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Computational Sciences and M.Sc. Chemistry, and working as teaching assistant in theoretical chemistry at FUB.", "id": 80158628, "node_id": "MDQ6VXNlcjgwMTU4NjI4", "avatar_url": "https://avatars.githubusercontent.com/u/80158628?v=4", "url": {"website": "", "github": "https://github.com/AAriam", "linkedin": "https://linkedin.com/in/armin-ariamajd", "twitter": "https://twitter.com/Al___Chemist", "researchgate": "https://researchgate.net/profile/Armin_Ariamajd", "orcid": "https://orcid.org/0000-0003-1563-6987"}, "publications": [{"doi": "10.1039/d2sc03130b", "url": "https://doi.org/10.1039/d2sc03130b", "type": "journal-article", "subtype": null, "cite": {"BibTex": "@article{Urner_2022,\n\tdoi = {10.1039/d2sc03130b},\n\turl = {https://doi.org/10.1039%2Fd2sc03130b},\n\tyear = 2022,\n\tpublisher = {Royal Society of Chemistry ({RSC})},\n\tvolume = {13},\n\tnumber = {35},\n\tpages = {10299--10307},\n\tauthor = {Leonhard H. Urner and Armin Ariamajd and Alex Weikum},\n\ttitle = {Combinatorial synthesis enables scalable designer detergents for membrane protein studies},\n\tjournal = {Chemical Science}\n}", "RIS": "TY - JOUR\nDO - 10.1039/d2sc03130b\nUR - http://dx.doi.org/10.1039/d2sc03130b\nTI - Combinatorial synthesis enables scalable designer detergents for membrane protein studies\nT2 - Chemical Science\nAU - Urner, Leonhard H.\nAU - Ariamajd, Armin\nAU - Weikum, Alex\nPY - 2022\nPB - Royal Society of Chemistry (RSC)\nSP - 10299-10307\nIS - 35\nVL - 13\nSN - 2041-6520\nSN - 2041-6539\nER - \n"}, "journal": "Chemical Science", "journal_abbr": "Chem. Sci.", "publisher": "Royal Society of Chemistry (RSC)", "title": "Combinatorial synthesis enables scalable designer detergents for membrane protein studies", "pages": "10299-10307", "volume": "13", "issue": "35", "date_tuple": [2022, 8, 30], "year": 2022, "date": "30 August 2022", "abstract": "Combinatorial detergent synthesis permits access to an unexplored part of the detergentome and provides new directions for the preparation of custom-made detergents for future applications."}, {"doi": "10.1093/nar/gkac267", "url": "https://doi.org/10.1093/nar/gkac267", "type": "journal-article", "subtype": null, "cite": {"BibTex": "@article{Sydow_2022,\n\tdoi = {10.1093/nar/gkac267},\n\turl = {https://doi.org/10.1093%2Fnar%2Fgkac267},\n\tyear = 2022,\n\tmonth = {may},\n\tpublisher = {Oxford University Press ({OUP})},\n\tvolume = {50},\n\tnumber = {W1},\n\tpages = {W753--W760},\n\tauthor = {Dominique Sydow and Jaime Rodr{\\'{\\i}}guez-Guerra and Talia~B Kimber and David Schaller and Corey~J Taylor and Yonghui Chen and Mareike Leja and Sakshi Misra and Michele Wichmann and Armin Ariamajd and Andrea Volkamer},\n\ttitle = {{TeachOpenCADD} 2022: open source and {FAIR} Python pipelines to assist in structural bioinformatics and cheminformatics research},\n\tjournal = {Nucleic Acids Research}\n}", "RIS": "TY - JOUR\nDO - 10.1093/nar/gkac267\nUR - http://dx.doi.org/10.1093/nar/gkac267\nTI - TeachOpenCADD 2022: open source and FAIR Python pipelines to assist in structural bioinformatics and cheminformatics research\nT2 - Nucleic Acids Research\nAU - Sydow, Dominique\nAU - Rodr\u00edguez-Guerra, Jaime\nAU - Kimber, Talia\u00a0B\nAU - Schaller, David\nAU - Taylor, Corey\u00a0J\nAU - Chen, Yonghui\nAU - Leja, Mareike\nAU - Misra, Sakshi\nAU - Wichmann, Michele\nAU - Ariamajd, Armin\nAU - Volkamer, Andrea\nPY - 2022\nDA - 2022/05/07\nPB - Oxford University Press (OUP)\nSP - W753-W760\nIS - W1\nVL - 50\nSN - 0305-1048\nSN - 1362-4962\nER - \n"}, "journal": "Nucleic Acids Research", "journal_abbr": "Nucleic Acids Res.", "publisher": "Oxford University Press (OUP)", "title": "TeachOpenCADD 2022: open source and FAIR Python pipelines to assist in structural bioinformatics and cheminformatics research", "pages": "W753-W760", "volume": "50", "issue": "W1", "date_tuple": [2022, 5, 7], "year": 2022, "date": "7 May 2022", "abstract": "Computational pipelines have become a crucial part of modern drug discovery campaigns. Setting up and maintaining such pipelines, however, can be challenging and time-consuming\u2014especially for novice scientists in this domain. TeachOpenCADD is a platform that aims to teach domain-specific skills and to provide pipeline templates as starting points for research projects. We offer Python-based solutions for common tasks in cheminformatics and structural bioinformatics in the form of Jupyter notebooks, based on open source resources only. Including the 12 newly released additions, TeachOpenCADD now contains 22 notebooks that cover both theoretical background as well as hands-on programming. To promote reproducible and reusable research, we apply software best practices to our notebooks such as testing with automated continuous integration and adhering to the idiomatic Python style. The new TeachOpenCADD website is available at https://projects.volkamerlab.org/teachopencadd and all code is deposited on GitHub."}, {"doi": "10.26434/chemrxiv-2021-8x13n", "url": "https://doi.org/10.26434/chemrxiv-2021-8x13n", "type": "posted-content", "subtype": "preprint", "cite": {"BibTex": "@article{Sydow_2021,\n\tdoi = {10.26434/chemrxiv-2021-8x13n},\n\turl = {https://doi.org/10.26434%2Fchemrxiv-2021-8x13n},\n\tyear = 2021,\n\tmonth = {dec},\n\tpublisher = {American Chemical Society ({ACS})},\n\tauthor = {Dominique Sydow and Jaime Rodr{\\'{\\i}}guez-Guerra and Talia B. Kimber and David Schaller and Corey J. Taylor and Yonghui Chen and Mareike Leja and Sakshi Misra and Michele Wichmann and Armin Ariamajd and Andrea Volkamer},\n\ttitle = {{TeachOpenCADD} 2021: Open Source and {FAIR} Python Pipelines to Assist in Structural Bioinformatics and Cheminformatics Research}\n}", "RIS": "TY - GENERIC\nDO - 10.26434/chemrxiv-2021-8x13n\nUR - http://dx.doi.org/10.26434/chemrxiv-2021-8x13n\nTI - TeachOpenCADD 2021: Open Source and FAIR Python Pipelines to Assist in Structural Bioinformatics and Cheminformatics Research\nAU - Sydow, Dominique\nAU - Rodr\u00edguez-Guerra, Jaime\nAU - Kimber, Talia B.\nAU - Schaller, David\nAU - Taylor, Corey J.\nAU - Chen, Yonghui\nAU - Leja, Mareike\nAU - Misra, Sakshi\nAU - Wichmann, Michele\nAU - Ariamajd, Armin\nAU - Volkamer, Andrea\nPY - 2021\nDA - 2021/12/13\nPB - American Chemical Society (ACS)\nER - \n"}, "journal": null, "journal_abbr": null, "publisher": "American Chemical Society (ACS)", "title": "TeachOpenCADD 2021: Open Source and FAIR Python Pipelines to Assist in Structural Bioinformatics and Cheminformatics Research", "pages": null, "volume": null, "issue": null, "date_tuple": [2021, 12, 13], "year": 2021, "date": "13 December 2021", "abstract": "Computational pipelines have become a crucial part of modern drug discovery campaigns. Setting up and maintaining such pipelines, however, can be challenging and time-consuming --- especially for novice scientists in this domain. TeachOpenCADD is a platform that aims to teach domain-specific skills and to provide pipeline templates as starting points for research projects. We offer Python-based solutions for common tasks in cheminformatics and structural bioinformatics in the form of Jupyter notebooks and based on open source resources only. Including the 12 newly released additions, TeachOpenCADD now contains 22 notebooks that each cover both theoretical background as well as hands-on programming. To promote reproducible and reusable research, we apply software best practices to our notebooks such as testing with an automated continuous integration and adhering to a more idiomatic Python style. The new TeachOpenCADD website is available at https://projects.volkamerlab.org/teachopencadd and all code is deposited on GitHub."}, {"doi": "10.3762/bjoc.17.8", "url": "https://doi.org/10.3762/bjoc.17.8", "type": "journal-article", "subtype": null, "cite": {"BibTex": "@article{Ariamajd_2021,\n\tdoi = {10.3762/bjoc.17.8},\n\turl = {https://doi.org/10.3762%2Fbjoc.17.8},\n\tyear = 2021,\n\tmonth = {jan},\n\tpublisher = {Beilstein Institut},\n\tvolume = {17},\n\tpages = {83--88},\n\tauthor = {Armin Ariamajd and Nils J Gerwien and Benjamin Schwabe and Stefan Dix and Matthew N Hopkinson},\n\ttitle = {Benzothiazolium salts as reagents for the deoxygenative perfluoroalkylthiolation of alcohols},\n\tjournal = {Beilstein Journal of Organic Chemistry}\n}", "RIS": "TY - JOUR\nDO - 10.3762/bjoc.17.8\nUR - http://dx.doi.org/10.3762/bjoc.17.8\nTI - Benzothiazolium salts as reagents for the deoxygenative perfluoroalkylthiolation of alcohols\nT2 - Beilstein Journal of Organic Chemistry\nAU - Ariamajd, Armin\nAU - Gerwien, Nils J\nAU - Schwabe, Benjamin\nAU - Dix, Stefan\nAU - Hopkinson, Matthew N\nPY - 2021\nDA - 2021/01/08\nPB - Beilstein Institut\nSP - 83-88\nVL - 17\nSN - 1860-5397\nER - \n"}, "journal": "Beilstein Journal of Organic Chemistry", "journal_abbr": "Beilstein J. Org. Chem.", "publisher": "Beilstein Institut", "title": "Benzothiazolium salts as reagents for the deoxygenative perfluoroalkylthiolation of alcohols", "pages": "83-88", "volume": "17", "issue": null, "date_tuple": [2021, 1, 8], "year": 2021, "date": "8 January 2021", "abstract": "A series of 2-(perfluoroalkylthio)benzothiazolium (BT-SRF) salts have been synthesized that serve as convenient sources of hitherto underexplored perfluoroalkylthiolate anions. An investigation of their reactivity in a deoxygenative nucleophilic substitution reaction led to the development of an unprecedented process that provides pentafluoroethyl and heptafluoropropyl thioethers directly from readily available alcohols."}]}]}, "tagline": "Python Projects Perfected: Innovate, Develop, and Deploy Effortlessly!", "description": "TemplateRepo is a free and open-source toolkit empowering the development of open-source Python projects on GitHub. It is a dynamic repository template that provides a complete, professional, and robust infrastructure for your project, where the only thing missing is your code. With TemplateRepo, you can solely focus on what truly matters: implementing your ideas and bringing your vision to life!", "keywords": ["python", "github", "packaging", "template", "dynamic repository", "repository template", "documentation", "testing", "deployment", "maintenance", "automation", "development", "infrastructure", "streamline"], "keynotes": [{"title": "Automation", "description": "TemplateRepo streamlines a remarkable portion of the process of creating, documenting, testing, publishing, and maintaining Python packages, making your project development a pleasant breeze!"}, {"title": "Synchronization", "description": "TemplateRepo gathers all your project's key information and configuration in one place, and dynamically updates them throughout your repository, Python package, and documentation website."}, {"title": "Configuration", "description": "TemplateRepo elevates your project by providing full configuration for your repository, Python package, and documentation website, according to the latest guidelines and best practices."}, {"title": "Customization", "description": "While carefully configured, TemplateRepo is also fully customizable, allowing you to tailor every aspect of your development pipeline to your specific needs"}, {"title": "Documentation", "description": "TemplateRepo comes with a professional website for your project, that is easily customizable, and automatically generated and deployed on your preferred platform."}, {"title": "Production", "description": "With TemplateRepo, the only remaining step to publishing a production-ready Python project is adding your code, unit-tests and documentation content."}], "name": "TemplateRepo", "license": {"shortname": "GNU AGPL v3.0+", "fullname": "GNU Affero General Public License v3.0 or later", "trove_classifier": "License :: OSI Approved :: GNU Affero General Public License v3 or later (AGPLv3+)", "text": " GNU AFFERO GENERAL PUBLIC LICENSE\n Version 3, 19 November 2007\n\n Copyright (C) 2007 Free Software Foundation, Inc. \n Everyone is permitted to copy and distribute verbatim copies\n of this license document, but changing it is not allowed.\n\n Preamble\n\n The GNU Affero General Public License is a free, copyleft license for\nsoftware and other kinds of works, specifically designed to ensure\ncooperation with the community in the case of network server software.\n\n The licenses for most software and other practical works are designed\nto take away your freedom to share and change the works. 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Conveying Non-Source Forms.\n\n You may convey a covered work in object code form under the terms\nof sections 4 and 5, provided that you also convey the\nmachine-readable Corresponding Source under the terms of this License,\nin one of these ways:\n\n a) Convey the object code in, or embodied in, a physical product\n (including a physical distribution medium), accompanied by the\n Corresponding Source fixed on a durable physical medium\n customarily used for software interchange.\n\n b) Convey the object code in, or embodied in, a physical product\n (including a physical distribution medium), accompanied by a\n written offer, valid for at least three years and valid for as\n long as you offer spare parts or customer support for that product\n model, to give anyone who possesses the object code either (1) a\n copy of the Corresponding Source for all the software in the\n product that is covered by this License, on a durable physical\n medium customarily used for software interchange, for a price no\n more than your reasonable cost of physically performing this\n conveying of source, or (2) access to copy the\n Corresponding Source from a network server at no charge.\n\n c) Convey individual copies of the object code with a copy of the\n written offer to provide the Corresponding Source. This\n alternative is allowed only occasionally and noncommercially, and\n only if you received the object code with such an offer, in accord\n with subsection 6b.\n\n d) Convey the object code by offering access from a designated\n place (gratis or for a charge), and offer equivalent access to the\n Corresponding Source in the same way through the same place at no\n further charge. You need not require recipients to copy the\n Corresponding Source along with the object code. If the place to\n copy the object code is a network server, the Corresponding Source\n may be on a different server (operated by you or a third party)\n that supports equivalent copying facilities, provided you maintain\n clear directions next to the object code saying where to find the\n Corresponding Source. Regardless of what server hosts the\n Corresponding Source, you remain obligated to ensure that it is\n available for as long as needed to satisfy these requirements.\n\n e) Convey the object code using peer-to-peer transmission, provided\n you inform other peers where the object code and Corresponding\n Source of the work are being offered to the general public at no\n charge under subsection 6d.\n\n A separable portion of the object code, whose source code is excluded\nfrom the Corresponding Source as a System Library, need not be\nincluded in conveying the object code work.\n\n A \"User Product\" is either (1) a \"consumer product\", which means any\ntangible personal property which is normally used for personal, family,\nor household purposes, or (2) anything designed or sold for incorporation\ninto a dwelling. In determining whether a product is a consumer product,\ndoubtful cases shall be resolved in favor of coverage. For a particular\nproduct received by a particular user, \"normally used\" refers to a\ntypical or common use of that class of product, regardless of the status\nof the particular user or of the way in which the particular user\nactually uses, or expects or is expected to use, the product. A product\nis a consumer product regardless of whether the product has substantial\ncommercial, industrial or non-consumer uses, unless such uses represent\nthe only significant mode of use of the product.\n\n \"Installation Information\" for a User Product means any methods,\nprocedures, authorization keys, or other information required to install\nand execute modified versions of a covered work in that User Product from\na modified version of its Corresponding Source. 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But this requirement does not apply\nif neither you nor any third party retains the ability to install\nmodified object code on the User Product (for example, the work has\nbeen installed in ROM).\n\n The requirement to provide Installation Information does not include a\nrequirement to continue to provide support service, warranty, or updates\nfor a work that has been modified or installed by the recipient, or for\nthe User Product in which it has been modified or installed. Access to a\nnetwork may be denied when the modification itself materially and\nadversely affects the operation of the network or violates the rules and\nprotocols for communication across the network.\n\n Corresponding Source conveyed, and Installation Information provided,\nin accord with this section must be in a format that is publicly\ndocumented (and with an implementation available to the public in\nsource code form), and must require no special password or key for\nunpacking, reading or copying.\n\n 7. Additional Terms.\n\n \"Additional permissions\" are terms that supplement the terms of this\nLicense by making exceptions from one or more of its conditions.\nAdditional permissions that are applicable to the entire Program shall\nbe treated as though they were included in this License, to the extent\nthat they are valid under applicable law. If additional permissions\napply only to part of the Program, that part may be used separately\nunder those permissions, but the entire Program remains governed by\nthis License without regard to the additional permissions.\n\n When you convey a copy of a covered work, you may at your option\nremove any additional permissions from that copy, or from any part of\nit. (Additional permissions may be written to require their own\nremoval in certain cases when you modify the work.) You may place\nadditional permissions on material, added by you to a covered work,\nfor which you have or can give appropriate copyright permission.\n\n Notwithstanding any other provision of this License, for material you\nadd to a covered work, you may (if authorized by the copyright holders of\nthat material) supplement the terms of this License with terms:\n\n a) Disclaiming warranty or limiting liability differently from the\n terms of sections 15 and 16 of this License; or\n\n b) Requiring preservation of specified reasonable legal notices or\n author attributions in that material or in the Appropriate Legal\n Notices displayed by works containing it; or\n\n c) Prohibiting misrepresentation of the origin of that material, or\n requiring that modified versions of such material be marked in\n reasonable ways as different from the original version; or\n\n d) Limiting the use for publicity purposes of names of licensors or\n authors of the material; or\n\n e) Declining to grant rights under trademark law for use of some\n trade names, trademarks, or service marks; or\n\n f) Requiring indemnification of licensors and authors of that\n material by anyone who conveys the material (or modified versions of\n it) with contractual assumptions of liability to the recipient, for\n any liability that these contractual assumptions directly impose on\n those licensors and authors.\n\n All other non-permissive additional terms are considered \"further\nrestrictions\" within the meaning of section 10. If the Program as you\nreceived it, or any part of it, contains a notice stating that it is\ngoverned by this License along with a term that is a further\nrestriction, you may remove that term. If a license document contains\na further restriction but permits relicensing or conveying under this\nLicense, you may add to a covered work material governed by the terms\nof that license document, provided that the further restriction does\nnot survive such relicensing or conveying.\n\n If you add terms to a covered work in accord with this section, you\nmust place, in the relevant source files, a statement of the\nadditional terms that apply to those files, or a notice indicating\nwhere to find the applicable terms.\n\n Additional terms, permissive or non-permissive, may be stated in the\nform of a separately written license, or stated as exceptions;\nthe above requirements apply either way.\n\n 8. Termination.\n\n You may not propagate or modify a covered work except as expressly\nprovided under this License. Any attempt otherwise to propagate or\nmodify it is void, and will automatically terminate your rights under\nthis License (including any patent licenses granted under the third\nparagraph of section 11).\n\n However, if you cease all violation of this License, then your\nlicense from a particular copyright holder is reinstated (a)\nprovisionally, unless and until the copyright holder explicitly and\nfinally terminates your license, and (b) permanently, if the copyright\nholder fails to notify you of the violation by some reasonable means\nprior to 60 days after the cessation.\n\n Moreover, your license from a particular copyright holder is\nreinstated permanently if the copyright holder notifies you of the\nviolation by some reasonable means, this is the first time you have\nreceived notice of violation of this License (for any work) from that\ncopyright holder, and you cure the violation prior to 30 days after\nyour receipt of the notice.\n\n Termination of your rights under this section does not terminate the\nlicenses of parties who have received copies or rights from you under\nthis License. If your rights have been terminated and not permanently\nreinstated, you do not qualify to receive new licenses for the same\nmaterial under section 10.\n\n 9. Acceptance Not Required for Having Copies.\n\n You are not required to accept this License in order to receive or\nrun a copy of the Program. Ancillary propagation of a covered work\noccurring solely as a consequence of using peer-to-peer transmission\nto receive a copy likewise does not require acceptance. However,\nnothing other than this License grants you permission to propagate or\nmodify any covered work. These actions infringe copyright if you do\nnot accept this License. Therefore, by modifying or propagating a\ncovered work, you indicate your acceptance of this License to do so.\n\n 10. Automatic Licensing of Downstream Recipients.\n\n Each time you convey a covered work, the recipient automatically\nreceives a license from the original licensors, to run, modify and\npropagate that work, subject to this License. You are not responsible\nfor enforcing compliance by third parties with this License.\n\n An \"entity transaction\" is a transaction transferring control of an\norganization, or substantially all assets of one, or subdividing an\norganization, or merging organizations. If propagation of a covered\nwork results from an entity transaction, each party to that\ntransaction who receives a copy of the work also receives whatever\nlicenses to the work the party's predecessor in interest had or could\ngive under the previous paragraph, plus a right to possession of the\nCorresponding Source of the work from the predecessor in interest, if\nthe predecessor has it or can get it with reasonable efforts.\n\n You may not impose any further restrictions on the exercise of the\nrights granted or affirmed under this License. For example, you may\nnot impose a license fee, royalty, or other charge for exercise of\nrights granted under this License, and you may not initiate litigation\n(including a cross-claim or counterclaim in a lawsuit) alleging that\nany patent claim is infringed by making, using, selling, offering for\nsale, or importing the Program or any portion of it.\n\n 11. Patents.\n\n A \"contributor\" is a copyright holder who authorizes use under this\nLicense of the Program or a work on which the Program is based. The\nwork thus licensed is called the contributor's \"contributor version\".\n\n A contributor's \"essential patent claims\" are all patent claims\nowned or controlled by the contributor, whether already acquired or\nhereafter acquired, that would be infringed by some manner, permitted\nby this License, of making, using, or selling its contributor version,\nbut do not include claims that would be infringed only as a\nconsequence of further modification of the contributor version. For\npurposes of this definition, \"control\" includes the right to grant\npatent sublicenses in a manner consistent with the requirements of\nthis License.\n\n Each contributor grants you a non-exclusive, worldwide, royalty-free\npatent license under the contributor's essential patent claims, to\nmake, use, sell, offer for sale, import and otherwise run, modify and\npropagate the contents of its contributor version.\n\n In the following three paragraphs, a \"patent license\" is any express\nagreement or commitment, however denominated, not to enforce a patent\n(such as an express permission to practice a patent or covenant not to\nsue for patent infringement). To \"grant\" such a patent license to a\nparty means to make such an agreement or commitment not to enforce a\npatent against the party.\n\n If you convey a covered work, knowingly relying on a patent license,\nand the Corresponding Source of the work is not available for anyone\nto copy, free of charge and under the terms of this License, through a\npublicly available network server or other readily accessible means,\nthen you must either (1) cause the Corresponding Source to be so\navailable, or (2) arrange to deprive yourself of the benefit of the\npatent license for this particular work, or (3) arrange, in a manner\nconsistent with the requirements of this License, to extend the patent\nlicense to downstream recipients. \"Knowingly relying\" means you have\nactual knowledge that, but for the patent license, your conveying the\ncovered work in a country, or your recipient's use of the covered work\nin a country, would infringe one or more identifiable patents in that\ncountry that you have reason to believe are valid.\n\n If, pursuant to or in connection with a single transaction or\narrangement, you convey, or propagate by procuring conveyance of, a\ncovered work, and grant a patent license to some of the parties\nreceiving the covered work authorizing them to use, propagate, modify\nor convey a specific copy of the covered work, then the patent license\nyou grant is automatically extended to all recipients of the covered\nwork and works based on it.\n\n A patent license is \"discriminatory\" if it does not include within\nthe scope of its coverage, prohibits the exercise of, or is\nconditioned on the non-exercise of one or more of the rights that are\nspecifically granted under this License. You may not convey a covered\nwork if you are a party to an arrangement with a third party that is\nin the business of distributing software, under which you make payment\nto the third party based on the extent of your activity of conveying\nthe work, and under which the third party grants, to any of the\nparties who would receive the covered work from you, a discriminatory\npatent license (a) in connection with copies of the covered work\nconveyed by you (or copies made from those copies), or (b) primarily\nfor and in connection with specific products or compilations that\ncontain the covered work, unless you entered into that arrangement,\nor that patent license was granted, prior to 28 March 2007.\n\n Nothing in this License shall be construed as excluding or limiting\nany implied license or other defenses to infringement that may\notherwise be available to you under applicable patent law.\n\n 12. No Surrender of Others' Freedom.\n\n If conditions are imposed on you (whether by court order, agreement or\notherwise) that contradict the conditions of this License, they do not\nexcuse you from the conditions of this License. If you cannot convey a\ncovered work so as to satisfy simultaneously your obligations under this\nLicense and any other pertinent obligations, then as a consequence you may\nnot convey it at all. For example, if you agree to terms that obligate you\nto collect a royalty for further conveying from those to whom you convey\nthe Program, the only way you could satisfy both those terms and this\nLicense would be to refrain entirely from conveying the Program.\n\n 13. Remote Network Interaction; Use with the GNU General Public License.\n\n Notwithstanding any other provision of this License, if you modify the\nProgram, your modified version must prominently offer all users\ninteracting with it remotely through a computer network (if your version\nsupports such interaction) an opportunity to receive the Corresponding\nSource of your version by providing access to the Corresponding Source\nfrom a network server at no charge, through some standard or customary\nmeans of facilitating copying of software. This Corresponding Source\nshall include the Corresponding Source for any work covered by version 3\nof the GNU General Public License that is incorporated pursuant to the\nfollowing paragraph.\n\n Notwithstanding any other provision of this License, you have\npermission to link or combine any covered work with a work licensed\nunder version 3 of the GNU General Public License into a single\ncombined work, and to convey the resulting work. The terms of this\nLicense will continue to apply to the part which is the covered work,\nbut the work with which it is combined will remain governed by version\n3 of the GNU General Public License.\n\n 14. Revised Versions of this License.\n\n The Free Software Foundation may publish revised and/or new versions of\nthe GNU Affero General Public License from time to time. Such new versions\nwill be similar in spirit to the present version, but may differ in detail to\naddress new problems or concerns.\n\n Each version is given a distinguishing version number. If the\nProgram specifies that a certain numbered version of the GNU Affero General\nPublic License \"or any later version\" applies to it, you have the\noption of following the terms and conditions either of that numbered\nversion or of any later version published by the Free Software\nFoundation. If the Program does not specify a version number of the\nGNU Affero General Public License, you may choose any version ever published\nby the Free Software Foundation.\n\n If the Program specifies that a proxy can decide which future\nversions of the GNU Affero General Public License can be used, that proxy's\npublic statement of acceptance of a version permanently authorizes you\nto choose that version for the Program.\n\n Later license versions may give you additional or different\npermissions. However, no additional obligations are imposed on any\nauthor or copyright holder as a result of your choosing to follow a\nlater version.\n\n 15. Disclaimer of Warranty.\n\n THERE IS NO WARRANTY FOR THE PROGRAM, TO THE EXTENT PERMITTED BY\nAPPLICABLE LAW. EXCEPT WHEN OTHERWISE STATED IN WRITING THE COPYRIGHT\nHOLDERS AND/OR OTHER PARTIES PROVIDE THE PROGRAM \"AS IS\" WITHOUT WARRANTY\nOF ANY KIND, EITHER EXPRESSED OR IMPLIED, INCLUDING, BUT NOT LIMITED TO,\nTHE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR\nPURPOSE. THE ENTIRE RISK AS TO THE QUALITY AND PERFORMANCE OF THE PROGRAM\nIS WITH YOU. SHOULD THE PROGRAM PROVE DEFECTIVE, YOU ASSUME THE COST OF\nALL NECESSARY SERVICING, REPAIR OR CORRECTION.\n\n 16. Limitation of Liability.\n\n IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING\nWILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MODIFIES AND/OR CONVEYS\nTHE PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES, INCLUDING ANY\nGENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING OUT OF THE\nUSE OR INABILITY TO USE THE PROGRAM (INCLUDING BUT NOT LIMITED TO LOSS OF\nDATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY YOU OR THIRD\nPARTIES OR A FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER PROGRAMS),\nEVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF\nSUCH DAMAGES.\n\n 17. Interpretation of Sections 15 and 16.\n\n If the disclaimer of warranty and limitation of liability provided\nabove cannot be given local legal effect according to their terms,\nreviewing courts shall apply local law that most closely approximates\nan absolute waiver of all civil liability in connection with the\nProgram, unless a warranty or assumption of liability accompanies a\ncopy of the Program in return for a fee.\n\n END OF TERMS AND CONDITIONS\n\n How to Apply These Terms to Your New Programs\n\n If you develop a new program, and you want it to be of the greatest\npossible use to the public, the best way to achieve this is to make it\nfree software which everyone can redistribute and change under these terms.\n\n To do so, attach the following notices to the program. It is safest\nto attach them to the start of each source file to most effectively\nstate the exclusion of warranty; and each file should have at least\nthe \"copyright\" line and a pointer to where the full notice is found.\n\n \n Copyright (C) \n\n This program is free software: you can redistribute it and/or modify\n it under the terms of the GNU Affero General Public License as published\n by the Free Software Foundation, either version 3 of the License, or\n (at your option) any later version.\n\n This program is distributed in the hope that it will be useful,\n but WITHOUT ANY WARRANTY; without even the implied warranty of\n MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\n GNU Affero General Public License for more details.\n\n You should have received a copy of the GNU Affero General Public License\n along with this program. If not, see .\n\nAlso add information on how to contact you by electronic and paper mail.\n\n If your software can interact with users remotely through a computer\nnetwork, you should also make sure that it provides a way for users to\nget its source. For example, if your program is a web application, its\ninterface could display a \"Source\" link that leads users to an archive\nof the code. There are many ways you could offer source, and different\nsolutions will be better for different programs; see section 13 for the\nspecific requirements.\n\n You should also get your employer (if you work as a programmer) or school,\nif any, to sign a \"copyright disclaimer\" for the program, if necessary.\nFor more information on this, and how to apply and follow the GNU AGPL, see\n.\n", "notice": "Copyright (C) 2023 Armin Ariamajd\n\nThis program is free software: you can redistribute it and/or modify\nit under the terms of the GNU Affero General Public License as published\nby the Free Software Foundation, either version 3 of the License, or\n(at your option) any later version.\n\nThis program is distributed in the hope that it will be useful,\nbut WITHOUT ANY WARRANTY; without even the implied warranty of\nMERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\nGNU Affero General Public License for more details.\n\nYou should have received a copy of the GNU Affero General Public License\nalong with this program. If not, see .\n"}, "copyright": {"year_start": 2023, "year_range": "2023", "owner": "Armin Ariamajd", "notice": "2023 Armin Ariamajd"}, "branch": {"default": {"name": "main", "protection_rules": {"allow_deletion": false, "allow_force_push": false}}, "group": {"release": {"prefix": "release/v", "protection_rules": {"allow_deletion": false, "allow_force_push": false}}, "pre_release": {"prefix": "pre-release/v", "protection_rules": {"allow_deletion": false, "allow_force_push": false}}, "dev": {"prefix": "dev/", "protection_rules": {"allow_deletion": true, "allow_force_push": true}}, "ci_pull": {"prefix": "ci-pull/", "protection_rules": {"allow_deletion": true, "allow_force_push": true}}}}, "changelog": {"package_public": {"name": "Public API", "path": "CHANGELOG.md", "title": "TemplateRepo Changelog (Public API)", "intro": "All notable changes to this project will be documented in this file.\n\nThe format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),\nand this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).\n", "entry": {"title": "[{ver_dist}] \u2013 {date}", "intro": "- Commit Type: {commit_type}\n- Commit Title: {commit_title}\n- Parent Commit: [{parent_commit_hash}]({parent_commit_url})\n"}, "sections": [{"id": "removed", "title": "\u26d4 Removed Features", "description": "Features that have been removed from the public API.\n"}, {"id": "changed", "title": "\ud83d\udeab Changed Features", "description": "Features that have been changed in the public API.\n"}, {"id": "deprecated", "title": "\u26a0\ufe0f Deprecated Features", "description": "Features that have been deprecated in the public API.\n"}, {"id": "added", "title": "\ud83c\udf31 New Features", "description": "Features that have been added to the public API.\n"}, {"id": "enhanced", "title": "\u2728 Enhanced Features", "description": "Features that have been enhanced in the public API.\n"}, {"id": "security", "title": "\ud83d\udee1\ufe0f Security Fixes", "description": "Security fixes that have been applied to the public API.\n"}, {"id": "fixed", "title": "\ud83d\udc1e Bug Fixes", "description": "Bug fixes that have been applied to the public API.\n"}, {"id": "improved", "title": "\ud83d\ude80 Performance Improvements", "description": "Performance improvements that have been applied to the public API.\n"}, {"id": "docs", "title": "\ud83d\udcdd Docstring Fixes", "description": "Docstring fixes that have been applied to the public API.\n"}, {"id": "notes", "title": "\ud83d\udcd4\ufe0f Release-Notes Fixes", "description": "Release-Notes fixes that have been applied to the public API.\n"}]}}, "commit": {"primary_action": {"package_major": {"description": "Remove features/components from - or introduce breaking changes to - the public API, \nand publish a new major release of the package.\n", "type": "major", "sub_types": {"any": ["remove", "change"], "exclude": ["ci", "meta-extensions", "meta-changelog", "meta-commits", "meta-issues", "meta-labels"]}}, "package_minor": {"description": "Add features/components to - or enhance/deprecate existing features in - the public API, \nand publish a new minor release of the package.\n", "type": "minor", "sub_types": {"any": ["deprecate", "feat", "enhance"]}}, "package_patch": {"description": "Fix bugs or security issues in the public API, \nor improve the performance of existing functionalities, \nand publish a new patch release of the package.\n", "type": "patch", "sub_types": {"any": ["secure", "fix", "perf"]}}, "package_post": {"description": "Fix documentation or release notes in a previous package release, \nand publish a new post release.\n", "type": "post", "sub_types": {"any": ["docs", "notes"]}}, "website": {"description": "Change the website content, design or backend.\n", "type": "web", "sub_types": {"any": ["web-content", "web-design", "web-backend"]}, "announcement": {"scope": "announcement", "changelog_id": "website", "changelog_section_id": "content"}}, "meta": {"description": "Change the meta content of the repository.\n", "type": "meta", "sub_types": {"any": ["meta-credits", "meta-extensions", "meta-intro", "meta-license", "meta-changelog", "meta-commits", "meta-issues", "meta-labels", "meta-maintainers", "meta-repo", "meta-workflows"]}}}, "primary_custom": {"package_private": {"description": "Change the private API, the build system, or refactor code, \nwithout affecting the public API, \nand without publishing a new package release.\n", "type": "pkg", "sub_types": {"any": ["priv-remove", "priv-change", "priv-feat", "priv-enhance", "priv-fix", "priv-perf", "priv-docs", "build", "refactor", "style"]}}, "tests": {"description": "Change the test-suite, without affecting the public API, \nand without publishing a new package release.\n", "type": "test", "sub_types": {"any": ["test-remove", "test-change", "test-feat", "test-enhance", "test-fix", "test-perf", "test-docs", "test-build", "test-refactor", "test-style"]}}, "workflows": {"description": "Change the GitHub workflows of the repository.\n", "type": "ci", "sub_types": {"any": ["ci"]}}}, "secondary_action": {"meta_sync": {"type": "meta-sync", "description": "Update the dynamic files of the repository.\n"}, "revert": {"type": "revert", "description": "Revert a previous commit.\n"}, "hook_fix": {"type": "hook-fix", "description": "Automatically refactor the code.\n"}}, "secondary_custom": {"remove": {"description": "Remove a feature/component from the public API.", "changelog_id": "package_public", "changelog_section_id": "removed"}, "change": {"description": "Change a feature/component in the public API.", "changelog_id": "package_public", "changelog_section_id": "changed"}, "deprecate": {"description": "Deprecate a feature/component from the public API.", "changelog_id": "package_public", "changelog_section_id": "deprecated"}, "feat": {"description": "Add a feature/component to the public API.", "changelog_id": "package_public", "changelog_section_id": "added"}, "enhance": {"description": "Enhance a feature/component in the public API.", "changelog_id": "package_public", "changelog_section_id": "enhanced"}, "secure": {"description": "Fix a security issue in the public API.", "changelog_id": "package_public", "changelog_section_id": "security"}, "fix": {"description": "Fix a bug in the public API.", "changelog_id": "package_public", "changelog_section_id": "fixed"}, "perf": {"description": "Improve performance in the public API.", "changelog_id": "package_public", "changelog_section_id": "improved"}, "docs": {"description": "Fix documentation.", "changelog_id": "package_public", "changelog_section_id": "docs"}, "notes": {"description": "Fix release notes.", "changelog_id": "package_public", "changelog_section_id": "notes"}, "web-content": {"description": "Change the website content.", "changelog_id": "website", "changelog_section_id": "content"}, "web-design": {"description": "Change the website design.", "changelog_id": "website", "changelog_section_id": "design"}, "web-backend": {"description": "Change the website backend.", "changelog_id": "website", "changelog_section_id": "backend"}, "priv-remove": {"description": "Remove a feature/component from the private API.", "changelog_id": "package_private", "changelog_section_id": "removed"}, "priv-change": {"description": "Change a feature/component in the private API.", "changelog_id": "package_private", "changelog_section_id": "changed"}, "priv-feat": {"description": "Add a feature/component to the private API.", "changelog_id": "package_private", "changelog_section_id": "added"}, "priv-enhance": {"description": "Enhance a feature/component in the private API.", "changelog_id": "package_private", "changelog_section_id": "enhanced"}, "priv-fix": {"description": "Fix a bug in the private API.", "changelog_id": "package_private", "changelog_section_id": "fixed"}, "priv-perf": {"description": "Improve performance in the private API.", "changelog_id": "package_private", "changelog_section_id": "improved"}, "priv-docs": {"description": "Fix documentation.", "changelog_id": "package_private", "changelog_section_id": "docs"}, "build": {"description": "Change the build system.", "changelog_id": "package_private", "changelog_section_id": "build"}, "refactor": {"description": "Refactor code.", "changelog_id": "package_private", "changelog_section_id": "refactor"}, "style": {"description": "Change text style and formatting without affecting the meaning.", "changelog_id": "package_private", "changelog_section_id": "style"}, "test-remove": {"description": "Remove a feature/component from the test-suite.", "changelog_id": "tests", "changelog_section_id": "removed"}, "test-change": {"description": "Change a feature/component in the test-suite.", "changelog_id": "tests", "changelog_section_id": "changed"}, "test-feat": {"description": "Add a feature/component to the test-suite.", "changelog_id": "tests", "changelog_section_id": "added"}, "test-enhance": {"description": "Enhance a feature/component in the test-suite.", "changelog_id": "tests", "changelog_section_id": "enhanced"}, "test-fix": {"description": "Fix a bug in the test-suite.", "changelog_id": "tests", "changelog_section_id": "fixed"}, "test-perf": {"description": "Improve performance in the test-suite.", "changelog_id": "tests", "changelog_section_id": "improved"}, "test-docs": {"description": "Fix documentation in the test-suite.", "changelog_id": "tests", "changelog_section_id": "docs"}, "test-build": {"description": "Change the test-suite build system.", "changelog_id": "tests", "changelog_section_id": "build"}, "test-refactor": {"description": "Refactor code in the test-suite.", "changelog_id": "tests", "changelog_section_id": "refactor"}, "test-style": {"description": "Change text style and formatting in the test-suite without affecting the meaning.", "changelog_id": "tests", "changelog_section_id": "style"}, "ci": {"description": "Change the CI configuration files and scripts.", "changelog_id": "workflows", "changelog_section_id": "workflows"}, "meta-credits": {"description": "Change credits meta content.", "changelog_id": "meta", "changelog_section_id": "credits"}, "meta-extensions": {"description": "Change extensions meta content.", "changelog_id": "meta", "changelog_section_id": "extensions"}, "meta-intro": {"description": "Change intro meta content.", "changelog_id": "meta", "changelog_section_id": "intro"}, "meta-license": {"description": "Change license meta content.", "changelog_id": "meta", "changelog_section_id": "license"}, "meta-changelog": {"description": "Change changelog meta content.", "changelog_id": "meta", "changelog_section_id": "changelog"}, "meta-commits": {"description": "Change commits meta content.", "changelog_id": "meta", "changelog_section_id": "commits"}, "meta-issues": {"description": "Change issues meta content.", "changelog_id": "meta", "changelog_section_id": "issues"}, "meta-labels": {"description": "Change labels meta content.", "changelog_id": "meta", "changelog_section_id": "labels"}, "meta-maintainers": {"description": "Change maintainers meta content.", "changelog_id": "meta", "changelog_section_id": "maintainers"}, "meta-repo": {"description": "Change repo meta content.", "changelog_id": "meta", "changelog_section_id": "repo"}, "meta-workflows": {"description": "Change workflows meta content.", "changelog_id": "meta", "changelog_section_id": "workflows"}, "meta-package": {"description": "Change package meta content.", "changelog_id": "meta", "changelog_section_id": "package"}, "meta-package-build": {"description": "Change package build meta content.", "changelog_id": "meta", "changelog_section_id": "package_build"}, "meta-package-tools": {"description": "Change package tools meta content.", "changelog_id": "meta", "changelog_section_id": "package_tools"}}}, "discussion": {"form": {"question_issues": {"title": "[General] ", "labels": ["General Introduction"], "body": [{"type": "markdown", "attributes": {"value": "This is text that will show up in the template!\n"}}, {"type": "textarea", "id": "improvements", "attributes": {"label": "Top 3 improvements", "description": "What are the top 3 improvements we could make to this project?", "value": "1.\n2.\n3.\n...\n", "render": "bash"}, "validations": {"required": true}}, {"type": "markdown", "attributes": {"value": "## Markdown header\nAnd some more markdown\n"}}, {"type": "input", "id": "has-id", "attributes": {"label": "Suggestions", "description": "A description about suggestions to help you"}, "validations": {"required": true}}, {"type": "dropdown", "id": "download", "attributes": {"label": "Which area of this project could be most improved?", "options": ["Documentation", "Pull request review time", "Bug fix time", "Release cadence"]}, "validations": {"required": true}}, {"type": "checkboxes", "attributes": {"label": "Check that box!", "options": [{"label": "This one!", "required": true}, {"label": "I won't stop you if you check this one, too"}]}}, {"type": "markdown", "attributes": {"value": "### The thrilling conclusion\n_to our template_\n"}}]}, "question_bug": {"title": "Is this a bug?", "labels": ["bug"], "body": [{"type": "markdown", "id": "bug", "attributes": {"value": "**Describe the bug**\n"}}]}}, "categories": []}, "issue": {"blank_enabled": false, "contact_links": [{"name": "\ud83c\udf93\ufe0f\u2002 Learn More", "about": "Not sure where to start? Read our contributing guide to learn more.", "url": "https://github.com/AAriam/TemplateRepo/blob/main/CONTRIBUTING.md"}, {"name": "\ud83d\udcac\u2002 Contact Us", "about": "Have another inquiry or need help? Contact us directly!", "url": "https://aariam.github.io/TemplateRepo/help/contact"}], "forms": [{"id": "app_bug_gui", "pre_process": {"if_any": [[]]}, "primary_commit_id": "package_patch", "sub_type": "gui", "name": "\u2002\ud83d\udda5\u2002App\u2002\ud83d\udc1e\u2002Bug Report\u2002\ud83d\uddb1\u2002GUI", "description": "Report a problem (e.g. errors and unexpected results) encountered while using the application's graphical user interface (GUI).", "body": [{"type": "markdown", "attributes": {"value": "

\n Thank you for taking the time to report a problem in TemplateRepo;\n we greatly appreciate your contribution! \u2764\ufe0f\ud83d\ude4f\n

\n

Terms and Conditions

\n Before submitting a report, please take a moment to review and accept our terms and conditions;\n they will help us process the issue as fast as possible,\n and not bother you with additional questions.\n

\n

\u26d4\u2002Choosing the right form

\n\n
\n \ud83d\udca1\u2002Contact us\n
\n

\n Can't find the right form or unsure about which one to choose? \n Ask a question and get help in the \n discussion forum.\n

\n
\n

\u26a0\ufe0f\u2002Verifying the bug

\nBefore submitting a report, please make sure that you are following our Bug Report Guidelines to verify that:
    \n
  1. \n The issue you are experiencing is in fact a bug, and not a documented expected behavior.\n
    2. \n
  2. \n The bug is reproducible in the latest version of the release, and has not yet been reported.\n
    3. \n
\n
\n \ud83d\udca1\u2002Open a discussion instead!\n
\n This verification process is non-trivial, and can be time-consuming.\n If you are not a collaborator and don't have the time to go through the process,\n you can always open a discussion instead; we will investigate the problem as soon as possible,\n and convert the discussion into an issue if the bug is verified.\n
\n

\ud83e\udd1d\u2002Code of conduct

\n

\n Please make sure that you are following our\n Code of Conduct,\n so that we can process the issue as soon as possible.\n

\n

\u2705\u2002Agreements

"}}, {"type": "checkboxes", "id": "terms", "attributes": {"label": "To submit an issue, please agree to the following terms and conditions:", "options": [{"label": "I have read the [Contributing Guidelines](https://github.com/AAriam/TemplateRepo/blob/main/CONTRIBUTING.md) and am following the [Bug Report Guidelines](https://aariam.github.io/TemplateRepo/contribute/feedback/report).", "required": true}, {"label": "I have read, understood, and agree to follow the [Code of Conduct](https://github.com/AAriam/TemplateRepo/blob/main/CODE_OF_CONDUCT.md).", "required": true}]}}, {"type": "markdown", "attributes": {"value": "

\ud83e\uddd1\u200d\ud83d\udcbb\u2002Collaborate

"}}, {"type": "checkboxes", "attributes": {"label": "Thank you again for filling this bug report.\nIf you are willing to collaborate on fixing the issue, please select the option below.\n", "options": [{"label": "I am willing to work on the issue and submit a pull request.", "required": false}]}}, {"type": "markdown", "attributes": {"value": "

System and Version Specifications

"}}, {"type": "dropdown", "id": "os", "attributes": {"label": "Operating System", "description": "Which operating systems have you tested?\nPlease select all options where you have encountered the bug.\n", "multiple": true, "options": []}, "validations": {"required": true}}, {"type": "dropdown", "id": "python_version", "attributes": {"label": "Python Version", "description": "Which Python versions have you tested?\nPlease select all versions where you have encountered the bug.\n", "multiple": true, "options": []}, "validations": {"required": true}}, {"type": "dropdown", "id": "package_manager", "attributes": {"label": "Package Manager", "description": "Which package manager have you used to download and install the package?\n", "multiple": false, "options": []}, "validations": {"required": true}}, {"type": "dropdown", "id": "version", "attributes": {"label": "Package Version", "description": "Which versions of our software are affected?\nPlease select all versions where you have encountered the bug.\n", "multiple": true, "options": []}, "validations": {"required": true}}, {"type": "textarea", "id": "environment", "attributes": {"label": "Environment", "description": "Please provide the details of all installed packages and their exact versions in the environment where you have encountered the bug. Follow the instructions below based on the package manager you have selected:\n1. **`pip`**: Run `pip freeze > requirements.txt` in your terminal within the environment, and copy the contents of the generated `requirements.txt` file here.\n2. **`conda`**: Run `conda env export > environment.yml` in your terminal within the environment (or alternatively `conda env export -n {YOUR_ENVIRONMENT_NAME} > environment.yml`), and copy the contents of the generated `environment.yml` file here."}, "validations": {"required": true}}, {"type": "markdown", "attributes": {"value": "
\n

Bug Report

\n"}}, {"type": "dropdown", "id": "gui_entry", "attributes": {"label": "GUI Entry Point", "description": "Which GUI entry point is causing the problem?\n", "multiple": false, "options": []}, "validations": {"required": true}}, {"type": "textarea", "id": "summary", "attributes": {"label": "Summary", "description": "Please provide a brief summary of the bug."}, "validations": {"required": true}}, {"type": "textarea", "id": "reproduce", "attributes": {"label": "Minimal Reproducible Example (MRE)", "description": "Please provide an exact step-by-step instruction to reproduce the bug. You can also include screenshots/recordings by dragging and dropping them here.", "value": "1. \n2. \n3.\n"}, "validations": {"required": true}}]}, {"id": "app_bug_cli", "primary_commit_id": "package_patch", "sub_type": "cli", "pre_process": {"if_any": [[]]}, "name": "\u2002\ud83d\udda5\u2002App\u2002\ud83d\udc1e\u2002Bug Report\u2002\u2328\ufe0f\u2002CLI", "description": "Report a problem (e.g. errors and unexpected results) encountered while using the application's command-line interface (CLI).", "body": [{"type": "markdown", "attributes": {"value": "

\n Thank you for taking the time to report a problem in TemplateRepo;\n we greatly appreciate your contribution! \u2764\ufe0f\ud83d\ude4f\n

\n

Terms and Conditions

\n

\n Before submitting a report, please take a moment to review and accept our terms and conditions;\n they will help us process the issue as fast as possible,\n and not bother you with additional questions.\n

\n

\u26d4\u2002Choosing the right form

\n\n
\n \ud83d\udca1\u2002Contact us\n
\n

\n Can't find the right form or unsure about which one to choose? \n Ask a question and get help in the \n discussion forum.\n

\n
\n

\u26a0\ufe0f\u2002Verifying the bug

\nBefore submitting a report, please make sure that you are following our Bug Report Guidelines to verify that:
    \n
  1. \n The issue you are experiencing is in fact a bug, and not a documented expected behavior.\n
    2. \n
  2. \n The bug is reproducible in the latest version of the release, and has not yet been reported.\n
    3. \n
\n
\n \ud83d\udca1 Open a discussion instead!\n
\n This verification process is non-trivial, and can be time-consuming.\n If you are not a collaborator and don't have the time to go through the process,\n you can always open a discussion instead; we will investigate the problem as soon as possible,\n and convert the discussion into an issue if the bug is verified.\n
\n

\ud83e\udd1d\u2002Code of conduct

\n

\n Please make sure that you are following our\n Code of Conduct,\n so that we can process the issue as soon as possible.\n

\n

\u2705\u2002Agreements

"}}, {"type": "checkboxes", "id": "terms", "attributes": {"label": "To submit an issue, please agree to the following terms and conditions:", "options": [{"label": "I have read the [Contributing Guidelines](https://github.com/AAriam/TemplateRepo/blob/main/CONTRIBUTING.md) and am following the [Bug Report Guidelines](https://aariam.github.io/TemplateRepo/contribute/feedback/report).", "required": true}, {"label": "I have read, understood, and agree to follow the [Code of Conduct](https://github.com/AAriam/TemplateRepo/blob/main/CODE_OF_CONDUCT.md).", "required": true}]}}, {"type": "markdown", "attributes": {"value": "

\ud83e\uddd1\u200d\ud83d\udcbb\u2002Collaborate

"}}, {"type": "checkboxes", "attributes": {"label": "Thank you again for filling this bug report.\nIf you are willing to collaborate on fixing the issue, please select the option below.\n", "options": [{"label": "I am willing to work on the issue and submit a pull request.", "required": false}]}}, {"type": "markdown", "attributes": {"value": "

System and Version Specifications

"}}, {"type": "dropdown", "id": "os", "attributes": {"label": "Operating System", "description": "Which operating systems have you tested?\nPlease select all options where you have encountered the bug.\n", "multiple": true, "options": []}, "validations": {"required": true}}, {"type": "dropdown", "id": "python_version", "attributes": {"label": "Python Version", "description": "Which Python versions have you tested?\nPlease select all versions where you have encountered the bug.\n", "multiple": true, "options": []}, "validations": {"required": true}}, {"type": "dropdown", "id": "package_manager", "attributes": {"label": "Package Manager", "description": "Which package manager have you used to download and install the package?\n", "multiple": false, "options": []}, "validations": {"required": true}}, {"type": "dropdown", "id": "version", "attributes": {"label": "Package Version", "description": "Which versions of our software are affected?\nPlease select all versions where you have encountered the bug.\n", "multiple": true, "options": []}, "validations": {"required": true}}, {"type": "textarea", "id": "environment", "attributes": {"label": "Environment", "description": "Please provide the details of all installed packages and their exact versions in the environment where you have encountered the bug. Follow the instructions below based on the package manager you have selected:\n1. **`pip`**: Run `pip freeze > requirements.txt` in your terminal within the environment, and copy the contents of the generated `requirements.txt` file here.\n2. **`conda`**: Run `conda env export > environment.yml` in your terminal within the environment (or alternatively `conda env export -n {YOUR_ENVIRONMENT_NAME} > environment.yml`), and copy the contents of the generated `environment.yml` file here."}, "validations": {"required": true}}, {"type": "markdown", "attributes": {"value": "
\n

Bug Report

\n"}}, {"type": "dropdown", "id": "cli_entry", "attributes": {"label": "CLI Entry Point", "description": "Which CLI entry point is causing the problem?\n", "multiple": false, "options": []}, "validations": {"required": true}}, {"type": "input", "attributes": {"label": "Console Command", "description": "Please provide the exact command (with all arguments) you are using.\n", "placeholder": "[] --help"}, "validations": {"required": true}}, {"type": "textarea", "id": "summary", "attributes": {"label": "Summary", "description": "Please provide a brief summary of the bug."}, "validations": {"required": true}}, {"type": "textarea", "id": "log", "attributes": {"label": "Console Output", "description": "Please provide the output of the command-line script.\n", "render": "shell"}, "validations": {"required": true}}]}, {"id": "app_bug_api", "primary_commit_id": "package_patch", "sub_type": "api", "name": "\u2002\ud83d\udda5\u2002App\u2002\ud83d\udc1e\u2002Bug Report\u2002\ud83d\udcf1\u2002API", "description": "Report a problem (e.g. errors and unexpected results) encountered while using the application's Python API.", "body": [{"type": "markdown", "attributes": {"value": "

\n Thank you for taking the time to report a problem in TemplateRepo;\n we greatly appreciate your contribution! \u2764\ufe0f\ud83d\ude4f\n

\n

Terms and Conditions

\n

\n Before submitting a report, please take a moment to review and accept our terms and conditions;\n they will help us process the issue as fast as possible,\n and not bother you with additional questions.\n

\n

\u26d4\u2002Choosing the right form

\n\n
\n \ud83d\udca1\u2002Contact us\n
\n

\n Can't find the right form or unsure about which one to choose? \n Ask a question and get help in the \n discussion forum.\n

\n
\n

\u26a0\ufe0f\u2002Verifying the bug

\nBefore submitting a report, please make sure that you are following our Bug Report Guidelines to verify that:
    \n
  1. \n The issue you are experiencing is in fact a bug, and not a documented expected behavior.\n
    2. \n
  2. \n The bug is reproducible in the latest version of the release, and has not yet been reported.\n
    3. \n
\n
\n \ud83d\udca1 Open a discussion instead!\n
\n This verification process is non-trivial, and can be time-consuming.\n If you are not a collaborator and don't have the time to go through the process,\n you can always open a discussion instead; we will investigate the problem as soon as possible,\n and convert the discussion into an issue if the bug is verified.\n
\n

\ud83e\udd1d\u2002Code of conduct

\n

\n Please make sure that you are following our\n Code of Conduct,\n so that we can process the issue as soon as possible.\n

\n

\u2705\u2002Agreements

"}}, {"type": "checkboxes", "id": "terms", "attributes": {"label": "To submit an issue, please agree to the following terms and conditions:", "options": [{"label": "I have read the [Contributing Guidelines](https://github.com/AAriam/TemplateRepo/blob/main/CONTRIBUTING.md) and am following the [Bug Report Guidelines](https://aariam.github.io/TemplateRepo/contribute/feedback/report).", "required": true}, {"label": "I have read, understood, and agree to follow the [Code of Conduct](https://github.com/AAriam/TemplateRepo/blob/main/CODE_OF_CONDUCT.md).", "required": true}]}}, {"type": "markdown", "attributes": {"value": "

\ud83e\uddd1\u200d\ud83d\udcbb\u2002Collaborate

"}}, {"type": "checkboxes", "id": "collab", "attributes": {"label": "Thank you again for filling this bug report.\nIf you are willing to collaborate on fixing the issue, please select the option below.\n", "options": [{"label": "I am willing to work on the issue and submit a pull request.", "required": false}]}}, {"type": "markdown", "attributes": {"value": "

System and Version Specifications

"}}, {"type": "dropdown", "id": "os", "attributes": {"label": "Operating System", "description": "Which operating systems have you tested?\nPlease select all options where you have encountered the bug.\n", "multiple": true, "options": []}, "validations": {"required": true}}, {"type": "dropdown", "id": "python_version", "attributes": {"label": "Python Version", "description": "Which Python versions have you tested?\nPlease select all versions where you have encountered the bug.\n", "multiple": true, "options": []}, "validations": {"required": true}}, {"type": "dropdown", "id": "package_manager", "attributes": {"label": "Package Manager", "description": "Which package manager have you used to download and install the package?\n", "multiple": false, "options": []}, "validations": {"required": true}}, {"type": "dropdown", "id": "version", "attributes": {"label": "Package Version", "description": "Which versions of our software are affected?\nPlease select all versions where you have encountered the bug.\n", "multiple": true, "options": []}, "validations": {"required": true}}, {"type": "textarea", "id": "environment", "attributes": {"label": "Environment", "description": "Please provide the details of all installed packages and their exact versions in the environment where you have encountered the bug. Follow the instructions below based on the package manager you have selected:\n1. **`pip`**: Run `pip freeze > requirements.txt` in your terminal within the environment, and copy the contents of the generated `requirements.txt` file here.\n2. **`conda`**: Run `conda env export > environment.yml` in your terminal within the environment (or alternatively `conda env export -n {YOUR_ENVIRONMENT_NAME} > environment.yml`), and copy the contents of the generated `environment.yml` file here."}, "validations": {"required": true}}, {"type": "markdown", "attributes": {"value": "
\n

Bug Report

\n"}}, {"type": "input", "id": "api_entry", "attributes": {"label": "Fully Qualified Name", "description": "Please provide the fully qualified name of the API endpoint that is causing the problem.\n", "value": "templaterepo."}, "validations": {"required": true}}, {"type": "textarea", "id": "summary", "attributes": {"label": "Summary", "description": "Please provide a brief summary of the bug."}, "validations": {"required": true}}, {"type": "textarea", "id": "code", "attributes": {"label": "Unit-Test / Minimal Reproducible Example (MRE)", "description": "Please provide a unit-test (preferred) or a minimal complete verifiable code example to test/reproduce the bug.", "value": "import ${{package.name]}\n\ndef unit_test():\n # write a unit-test here to reproduce the bug\n ...\n assert ...\n", "render": "python"}, "validations": {"required": true}}, {"type": "textarea", "id": "log", "attributes": {"label": "Error Message", "description": "Please provide the full traceback of the error message.\n", "render": "shell"}, "validations": {"required": true}}], "post_process": {"assign_creator": {"if_checkbox": {"id": "collab", "number": 1, "is_checked": true}}, "body": "

Bug Location

\n
    \n
  • Package Version: {version}
    • \n
  • Fully Qualified Name: {api_entry}
    • \n
\n

System and Version Specifications

\n
  • Operating System: {os}
    • \n
  • Python Version: {python_version}
    • \n
  • Package Manager: {package_manager}
    • \n
  • \n
    \nEnvironment\n\n```\n{environment}\n```\n\n
    • \n\n

    Bug Summary

    \n\n{summary}\n\n

    Unit-Test / Minimal Reproducible Example (MRE)

    \n \n{code}\n\n

    Error Message

    \n\n{log}\n"}}, {"id": "app_bug_setup", "primary_commit_id": "package_patch", "sub_type": "setup", "name": "\u2002\ud83d\udda5\u2002App\u2002\ud83d\udc1e\u2002Bug Report\u2002\u2699\ufe0f\u2002Setup", "description": "Report a problem in downloading, installation, or initialization of the application.", "body": [{"type": "markdown", "attributes": {"value": "

    \n Thank you for taking the time to report a problem in TemplateRepo;\n we greatly appreciate your contribution! \u2764\ufe0f\ud83d\ude4f\n

    \n

    Terms and Conditions

    \n

    \n Before submitting a report, please take a moment to review and accept our terms and conditions;\n they will help us process the issue as fast as possible,\n and not bother you with additional questions.\n

    \n

    \u26d4\u2002Choosing the right form

    \n
      \n
    • \n

      \n Please note that this form is specifically for reporting a non-security-related bug\n in the TemplateRepo setup process, i.e. an unexpected behavior that occurs during the \n download, installation, or initialization of the application.\n

      \n
      • \n
    • \n

      \n To \ud83d\udea8 report a security vulnerability\n \ud83d\udea8 please first read our\n security policy, and fill a\n private security advisory form instead.\n

      \n
      • \n
    • \n

      \n For other types of issues, such as problems in the\n Python API,\n website, or\n documentation,\n or for requesting new features and enhancements, please select the appropriate form \n from the issue template chooser.\n

      \n
      • \n
    \n
    \n \ud83d\udca1\u2002Contact us\n
    \n

    \n Can't find the right form or unsure about which one to choose? \n Ask a question and get help in the \n discussion forum.\n

    \n
    \n

    \u26a0\ufe0f\u2002Verifying the bug

    \nBefore submitting a report, please make sure that you are following our Bug Report Guidelines to verify that:
      \n
    1. \n The issue you are experiencing is in fact a bug, and not a documented expected behavior.\n
      2. \n
    2. \n The bug is reproducible in the latest version of the release, and has not yet been reported.\n
      3. \n
    \n
    \n \ud83d\udca1 Open a discussion instead!\n
    \n This verification process is non-trivial, and can be time-consuming.\n If you are not a collaborator and don't have the time to go through the process,\n you can always open a discussion instead; we will investigate the problem as soon as possible,\n and convert the discussion into an issue if the bug is verified.\n
    \n

    \ud83e\udd1d\u2002Code of conduct

    \n

    \n Please make sure that you are following our\n Code of Conduct,\n so that we can process the issue as soon as possible.\n

    \n

    \u2705\u2002Agreements

    "}}, {"type": "checkboxes", "id": "terms", "attributes": {"label": "To submit an issue, please agree to the following terms and conditions:", "options": [{"label": "I have read the [Contributing Guidelines](https://github.com/AAriam/TemplateRepo/blob/main/CONTRIBUTING.md) and am following the [Bug Report Guidelines](https://aariam.github.io/TemplateRepo/contribute/feedback/report).", "required": true}, {"label": "I have read, understood, and agree to follow the [Code of Conduct](https://github.com/AAriam/TemplateRepo/blob/main/CODE_OF_CONDUCT.md).", "required": true}]}}, {"type": "markdown", "attributes": {"value": "

    \ud83e\uddd1\u200d\ud83d\udcbb\u2002Collaborate

    "}}, {"type": "checkboxes", "attributes": {"label": "Thank you again for filling this bug report.\nIf you are willing to collaborate on fixing the issue, please select the option below.\n", "options": [{"label": "I am willing to work on the issue and submit a pull request.", "required": false}]}}, {"type": "markdown", "attributes": {"value": "

    System and Version Specifications

    "}}, {"type": "dropdown", "id": "os", "attributes": {"label": "Operating System", "description": "Which operating systems have you tested?\nPlease select all options where you have encountered the bug.\n", "multiple": true, "options": []}, "validations": {"required": true}}, {"type": "dropdown", "id": "python_version", "attributes": {"label": "Python Version", "description": "Which Python versions have you tested?\nPlease select all versions where you have encountered the bug.\n", "multiple": true, "options": []}, "validations": {"required": true}}, {"type": "dropdown", "id": "package_manager", "attributes": {"label": "Package Manager", "description": "Which package manager have you used to download and install the package?\n", "multiple": false, "options": []}, "validations": {"required": true}}, {"type": "dropdown", "id": "version", "attributes": {"label": "Package Version", "description": "Which versions of our software are affected?\nPlease select all versions where you have encountered the bug.\n", "multiple": true, "options": []}, "validations": {"required": true}}, {"type": "textarea", "id": "environment", "attributes": {"label": "Environment", "description": "Please provide the details of all installed packages and their exact versions in the environment where you have encountered the bug. Follow the instructions below based on the package manager you have selected:\n1. **`pip`**: Run `pip freeze > requirements.txt` in your terminal within the environment, and copy the contents of the generated `requirements.txt` file here.\n2. **`conda`**: Run `conda env export > environment.yml` in your terminal within the environment (or alternatively `conda env export -n {YOUR_ENVIRONMENT_NAME} > environment.yml`), and copy the contents of the generated `environment.yml` file here."}, "validations": {"required": true}}, {"type": "markdown", "attributes": {"value": "
    \n

    Bug Report

    \n"}}, {"type": "textarea", "id": "summary", "attributes": {"label": "Summary", "description": "Please provide a brief summary of the bug, and the steps necessary to reproduce it."}, "validations": {"required": true}}, {"type": "textarea", "id": "log", "attributes": {"label": "Error Message", "description": "If applicable, provide the full traceback of the error message.\n", "render": "shell"}, "validations": {"required": false}}]}, {"id": "app_request_enhancement", "primary_commit_id": "package_minor", "sub_type": "enhancement", "name": "\u2002\ud83d\udda5\u2002App\u2002\ud83d\udd14\u2002Request\u2002\ud83d\ude80\u2002Enhancement", "description": "Request an improvement to an existing feature in the application, for example in terms of performance, functionality, or ease of use.", "body": [{"type": "markdown", "attributes": {"value": "

    \n Thank you for taking the time to report a problem in TemplateRepo;\n we greatly appreciate your contribution! \u2764\ufe0f\ud83d\ude4f\n

    \n

    Terms and Conditions

    \n

    \n Before submitting a report, please take a moment to review and accept our terms and conditions;\n they will help us process the issue as fast as possible,\n and not bother you with additional questions.\n

    \n

    \u26d4\u2002Choosing the right form

    \n\n
    \n \ud83d\udca1\u2002Contact us\n
    \n

    \n Can't find the right form or unsure about which one to choose? \n Ask a question and get help in the \n discussion forum.\n

    \n
    \n

    \u26a0\ufe0f\u2002Verifying the request

    \nBefore submitting a report, please make sure that you are following our Contributing Guidelines to verify that:
      \n
    1. \n Your request is in fact for a non-breaking enhancement, and not a breaking change or new feature.\n
      2. \n
    2. \n The request is not implemented in the latest version of the release, \n and has not yet been filed by another person.\n
      3. \n
    \n
    \n \ud83d\udca1 Open a discussion instead!\n
    \n This verification process is non-trivial, and can be time-consuming.\n If you are not a collaborator and don't have the time to go through the process,\n you can always open a discussion instead; we will investigate the problem as soon as possible,\n and convert the discussion into an issue if the request is valid.\n
    \n

    \ud83e\udd1d\u2002Code of conduct

    \n

    \n Please make sure that you are following our\n Code of Conduct,\n so that we can process the issue as soon as possible.\n

    \n

    \u2705\u2002Agreements

    "}}, {"type": "checkboxes", "id": "terms", "attributes": {"label": "To submit an issue, please agree to the following terms and conditions:", "options": [{"label": "I have read the [Contributing Guidelines](https://github.com/AAriam/TemplateRepo/blob/main/CONTRIBUTING.md) and am following the [Bug Report Guidelines](https://aariam.github.io/TemplateRepo/contribute/feedback/report).", "required": true}, {"label": "I have read, understood, and agree to follow the [Code of Conduct](https://github.com/AAriam/TemplateRepo/blob/main/CODE_OF_CONDUCT.md).", "required": true}]}}, {"type": "markdown", "attributes": {"value": "

    \ud83e\uddd1\u200d\ud83d\udcbb\u2002Collaborate

    "}}, {"type": "checkboxes", "attributes": {"label": "Thank you again for filling this bug report.\nIf you are willing to collaborate on fixing the issue, please select the option below.\n", "options": [{"label": "I am willing to work on the issue and submit a pull request.", "required": false}]}}, {"type": "markdown", "attributes": {"value": "

    System and Version Specifications

    "}}, {"type": "dropdown", "id": "os", "attributes": {"label": "Operating System", "description": "Does this enhancement request apply to a specific operating system?\nIf so, please select the appropriate option.\n", "multiple": false, "options": []}, "validations": {"required": false}}, {"type": "dropdown", "id": "python_version", "attributes": {"label": "Python Version", "description": "Does this enhancement request apply to a specific Python version?\nIf so, please select the appropriate option.\n", "multiple": false, "options": []}, "validations": {"required": false}}, {"type": "dropdown", "id": "package_manager", "attributes": {"label": "Package Manager", "description": "Does this enhancement request apply to a specific package manager?\nIf so, please select the appropriate option.\n", "multiple": false, "options": []}, "validations": {"required": true}}, {"type": "markdown", "attributes": {"value": "
    \n

    Enhancement Request

    \n"}}, {"type": "dropdown", "id": "version", "attributes": {"label": "Package Version", "description": "Which version of our software is this request for?\n", "multiple": false, "options": []}, "validations": {"required": true}}, {"type": "dropdown", "id": "package_interface", "pre_process": {"if_any": [false]}, "attributes": {"label": "Package Interface", "description": "Which interface of our software is this request for?\n", "multiple": true, "options": ["Python API"]}, "validations": {"required": true}}, {"type": "textarea", "id": "summary", "attributes": {"label": "Summary", "description": "Please provide a brief summary of your enhancement request,\nincluding the motivation, use case, or problem it solves.\n"}, "validations": {"required": true}}]}, {"id": "app_request_feature", "primary_commit_id": "package_minor", "sub_type": "feat", "name": "\u2002\ud83d\udda5\u2002App\u2002\ud83d\udd14\u2002Request\u2002\u2728\u2002New Feature", "description": "Request a brand new feature that is not yet available in the application.", "body": [{"type": "markdown", "attributes": {"value": "

    \n Thank you for taking the time to report a problem in TemplateRepo;\n we greatly appreciate your contribution! \u2764\ufe0f\ud83d\ude4f\n

    \n

    Terms and Conditions

    \n

    \n Before submitting a report, please take a moment to review and accept our terms and conditions;\n they will help us process the issue as fast as possible,\n and not bother you with additional questions.\n

    \n

    \u26d4\u2002Choosing the right form

    \n\n
    \n \ud83d\udca1\u2002Contact us\n
    \n

    \n Can't find the right form or unsure about which one to choose? \n Ask a question and get help in the \n discussion forum.\n

    \n
    \n

    \u26a0\ufe0f\u2002Verifying the request

    \nBefore submitting a report, please make sure that you are following our Contributing Guidelines to verify that:
      \n
    1. \n Your request is in fact for a non-breaking new feature, and not a breaking change or an enhancement.\n
      2. \n
    2. \n The feature is not implemented in the latest version of the release, \n and has not yet been requested by another person.\n
      3. \n
    \n
    \n \ud83d\udca1 Open a discussion instead!\n
    \n This verification process is non-trivial, and can be time-consuming.\n If you are not a collaborator and don't have the time to go through the process,\n you can always open a discussion instead; we will investigate the problem as soon as possible,\n and convert the discussion into an issue if the request is valid.\n
    \n

    \ud83e\udd1d\u2002Code of conduct

    \n

    \n Please make sure that you are following our\n Code of Conduct,\n so that we can process the issue as soon as possible.\n

    \n

    \u2705\u2002Agreements

    "}}, {"type": "checkboxes", "id": "terms", "attributes": {"label": "To submit an issue, please agree to the following terms and conditions:", "options": [{"label": "I have read the [Contributing Guidelines](https://github.com/AAriam/TemplateRepo/blob/main/CONTRIBUTING.md) and am following the [Bug Report Guidelines](https://aariam.github.io/TemplateRepo/contribute/feedback/report).", "required": true}, {"label": "I have read, understood, and agree to follow the [Code of Conduct](https://github.com/AAriam/TemplateRepo/blob/main/CODE_OF_CONDUCT.md).", "required": true}]}}, {"type": "markdown", "attributes": {"value": "

    \ud83e\uddd1\u200d\ud83d\udcbb\u2002Collaborate

    "}}, {"type": "checkboxes", "id": "collab", "attributes": {"label": "Thank you again for filling this feature request.\nIf you are willing to collaborate on implementing the new feature, please select the option below.\n", "options": [{"label": "I am willing to work on the issue and submit a pull request.", "required": false}]}}, {"type": "markdown", "attributes": {"value": "

    System and Version Specifications

    "}}, {"type": "dropdown", "id": "os", "attributes": {"label": "Operating System", "description": "Does this feature request apply to a specific operating system?\nIf so, please select the appropriate option.\n", "multiple": false, "options": []}, "validations": {"required": false}}, {"type": "dropdown", "id": "python_version", "attributes": {"label": "Python Version", "description": "Does this feature request apply to a specific Python version?\nIf so, please select the appropriate option.\n", "multiple": false, "options": []}, "validations": {"required": false}}, {"type": "dropdown", "id": "package_manager", "attributes": {"label": "Package Manager", "description": "Does this feature request apply to a specific package manager?\nIf so, please select the appropriate option.\n", "multiple": false, "options": []}, "validations": {"required": false}}, {"type": "markdown", "attributes": {"value": "
    \n

    Feature Request

    \n"}}, {"type": "dropdown", "id": "version", "attributes": {"label": "Package Version", "description": "Which version of our software is this request for?\n", "multiple": false, "options": []}, "validations": {"required": true}}, {"type": "dropdown", "id": "package_interface", "pre_process": {"if_any": [false]}, "attributes": {"label": "Package Interface", "description": "Which interface of our software is this request for?\n", "multiple": true, "options": ["Python API"]}, "validations": {"required": true}}, {"type": "textarea", "id": "summary", "attributes": {"label": "Summary", "description": "Please provide a brief summary of your request,\nincluding the motivation, use case, or problem it solves.\n"}, "validations": {"required": true}}], "post_process": {"assign_creator": {"if_checkbox": {"id": "collab", "number": 1, "is_checked": true}}, "body": "

    Feature Location

    \n
      \n
    • Package Version: {version}
      • \n
    • Package Interface: {package_interface}
      • \n
    • Operating System: {os}
      • \n
    • Python Version: {python_version}
      • \n
    • Package Manager: {package_manager}
      • \n
    \n

    Request Summary

    \n\n{summary}\n"}}, {"id": "app_request_breaking", "primary_commit_id": "package_major", "sub_type": "breaking", "name": "\u2002\ud83d\udda5\u2002App\u2002\ud83d\udd14\u2002Request\u2002\ud83d\udca5\u2002Breaking Change", "description": "Request a backward-incompatible change to the API, such as a change in the behavior of an existing functionality.", "body": [{"type": "markdown", "attributes": {"value": "

    \n Thank you for taking the time to report a problem in TemplateRepo;\n we greatly appreciate your contribution! \u2764\ufe0f\ud83d\ude4f\n

    \n

    Terms and Conditions

    \n

    \n Before submitting a report, please take a moment to review and accept our terms and conditions;\n they will help us process the issue as fast as possible,\n and not bother you with additional questions.\n

    \n

    \u26d4\u2002Choosing the right form

    \n\n
    \n \ud83d\udca1\u2002Contact us\n
    \n

    \n Can't find the right form or unsure about which one to choose? \n Ask a question and get help in the \n discussion forum.\n

    \n
    \n

    \u26a0\ufe0f\u2002Verifying the request

    \nBefore submitting a report, please make sure that you are following our Contributing Guidelines to verify that:
      \n
    1. \n Your request is in fact for a breaking change, and not a new feature or an enhancement.\n
      2. \n
    2. \n The request has not yet been filed by another person.\n
      3. \n
    \n
    \n \ud83d\udca1 Open a discussion instead!\n
    \n This verification process is non-trivial, and can be time-consuming.\n If you are not a collaborator and don't have the time to go through the process,\n you can always open a discussion instead; we will investigate the problem as soon as possible,\n and convert the discussion into an issue if the request is valid.\n
    \n

    \ud83e\udd1d\u2002Code of conduct

    \n

    \n Please make sure that you are following our\n Code of Conduct,\n so that we can process the issue as soon as possible.\n

    \n

    \u2705\u2002Agreements

    "}}, {"type": "checkboxes", "id": "terms", "attributes": {"label": "To submit an issue, please agree to the following terms and conditions:", "options": [{"label": "I have read the [Contributing Guidelines](https://github.com/AAriam/TemplateRepo/blob/main/CONTRIBUTING.md) and am following the [Bug Report Guidelines](https://aariam.github.io/TemplateRepo/contribute/feedback/report).", "required": true}, {"label": "I have read, understood, and agree to follow the [Code of Conduct](https://github.com/AAriam/TemplateRepo/blob/main/CODE_OF_CONDUCT.md).", "required": true}]}}, {"type": "markdown", "attributes": {"value": "

    \ud83e\uddd1\u200d\ud83d\udcbb\u2002Collaborate

    "}}, {"type": "checkboxes", "attributes": {"label": "Thank you again for filling this feature request.\nIf you are willing to collaborate on implementing the new feature, please select the option below.\n", "options": [{"label": "I am willing to work on the issue and submit a pull request.", "required": false}]}}, {"type": "markdown", "attributes": {"value": "

    System and Version Specifications

    "}}, {"type": "dropdown", "id": "os", "attributes": {"label": "Operating System", "description": "Does this request apply to a specific operating system?\nIf so, please select the appropriate option.\n", "multiple": false, "options": []}, "validations": {"required": false}}, {"type": "dropdown", "id": "python_version", "attributes": {"label": "Python Version", "description": "Does this request apply to a specific Python version?\nIf so, please select the appropriate option.\n", "multiple": false, "options": []}, "validations": {"required": false}}, {"type": "dropdown", "id": "package_manager", "attributes": {"label": "Package Manager", "description": "Does this request apply to a specific package manager?\nIf so, please select the appropriate option.\n", "multiple": false, "options": []}, "validations": {"required": true}}, {"type": "markdown", "attributes": {"value": "
    \n

    Modification Request

    \n"}}, {"type": "dropdown", "id": "version", "attributes": {"label": "Package Version", "description": "Which version of our software is this request for?\n", "multiple": false, "options": []}, "validations": {"required": true}}, {"type": "dropdown", "id": "package_interface", "pre_process": {"if_any": [false]}, "attributes": {"label": "Package Interface", "description": "Which interface of our software is this request for?\n", "multiple": true, "options": ["Python API"]}, "validations": {"required": true}}, {"type": "textarea", "id": "summary", "attributes": {"label": "Summary", "description": "Please provide a brief summary of your request,\nincluding the motivation, use case, or problem it solves.\n"}, "validations": {"required": true}}]}]}, "label": {"auto_group": {"version": {"prefix": "Version: ", "color": "0366d6", "description": "Related to this specific version of the package."}, "target": {"prefix": "Target: ", "color": "0366d6", "description": "Related to this specific 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"stages": ["pre-commit", "manual"], "verbose": true}]}, {"repo": "https://github.com/astral-sh/ruff-pre-commit", "rev": "v0.0.290", "hooks": [{"id": "ruff", "stages": ["pre-commit", "manual"], "args": ["--fix", "--exit-non-zero-on-fix"], "types_or": ["python", "pyi", "jupyter"], "verbose": true}]}, {"repo": "https://github.com/pycqa/isort", "rev": "5.12.0", "hooks": [{"id": "isort", "stages": ["pre-commit", "manual"], "args": ["--settings-path", "pyproject.toml"], "verbose": true}]}, {"repo": "https://github.com/psf/black-pre-commit-mirror", "rev": "23.9.1", "hooks": [{"id": "black-jupyter", "stages": ["pre-commit", "manual"], "args": ["--config", "pyproject.toml"], "verbose": true}]}]}}, "codecov": {"coverage": {"precision": 2, "round": "nearest", "range": "90...100", "status": {"project": {"default": {"target": "100%", "threshold": "5%"}}}}, "comment": {"layout": "header, diff, flags, files", "require_changes": false, "behavior": "default"}}}, "package": {"conda": {"about": {"summary": "binary diff and patch using the BSDIFF4-format", "description": "A Python library for structural cheminformatics\n", "home": "https://github.com/ilanschnell/bsdiff4", "doc_url": "https://numpy.org/doc/stable/", "dev_url": "https://github.com/numpy/numpy", "license": "MIT", "license_family": "MIT", "license_file": ["LICENSE"], "prelink_message": ["prelink_message_file.txt", "folder-with-all-prelink-messages/"]}, "extra": {"recipe-maintainers": ["jakirkham"], "feedstock-name": "scipy"}}, "dev_config": {"max_line_length": 100}, "docs": {"main_init": "TemplateRepo\n\nPython Projects Perfected: Innovate, Develop, and Deploy Effortlessly!\n\nTemplateRepo is a free and open-source toolkit empowering the development of open-source Python projects on GitHub. It is a dynamic repository template that provides a complete, professional, and robust infrastructure for your project, where the only thing missing is your code. With TemplateRepo, you can solely focus on what truly matters: implementing your ideas and bringing your vision to life!\n\nCopyright 2023 Armin Ariamajd\n\nCopyright (C) 2023 Armin Ariamajd\n\nThis program is free software: you can redistribute it and/or modify\nit under the terms of the GNU Affero General Public License as published\nby the Free Software Foundation, either version 3 of the License, or\n(at your option) any later version.\n\nThis program is distributed in the hope that it will be useful,\nbut WITHOUT ANY WARRANTY; without even the implied warranty of\nMERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\nGNU Affero General Public License for more details.\n\nYou should have received a copy of the GNU Affero General Public License\nalong with this program. If not, see .\n"}, "manifest": ["graft src/templaterepo", "include CODE_OF_CONDUCT.md", "global-exclude *.py[cod] __pycache__ *.so"], "typed": true, "trove_classifiers": ["License :: OSI Approved :: GNU Affero General Public License v3 or later (AGPLv3+)", "Natural Language :: English", "Operating System :: MacOS", "Operating System :: Microsoft :: Windows", "Operating System :: POSIX :: Linux", "Programming Language :: Python :: 3 :: Only", "Programming Language :: Python :: 3.10", "Programming Language :: Python :: 3.11", "Programming Language :: Python :: 3.12", "Programming Language :: Python :: 3.9", "Typing :: Typed"], "urls": {"Homepage": "https://aariam.github.io/TemplateRepo", "Download": "https://github.com/AAriam/TemplateRepo/releases", "News": "https://aariam.github.io/TemplateRepo/news", "Documentation": "https://aariam.github.io/TemplateRepo", "Issue-Tracker": "https://github.com/AAriam/TemplateRepo/issues", "Sponsor": "https://aariam.github.io/TemplateRepo/contribute/collaborate/maintain/sponsor", "Source": "https://github.com/AAriam/TemplateRepo"}, "python_version_min": "3.9", "operating_systems": {"linux": {"runner": "ubuntu-latest"}, "macos": null, "windows": null}, "core_dependencies": [{"pip_spec": "numpy >= 1.21.2", "usage": "Numerical computing.", "url_source": "", "url_homepage": "", "url_docs": "", "conda_spec": "", "conda_channel": ""}], "name": "templaterepo", "python_version_max": "3.12", "python_versions": ["3.9", "3.10", "3.11", "3.12"], "python_versions_py3x": ["py39", "py310", "py311", "py312"], "python_versions_int": [[3, 9], [3, 10], [3, 11], [3, 12]], "os_titles": ["Linux", "macOS", "Windows"], "os_independent": false, "pure_python": true, "github_runners": ["ubuntu-latest", "macos-latest", "windows-latest"], "releases": {"per_branch": [], "branch_names": [], "os_titles": [], "python_versions": [], "package_versions": [], "package_managers": [], "cli_scripts": [], "gui_scripts": [], "has_scripts": false, "interfaces": ["Python API"]}}, "health_file": {"code_of_conduct": {"path": ".", "text": "# Contributor Covenant Code of Conduct\n\n## Our Pledge\n\nWe, the members, contributors, maintainers, and creators of ***TemplateRepo***,\npledge to act and interact in ways that contribute to an open, welcoming,\ndiverse, inclusive, healthy, and harassment-free community for every person involved in this project.\n\n## Our Standards\n\nExamples of behavior that contributes to a positive environment for our\ncommunity include:\n\n* Demonstrating empathy and kindness toward other people.\n* Being respectful of differing opinions, viewpoints, and experiences.\n* Giving and gracefully accepting constructive feedback.\n* Accepting responsibility and apologizing to those affected by our mistakes,\n and learning from the experience.\n* Focusing on what is best not just for us as individuals, but for the\n overall community.\n\nExamples of unacceptable behavior include:\n\n* The use of sexualized language or imagery, and sexual attention or\n advances of any kind.\n* Trolling, insulting or derogatory comments, and personal or political attacks.\n* Public or private harassment.\n* Publishing others' private information, such as a physical or email\n address, without their explicit permission.\n* Other conduct which could reasonably be considered inappropriate in a\n professional setting.\n\n## Enforcement Responsibilities\n\nCommunity leaders are responsible for clarifying and enforcing our standards of\nacceptable behavior and will take appropriate and fair corrective action in\nresponse to any behavior that they deem inappropriate, threatening, offensive,\nor harmful.\n\nCommunity leaders have the right and responsibility to remove, edit, or reject\ncomments, commits, code, wiki edits, issues, and other contributions that are\nnot aligned to this Code of Conduct, and will communicate reasons for moderation\ndecisions when appropriate.\n\n## Scope\n\nThis Code of Conduct applies within all community spaces, and also applies when\nan individual is officially representing the community in public spaces.\nExamples of representing our community include using an official e-mail address,\nposting via an official social media account, or acting as an appointed\nrepresentative at an online or offline event.\n\n## Enforcement\n\nInstances of abusive, harassing, or otherwise unacceptable behavior may be\nreported to the community leaders responsible for enforcement,\nat [None](mailto:None).\nAll complaints will be reviewed and investigated promptly and fairly.\n\nAll community leaders are obligated to respect the privacy and security of the\nreporter of any incident.\n\n## Enforcement Guidelines\n\nCommunity leaders will follow these Community Impact Guidelines in determining\nthe consequences for any action they deem in violation of this Code of Conduct:\n\n### 1. Correction\n\n**Community Impact**: Use of inappropriate language or other behavior deemed\nunprofessional or unwelcome in the community.\n\n**Consequence**: A private, written warning from community leaders, providing\nclarity around the nature of the violation and an explanation of why the\nbehavior was inappropriate. A public apology may be requested.\n\n### 2. Warning\n\n**Community Impact**: A violation through a single incident or series\nof actions.\n\n**Consequence**: A warning with consequences for continued behavior. No\ninteraction with the people involved, including unsolicited interaction with\nthose enforcing the Code of Conduct, for a specified period of time. This\nincludes avoiding interactions in community spaces as well as external channels\nlike social media. Violating these terms may lead to a temporary or\npermanent ban.\n\n### 3. Temporary Ban\n\n**Community Impact**: A serious violation of community standards, including\nsustained inappropriate behavior.\n\n**Consequence**: A temporary ban from any sort of interaction or public\ncommunication with the community for a specified period of time. No public or\nprivate interaction with the people involved, including unsolicited interaction\nwith those enforcing the Code of Conduct, is allowed during this period.\nViolating these terms may lead to a permanent ban.\n\n### 4. Permanent Ban\n\n**Community Impact**: Demonstrating a pattern of violation of community\nstandards, including sustained inappropriate behavior, harassment of an\nindividual, or aggression toward or disparagement of classes of individuals.\n\n**Consequence**: A permanent ban from any sort of public interaction within\nthe community.\n\n## Attribution\n\nThis Code of Conduct is adapted from the [Contributor Covenant][homepage],\nversion 2.0, available at\nhttps://www.contributor-covenant.org/version/2/0/code_of_conduct.html.\n\nCommunity Impact Guidelines were inspired by [Mozilla's code of conduct\nenforcement ladder](https://github.com/mozilla/diversity).\n\n[homepage]: https://www.contributor-covenant.org\n\nFor answers to common questions about this code of conduct, see the FAQ at\nhttps://www.contributor-covenant.org/faq. Translations are available at\nhttps://www.contributor-covenant.org/translations.\n"}, "contributing": {"path": ".", "text": "# Contributing Guidelines\n\n

    \n Welcome to the TemplateRepo community!\n We are excited to have you here,\n and grateful that you are considering contributing.\n TemplateRepo is a free and open-source project that evolves with the needs of its users,\n and can only survive and grow through the help of great members like you.\n

    \n\n
    \n \u2764\ufe0f\ud83d\ude4f We Appreciate All Your Work!\n
    \n We follow the All Contributors\n specifications; all types of contributions are encouraged and valued, and all contributors are\n acknowledged on our public website\n and repository.\n
    \n\n## How To Contribute\n\n

    \n To keep all documentation on our project organized and easy to find, the complete\n contribution guide is hosted on our website.\n

    \n"}, "governance": {"path": ".", "text": ""}, "security": {"path": ".", "text": "# TemplateRepo Security and Vulnerability Disclosure Policy\n\nTemplateRepo takes the security and privacy of all its users and members very seriously,\nand is committed to ensuring the safety of its products and services.\nIn case a security vulnerability is detected that may affect users, we take immediate action to:\n1. fix the issue as soon as possible,\n2. publish a new security patch release in case a published application was affected,\n3. release a security advisory, detailing the vulnerability,\nas well as guidelines for end-users to protect themselves.\nSecurity advisories are accessible on our website and repository, as well as via a feed.\n\n\nhttps://aariam.github.io/TemplateRepo/contribute/collaborate/maintain/security\n\n
    \n \ud83d\udee1\ufe0f**Supported Versions**\n

    \n Currently supported versions for security updates are:\n
    \n\nThis policy is intended to give users, contributors, and security researchers clear guidelines for\n[reporting potential security vulnerabilities](#reporting-a-potential-vulnerability),\nand [conducting vulnerability discovery activities](#testing-for-vulnerabilities).\nIt describes what systems and types of research are covered under this policy,\nhow to send us vulnerability reports and what information to include,\nand how long we ask security researchers to wait before publicly disclosing vulnerabilities.\n\n
    \n \ud83d\udee1\ufe0f**Supported Versions**\n

    \n Questions regarding this policy may be sent to security@agency.gov.\n We also invite you to contact us with suggestions for improving this policy.\n
    \n\n\n## Reporting a Potential Vulnerability\nIf you have found a potential vulnerability in our application, website, or repository,\nplease report it as soon as possible, following the guidelines described here.\nPlease DO NOT\n\n### Where to Report\nWe use [GitHub's security advisories feature](https://docs.github.com/en/code-security/security-advisories/repository-security-advisories/about-repository-security-advisories)\nof our repository to securely discuss, fix and publish information about security vulnerabilities\nin TemplateRepo. To privately report a security vulnerability,\nfollow the [documentation on Github](https://docs.github.com/en/code-security/security-advisories/guidance-on-reporting-and-writing/privately-reporting-a-security-vulnerability#privately-reporting-a-security-vulnerability)\nor [**click here to directly open a private report form**](https://github.com/AAriam/TemplateRepo/security/advisories/new).\n\n
    \n \ud83e\udd77\ud83c\udffe Prefer Anonymity?\n

    \n Our vulnerability management team also welcomes anonymous emails sent to\n None.\n
    \n\n---Thank you for reporting a security vulnerability. Please provide as much information as you can under the sections listed below. Texts like this that are surrounded by three hyphens are instructions and should be deleted before sending the email.---\n\n1. Summary\n---Provide a short summary of the problem. Make the impact and severity as clear as possible. For example: An unsafe deserialization vulnerability allows any unauthenticated user to execute arbitrary code on the server.---\n\n2. Details\n---Give all details on the vulnerability. Pointing to the incriminated source code is very helpful for the maintainer.---\n\n3. PoC\n---Complete instructions, including specific configuration details, to reproduce the vulnerability.---\n\n4. Impact\n---What kind of vulnerability is it? Who is impacted?---\n\n5. Affected Products\n---For each affected product, name the ecosystem (e.g. pip, GitHub Actions), package- or filename, and affected versions.---\n\n6. Severity\n---Asses the severity of the issue, e.g. using a CVSS vector string (learn more at https://www.first.org/cvss/v3.1/user-guide).---\n\n7. Weaknesses\n---Provide Common Weakness Enumerator (CWE; learn more at https://docs.github.com/en/code-security/security-advisories/repository-security-advisories/about-repository-security-advisories#cve-identification-numbers).---\n\n8. Mitigation\n---Provide necessary steps to mitigate the problem.---\n\n\n### What to Include\nIn order to help us triage and prioritize submissions, we recommend that your reports:\n* Describe the location the vulnerability was discovered,\naffected components/versions, and the potential impact of exploitation.\n* Offer a detailed description of the vulnerability and the steps needed to reproduce it\n(proof of concept scripts or screenshots can be helpful).\n* if known, necessary steps to mitigate the issue.\n\nFor more information, see GitHub Documentations on [creating a repository security advisory](https://docs.github.com/en/code-security/security-advisories/repository-security-advisories/creating-a-repository-security-advisory)\nand [best practices for writing repository security advisories](https://docs.github.com/en/code-security/security-advisories/guidance-on-reporting-and-writing/best-practices-for-writing-repository-security-advisories).\n\n### Response Policy\nWhen you choose to share your contact information with us,\nwe commit to coordinating with you as openly and as quickly as possible:\n* Within a week, our vulnerability management team will acknowledge receiving your report.\n* To the best of our ability, we will confirm the existence of the vulnerability to you\nand be as transparent as possible about what steps we are taking during the remediation process,\nincluding on issues or challenges that may delay resolution.\n* We will maintain an open dialogue to discuss issues.\n\n### Disclosure Policy\nThis project follows a 90-day disclosure timeline.\nIf you are a security researcher and would like to disclose the vulnerability you detected,\nwe request that you allow us at least 90 days prior to any public exposure.\nThis helps the project contributors to resolve the vulnerability and issue a new release,\nand provides our users a chance to update their applications and protect themselves.\n\n\n\n## Testing for Vulnerabilities\nTemplateRepo is a free and open-source project.\nWe encourage security researchers to help us improve our security measures\nby conducting vulnerability discovery activities on our application, website, and repository.\nBefore starting, please read the [guidelines](#testing-for-vulnerabilities) below,\ndescribing what systems and types of research are covered under this policy.\n\n### Authorization\nIf you make a good faith effort to comply with this policy during your security research,\nwe will consider your research to be authorized, will work with you to understand and resolve the issue quickly,\nand will not recommend or pursue legal action related to your research.\nShould legal action be initiated by a third party against you for activities that were conducted\nin accordance with this policy, we will make this authorization known.\n\n### Guidelines\nUnder this policy, \"research\" and \"vulnerability discovery\" means activities in which you:\n* notify us as soon as possible after you discover a real or potential security issue,\n* make every effort to avoid privacy violations, degradation of user experience,\ndisruption to production systems, and destruction or manipulation of data,\n* only use exploits to the extent necessary to confirm a vulnerability's presence,\n* do not use an exploit to compromise or exfiltrate data, establish persistent command line access,\nor use the exploit to pivot to other systems,\n* provide us a reasonable amount of time to resolve the issue before you disclose it publicly,\n* do not submit a high volume of low-quality reports.\n\nOnce you've established that a vulnerability exists or encounter\nany sensitive data (including personally identifiable information, financial information,\nor proprietary information or secrets of any kind), you must:\n* stop your test,\n* notify us immediately,\n* and not disclose this data to anyone else.\n\n### Test Methods\nThe following test methods are not authorized:\n* Network denial of service (DoS or DDoS) tests or other tests that\nimpair access to or damage a system or data.\n* Social engineering (e.g. phishing, vishing), or any other non-technical vulnerability testing.\n\n### Scope\nThis policy applies to the following systems and services:\n* Source code at https://github.com/AAriam/TemplateRepo\n\nAny service not expressly listed above, such as any connected services, are excluded from scope\nand are not authorized for testing. Additionally, vulnerabilities found in systems from our vendors\nfall outside of this policy's scope and should be reported directly to the vendor according to their\ndisclosure policy (if any). If you aren't sure whether a system is in scope or not,\nor there is a particular system not in scope that you think merits testing,\nplease contact us at None to discuss it first, before starting your research.\n"}, "support": {"path": ".", "text": ""}, "codeowners": {"path": ".github"}}, "readme": {"repo": {"header": {"style": "vertical"}, "body": {"style": "ver", "sections": [{"id": "ci"}]}}, "package": {}, "dir": {".github": "# GitHub Directory\n", ".github/DISCUSSION_TEMPLATE": "# Discussion Category Forms\n[Discussion category forms](https://docs.github.com/en/discussions/managing-discussions-for-your-community/creating-discussion-category-forms)\ncustomize the templates that are available for community members to use\nwhen they open new discussions in the repository.\nIt encourages community members to include specific, structured information\nin their discussions by using customizable web form fields.\n\nTo be recognized by GitHub, discussion category forms must be stored in the directory `/.github/DISCUSSION_TEMPLATE/`\n(i.e. this directory). Each YAML file defines a form for a specific discussion category, indicated by the\nfilename, which must correspond with the slug for one of the discussion categories.\nFor example, the template for the \"New Announcements\" category should be stored in `.github/DISCUSSION_TEMPLATE/new-announcements.yml`.\nDiscussion forms, like issue forms, are written in YAML, using the\nGitHub [form schema](https://docs.github.com/en/communities/using-templates-to-encourage-useful-issues-and-pull-requests/syntax-for-githubs-form-schema).\n", ".github/ISSUE_TEMPLATE": "# GitHub Issues Settings\nThis directory contains templates and configurations used when an issue is opened in the repository.\n\n## Templates\nThe issues templates use the GitHub's [issue forms](https://docs.github.com/en/communities/using-templates-to-encourage-useful-issues-and-pull-requests/configuring-issue-templates-for-your-repository#creating-issue-forms)\nto create customizable web form fields. Each `.yml` file (other than `config.yml`) provides a template for\na specific issue type. The issue forms use the YAML format, with a series of defined [top-level keys](https://docs.github.com/en/communities/using-templates-to-encourage-useful-issues-and-pull-requests/syntax-for-issue-forms#top-level-syntax)\nsuch as `name`, `description` and `labels`, and a [body syntax](https://docs.github.com/en/communities/using-templates-to-encourage-useful-issues-and-pull-requests/syntax-for-githubs-form-schema)\nto define the form fields.\n\nAny YAML file created in this directory using the specified syntax will be automatically added to the list of possible\nissue forms that users can select from when opening a new issue in the repository.\n\n\n## Configurations\nThe [config.yml](../../.meta/config/issues_template_chooser.yaml) file contains the configurations for the\n[template chooser](https://docs.github.com/en/communities/using-templates-to-encourage-useful-issues-and-pull-requests/configuring-issue-templates-for-your-repository#configuring-the-template-chooser),\ni.e. the landing page of the repository's 'Issues' section.\n\n### Options\n- `blank_issues_enabled`: A boolean value defining whether free-form issues can be opened by users.\n- `contact_links`: An array of dictionaries, defining additional external links for opening issues.\nThese options will be displayed alongside the available templates in the 'Issues' section of the repository.\n\n## References\n- [GitHub Documentation](https://docs.github.com/en/communities/using-templates-to-encourage-useful-issues-and-pull-requests/about-issue-and-pull-request-templates)\n", ".github/PULL_REQUEST_TEMPLATE": "# GitHub Pull Requests Templates\nThis directory contains additional templates for pull requests.\n\nBy default, the template defined at [./github/pull_request_template.md](./github/pull_request_template.md)\nis used when opening a pull request. To use the extra templates in this directory,\nthe `template` [query parameter](https://docs.github.com/en/pull-requests/collaborating-with-pull-requests/proposing-changes-to-your-work-with-pull-requests/using-query-parameters-to-create-a-pull-request)\nmust be added to the URL of the pull request form, defining the name of the template to use.\nFor example, to use a template file named `my_custom_template.md`, add the following query string at the end of the\nURL: `?template=my_custom_template.md`. A full URL may e.g. look like this:\nhttps://github.com/my-username/my-repo/compare/main...my-branch?template=my_custom_template.md\n\n## Notes\n- Pull request template filenames are not case-sensitive, and can have an extension such as `.md` or `.txt`.\n- The YAML syntax used for issue forms is not supported for pull requests templates.\n\n## References\n- [GitHub Documentation](https://docs.github.com/en/communities/using-templates-to-encourage-useful-issues-and-pull-requests/creating-a-pull-request-template-for-your-repository)\n", ".github/workflows": "# GitHub Actions Workflows\nThis directory contains [workflows](https://docs.github.com/en/actions/using-workflows/about-workflows)\nused in the CI/CD operations of the repository.\n\n## [docs_rtd_pr_preview](_docs_rtd-pr-preview.yaml)\nhttps://docs.readthedocs.io/en/latest/pull-requests.html\nhttps://docs.readthedocs.io/en/latest/guides/pull-requests.html\n\n## Releases\nGitHub has [built-in functionality](https://docs.github.com/en/repositories/releasing-projects-on-github/automatically-generated-release-notes)\nto automatically generate release notes.\n\n## Used Actions\n\n### setup-python\nhttps://github.com/marketplace/actions/setup-python\n\n### setup-micromamba\nhttps://github.com/mamba-org/setup-micromamba\nreplacing [provision-with-micromamba](https://github.com/mamba-org/provision-with-micromamba)\n\n## Syntax\n\n### on: schedule: cron\nschedule : https://docs.github.com/en/actions/using-workflows/events-that-trigger-workflows#schedule\ncron tasks: https://pubs.opengroup.org/onlinepubs/9699919799/utilities/crontab.html#tag_20_25_07\n\n## References\n- [GitHub Actions Documentation](https://docs.github.com/en/actions)\n- [Workflow Syntax](https://docs.github.com/en/actions/using-workflows/workflow-syntax-for-github-actions)\n\n## Useful Links\n- [Workflow security: `pull_request` vs `pull_request_target`](https://securitylab.github.com/research/github-actions-preventing-pwn-requests/)\n", ".meta": "# Meta Directory\nThis directory contains all the meta content of the repository.\n\n## PyPI\n\n### dependencies\nEither a list of dependencies, or a string representing the filepath (from root) to a txt file containing one\ndependency per line.\n\n### optional_dependencies\nEither a dictionary, where keys are the name of the group of optional dependencies, and the values are lists of\ncorresponding dependencies, or a string representing the path (from root) to a directory containing one\ntxt file (named .txt) with one dependency per line, for each dependency group.\n", "docs/website": "# Documentation Website\n\n## Requirements\n\n### sphinxext-opengraph\nTo add [Open Graph](https://ogp.me/) meta tags to each HTML page of the site.\n\nPyPI: https://pypi.org/project/sphinxext-opengraph\nconda-forge: https://anaconda.org/conda-forge/sphinxext-opengraph\nGitHub: https://github.com/wpilibsuite/sphinxext-opengraph\nDocs: https://sphinxext-opengraph.readthedocs.io/en/latest/\n\n### Extra Requirements\nfrom 'apt': \"librsvg2-bin\"\n"}}, "color": {"primary": ["135400", "459B24"], "secondary": ["055005", "9CCC00"]}, "web": {"base_url": "", "readthedocs": {"name": "templaterepo", "version": 2, "build": {"os": "ubuntu-22.04", "tools": {"python": "mambaforge-4.10"}, "jobs": {"post_checkout": ["git fetch --unshallow"]}}, "conda": {"environment": "docs/website/requirements.yaml"}, "python": {"install": [{"method": "pip", "path": "."}]}, "sphinx": {"configuration": "docs/website/source/conf.py", "builder": "dirhtml", "fail_on_warning": false}, "formats": "all"}, "announcement_retention_days": 30, "navbar_icons": [{"id": "pypi"}, {"id": "conda"}, {"id": "repo"}, {"id": "issues"}, {"id": "pull_requests"}, {"id": "discussions"}, {"id": "email"}, {"id": "license"}, {"id": "twitter"}, {"id": "linkedin"}, {"id": "researchgate"}, {"id": "orcid"}], "quicklinks": [[{"title": "Install", "path": "manual/install", "include_in_readme": true}], [{"title": "Releases", "path": "news/category/release", "include_in_readme": true}], [{"title": "Q&A", "path": "help/ask", "include_in_readme": true}]], "analytics": {"plausible": {"domain": "", "url": ""}, "google_id": "G-0X66W6TGL2"}, "path": {"contact": "help/contact", "news": "news", "contributors": "about/#contributors", "contributing": "contribute", "bug_report": "contribute/feedback/report", "license": "license", "security_measures": "contribute/collaborate/maintain/security", "sponsor": "contribute/collaborate/maintain/sponsor"}}, "path": {"dir": {"source": "src", "tests": "tests", "website": "docs/website", "local": {"root": ".local", "cache": {"root": ".local/cache", "repodynamics": ".local/cache/repodynamics", "coverage": ".local/cache/coverage", "mypy": ".local/cache/mypy", "pylint": ".local/cache/pylint", "pytest": ".local/cache/pytest", "ruff": ".local/cache/ruff"}, "report": {"root": ".local/report", "repodynamics": ".local/report/repodynamics", "coverage": ".local/report/coverage", "mypy": ".local/report/mypy", "pylint": ".local/report/pylint", "pytest": ".local/report/pytest", "ruff": ".local/report/ruff"}}, "meta": ".meta"}, "file": {"website_announcement": "docs/website/announcement.html"}}, "owner": {"username": "aariam", "name": "Armin Ariamajd", "company": "Freie Universit\u00e4t Berlin (FUB)", "location": "Berlin", "email": null, "bio": "Studying M.Sc. Computational Sciences and M.Sc. Chemistry, and working as teaching assistant in theoretical chemistry at FUB.", "id": 80158628, "node_id": "MDQ6VXNlcjgwMTU4NjI4", "avatar_url": "https://avatars.githubusercontent.com/u/80158628?v=4", "url": {"website": "", "github": "https://github.com/AAriam", "linkedin": "https://linkedin.com/in/armin-ariamajd", "twitter": "https://twitter.com/Al___Chemist", "researchgate": "https://researchgate.net/profile/Armin_Ariamajd", "orcid": "https://orcid.org/0000-0003-1563-6987"}, "publications": [{"doi": "10.1039/d2sc03130b", "url": "https://doi.org/10.1039/d2sc03130b", "type": "journal-article", "subtype": null, "cite": {"BibTex": "@article{Urner_2022,\n\tdoi = {10.1039/d2sc03130b},\n\turl = {https://doi.org/10.1039%2Fd2sc03130b},\n\tyear = 2022,\n\tpublisher = {Royal Society of Chemistry ({RSC})},\n\tvolume = {13},\n\tnumber = {35},\n\tpages = {10299--10307},\n\tauthor = {Leonhard H. Urner and Armin Ariamajd and Alex Weikum},\n\ttitle = {Combinatorial synthesis enables scalable designer detergents for membrane protein studies},\n\tjournal = {Chemical Science}\n}", "RIS": "TY - JOUR\nDO - 10.1039/d2sc03130b\nUR - http://dx.doi.org/10.1039/d2sc03130b\nTI - Combinatorial synthesis enables scalable designer detergents for membrane protein studies\nT2 - Chemical Science\nAU - Urner, Leonhard H.\nAU - Ariamajd, Armin\nAU - Weikum, Alex\nPY - 2022\nPB - Royal Society of Chemistry (RSC)\nSP - 10299-10307\nIS - 35\nVL - 13\nSN - 2041-6520\nSN - 2041-6539\nER - \n"}, "journal": "Chemical Science", "journal_abbr": "Chem. Sci.", "publisher": "Royal Society of Chemistry (RSC)", "title": "Combinatorial synthesis enables scalable designer detergents for membrane protein studies", "pages": "10299-10307", "volume": "13", "issue": "35", "date_tuple": [2022, 8, 30], "year": 2022, "date": "30 August 2022", "abstract": "Combinatorial detergent synthesis permits access to an unexplored part of the detergentome and provides new directions for the preparation of custom-made detergents for future applications."}, {"doi": "10.1093/nar/gkac267", "url": "https://doi.org/10.1093/nar/gkac267", "type": "journal-article", "subtype": null, "cite": {"BibTex": "@article{Sydow_2022,\n\tdoi = {10.1093/nar/gkac267},\n\turl = {https://doi.org/10.1093%2Fnar%2Fgkac267},\n\tyear = 2022,\n\tmonth = {may},\n\tpublisher = {Oxford University Press ({OUP})},\n\tvolume = {50},\n\tnumber = {W1},\n\tpages = {W753--W760},\n\tauthor = {Dominique Sydow and Jaime Rodr{\\'{\\i}}guez-Guerra and Talia~B Kimber and David Schaller and Corey~J Taylor and Yonghui Chen and Mareike Leja and Sakshi Misra and Michele Wichmann and Armin Ariamajd and Andrea Volkamer},\n\ttitle = {{TeachOpenCADD} 2022: open source and {FAIR} Python pipelines to assist in structural bioinformatics and cheminformatics research},\n\tjournal = {Nucleic Acids Research}\n}", "RIS": "TY - JOUR\nDO - 10.1093/nar/gkac267\nUR - http://dx.doi.org/10.1093/nar/gkac267\nTI - TeachOpenCADD 2022: open source and FAIR Python pipelines to assist in structural bioinformatics and cheminformatics research\nT2 - Nucleic Acids Research\nAU - Sydow, Dominique\nAU - Rodr\u00edguez-Guerra, Jaime\nAU - Kimber, Talia\u00a0B\nAU - Schaller, David\nAU - Taylor, Corey\u00a0J\nAU - Chen, Yonghui\nAU - Leja, Mareike\nAU - Misra, Sakshi\nAU - Wichmann, Michele\nAU - Ariamajd, Armin\nAU - Volkamer, Andrea\nPY - 2022\nDA - 2022/05/07\nPB - Oxford University Press (OUP)\nSP - W753-W760\nIS - W1\nVL - 50\nSN - 0305-1048\nSN - 1362-4962\nER - \n"}, "journal": "Nucleic Acids Research", "journal_abbr": "Nucleic Acids Res.", "publisher": "Oxford University Press (OUP)", "title": "TeachOpenCADD 2022: open source and FAIR Python pipelines to assist in structural bioinformatics and cheminformatics research", "pages": "W753-W760", "volume": "50", "issue": "W1", "date_tuple": [2022, 5, 7], "year": 2022, "date": "7 May 2022", "abstract": "Computational pipelines have become a crucial part of modern drug discovery campaigns. Setting up and maintaining such pipelines, however, can be challenging and time-consuming\u2014especially for novice scientists in this domain. TeachOpenCADD is a platform that aims to teach domain-specific skills and to provide pipeline templates as starting points for research projects. We offer Python-based solutions for common tasks in cheminformatics and structural bioinformatics in the form of Jupyter notebooks, based on open source resources only. Including the 12 newly released additions, TeachOpenCADD now contains 22 notebooks that cover both theoretical background as well as hands-on programming. To promote reproducible and reusable research, we apply software best practices to our notebooks such as testing with automated continuous integration and adhering to the idiomatic Python style. The new TeachOpenCADD website is available at https://projects.volkamerlab.org/teachopencadd and all code is deposited on GitHub."}, {"doi": "10.26434/chemrxiv-2021-8x13n", "url": "https://doi.org/10.26434/chemrxiv-2021-8x13n", "type": "posted-content", "subtype": "preprint", "cite": {"BibTex": "@article{Sydow_2021,\n\tdoi = {10.26434/chemrxiv-2021-8x13n},\n\turl = {https://doi.org/10.26434%2Fchemrxiv-2021-8x13n},\n\tyear = 2021,\n\tmonth = {dec},\n\tpublisher = {American Chemical Society ({ACS})},\n\tauthor = {Dominique Sydow and Jaime Rodr{\\'{\\i}}guez-Guerra and Talia B. Kimber and David Schaller and Corey J. Taylor and Yonghui Chen and Mareike Leja and Sakshi Misra and Michele Wichmann and Armin Ariamajd and Andrea Volkamer},\n\ttitle = {{TeachOpenCADD} 2021: Open Source and {FAIR} Python Pipelines to Assist in Structural Bioinformatics and Cheminformatics Research}\n}", "RIS": "TY - GENERIC\nDO - 10.26434/chemrxiv-2021-8x13n\nUR - http://dx.doi.org/10.26434/chemrxiv-2021-8x13n\nTI - TeachOpenCADD 2021: Open Source and FAIR Python Pipelines to Assist in Structural Bioinformatics and Cheminformatics Research\nAU - Sydow, Dominique\nAU - Rodr\u00edguez-Guerra, Jaime\nAU - Kimber, Talia B.\nAU - Schaller, David\nAU - Taylor, Corey J.\nAU - Chen, Yonghui\nAU - Leja, Mareike\nAU - Misra, Sakshi\nAU - Wichmann, Michele\nAU - Ariamajd, Armin\nAU - Volkamer, Andrea\nPY - 2021\nDA - 2021/12/13\nPB - American Chemical Society (ACS)\nER - \n"}, "journal": null, "journal_abbr": null, "publisher": "American Chemical Society (ACS)", "title": "TeachOpenCADD 2021: Open Source and FAIR Python Pipelines to Assist in Structural Bioinformatics and Cheminformatics Research", "pages": null, "volume": null, "issue": null, "date_tuple": [2021, 12, 13], "year": 2021, "date": "13 December 2021", "abstract": "Computational pipelines have become a crucial part of modern drug discovery campaigns. Setting up and maintaining such pipelines, however, can be challenging and time-consuming --- especially for novice scientists in this domain. TeachOpenCADD is a platform that aims to teach domain-specific skills and to provide pipeline templates as starting points for research projects. We offer Python-based solutions for common tasks in cheminformatics and structural bioinformatics in the form of Jupyter notebooks and based on open source resources only. Including the 12 newly released additions, TeachOpenCADD now contains 22 notebooks that each cover both theoretical background as well as hands-on programming. To promote reproducible and reusable research, we apply software best practices to our notebooks such as testing with an automated continuous integration and adhering to a more idiomatic Python style. The new TeachOpenCADD website is available at https://projects.volkamerlab.org/teachopencadd and all code is deposited on GitHub."}, {"doi": "10.3762/bjoc.17.8", "url": "https://doi.org/10.3762/bjoc.17.8", "type": "journal-article", "subtype": null, "cite": {"BibTex": "@article{Ariamajd_2021,\n\tdoi = {10.3762/bjoc.17.8},\n\turl = {https://doi.org/10.3762%2Fbjoc.17.8},\n\tyear = 2021,\n\tmonth = {jan},\n\tpublisher = {Beilstein Institut},\n\tvolume = {17},\n\tpages = {83--88},\n\tauthor = {Armin Ariamajd and Nils J Gerwien and Benjamin Schwabe and Stefan Dix and Matthew N Hopkinson},\n\ttitle = {Benzothiazolium salts as reagents for the deoxygenative perfluoroalkylthiolation of alcohols},\n\tjournal = {Beilstein Journal of Organic Chemistry}\n}", "RIS": "TY - JOUR\nDO - 10.3762/bjoc.17.8\nUR - http://dx.doi.org/10.3762/bjoc.17.8\nTI - Benzothiazolium salts as reagents for the deoxygenative perfluoroalkylthiolation of alcohols\nT2 - Beilstein Journal of Organic Chemistry\nAU - Ariamajd, Armin\nAU - Gerwien, Nils J\nAU - Schwabe, Benjamin\nAU - Dix, Stefan\nAU - Hopkinson, Matthew N\nPY - 2021\nDA - 2021/01/08\nPB - Beilstein Institut\nSP - 83-88\nVL - 17\nSN - 1860-5397\nER - \n"}, "journal": "Beilstein Journal of Organic Chemistry", "journal_abbr": "Beilstein J. Org. Chem.", "publisher": "Beilstein Institut", "title": "Benzothiazolium salts as reagents for the deoxygenative perfluoroalkylthiolation of alcohols", "pages": "83-88", "volume": "17", "issue": null, "date_tuple": [2021, 1, 8], "year": 2021, "date": "8 January 2021", "abstract": "A series of 2-(perfluoroalkylthio)benzothiazolium (BT-SRF) salts have been synthesized that serve as convenient sources of hitherto underexplored perfluoroalkylthiolate anions. An investigation of their reactivity in a deoxygenative nucleophilic substitution reaction led to the development of an unprecedented process that provides pentafluoroethyl and heptafluoropropyl thioethers directly from readily available alcohols."}]}, "keyword_slugs": ["python", "github", "packaging", "template", "dynamic-repository", "repository-template", "documentation", "testing", "deployment", "maintenance", "automation", "development", "infrastructure", "streamline"], "url": {"github": {"home": "https://github.com/AAriam/TemplateRepo", "issues": {"home": "https://github.com/AAriam/TemplateRepo/issues", "template_chooser": "https://github.com/AAriam/TemplateRepo/issues/new/choose", "new": {"app_bug_gui": "https://github.com/AAriam/TemplateRepo/issues/new?template=01_app_bug_gui.yaml", "app_bug_cli": "https://github.com/AAriam/TemplateRepo/issues/new?template=02_app_bug_cli.yaml", "app_bug_api": "https://github.com/AAriam/TemplateRepo/issues/new?template=03_app_bug_api.yaml", "app_bug_setup": "https://github.com/AAriam/TemplateRepo/issues/new?template=04_app_bug_setup.yaml", "app_request_enhancement": "https://github.com/AAriam/TemplateRepo/issues/new?template=05_app_request_enhancement.yaml", "app_request_feature": "https://github.com/AAriam/TemplateRepo/issues/new?template=06_app_request_feature.yaml", "app_request_breaking": "https://github.com/AAriam/TemplateRepo/issues/new?template=07_app_request_breaking.yaml"}}, "pulls": {"home": "https://github.com/AAriam/TemplateRepo/pulls"}, "discussions": {"home": "https://github.com/AAriam/TemplateRepo/discussions", "new": {"question_issues": "https://github.com/AAriam/TemplateRepo/discussions/new?category=question_issues", "question_bug": "https://github.com/AAriam/TemplateRepo/discussions/new?category=question_bug"}}, "actions": {"home": "https://github.com/AAriam/TemplateRepo/actions"}, "releases": {"home": "https://github.com/AAriam/TemplateRepo/releases"}, "security": {"home": "https://github.com/AAriam/TemplateRepo/security", "policy": "https://github.com/AAriam/TemplateRepo/security/policy", "advisories": "https://github.com/AAriam/TemplateRepo/security/advisories", "new_advisory": "https://github.com/AAriam/TemplateRepo/security/advisories/new"}, "tree": "https://github.com/AAriam/TemplateRepo/tree/main", "blob": "https://github.com/AAriam/TemplateRepo/blob/main", "raw": "https://raw.githubusercontent.com/AAriam/TemplateRepo/main", "health_file": {"code_of_conduct": "https://github.com/AAriam/TemplateRepo/blob/main/CODE_OF_CONDUCT.md", "contributing": "https://github.com/AAriam/TemplateRepo/blob/main/CONTRIBUTING.md", "governance": "https://github.com/AAriam/TemplateRepo/blob/main/GOVERNANCE.md", "security": "https://github.com/AAriam/TemplateRepo/blob/main/SECURITY.md", "support": "https://github.com/AAriam/TemplateRepo/blob/main/SUPPORT.md", "codeowners": "https://github.com/AAriam/TemplateRepo/blob/main/.github/CODEOWNERS"}}, "website": {"base": "https://aariam.github.io/TemplateRepo", "home": "https://aariam.github.io/TemplateRepo", "announcement": "https://raw.githubusercontent.com/AAriam/TemplateRepo/main/docs/website/announcement.html", "contact": "https://aariam.github.io/TemplateRepo/help/contact", "news": "https://aariam.github.io/TemplateRepo/news", "contributors": "https://aariam.github.io/TemplateRepo/about/#contributors", "contributing": "https://aariam.github.io/TemplateRepo/contribute", "bug_report": "https://aariam.github.io/TemplateRepo/contribute/feedback/report", "license": "https://aariam.github.io/TemplateRepo/license", "security_measures": "https://aariam.github.io/TemplateRepo/contribute/collaborate/maintain/security", "sponsor": "https://aariam.github.io/TemplateRepo/contribute/collaborate/maintain/sponsor"}, "pypi": "https://pypi.org/project/templaterepo/", "conda": "https://anaconda.org/conda-forge/templaterepo/"}} diff --git a/.github/.pre-commit-config-dev.yaml b/.github/.pre-commit-config-dev.yaml new file mode 100644 index 00000000..b602165e --- /dev/null +++ b/.github/.pre-commit-config-dev.yaml @@ -0,0 +1,120 @@ +default_language_version: + python: python3.11 +minimum_pre_commit_version: 3.3.3 +repos: +- repo: https://github.com/pre-commit/pre-commit-hooks + rev: v4.4.0 + hooks: + - id: check-ast + stages: + - pre-commit + - manual + verbose: true + - id: check-case-conflict + stages: + - pre-commit + - manual + verbose: true + - id: check-executables-have-shebangs + stages: + - pre-commit + - manual + verbose: true + - id: check-json + stages: + - pre-commit + - manual + verbose: true + - id: check-shebang-scripts-are-executable + stages: + - pre-commit + - manual + verbose: true + - id: check-symlinks + stages: + - pre-commit + - manual + verbose: true + - id: check-toml + stages: + - pre-commit + - manual + verbose: true + - id: check-xml + stages: + - pre-commit + - manual + verbose: true + - id: check-yaml + stages: + - pre-commit + - manual + verbose: true + - id: end-of-file-fixer + stages: + - pre-commit + - manual + verbose: true + - id: mixed-line-ending + stages: + - pre-commit + - manual + verbose: true + - id: name-tests-test + stages: + - pre-commit + - manual + args: + - --pytest + verbose: true + - id: no-commit-to-branch + stages: + - pre-commit + args: + - --branch + - main + - --pattern + - release/.* + verbose: true + - id: trailing-whitespace + stages: + - pre-commit + - manual + verbose: true +- repo: https://github.com/astral-sh/ruff-pre-commit + rev: v0.0.290 + hooks: + - id: ruff + stages: + - pre-commit + - manual + args: + - --fix + - --exit-non-zero-on-fix + types_or: + - python + - pyi + - jupyter + verbose: true +- repo: https://github.com/pycqa/isort + rev: 5.12.0 + hooks: + - id: isort + stages: + - pre-commit + - manual + args: + - --settings-path + - pyproject.toml + verbose: true +- repo: https://github.com/psf/black-pre-commit-mirror + rev: 23.9.1 + hooks: + - id: black-jupyter + stages: + - pre-commit + - manual + args: + - --config + - pyproject.toml + verbose: true diff --git a/.github/.pre-commit-config-main.yaml b/.github/.pre-commit-config-main.yaml new file mode 100644 index 00000000..b602165e --- /dev/null +++ b/.github/.pre-commit-config-main.yaml @@ -0,0 +1,120 @@ +default_language_version: + python: python3.11 +minimum_pre_commit_version: 3.3.3 +repos: +- repo: https://github.com/pre-commit/pre-commit-hooks + rev: v4.4.0 + hooks: + - id: check-ast + stages: + - pre-commit + - manual + verbose: true + - id: check-case-conflict + stages: + - pre-commit + - manual + verbose: true + - id: check-executables-have-shebangs + stages: + - pre-commit + - manual + verbose: true + - id: check-json + stages: + - pre-commit + - manual + verbose: true + - id: check-shebang-scripts-are-executable + stages: + - pre-commit + - manual + verbose: true + - id: check-symlinks + stages: + - pre-commit + - manual + verbose: true + - id: check-toml + stages: + - pre-commit + - manual + verbose: true + - id: check-xml + stages: + - pre-commit + - manual + verbose: true + - id: check-yaml + stages: + - pre-commit + - manual + verbose: true + - id: end-of-file-fixer + stages: + - pre-commit + - manual + verbose: true + - id: mixed-line-ending + stages: + - pre-commit + - manual + verbose: true + - id: name-tests-test + stages: + - pre-commit + - manual + args: + - --pytest + verbose: true + - id: no-commit-to-branch + stages: + - pre-commit + args: + - --branch + - main + - --pattern + - release/.* + verbose: true + - id: trailing-whitespace + stages: + - pre-commit + - manual + verbose: true +- repo: https://github.com/astral-sh/ruff-pre-commit + rev: v0.0.290 + hooks: + - id: ruff + stages: + - pre-commit + - manual + args: + - --fix + - --exit-non-zero-on-fix + types_or: + - python + - pyi + - jupyter + verbose: true +- repo: https://github.com/pycqa/isort + rev: 5.12.0 + hooks: + - id: isort + stages: + - pre-commit + - manual + args: + - --settings-path + - pyproject.toml + verbose: true +- repo: https://github.com/psf/black-pre-commit-mirror + rev: 23.9.1 + hooks: + - id: black-jupyter + stages: + - pre-commit + - manual + args: + - --config + - pyproject.toml + verbose: true diff --git a/.github/.pre-commit-config-other.yaml b/.github/.pre-commit-config-other.yaml new file mode 100644 index 00000000..b602165e --- /dev/null +++ b/.github/.pre-commit-config-other.yaml @@ -0,0 +1,120 @@ +default_language_version: + python: python3.11 +minimum_pre_commit_version: 3.3.3 +repos: +- repo: https://github.com/pre-commit/pre-commit-hooks + rev: v4.4.0 + hooks: + - id: check-ast + stages: + - pre-commit + - manual + verbose: true + - id: check-case-conflict + stages: + - pre-commit + - manual + verbose: true + - id: check-executables-have-shebangs + stages: + - pre-commit + - manual + verbose: true + - id: check-json + stages: + - pre-commit + - manual + verbose: true + - id: check-shebang-scripts-are-executable + stages: + - pre-commit + - manual + verbose: true + - id: check-symlinks + stages: + - pre-commit + - manual + verbose: true + - id: check-toml + stages: + - pre-commit + - manual + verbose: true + - id: check-xml + stages: + - pre-commit + - manual + verbose: true + - id: check-yaml + stages: + - pre-commit + - manual + verbose: true + - id: end-of-file-fixer + stages: + - pre-commit + - manual + verbose: true + - id: mixed-line-ending + stages: + - pre-commit + - manual + verbose: true + - id: name-tests-test + stages: + - pre-commit + - manual + args: + - --pytest + verbose: true + - id: no-commit-to-branch + stages: + - pre-commit + args: + - --branch + - main + - --pattern + - release/.* + verbose: true + - id: trailing-whitespace + stages: + - pre-commit + - manual + verbose: true +- repo: https://github.com/astral-sh/ruff-pre-commit + rev: v0.0.290 + hooks: + - id: ruff + stages: + - pre-commit + - manual + args: + - --fix + - --exit-non-zero-on-fix + types_or: + - python + - pyi + - jupyter + verbose: true +- repo: https://github.com/pycqa/isort + rev: 5.12.0 + hooks: + - id: isort + stages: + - pre-commit + - manual + args: + - --settings-path + - pyproject.toml + verbose: true +- repo: https://github.com/psf/black-pre-commit-mirror + rev: 23.9.1 + hooks: + - id: black-jupyter + stages: + - pre-commit + - manual + args: + - --config + - pyproject.toml + verbose: true diff --git a/.github/.pre-commit-config-release.yaml b/.github/.pre-commit-config-release.yaml new file mode 100644 index 00000000..b602165e --- /dev/null +++ b/.github/.pre-commit-config-release.yaml @@ -0,0 +1,120 @@ +default_language_version: + python: python3.11 +minimum_pre_commit_version: 3.3.3 +repos: +- repo: https://github.com/pre-commit/pre-commit-hooks + rev: v4.4.0 + hooks: + - id: check-ast + stages: + - pre-commit + - manual + verbose: true + - id: check-case-conflict + stages: + - pre-commit + - manual + verbose: true + - id: check-executables-have-shebangs + stages: + - pre-commit + - manual + verbose: true + - id: check-json + stages: + - pre-commit + - manual + verbose: true + - id: check-shebang-scripts-are-executable + stages: + - pre-commit + - manual + verbose: true + - id: check-symlinks + stages: + - pre-commit + - manual + verbose: true + - id: check-toml + stages: + - pre-commit + - manual + verbose: true + - id: check-xml + stages: + - pre-commit + - manual + verbose: true + - id: check-yaml + stages: + - pre-commit + - manual + verbose: true + - id: end-of-file-fixer + stages: + - pre-commit + - manual + verbose: true + - id: mixed-line-ending + stages: + - pre-commit + - manual + verbose: true + - id: name-tests-test + stages: + - pre-commit + - manual + args: + - --pytest + verbose: true + - id: no-commit-to-branch + stages: + - pre-commit + args: + - --branch + - main + - --pattern + - release/.* + verbose: true + - id: trailing-whitespace + stages: + - pre-commit + - manual + verbose: true +- repo: https://github.com/astral-sh/ruff-pre-commit + rev: v0.0.290 + hooks: + - id: ruff + stages: + - pre-commit + - manual + args: + - --fix + - --exit-non-zero-on-fix + types_or: + - python + - pyi + - jupyter + verbose: true +- repo: https://github.com/pycqa/isort + rev: 5.12.0 + hooks: + - id: isort + stages: + - pre-commit + - manual + args: + - --settings-path + - pyproject.toml + verbose: true +- repo: https://github.com/psf/black-pre-commit-mirror + rev: 23.9.1 + hooks: + - id: black-jupyter + stages: + - pre-commit + - manual + args: + - --config + - pyproject.toml + verbose: true diff --git a/.github/.readthedocs.yaml b/.github/.readthedocs.yaml new file mode 100644 index 00000000..fd947d4c --- /dev/null +++ b/.github/.readthedocs.yaml @@ -0,0 +1,19 @@ +version: 2 +build: + os: ubuntu-22.04 + tools: + python: mambaforge-4.10 + jobs: + post_checkout: + - git fetch --unshallow +conda: + environment: docs/website/requirements.yaml +python: + install: + - method: pip + path: . +sphinx: + configuration: docs/website/source/conf.py + builder: dirhtml + fail_on_warning: false +formats: all diff --git a/.github/CODEOWNERS b/.github/CODEOWNERS new file mode 100644 index 00000000..03e2326f --- /dev/null +++ b/.github/CODEOWNERS @@ -0,0 +1,3 @@ +* @aariam +/* @aariam +/.github/ @aariam diff --git a/.github/DISCUSSION_TEMPLATE/README.md b/.github/DISCUSSION_TEMPLATE/README.md new file mode 100644 index 00000000..fbf08f47 --- /dev/null +++ b/.github/DISCUSSION_TEMPLATE/README.md @@ -0,0 +1,13 @@ +# Discussion Category Forms +[Discussion category forms](https://docs.github.com/en/discussions/managing-discussions-for-your-community/creating-discussion-category-forms) +customize the templates that are available for community members to use +when they open new discussions in the repository. +It encourages community members to include specific, structured information +in their discussions by using customizable web form fields. + +To be recognized by GitHub, discussion category forms must be stored in the directory `/.github/DISCUSSION_TEMPLATE/` +(i.e. this directory). Each YAML file defines a form for a specific discussion category, indicated by the +filename, which must correspond with the slug for one of the discussion categories. +For example, the template for the "New Announcements" category should be stored in `.github/DISCUSSION_TEMPLATE/new-announcements.yml`. +Discussion forms, like issue forms, are written in YAML, using the +GitHub [form schema](https://docs.github.com/en/communities/using-templates-to-encourage-useful-issues-and-pull-requests/syntax-for-githubs-form-schema). diff --git a/.github/DISCUSSION_TEMPLATE/question_bug.yaml b/.github/DISCUSSION_TEMPLATE/question_bug.yaml new file mode 100644 index 00000000..83af46dd --- /dev/null +++ b/.github/DISCUSSION_TEMPLATE/question_bug.yaml @@ -0,0 +1,8 @@ +title: Is this a bug? +labels: +- bug +body: +- type: markdown + id: bug + attributes: + value: "**Describe the bug**\n" diff --git a/.github/DISCUSSION_TEMPLATE/question_issues.yaml b/.github/DISCUSSION_TEMPLATE/question_issues.yaml new file mode 100644 index 00000000..6d25d7e0 --- /dev/null +++ b/.github/DISCUSSION_TEMPLATE/question_issues.yaml @@ -0,0 +1,47 @@ +title: '[General] ' +labels: +- General Introduction +body: +- type: markdown + attributes: + value: "This is text that will show up in the template!\n" +- type: textarea + id: improvements + attributes: + label: Top 3 improvements + description: What are the top 3 improvements we could make to this project? + value: "1.\n2.\n3.\n...\n" + render: bash + validations: + required: true +- type: markdown + attributes: + value: "## Markdown header\nAnd some more markdown\n" +- type: input + id: has-id + attributes: + label: Suggestions + description: A description about suggestions to help you + validations: + required: true +- type: dropdown + id: download + attributes: + label: Which area of this project could be most improved? + options: + - Documentation + - Pull request review time + - Bug fix time + - Release cadence + validations: + required: true +- type: checkboxes + attributes: + label: Check that box! + options: + - label: This one! + required: true + - label: I won't stop you if you check this one, too +- type: markdown + attributes: + value: "### The thrilling conclusion\n_to our template_\n" diff --git a/.github/FUNDING.yml b/.github/FUNDING.yml new file mode 100644 index 00000000..5d66a5b6 --- /dev/null +++ b/.github/FUNDING.yml @@ -0,0 +1 @@ +github: aariam diff --git a/.github/ISSUE_TEMPLATE/03_app_bug_api.yaml b/.github/ISSUE_TEMPLATE/03_app_bug_api.yaml new file mode 100644 index 00000000..dd527791 --- /dev/null +++ b/.github/ISSUE_TEMPLATE/03_app_bug_api.yaml @@ -0,0 +1,169 @@ +name:  🖥 App 🐞 Bug Report 📱 API +description: Report a problem (e.g. errors and unexpected results) encountered while + using the application's Python API. +labels: +- 'Type: patch-release' +- 'SubType: api' +- 'Status: triage' +assignees: +- aariam +body: +- type: markdown + attributes: + value: "

    \n Thank you for taking the time to report a problem + in TemplateRepo;\n we greatly appreciate your contribution! ❤️🙏\n

    \n

    Terms + and Conditions

    \n

    \n Before submitting a report, please + take a moment to review and accept our terms and conditions;\n they will help + us process the issue as fast as possible,\n and not bother you with additional + questions.\n

    \n

    ⛔ Choosing the right form

    \n\n
    \n 💡 Contact us\n\ + \
    \n

    \n Can't find the right form or unsure about + which one to choose? \n Ask a question and get help in the \n discussion forum.\n

    \n
    \n

    ⚠️ Verifying the bug

    \n + Before submitting a report, please make sure that you are following our Bug Report + Guidelines to verify that:
      \n
    1. \n The issue you are experiencing + is in fact a bug, and not a documented expected behavior.\n
      2. \n
    2. \n\ + \ The bug is reproducible in the latest version of the release, and has not + yet been reported.\n
      3. \n
    \n
    \n 💡 Open a discussion instead!\n
    \n This verification process + is non-trivial, and can be time-consuming.\n If you are not a collaborator + and don't have the time to go through the process,\n you can always open + a discussion instead; we will investigate the problem as soon as possible,\n\ + \ and convert the discussion into an issue if the bug is verified.\n
    \n +

    🤝 Code of conduct

    \n

    \n Please make sure that you + are following our\n Code of Conduct,\n so that we can process the issue as soon as possible.\n\ +

    \n

    ✅ Agreements

    " +- type: checkboxes + id: terms + attributes: + label: 'To submit an issue, please agree to the following terms and conditions:' + options: + - label: I have read the [Contributing Guidelines](https://github.com/AAriam/TemplateRepo/blob/main/CONTRIBUTING.md) and + am following the [Bug Report Guidelines](https://aariam.github.io/TemplateRepo/contribute/feedback/report). + required: true + - label: I have read, understood, and agree to follow the [Code of Conduct](https://github.com/AAriam/TemplateRepo/blob/main/CODE_OF_CONDUCT.md). + required: true +- type: markdown + attributes: + value:

    🧑‍💻 Collaborate

    +- type: checkboxes + id: collab + attributes: + label: "Thank you again for filling this bug report.\nIf you are willing to collaborate + on fixing the issue, please select the option below.\n" + options: + - label: I am willing to work on the issue and submit a pull request. + required: false +- type: markdown + attributes: + value:

    System and Version Specifications

    +- type: dropdown + id: os + attributes: + label: Operating System + description: "Which operating systems have you tested?\nPlease select all options + where you have encountered the bug.\n" + multiple: true + options: [] + validations: + required: true +- type: dropdown + id: python_version + attributes: + label: Python Version + description: "Which Python versions have you tested?\nPlease select all versions + where you have encountered the bug.\n" + multiple: true + options: [] + validations: + required: true +- type: dropdown + id: package_manager + attributes: + label: Package Manager + description: "Which package manager have you used to download and install the + package?\n" + multiple: false + options: [] + validations: + required: true +- type: dropdown + id: version + attributes: + label: Package Version + description: "Which versions of our software are affected?\nPlease select all + versions where you have encountered the bug.\n" + multiple: true + options: [] + validations: + required: true +- type: textarea + id: environment + attributes: + label: Environment + description: "Please provide the details of all installed packages and their exact + versions in the environment where you have encountered the bug. Follow the + instructions below based on the package manager you have selected:\n1. **`pip`**: + Run `pip freeze > requirements.txt` in your terminal within the environment, + and copy the contents of the generated `requirements.txt` file here.\n2. **`conda`**: + Run `conda env export > environment.yml` in your terminal within the environment + (or alternatively `conda env export -n {YOUR_ENVIRONMENT_NAME} > environment.yml`),\ + \ and copy the contents of the generated `environment.yml` file here." + validations: + required: true +- type: markdown + attributes: + value: "
    \n

    Bug Report

    \n" +- type: input + id: api_entry + attributes: + label: Fully Qualified Name + description: "Please provide the fully qualified name of the API endpoint that + is causing the problem.\n" + value: templaterepo. + validations: + required: true +- type: textarea + id: summary + attributes: + label: Summary + description: Please provide a brief summary of the bug. + validations: + required: true +- type: textarea + id: code + attributes: + label: Unit-Test / Minimal Reproducible Example (MRE) + description: Please provide a unit-test (preferred) or a minimal complete verifiable + code example to test/reproduce the bug. + value: "import ${{package.name]}\n\ndef unit_test():\n # write a unit-test + here to reproduce the bug\n ...\n assert ...\n" + render: python + validations: + required: true +- type: textarea + id: log + attributes: + label: Error Message + description: "Please provide the full traceback of the error message.\n" + render: shell + validations: + required: true diff --git a/.github/ISSUE_TEMPLATE/04_app_bug_setup.yaml b/.github/ISSUE_TEMPLATE/04_app_bug_setup.yaml new file mode 100644 index 00000000..cdd8ff82 --- /dev/null +++ b/.github/ISSUE_TEMPLATE/04_app_bug_setup.yaml @@ -0,0 +1,150 @@ +name:  🖥 App 🐞 Bug Report ⚙️ Setup +description: Report a problem in downloading, installation, or initialization of the + application. +labels: +- 'Type: patch-release' +- 'SubType: setup' +- 'Status: triage' +assignees: +- aariam +body: +- type: markdown + attributes: + value: "

    \n Thank you for taking the time to report a problem + in TemplateRepo;\n we greatly appreciate your contribution! ❤️🙏\n

    \n

    Terms + and Conditions

    \n

    \n Before submitting a report, please + take a moment to review and accept our terms and conditions;\n they will help + us process the issue as fast as possible,\n and not bother you with additional + questions.\n

    \n

    ⛔ Choosing the right form

    \n
      \n
    • \n

      \n Please note that this form is specifically for reporting a + non-security-related bug\n in the TemplateRepo setup process, i.e. + an unexpected behavior that occurs during the \n download, installation, + or initialization of the application.\n

      \n
      • \n
    • \n

      \n To 🚨 report a security vulnerability\n 🚨 please first read our\n\ + \ security + policy, and fill a\n private security advisory form instead.\n

      \n
      • \n
    • \n \ + \

      \n For other types of issues, such as problems + in the\n Python API,\n\ + \ website, or\n\ + \ documentation,\n\ + \ or for requesting new features and enhancements, please select the appropriate + form \n from the issue + template chooser.\n

      \n
      • \n
    \n
    \n 💡 Contact us\n\ + \
    \n

    \n Can't find the right form or unsure about + which one to choose? \n Ask a question and get help in the \n discussion forum.\n

    \n
    \n

    ⚠️ Verifying the bug

    \n + Before submitting a report, please make sure that you are following our Bug Report + Guidelines to verify that:
      \n
    1. \n The issue you are experiencing + is in fact a bug, and not a documented expected behavior.\n
      2. \n
    2. \n\ + \ The bug is reproducible in the latest version of the release, and has not + yet been reported.\n
      3. \n
    \n
    \n 💡 Open a discussion instead!\n
    \n This verification process + is non-trivial, and can be time-consuming.\n If you are not a collaborator + and don't have the time to go through the process,\n you can always open + a discussion instead; we will investigate the problem as soon as possible,\n\ + \ and convert the discussion into an issue if the bug is verified.\n
    \n +

    🤝 Code of conduct

    \n

    \n Please make sure that you + are following our\n Code of Conduct,\n so that we can process the issue as soon as possible.\n\ +

    \n

    ✅ Agreements

    " +- type: checkboxes + id: terms + attributes: + label: 'To submit an issue, please agree to the following terms and conditions:' + options: + - label: I have read the [Contributing Guidelines](https://github.com/AAriam/TemplateRepo/blob/main/CONTRIBUTING.md) and + am following the [Bug Report Guidelines](https://aariam.github.io/TemplateRepo/contribute/feedback/report). + required: true + - label: I have read, understood, and agree to follow the [Code of Conduct](https://github.com/AAriam/TemplateRepo/blob/main/CODE_OF_CONDUCT.md). + required: true +- type: markdown + attributes: + value:

    🧑‍💻 Collaborate

    +- type: checkboxes + attributes: + label: "Thank you again for filling this bug report.\nIf you are willing to collaborate + on fixing the issue, please select the option below.\n" + options: + - label: I am willing to work on the issue and submit a pull request. + required: false +- type: markdown + attributes: + value:

    System and Version Specifications

    +- type: dropdown + id: os + attributes: + label: Operating System + description: "Which operating systems have you tested?\nPlease select all options + where you have encountered the bug.\n" + multiple: true + options: [] + validations: + required: true +- type: dropdown + id: python_version + attributes: + label: Python Version + description: "Which Python versions have you tested?\nPlease select all versions + where you have encountered the bug.\n" + multiple: true + options: [] + validations: + required: true +- type: dropdown + id: package_manager + attributes: + label: Package Manager + description: "Which package manager have you used to download and install the + package?\n" + multiple: false + options: [] + validations: + required: true +- type: dropdown + id: version + attributes: + label: Package Version + description: "Which versions of our software are affected?\nPlease select all + versions where you have encountered the bug.\n" + multiple: true + options: [] + validations: + required: true +- type: textarea + id: environment + attributes: + label: Environment + description: "Please provide the details of all installed packages and their exact + versions in the environment where you have encountered the bug. Follow the + instructions below based on the package manager you have selected:\n1. **`pip`**: + Run `pip freeze > requirements.txt` in your terminal within the environment, + and copy the contents of the generated `requirements.txt` file here.\n2. **`conda`**: + Run `conda env export > environment.yml` in your terminal within the environment + (or alternatively `conda env export -n {YOUR_ENVIRONMENT_NAME} > environment.yml`),\ + \ and copy the contents of the generated `environment.yml` file here." + validations: + required: true +- type: markdown + attributes: + value: "
    \n

    Bug Report

    \n" +- type: textarea + id: summary + attributes: + label: Summary + description: Please provide a brief summary of the bug, and the steps necessary + to reproduce it. + validations: + required: true +- type: textarea + id: log + attributes: + label: Error Message + description: "If applicable, provide the full traceback of the error message.\n" + render: shell + validations: + required: false diff --git a/.github/ISSUE_TEMPLATE/05_app_request_enhancement.yaml b/.github/ISSUE_TEMPLATE/05_app_request_enhancement.yaml new file mode 100644 index 00000000..1d1e985c --- /dev/null +++ b/.github/ISSUE_TEMPLATE/05_app_request_enhancement.yaml @@ -0,0 +1,121 @@ +name:  🖥 App 🔔 Request 🚀 Enhancement +description: Request an improvement to an existing feature in the application, for + example in terms of performance, functionality, or ease of use. +labels: +- 'Type: minor-release' +- 'SubType: enhancement' +- 'Status: triage' +assignees: +- aariam +body: +- type: markdown + attributes: + value: "

    \n Thank you for taking the time to report a problem + in TemplateRepo;\n we greatly appreciate your contribution! ❤️🙏\n

    \n

    Terms + and Conditions

    \n

    \n Before submitting a report, please + take a moment to review and accept our terms and conditions;\n they will help + us process the issue as fast as possible,\n and not bother you with additional + questions.\n

    \n

    ⛔ Choosing the right form

    \n
      \n
    • \n

      \n Please note that this form is specifically for requesting + a non-breaking enhancement\n in one of TemplateRepo's existing features + and functionalities.\n

      \n
      • \n
    • \n

      \n\ + \ For other types of issues, such as requesting\n new features,\n breaking changes, and\n changes in the website content,\n or for reporting bugs, please select + the appropriate form \n from the issue template chooser.\n

      \n
      • \n
    \n
    \n 💡 Contact us\n\ + \
    \n

    \n Can't find the right form or unsure about + which one to choose? \n Ask a question and get help in the \n discussion forum.\n

    \n
    \n

    ⚠️ Verifying the request

    \n + Before submitting a report, please make sure that you are following our Contributing Guidelines + to verify that:
      \n
    1. \n Your request is in fact for a non-breaking + enhancement, and not a breaking change or new feature.\n
      2. \n
    2. \n \ + \ The request is not implemented in the latest version of the release, \n \ + \ and has not yet been filed by another person.\n
      3. \n
    \n
    \n\ + \ 💡 Open a discussion instead!\n
    \n This verification process + is non-trivial, and can be time-consuming.\n If you are not a collaborator + and don't have the time to go through the process,\n you can always open + a discussion instead; we will investigate the problem as soon as possible,\n\ + \ and convert the discussion into an issue if the request is valid.\n
    \n +

    🤝 Code of conduct

    \n

    \n Please make sure that you + are following our\n Code of Conduct,\n so that we can process the issue as soon as possible.\n\ +

    \n

    ✅ Agreements

    " +- type: checkboxes + id: terms + attributes: + label: 'To submit an issue, please agree to the following terms and conditions:' + options: + - label: I have read the [Contributing Guidelines](https://github.com/AAriam/TemplateRepo/blob/main/CONTRIBUTING.md) and + am following the [Bug Report Guidelines](https://aariam.github.io/TemplateRepo/contribute/feedback/report). + required: true + - label: I have read, understood, and agree to follow the [Code of Conduct](https://github.com/AAriam/TemplateRepo/blob/main/CODE_OF_CONDUCT.md). + required: true +- type: markdown + attributes: + value:

    🧑‍💻 Collaborate

    +- type: checkboxes + attributes: + label: "Thank you again for filling this bug report.\nIf you are willing to collaborate + on fixing the issue, please select the option below.\n" + options: + - label: I am willing to work on the issue and submit a pull request. + required: false +- type: markdown + attributes: + value:

    System and Version Specifications

    +- type: dropdown + id: os + attributes: + label: Operating System + description: "Does this enhancement request apply to a specific operating system?\n + If so, please select the appropriate option.\n" + multiple: false + options: [] + validations: + required: false +- type: dropdown + id: python_version + attributes: + label: Python Version + description: "Does this enhancement request apply to a specific Python version?\n + If so, please select the appropriate option.\n" + multiple: false + options: [] + validations: + required: false +- type: dropdown + id: package_manager + attributes: + label: Package Manager + description: "Does this enhancement request apply to a specific package manager?\n + If so, please select the appropriate option.\n" + multiple: false + options: [] + validations: + required: true +- type: markdown + attributes: + value: "
    \n

    Enhancement Request

    \n" +- type: dropdown + id: version + attributes: + label: Package Version + description: "Which version of our software is this request for?\n" + multiple: false + options: [] + validations: + required: true +- type: textarea + id: summary + attributes: + label: Summary + description: "Please provide a brief summary of your enhancement request,\nincluding + the motivation, use case, or problem it solves.\n" + validations: + required: true diff --git a/.github/ISSUE_TEMPLATE/06_app_request_feature.yaml b/.github/ISSUE_TEMPLATE/06_app_request_feature.yaml new file mode 100644 index 00000000..e519b449 --- /dev/null +++ b/.github/ISSUE_TEMPLATE/06_app_request_feature.yaml @@ -0,0 +1,121 @@ +name:  🖥 App 🔔 Request ✨ New Feature +description: Request a brand new feature that is not yet available in the application. +labels: +- 'Type: minor-release' +- 'SubType: feat' +- 'Status: triage' +assignees: +- aariam +body: +- type: markdown + attributes: + value: "

    \n Thank you for taking the time to report a problem + in TemplateRepo;\n we greatly appreciate your contribution! ❤️🙏\n

    \n

    Terms + and Conditions

    \n

    \n Before submitting a report, please + take a moment to review and accept our terms and conditions;\n they will help + us process the issue as fast as possible,\n and not bother you with additional + questions.\n

    \n

    ⛔ Choosing the right form

    \n\n
    \n 💡 Contact us\n\ + \
    \n

    \n Can't find the right form or unsure about + which one to choose? \n Ask a question and get help in the \n discussion forum.\n

    \n
    \n

    ⚠️ Verifying the request

    \n + Before submitting a report, please make sure that you are following our Contributing Guidelines + to verify that:
      \n
    1. \n Your request is in fact for a non-breaking + new feature, and not a breaking change or an enhancement.\n
      2. \n
    2. \n\ + \ The feature is not implemented in the latest version of the release, \n\ + \ and has not yet been requested by another person.\n
      3. \n
    \n
    \n\ + \ 💡 Open a discussion instead!\n
    \n This verification process + is non-trivial, and can be time-consuming.\n If you are not a collaborator + and don't have the time to go through the process,\n you can always open + a discussion instead; we will investigate the problem as soon as possible,\n\ + \ and convert the discussion into an issue if the request is valid.\n
    \n +

    🤝 Code of conduct

    \n

    \n Please make sure that you + are following our\n Code of Conduct,\n so that we can process the issue as soon as possible.\n\ +

    \n

    ✅ Agreements

    " +- type: checkboxes + id: terms + attributes: + label: 'To submit an issue, please agree to the following terms and conditions:' + options: + - label: I have read the [Contributing Guidelines](https://github.com/AAriam/TemplateRepo/blob/main/CONTRIBUTING.md) and + am following the [Bug Report Guidelines](https://aariam.github.io/TemplateRepo/contribute/feedback/report). + required: true + - label: I have read, understood, and agree to follow the [Code of Conduct](https://github.com/AAriam/TemplateRepo/blob/main/CODE_OF_CONDUCT.md). + required: true +- type: markdown + attributes: + value:

    🧑‍💻 Collaborate

    +- type: checkboxes + id: collab + attributes: + label: "Thank you again for filling this feature request.\nIf you are willing + to collaborate on implementing the new feature, please select the option below.\n" + options: + - label: I am willing to work on the issue and submit a pull request. + required: false +- type: markdown + attributes: + value:

    System and Version Specifications

    +- type: dropdown + id: os + attributes: + label: Operating System + description: "Does this feature request apply to a specific operating system?\n + If so, please select the appropriate option.\n" + multiple: false + options: [] + validations: + required: false +- type: dropdown + id: python_version + attributes: + label: Python Version + description: "Does this feature request apply to a specific Python version?\n + If so, please select the appropriate option.\n" + multiple: false + options: [] + validations: + required: false +- type: dropdown + id: package_manager + attributes: + label: Package Manager + description: "Does this feature request apply to a specific package manager?\n + If so, please select the appropriate option.\n" + multiple: false + options: [] + validations: + required: false +- type: markdown + attributes: + value: "
    \n

    Feature Request

    \n" +- type: dropdown + id: version + attributes: + label: Package Version + description: "Which version of our software is this request for?\n" + multiple: false + options: [] + validations: + required: true +- type: textarea + id: summary + attributes: + label: Summary + description: "Please provide a brief summary of your request,\nincluding the motivation, + use case, or problem it solves.\n" + validations: + required: true diff --git a/.github/ISSUE_TEMPLATE/07_app_request_breaking.yaml b/.github/ISSUE_TEMPLATE/07_app_request_breaking.yaml new file mode 100644 index 00000000..6ee995dc --- /dev/null +++ b/.github/ISSUE_TEMPLATE/07_app_request_breaking.yaml @@ -0,0 +1,120 @@ +name:  🖥 App 🔔 Request 💥 Breaking Change +description: Request a backward-incompatible change to the API, such as a change in + the behavior of an existing functionality. +labels: +- 'Type: major-release' +- 'SubType: breaking' +- 'Status: triage' +assignees: +- aariam +body: +- type: markdown + attributes: + value: "

    \n Thank you for taking the time to report a problem + in TemplateRepo;\n we greatly appreciate your contribution! ❤️🙏\n

    \n

    Terms + and Conditions

    \n

    \n Before submitting a report, please + take a moment to review and accept our terms and conditions;\n they will help + us process the issue as fast as possible,\n and not bother you with additional + questions.\n

    \n

    ⛔ Choosing the right form

    \n\n
    \n 💡 Contact us\n\ + \
    \n

    \n Can't find the right form or unsure about + which one to choose? \n Ask a question and get help in the \n discussion forum.\n

    \n
    \n

    ⚠️ Verifying the request

    \n + Before submitting a report, please make sure that you are following our Contributing Guidelines + to verify that:
      \n
    1. \n Your request is in fact for a breaking change, + and not a new feature or an enhancement.\n
      2. \n
    2. \n The request has + not yet been filed by another person.\n
      3. \n
    \n
    \n 💡 Open a discussion instead!\n
    \n This verification process + is non-trivial, and can be time-consuming.\n If you are not a collaborator + and don't have the time to go through the process,\n you can always open + a discussion instead; we will investigate the problem as soon as possible,\n\ + \ and convert the discussion into an issue if the request is valid.\n
    \n +

    🤝 Code of conduct

    \n

    \n Please make sure that you + are following our\n Code of Conduct,\n so that we can process the issue as soon as possible.\n\ +

    \n

    ✅ Agreements

    " +- type: checkboxes + id: terms + attributes: + label: 'To submit an issue, please agree to the following terms and conditions:' + options: + - label: I have read the [Contributing Guidelines](https://github.com/AAriam/TemplateRepo/blob/main/CONTRIBUTING.md) and + am following the [Bug Report Guidelines](https://aariam.github.io/TemplateRepo/contribute/feedback/report). + required: true + - label: I have read, understood, and agree to follow the [Code of Conduct](https://github.com/AAriam/TemplateRepo/blob/main/CODE_OF_CONDUCT.md). + required: true +- type: markdown + attributes: + value:

    🧑‍💻 Collaborate

    +- type: checkboxes + attributes: + label: "Thank you again for filling this feature request.\nIf you are willing + to collaborate on implementing the new feature, please select the option below.\n" + options: + - label: I am willing to work on the issue and submit a pull request. + required: false +- type: markdown + attributes: + value:

    System and Version Specifications

    +- type: dropdown + id: os + attributes: + label: Operating System + description: "Does this request apply to a specific operating system?\nIf so, + please select the appropriate option.\n" + multiple: false + options: [] + validations: + required: false +- type: dropdown + id: python_version + attributes: + label: Python Version + description: "Does this request apply to a specific Python version?\nIf so, please + select the appropriate option.\n" + multiple: false + options: [] + validations: + required: false +- type: dropdown + id: package_manager + attributes: + label: Package Manager + description: "Does this request apply to a specific package manager?\nIf so, please + select the appropriate option.\n" + multiple: false + options: [] + validations: + required: true +- type: markdown + attributes: + value: "
    \n

    Modification Request

    \n" +- type: dropdown + id: version + attributes: + label: Package Version + description: "Which version of our software is this request for?\n" + multiple: false + options: [] + validations: + required: true +- type: textarea + id: summary + attributes: + label: Summary + description: "Please provide a brief summary of your request,\nincluding the motivation, + use case, or problem it solves.\n" + validations: + required: true diff --git a/.github/ISSUE_TEMPLATE/README.md b/.github/ISSUE_TEMPLATE/README.md new file mode 100644 index 00000000..79a3540c --- /dev/null +++ b/.github/ISSUE_TEMPLATE/README.md @@ -0,0 +1,26 @@ +# GitHub Issues Settings +This directory contains templates and configurations used when an issue is opened in the repository. + +## Templates +The issues templates use the GitHub's [issue forms](https://docs.github.com/en/communities/using-templates-to-encourage-useful-issues-and-pull-requests/configuring-issue-templates-for-your-repository#creating-issue-forms) +to create customizable web form fields. Each `.yml` file (other than `config.yml`) provides a template for +a specific issue type. The issue forms use the YAML format, with a series of defined [top-level keys](https://docs.github.com/en/communities/using-templates-to-encourage-useful-issues-and-pull-requests/syntax-for-issue-forms#top-level-syntax) +such as `name`, `description` and `labels`, and a [body syntax](https://docs.github.com/en/communities/using-templates-to-encourage-useful-issues-and-pull-requests/syntax-for-githubs-form-schema) +to define the form fields. + +Any YAML file created in this directory using the specified syntax will be automatically added to the list of possible +issue forms that users can select from when opening a new issue in the repository. + + +## Configurations +The [config.yml](../../.meta/config/issues_template_chooser.yaml) file contains the configurations for the +[template chooser](https://docs.github.com/en/communities/using-templates-to-encourage-useful-issues-and-pull-requests/configuring-issue-templates-for-your-repository#configuring-the-template-chooser), +i.e. the landing page of the repository's 'Issues' section. + +### Options +- `blank_issues_enabled`: A boolean value defining whether free-form issues can be opened by users. +- `contact_links`: An array of dictionaries, defining additional external links for opening issues. +These options will be displayed alongside the available templates in the 'Issues' section of the repository. + +## References +- [GitHub Documentation](https://docs.github.com/en/communities/using-templates-to-encourage-useful-issues-and-pull-requests/about-issue-and-pull-request-templates) diff --git a/.github/ISSUE_TEMPLATE/config.yml b/.github/ISSUE_TEMPLATE/config.yml new file mode 100644 index 00000000..44b90d6b --- /dev/null +++ b/.github/ISSUE_TEMPLATE/config.yml @@ -0,0 +1,8 @@ +blank_issues_enabled: false +contact_links: +- name: 🎓️  Learn More + about: Not sure where to start? Read our contributing guide to learn more. + url: https://github.com/AAriam/TemplateRepo/blob/main/CONTRIBUTING.md +- name: 💬  Contact Us + about: Have another inquiry or need help? Contact us directly! + url: https://aariam.github.io/TemplateRepo/help/contact diff --git a/.github/PULL_REQUEST_TEMPLATE.md b/.github/PULL_REQUEST_TEMPLATE.md new file mode 100644 index 00000000..2ad6146b --- /dev/null +++ b/.github/PULL_REQUEST_TEMPLATE.md @@ -0,0 +1,16 @@ +## Description +Provide a brief description of the PR's purpose here. + +## Content +Notable points that this PR has either accomplished or will accomplish. +- [ ] TODO 1 + +## Questions +- [ ] Question1 + +## Status + - [ ] Tests + - [ ] Docs + - [ ] CHANGELOG updated + - [ ] Issue raised/referenced + - [ ] Ready to merge diff --git a/.github/PULL_REQUEST_TEMPLATE/README.md b/.github/PULL_REQUEST_TEMPLATE/README.md new file mode 100644 index 00000000..0221715a --- /dev/null +++ b/.github/PULL_REQUEST_TEMPLATE/README.md @@ -0,0 +1,17 @@ +# GitHub Pull Requests Templates +This directory contains additional templates for pull requests. + +By default, the template defined at [./github/pull_request_template.md](./github/pull_request_template.md) +is used when opening a pull request. To use the extra templates in this directory, +the `template` [query parameter](https://docs.github.com/en/pull-requests/collaborating-with-pull-requests/proposing-changes-to-your-work-with-pull-requests/using-query-parameters-to-create-a-pull-request) +must be added to the URL of the pull request form, defining the name of the template to use. +For example, to use a template file named `my_custom_template.md`, add the following query string at the end of the +URL: `?template=my_custom_template.md`. A full URL may e.g. look like this: +https://github.com/my-username/my-repo/compare/main...my-branch?template=my_custom_template.md + +## Notes +- Pull request template filenames are not case-sensitive, and can have an extension such as `.md` or `.txt`. +- The YAML syntax used for issue forms is not supported for pull requests templates. + +## References +- [GitHub Documentation](https://docs.github.com/en/communities/using-templates-to-encourage-useful-issues-and-pull-requests/creating-a-pull-request-template-for-your-repository) diff --git a/.github/_README.md b/.github/_README.md new file mode 100644 index 00000000..ea87c0e3 --- /dev/null +++ b/.github/_README.md @@ -0,0 +1 @@ +# GitHub Directory diff --git a/.github/workflow_requirements/bandit.txt b/.github/workflow_requirements/bandit.txt new file mode 100644 index 00000000..59f7028e --- /dev/null +++ b/.github/workflow_requirements/bandit.txt @@ -0,0 +1,2 @@ +bandit[toml] +bandit-sarif-formatter diff --git a/.github/workflow_requirements/mypy.txt b/.github/workflow_requirements/mypy.txt new file mode 100644 index 00000000..0740b4ae --- /dev/null +++ b/.github/workflow_requirements/mypy.txt @@ -0,0 +1 @@ +mypy[reports] >= 1.6, < 2 diff --git a/.github/workflow_requirements/pylint.txt b/.github/workflow_requirements/pylint.txt new file mode 100644 index 00000000..7b85395f --- /dev/null +++ b/.github/workflow_requirements/pylint.txt @@ -0,0 +1 @@ +pylint[spelling] >= 3.0, < 4 diff --git a/.github/workflows/README.md b/.github/workflows/README.md new file mode 100644 index 00000000..16822a88 --- /dev/null +++ b/.github/workflows/README.md @@ -0,0 +1,33 @@ +# GitHub Actions Workflows +This directory contains [workflows](https://docs.github.com/en/actions/using-workflows/about-workflows) +used in the CI/CD operations of the repository. + +## [docs_rtd_pr_preview](_docs_rtd-pr-preview.yaml) +https://docs.readthedocs.io/en/latest/pull-requests.html +https://docs.readthedocs.io/en/latest/guides/pull-requests.html + +## Releases +GitHub has [built-in functionality](https://docs.github.com/en/repositories/releasing-projects-on-github/automatically-generated-release-notes) +to automatically generate release notes. + +## Used Actions + +### setup-python +https://github.com/marketplace/actions/setup-python + +### setup-micromamba +https://github.com/mamba-org/setup-micromamba +replacing [provision-with-micromamba](https://github.com/mamba-org/provision-with-micromamba) + +## Syntax + +### on: schedule: cron +schedule : https://docs.github.com/en/actions/using-workflows/events-that-trigger-workflows#schedule +cron tasks: https://pubs.opengroup.org/onlinepubs/9699919799/utilities/crontab.html#tag_20_25_07 + +## References +- [GitHub Actions Documentation](https://docs.github.com/en/actions) +- [Workflow Syntax](https://docs.github.com/en/actions/using-workflows/workflow-syntax-for-github-actions) + +## Useful Links +- [Workflow security: `pull_request` vs `pull_request_target`](https://securitylab.github.com/research/github-actions-preventing-pwn-requests/) diff --git a/.gitignore b/.gitignore index 78b295f9..adf38109 100644 --- a/.gitignore +++ b/.gitignore @@ -1,14 +1,7 @@ -# Ref: https://github.com/github/gitignore - -# Byte-compiled / optimized / DLL files __pycache__/ *.py[cod] *$py.class - -# C extensions *.so - -# Distribution / packaging .Python build/ develop-eggs/ @@ -26,18 +19,10 @@ share/python-wheels/ *.egg-info/ .installed.cfg *.egg - -# PyInstaller -# Usually these files are written by a python script from a template -# before PyInstaller builds the exe, so as to inject date/other infos into it. *.manifest *.spec - -# Installer logs pip-log.txt pip-delete-this-directory.txt - -# Unit test / coverage reports htmlcov/ .tox/ .nox/ @@ -50,50 +35,26 @@ coverage.xml .hypothesis/ .pytest_cache cover/ - -# Translations *.mo *.pot - -# Django stuff: *.log local_settings.py db.sqlite3 db.sqlite3-journal - -# Flask stuff: instance/ .webassets-cache - -# Scrapy stuff: .scrapy - -# Sphinx documentation docs/website/_build/ docs/website/source/api/_autosummary - -# PyBuilder .pybuilder/ target/ - -# Jupyter Notebook .ipynb_checkpoints - -# IPython profile_default/ ipython_config.py - -# pyenv .python-version - -# Celery stuff celerybeat-schedule celerybeat.pid - -# SageMath parsed files *.sage.py - -# Environments .env .venv env/ @@ -101,49 +62,22 @@ venv/ ENV/ env.bak/ venv.bak/ - -# Spyder project settings .spyderproject .spyproject - -# Rope project settings .ropeproject - -# mkdocs documentation /site - -# mypy .mypy_cache/ .dmypy.json dmypy.json - -# Pyre type checker -# There are reports this comes from LLVM profiling, but also Xcode 9. .pyre/ - -# pytype static type analyzer .pytype/ - -# Cython debug symbols cython_debug/ - -# profraw files from LLVM? Unclear exactly what triggers this -# There are reports this comes from LLVM profiling, but also Xcode 9. *profraw - -# In-tree generated files */_version.py - -# VSCode .vscode/ - -# PyCharm .idea/ - -# MacOS system files .DS_Store - -# RepoDynamics -#.local/** -#!.local/README.md -!/.dev/build/ +.local/** +!.local/**/ +!.local/**/README.md +!.local/config.yaml diff --git a/.local/cache/repodynamics/api_cache.yaml b/.local/cache/repodynamics/api_cache.yaml index 08870bec..9cbb46c2 100644 --- a/.local/cache/repodynamics/api_cache.yaml +++ b/.local/cache/repodynamics/api_cache.yaml @@ -29,7 +29,7 @@ doi_10.1039/d2sc03130b: url: https://doi.org/10.1039/d2sc03130b volume: '13' year: 2022 - timestamp: '2023_11_09_00_29_59' + timestamp: '2023_11_10_21_38_27' doi_10.1093/nar/gkac267: data: &id002 abstract: Computational pipelines have become a crucial part of modern drug discovery @@ -78,7 +78,7 @@ doi_10.1093/nar/gkac267: url: https://doi.org/10.1093/nar/gkac267 volume: '50' year: 2022 - timestamp: '2023_11_09_00_29_57' + timestamp: '2023_11_10_21_38_26' doi_10.26434/chemrxiv-2021-8x13n: data: &id003 abstract: Computational pipelines have become a crucial part of modern drug discovery @@ -125,7 +125,7 @@ doi_10.26434/chemrxiv-2021-8x13n: url: https://doi.org/10.26434/chemrxiv-2021-8x13n volume: null year: 2021 - timestamp: '2023_11_09_00_30_03' + timestamp: '2023_11_10_21_38_30' doi_10.3762/bjoc.17.8: data: &id004 abstract: A series of 2-(perfluoroalkylthio)benzothiazolium (BT-SRF) @@ -162,10 +162,10 @@ doi_10.3762/bjoc.17.8: url: https://doi.org/10.3762/bjoc.17.8 volume: '17' year: 2021 - timestamp: '2023_11_09_00_30_01' + timestamp: '2023_11_10_21_38_29' publications_orcid_https://orcid.org/0000-0003-1563-6987: data: [10.1093/nar/gkac267, 10.1039/d2sc03130b, 10.3762/bjoc.17.8, 10.26434/chemrxiv-2021-8x13n] - timestamp: '2023_11_09_00_29_55' + timestamp: '2023_11_10_21_38_23' python_versions: data: - [3, 0, 1] @@ -304,12 +304,12 @@ python_versions: - [3, 11, 5] - [3, 11, 6] - [3, 12, 0] - timestamp: '2023_11_09_00_30_04' + timestamp: '2023_11_10_21_38_32' repo__aariam_templaterepo_source: data: {created_at: '2023-05-14T17:39:52Z', default_branch: main, full_name: AAriam/TemplateRepo, html_url: 'https://github.com/AAriam/TemplateRepo', id: 640622662, name: TemplateRepo, node_id: R_kgDOJi8gRg, owner: AAriam} - timestamp: '2023_11_09_00_29_54' + timestamp: '2023_11_10_21_38_21' user__aariam: data: avatar_url: https://avatars.githubusercontent.com/u/80158628?v=4 @@ -330,4 +330,4 @@ user__aariam: orcid: 'https://orcid.org/0000-0003-1563-6987', researchgate: 'https://researchgate.net/profile/Armin_Ariamajd', twitter: 'https://twitter.com/Al___Chemist', website: ''} username: aariam - timestamp: '2023_11_09_00_29_54' + timestamp: '2023_11_10_21_38_22' diff --git a/.meta/README.md b/.meta/README.md new file mode 100644 index 00000000..b00fd6ba --- /dev/null +++ b/.meta/README.md @@ -0,0 +1,13 @@ +# Meta Directory +This directory contains all the meta content of the repository. + +## PyPI + +### dependencies +Either a list of dependencies, or a string representing the filepath (from root) to a txt file containing one +dependency per line. + +### optional_dependencies +Either a dictionary, where keys are the name of the group of optional dependencies, and the values are lists of +corresponding dependencies, or a string representing the path (from root) to a directory containing one +txt file (named .txt) with one dependency per line, for each dependency group. diff --git a/CODE_OF_CONDUCT.md b/CODE_OF_CONDUCT.md new file mode 100644 index 00000000..2cf702f9 --- /dev/null +++ b/CODE_OF_CONDUCT.md @@ -0,0 +1,122 @@ +# Contributor Covenant Code of Conduct + +## Our Pledge + +We, the members, contributors, maintainers, and creators of ***TemplateRepo***, +pledge to act and interact in ways that contribute to an open, welcoming, +diverse, inclusive, healthy, and harassment-free community for every person involved in this project. + +## Our Standards + +Examples of behavior that contributes to a positive environment for our +community include: + +* Demonstrating empathy and kindness toward other people. +* Being respectful of differing opinions, viewpoints, and experiences. +* Giving and gracefully accepting constructive feedback. +* Accepting responsibility and apologizing to those affected by our mistakes, + and learning from the experience. +* Focusing on what is best not just for us as individuals, but for the + overall community. + +Examples of unacceptable behavior include: + +* The use of sexualized language or imagery, and sexual attention or + advances of any kind. +* Trolling, insulting or derogatory comments, and personal or political attacks. +* Public or private harassment. +* Publishing others' private information, such as a physical or email + address, without their explicit permission. +* Other conduct which could reasonably be considered inappropriate in a + professional setting. + +## Enforcement Responsibilities + +Community leaders are responsible for clarifying and enforcing our standards of +acceptable behavior and will take appropriate and fair corrective action in +response to any behavior that they deem inappropriate, threatening, offensive, +or harmful. + +Community leaders have the right and responsibility to remove, edit, or reject +comments, commits, code, wiki edits, issues, and other contributions that are +not aligned to this Code of Conduct, and will communicate reasons for moderation +decisions when appropriate. + +## Scope + +This Code of Conduct applies within all community spaces, and also applies when +an individual is officially representing the community in public spaces. +Examples of representing our community include using an official e-mail address, +posting via an official social media account, or acting as an appointed +representative at an online or offline event. + +## Enforcement + +Instances of abusive, harassing, or otherwise unacceptable behavior may be +reported to the community leaders responsible for enforcement, +at [None](mailto:None). +All complaints will be reviewed and investigated promptly and fairly. + +All community leaders are obligated to respect the privacy and security of the +reporter of any incident. + +## Enforcement Guidelines + +Community leaders will follow these Community Impact Guidelines in determining +the consequences for any action they deem in violation of this Code of Conduct: + +### 1. Correction + +**Community Impact**: Use of inappropriate language or other behavior deemed +unprofessional or unwelcome in the community. + +**Consequence**: A private, written warning from community leaders, providing +clarity around the nature of the violation and an explanation of why the +behavior was inappropriate. A public apology may be requested. + +### 2. Warning + +**Community Impact**: A violation through a single incident or series +of actions. + +**Consequence**: A warning with consequences for continued behavior. No +interaction with the people involved, including unsolicited interaction with +those enforcing the Code of Conduct, for a specified period of time. This +includes avoiding interactions in community spaces as well as external channels +like social media. Violating these terms may lead to a temporary or +permanent ban. + +### 3. Temporary Ban + +**Community Impact**: A serious violation of community standards, including +sustained inappropriate behavior. + +**Consequence**: A temporary ban from any sort of interaction or public +communication with the community for a specified period of time. No public or +private interaction with the people involved, including unsolicited interaction +with those enforcing the Code of Conduct, is allowed during this period. +Violating these terms may lead to a permanent ban. + +### 4. Permanent Ban + +**Community Impact**: Demonstrating a pattern of violation of community +standards, including sustained inappropriate behavior, harassment of an +individual, or aggression toward or disparagement of classes of individuals. + +**Consequence**: A permanent ban from any sort of public interaction within +the community. + +## Attribution + +This Code of Conduct is adapted from the [Contributor Covenant][homepage], +version 2.0, available at +https://www.contributor-covenant.org/version/2/0/code_of_conduct.html. + +Community Impact Guidelines were inspired by [Mozilla's code of conduct +enforcement ladder](https://github.com/mozilla/diversity). + +[homepage]: https://www.contributor-covenant.org + +For answers to common questions about this code of conduct, see the FAQ at +https://www.contributor-covenant.org/faq. Translations are available at +https://www.contributor-covenant.org/translations. diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md new file mode 100644 index 00000000..4a04c931 --- /dev/null +++ b/CONTRIBUTING.md @@ -0,0 +1,25 @@ +# Contributing Guidelines + +

    + Welcome to the TemplateRepo community! + We are excited to have you here, + and grateful that you are considering contributing. + TemplateRepo is a free and open-source project that evolves with the needs of its users, + and can only survive and grow through the help of great members like you. +

    + +
    + ❤️🙏 We Appreciate All Your Work! +
    + We follow the All Contributors + specifications; all types of contributions are encouraged and valued, and all contributors are + acknowledged on our public website + and repository. +
    + +## How To Contribute + +

    + To keep all documentation on our project organized and easy to find, the complete + contribution guide is hosted on our website. +

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Remote Network Interaction; Use with the GNU General Public License. + + Notwithstanding any other provision of this License, if you modify the +Program, your modified version must prominently offer all users +interacting with it remotely through a computer network (if your version +supports such interaction) an opportunity to receive the Corresponding +Source of your version by providing access to the Corresponding Source +from a network server at no charge, through some standard or customary +means of facilitating copying of software. This Corresponding Source +shall include the Corresponding Source for any work covered by version 3 +of the GNU General Public License that is incorporated pursuant to the +following paragraph. + + Notwithstanding any other provision of this License, you have +permission to link or combine any covered work with a work licensed +under version 3 of the GNU General Public License into a single +combined work, and to convey the resulting work. The terms of this +License will continue to apply to the part which is the covered work, +but the work with which it is combined will remain governed by version +3 of the GNU General Public License. + + 14. Revised Versions of this License. + + The Free Software Foundation may publish revised and/or new versions of +the GNU Affero General Public License from time to time. Such new versions +will be similar in spirit to the present version, but may differ in detail to +address new problems or concerns. + + Each version is given a distinguishing version number. If the +Program specifies that a certain numbered version of the GNU Affero General +Public License "or any later version" applies to it, you have the +option of following the terms and conditions either of that numbered +version or of any later version published by the Free Software +Foundation. If the Program does not specify a version number of the +GNU Affero General Public License, you may choose any version ever published +by the Free Software Foundation. + + If the Program specifies that a proxy can decide which future +versions of the GNU Affero General Public License can be used, that proxy's +public statement of acceptance of a version permanently authorizes you +to choose that version for the Program. + + Later license versions may give you additional or different +permissions. However, no additional obligations are imposed on any +author or copyright holder as a result of your choosing to follow a +later version. + + 15. Disclaimer of Warranty. + + THERE IS NO WARRANTY FOR THE PROGRAM, TO THE EXTENT PERMITTED BY +APPLICABLE LAW. EXCEPT WHEN OTHERWISE STATED IN WRITING THE COPYRIGHT +HOLDERS AND/OR OTHER PARTIES PROVIDE THE PROGRAM "AS IS" WITHOUT WARRANTY +OF ANY KIND, EITHER EXPRESSED OR IMPLIED, INCLUDING, BUT NOT LIMITED TO, +THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR +PURPOSE. THE ENTIRE RISK AS TO THE QUALITY AND PERFORMANCE OF THE PROGRAM +IS WITH YOU. SHOULD THE PROGRAM PROVE DEFECTIVE, YOU ASSUME THE COST OF +ALL NECESSARY SERVICING, REPAIR OR CORRECTION. + + 16. Limitation of Liability. + + IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING +WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MODIFIES AND/OR CONVEYS +THE PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES, INCLUDING ANY +GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING OUT OF THE +USE OR INABILITY TO USE THE PROGRAM (INCLUDING BUT NOT LIMITED TO LOSS OF +DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY YOU OR THIRD +PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER PROGRAMS), +EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF +SUCH DAMAGES. + + 17. Interpretation of Sections 15 and 16. + + If the disclaimer of warranty and limitation of liability provided +above cannot be given local legal effect according to their terms, +reviewing courts shall apply local law that most closely approximates +an absolute waiver of all civil liability in connection with the +Program, unless a warranty or assumption of liability accompanies a +copy of the Program in return for a fee. + + END OF TERMS AND CONDITIONS + + How to Apply These Terms to Your New Programs + + If you develop a new program, and you want it to be of the greatest +possible use to the public, the best way to achieve this is to make it +free software which everyone can redistribute and change under these terms. + + To do so, attach the following notices to the program. It is safest +to attach them to the start of each source file to most effectively +state the exclusion of warranty; and each file should have at least +the "copyright" line and a pointer to where the full notice is found. + + + Copyright (C) + + This program is free software: you can redistribute it and/or modify + it under the terms of the GNU Affero General Public License as published + by the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + + This program is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU Affero General Public License for more details. + + You should have received a copy of the GNU Affero General Public License + along with this program. If not, see . + +Also add information on how to contact you by electronic and paper mail. + + If your software can interact with users remotely through a computer +network, you should also make sure that it provides a way for users to +get its source. For example, if your program is a web application, its +interface could display a "Source" link that leads users to an archive +of the code. There are many ways you could offer source, and different +solutions will be better for different programs; see section 13 for the +specific requirements. + + You should also get your employer (if you work as a programmer) or school, +if any, to sign a "copyright disclaimer" for the program, if necessary. +For more information on this, and how to apply and follow the GNU AGPL, see +. diff --git a/MANIFEST.in b/MANIFEST.in new file mode 100644 index 00000000..6c2c0e62 --- /dev/null +++ b/MANIFEST.in @@ -0,0 +1,3 @@ +graft src/templaterepo +include CODE_OF_CONDUCT.md +global-exclude *.py[cod] __pycache__ *.so diff --git a/README.md b/README.md index 7e78e8bb..3b5fe077 100644 --- a/README.md +++ b/README.md @@ -1,5 +1,5 @@
    -TemplateRepo: Python Projects Perfected: Innovate, Develop, and Deploy Effortlessly! +TemplateRepo: Python Projects Perfected: Innovate, Develop, and Deploy Effortlessly!
    @@ -9,37 +9,37 @@ Intro -   +   Manual -   +   API -   +   News -   +   Contribute -   +   About -   +   @@ -49,43 +49,43 @@
    -

    PyPackIT is a free and open-source toolkit empowering the development of open-source Python projects on GitHub. It is a dynamic repository template that provides a complete, professional, and robust infrastructure for your project, where the only thing missing is your code. With PyPackIT, you can solely focus on what truly matters: implementing your ideas and bringing your vision to life!

    +

    TemplateRepo is a free and open-source toolkit empowering the development of open-source Python projects on GitHub. It is a dynamic repository template that provides a complete, professional, and robust infrastructure for your project, where the only thing missing is your code. With TemplateRepo, you can solely focus on what truly matters: implementing your ideas and bringing your vision to life!

    Automation -

    PyPackIT streamlines a remarkable portion of the process of creating, documenting, testing, publishing, and maintaining Python packages, making your project development a pleasant breeze!

    +

    TemplateRepo streamlines a remarkable portion of the process of creating, documenting, testing, publishing, and maintaining Python packages, making your project development a pleasant breeze!

    Synchronization -

    PyPackIT gathers all your project's key information and configuration in one place, and dynamically updates them throughout your repository, Python package, and documentation website.

    +

    TemplateRepo gathers all your project's key information and configuration in one place, and dynamically updates them throughout your repository, Python package, and documentation website.

    Configuration -

    PyPackIT elevates your project by providing full configuration for your repository, Python package, and documentation website, according to the latest guidelines and best practices.

    +

    TemplateRepo elevates your project by providing full configuration for your repository, Python package, and documentation website, according to the latest guidelines and best practices.

    Customization -

    While carefully configured, PyPackIT is also fully customizable, allowing you to tailor every aspect of your development pipeline to your specific needs

    +

    While carefully configured, TemplateRepo is also fully customizable, allowing you to tailor every aspect of your development pipeline to your specific needs

    Documentation -

    PyPackIT comes with a professional website for your project, that is easily customizable, and automatically generated and deployed on your preferred platform.

    +

    TemplateRepo comes with a professional website for your project, that is easily customizable, and automatically generated and deployed on your preferred platform.

    Production -

    With PyPackIT, the only remaining step to publishing a production-ready Python project is adding your code, unit-tests and documentation content.

    +

    With TemplateRepo, the only remaining step to publishing a production-ready Python project is adding your code, unit-tests and documentation content.

    @@ -95,13 +95,13 @@ Install -   +   Releases -   +   diff --git a/SECURITY.md b/SECURITY.md new file mode 100644 index 00000000..580df59b --- /dev/null +++ b/SECURITY.md @@ -0,0 +1,188 @@ +# TemplateRepo Security and Vulnerability Disclosure Policy + +TemplateRepo takes the security and privacy of all its users and members very seriously, +and is committed to ensuring the safety of its products and services. +In case a security vulnerability is detected that may affect users, we take immediate action to: +1. fix the issue as soon as possible, +2. publish a new security patch release in case a published application was affected, +3. release a security advisory, detailing the vulnerability, +as well as guidelines for end-users to protect themselves. +Security advisories are accessible on our website and repository, as well as via a feed. + + +https://aariam.github.io/TemplateRepo/contribute/collaborate/maintain/security + +
    + 🛡️**Supported Versions** +

    + Currently supported versions for security updates are: +
    + +This policy is intended to give users, contributors, and security researchers clear guidelines for +[reporting potential security vulnerabilities](#reporting-a-potential-vulnerability), +and [conducting vulnerability discovery activities](#testing-for-vulnerabilities). +It describes what systems and types of research are covered under this policy, +how to send us vulnerability reports and what information to include, +and how long we ask security researchers to wait before publicly disclosing vulnerabilities. + +
    + 🛡️**Supported Versions** +

    + Questions regarding this policy may be sent to security@agency.gov. + We also invite you to contact us with suggestions for improving this policy. +
    + + +## Reporting a Potential Vulnerability +If you have found a potential vulnerability in our application, website, or repository, +please report it as soon as possible, following the guidelines described here. +Please DO NOT + +### Where to Report +We use [GitHub's security advisories feature](https://docs.github.com/en/code-security/security-advisories/repository-security-advisories/about-repository-security-advisories) +of our repository to securely discuss, fix and publish information about security vulnerabilities +in TemplateRepo. To privately report a security vulnerability, +follow the [documentation on Github](https://docs.github.com/en/code-security/security-advisories/guidance-on-reporting-and-writing/privately-reporting-a-security-vulnerability#privately-reporting-a-security-vulnerability) +or [**click here to directly open a private report form**](https://github.com/AAriam/TemplateRepo/security/advisories/new). + +
    + 🥷🏾 Prefer Anonymity? +

    + Our vulnerability management team also welcomes anonymous emails sent to +     None. +
    + +---Thank you for reporting a security vulnerability. Please provide as much information as you can under the sections listed below. Texts like this that are surrounded by three hyphens are instructions and should be deleted before sending the email.--- + +1. Summary +---Provide a short summary of the problem. Make the impact and severity as clear as possible. For example: An unsafe deserialization vulnerability allows any unauthenticated user to execute arbitrary code on the server.--- + +2. Details +---Give all details on the vulnerability. Pointing to the incriminated source code is very helpful for the maintainer.--- + +3. PoC +---Complete instructions, including specific configuration details, to reproduce the vulnerability.--- + +4. Impact +---What kind of vulnerability is it? Who is impacted?--- + +5. Affected Products +---For each affected product, name the ecosystem (e.g. pip, GitHub Actions), package- or filename, and affected versions.--- + +6. Severity +---Asses the severity of the issue, e.g. using a CVSS vector string (learn more at https://www.first.org/cvss/v3.1/user-guide).--- + +7. Weaknesses +---Provide Common Weakness Enumerator (CWE; learn more at https://docs.github.com/en/code-security/security-advisories/repository-security-advisories/about-repository-security-advisories#cve-identification-numbers).--- + +8. Mitigation +---Provide necessary steps to mitigate the problem.--- + + +### What to Include +In order to help us triage and prioritize submissions, we recommend that your reports: +* Describe the location the vulnerability was discovered, +affected components/versions, and the potential impact of exploitation. +* Offer a detailed description of the vulnerability and the steps needed to reproduce it +(proof of concept scripts or screenshots can be helpful). +* if known, necessary steps to mitigate the issue. + +For more information, see GitHub Documentations on [creating a repository security advisory](https://docs.github.com/en/code-security/security-advisories/repository-security-advisories/creating-a-repository-security-advisory) +and [best practices for writing repository security advisories](https://docs.github.com/en/code-security/security-advisories/guidance-on-reporting-and-writing/best-practices-for-writing-repository-security-advisories). + +### Response Policy +When you choose to share your contact information with us, +we commit to coordinating with you as openly and as quickly as possible: +* Within a week, our vulnerability management team will acknowledge receiving your report. +* To the best of our ability, we will confirm the existence of the vulnerability to you +and be as transparent as possible about what steps we are taking during the remediation process, +including on issues or challenges that may delay resolution. +* We will maintain an open dialogue to discuss issues. + +### Disclosure Policy +This project follows a 90-day disclosure timeline. +If you are a security researcher and would like to disclose the vulnerability you detected, +we request that you allow us at least 90 days prior to any public exposure. +This helps the project contributors to resolve the vulnerability and issue a new release, +and provides our users a chance to update their applications and protect themselves. + + + +## Testing for Vulnerabilities +TemplateRepo is a free and open-source project. +We encourage security researchers to help us improve our security measures +by conducting vulnerability discovery activities on our application, website, and repository. +Before starting, please read the [guidelines](#testing-for-vulnerabilities) below, +describing what systems and types of research are covered under this policy. + +### Authorization +If you make a good faith effort to comply with this policy during your security research, +we will consider your research to be authorized, will work with you to understand and resolve the issue quickly, +and will not recommend or pursue legal action related to your research. +Should legal action be initiated by a third party against you for activities that were conducted +in accordance with this policy, we will make this authorization known. + +### Guidelines +Under this policy, "research" and "vulnerability discovery" means activities in which you: +* notify us as soon as possible after you discover a real or potential security issue, +* make every effort to avoid privacy violations, degradation of user experience, +disruption to production systems, and destruction or manipulation of data, +* only use exploits to the extent necessary to confirm a vulnerability's presence, +* do not use an exploit to compromise or exfiltrate data, establish persistent command line access, +or use the exploit to pivot to other systems, +* provide us a reasonable amount of time to resolve the issue before you disclose it publicly, +* do not submit a high volume of low-quality reports. + +Once you've established that a vulnerability exists or encounter +any sensitive data (including personally identifiable information, financial information, +or proprietary information or secrets of any kind), you must: +* stop your test, +* notify us immediately, +* and not disclose this data to anyone else. + +### Test Methods +The following test methods are not authorized: +* Network denial of service (DoS or DDoS) tests or other tests that +impair access to or damage a system or data. +* Social engineering (e.g. phishing, vishing), or any other non-technical vulnerability testing. + +### Scope +This policy applies to the following systems and services: +* Source code at https://github.com/AAriam/TemplateRepo + +Any service not expressly listed above, such as any connected services, are excluded from scope +and are not authorized for testing. Additionally, vulnerabilities found in systems from our vendors +fall outside of this policy's scope and should be reported directly to the vendor according to their +disclosure policy (if any). If you aren't sure whether a system is in scope or not, +or there is a particular system not in scope that you think merits testing, +please contact us at None to discuss it first, before starting your research. diff --git a/docs/website/README.md b/docs/website/README.md new file mode 100644 index 00000000..463757bf --- /dev/null +++ b/docs/website/README.md @@ -0,0 +1,14 @@ +# Documentation Website + +## Requirements + +### sphinxext-opengraph +To add [Open Graph](https://ogp.me/) meta tags to each HTML page of the site. + +PyPI: https://pypi.org/project/sphinxext-opengraph +conda-forge: https://anaconda.org/conda-forge/sphinxext-opengraph +GitHub: https://github.com/wpilibsuite/sphinxext-opengraph +Docs: https://sphinxext-opengraph.readthedocs.io/en/latest/ + +### Extra Requirements +from 'apt': "librsvg2-bin" diff --git a/pyproject.toml b/pyproject.toml new file mode 100644 index 00000000..973ac8f4 --- /dev/null +++ b/pyproject.toml @@ -0,0 +1,259 @@ +[build-system] +requires = ["setuptools>=61.0", "versioningit"] +build-backend = "setuptools.build_meta" + +[tool] +[tool.setuptools] +include-package-data = true +zip-safe = false + +[tool.setuptools.packages.find] +where = ["src"] +namespaces = true + +[tool.versioningit] +[tool.versioningit.vcs] +method = "git" +match = ["ver/[0-9]*.[0-9]*.[0-9]*"] + +[tool.versioningit.tag2version] +rmprefix = "ver/" + +[tool.versioningit.format] +distance = "{base_version}+{distance}-{revision}" +dirty = "{base_version}.dirty" +distance-dirty = "{base_version}+{distance}-{revision}.dirty" + +[tool.versioningit.onbuild] +method = "replace-version" +regex = "^\\s*__version_details__\\s*=\\s*(?P.*)" +require-match = true +replacement = "dict(\n version=\"{version}\",\n version_tuple={version_tuple},\n author_date=\"{author_date:%Y.%m.%d}\",\n build_date=\"{build_date:%Y.%m.%d}\",\n branch=\"{branch}\",\n distance=\"{distance}\",\n head_commit_hash=\"{revision}\",\n)" +source-file = "src/templaterepo/__init__.py" +build-file = "templaterepo/__init__.py" + +[tool.mypy] +packages = ["templaterepo"] +warn_return_any = true +strict = true +show_error_context = true +show_column_numbers = true +pretty = true +color_output = true +cache_dir = ".local/cache/mypy" +show_traceback = true +raise_exceptions = true +any_exprs_report = ".local/report/mypy" +html_report = ".local/report/mypy" +linecount_report = ".local/report/mypy" +linecoverage_report = ".local/report/mypy" +lineprecision_report = ".local/report/mypy" +txt_report = ".local/report/mypy" +verbosity = 2 + +[tool.bandit] +targets = ["src"] + +[tool.isort] +profile = "black" +line_length = 100 +src_paths = ["src", "tests"] +skip_gitignore = true +lines_before_imports = 2 +lines_after_imports = 2 +lines_between_sections = 0 +verbose = true +color_output = true +only_modified = true +filter_files = true +no_lines_before = ["future", "stdlib", "thirdparty", "firstparty", "localfolder"] +dedup_headings = true +overwrite_in_place = true + +[tool.isort.import_headings] +future = "Futures" +stdlib = "Standard libraries" +thirdparty = "Non-standard libraries" +firstparty = "Self" + +[tool.pytest.ini_options] +addopts = "-r a --verbose --color=yes --full-trace --cov --cov-config=pyproject.toml --cov-report=term-missing:skip-covered --cov-report=html --cov-report=xml --strict-config --strict-markers" +cache_dir = ".local/cache/pytest" +console_output_style = "count" +log_auto_indent = true +log_cli = true +log_cli_format = "%(levelname)s %(message)s" +log_cli_level = "INFO" +log_file = ".local/report/pytest/log.txt" +log_file_date_format = "%Y-%m-%d %H:%M:%S" +log_file_format = "%(asctime)s %(levelname)s %(message)s" +log_file_level = "DEBUG" +log_format = "%(asctime)s %(levelname)s %(message)s" +log_level = "DEBUG" +minversion = "7.4.2" +python_classes = ["Test*", "*Test"] +python_files = ["test_*.py", "tests_*.py", "*_test.py", "*_tests.py"] +python_functions = ["test_*", "tests_*", "*_test", "*_tests"] +required_plugins = ["pytest-cov>=4.1.0,<5"] +testpaths = ["tests"] + +[tool.coverage] +[tool.coverage.run] +branch = true +data_file = ".local/cache/coverage/.coverage" +source_pkgs = ["templaterepo"] + +[tool.coverage.report] +exclude_also = ["def __repr__", "if self\\.debug", "raise AssertionError", "raise NotImplementedError", "if 0:", "if __name__ == .__main__.:", "@(abc\\.)?abstractmethod"] +show_missing = true + +[tool.coverage.html] +directory = ".local/report/coverage" + +[tool.coverage.xml] +output = ".local/report/coverage/coverage.xml" + +[tool.pylint] +[tool.pylint.main] +fail-under = 10 +jobs = 0 +limit-inference-results = 500 +load-plugins = ["pylint.extensions.broad_try_clause", "pylint.extensions.code_style", "pylint.extensions.comparison_placement", "pylint.extensions.confusing_elif", "pylint.extensions.for_any_all", "pylint.extensions.consider_refactoring_into_while_condition", "pylint.extensions.consider_ternary_expression", "pylint.extensions.bad_builtin", "pylint.extensions.mccabe", "pylint.extensions.dict_init_mutate", "pylint.extensions.docstyle", "pylint.extensions.dunder", "pylint.extensions.check_elif", "pylint.extensions.empty_comment", "pylint.extensions.eq_without_hash", "pylint.extensions.private_import", "pylint.extensions.magic_value", "pylint.extensions.redefined_variable_type", "pylint.extensions.no_self_use", "pylint.extensions.overlapping_exceptions", "pylint.extensions.docparams", "pylint.extensions.redefined_loop_name", "pylint.extensions.set_membership", "pylint.extensions.typing", "pylint.extensions.while_used"] +persistent = true +py-version = "3.9" +recursive = true +source-roots = ["src"] + +[tool.pylint.basic] +good-names = ["i", "j", "k", "x", "y", "z", "ex", "Run", "_"] + +[tool.pylint.design] +max-args = 10 +max-attributes = 20 +max-bool-expr = 5 +max-branches = 15 +max-locals = 15 +max-public-methods = 50 +max-returns = 10 +max-statements = 50 +min-public-methods = 1 + +[tool.pylint.format] +max-line-length = 100 +max-module-lines = 2000 + +[tool.pylint.imports] +import-graph = ".local/report/pylint/import_graph_total.svg" +int-import-graph = ".local/report/pylint/import_graph_internal.svg" +ext-import-graph = ".local/report/pylint/import_graph_external.svg" + +[tool.pylint.logging] +logging-format-style = "new" + +[tool.pylint."messages control"] +confidence = ["HIGH", "CONTROL_FLOW", "INFERENCE", "INFERENCE_FAILURE", "UNDEFINED"] + +[tool.pylint.reports] +reports = true +score = true +msg-template = "{path}\nL[{line}:{end_line}] - Col[{column}:{end_column}] - Obj: {obj}\n\t{msg_id}: {category} - {symbol}\n\t{msg}\n" +output-format = ["json:.local/report/pylint/report_json.json", "text:.local/report/pylint/report_text.txt", "parseable:.local/report/pylint/report_parseable.txt", "msvs:.local/report/pylint/report_msvs.txt", "colorized"] + +[tool.pylint.similarities] +ignore-comments = true +min-similarity-lines = 8 + +[tool.black] +required-version = "23.9.1" +target-version = ["py39", "py310", "py311", "py312"] +line-length = 100 +verbose = true + +[tool.ruff] +required-version = "0.0.290" +cache-dir = ".local/cache/ruff" +format = "grouped" +ignore-init-module-imports = true +line-length = 100 +show-fixes = true +show-source = true +select = ["F", "E", "W", "N", "D", "UP", "YTT", "S", "BLE", "FBT", "B", "COM", "C4", "DTZ", "EM", "EXE", "ICN", "PIE", "PT", "RSE", "RET", "SIM", "ARG", "PTH", "TD", "FIX", "ERA", "PD", "PGH", "PL", "RUF"] +src = ["src", "tests"] +include = ["*.py", "*.pyi", "**/pyproject.toml", "*.ipynb"] + +[tool.ruff.flake8-annotations] +allow-star-arg-any = true +suppress-dummy-args = true +suppress-none-returning = true + +[tool.ruff.flake8-comprehensions] +allow-dict-calls-with-keyword-arguments = true + +[tool.ruff.flake8-quotes] +docstring-quotes = "single" +multiline-quotes = "single" + +[tool.ruff.pydocstyle] +convention = "numpy" + +[tool.ruff.pylint] +max-args = 10 +max-public-methods = 50 +max-returns = 10 + +[project] +name = "templaterepo" +dynamic = [ + 'version', +] +description = "Python Projects Perfected: Innovate, Develop, and Deploy Effortlessly!" +readme = "src/readme_pypi.md" +requires-python = ">= 3.9" +authors = [ + {name = "Armin Ariamajd"}, +] +maintainers = [ + {name = "Armin Ariamajd"}, +] +keywords = [ + 'python', + 'github', + 'packaging', + 'template', + 'dynamic repository', + 'repository template', + 'documentation', + 'testing', + 'deployment', + 'maintenance', + 'automation', + 'development', + 'infrastructure', + 'streamline', +] +classifiers = [ + 'License :: OSI Approved :: GNU Affero General Public License v3 or later (AGPLv3+)', + 'Natural Language :: English', + 'Operating System :: MacOS', + 'Operating System :: Microsoft :: Windows', + 'Operating System :: POSIX :: Linux', + 'Programming Language :: Python :: 3 :: Only', + 'Programming Language :: Python :: 3.10', + 'Programming Language :: Python :: 3.11', + 'Programming Language :: Python :: 3.12', + 'Programming Language :: Python :: 3.9', + 'Typing :: Typed', +] +dependencies = [ + 'numpy >= 1.21.2', +] +license = {file = "LICENSE"} + +[project.urls] +Homepage = "https://aariam.github.io/TemplateRepo" +Download = "https://github.com/AAriam/TemplateRepo/releases" +News = "https://aariam.github.io/TemplateRepo/news" +Documentation = "https://aariam.github.io/TemplateRepo" +Issue-Tracker = "https://github.com/AAriam/TemplateRepo/issues" +Sponsor = "https://aariam.github.io/TemplateRepo/contribute/collaborate/maintain/sponsor" +Source = "https://github.com/AAriam/TemplateRepo" diff --git a/requirements.txt b/requirements.txt new file mode 100644 index 00000000..950e3bdf --- /dev/null +++ b/requirements.txt @@ -0,0 +1 @@ +numpy >= 1.21.2 diff --git a/src/templaterepo/__init__.py b/src/templaterepo/__init__.py index 8a835674..6c741108 100644 --- a/src/templaterepo/__init__.py +++ b/src/templaterepo/__init__.py @@ -2,25 +2,38 @@ Python Projects Perfected: Innovate, Develop, and Deploy Effortlessly! -PyPackIT is a free and open-source toolkit empowering the development of open-source Python projects on GitHub. It is a dynamic repository template that provides a complete, professional, and robust infrastructure for your project, where the only thing missing is your code. With PyPackIT, you can solely focus on what truly matters: implementing your ideas and bringing your vision to life! +TemplateRepo +is a free and open-source toolkit empowering the development of open-source Python projects on +GitHub. It is a dynamic repository template that provides a complete, professional, and +robust infrastructure for your project, where the only thing missing is your code. With +TemplateRepo, you can solely focus on what truly matters: implementing your ideas and bringing your +vision to life! Copyright 2023 Armin Ariamajd Copyright (C) 2023 Armin Ariamajd -This program is free software: you can redistribute it and/or modify -it under the terms of the GNU Affero General Public License as published +This program is +free software: you can redistribute it and/or modify +it under the terms of the GNU Affero General +Public License as published by the Free Software Foundation, either version 3 of the License, or -(at your option) any later version. +(at +your option) any later version. This program is distributed in the hope that it will be useful, -but WITHOUT ANY WARRANTY; without even the implied warranty of -MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +but +WITHOUT ANY WARRANTY; without even the implied warranty of +MERCHANTABILITY or FITNESS FOR A +PARTICULAR PURPOSE. See the GNU Affero General Public License for more details. -You should have received a copy of the GNU Affero General Public License -along with this program. If not, see . +You should have +received a copy of the GNU Affero General Public License +along with this program. If not, see +. """ + __version_details__ = {"version": "0.0.0"} __version__ = __version_details__["version"] diff --git a/tests/pyproject.toml b/tests/pyproject.toml new file mode 100644 index 00000000..e8782e92 --- /dev/null +++ b/tests/pyproject.toml @@ -0,0 +1,43 @@ +[build-system] +requires = ["setuptools>=61.0", "versioningit"] +build-backend = "setuptools.build_meta" + +[build-system.project] +name = "templaterepo_tests" +dynamic = ["version"] +dependencies = ["pytest >= 7.4.2, < 8", "pytest-cov >= 4.1.0, < 5"] + +[tool] +[tool.setuptools] +include-package-data = true +zip-safe = false + +[tool.setuptools.packages.find] +where = ["src"] +namespaces = true + +[tool.versioningit] +[tool.versioningit.vcs] +method = "git" +match = ["ver/[0-9]*.[0-9]*.[0-9]*"] + +[tool.versioningit.tag2version] +rmprefix = "ver/" + +[tool.versioningit.format] +distance = "{base_version}+{distance}-{revision}" +dirty = "{base_version}.dirty" +distance-dirty = "{base_version}+{distance}-{revision}.dirty" + +[tool.versioningit.onbuild] +method = "replace-version" +regex = "^\\s*__version_details__\\s*=\\s*(?P.*)" +require-match = true +replacement = "dict(\n version=\"{version}\",\n version_tuple={version_tuple},\n author_date=\"{author_date:%Y.%m.%d}\",\n build_date=\"{build_date:%Y.%m.%d}\",\n branch=\"{branch}\",\n distance=\"{distance}\",\n head_commit_hash=\"{revision}\",\n)" +source-file = "tests/src/templaterepo_tests/__init__.py" +build-file = "templaterepo_tests/__init__.py" + +[project] +name = "templaterepo_tests" +dynamic = ["version"] +dependencies = ["pytest >= 7.4.2, < 8", "pytest-cov >= 4.1.0, < 5", "pipreqs"] diff --git a/tests/src/pypackit_tests/__main__.py b/tests/src/pypackit_tests/__main__.py deleted file mode 100644 index ea633c5e..00000000 --- a/tests/src/pypackit_tests/__main__.py +++ /dev/null @@ -1,3 +0,0 @@ -import pypackit_tests as testsuite - -testsuite.run() diff --git a/tests/src/pypackit_tests/__init__.py b/tests/src/templaterepo_tests/__init__.py similarity index 100% rename from tests/src/pypackit_tests/__init__.py rename to tests/src/templaterepo_tests/__init__.py diff --git a/tests/src/templaterepo_tests/__main__.py b/tests/src/templaterepo_tests/__main__.py new file mode 100644 index 00000000..349d8e72 --- /dev/null +++ b/tests/src/templaterepo_tests/__main__.py @@ -0,0 +1,3 @@ +import templaterepo_tests as testsuite + +testsuite.run() diff --git a/tests/src/pypackit_tests/general_tests.py b/tests/src/templaterepo_tests/general_tests.py similarity index 84% rename from tests/src/pypackit_tests/general_tests.py rename to tests/src/templaterepo_tests/general_tests.py index 52138411..f85c5178 100644 --- a/tests/src/pypackit_tests/general_tests.py +++ b/tests/src/templaterepo_tests/general_tests.py @@ -1,4 +1,4 @@ -import pypackit as pkg +import templaterepo as pkg def version_test():