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rerun advection-diffusion-2d and -1d notebooks; fix hdf5-mpi paths on macOS CI (homebrew); cleanup Trixi comparison notebook; pin CI upper Python version to 3.13.12 (since 3.13.13 errs with a base64 failure) #681

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Merged
slayoo merged 5 commits into from
May 1, 2026
Merged

rerun advection-diffusion-2d and -1d notebooks; fix hdf5-mpi paths on macOS CI (homebrew); cleanup Trixi comparison notebook; pin CI upper Python version to 3.13.12 (since 3.13.13 errs with a base64 failure) #681

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792ec08
rerun notebooks
AgnieszkaZaba Apr 27, 2026
6df1fdb
try to specify version of libhdf5-mpi==2.0.0
AgnieszkaZaba Apr 27, 2026
5ad1d57
revert previous commit and change installation on macOS, hope it will…
AgnieszkaZaba Apr 27, 2026
f9a6ec1
Remove try-except blocks for file handling
slayoo Apr 28, 2026
e490d2f
pin Python version to 3.13.12 in workflows (to workaround base64 issues)
slayoo May 1, 2026
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6 changes: 5 additions & 1 deletion .github/workflows/mpi.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -158,7 +158,11 @@ jobs:
sudo apt-get update && sudo apt-get install -y libhdf5-mpi$_ch-dev pkg-config
echo NUMBA_THREADING_LAYER=omp >> $GITHUB_ENV
- if: startsWith(matrix.platform, 'macos-')
run: brew install hdf5-mpi && echo HDF5_DIR=/opt/homebrew >> $GITHUB_ENV
run: |
brew install hdf5-mpi
echo HDF5_DIR=$(brew --prefix hdf5-mpi) >> $GITHUB_ENV
echo DYLD_FALLBACK_LIBRARY_PATH=$(brew --prefix hdf5-mpi)/lib:$DYLD_FALLBACK_LIBRARY_PATH >> $GITHUB_ENV

- if: matrix.platform == 'macos-14'
run: echo DYLD_FALLBACK_LIBRARY_PATH=/opt/homebrew/lib:/usr/local/lib:/usr/lib:$DYLD_FALLBACK_LIBRARY_PATH >> $GITHUB_ENV
- run: python -We -c "import PyMPDATA_MPI"
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10 changes: 5 additions & 5 deletions .github/workflows/tests.yml
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Expand Up @@ -81,7 +81,7 @@ jobs:
needs: [ precommit, pylint, devops ]
strategy:
matrix:
python-version: ["3.10", "3.13"]
python-version: ["3.10", "3.13.12"]
runs-on: ubuntu-latest
env:
NUMBA_DISABLE_JIT: 1
Expand Down Expand Up @@ -113,7 +113,7 @@ jobs:
strategy:
matrix:
platform: [ubuntu-latest, macos-15-intel, macos-14, windows-latest]
python-version: ["3.10", "3.13"]
python-version: ["3.10", "3.13.12"]
exclude:
- platform: macos-14
python-version: "3.10"
Expand Down Expand Up @@ -154,7 +154,7 @@ jobs:
strategy:
matrix:
platform: [ubuntu-latest, macos-15-intel, macos-14, windows-latest]
python-version: ["3.10", "3.13"]
python-version: ["3.10", "3.13.12"]
fail-fast: false
runs-on: ${{ matrix.platform }}
steps:
Expand Down Expand Up @@ -191,7 +191,7 @@ jobs:
NUMBA_OPT: 1
run: python -m pytest --durations=10 -p no:unraisableexception -We tests/devops_tests/test_notebooks.py

- if: ${{ matrix.platform == 'ubuntu-latest' && matrix.python-version == '3.13'}}
- if: ${{ matrix.platform == 'ubuntu-latest' && matrix.python-version == '3.13.12'}}
run: |
mkdir -p /home/runner/work/_temp/_github_home/figures
rm /tmp/pytest-of-runner/pytest-current/test_run_notebooks_examples_Pycurrent
Expand All @@ -206,7 +206,7 @@ jobs:
# with:
# limit-access-to-actor: true

- if: ${{ github.ref == 'refs/heads/main' && matrix.platform == 'ubuntu-latest' && matrix.python-version == '3.13'}}
- if: ${{ github.ref == 'refs/heads/main' && matrix.platform == 'ubuntu-latest' && matrix.python-version == '3.13.12'}}
uses: eine/tip@master
with:
token: ${{ secrets.GITHUB_TOKEN }}
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9,846 changes: 9,815 additions & 31 deletions examples/PyMPDATA_examples/advection_diffusion_1d/demo.ipynb
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147 changes: 81 additions & 66 deletions examples/PyMPDATA_examples/advection_diffusion_2d/advection-diffusion-2d.ipynb
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23 changes: 7 additions & 16 deletions examples/PyMPDATA_examples/trixi_comparison/advection_comparison.ipynb
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Expand Up @@ -504,14 +504,10 @@
},
"cell_type": "code",
"source": [
"try:\n",
" vtu_filename = [f for f in os.listdir(\"./\") if \"vtu\" in f and \"celldata\" not in f][0]\n",
" mesh = meshio.read(vtu_filename)\n",
" trixi_points = ((mesh.points[:,:2] + 1)*SETUP[\"nx\"]*SETUP[\"polydeg\"]/2).round().astype(np.int16)\n",
" assert trixi_points.shape[0] == SETUP[\"nx\"]**2 * (SETUP[\"polydeg\"] + 1)**2\n",
"except Exception as e:\n",
" e.args += (list(os.walk(os.path.curdir)),)\n",
" raise e"
"vtu_filename = [f for f in os.listdir(\"./\") if \"vtu\" in f and \"celldata\" not in f][0]\n",
"mesh = meshio.read(vtu_filename)\n",
"trixi_points = ((mesh.points[:,:2] + 1)*SETUP[\"nx\"]*SETUP[\"polydeg\"]/2).round().astype(np.int16)\n",
"assert trixi_points.shape[0] == SETUP[\"nx\"]**2 * (SETUP[\"polydeg\"] + 1)**2\n"
],
"id": "451911db51e18682",
"outputs": [],
Expand All @@ -526,14 +522,9 @@
},
"cell_type": "code",
"source": [
"try:\n",
" trixi_output = np.zeros_like(pympdata_result_state)\n",
" for i in range(trixi_points.shape[0]):\n",
" trixi_output[trixi_points[i][0], trixi_points[i][1]] = mesh.point_data['scalar'][i][0]\n",
"except Exception as e:\n",
" e.args += (list(mesh.point_data.keys()),)\n",
" e.args += (list(mesh.points.shape),)\n",
" raise e"
"trixi_output = np.zeros_like(pympdata_result_state)\n",
"for i in range(trixi_points.shape[0]):\n",
" trixi_output[trixi_points[i][0], trixi_points[i][1]] = mesh.point_data['scalar'][i][0]\n"
],
"id": "58595cff705f196c",
"outputs": [],
Expand Down
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