diff --git a/CHANGELOG.rst b/CHANGELOG.rst index 2ddae3d6..4a1594f3 100644 --- a/CHANGELOG.rst +++ b/CHANGELOG.rst @@ -19,9 +19,9 @@ Development * Fix a bug in pytest where we used `scope` as a positional argument * Update the SubFactoryList to a new version that works with newer FactoryBoy versions -.. _[#430]: https://github.com/ewels/MegaQC/issues/430 -.. _[#440]: https://github.com/ewels/MegaQC/pull/440 -.. _[#433]: https://github.com/ewels/MegaQC/pull/433 +.. _[#430]: https://github.com/MultiQC/MegaQC/issues/430 +.. _[#440]: https://github.com/MultiQC/MegaQC/pull/440 +.. _[#433]: https://github.com/MultiQC/MegaQC/pull/433 ======= @@ -87,12 +87,12 @@ Internal Changes - Many and more dependency updates -.. _[#69]: https://github.com/ewels/MegaQC/issues/69 -.. _[#138]: https://github.com/ewels/MegaQC/issues/138 -.. _[#139]: https://github.com/ewels/MegaQC/issues/139 -.. _[#140]: https://github.com/ewels/MegaQC/issues/140 -.. _[#148]: https://github.com/ewels/MegaQC/issues/148 -.. _[#156]: https://github.com/ewels/MegaQC/issues/156 -.. _[#170]: https://github.com/ewels/MegaQC/issues/170 -.. _[#194]: https://github.com/ewels/MegaQC/issues/194 -.. _[#443]: https://github.com/ewels/MegaQC/pull/443 +.. _[#69]: https://github.com/MultiQC/MegaQC/issues/69 +.. _[#138]: https://github.com/MultiQC/MegaQC/issues/138 +.. _[#139]: https://github.com/MultiQC/MegaQC/issues/139 +.. _[#140]: https://github.com/MultiQC/MegaQC/issues/140 +.. _[#148]: https://github.com/MultiQC/MegaQC/issues/148 +.. _[#156]: https://github.com/MultiQC/MegaQC/issues/156 +.. _[#170]: https://github.com/MultiQC/MegaQC/issues/170 +.. _[#194]: https://github.com/MultiQC/MegaQC/issues/194 +.. _[#443]: https://github.com/MultiQC/MegaQC/pull/443 diff --git a/README.rst b/README.rst index 1d430cb1..e57d1593 100644 --- a/README.rst +++ b/README.rst @@ -20,7 +20,7 @@ MegaQC is a web application that you can install and run on your own network. It collects and visualises data parsed by MultiQC across multiple runs. The MegaQC home page looks something like this: -.. figure:: https://raw.githubusercontent.com/ewels/MegaQC/master/docs/source/images/megaqc_homepage.png +.. figure:: https://raw.githubusercontent.com/MultiQC/MegaQC/master/docs/source/images/megaqc_homepage.png :alt: MegaQC homepage Screenshot of the MegaQC home page. @@ -37,7 +37,7 @@ to learn how to install, deploy and use MegaQC. .. _MultiQC website: http://multiqc.info .. _GitHub repository: https://github.com/ewels/MultiQC -.. |MegaQC| image:: https://raw.githubusercontent.com/ewels/MegaQC/master/megaqc/static/img/MegaQC_logo.png +.. |MegaQC| image:: https://raw.githubusercontent.com/MultiQC/MegaQC/master/megaqc/static/img/MegaQC_logo.png .. |Docker| image:: https://img.shields.io/docker/automated/ewels/megaqc.svg?style=flat-square :target: https://hub.docker.com/r/ewels/megaqc/ .. |Build Status| image:: https://travis-ci.org/ewels/MegaQC.svg?branch=master diff --git a/docs/source/_templates/index.html b/docs/source/_templates/index.html index 63521763..1e8dd75f 100644 --- a/docs/source/_templates/index.html +++ b/docs/source/_templates/index.html @@ -27,7 +27,7 @@

Docs
  • MultiQC
  • Gitter
    • -
  • GitHub
    • +
  • GitHub
    • @@ -186,7 +186,7 @@

    Still not sure?

    diff --git a/docs/source/conf.py b/docs/source/conf.py index ba5cd031..0012738c 100644 --- a/docs/source/conf.py +++ b/docs/source/conf.py @@ -98,4 +98,4 @@ def find_source(): tag = "master" # TODO use this after the first release: tag = 'master' if 'dev' in release else ('v' + release) - return "https://github.com/ewels/megaqc/blob/%s/%s" % (tag, filename) + return "https://github.com/MultiQC/MegaQC/blob/%s/%s" % (tag, filename) diff --git a/docs/source/docs/dev/backend.rst b/docs/source/docs/dev/backend.rst index 1b796032..389e3745 100644 --- a/docs/source/docs/dev/backend.rst +++ b/docs/source/docs/dev/backend.rst @@ -13,7 +13,7 @@ will likely be SQLite. Database models are located in `model/models.py`_ and `user/models.py`_. -Database schema migrations +Database schema migrations ^^^^^^^^^^^^^^^^^^^^^^^^^^^^ You need to generate a new migration whenever the database schema (ie @@ -61,16 +61,16 @@ be done inside `test_api.py`_, which tests all REST API endpoints. .. _flask: https://www.palletsprojects.com/p/flask/ .. _SQLAlchemy: https://docs.sqlalchemy.org/ -.. _model/models.py: https://github.com/ewels/MegaQC/blob/master/megaqc/model/models.py -.. _user/models.py: https://github.com/ewels/MegaQC/blob/master/megaqc/user/models.py -.. _megaqc/api: https://github.com/ewels/MegaQC/tree/master/megaqc/api -.. _megaqc/rest_api: https://github.com/ewels/MegaQC/tree/master/megaqc/rest_api -.. _views.py: https://github.com/ewels/MegaQC/blob/master/megaqc/rest_api/views.py +.. _model/models.py: https://github.com/MultiQC/MegaQC/blob/master/megaqc/model/models.py +.. _user/models.py: https://github.com/MultiQC/MegaQC/blob/master/megaqc/user/models.py +.. _megaqc/api: https://github.com/MultiQC/MegaQC/tree/master/megaqc/api +.. _megaqc/rest_api: https://github.com/MultiQC/MegaQC/tree/master/megaqc/rest_api +.. _views.py: https://github.com/MultiQC/MegaQC/blob/master/megaqc/rest_api/views.py .. _flapison: https://github.com/TMiguelT/flapison -.. _schemas.py: https://github.com/ewels/MegaQC/tree/master/megaqc/rest_api/schemas.py -.. _public/views.py: https://github.com/ewels/MegaQC/tree/master/megaqc/public/views.py -.. _user/views.py: https://github.com/ewels/MegaQC/tree/master/megaqc/user/views.py +.. _schemas.py: https://github.com/MultiQC/MegaQC/tree/master/megaqc/rest_api/schemas.py +.. _public/views.py: https://github.com/MultiQC/MegaQC/tree/master/megaqc/public/views.py +.. _user/views.py: https://github.com/MultiQC/MegaQC/tree/master/megaqc/user/views.py .. _Jinja2: https://jinja.palletsprojects.com/en/2.11.x/ .. _frontend: ./frontend.md -.. _python_tests: https://github.com/ewels/MegaQC/tree/master/tests -.. _test_api.py: https://github.com/ewels/MegaQC/tree/master/megaqc/api/test_api.py +.. _python_tests: https://github.com/MultiQC/MegaQC/tree/master/tests +.. _test_api.py: https://github.com/MultiQC/MegaQC/tree/master/megaqc/api/test_api.py diff --git a/docs/source/docs/dev/documentation.rst b/docs/source/docs/dev/documentation.rst index 6bc8dcca..8c6b6ea4 100644 --- a/docs/source/docs/dev/documentation.rst +++ b/docs/source/docs/dev/documentation.rst @@ -10,8 +10,8 @@ Building the documentation locally The MegaQC documentation requires 1. An installation of MegaQC to fetch the API endpoints and the Click commands. -2. All dependencies specified in the `docs requirements.txt `_. - Install them by invoking: ``pip install -r docs/requirements.txt``. +2. All dependencies specified in the `docs requirements.txt `_. + Install them by invoking: ``pip install -r docs/requirements.txt``. After having installed all requirements run ``make api-docs && make html`` in the ``docs`` directory. The generated ``html`` files are found in the ``docs/_build/html`` subfolder. @@ -23,4 +23,4 @@ Publishing the documentation On pushes to the ``master`` branch, the documentation is automatically built and pushed to the ``gh-pages`` branch. The static html files on this branch are then deployed to Github Pages and displayed to the outside world. -All of this is done with the `Publish Docs Github Actions workflow `. +All of this is done with the `Publish Docs Github Actions workflow `. diff --git a/docs/source/docs/dev/frontend.rst b/docs/source/docs/dev/frontend.rst index 8ac647c4..f2465ccd 100644 --- a/docs/source/docs/dev/frontend.rst +++ b/docs/source/docs/dev/frontend.rst @@ -22,7 +22,7 @@ Note that all new pages going forward should be written using React, to improve the maintainability of the frontend. .. _React: https://reactjs.org/ -.. _templates: https://github.com/ewels/MegaQC/tree/master/megaqc/templates -.. _static: https://github.com/ewels/MegaQC/tree/master/megaqc/static -.. _react.html: https://github.com/ewels/MegaQC/tree/master/megaqc/templates/public/react.html -.. _src: https://github.com/ewels/MegaQC/tree/master/src \ No newline at end of file +.. _templates: https://github.com/MultiQC/MegaQC/tree/master/megaqc/templates +.. _static: https://github.com/MultiQC/MegaQC/tree/master/megaqc/static +.. _react.html: https://github.com/MultiQC/MegaQC/tree/master/megaqc/templates/public/react.html +.. _src: https://github.com/MultiQC/MegaQC/tree/master/src diff --git a/docs/source/docs/index.rst b/docs/source/docs/index.rst index 0801d53f..4c623c2a 100644 --- a/docs/source/docs/index.rst +++ b/docs/source/docs/index.rst @@ -23,4 +23,4 @@ Indices and tables * :ref:`modindex` * :ref:`search` -.. |MegaQC| image:: https://raw.githubusercontent.com/ewels/MegaQC/master/megaqc/static/img/MegaQC_logo.png +.. |MegaQC| image:: https://raw.githubusercontent.com/MultiQC/MegaQC/master/megaqc/static/img/MegaQC_logo.png diff --git a/docs/source/docs/installation/installation_dev.rst b/docs/source/docs/installation/installation_dev.rst index 76457f1b..86149404 100644 --- a/docs/source/docs/installation/installation_dev.rst +++ b/docs/source/docs/installation/installation_dev.rst @@ -17,7 +17,7 @@ If you’re doing development work, you need access to the source code .. code:: bash - git clone https://github.com/ewels/MegaQC + git clone https://github.com/MultiQC/MegaQC/ 2. Install Dependencies ------------------------------------------------ diff --git a/docs/source/docs/installation/installation_docker.rst b/docs/source/docs/installation/installation_docker.rst index f6933906..39fd197d 100644 --- a/docs/source/docs/installation/installation_docker.rst +++ b/docs/source/docs/installation/installation_docker.rst @@ -14,10 +14,10 @@ The MegaQC Docker container Overview ~~~~~~~~~~ -The MegaQC container is based on the `Node container `_ +The MegaQC container is based on the `Node container `_ to compile all Javascript scripts and the `Gunicorn Flask container `_ providing Gunicorn, Flask and MegaQC preconfigured for production deployments. -The `Gunicorn Flask `_ container +The `Gunicorn Flask `_ container is also the one spinning up the final server. Pulling the docker image from dockerhub @@ -53,10 +53,10 @@ You can then run MegaQC as described above: Configuration ~~~~~~~~~~~~~~~ -Besides the sections below it is also recommended to read the +Besides the sections below it is also recommended to read the `Gunicorn Flask container documentation `_, which explains how to customize the ``host`` IP where Gunicorn listens -to requests, the ``port`` the container should listen on and ``bind``, the actual +to requests, the ``port`` the container should listen on and ``bind``, the actual host and port passed to gunicorn, let alone custom Gunicorn configuration files. Environment variables @@ -199,15 +199,15 @@ Overview The `docker-compose`_ configuration can be accessed in the `deployment folder`_. The docker-compose configuration provides the :ref:`megaqc_docker_container`, -a `postgres container `_ for the SQL database +a `postgres container `_ for the SQL database and a `nginx container `_ for the reverse proxy setup. Usage ~~~~~~~~ Inside the `deployment folder`_ the `docker-compose`_ configuration -together with the associated `.env `_ file -are found. To spin up all containers simply run from inside the `deployment folder `_: +together with the associated `.env `_ file +are found. To spin up all containers simply run from inside the `deployment folder `_: .. code:: bash @@ -229,18 +229,18 @@ Environment variables ^^^^^^^^^^^^^^^^^^^^^^^^^^ The default environment variables for MegaQC used when starting the :ref:`megaqc_docker_container` -are defined inside the `.env `_ file. +are defined inside the `.env `_ file. Simply edit the file and the new environment variables will be passed to the :ref:`megaqc_docker_container`. Further runtime arguments ^^^^^^^^^^^^^^^^^^^^^^^^^^^ -Further runtime arguments can be added to a +Further runtime arguments can be added to a `command section `_ inside the `docker-compose`_ configuration file. -.. _deployment_folder: https://github.com/ewels/MegaQC/blob/master/deployment -.. _docker-compose: https://github.com/ewels/MegaQC/blob/master/deployment/docker-compose.yml +.. _deployment_folder: https://github.com/MultiQC/MegaQC/blob/master/deployment +.. _docker-compose: https://github.com/MultiQC/MegaQC/blob/master/deployment/docker-compose.yml .. _dockerhub: https://hub.docker.com/r/ewels/megaqc/ HTTPS @@ -256,4 +256,4 @@ Then, edit these lines to the full filepath of the respective ``.crt`` and ``.ke CRT_PATH=./nginx-selfsigned.crt KEY_PATH=./nginx-selfsigned.key -After this, run the stack as described above, and then you should be able to access MegaQC on ``https://your_hostname``. \ No newline at end of file +After this, run the stack as described above, and then you should be able to access MegaQC on ``https://your_hostname``. diff --git a/docs/source/docs/installation/installation_prod.rst b/docs/source/docs/installation/installation_prod.rst index 89354cf2..2994fa14 100644 --- a/docs/source/docs/installation/installation_prod.rst +++ b/docs/source/docs/installation/installation_prod.rst @@ -2,8 +2,8 @@ Production ============= This section explains how to set up a production environment without -the usage of container technologies. If you want to run MegaQC in a -containerized environment please refer to :ref:`docker_installation`. +the usage of container technologies. If you want to run MegaQC in a +containerized environment please refer to :ref:`docker_installation`. 1. Install the MegaQC package ----------------------------- @@ -169,5 +169,5 @@ If you run an older OS, ensure that the package is installed. .. _Python MySQL connector: https://dev.mysql.com/downloads/connector/python/2.1.html .. _PyPI package: https://pypi.python.org/pypi/mysql-connector-python/2.0.4 -.. _create an issue: https://github.com/ewels/MegaQC/issues/new -.. _deployment_folder: https://github.com/ewels/MegaQC/blob/master/deployment +.. _create an issue: https://github.com/MultiQC/MegaQC/issues/new +.. _deployment_folder: https://github.com/MultiQC/MegaQC/blob/master/deployment diff --git a/docs/source/docs/troubleshooting.rst b/docs/source/docs/troubleshooting.rst index 52095665..4327a39e 100644 --- a/docs/source/docs/troubleshooting.rst +++ b/docs/source/docs/troubleshooting.rst @@ -18,9 +18,9 @@ Usage - When creating a violin plot I get an error. - - This is a known issue: https://github.com/ewels/MegaQC/issues/31 + - This is a known issue: https://github.com/MultiQC/MegaQC/issues/31 - TypeError: '<' not supported between instances of 'NoneType' and 'float' when trying to compare data - - This is a known issue: https://github.com/ewels/MegaQC/issues/156 + - This is a known issue: https://github.com/MultiQC/MegaQC/issues/156 - Please ensure that your reports do not have missing fields diff --git a/megaqc/templates/footer.html b/megaqc/templates/footer.html index dc482720..9c7add40 100644 --- a/megaqc/templates/footer.html +++ b/megaqc/templates/footer.html @@ -6,7 +6,7 @@

    MegaQC v{{ version }} - Written by Phil Ewels, Denis Moreno, Michael Milton, Tor Solli-Nowlan and Lukas Heumos, - available on GitHub. + available on GitHub.

    MegaQC uses diff --git a/megaqc/templates/public/home.html b/megaqc/templates/public/home.html index 68c7ae4c..e632f6d2 100644 --- a/megaqc/templates/public/home.html +++ b/megaqc/templates/public/home.html @@ -24,7 +24,7 @@

    MegaQC is a web application that collects results from multiple runs of MultiQC and allows bulk visualisation.

    -

    See the MegaQC GitHub repository for installation instructions and documentation: https://github.com/ewels/MegaQC

    +

    See the MegaQC GitHub repository for installation instructions and documentation: https://github.com/MultiQC/MegaQC/

    diff --git a/pyproject.toml b/pyproject.toml index 111a008c..4d0a2cce 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -14,7 +14,7 @@ keywords = [ "quality control", ] homepage = "https://megaqc.info/" -repository = "https://github.com/ewels/MegaQC/" +repository = "https://github.com/MultiQC/MegaQC" documentation = "https://megaqc.info/docs/index.html" classifiers = [ "Development Status :: 4 - Beta", diff --git a/setup.py b/setup.py index 903eab11..cfc93c21 100644 --- a/setup.py +++ b/setup.py @@ -61,7 +61,7 @@ "quality control", ], url="https://megaqc.info/", - download_url="https://github.com/ewels/MegaQC/releases", + download_url="https://github.com/MultiQC/MegaQC/releases", license="GPLv3", packages=["megaqc"], include_package_data=True,