Merge pull request #109 from kavitasinghnih/plotting-userstory

add basic dynamicpet usage jupyter notebook and fix checks

add jupyter notebook checks
add jupytext to generate py from ipynb for easy code diff
configure CI to run kinfitr tests on macOS
skip R install on windows
fix coverage checks

.github/workflows/tests.yml

@@ -46,6 +46,21 @@ jobs:
       - name: Check out the repository
         uses: actions/checkout@v4
 
+      - name: Set up R if not on Windows
+        if: matrix.os != 'windows-latest'
+        uses: r-lib/actions/setup-r@v2
+
+      - name: Install remotes R package if on MacOS
+        if: matrix.os == 'macos-latest'
+        uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          packages: remotes
+
+      - name: Install kinfitr if on MacOS
+        if: matrix.os == 'macos-latest'
+        run: |
+          Rscript -e "remotes::install_url('https://github.com/mathesong/kinfitr/archive/refs/tags/v0.8.0.tar.gz')"
+
       - name: Set up Python ${{ matrix.python }}
         uses: actions/setup-python@v5
         with:
@@ -110,6 +125,7 @@ jobs:
         with:
           name: coverage-data
           path: ".coverage.*"
+          include-hidden-files: true
 
       - name: Upload documentation
         if: matrix.session == 'docs-build'

.gitignore

@@ -6,6 +6,8 @@
 /.pytype/
 /dist/
 /docs/_build/
+/docs/jupyter_execute/
+/docs/notebooks/nb_data/
 /src/*.egg-info/
 __pycache__/
 /.vscode

.pre-commit-config.yaml

@@ -7,6 +7,7 @@ repos:
         language: system
         types: [python]
         require_serial: true
+        exclude: ^docs/notebooks/
       - id: check-added-large-files
         name: Check for added large files
         entry: check-added-large-files
@@ -27,6 +28,7 @@ repos:
         language: system
         types: [python]
         stages: [manual]
+        exclude: ^docs/notebooks/
       - id: end-of-file-fixer
         name: Fix End of Files
         entry: end-of-file-fixer
@@ -40,26 +42,51 @@ repos:
         types: [python]
         require_serial: true
         args: [--darglint-ignore-regex, .*]
+        exclude: ^docs/notebooks/
       - id: isort
         name: isort
         entry: isort
         require_serial: true
         language: system
         types_or: [cython, pyi, python]
         args: ["--filter-files"]
+        exclude: ^docs/notebooks/
       - id: pyupgrade
         name: pyupgrade
         description: Automatically upgrade syntax for newer versions.
         entry: pyupgrade
         language: system
         types: [python]
         args: [--py37-plus]
+        exclude: ^docs/notebooks/
       - id: trailing-whitespace
         name: Trim Trailing Whitespace
         entry: trailing-whitespace-fixer
         language: system
         types: [text]
         stages: [commit, push, manual]
+  - repo: https://github.com/nbQA-dev/nbQA
+    rev: 1.9.0
+    hooks:
+      - id: nbqa-black
+      - id: nbqa-check-ast
+      - id: nbqa-flake8
+        args: ["--extend-ignore=E402"]
+      - id: nbqa-pyupgrade
+        args: ["--py37-plus"]
+      - id: nbqa-isort
+  - repo: https://github.com/mwouts/jupytext
+    rev: v1.16.4
+    hooks:
+      - id: jupytext
+        name: jupytext
+        description: Runs jupytext on all notebooks and paired files
+        language: python
+        entry: jupytext --pre-commit-mode --set-formats "ipynb,py:percent"
+        require_serial: true
+        types_or: [jupyter, python]
+        files: ^docs/notebooks/ # Only apply this under docs/notebooks/
+        fail_fast: true
   - repo: https://github.com/pre-commit/mirrors-prettier
     rev: v2.6.0
     hooks:

codecov.yml

@@ -3,7 +3,7 @@ coverage:
   status:
     project:
       default:
-        target: "100"
+        target: "80"
     patch:
       default:
-        target: "100"
+        target: "80"

docs/conf.py

@@ -7,7 +7,7 @@
     "sphinx.ext.autodoc",
     "sphinx.ext.napoleon",
     "sphinx_click",
-    "myst_parser",
+    "myst_nb",
 ]
 autodoc_typehints = "description"
 autosummary_generate = True

docs/index.md

@@ -11,7 +11,8 @@ end-before: <!-- github-only -->
 ```{toctree}
 ---
 hidden:
-maxdepth: 1
+maxdepth: 2
+caption: Contents:
 ---
 
 usage
@@ -21,3 +22,12 @@ Code of Conduct <codeofconduct>
 License <license>
 Changelog <https://github.com/bilgelm/dynamicpet/releases>
 ```
+
+```{toctree}
+---
+maxdepth: 1
+caption: Notebooks:
+---
+
+notebooks/basics
+```