Merge pull request #125 from AllenCellModeling/fix/docs-replace-m2r2

use myst_parser instead of m2r2

Author: toloudis

.github/workflows/build-docs-pr.yml

@@ -0,0 +1,28 @@
+name: Docs
+
+on: [pull_request]
+
+jobs:
+  docs:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          submodules: true
+      - name: Setup Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.10"
+      - name: Install Dependencies
+        run: |
+          pip install --upgrade pip setuptools
+          pip install .[dev]
+      - name: Generate Docs
+        env:
+          BUILD_DOCS: true
+        run: |
+          mkdir cmake_build_debug
+          cd cmake_build_debug
+          cmake ..
+          cmake --build . --target docs
+        shell: bash

.gitignore

@@ -121,3 +121,4 @@ dummy_test.py
 *.ipynb
 .DS_Store
 cmake-build-debug/
+cmake_build_debug/

docs/conf.py.in

@@ -18,6 +18,7 @@
 # relative to the documentation root, use os.path.abspath to make it
 # absolute, like shown here.
 #
+from datetime import datetime
 import os
 import sys
 
@@ -40,12 +41,13 @@ extensions = [
     "sphinx.ext.autodoc",
     "sphinx.ext.viewcode",
     "sphinx.ext.mathjax",
-    "m2r2",
+    "myst_parser",
 ]
 
 # Control napoleon
 napoleon_google_docstring = False
-napolean_include_init_with_doc = True
+napoleon_numpy_docstring = True
+napoleon_include_init_with_doc = True
 napoleon_use_ivar = True
 napoleon_use_param = False
 
@@ -60,7 +62,7 @@ templates_path = ["_templates"]
 #
 source_suffix = {
     ".rst": "restructuredtext",
-    ".txt": "markdown",
+    # ".txt": "markdown",
     ".md": "markdown",
 }
 
@@ -69,7 +71,7 @@ master_doc = "index"
 
 # General information about the project.
 project = u"aicspylibczi"
-copyright = u'2019, Allen Institute for Cell Science'
+project_copyright = f'2019-{datetime.now().year}, Allen Institute for Cell Science'
 author = u"Allen Institute for Cell Science"
 
 # The version info for the project you"re documenting, acts as replacement

docs/contributing.rst

@@ -1 +1,2 @@
-.. mdinclude:: ../CONTRIBUTING.md
+.. include:: ../CONTRIBUTING.md
+   :parser: myst_parser.docutils_

docs/index.rst

@@ -33,7 +33,8 @@ Welcome to aicspylibczi's documentation!
    Package modules <modules>
    contributing
 
-.. mdinclude:: ../README.md
+.. include:: ../README.md
+   :parser: myst_parser.docutils_
 
 
 Indices and tables

setup.py

@@ -29,7 +29,7 @@
     "coverage>=5.0a4",
     "flake8>=3.7.7",
     "ipython>=7.5.0",
-    "m2r2>=0.2.7",
+    "myst-parser>=4.0.0",
     "pytest>=4.3.0",
     "pytest-cov==2.6.1",
     "pytest-raises>=0.10",