Merge branch 'crossdock' of github.com:molecularmachines/moleculib in…

…to crossdock

.github/workflows/sphinx.yml

@@ -0,0 +1,27 @@
+name: "Sphinx: Render docs"
+
+on: push
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    permissions:
+      contents: write
+    steps:
+      - uses: actions/checkout@v4
+      - name: Install Theme
+        run: |
+          pip install sphinx sphinx_rtd_theme
+          pip install git+https://github.com/AllanSCosta/insegel-updated
+          pip install -e .
+      - name: Sphinx build
+        run: |
+          sphinx-build docs _build
+      - name: Deploy
+        uses: peaceiris/actions-gh-pages@v3
+        if: ${{ github.event_name == 'push' && github.ref == 'refs/heads/master' }}
+        with:
+          publish_branch: gh-pages
+          github_token: ${{ secrets.GITHUB_TOKEN }}
+          publish_dir: _build/
+          force_orphan: true

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/abstract.rst

@@ -0,0 +1,29 @@
+abstract package
+================
+
+Submodules
+----------
+
+abstract.dataset module
+-----------------------
+
+.. automodule:: abstract.dataset
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+abstract.transform module
+-------------------------
+
+.. automodule:: abstract.transform
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+Module contents
+---------------
+
+.. automodule:: abstract
+   :members:
+   :undoc-members:
+   :show-inheritance:

docs/assembly.rst

@@ -0,0 +1,37 @@
+assembly package
+================
+
+Submodules
+----------
+
+assembly.dataset module
+-----------------------
+
+.. automodule:: assembly.dataset
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+assembly.datum module
+---------------------
+
+.. automodule:: assembly.datum
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+assembly.transform module
+-------------------------
+
+.. automodule:: assembly.transform
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+Module contents
+---------------
+
+.. automodule:: assembly
+   :members:
+   :undoc-members:
+   :show-inheritance:

docs/conf.py

@@ -0,0 +1,37 @@
+# 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
+
+import os
+import sys
+sys.path.insert(0, os.path.abspath('../moleculib'))
+
+project = 'moleculib'
+copyright = '2024, Center for Bits and Atoms, MIT Media Lab Molecular Machines'
+author = 'Molecular Machines'
+release = '-'
+
+# -- General configuration ---------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration
+
+extensions = [
+    'sphinx.ext.autodoc',
+    'sphinx.ext.viewcode',
+    'sphinx.ext.napoleon'
+]
+
+
+templates_path = ['_templates']
+exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store']
+
+
+# -- Options for HTML output -------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#options-for-html-output
+
+html_theme = 'insegel'
+html_static_path = ['_static']
+html_logo = '_static/logo.svg'

docs/index.rst

@@ -0,0 +1,18 @@
+.. moleculib documentation master file, created by
+   sphinx-quickstart on Sun Feb 25 21:41:42 2024.
+   You can adapt this file completely to your liking, but it should at least
+   contain the root `toctree` directive.
+
+**moleculib** is a comprehensive Python package designed to streamline the processing and management of biomolecular data within machine learning workflows. It empowers researchers and developers with a robust set of functionalities, simplifying complex data pipelines and accelerating the journey from raw biomolecular data to valuable insights.
+
+* **Data Processing**: preprocessing and cleaning capabilities for data normalization and feature engineering.
+* **Machine Learning-First**: designed to readily integrate with Jax and pytrees in machine learning pipelines.
+* **Reproducibility**: modular classes and workflows for better organization and reproducibility.
+
+.. toctree::
+   :maxdepth: 2
+   :caption: Contents:
+
+   modules
+
+* :ref:`genindex`

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
+
+%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

docs/modules.rst

@@ -0,0 +1,41 @@
+Assembly
+=======
+.. toctree::
+   :maxdepth: 4
+
+   assembly
+
+Protein
+=======
+
+.. toctree::
+   :maxdepth: 4
+
+   protein
+
+Sequence
+=======
+.. toctree::
+   :maxdepth: 4
+
+   sequence
+
+Molecule
+=======
+.. toctree::
+   :maxdepth: 4
+
+   molecule
+
+Nucleic
+=======
+.. toctree::
+   :maxdepth: 4
+   nucleic
+
+Abstract
+=======
+.. toctree::
+   :maxdepth: 4
+
+   abstract

docs/molecule.rst

@@ -0,0 +1,69 @@
+molecule package
+================
+
+Subpackages
+-----------
+
+.. toctree::
+   :maxdepth: 4
+
+   molecule.tests
+
+Submodules
+----------
+
+molecule.alphabet module
+------------------------
+
+.. automodule:: molecule.alphabet
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+molecule.batch module
+---------------------
+
+.. automodule:: molecule.batch
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+molecule.dataset module
+-----------------------
+
+.. automodule:: molecule.dataset
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+molecule.datum module
+---------------------
+
+.. automodule:: molecule.datum
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+molecule.transform module
+-------------------------
+
+.. automodule:: molecule.transform
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+molecule.utils module
+---------------------
+
+.. automodule:: molecule.utils
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+Module contents
+---------------
+
+.. automodule:: molecule
+   :members:
+   :undoc-members:
+   :show-inheritance:

docs/molecule.tests.rst

@@ -0,0 +1,21 @@
+molecule.tests package
+======================
+
+Submodules
+----------
+
+molecule.tests.loader\_test module
+----------------------------------
+
+.. automodule:: molecule.tests.loader_test
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+Module contents
+---------------
+
+.. automodule:: molecule.tests
+   :members:
+   :undoc-members:
+   :show-inheritance: