Set of commits to be tagged v0.7

.github/workflows/ci.yml

@@ -18,7 +18,7 @@ jobs:
           - ubuntu-latest
           - macos-latest
           - windows-latest
-        python-version: ["3.8", "3.9", "3.10", "3.11", "3.12", "3.13"]
+        python-version: ["3.9", "3.10", "3.11", "3.12", "3.13", "3.14"]
       fail-fast: true
 
     steps:

.gitignore

@@ -8,6 +8,8 @@ __pycache__/
 dist/
 build/
 _build/
+poetry.lock
+uv.lock
 
 # anything hidden should be manually added
 .*
@@ -28,6 +30,7 @@ _build/
 
 # notebooks
 *.ipynb
+notebooks/data-examples/
 
 # singularity containers
 *.sif

README.md

@@ -9,7 +9,7 @@ An attempt to rewrite the project documentation is available as a [separate proj
 
 ## Installation
 
-You will need Python >= 3.8.
+You will need Python >= 3.9.
 
 ### Windows users
 

containers/available_images.md

@@ -1,196 +1,6 @@
-Available singularity images are:
+Available Apptainer images are:
 
-* tramway-hpc-220312-py3{6,7,[8](http://dl.pasteur.fr/fop/n2SSFwr5/tramway-hpc-220312-py38.sif),[9](http://dl.pasteur.fr/fop/W6GcBTqk/tramway-hpc-220312-py39.sif),[10](http://dl.pasteur.fr/fop/Cmmobhil/tramway-hpc-220312-py310.sif)}.sif
-
-  *tramway0.6.4* image with targets *hpc-minimal* and *animate*, and *scikit-learn* as an additional package.
-  Python is available as *python3.x*, with *x* any of *6*, *7*, *8*, *9*, *10* depending on the container file.
-  The run command admits option *-s*, passed to Python,
-  resulting in command (e.g.) `python3.8 -s -m tramway $@`.
-  The included Python dependencies are the following:
-
-```
-cached-property==1.5.2 # <=py38
-certifi==2019.11.28
-chardet==3.0.4
-cvxopt==1.3.0
-cycler==0.11.0
-dbus-python==1.2.16
-decorator==4.4.2 # py36 only
-fonttools==4.30.0 # >=py37
-h5py==3.1.0 # py36 only
-h5py==3.6.0 # >=py37
-idna==2.8
-imageio==2.15.0 # py36 only
-imageio==2.16.1 # >=py37
-importlib-resources==5.4.0 # py36 only
-joblib==1.1.0
-kiwisolver==1.3.1 # py36 only
-kiwisolver==1.3.2 # >=py37
-matplotlib==3.3.4 # py36 only
-matplotlib==3.5.1 # >=py37
-networkx==2.5.1 # py36 only
-networkx==2.6.3 # py37 only
-networkx==2.7.1 # >=py38
-numpy==1.19.5 # py36 only
-numpy==1.21.5 # py37 only
-numpy==1.22.3 # >=py38
-opencv-python==4.5.5.64
-packaging==21.3 # >=py37
-pandas==1.1.5 # py36 only
-pandas==1.3.5 # py37 only
-pandas==1.4.1 # >=py38
-Pillow==8.4.0 # py36 only
-Pillow==9.0.1 # >=py37
-polytope==0.2.3
-PyGObject==3.36.0
-pyparsing==3.0.7
-python-apt==2.0.0+ubuntu0.20.4.7
-python-dateutil==2.8.2
-pytz==2021.3
-PyWavelets==1.1.1 # py36 only
-PyWavelets==1.3.0 # >=py37
-requests==2.22.0
-requests-unixsocket==0.2.0
-rwa-python==0.9.1
-scikit-image==0.17.2 # py36 only
-scikit-image==0.19.2 # >=py37
-scikit-learn==0.24.2 # py36 only
-scikit-learn==1.0.2 # >=py37
-scipy==1.5.4 # py36 only
-scipy==1.7.3 # py37 only
-scipy==1.8.0 # >=py38
-six==1.14.0
-stopit==1.1.2
-threadpoolctl==3.1.0
-tifffile==2020.9.3 # py36 only
-tifffile==2021.11.2 # py37 only
-tifffile==2022.2.9 # >=py38
-tqdm==4.63.0
-urllib3==1.25.8
-zipp==3.6.0 # py36 only
-```
-
-* tramway-hpc-230609-py3{8,9,[10](https://dl.pasteur.fr/fop/keDoKINW/tramway-hpc-230609-py310.sif),[11](https://dl.pasteur.fr/fop/znbYr11f/tramway-hpc-230609-py311.sif)}.sif
-
-  *tramway0.6.7* image with targets *hpc-minimal* and *animate*, and *scikit-learn* as an additional package.
-  Python is available as *python3.x*, with *x* any of *8*, *9*, *10*, *11* depending on the container file.
-  The run command admits option *-s*, passed to Python,
-  resulting in command (e.g.) `python3.x -s -m tramway $@`.
-  The included Python dependencies are the following:
-
-```
-certifi==2019.11.28
-chardet==3.0.4
-contourpy==1.0.7
-cvxopt==1.3.1
-cycler==0.11.0
-dbus-python==1.2.16
-fonttools==4.40.0
-h5py==3.8.0
-idna==2.8
-imageio==2.31.1
-importlib-resources==5.12.0 # py<310
-joblib==1.2.0
-kiwisolver==1.4.4
-lazy_loader==0.2
-matplotlib==3.7.1
-networkx==3.1
-numpy==1.24.3
-opencv-python==4.7.0.72
-packaging==23.1
-pandas==2.0.2
-Pillow==9.5.0
-polytope==0.2.3
-PyGObject==3.36.0
-pyparsing==3.0.9
-python-apt==2.0.1+ubuntu0.20.4.1
-python-dateutil==2.8.2
-pytz==2023.3
-PyWavelets==1.4.1
-requests==2.22.0
-requests-unixsocket==0.2.0
-rwa-python==0.9.3
-scikit-image==0.20.0
-scikit-learn==1.2.2
-scipy==1.9.1 # py<310
-scipy==1.10.1 # py>39
-six==1.16.0
-stopit==1.1.2
-threadpoolctl==3.1.0
-tifffile==2023.4.12
-tqdm==4.65.0
-tzdata==2023.3
-urllib3==1.25.8
-zipp==3.15.0 # py<310
-```
-
-* tramway-hpc-240423-py3{[8](https://dl.pasteur.fr/fop/B3LCHpTL/tramway-hpc-240423-py38.sif),[9](https://dl.pasteur.fr/fop/crbAgtuu/tramway-hpc-240423-py39.sif),[10](https://dl.pasteur.fr/fop/zZ2nrnKP/tramway-hpc-240423-py310.sif),[11](https://dl.pasteur.fr/fop/7F8PPD7j/tramway-hpc-240423-py311.sif),[12](https://dl.pasteur.fr/fop/lRWEB8oR/tramway-hpc-240423-py312.sif)}.sif
-
-  *tramway0.6.8* image with targets *hpc-minimal* and *animate*, and *scikit-learn* as an additional package.
-  Python is available as *python3.x*, with *x* any of *8*, *9*, *10*, *11*, *12* depending on the container file.
-  The run command admits option *-s*, passed to Python,
-  resulting in command (e.g.) `python3.x -s -m tramway $@`.
-  The included Python dependencies are the following:
-
-```
-certifi==2019.11.28
-chardet==3.0.4
-contourpy==1.1.1 # py38 only
-contourpy==1.2.1 # py>38
-cvxopt==1.3.2
-cycler==0.12.1
-dbus-python==1.2.16
-fonttools==4.51.0
-h5py==3.11.0
-idna==2.8
-imageio==2.34.1
-importlib-resources==6.4.0 # py<312
-joblib==1.4.0
-kiwisolver==1.4.5
-lazy_loader==0.4
-matplotlib==3.7.5 # py38 only
-matplotlib==3.8.4 # py>38
-networkx==3.1 # py38 only
-networkx==3.2.1 # py39 only
-networkx==3.3 # py>39
-numpy==1.24.4 # py38 only
-numpy==1.26.4 # py>38
-opencv-python==4.9.0.80
-packaging==24.0
-pandas==2.0.3 # py38 only
-pandas==2.2.2 # py>38
-pillow==10.3.0
-polytope==0.2.5
-PyGObject==3.36.0
-pyparsing==3.1.2
-python-apt==2.0.1+ubuntu0.20.4.1
-python-dateutil==2.9.0.post0
-pytz==2024.1
-PyWavelets==1.4.1
-requests==2.22.0
-requests-unixsocket==0.2.0
-rwa-python==0.9.3
-scikit-image==0.21.0 # py38 only
-scikit-image==0.22.0 # py39 only
-scikit-image==0.23.2 # py>39
-scikit-learn==1.3.2 # py38 only
-scikit-learn==1.4.2 # py>38
-scipy==1.10.1 # py38 only
-scipy==1.13.0 # py>38
-setuptools==69.5.1 # py312 only
-six==1.16.0
-stopit==1.1.2
-threadpoolctl==3.4.0
-tifffile==2023.7.10 # py38 only
-tifffile==2024.4.18 # py>38
-tqdm==4.66.2
-tzdata==2024.1
-urllib3==1.25.8
-wheel==0.43.0 # py312 only
-zipp==3.18.1 # py<310 only
-```
-
-* tramway-hpc-250124-py3{[8](https://dl.pasteur.fr/fop/xVjMGhTa/tramway-hpc-2501024-py38.sif),[9](https://dl.pasteur.fr/fop/AyK3JTC0/tramway-hpc-2501024-py39.sif),[10](https://dl.pasteur.fr/fop/jEmrwWhp/tramway-hpc-2501024-py310.sif),[11](https://dl.pasteur.fr/fop/QmL7TE6w/tramway-hpc-2501024-py311.sif),[12](https://dl.pasteur.fr/fop/elytCrRB/tramway-hpc-2501024-py312.sif),[13](https://dl.pasteur.fr/fop/hSeIMslv/tramway-hpc-2501024-py313.sif)}.sif
+* tramway-hpc-250124-py3{[8](https://dl.pasteur.fr/fop/fnQY9aI4/tramway-hpc-250124-py38.sif),[9](https://dl.pasteur.fr/fop/bqIvcQOu/tramway-hpc-250124-py39.sif),[10](https://dl.pasteur.fr/fop/CGSBWArs/tramway-hpc-250124-py310.sif),[11](https://dl.pasteur.fr/fop/AFE8uuyA/tramway-hpc-250124-py311.sif),[12](https://dl.pasteur.fr/fop/4KuTx4gX/tramway-hpc-250124-py312.sif),[13](https://dl.pasteur.fr/fop/5XftLW2h/tramway-hpc-250124-py313.sif)}.sif
 
   *tramway0.6.9* image with targets *hpc-minimal* and *animate*, and *scikit-learn* as an additional package.
   Python is available as *python3.x*, with *x* any of *8*, *9*, *10*, *11*, *12*, *13* depending on the container file.
@@ -266,3 +76,103 @@ zipp==3.20.2 # py == 3.8
 zipp==3.21.0 # py == 3.9
 ```
 
+* tramway-hpc-260217-py3{[9](https://dl.pasteur.fr/fop/vk2BlcFV/tramway-hpc-260217-py39.sif),[10](https://dl.pasteur.fr/fop/vt7BJqDk/tramway-hpc-260217-py310.sif),[11](https://dl.pasteur.fr/fop/yZNQ1Wn4/tramway-hpc-260217-py311.sif),[12](https://dl.pasteur.fr/fop/X4Pqd1Bk/tramway-hpc-260217-py312.sif),[13](https://dl.pasteur.fr/fop/FBEYEP0E/tramway-hpc-260217-py313.sif),[14](https://dl.pasteur.fr/fop/NbJmUfmQ/tramway-hpc-260217-py314.sif)}.sif
+
+  *tramway0.7* image with targets *hpc-minimal* and *animate*, and *scikit-learn* as an additional package.
+  Python is available as *python3.x*, with *x* any of *9*, *10*, *11*, *12*, *13*, *14* depending on the container file.
+  The run command admits option *-s*, passed to Python,
+  resulting in command (e.g.) `python3.x -s -m tramway $@`.
+  The included Python dependencies are the following:
+
+```
+blinker==1.4  # py >= 3.10
+certifi==2019.11.28  # py == 3.9
+chardet==3.0.4  # py == 3.9
+contourpy==1.3.0  # py == 3.9
+contourpy==1.3.2  # py == 3.10
+contourpy==1.3.3  # py >= 3.11
+cryptography==3.4.8  # py >= 3.10
+cvxopt==1.3.3
+cycler==0.12.1
+dbus-python==1.2.16  # py == 3.9
+dbus-python==1.2.18  # py >= 3.10
+dill==0.4.1
+distro==1.7.0  # py >= 3.10
+exceptiongroup==1.3.1  # py == 3.9
+fonttools==4.60.2  # py == 3.9
+fonttools==4.61.1  # py >= 3.10
+h5py==3.14.0  # py == 3.9
+h5py==3.15.1  # py >= 3.10
+httplib2==0.20.2  # py >=3.10
+idna==2.8  # py == 3.9
+ImageIO==2.37.2
+importlib_resources==6.5.2  # py == 3.9
+importlib-metadata==4.6.4  # py >= 3.10
+iniconfig==2.1.0  # py == 3.9
+jeepney==0.7.1  # py >= 3.10
+joblib==1.5.3
+keyring==23.5.0  # py >= 3.10
+kiwisolver==1.4.7  # py == 3.9
+kiwisolver==1.4.9  # py >= 3.10
+launchpadlib==1.10.16  # py >= 3.10
+lazr.restfulclient==0.14.4  # py >= 3.10
+lazr.uri==1.0.6  # py >= 3.10
+lazy_loader==0.4
+matplotlib==3.9.4  # py == 3.9
+matplotlib==3.10.8  # py >= 3.10
+more-itertools==8.10.0  # py >= 3.10
+multiprocess==0.70.19
+networkx==3.2.1  # py == 3.9
+networkx==3.4.2  # py == 3.10
+networkx==3.6.1  # py >= 3.11
+numpy==2.0.2  # py == 3.9
+numpy==2.2.6  # py == 3.10
+numpy==2.4.2  # py >= 3.11
+oauthlib==3.2.0  # py >= 3.10
+opencv-python==4.13.0.92
+packaging==26.0
+pandas==2.3.3
+pillow==11.3.0  # py == 3.9
+pillow==12.1.1  # py >= 3.10
+pluggy==1.6.0  # py == 3.9
+polytope==0.2.5
+Pygments==2.19.2  # py == 3.9
+PyGObject==3.36.0  # py == 3.9
+PyGObject==3.42.1  # py >= 3.10
+PyJWT==2.3.0  # py >= 3.10
+pyparsing==3.3.2
+pytest==8.4.2  # py == 3.9
+python-apt==2.0.1+ubuntu0.20.4.1  # py == 3.9
+python-apt==2.4.0+ubuntu4.1  # py >= 3.10
+python-dateutil==2.9.0.post0
+pytz==2025.2
+requests==2.22.0  # py == 3.9
+requests-unixsocket==0.2.0  # py == 3.9
+rwa-python==0.10
+scikit-image==0.24.0  # py == 3.9
+scikit-image==0.25.2  # py == 3.10
+scikit-image==0.26.0  # py >= 3.11
+scikit-learn==1.6.1  # py == 3.9
+scikit-learn==1.7.2  # py == 3.10
+scikit-learn==1.8.0  # py >= 3.11
+scipy==1.13.1  # py == 3.9
+scipy==1.15.3  # py == 3.10
+scipy==1.17.0  # py >= 3.11
+SecretStorage==3.3.1  # py >= 3.10
+setuptools==82.0.0  # py >= 3.12
+six==1.17.0  # py == 3.9
+six==1.16.0  # py >= 3.10
+stopit==1.1.2
+threadpoolctl==3.6.0
+tifffile==2024.8.30  # py == 3.9
+tifffile==2025.5.10  # py == 3.10
+tifffile==2026.2.16  # py >= 3.11
+tomli==2.4.0  # py == 3.9
+tqdm==4.67.3
+typing_extensions==4.15.0  # py == 3.9
+tzdata==2025.3
+urllib3==1.25.8  # py == 3.9
+wadllib==1.3.6  # py >= 3.10
+zipp==3.23.0  # py == 3.9
+zipp==1.0.0  # py >= 3.10
+```

containers/container-pip-freeze.sh

@@ -1,15 +1,15 @@
 #!/bin/bash
 
 if [ -z $1 ]; then
-  echo "usage: $0 CONTAINER_FILE [PATH_TO_SINGULARITY]"
+  echo "usage: $0 CONTAINER_FILE [PATH_TO_APPTAINER]" >&2
   exit 1
 fi
 
 CONTAINER=$1
 shift
 
 if [ -z $1 ]; then
-  SINGULARITY="singularity exec"
+  SINGULARITY="apptainer exec"
 else
   SINGULARITY="$1 exec"
 fi

containers/detect_python.sh

@@ -1,6 +1,6 @@
 #!/bin/bash
 
-for ((minor=13;6<=minor;minor--)); do
+for ((minor=14;6<=minor;minor--)); do
 py=python3.$minor
 if command -v $py &>/dev/null; then
 if $py -m pip freeze | grep tramway &>/dev/null; then

containers/test-maestro.sh

@@ -0,0 +1,28 @@
+#!/bin/sh
+
+## to get and run the present script, on Maestro:
+# cd $MYSCRATCH
+# rm -rf TRamWAy; git clone --branch dev https://github.com/DecBayComp/TRamWAy && cd $_
+# tests/test-maestro.sh
+
+set -e
+
+version=260217
+pyminor=9
+container="containers/tramway-hpc-$version-py3$pyminor.sif"
+testdata=tests/test_analyzer_200803
+slurmopts="-p dbc -q dbc"
+
+[ "`pwd`" = "$MYSCRATCH/TRamWAy" ] || exit 1
+
+# TODO make the data available online again
+[ -d "$testdata" ] || cp -r ~/Projects/Tramway/TRamWAy/"$testdata" tests/
+
+module load apptainer
+rm -f $container; srun $slurmopts apptainer build $container "containers/tramway-hpc-py3$pyminor"
+
+mkdir -p containers/tmp
+srun $slurmopts apptainer exec \
+  --bind "$testdata:/root/TRamWAy/$testdata" \
+  --cwd=/root/TRamWAy --overlay=containers/tmp $container \
+  "python3.$pyminor" -m pytest --ignore=tests/test_analyzer_pipeline.py