VariantEffect · EstelleDa · Sep 16, 2022 · Sep 16, 2022 · Sep 16, 2022 · Sep 16, 2022
diff --git a/.gitignore b/.gitignore
@@ -127,3 +127,6 @@ dmypy.json
 
 # Pyre type checker
 .pyre/
+
+# PyCharm
+.idea/
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -0,0 +1,18 @@
+repos:
+-   repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.0.1
+    hooks:
+    -   id: check-yaml
+    -   id: check-json
+    -   id: debug-statements
+    -   id: detect-private-key
+    -   id: end-of-file-fixer
+        files: \.py$
+    -   id: pretty-format-json
+    -   id: trailing-whitespace
+        files: \.py$
+-   repo: https://github.com/psf/black
+    rev: 22.3.0
+    hooks:
+    -   id: black
+        language_version: python3
diff --git a/.travis.yml b/.travis.yml
@@ -0,0 +1,28 @@
+language: python
+matrix:
+  include:
+    - python: "3.6"
+    - python: "3.7"
+    - python: "3.8"
+    - python: "3.9"
+    - python: "3.9-dev"
+    - python: "3.10-dev"
+    - python: "pypy3"
+      env: NO_MYPY=true
+  allow_failures:
+    - python: "3.9"
+    - python: "3.9-dev"
+    - python: "3.10-dev"
+    - python: "pypy3"
+      env: NO_MYPY=true
+install:
+  - pip3 install .
+before_script:
+  - pip3 install coverage
+  - pip3 install coveralls
+  - if ! $NO_MYPY; then pip3 install mypy; fi
+script:
+  - coverage run --source mavecore -m unittest
+  - if ! $NO_MYPY; then mypy mavecore tests; fi
+after_success:
+  - coveralls
diff --git a/README.md b/README.md
@@ -1,2 +1,17 @@
 # MaveCore
 Shared MaveDB and MaveTools functionality
+
+## Contributing
+
+To contribute to MaveCore development, please install the additional requirements:
+```
+pip install -r requirements-dev.txt
+```
+
+To run the tests and generate an HTML coverage report use:
+```
+coverage run -m unittest && coverage html
+```
+
+By default, the coverage report will be located at `htmlcov/index.html`.
+Open this file in your browser to identify lines that have not been adequately covered by the test suite.
diff --git a/docs/Makefile b/docs/Makefile
@@ -0,0 +1,20 @@
+# Minimal makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line, and also
+# from the environment for the first two.
+SPHINXOPTS    ?=
+SPHINXBUILD   ?= sphinx-build
+SOURCEDIR     = source
+BUILDDIR      = _build
+
+# Put it first so that "make" without argument is like "make help".
+help:
+	@$(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)
diff --git a/docs/make.bat b/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=source
+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.https://www.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
diff --git a/docs/source/conf.py b/docs/source/conf.py
@@ -0,0 +1,68 @@
+# 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 = "MaveCore"
+copyright = "2022, Alan F Rubin"
+author = "Alan F Rubin"
+
+# The full version, including alpha/beta/rc tags
+release = "0.0.1"
+
+
+# -- 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.napoleon",
+    "sphinx.ext.intersphinx",
+    "sphinx.ext.autosectionlabel",
+]
+nbsphinx_allow_errors = True
+
+# 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"]
+
+# Intersphinx information for documentation from other packages
+intersphinx_mapping = {"python": ("https://docs.python.org/3", None)}
+
+
+# -- 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 = "pyramid"
+
+# 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"]
+
+
+def setup(app):
+    app.add_css_file("styles.css")
diff --git a/docs/source/dataset_validators.rst b/docs/source/dataset_validators.rst
@@ -0,0 +1,8 @@
+dataset validation
+==================
+
+Dataset validation contains validation code for datasets.
+
+
+.. automodule:: mavecore.validation.dataset_validators
+   :members:
diff --git a/docs/source/genome_validators.rst b/docs/source/genome_validators.rst
@@ -0,0 +1,8 @@
+genome validation
+=================
+
+Genome validation contains validation functions relating to wild type sequences,
+reference genomes, target genes, reference maps, and genomic intervals.
+
+.. automodule:: mavecore.validation.genome_validators
+   :members:
diff --git a/docs/source/index.rst b/docs/source/index.rst
@@ -0,0 +1,31 @@
+.. MaveCore documentation master file, created by
+   sphinx-quickstart on Tue Mar 1 14:20:15 2022.
+   You can adapt this file completely to your liking, but it should at least
+   contain the root `toctree` directive.
+
+MaveCore
+========
+MaveCore is a pure Python Module for bioinformatics and computational biology.
+It features all the shared functionality of MaveDB and MaveTools.
+
+Install MaveCore using pip::
+
+    pip3 install MaveCore
+
+Building a local copy of the documentation requires the following additional packages::
+
+    pip3 install sphinx
+
+.. toctree::
+   :maxdepth: 2
+   :caption: Contents:
+
+   validation
+
+
+Indices and tables
+==================
+
+* :ref:`genindex`
+* :ref:`modindex`
+* :ref:`search`
diff --git a/docs/source/metadata_validators.rst b/docs/source/metadata_validators.rst
@@ -0,0 +1,8 @@
+metadata validation
+===================
+
+Metadata validation contains functions designed to check the validity of metadata relating to
+sra, keyword, pubmed, doi, ensembl, uniprot, refseq and genome identifiers and lists.
+
+.. automodule:: mavecore.validation.metadata_validators
+   :members:
diff --git a/docs/source/static/lato-fonts.css b/docs/source/static/lato-fonts.css
@@ -0,0 +1,108 @@
+/* latin-ext */
+@font-face {
+  font-family: 'Lato';
+  font-style: italic;
+  font-weight: 300;
+  font-display: swap;
+  src: url(https://fonts.gstatic.com/s/lato/v20/S6u_w4BMUTPHjxsI9w2_FQft1dw.woff2) format('woff2');
+  unicode-range: U+0100-024F, U+0259, U+1E00-1EFF, U+2020, U+20A0-20AB, U+20AD-20CF, U+2113, U+2C60-2C7F, U+A720-A7FF;
+}
+/* latin */
+@font-face {
+  font-family: 'Lato';
+  font-style: italic;
+  font-weight: 300;
+  font-display: swap;
+  src: url(https://fonts.gstatic.com/s/lato/v20/S6u_w4BMUTPHjxsI9w2_Gwft.woff2) format('woff2');
+  unicode-range: U+0000-00FF, U+0131, U+0152-0153, U+02BB-02BC, U+02C6, U+02DA, U+02DC, U+2000-206F, U+2074, U+20AC, U+2122, U+2191, U+2193, U+2212, U+2215, U+FEFF, U+FFFD;
+}
+/* latin-ext */
+@font-face {
+  font-family: 'Lato';
+  font-style: italic;
+  font-weight: 400;
+  font-display: swap;
+  src: url(https://fonts.gstatic.com/s/lato/v20/S6u8w4BMUTPHjxsAUi-qJCY.woff2) format('woff2');
+  unicode-range: U+0100-024F, U+0259, U+1E00-1EFF, U+2020, U+20A0-20AB, U+20AD-20CF, U+2113, U+2C60-2C7F, U+A720-A7FF;
+}
+/* latin */
+@font-face {
+  font-family: 'Lato';
+  font-style: italic;
+  font-weight: 400;
+  font-display: swap;
+  src: url(https://fonts.gstatic.com/s/lato/v20/S6u8w4BMUTPHjxsAXC-q.woff2) format('woff2');
+  unicode-range: U+0000-00FF, U+0131, U+0152-0153, U+02BB-02BC, U+02C6, U+02DA, U+02DC, U+2000-206F, U+2074, U+20AC, U+2122, U+2191, U+2193, U+2212, U+2215, U+FEFF, U+FFFD;
+}
+/* latin-ext */
+@font-face {
+  font-family: 'Lato';
+  font-style: italic;
+  font-weight: 700;
+  font-display: swap;
+  src: url(https://fonts.gstatic.com/s/lato/v20/S6u_w4BMUTPHjxsI5wq_FQft1dw.woff2) format('woff2');
+  unicode-range: U+0100-024F, U+0259, U+1E00-1EFF, U+2020, U+20A0-20AB, U+20AD-20CF, U+2113, U+2C60-2C7F, U+A720-A7FF;
+}
+/* latin */
+@font-face {
+  font-family: 'Lato';
+  font-style: italic;
+  font-weight: 700;
+  font-display: swap;
+  src: url(https://fonts.gstatic.com/s/lato/v20/S6u_w4BMUTPHjxsI5wq_Gwft.woff2) format('woff2');
+  unicode-range: U+0000-00FF, U+0131, U+0152-0153, U+02BB-02BC, U+02C6, U+02DA, U+02DC, U+2000-206F, U+2074, U+20AC, U+2122, U+2191, U+2193, U+2212, U+2215, U+FEFF, U+FFFD;
+}
+/* latin-ext */
+@font-face {
+  font-family: 'Lato';
+  font-style: normal;
+  font-weight: 300;
+  font-display: swap;
+  src: url(https://fonts.gstatic.com/s/lato/v20/S6u9w4BMUTPHh7USSwaPGR_p.woff2) format('woff2');
+  unicode-range: U+0100-024F, U+0259, U+1E00-1EFF, U+2020, U+20A0-20AB, U+20AD-20CF, U+2113, U+2C60-2C7F, U+A720-A7FF;
+}
+/* latin */
+@font-face {
+  font-family: 'Lato';
+  font-style: normal;
+  font-weight: 300;
+  font-display: swap;
+  src: url(https://fonts.gstatic.com/s/lato/v20/S6u9w4BMUTPHh7USSwiPGQ.woff2) format('woff2');
+  unicode-range: U+0000-00FF, U+0131, U+0152-0153, U+02BB-02BC, U+02C6, U+02DA, U+02DC, U+2000-206F, U+2074, U+20AC, U+2122, U+2191, U+2193, U+2212, U+2215, U+FEFF, U+FFFD;
+}
+/* latin-ext */
+@font-face {
+  font-family: 'Lato';
+  font-style: normal;
+  font-weight: 400;
+  font-display: swap;
+  src: url(https://fonts.gstatic.com/s/lato/v20/S6uyw4BMUTPHjxAwXjeu.woff2) format('woff2');
+  unicode-range: U+0100-024F, U+0259, U+1E00-1EFF, U+2020, U+20A0-20AB, U+20AD-20CF, U+2113, U+2C60-2C7F, U+A720-A7FF;
+}
+/* latin */
+@font-face {
+  font-family: 'Lato';
+  font-style: normal;
+  font-weight: 400;
+  font-display: swap;
+  src: url(https://fonts.gstatic.com/s/lato/v20/S6uyw4BMUTPHjx4wXg.woff2) format('woff2');
+  unicode-range: U+0000-00FF, U+0131, U+0152-0153, U+02BB-02BC, U+02C6, U+02DA, U+02DC, U+2000-206F, U+2074, U+20AC, U+2122, U+2191, U+2193, U+2212, U+2215, U+FEFF, U+FFFD;
+}
+/* latin-ext */
+@font-face {
+  font-family: 'Lato';
+  font-style: normal;
+  font-weight: 700;
+  font-display: swap;
+  src: url(https://fonts.gstatic.com/s/lato/v20/S6u9w4BMUTPHh6UVSwaPGR_p.woff2) format('woff2');
+  unicode-range: U+0100-024F, U+0259, U+1E00-1EFF, U+2020, U+20A0-20AB, U+20AD-20CF, U+2113, U+2C60-2C7F, U+A720-A7FF;
+}
+/* latin */
+@font-face {
+  font-family: 'Lato';
+  font-style: normal;
+  font-weight: 700;
+  font-display: swap;
+  src: url(https://fonts.gstatic.com/s/lato/v20/S6u9w4BMUTPHh6UVSwiPGQ.woff2) format('woff2');
+  unicode-range: U+0000-00FF, U+0131, U+0152-0153, U+02BB-02BC, U+02C6, U+02DA, U+02DC, U+2000-206F, U+2074, U+20AC, U+2122, U+2191, U+2193, U+2212, U+2215, U+FEFF, U+FFFD;
+}
-Original file line number
+Diff line change
@@ Expand Up / @@ -127,3 +127,6 @@ dmypy.json @@
     # Pyre type checker
     .pyre/
+    # PyCharm
+    .idea/