add documentation

Author: mffrank

.github/workflows/docs.yml

@@ -0,0 +1,40 @@
+name: Build and Deploy Documentation
+on:
+  push:
+    branches:
+      - main
+  pull_request:
+    branches:
+      - main
+
+permissions:
+  contents: write
+
+jobs:
+  build-and-deploy:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Set up Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: '3.9'
+
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install ".[docs]"  # Install package with docs dependencies
+
+      - name: Build Documentation
+        run: |
+          cd docs
+          make html
+          touch build/html/.nojekyll
+
+      - name: Deploy to GitHub Pages
+        if: github.event_name == 'push'
+        uses: JamesIves/github-pages-deploy-action@v4
+        with:
+          folder: docs/build/html
+          branch: gh-pages 

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/_static/img/grassp_logo.png

@@ -0,0 +1 @@
+# Datasets

docs/source/_static/img/grassp_logo.webp

@@ -0,0 +1,18 @@
+# API
+
+Import grassp as:
+
+```
+import grassp as gr
+```
+
+
+```{toctree}
+:maxdepth: 2
+
+preprocessing
+tools
+plotting
+io
+datasets
+```

docs/source/api/datasets.md

@@ -0,0 +1 @@
+# IO

docs/source/api/index.md

@@ -0,0 +1,38 @@
+## Plotting: `pl`
+
+```{eval-rst}
+.. module:: grassp.pl
+```
+
+```{eval-rst}
+.. currentmodule:: grassp
+```
+
+This module provides visualization functions for proteomics data.
+
+```{note}
+Many of scanpy's plotting functions can be directly used with grassp AnnData objects. So if you are looking for a specific plot, it is worth checking if it is already implemented in scanpy.
+```
+
+### Preprocessing
+
+```{eval-rst}
+.. autosummary::
+   :nosignatures:
+   :toctree: ../generated/
+
+   pl.highly_variable_proteins
+   pl.bait_volcano_plots
+   pl.protein_clustermap
+```
+
+### Integration
+```{eval-rst}
+.. autosummary::
+   :nosignatures:
+   :toctree: ../generated/
+
+   pl.aligned_umap
+   pl.remodeling_score
+   pl.remodeling_sankey
+``` 

docs/source/api/io.md

@@ -0,0 +1,41 @@
+## Preprocessing: `pp`
+
+```{eval-rst}
+.. module:: grassp.pp
+```
+
+```{eval-rst}
+.. currentmodule:: grassp
+```
+
+Any transformation of the data matrix that is not a *tool*. Other than *tools*, preprocessing steps usually don't return an easily interpretable annotation, but perform a basic transformation on the data matrix.
+
+### Basic Preprocessing
+
+
+```{eval-rst}
+.. autosummary::
+   :nosignatures:
+   :toctree: ../generated/
+
+   pp.calculate_qc_metrics
+   pp.filter_samples
+   pp.filter_proteins
+   pp.highly_variable_proteins
+   pp.filter_proteins_per_replicate
+   pp.aggregate_proteins
+   pp.aggregate_samples
+   pp.normalize_total
+   pp.drop_excess_MQ_metadata
+   pp.remove_contaminants
+```
+
+### Imputation
+
+```{eval-rst}
+.. autosummary::
+   :nosignatures:
+   :toctree: ../generated/
+
+   pp.impute_gaussian
+```