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Add new pre-commit hook for notebook structure check; pre-commit autoupdate only for schedulled builds #663

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Add new pre-commit hook for notebook structure check; pre-commit autoupdate only for schedulled builds #663

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d4d8d0c
Add new pre-commit hook for notebook structure check
AgnieszkaZaba Feb 15, 2026
4c6e844
pre-commit autoupdate only for scheduled builds
AgnieszkaZaba Feb 15, 2026
dc6a347
fix colab headers
AgnieszkaZaba Feb 17, 2026
b8a1a34
update hook version
AgnieszkaZaba Feb 21, 2026
ff86995
commentoverwriting variable hdf5_dir
AgnieszkaZaba Feb 21, 2026
42de263
revert and rerun
AgnieszkaZaba Feb 21, 2026
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11 changes: 8 additions & 3 deletions .github/workflows/tests.yml
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Expand Up @@ -28,9 +28,14 @@ jobs:
python-version: "3.10"
- run: |
pip install pre-commit
pre-commit clean
pre-commit autoupdate
pre-commit run --all-files

# avoiding failures unrelated to PR contents
if [ "${{ github.event_name }}" = "schedule" ]; then
pre-commit clean
pre-commit autoupdate
fi

pre-commit run --all-files --show-diff-on-failure

pylint:
runs-on: ubuntu-latest
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7 changes: 7 additions & 0 deletions .pre-commit-config.yaml
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Expand Up @@ -22,3 +22,10 @@ repos:
- id: debug-statements
- id: check-json
files: '.json'

- repo: https://github.com/AgnieszkaZaba/devops_tests
rev: dc88fdee2a5a3e4bd1e6e8b2a1c7c7418ea5fbf5
hooks:
- id: check-notebook-open-atmos-structure
name: check notebook has open-atmos structure
args: [--repo-name=PyMPDATA]
5 changes: 3 additions & 2 deletions examples/PyMPDATA_examples/Arabas_and_Farhat_2020/fig_1.ipynb
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Expand Up @@ -29,11 +29,12 @@
},
"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('PyMPDATA-examples')"
" pip_install_on_colab('PyMPDATA-examples', 'PyMPDATA')"
]
},
{
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5 changes: 3 additions & 2 deletions examples/PyMPDATA_examples/Arabas_and_Farhat_2020/fig_2.ipynb
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Expand Up @@ -29,11 +29,12 @@
},
"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('PyMPDATA-examples')"
" pip_install_on_colab('PyMPDATA-examples', 'PyMPDATA')"
]
},
{
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5 changes: 3 additions & 2 deletions examples/PyMPDATA_examples/Arabas_and_Farhat_2020/fig_3.ipynb
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Expand Up @@ -29,11 +29,12 @@
},
"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('PyMPDATA-examples')"
" pip_install_on_colab('PyMPDATA-examples', 'PyMPDATA')"
]
},
{
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5 changes: 3 additions & 2 deletions examples/PyMPDATA_examples/Arabas_and_Farhat_2020/tab_1.ipynb
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Expand Up @@ -29,11 +29,12 @@
},
"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('PyMPDATA-examples')"
" pip_install_on_colab('PyMPDATA-examples', 'PyMPDATA')"
]
},
{
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5 changes: 3 additions & 2 deletions examples/PyMPDATA_examples/Bartman_et_al_2022/fig_X.ipynb
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Expand Up @@ -22,11 +22,12 @@
"metadata": {},
"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('PyMPDATA-examples')"
" pip_install_on_colab('PyMPDATA-examples', 'PyMPDATA')"
]
},
{
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5 changes: 3 additions & 2 deletions examples/PyMPDATA_examples/DPDC/demo.ipynb
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Expand Up @@ -22,11 +22,12 @@
"metadata": {},
"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('PyMPDATA-examples')"
" pip_install_on_colab('PyMPDATA-examples', 'PyMPDATA')"
]
},
{
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5 changes: 3 additions & 2 deletions examples/PyMPDATA_examples/Jarecka_et_al_2015/fig_6.ipynb
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Expand Up @@ -27,11 +27,12 @@
"metadata": {},
"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('PyMPDATA-examples')"
" pip_install_on_colab('PyMPDATA-examples', 'PyMPDATA')"
]
},
{
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5 changes: 3 additions & 2 deletions examples/PyMPDATA_examples/Jaruga_et_al_2015/fig19.ipynb
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Expand Up @@ -45,11 +45,12 @@
"metadata": {},
"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('PyMPDATA-examples')"
" pip_install_on_colab('PyMPDATA-examples', 'PyMPDATA')"
]
},
{
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5 changes: 3 additions & 2 deletions examples/PyMPDATA_examples/Magnuszewski_et_al_2025/convergence_analysis.ipynb
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Expand Up @@ -32,11 +32,12 @@
},
"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('PyMPDATA-examples')"
" pip_install_on_colab('PyMPDATA-examples', 'PyMPDATA')"
]
},
{
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5 changes: 3 additions & 2 deletions examples/PyMPDATA_examples/Magnuszewski_et_al_2025/figs.ipynb
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Expand Up @@ -35,11 +35,12 @@
},
"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('PyMPDATA-examples')"
" pip_install_on_colab('PyMPDATA-examples', 'PyMPDATA')"
]
},
{
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5 changes: 3 additions & 2 deletions examples/PyMPDATA_examples/Magnuszewski_et_al_2025/table_1.ipynb
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Expand Up @@ -27,11 +27,12 @@
"metadata": {},
"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('PyMPDATA-examples')"
" pip_install_on_colab('PyMPDATA-examples', 'PyMPDATA')"
]
},
{
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5 changes: 3 additions & 2 deletions examples/PyMPDATA_examples/Molenkamp_test_as_in_Jaruga_et_al_2015_Fig_12/demo.ipynb
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Expand Up @@ -26,11 +26,12 @@
"metadata": {},
"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('PyMPDATA-examples')"
" pip_install_on_colab('PyMPDATA-examples', 'PyMPDATA')"
]
},
{
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5 changes: 3 additions & 2 deletions examples/PyMPDATA_examples/Olesik_et_al_2022/demo_analytical_solution.ipynb
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Expand Up @@ -22,11 +22,12 @@
"metadata": {},
"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('PyMPDATA-examples')"
" pip_install_on_colab('PyMPDATA-examples', 'PyMPDATA')"
]
},
{
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5 changes: 3 additions & 2 deletions examples/PyMPDATA_examples/Olesik_et_al_2022/demo_make_convergences.ipynb
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Expand Up @@ -22,11 +22,12 @@
"metadata": {},
"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('PyMPDATA-examples')"
" pip_install_on_colab('PyMPDATA-examples', 'PyMPDATA')"
]
},
{
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5 changes: 3 additions & 2 deletions examples/PyMPDATA_examples/Olesik_et_al_2022/demo_make_dispersion_ratio.ipynb
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Expand Up @@ -22,11 +22,12 @@
"metadata": {},
"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('PyMPDATA-examples')"
" pip_install_on_colab('PyMPDATA-examples', 'PyMPDATA')"
]
},
{
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5 changes: 3 additions & 2 deletions examples/PyMPDATA_examples/Olesik_et_al_2022/demo_make_plots.ipynb
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Expand Up @@ -22,11 +22,12 @@
"metadata": {},
"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('PyMPDATA-examples')"
" pip_install_on_colab('PyMPDATA-examples', 'PyMPDATA')"
]
},
{
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5 changes: 3 additions & 2 deletions examples/PyMPDATA_examples/Olesik_et_al_2022/demo_wall_times.ipynb
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Expand Up @@ -22,11 +22,12 @@
"metadata": {},
"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('PyMPDATA-examples')"
" pip_install_on_colab('PyMPDATA-examples', 'PyMPDATA')"
]
},
{
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5 changes: 3 additions & 2 deletions examples/PyMPDATA_examples/Shipway_and_Hill_2012/fig_1.ipynb
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Expand Up @@ -26,11 +26,12 @@
},
"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('PyMPDATA-examples')"
" pip_install_on_colab('PyMPDATA-examples', 'PyMPDATA')"
]
},
{
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5 changes: 3 additions & 2 deletions examples/PyMPDATA_examples/Smolarkiewicz_1984/figs_13-14.ipynb
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Expand Up @@ -26,11 +26,12 @@
"metadata": {},
"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('PyMPDATA-examples')"
" pip_install_on_colab('PyMPDATA-examples', 'PyMPDATA')"
]
},
{
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5 changes: 3 additions & 2 deletions examples/PyMPDATA_examples/Smolarkiewicz_2006_Figs_3_4_10_11_12/demo.ipynb
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Expand Up @@ -26,11 +26,12 @@
"metadata": {},
"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('PyMPDATA-examples')"
" pip_install_on_colab('PyMPDATA-examples', 'PyMPDATA')"
]
},
{
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5 changes: 3 additions & 2 deletions ...xamples/Williamson_and_Rasch_1989_as_in_Jaruga_et_al_2015_Fig_14/demo_over_the_pole.ipynb
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Expand Up @@ -23,11 +23,12 @@
"metadata": {},
"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('PyMPDATA-examples')"
" pip_install_on_colab('PyMPDATA-examples', 'PyMPDATA')"
]
},
{
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5 changes: 3 additions & 2 deletions examples/PyMPDATA_examples/advection_diffusion_1d/demo.ipynb
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Expand Up @@ -22,11 +22,12 @@
"metadata": {},
"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('PyMPDATA-examples')"
" pip_install_on_colab('PyMPDATA-examples', 'PyMPDATA')"
]
},
{
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