add check-badges hook; set NUMBA_THREADING_LAYER to 'workqueue' in all notebooks with uniform experience across all OSes in mind (#1748)

Co-authored-by: Sylwester Arabas <sylwester.arabas@agh.edu.pl>

Author: AgnieszkaZaba

.github/actions/env-setup/action.yml

@@ -43,6 +43,10 @@ runs:
             exit(0)
         EOF
       shell: bash
+    
+    - name: set NUMBA_THREADING_LAYER
+      run: echo NUMBA_THREADING_LAYER=workqueue >> $GITHUB_ENV
+      shell: bash
 
     - uses: actions/cache/save@v4
       if: steps.cache.outputs.cache-hit != 'true'

.github/workflows/readme_snippets.yml

@@ -66,7 +66,7 @@ jobs:
         with:
           python-version: "3.12"
 
-      - run: echo NUMBA_THREADING_LAYER=omp >> $GITHUB_ENV
+      - run: echo NUMBA_THREADING_LAYER=workqueue >> $GITHUB_ENV
 
       - run: pip install -e .
       - run: pip install pytest-codeblocks pytest

.github/workflows/tests.yml

@@ -84,7 +84,7 @@ jobs:
         pylint --max-module-lines=550 --unsafe-load-any-extension=y --disable=fixme,too-many-function-args,unsubscriptable-object,consider-using-with,protected-access,too-many-statements,too-many-public-methods,too-many-branches,duplicate-code,invalid-name,missing-function-docstring,missing-module-docstring,missing-class-docstring,too-many-locals,too-many-instance-attributes,too-few-public-methods,too-many-arguments,c-extension-no-member $(git ls-files '*.py' | grep ^examples)
     - run: |
         # TODO #682
-        nbqa pylint --unsafe-load-any-extension=y --disable=fixme,duplicate-code,invalid-name,trailing-whitespace,line-too-long,missing-function-docstring,wrong-import-position,missing-module-docstring,wrong-import-order,ungrouped-imports,no-member,too-many-locals,unnecessary-lambda-assignment $(git ls-files '*.ipynb')
+        nbqa pylint --unsafe-load-any-extension=y --disable=fixme,duplicate-code,invalid-name,trailing-whitespace,line-too-long,missing-function-docstring,wrong-import-position,missing-module-docstring,wrong-import-order,ungrouped-imports,no-member,too-many-locals,unnecessary-lambda-assignment,multiple-imports $(git ls-files '*.ipynb')
 
   unit-tests-without-jit-plus-codecov:
     needs: env-unit-tests-setup
@@ -138,8 +138,6 @@ jobs:
         with:
           python-version: ${{ matrix.python-version }}
           setup-name: unit-tests-${{ matrix.platform }}-${{ matrix.python-version }}
-      - if: startsWith(matrix.platform, 'ubuntu-')
-        run: echo NUMBA_THREADING_LAYER=omp >> $GITHUB_ENV
       - name: Run pytest
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
@@ -199,9 +197,6 @@ jobs:
         with:
           python-version: ${{ matrix.python-version }}
           setup-name: nonunit-tests-${{ matrix.platform }}-${{ matrix.python-version }}
-
-      - if: startsWith(matrix.platform, 'ubuntu-')
-        run: echo NUMBA_THREADING_LAYER=omp >> $GITHUB_ENV
       - name: Run pytest
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
@@ -243,7 +238,7 @@ jobs:
             test-suite: "multi-process_e"
       fail-fast: true
     runs-on: ${{ matrix.platform }}
-    timeout-minutes: ${{ startsWith(matrix.platform, 'windows-') && 28 || 30 }}
+    timeout-minutes: ${{ startsWith(matrix.platform, 'windows-') && 30 || 32 }}
     steps:
       - name: Debug contexts
         run: |
@@ -261,8 +256,6 @@ jobs:
           python-version: ${{ matrix.python-version }}
           setup-name: nonunit-tests-${{ matrix.platform }}-${{ matrix.python-version }}
           # https://github.com/numba/numba/issues/6350#issuecomment-728174860
-      - if: startsWith(matrix.platform, 'ubuntu-')
-        run: echo NUMBA_THREADING_LAYER=omp >> $GITHUB_ENV
 
       - if: startsWith(matrix.platform, 'ubuntu-') && (contains(matrix.test-suite, 'multi-process_a') || contains(matrix.test-suite, 'multi-process_b'))
         run: |

.pre-commit-config.yaml

@@ -28,3 +28,9 @@ repos:
     - id: detect-missing-init
       args: ['--create', "--track", "--python-folders", "tests,PySDM,examples/PySDM_examples"]
 
+  - repo: https://github.com/open-atmos/devops_tests
+    rev: v0.0.2
+    hooks:
+      - id: check-badges
+        name: check badges
+        args: [--fix-header, --repo-name=PySDM]

examples/PySDM_examples/Abade_and_Albuquerque_2024/fig_2.ipynb

@@ -41,11 +41,12 @@
    },
    "outputs": [],
    "source": [
-    "import sys\n",
+    "import os, sys\n",
+    "os.environ['NUMBA_THREADING_LAYER'] = 'workqueue'  # PySDM & PyMPDATA don't work with TBB; OpenMP has extra dependencies on macOS\n",
     "if 'google.colab' in sys.modules:\n",
     "    !pip --quiet install open-atmos-jupyter-utils\n",
     "    from open_atmos_jupyter_utils import pip_install_on_colab\n",
-    "    pip_install_on_colab('PySDM-examples')"
+    "    pip_install_on_colab('PySDM-examples', 'PySDM')"
    ]
   },
   {
@@ -55,7 +56,6 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "import os\n",
     "import numpy as np\n",
     "from matplotlib import pyplot\n",
     "from scipy.interpolate import interp1d\n",