Merge branch 'main' of https://github.com/aidos-lab/mantra

.github/workflows/black.yaml

@@ -9,7 +9,7 @@ jobs:
       - uses: actions/checkout@v4
       - uses: psf/black@stable
         with:
-          options: "--check --verbose --line-length 80"
+          options: "--check --verbose --line-length 80 --exclude docs/"
           # Ignore Jupyter notebooks for now to simplify rapid
           # prototyping.
           jupyter: false

.github/workflows/docs.yaml

@@ -0,0 +1,62 @@
+name: Build the documentation.
+
+# build the documentation whenever there are new commits on main
+on:
+  push:
+    # Alternative: only build for tags.
+    tags:
+      - '*'
+  workflow_dispatch:
+
+# security: restrict permissions for CI jobs.
+permissions:
+  contents: read
+
+jobs:
+  # Build the documentation and upload the static HTML files as an artifact.
+  build:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
+        with:
+          python-version: '3.10.11'
+          cache: 'pip'
+      - name: Install dependencies
+        run: |
+          pip install torch==2.2.0
+          pip install numpy
+          pip install git+https://github.com/Lezcano/geotorch/
+          pip install pdoc
+
+      # ADJUST THIS: install all dependencies (including pdoc)
+      - name: Install mantra
+        run: |
+          pip install -e .
+
+      - name: Install sphinx
+        run: |
+          pip install sphinx sphinx_rtd_theme myst_parser
+
+      - name: Sphinx build
+        run: |
+          sphinx-build docs/source docs/build
+
+      - uses: actions/upload-pages-artifact@v3
+        with:
+          path: docs/build
+
+  # Deploy the artifact to GitHub pages.
+  # This is a separate job so that only actions/deploy-pages has the necessary permissions.
+  deploy:
+    needs: build
+    runs-on: ubuntu-latest
+    permissions:
+      pages: write
+      id-token: write
+    environment:
+      name: github-pages
+      url: ${{ steps.deployment.outputs.page_url }}
+    steps:
+      - id: deployment
+        uses: actions/deploy-pages@v4

.gitignore

@@ -11,4 +11,6 @@ scratch_**
 
 /build
 /visualization 
-/tables
+/tables
+
+docs/build

CNAME

@@ -0,0 +1 @@
+mantra.aidos.group

README.md

@@ -19,9 +19,9 @@ pip install mantra-dataset
 After installation the dataset can be used with the follwing snippet.
 
 ```python
-from mantra.simplicial import SimplicialDataset
+from mantra.datasets import ManifoldTriangulations
 
-dataset = SimplicialDataset(root="./data", manifold="2", version="latest")
+dataset = ManifoldTriangulations(root="./data", manifold="2", version="latest")
 ```
 
 ## Folder Structure
@@ -52,7 +52,7 @@ triangulation having the following attributes:
 
 * `betti_numbers` (required, `list` of `int`): A list of the [Betti
   numbers](https://en.wikipedia.org/wiki/Betti_number) of the
-  triangulation, computed using $Z_2$ coefficients. This implies that
+  triangulation, computed using $Z$ coefficients. This implies that
   [torsion](https://en.wikipedia.org/wiki/Homology_(mathematics))
   coefficients are stored in another attribute.
 

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 +1,45 @@
+# 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 = "MANTRA"
+copyright = "2024, Ernst Röell, Daniel Bin Schmid, Bastian Rieck"
+author = "Ernst Röell, Daniel Bin Schmid, Bastian Rieck"
+
+# -- General configuration ---------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration
+
+extensions = [
+    "sphinx.ext.autodoc",
+    "sphinx_rtd_theme",
+]
+
+templates_path = ["_templates"]
+exclude_patterns = ["build", "Thumbs.db", ".DS_Store"]
+
+
+# Ensure that member functions are documented. These are sane defaults.
+autodoc_default_options = {
+    "members": True,
+    "member-order": "bysource",
+    "special-members": "__init__",
+    "undoc-members": True,
+    "exclude-members": "__weakref__",
+}
+
+# Tries to assign some semantic meaning to arguments provided with
+# single backtics, such as `x`. This way, we can ignore `func` and
+# `class` targets etc. (They still work, though!)
+default_role = "obj"
+
+# -- Options for HTML output -------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#options-for-html-output
+
+html_theme = "sphinx_rtd_theme"
+html_static_path = ["_static"]
+
+modindex_common_prefix = ["mantra."]

docs/source/datasets.rst

@@ -0,0 +1,6 @@
+mantra.datasets
+===============
+
+.. automodule:: mantra.datasets
+   :members:
+

docs/source/index.rst

@@ -0,0 +1,20 @@
+
+MANTRA
+======
+
+.. toctree::
+   :maxdepth: 2
+   :caption: Contents:
+
+.. toctree::
+   :maxdepth: 2
+   :caption: Modules
+
+   datasets
+
+Indices and tables
+==================
+
+* :ref:`genindex`
+* :ref:`modindex`
+* :ref:`search`

mantra/__init__.py

@@ -0,0 +1,3 @@
+"""
+.. include:: ../README.md
+"""

mantra/simplicial.py → mantra/datasets.py

@@ -1,7 +1,7 @@
-"""
-The dataset class for the manifolds. It consists of 2 and 3 manifolds
-along with the topological information. We follow the pytorch geometric
-conventions for the dataset.
+"""Datasets module
+
+This module contains datasets describing triangulations of manifolds,
+following the API `pytorch-geometric`.
 """
 
 import os
@@ -15,7 +15,7 @@
 )
 
 
-class SimplicialDataset(InMemoryDataset):
+class ManifoldTriangulations(InMemoryDataset):
 
     def __init__(
         self,