Merge pull request #1357 from MridulS/pre_commit_clean_up

Add linting action to run pre-commit

.github/workflows/documentation.yml

@@ -26,73 +26,73 @@ jobs:
       contents: write
 
     steps:
-    - uses: actions/checkout@v3
-
-    - name: Set up Python 3.10
-      uses: actions/setup-python@v4
-      with:
-        python-version: "3.10"  # Interpolation.py doesn't support Python 3.11 [2023-07]
-        cache: 'pip'
-        cache-dependency-path: |
-          requirements/base.txt
-          requirements/doc.txt
-
-    - name: Install Pandoc
-      run: sudo apt-get install --yes pandoc
-
-    - name: Update pip
-      run: python -m pip install --upgrade pip
-
-    - name: Install HARK
-      run: python -m pip install .[doc]
-
-    - name: Run Sphinx
-      run: >
-        sphinx-build
-        -M html Documentation HARK-docs
-        -T
-        -W
-        -j auto
-
-    - name: Set up git for deployment
-      run: |
-        git config user.name "${{ github.actor }}"
-        git config user.email "${{ github.actor }}@users.noreply.github.com"
-        git config --local --unset-all http.https://github.com/.extraheader
-
-    - name: Commit all rendered HTML files
-      run: |
-        git switch --orphan gh-pages
-        git add --all HARK-docs/html
-        git commit -qm "Documentation from @ ${{ github.repository }}@${{ github.sha }}"
-
-    - 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')
-      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
+      - uses: actions/checkout@v3
+
+      - name: Set up Python 3.10
+        uses: actions/setup-python@v4
+        with:
+          python-version: "3.10" # Interpolation.py doesn't support Python 3.11 [2023-07]
+          cache: "pip"
+          cache-dependency-path: |
+            requirements/base.txt
+            requirements/doc.txt
+
+      - name: Install Pandoc
+        run: sudo apt-get install --yes pandoc
+
+      - name: Update pip
+        run: python -m pip install --upgrade pip
+
+      - name: Install HARK
+        run: python -m pip install .[doc]
+
+      - name: Run Sphinx
+        run: >
+          sphinx-build
+          -M html Documentation HARK-docs
+          -T
+          -W
+          -j auto
+
+      - name: Set up git for deployment
+        run: |
+          git config user.name "${{ github.actor }}"
+          git config user.email "${{ github.actor }}@users.noreply.github.com"
+          git config --local --unset-all http.https://github.com/.extraheader
+
+      - name: Commit all rendered HTML files
+        run: |
+          git switch --orphan gh-pages
+          git add --all HARK-docs/html
+          git commit -qm "Documentation from @ ${{ github.repository }}@${{ github.sha }}"
+
+      - 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')
+        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
 
   lint:
     runs-on: ubuntu-latest
 
     steps:
-    - uses: actions/checkout@v3
-    - name: Set up Python
-      uses: actions/setup-python@v4
-      with:
-        python-version: 3
-    - name: Install dependencies
-      run: |
-        python -m pip install --upgrade pip
-        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/
+      - uses: actions/checkout@v3
+      - name: Set up Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: 3
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          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/

.github/workflows/execute-notebooks.yml

@@ -5,7 +5,7 @@ on:
   workflow_dispatch:
   # 6.49 am (GMT) every Monday; time chosen at random
   schedule:
-  - cron: "49 6 * * MON"
+    - cron: "49 6 * * MON"
 
 # Limit workflow permissions
 permissions:
@@ -29,47 +29,47 @@ jobs:
       pull-requests: write
 
     steps:
-    - uses: actions/checkout@v3
-    - name: Set up Python 3.10
-      uses: actions/setup-python@v4
-      with:
-        python-version: "3.10"  # Numba doesn't support Python 3.11 [2023-05]
-        cache: 'pip'
-        cache-dependency-path: |
-          requirements/base.txt
-          .github/workflows/execute-notebooks.yml
+      - uses: actions/checkout@v3
+      - name: Set up Python 3.10
+        uses: actions/setup-python@v4
+        with:
+          python-version: "3.10" # Numba doesn't support Python 3.11 [2023-05]
+          cache: "pip"
+          cache-dependency-path: |
+            requirements/base.txt
+            .github/workflows/execute-notebooks.yml
 
-    - name: Install dependencies
-      run: |
-        python -m pip install --upgrade pip
-        python -m pip install .
-        # For LabeledModels.ipynb
-        python -m pip install estimagic
-        # For nbstripout
-        python -m pip install nbstripout
-        # For nb_exec.py
-        python -m pip install ipykernel nbclient nbformat
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          python -m pip install .
+          # For LabeledModels.ipynb
+          python -m pip install estimagic
+          # For nbstripout
+          python -m pip install nbstripout
+          # For nb_exec.py
+          python -m pip install ipykernel nbclient nbformat
 
-    - name: Strip output
-      run: nbstripout examples/**/*.ipynb
+      - name: Strip output
+        run: nbstripout examples/**/*.ipynb
 
-    # This step takes c. 20 minutes
-    - name: Execute notebooks
-      run: python tools/nb_exec.py examples/**/*.ipynb
-      env:
-        PYTHONUNBUFFERED: "1"
+      # This step takes c. 20 minutes
+      - name: Execute notebooks
+        run: python tools/nb_exec.py examples/**/*.ipynb
+        env:
+          PYTHONUNBUFFERED: "1"
 
-    - name: Open PR
-      uses: peter-evans/create-pull-request@v5
-      with:
-        author: "Econ-ARK Bot <noreply@econ-ark.org>"
-        branch: "bot/update-notebooks"
-        commit-message: "[bot] updated notebooks"
-        delete-branch: true
-        title: "[bot] Execute example notebooks"
-        # language=Markdown
-        body: >
-          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
+      - name: Open PR
+        uses: peter-evans/create-pull-request@v5
+        with:
+          author: "Econ-ARK Bot <noreply@econ-ark.org>"
+          branch: "bot/update-notebooks"
+          commit-message: "[bot] updated notebooks"
+          delete-branch: true
+          title: "[bot] Execute example notebooks"
+          # language=Markdown
+          body: >
+            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

.github/workflows/lint.yml

@@ -0,0 +1,27 @@
+name: pre-commit
+
+on: [push, pull_request]
+
+jobs:
+  format:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ["3.10"]
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v4
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: Install packages
+        run: |
+          python -m pip install --upgrade pip
+          python -m pip install ".[dev]"
+          pip list
+
+      - name: Lint
+        run: pre-commit run --all-files --show-diff-on-failure --color always

.pre-commit-config.yaml

@@ -1,13 +1,14 @@
 exclude: Documentation/example_notebooks/
 
 repos:
-  - repo: https://github.com/mwouts/jupytext
-    rev: v1.15.0
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.1.4
     hooks:
-      - id: jupytext
-        args: [--sync, --set-formats, "ipynb", --pipe, black, --execute]
-        additional_dependencies: [jupytext, black, nbconvert]
-        files: ^examples/.*\.ipynb$
+      - id: ruff
+        types_or: [jupyter]
+      - id: ruff-format
+        args: [--check]
+        types_or: [jupyter]
 
   - repo: https://github.com/psf/black
     rev: 23.7.0

Documentation/_static/override-nbsphinx-gallery.css

@@ -1,3 +1,3 @@
 .nbsphinx-gallery {
-    grid-template-columns: repeat(auto-fill, minmax(200px, 1fr));
+  grid-template-columns: repeat(auto-fill, minmax(200px, 1fr));
 }

Documentation/conf.py

@@ -1,17 +1,19 @@
-from datetime import date
 import warnings
+from datetime import date
 
 try:
     import numba
 except ImportError:
     pass
 else:
-    warnings.filterwarnings("ignore",
-                            message="numba.generated_jit.*",
-                            category=numba.NumbaDeprecationWarning)
-    warnings.filterwarnings("ignore",
-                            message=".* 'nopython' .*",
-                            category=numba.NumbaDeprecationWarning)
+    warnings.filterwarnings(
+        "ignore",
+        message="numba.generated_jit.*",
+        category=numba.NumbaDeprecationWarning,
+    )
+    warnings.filterwarnings(
+        "ignore", message=".* 'nopython' .*", category=numba.NumbaDeprecationWarning
+    )
 
 # Project information
 project = "HARK"
@@ -64,7 +66,7 @@
 html_theme = "pydata_sphinx_theme"
 html_static_path = ["_static"]
 html_css_files = [
-    'override-nbsphinx-gallery.css',
+    "override-nbsphinx-gallery.css",
 ]
 
 html_theme_options = {
@@ -95,7 +97,7 @@
             "type": "local",
             "attributes": {"target": "_blank"},
         },
-    ]
+    ],
 }
 
 # Point to Econ-ARK repo for edit buttons

Documentation/overview/ARKitecture.md

@@ -45,7 +45,6 @@ After you [installed](https://docs.econ-ark.org/guides/quick_start.html) and [cl
 HARK's root directory contains six tool modules, [^1] each containing a variety of functions and classes that can be used in many economic models-- or even for mathematical purposes that have nothing to do with economics. Some of the tool modules are very sparely populated at this time, while others are quite large. We expect that all of these modules will grow considerably in the near future, as new tools are ''low hanging fruit'' for contribution to the project. [^2]
 
 [^1]: The ''taxonomy'' of these modules is in flux; the functions described here could be combined into fewer modules or further divided by purpose.
-
 [^2]: That is, as the foundational, building-block elements of HARK, new tools are not difficult to program and do not require extensive integration with many moving parts.
 
 #### HARK.core
@@ -87,7 +86,6 @@ Methods for optimizing an objective function for the purposes of estimating a mo
 By default, processes in Python are single-threaded, using only a single CPU core. The **_HARK.parallel_** module provides basic tools for using multiple CPU cores simultaneously, with minimal effort. [^4] In particular, it provides the function **_multiThreadCommands_**, which takes two arguments: a list of **_AgentType_**s and a list of commands as strings; each command should be a method of the **_AgentType_**s. The function simply distributes the **_AgentType_**s across threads on different cores and executes each command in order, returning no output (the **_AgentType_**s themselves are changed by running the commands). Equivalent results would be achieved by simply looping over each type and running each method in the list. Indeed, **_HARK.parallel_** also has a function called **_multiThreadCommandsFake_** that does just that, with identical syntax to **_multiThreadCommands_**; multithreading in HARK can thus be easily turned on and off. [^5] The module also has functions for a parallel implementation of the Nelder-Mead simplex algorithm, as described in Wiswall and Lee (2011). See [here](https://docs.econ-ark.org/reference/tools/parallel.html) for full documentation.
 
 [^4]: **_HARK.parallel_** uses two packages that aren't included in the default distribution of Anaconda: **_joblib_** and **_dill_**; see [here](https://docs.econ-ark.org/guides/quick_start.html#using-hark-with-anaconda) for instructions on how to install them.
-
 [^5]: In the future, **_HARK.parallel_** might be absorbed into **_HARK.core_** and **_HARK.estimation_**, particularly if **_joblib_** and **_dill_** become part of the standard Anaconda distribution.
 
 ### AgentType Class

HARK/Calibration/Income/tests/test_IncomeTools.py

@@ -203,7 +203,7 @@ def test_Cagetti(self):
             age_max=age_max,
             adjust_infl_to=adjust_infl_to,
             start_year=start_year,
-            **spec
+            **spec,
         )
         MeanP = find_profile(params["PermGroFac"], params["P0"])