[WIP] Cookie

.copier-answers.yml

@@ -0,0 +1,12 @@
+# Changes here will be overwritten by Copier; NEVER EDIT MANUALLY
+_commit: 2024.08.19
+_src_path: gh:scientific-python/cookie
+backend: hatch
+email: econ-ark@jhuecon.org
+full_name: Econ-ARK Team
+license: MIT
+org: econ-ark
+project_name: HARK
+project_short_description: Heterogeneous Agents Resources and toolKit
+url: https://github.com/econ-ark/HARK
+vcs: true

.git_archival.txt

@@ -0,0 +1,3 @@
+node: $Format:%H$
+node-date: $Format:%cI$
+describe-name: $Format:%(describe:tags=true,match=*[0-9]*)$

.gitattributes

@@ -0,0 +1 @@
+.git_archival.txt  export-subst

.github/CONTRIBUTING.md

@@ -0,0 +1,89 @@
+See the [Scientific Python Developer Guide][spc-dev-intro] for a detailed
+description of best practices for developing scientific packages.
+
+[spc-dev-intro]: https://learn.scientific-python.org/development/
+
+# Quick development
+
+The fastest way to start with development is to use nox. If you don't have nox,
+you can use `pipx run nox` to run it without installing, or `pipx install nox`.
+If you don't have pipx (pip for applications), then you can install with
+`pip install pipx` (the only case were installing an application with regular
+pip is reasonable). If you use macOS, then pipx and nox are both in brew, use
+`brew install pipx nox`.
+
+To use, run `nox`. This will lint and test using every installed version of
+Python on your system, skipping ones that are not installed. You can also run
+specific jobs:
+
+```console
+$ nox -s lint  # Lint only
+$ nox -s tests  # Python tests
+$ nox -s docs -- --serve  # Build and serve the docs
+$ nox -s build  # Make an SDist and wheel
+```
+
+Nox handles everything for you, including setting up an temporary virtual
+environment for each run.
+
+# Setting up a development environment manually
+
+You can set up a development environment by running:
+
+```bash
+python3 -m venv .venv
+source ./.venv/bin/activate
+pip install -v -e .[dev]
+```
+
+If you have the
+[Python Launcher for Unix](https://github.com/brettcannon/python-launcher), you
+can instead do:
+
+```bash
+py -m venv .venv
+py -m install -v -e .[dev]
+```
+
+# Pre-commit
+
+You should prepare pre-commit, which will help you by checking that commits pass
+required checks:
+
+```bash
+pip install pre-commit # or brew install pre-commit on macOS
+pre-commit install # Will install a pre-commit hook into the git repo
+```
+
+You can also/alternatively run `pre-commit run` (changes only) or
+`pre-commit run --all-files` to check even without installing the hook.
+
+# Testing
+
+Use pytest to run the unit checks:
+
+```bash
+pytest
+```
+
+# Coverage
+
+Use pytest-cov to generate coverage reports:
+
+```bash
+pytest --cov=HARK
+```
+
+# Building docs
+
+You can build the docs using:
+
+```bash
+nox -s docs
+```
+
+You can see a preview with:
+
+```bash
+nox -s docs -- --serve
+```

.github/dependabot.yml

@@ -0,0 +1,11 @@
+version: 2
+updates:
+  # Maintain dependencies for GitHub Actions
+  - package-ecosystem: "github-actions"
+    directory: "/"
+    schedule:
+      interval: "weekly"
+    groups:
+      actions:
+        patterns:
+          - "*"

.github/release.yml

@@ -0,0 +1,5 @@
+changelog:
+  exclude:
+    authors:
+      - dependabot
+      - pre-commit-ci

.github/workflows/cd.yml

@@ -0,0 +1,60 @@
+name: CD
+
+on:
+  workflow_dispatch:
+  pull_request:
+  push:
+    branches:
+      - main
+  release:
+    types:
+      - published
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+env:
+  # Many color libraries just need this to be set to any value, but at least
+  # one distinguishes color depth, where "3" -> "256-bit color".
+  FORCE_COLOR: 3
+
+jobs:
+  dist:
+    name: Distribution build
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+
+      - uses: hynek/build-and-inspect-python-package@v2
+
+  publish:
+    needs: [dist]
+    name: Publish to PyPI
+    environment: pypi
+    permissions:
+      id-token: write
+      attestations: write
+      contents: read
+    runs-on: ubuntu-latest
+    if: github.event_name == 'release' && github.event.action == 'published'
+
+    steps:
+      - uses: actions/download-artifact@v4
+        with:
+          name: Packages
+          path: dist
+
+      - name: Generate artifact attestation for sdist and wheel
+        uses: actions/attest-build-provenance@v1.4.1
+        with:
+          subject-path: "dist/*"
+
+      - uses: pypa/gh-action-pypi-publish@release/v1
+        with:
+          # Remember to tell (test-)pypi about this repo before publishing
+          # Remove this line to publish to PyPI
+          repository-url: https://test.pypi.org/legacy/

.github/workflows/ci.yml

@@ -0,0 +1,67 @@
+name: CI
+
+on:
+  workflow_dispatch:
+  pull_request:
+  push:
+    branches:
+      - main
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+env:
+  # Many color libraries just need this to be set to any value, but at least
+  # one distinguishes color depth, where "3" -> "256-bit color".
+  FORCE_COLOR: 3
+
+jobs:
+  pre-commit:
+    name: Format
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+      - uses: actions/setup-python@v5
+        with:
+          python-version: "3.x"
+      - uses: pre-commit/action@v3.0.1
+        with:
+          extra_args: --hook-stage manual --all-files
+      - name: Run PyLint
+        run: pipx run nox -s pylint -- --output-format=github
+
+  checks:
+    name: Check Python ${{ matrix.python-version }} on ${{ matrix.runs-on }}
+    runs-on: ${{ matrix.runs-on }}
+    needs: [pre-commit]
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ["3.10", "3.11", "3.12"]
+        runs-on: [ubuntu-latest, windows-latest, macos-14]
+
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+
+      - uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+          allow-prereleases: true
+
+      - name: Install package
+        run: python -m pip install .[test]
+
+      - name: Test package
+        run: >-
+          python -m pytest -ra --cov --cov-report=xml --cov-report=term
+          --durations=20
+
+      - name: Upload coverage report
+        uses: codecov/codecov-action@v4.5.0
+        with:
+          token: ${{ secrets.CODECOV_TOKEN }}

.github/workflows/documentation.yml

@@ -35,7 +35,7 @@ jobs:
           cache: "pip"
           cache-dependency-path: |
             requirements/base.txt
-            requirements/doc.txt
+            requirements/docs.txt
 
       - name: Install Pandoc
         run: sudo apt-get install --yes pandoc
@@ -44,16 +44,11 @@ jobs:
         run: python -m pip install --upgrade pip
 
       - name: Install HARK
-        run: python -m pip install .[doc]
+        run: python -m pip install .[docs]
 
       - name: Run Sphinx
         run: >
-          sphinx-build
-          -M html . HARK-docs
-          -T
-          -c Documentation
-          -W
-          -j 1
+          sphinx-build -M html docs HARK-docs -T -c docs -j 1
 
       - name: Set up git for deployment
         run: |
@@ -69,12 +64,13 @@ jobs:
 
       - name: Deploy to GitHub Pages
         # Only deploy to Pages on pushes to HEAD
-        if: (github.repository_owner == 'Econ-ARK') && (github.event_name == 'push') && (github.ref_name == 'master')
+        if:
+          (github.repository_owner == 'Econ-ARK') && (github.event_name ==
+          'push') && (github.ref_name == 'master')
         run: >
-          git push
-          --force
-          https://x-access-token:${{ github.token }}@github.com/${{ github.repository }}
-          `git subtree split --prefix HARK-docs/html gh-pages`:refs/heads/gh-pages
+          git push --force https://x-access-token:${{ github.token
+          }}@github.com/${{ github.repository }} `git subtree split --prefix
+          HARK-docs/html gh-pages`:refs/heads/gh-pages
 
   lint:
     runs-on: ubuntu-latest
@@ -91,9 +87,5 @@ jobs:
           python -m pip install --upgrade sphinx-lint
       - name: Lint documentation with sphinx-lint
         run: >
-          sphinx-lint
-          --ignore Documentation/example_notebooks/GenIncProcessModel.py
-          --enable all
-          --max-line-length 85
-          README.md
-          Documentation/
+          sphinx-lint --ignore docs/example_notebooks/GenIncProcessModel.py
+          --enable all --max-line-length 85 README.md docs/

.github/workflows/examples.yml

@@ -6,13 +6,13 @@ on:
       - master
     paths-ignore:
       - ".github/workflows/documentation.yml"
-      - "Documentation/**"
+      - "docs/**"
   pull_request:
     branches:
       - master
     paths-ignore:
       - ".github/workflows/documentation.yml"
-      - "Documentation/**"
+      - "docs/**"
   schedule:
     - cron: 0 0 * * *
 
@@ -35,4 +35,4 @@ jobs:
           pip install ".[dev]"
       - name: Run examples
         run: |
-          pytest --nbval-lax --nbval-current-env --dist loadscope -n auto examples/
+          pytest --nbval-lax --nbval-current-env --dist loadscope -n auto docs/examples/

.github/workflows/execute-notebooks.yml

@@ -49,11 +49,11 @@ jobs:
           python -m pip install ipykernel nbclient nbformat
 
       - name: Strip output
-        run: nbstripout examples/**/*.ipynb
+        run: nbstripout docs/examples/**/*.ipynb
 
       # This step takes c. 20 minutes
       - name: Execute notebooks
-        run: python tools/nb_exec.py examples/**/*.ipynb
+        run: python tools/nb_exec.py docs/examples/**/*.ipynb
         env:
           PYTHONUNBUFFERED: "1"
 
@@ -67,7 +67,8 @@ jobs:
           title: "[bot] Execute example notebooks"
           # language=Markdown
           body: >
-            This PR was [automatically generated] to re-execute
-            the example notebooks for use in the documentation.
+            This PR was [automatically generated] to re-execute the example
+            notebooks for use in the documentation.
 
-            [automatically generated]: https://github.com/Econ-ARK/HARK/actions/workflows/execute-notebooks.yml
+            [automatically generated]:
+            https://github.com/Econ-ARK/HARK/actions/workflows/execute-notebooks.yml