Merge pull request #11 from ptynecki/feature/v0.0.8

Migration to Python 3.8 with initial Sphinx docs

.gitignore

@@ -132,3 +132,4 @@ bert_model/
 bsp_model/
 word2vec_model/
 .pypirc
+docs/_build

.travis.yml

@@ -1,21 +1,20 @@
 language: python
 python:
-  - "3.6"
-  - "3.7"
   - "3.8"
 
 before_install:
   - python --version
   - pip install -U pytest
   - pip install codecov
   - pip install -U "bio-embeddings[all] @ git+https://github.com/sacdallago/bio_embeddings.git"
+  - pip install git+https://github.com/facebookresearch/esm.git
 install:
   - pip install -r requirements.txt
 
 env:
   - CODECOV_TOKEN=4f9eafa3-0ca3-48e4-9841-8fb25ff5d7c6
 
 script:
-  - pytest --verbose --color=yes phages2050
+  - pytest --verbose --color=yes phages2050/features
 after_success:
   - codecov

CHANGELOG.md

@@ -2,6 +2,14 @@
 All notable changes to this project will be documented in this file.
 
 
+## [0.0.8] - 11.10.2020
+### Added
+* Initial online documentation;
+
+### Changed
+* Migrated the codebase to Python 3.8+; 
+
+
 ## [0.0.7] - 18.09.2020
 ### Added
 * new extention for `embedding` module with ESM transformer-based protein embedding model;

README.md

@@ -4,7 +4,7 @@
 
 > "Keep calm, use AI for phages and stop AMR"
 
-PHAGES2050 is a novel [Python 3.6+ programming language](https://python.org) framework to boost bacteriophage research & therapy and infrastructure in order to achieve the full potential to fight against antimicrobial resistant bacteria within **Natural Language Processing (NLP)** and **Deep Learning**.
+PHAGES2050 is a novel [Python 3.8+ programming language](https://python.org) framework to boost bacteriophage research & therapy and infrastructure in order to achieve the full potential to fight against antimicrobial resistant bacteria within **Natural Language Processing (NLP)** and **Deep Learning**.
 
 Our project is about developing a AI-based framework for microbiologists and bioinformaticians who hunt, explore and classify phages. Applying the framework will shorten the duration of computational methods required to match phages with bacteria for specific patient cases. Having such organised framework at hand and freely-available will help develop personalized phage therapy and make it accessible to people worldwide.
 
@@ -73,7 +73,7 @@ _PHAGES2050_ can be installed by running:
 pip install phages2050
 ```
 
-It requires Python 3.6.0+ to run. You can also use Conda:
+It requires Python 3.8.0+ to run. You can also use Conda:
 
 ```
 conda install -c conda-forge phages2050
@@ -98,7 +98,7 @@ pip install git+https://github.com/facebookresearch/esm.git
 
 ## Community and Contributions
 
-Happy to see you willing to make the PHAGES2050 better. Development on the latest stable version of Python 3+ is preferred. As of this writing it's 3.6. You can use any operating system.
+Happy to see you willing to make the PHAGES2050 better. Development on the latest stable version of Python 3+ is preferred. As of this writing it's 3.8. You can use any operating system.
 
 If you're fixing a bug or adding a new feature, add a test with *[pytest](https://github.com/pytest-dev/pytest)* and check the code with *[Black](https://github.com/psf/black/)* and *[mypy](https://github.com/python/mypy)*. Before adding any large feature, first open an issue for us to discuss the idea with the core devs and community.
 

docs/Makefile

@@ -0,0 +1,20 @@
+# Minimal makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line, and also
+# from the environment for the first two.
+SPHINXOPTS    ?=
+SPHINXBUILD   ?= sphinx-build
+SOURCEDIR     = .
+BUILDDIR      = _build
+
+# Put it first so that "make" without argument is like "make help".
+help:
+	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+.PHONY: help Makefile
+
+# Catch-all target: route all unknown targets to Sphinx using the new
+# "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
+%: Makefile
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)

docs/conf.py

@@ -0,0 +1,61 @@
+# Configuration file for the Sphinx documentation builder.
+#
+# This file only contains a selection of the most common options. For a full
+# list see the documentation:
+# https://www.sphinx-doc.org/en/master/usage/configuration.html
+
+# -- Path setup --------------------------------------------------------------
+
+# If extensions (or modules to document with autodoc) are in another directory,
+# add these directories to sys.path here. If the directory is relative to the
+# documentation root, use os.path.abspath to make it absolute, like shown here.
+#
+import os
+import sys
+sys.path.insert(0, os.path.abspath('..'))
+
+
+# -- Project information -----------------------------------------------------
+
+project = 'PHAGES2050'
+copyright = '2020, Piotr Tynecki, Iwona Świętochowska, Yana Minina, Przemysław Mitura, Wojciech Łaguna'
+author = 'Piotr Tynecki, Iwona Świętochowska, Yana Minina, Przemysław Mitura, Wojciech Łaguna'
+
+# The full version, including alpha/beta/rc tags
+release = version = '0.0.8'
+
+
+# -- General configuration ---------------------------------------------------
+
+# Add any Sphinx extension module names here, as strings. They can be
+# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
+# ones.
+extensions = [
+    'sphinx.ext.autodoc',
+    'sphinx.ext.viewcode'
+]
+
+# Add any paths that contain templates here, relative to this directory.
+templates_path = ['_templates']
+
+# List of patterns, relative to source directory, that match files and
+# directories to ignore when looking for source files.
+# This pattern also affects html_static_path and html_extra_path.
+exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store']
+
+
+# -- Options for HTML output -------------------------------------------------
+
+# The theme to use for HTML and HTML Help pages.  See the documentation for
+# a list of builtin themes.
+#
+html_theme = 'sphinx_rtd_theme'
+
+# Add any paths that contain custom static files (such as style sheets) here,
+# relative to this directory. They are copied after the builtin static files,
+# so a file named "default.css" will overwrite the builtin "default.css".
+html_static_path = ['_static']
+
+html_logo = '_static/images/phages2050-logo.png'
+
+master_doc = 'index'

docs/index.rst

@@ -0,0 +1,17 @@
+Welcome to PHAGES2050's documentation!
+======================================
+
+PHAGES2050 is a novel Python 3.8+ programming language framework to boost bacteriophage research & therapy.
+
+.. toctree::
+   :maxdepth: 2
+   :caption: Contents:
+
+   modules
+
+Indices and tables
+==================
+
+* :ref:`genindex`
+* :ref:`modindex`
+* :ref:`search`

docs/make.bat

@@ -0,0 +1,35 @@
+@ECHO OFF
+
+pushd %~dp0
+
+REM Command file for Sphinx documentation
+
+if "%SPHINXBUILD%" == "" (
+	set SPHINXBUILD=sphinx-build
+)
+set SOURCEDIR=.
+set BUILDDIR=_build
+
+if "%1" == "" goto help
+
+%SPHINXBUILD% >NUL 2>NUL
+if errorlevel 9009 (
+	echo.
+	echo.The 'sphinx-build' command was not found. Make sure you have Sphinx
+	echo.installed, then set the SPHINXBUILD environment variable to point
+	echo.to the full path of the 'sphinx-build' executable. Alternatively you
+	echo.may add the Sphinx directory to PATH.
+	echo.
+	echo.If you don't have Sphinx installed, grab it from
+	echo.http://sphinx-doc.org/
+	exit /b 1
+)
+
+%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+goto end
+
+:help
+%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+
+:end
+popd

docs/modules.rst

@@ -0,0 +1,8 @@
+PHAGES2050
+==========
+
+.. toctree::
+   :maxdepth: 4
+
+   phages2050
+   setup

docs/phages2050.classifiers.proteins.rst

@@ -0,0 +1,21 @@
+phages2050.classifiers.proteins package
+=======================================
+
+Submodules
+----------
+
+phages2050.classifiers.proteins.structural\_protein module
+----------------------------------------------------------
+
+.. automodule:: phages2050.classifiers.proteins.structural_protein
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+Module contents
+---------------
+
+.. automodule:: phages2050.classifiers.proteins
+   :members:
+   :undoc-members:
+   :show-inheritance:

docs/phages2050.classifiers.rst

@@ -0,0 +1,18 @@
+phages2050.classifiers package
+==============================
+
+Subpackages
+-----------
+
+.. toctree::
+   :maxdepth: 4
+
+   phages2050.classifiers.proteins
+
+Module contents
+---------------
+
+.. automodule:: phages2050.classifiers
+   :members:
+   :undoc-members:
+   :show-inheritance:

docs/phages2050.crawlers.millardlab.rst

@@ -0,0 +1,21 @@
+phages2050.crawlers.millardlab package
+======================================
+
+Submodules
+----------
+
+phages2050.crawlers.millardlab.crawler module
+---------------------------------------------
+
+.. automodule:: phages2050.crawlers.millardlab.crawler
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+Module contents
+---------------
+
+.. automodule:: phages2050.crawlers.millardlab
+   :members:
+   :undoc-members:
+   :show-inheritance:

docs/phages2050.crawlers.ncbi.rst

@@ -0,0 +1,10 @@
+phages2050.crawlers.ncbi package
+================================
+
+Module contents
+---------------
+
+.. automodule:: phages2050.crawlers.ncbi
+   :members:
+   :undoc-members:
+   :show-inheritance:

docs/phages2050.crawlers.rst

@@ -0,0 +1,19 @@
+phages2050.crawlers package
+===========================
+
+Subpackages
+-----------
+
+.. toctree::
+   :maxdepth: 4
+
+   phages2050.crawlers.millardlab
+   phages2050.crawlers.ncbi
+
+Module contents
+---------------
+
+.. automodule:: phages2050.crawlers
+   :members:
+   :undoc-members:
+   :show-inheritance:

docs/phages2050.embeddings.nucleotides.rst

@@ -0,0 +1,21 @@
+phages2050.embeddings.nucleotides package
+=========================================
+
+Submodules
+----------
+
+phages2050.embeddings.nucleotides.word2vec module
+-------------------------------------------------
+
+.. automodule:: phages2050.embeddings.nucleotides.word2vec
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+Module contents
+---------------
+
+.. automodule:: phages2050.embeddings.nucleotides
+   :members:
+   :undoc-members:
+   :show-inheritance:

docs/phages2050.embeddings.proteins.rst

@@ -0,0 +1,29 @@
+phages2050.embeddings.proteins package
+======================================
+
+Submodules
+----------
+
+phages2050.embeddings.proteins.bert module
+------------------------------------------
+
+.. automodule:: phages2050.embeddings.proteins.bert
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+phages2050.embeddings.proteins.esm module
+-----------------------------------------
+
+.. automodule:: phages2050.embeddings.proteins.esm
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+Module contents
+---------------
+
+.. automodule:: phages2050.embeddings.proteins
+   :members:
+   :undoc-members:
+   :show-inheritance:

docs/phages2050.embeddings.rst

@@ -0,0 +1,19 @@
+phages2050.embeddings package
+=============================
+
+Subpackages
+-----------
+
+.. toctree::
+   :maxdepth: 4
+
+   phages2050.embeddings.nucleotides
+   phages2050.embeddings.proteins
+
+Module contents
+---------------
+
+.. automodule:: phages2050.embeddings
+   :members:
+   :undoc-members:
+   :show-inheritance: