docs

README.md

@@ -1,4 +1,4 @@
-# LOBSTER
+# LOBSTER 🦞
 **L**anguage m**O**dels for **B**iological **S**equence **T**ransformation and **E**volutionary **R**epresentation
 
 ## A language model library for rapid pre-training from scratch.
@@ -43,10 +43,9 @@ causal_language_model = PrescientPCLM.load_from_checkpoint(<path to ckpt>)
 TODO: update
 
 **Datasets**
-- all models are trained on heavy and light chains separately, no pairing
-- public antibodies: antiberty dataset (paired and unpaired OAS)
-- private antibodies: all tenx (paired) and bulk (unpaired) ngs data
-- aho: these models expect aho aligned inputs from anarci
+- all antibody models are trained on heavy and light chains separately, no pairing
+- antibodies: antiberty dataset (paired and unpaired OAS)
+- aho: these models expect aho aligned antibody inputs from anarci
 - uniref50: general protein universe
 - pdb complexes: pdb sequences with `.` tokens indicating complexes
 
@@ -92,22 +91,28 @@ To train an MLM on a fasta file of sequences on an interactive GPU node, cd into
 lobster_train data.path_to_fasta="test_data/query.fasta" logger=csv paths.root_dir="."
 ```
 
-## License
-Copyright © 2024 Genentech, Inc.
-
-Permission is hereby granted, free of charge, to any person obtaining a copy of
-this software and associated documentation files (the “Software”), to deal in
-the Software without restriction, including without limitation the rights to
-use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of
-the Software, and to permit persons to whom the Software is furnished to do so,
-subject to the following conditions:
-
-The above copyright notice and this permission notice shall be included in all
-copies or substantial portions of the Software.
-
-THE SOFTWARE IS PROVIDED “AS IS”, WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
-IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS
-FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR
-COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER
-IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
-CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+## Contributing
+Contributions are welcome! We ask that all users and contributors remember that the LOBSTER team are all full-time drug hunters, and our open-source efforts are a labor of love because we care deeply about open science and scientific progress.
+
+### Install dev requirements and pre-commit hooks
+
+```bash
+python -m pip install -r requirements-dev.in
+pre-commit install
+```
+
+### Testing
+
+```bash
+python -m pytest -v --cov-report term-missing --cov=./lobster ./tests
+```
+
+### Build and browse docs locally
+
+```bash
+make -C docs html
+cd docs/build/html
+python -m http.server
+```
+
+Then open `http://localhost:8000` in your browser.

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)

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

docs/source/conf.py

@@ -0,0 +1,28 @@
+# 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 = "lobster"
+copyright = "2024, Nathan C. Frey"
+author = "Nathan C. Frey"
+
+# -- General configuration ---------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration
+
+extensions = ["autoapi.extension", "sphinx.ext.napoleon"]
+
+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 = "alabaster"
+html_static_path = ["_static"]
+
+autoapi_dirs = ["../../src/lobster"]

requirements-dev.in

@@ -2,3 +2,6 @@ mypy
 pytest
 pytest-cov
 pre-commit
+sphinx
+sphinx-rtd-theme
+sphinx-autoapi