cancervariants · jsstevenson · Aug 13, 2024 · Jul 24, 2024 · Aug 12, 2024 · Aug 12, 2024
diff --git a/.readthedocs.yaml b/.readthedocs.yaml
@@ -0,0 +1,16 @@
+version: 2
+
+build:
+  os: "ubuntu-20.04"
+  tools:
+    python: "3.11"
+
+python:
+  install:
+    - method: pip
+      path: .
+      extra_requirements:
+        - docs
+
+sphinx:
+  configuration: docs/source/conf.py
diff --git a/LICENSE b/LICENSE
@@ -1,7 +1,7 @@
 
 MIT License
 
-Copyright (c) 2021-2023 VICC
+Copyright (c) 2021-2024 VICC
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal

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
+
+%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
+)
+
+if "%1" == "" goto help
+
+%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+goto end
+
+:help
+%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+
+:end
+popd
diff --git a/docs/source/_templates/module_summary.rst b/docs/source/_templates/module_summary.rst
@@ -0,0 +1,7 @@
+{{ fullname | underline }}
+
+.. automodule:: {{ fullname }}
+   :members:
+   :undoc-members:
+   :special-members: __init__
+   :exclude-members: model_fields, model_config
diff --git a/docs/source/changelog.rst b/docs/source/changelog.rst
@@ -0,0 +1,7 @@
+Changelog
+---------
+
+.. changelog::
+    :changelog-url: https://fusor.readthedocs.io/en/stable/#changelog
+    :github: https://github.com/cancervariants/fusor/releases/
+    :pypi: https://pypi.org/project/fusor/
diff --git a/docs/source/conf.py b/docs/source/conf.py
@@ -0,0 +1,79 @@
+# Configuration file for the Sphinx documentation builder.
+#
+# For the full list of built-in configuration values, see the documentation:
+# https://www.sphinx-doc.org/en/master/usage/configuration.html
+
+# -- Project information -----------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#project-information
+
+project = "FUSOR"
+copyright = "2024, Wagner Lab"
+author = "Wagner Lab"
+html_title = "FUSOR"
+
+# -- General configuration ---------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration
+
+extensions = [
+    "sphinx.ext.autodoc",
+    "sphinx_autodoc_typehints",
+    "sphinx.ext.linkcode",
+    "sphinx_copybutton",
+    "sphinx.ext.autosummary",
+    "sphinx_github_changelog",
+]
+
+templates_path = ["_templates"]
+exclude_patterns = []
+
+# -- Options for HTML output -------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#options-for-html-output
+
+html_theme = "furo"
+html_static_path = []
+html_css_files = [
+    "https://cdnjs.cloudflare.com/ajax/libs/font-awesome/6.0.0/css/fontawesome.min.css",
+    "https://cdnjs.cloudflare.com/ajax/libs/font-awesome/6.0.0/css/solid.min.css",
+    "https://cdnjs.cloudflare.com/ajax/libs/font-awesome/6.0.0/css/brands.min.css",
+]
+html_theme_options = {
+    "footer_icons": [
+        {
+            "name": "GitHub",
+            "url": "https://github.com/cancervariants/fusor",
+            "html": "",
+            "class": "fa-brands fa-solid fa-github",
+        },
+        {
+            "name": "Wagner Lab",
+            "url": "https://www.nationwidechildrens.org/specialties/institute-for-genomic-medicine/research-labs/wagner-lab",
+            "html": "",
+            "class": "fa-solid fa-house",
+        }
+    ],
+}
+# -- autodoc things ----------------------------------------------------------
+import os
+import sys
+
+sys.path.insert(0, os.path.abspath("../../"))
+autodoc_preserve_defaults = True
+
+# -- get version -------------------------------------------------------------
+from importlib.metadata import version
+
+release = version = version("fusor")
+
+# -- linkcode ----------------------------------------------------------------
+def linkcode_resolve(domain, info):
+    if domain != "py":
+        return None
+    if not info["module"]:
+        return None
+    filename = info["module"].replace(".", "/")
+    return f"https://github.com/cancervariants/fusor/blob/main/src/{filename}.py"
+
+
+# -- code block style --------------------------------------------------------
+pygments_style = "default"
+pygements_dark_style = "monokai"
diff --git a/docs/source/contributing.rst b/docs/source/contributing.rst
@@ -0,0 +1,56 @@
+.. _contributing:
+
+Contributing
+============
+
+Bug reports and feature requests
+--------------------------------
+
+Bugs and new feature requests can be submitted to the `issue tracker on GitHub <https://github.com/cancervariants/fusor/issues>`_. See `this StackOverflow post <https://stackoverflow.com/help/minimal-reproducible-example>`_ for tips on how to craft a helpful bug report.
+
+Development setup
+-----------------
+
+Clone the repository: ::
+
+    git clone https://github.com/cancervariants/fusor
+    cd fusor
+
+Then initialize a virtual environment: ::
+
+    python3 -m virtualenv venv
+    source venv/bin/activate
+    python3 -m pip install -e '.[dev,tests,docs]'
+
+We use `pre-commit <https://pre-commit.com/#usage>`_ to run conformance tests before commits. This provides checks for:
+
+* Code format and style
+* Added large files
+* AWS credentials
+* Private keys
+
+Before your first commit, run: ::
+
+    pre-commit install
+
+Style
+-----
+
+Code style is managed by `Ruff <https://github.com/astral-sh/ruff>`_, and should be checked via pre-commit hook before commits. Final QC is applied with GitHub Actions to every pull request.
+
+Tests
+-----
+
+Tests are executed with `pytest <https://docs.pytest.org/en/7.1.x/getting-started.html>`_: ::
+
+    pytest
+
+Documentation
+-------------
+
+The documentation is built with Sphinx, which is included as part of the ``docs`` dependency group. Navigate to the ``docs/`` subdirectory and use ``make`` to build the HTML version: ::
+
+    cd docs
+    make html
+
+See the `Sphinx documentation <https://www.sphinx-doc.org/en/master/>`_ for more information.
diff --git a/docs/source/index.rst b/docs/source/index.rst
@@ -0,0 +1,30 @@
+FUSOR |version|
+=========================
+
+.. image:: https://img.shields.io/pypi/v/fusor.svg
+   :alt: PyPI version
+   :target: https://pypi.python.org/pypi/fusor
+
+.. image:: https://img.shields.io/pypi/l/fusor.svg
+   :alt: License
+   :target: https://github.com/cancervariants/fusor/blob/main/LICENSE
+
+.. image:: https://img.shields.io/pypi/pyversions/fusor?color=gr
+   :alt: PyPI - supported Python versions
+
+.. image:: https://github.com/cancervariants/fusor/actions/workflows/checks.yaml/badge.svg
+   :alt: tests status
+   :target: https://github.com/cancervariants/fusor/actions/workflows/checks.yaml
+
+TODO
+
+.. toctree::
+   :hidden:
+   :maxdepth: 2
+
+    Installation<install>
+    Usage<usage>
+    API Reference<reference/index>
+    Changelog<changelog>
+    Contributing<contributing>
+    License<license>
diff --git a/docs/source/install.rst b/docs/source/install.rst
@@ -0,0 +1,56 @@
+.. _install:
+
+Installation
+============
+
+Prerequisites
+-------------
+
+* Python 3.10+
+* A UNIX-like environment (e.g. MacOS, WSL, Ubuntu)
+* A recent version of PostgreSQL (ideally at least 11+)
+* A modern Java runtime (if using DynamoDB for the Gene Normalizer database)
+
+Library installation
+--------------------
+
+Install ``FUSOR`` from `PyPI <https://pypi.org/project/fusor/>`_:
+
+.. code-block:: shell
+
+    pip install fusor
+
+Data setup
+----------
+
+Universal Transcript Archive (UTA)
+++++++++++++++++++++++++++++++++++
+
+The `UTA <https://github.com/biocommons/uta>`_ is a dataset of genome-transcript aligned data supplied as a PostgreSQL database. Access in FUSOR is supplied by way of ``Cool-Seq-Tool``; see the `Cool-Seq-Tool UTA docs <https://coolseqtool.readthedocs.io/stable/install.html#set-up-uta>`_ for some opinionated setup instructions.
+
+At runtime, UTA connection information can be relayed to FUSOR (by way of Cool-Seq-Tool) either as an initialization argument or via the environment variable ``UTA_DB_URL``. By default, it is set to ``postgresql://uta_admin:uta@localhost:5432/uta/uta_20210129b``. See the `Cool-Seq-Tool configuration docs <https://coolseqtool.readthedocs.io/stable/usage.html#environment-configuration>`_ for more info.
+
+SeqRepo
++++++++
+
+`SeqRepo <https://github.com/biocommons/biocommons.seqrepo>`_ is a controlled dataset of biological sequences. As with UTA, access in FUSOR is given via `Cool-Seq-Tool`, which provides `documentation <https://coolseqtool.readthedocs.io/stable/install.html#set-up-seqrepo>`_ on getting it set up.
+
+At runtime, the file location of the SeqRepo instance directory can be defined (by way of Cool-Seq-Tool) either as an initialization argument or via the environment variable ``SEQREPO_ROOT_DIR``. By default, it's expected to be ``/usr/local/share/seqrepo/latest``. See the `Cool-Seq-Tool configuration docs <https://coolseqtool.readthedocs.io/stable/usage.html#environment-configuration>`_ for more info.
+
+Gene Normalizer
++++++++++++++++
+
+Finally, ``FUSOR`` uses the `Gene Normalizer <https://github.com/cancervariants/gene-normalization>`_ to ground gene terms. See the `Gene Normalizer documentation <https://gene-normalizer.readthedocs.io/stable/install.html>`_ for setup instructions.
+
+Connection information for the normalizer database can be set using the environment variable ``GENE_NORM_DB_URL``. See the `Gene Normalizer docs <https://gene-normalizer.readthedocs.io/stable/reference/api/database/gene.database.database.html#gene.database.database.create_db>`_ for more information on connection configuration.
+
+Check data availability
++++++++++++++++++++++++
+
+Use the :py:meth:`fusor.tools.check_data_resources` method to verify that all data dependencies are available:
+
+.. code-block:: pycon
+
+   >>> from fusor.tools import check_data_resources
+   >>> status = await check_data_resources()
+   >>> assert all(status)  # passes if all resources can be acquired successfully
diff --git a/docs/source/license.rst b/docs/source/license.rst
@@ -0,0 +1,4 @@
+License
+=======
+
+.. include:: ../../LICENSE
diff --git a/docs/source/reference/api/fusor.exceptions.rst b/docs/source/reference/api/fusor.exceptions.rst
@@ -0,0 +1,8 @@
+fusor.exceptions
+================
+
+.. automodule:: fusor.exceptions
+   :members:
+   :undoc-members:
+   :special-members: __init__
+   :exclude-members: model_fields, model_config
diff --git a/docs/source/reference/api/fusor.fusor.rst b/docs/source/reference/api/fusor.fusor.rst
@@ -0,0 +1,8 @@
+fusor.fusor
+===========
+
+.. automodule:: fusor.fusor
+   :members:
+   :undoc-members:
+   :special-members: __init__
+   :exclude-members: model_fields, model_config
diff --git a/docs/source/reference/api/fusor.models.rst b/docs/source/reference/api/fusor.models.rst
@@ -0,0 +1,8 @@
+fusor.models
+============
+
+.. automodule:: fusor.models
+   :members:
+   :undoc-members:
+   :special-members: __init__
+   :exclude-members: model_fields, model_config
diff --git a/docs/source/reference/api/fusor.nomenclature.rst b/docs/source/reference/api/fusor.nomenclature.rst
@@ -0,0 +1,8 @@
+fusor.nomenclature
+==================
+
+.. automodule:: fusor.nomenclature
+   :members:
+   :undoc-members:
+   :special-members: __init__
+   :exclude-members: model_fields, model_config
diff --git a/docs/source/reference/api/fusor.tools.rst b/docs/source/reference/api/fusor.tools.rst
@@ -0,0 +1,8 @@
+fusor.tools
+===========
+
+.. automodule:: fusor.tools
+   :members:
+   :undoc-members:
+   :special-members: __init__
+   :exclude-members: model_fields, model_config
diff --git a/docs/source/reference/index.rst b/docs/source/reference/index.rst
@@ -0,0 +1,15 @@
+.. _api_reference:
+
+API Reference
+=============
+
+.. autosummary::
+   :nosignatures:
+   :toctree: api/
+   :template: module_summary.rst
+
+   fusor.exceptions
+   fusor.fusor
+   fusor.models
+   fusor.nomenclature
+   fusor.tools