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Merge remote-tracking branch 'ttk/dev' into HEAD
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‎.github/actions/install-spectra-unix/action.yml‎

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name: 'Install dependencies for Unix'
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description: 'Install Spectra optional dependencies'
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runs:
4+
using: "composite"
5+
steps:
6+
7+
- name: Install Spectra dependency
8+
shell: bash
9+
run: |
10+
wget https://github.com/yixuan/spectra/archive/v1.1.0.tar.gz
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tar xvf v1.1.0.tar.gz
12+
mkdir build_spectra && cd build_spectra
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cmake ../spectra-1.1.0
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sudo cmake --build . --target install --parallel

.github/actions/install-deps-unix/action.yml renamed to .github/actions/install-zfp-unix/action.yml

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name: 'Install dependencies for Unix'
2-
description: 'Install TTK optional dependencies on Ubuntu & macOS'
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description: 'Install ZFP optional dependencies'
33
runs:
44
using: "composite"
55
steps:
66

7-
- name: Install Spectra dependency
8-
shell: bash
9-
run: |
10-
wget https://github.com/yixuan/spectra/archive/v1.1.0.tar.gz
11-
tar xvf v1.1.0.tar.gz
12-
mkdir build_spectra && cd build_spectra
13-
cmake ../spectra-1.1.0
14-
sudo cmake --build . --target install --parallel
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- name: Install ZFP dependency
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shell: bash
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run: |

‎.github/actions/test-ttk-macos/action.yml‎

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name: 'Test TTK for Unix'
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description: 'Test TTK standalone, examples & states on Ubuntu & macOS'
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runs:
4+
using: "composite"
5+
steps:
6+
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- name: Test C++ example
8+
shell: bash
9+
run: |
10+
cd $GITHUB_WORKSPACE/examples/c++
11+
mkdir build && cd build
12+
cmake .. \
13+
-DOpenMP_C_FLAGS="-Xpreprocessor -fopenmp -I/opt/homebrew/opt/libomp/include" \
14+
-DOpenMP_C_LIB_NAMES="omp" \
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-DOpenMP_CXX_FLAGS="-Xpreprocessor -fopenmp -I/opt/homebrew/opt/libomp/include" \
16+
-DOpenMP_CXX_LIB_NAMES="omp" \
17+
-DOpenMP_omp_LIBRARY=/opt/homebrew/opt/libomp/lib/libomp.dylib \
18+
-DCMAKE_EXE_LINKER_FLAGS="-L/opt/homebrew/opt/libomp/lib -lomp"
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cmake --build . --parallel
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./ttkExample-c++ -i ../../data/inputData.off
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- name: Test VTK-C++ example
23+
shell: bash
24+
run: |
25+
cd $GITHUB_WORKSPACE/examples/vtk-c++
26+
mkdir build && cd build
27+
cmake .. \
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-DOpenMP_C_FLAGS="-Xpreprocessor -fopenmp -I/opt/homebrew/opt/libomp/include" \
29+
-DOpenMP_C_LIB_NAMES="omp" \
30+
-DOpenMP_CXX_FLAGS="-Xpreprocessor -fopenmp -I/opt/homebrew/opt/libomp/include" \
31+
-DOpenMP_CXX_LIB_NAMES="omp" \
32+
-DOpenMP_omp_LIBRARY=/opt/homebrew/opt/libomp/lib/libomp.dylib \
33+
-DCMAKE_EXE_LINKER_FLAGS="-L/opt/homebrew/opt/libomp/lib -lomp"
34+
cmake --build . --parallel
35+
./ttkExample-vtk-c++ -i ../../data/inputData.vtu
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- name: Test Python example
38+
shell: bash
39+
run: |
40+
cd $GITHUB_WORKSPACE/examples/python
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python3 example.py ../data/inputData.vtu
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- name: Test pvpython example
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shell: bash
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run: |
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cd $GITHUB_WORKSPACE/examples/pvpython
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pvpython example.py ../data/inputData.vtu
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- name: Test standalone
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shell: bash
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run: |
52+
cd $GITHUB_WORKSPACE
53+
ttkHelloWorldCmd -i examples/data/inputData.vtu

.github/actions/test-ttk-unix/action.yml renamed to .github/actions/test-ttk-ubuntu/action.yml

File renamed without changes.

‎.github/workflows/check.yml‎

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@@ -1,34 +1,16 @@
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name: check_code
22

33
on:
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push:
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# triggered on tag pushes with tags beginning with either "v" or "dev"
6-
branch-ignore:
7-
- '*'
8-
tags:
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- 'v*'
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- 'dev*'
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- 'ci*'
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- 'check*'
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pull_request:
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# also triggered by pull requests on the "dev" & "mpi" branches
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branches:
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- 'dev'
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- 'mpi'
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concurrency:
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group: ${{ github.workflow }}-${{ github.ref }}
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cancel-in-progress: true
4+
workflow_call:
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workflow_dispatch:
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env:
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PV_TAG: v5.13.0-headless
8+
PV_TAG: v6.0.1-headless
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PV_REPO: topology-tool-kit/ttk-paraview
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jobs:
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# ----------------------- #
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# Check source formatting #
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# ----------------------- #
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doxygen \
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clang-tidy
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- name: Install optional dependencies
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uses: ./.github/actions/install-deps-unix
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- name: Install optional Spectra dependency
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uses: ./.github/actions/install-spectra-unix
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- name: Install optional ZFP dependency
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uses: ./.github/actions/install-zfp-unix
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- name: Fetch TTK-ParaView headless Debian package
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run: |
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# Check compiler warnings #
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# ----------------------- #
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check-warnings:
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runs-on: ubuntu-22.04
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runs-on: ubuntu-24.04
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strategy:
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matrix:
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kamikaze: [KAMIKAZE=TRUE, KAMIKAZE=FALSE]
@@ -207,13 +192,16 @@ jobs:
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clang-tools \
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libomp-dev
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- name: Install optional dependencies
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uses: ./.github/actions/install-deps-unix
195+
- name: Install optional Spectra dependency
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uses: ./.github/actions/install-spectra-unix
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- name: Install optional ZFP dependency
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uses: ./.github/actions/install-zfp-unix
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- name: Fetch TTK-ParaView headless Debian package
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run: |
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wget -O ttk-paraview-headless.deb \
216-
https://github.com/${{ env.PV_REPO }}/releases/download/${{ env.PV_TAG }}/ttk-paraview-headless-ubuntu-22.04.deb
204+
https://github.com/${{ env.PV_REPO }}/releases/download/${{ env.PV_TAG }}/ttk-paraview-headless-ubuntu-24.04.deb
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- name: Install ParaView .deb
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run: |

‎.github/workflows/package.yml‎

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- 'pack*'
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env:
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PV_TAG: v5.13.0
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PV_TAG: v6.0.1
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PV_REPO: topology-tool-kit/ttk-paraview
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jobs:
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libqhull-dev \
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dpkg-dev
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- name: Install optional dependencies
51-
uses: ./.github/actions/install-deps-unix
50+
- name: Install optional Spectra dependency
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uses: ./.github/actions/install-spectra-unix
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53+
- name: Install optional ZFP dependency
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uses: ./.github/actions/install-zfp-unix
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- name: Fetch TTK-ParaView headless Debian package
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run: |
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134137
echo "PYTHONPATH=/usr/lib/python3/dist-packages:$PYTHONPATH" >> $GITHUB_ENV
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- name: Run TTK tests
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uses: ./.github/actions/test-ttk-unix
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uses: ./.github/actions/test-ttk-ubuntu
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- uses: actions/checkout@v4
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with:
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rm python/nestedTrackingFromOverlap.py
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# remove examples which fill up the memory
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rm python/topologicalOptimization_darkSky.py
167-
python3 -u python/run.py
170+
pvpython -u python/run.py
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- name: Test ttk-data Python scripts results [NOT ENFORCED]
170173
continue-on-error: true
@@ -181,7 +184,7 @@ jobs:
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runs-on: ${{ matrix.os }}
182185
strategy:
183186
matrix:
184-
os: [macos-13, macos-14, macos-15]
187+
os: [macos-14, macos-15]
185188
env:
186189
DYLD_LIBRARY_PATH: /usr/local/lib
187190

@@ -191,13 +194,13 @@ jobs:
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- uses: actions/setup-python@v5
193196
with:
194-
python-version: '3.12'
197+
python-version: '3.13'
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196199
- name: Install macOS dependencies
197200
run: |
198201
# ParaView dependencies
199202
brew install --cask xquartz
200-
brew install llvm mesa glew qt@5 ninja
203+
brew install mesa glew qt@5 ninja libomp
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# TTK dependencies
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brew install boost cgal eigen graphviz spectra sqlite zlib numpy qhull
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with:
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key: macos-0
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- name: Install optional dependencies
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uses: ./.github/actions/install-deps-unix
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- name: Install optional Spectra dependency
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uses: ./.github/actions/install-spectra-unix
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215+
- name: Install optional ZFP dependency
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uses: ./.github/actions/install-zfp-unix
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212218
- name: Fetch & install TTK-ParaView
213219
run: |
214220
wget https://github.com/${{ env.PV_REPO }}/releases/download/${{ env.PV_TAG }}/ttk-paraview-${{ env.PV_TAG }}-${{ matrix.os }}.tar.gz
215221
tar xzf ttk-paraview-${{ env.PV_TAG }}-${{ matrix.os }}.tar.gz
216222
sudo cp -r ttk-paraview/* /usr/local
217223
# pvpython does not embed the correct PYTHONPATH
218-
echo "PYTHONPATH=/usr/local/lib/python3.12/site-packages:$PYTHONPATH" >> $GITHUB_ENV
224+
echo "PYTHONPATH=/usr/local/lib/python3.13/site-packages:$PYTHONPATH" >> $GITHUB_ENV
219225
pvpython -m pip install --break-system-packages scikit-learn
220226
# pvpython is expecting a vtkpython executable at this path
221-
sudo ln -s /usr/local/bin/pvpython /Library/Frameworks/Python.framework/Versions/3.12/vtkpython
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223-
- name: Set compilers as environment variables
224-
run: |
225-
echo "CC=$(brew --prefix llvm)/bin/clang" >> $GITHUB_ENV
226-
echo "CXX=$(brew --prefix llvm)/bin/clang++" >> $GITHUB_ENV
227+
sudo ln -s /usr/local/bin/pvpython /Library/Frameworks/Python.framework/Versions/3.13/vtkpython
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- name: Create & configure TTK build directory
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run: |
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232233
cmake \
233234
-DCMAKE_BUILD_TYPE=Release \
234235
-DQt5_DIR=$(brew --prefix qt@5)/lib/cmake/Qt5 \
236+
-DOpenMP_C_FLAGS="-Xpreprocessor -fopenmp -I/opt/homebrew/opt/libomp/include" \
237+
-DOpenMP_C_LIB_NAMES="omp" \
238+
-DOpenMP_CXX_FLAGS="-Xpreprocessor -fopenmp -I/opt/homebrew/opt/libomp/include" \
239+
-DOpenMP_CXX_LIB_NAMES="omp" \
240+
-DOpenMP_omp_LIBRARY=/opt/homebrew/opt/libomp/lib/libomp.dylib \
241+
-DCMAKE_EXE_LINKER_FLAGS="-L/opt/homebrew/opt/libomp/lib -lomp" \
235242
-DTTK_BUILD_PARAVIEW_PLUGINS=TRUE \
236243
-DTTK_BUILD_VTK_WRAPPERS=TRUE \
237244
-DTTK_BUILD_STANDALONE_APPS=TRUE \
@@ -266,7 +273,7 @@ jobs:
266273
runs-on: ${{ matrix.os }}
267274
strategy:
268275
matrix:
269-
os: [macos-13, macos-14, macos-15]
276+
os: [macos-14, macos-15]
270277
env:
271278
DYLD_LIBRARY_PATH: /usr/local/lib
272279
steps:
@@ -275,13 +282,13 @@ jobs:
275282

276283
- uses: actions/setup-python@v5
277284
with:
278-
python-version: '3.12'
285+
python-version: '3.13'
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280287
- name: Install macOS dependencies
281288
run: |
282289
# ParaView dependencies
283290
brew install --cask xquartz
284-
brew install llvm mesa glew qt@5 ninja
291+
brew install mesa glew qt@5 ninja libomp
285292
# TTK dependencies
286293
brew install boost cgal eigen graphviz spectra sqlite zlib numpy qhull
287294
@@ -290,8 +297,11 @@ jobs:
290297
with:
291298
key: macos-0
292299

293-
- name: Install optional dependencies
294-
uses: ./.github/actions/install-deps-unix
300+
- name: Install optional Spectra dependency
301+
uses: ./.github/actions/install-spectra-unix
302+
303+
- name: Install optional ZFP dependency
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uses: ./.github/actions/install-zfp-unix
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296306
- name: Fetch TTK-ParaView
297307
run: |
@@ -312,16 +322,14 @@ jobs:
312322
313323
- name: Set environment variables
314324
run: |
315-
echo "CC=$(brew --prefix llvm)/bin/clang" >> $GITHUB_ENV
316-
echo "CXX=$(brew --prefix llvm)/bin/clang++" >> $GITHUB_ENV
317325
echo "CMAKE_PREFIX_PATH=$(brew --prefix qt@5)/lib/cmake:$CMAKE_PREFIX_PATH" >> $GITHUB_ENV
318326
# pvpython does not embed the correct PYTHONPATH
319-
echo "PYTHONPATH=/usr/local/lib/python3.12/site-packages:$PYTHONPATH" >> $GITHUB_ENV
327+
echo "PYTHONPATH=/usr/local/lib/python3.13/site-packages:$PYTHONPATH" >> $GITHUB_ENV
320328
# pvpython is expecting a vtkpython executable at this path
321-
sudo ln -s /usr/local/bin/pvpython /Library/Frameworks/Python.framework/Versions/3.12/vtkpython
329+
sudo ln -s /usr/local/bin/pvpython /Library/Frameworks/Python.framework/Versions/3.13/vtkpython
322330
323331
- name: Run TTK tests
324-
uses: ./.github/actions/test-ttk-unix
332+
uses: ./.github/actions/test-ttk-macos
325333

326334
- uses: actions/checkout@v4
327335
with:
@@ -339,12 +347,6 @@ jobs:
339347
# remove examples which fill up the memory
340348
rm python/topologicalOptimization_darkSky.py
341349
# some cases fail only with version 12
342-
if [[ "${{ matrix.os }}" == "macos-13" ]]; then
343-
rm python/contourTreeAlignment.py
344-
rm python/geometryApproximation.py
345-
rm python/harmonicSkeleton.py
346-
rm python/topologicalOptimization_torus.py
347-
fi
348350
# remove sklearn examples -- buggy on MacOS since sklearn-1.7
349351
rm python/1manifoldLearning.py python/clusteringKelvinHelmholtzInstabilities.py python/karhunenLoveDigits64Dimensions.py python/mergeTreeClustering.py python/persistentGenerators_householdAnalysis.py python/persistentGenerators_periodicPicture.py
350352
pvpython -u python/run.py
@@ -588,8 +590,12 @@ jobs:
588590
set PV_PLUGIN_PATH=%TTK_DIR%\bin\plugins
589591
cd ttk-data
590592
rm python/nestedTrackingFromOverlap.py
593+
# tmp removal of mpi example
594+
rm python/mpiExample.py
591595
# remove examples which fill up the memory
592596
rm python/topologicalOptimization_darkSky.py
597+
# remove examples using raster features
598+
rm python/geometryApproximation.py
593599
pvpython.exe -u python\run.py
594600
595601
- name: Test ttk-data Python scripts results [NOT ENFORCED]
@@ -655,14 +661,6 @@ jobs:
655661
file: ttk-ubuntu-24.04.deb/ttk.deb
656662
asset_name: ttk-$tag-ubuntu-24.04.deb
657663

658-
- name: Upload MacOS 13 binary archives as Release Asset
659-
uses: svenstaro/upload-release-action@v2
660-
with:
661-
repo_token: ${{ secrets.GITHUB_TOKEN }}
662-
tag: ${{ github.ref }}
663-
file: ttk-macos-13.tar.gz/ttk.tar.gz
664-
asset_name: ttk-$tag-macos-13.tar.gz
665-
666664
- name: Upload MacOS 14 binary archives as Release Asset
667665
uses: svenstaro/upload-release-action@v2
668666
with:

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