fixes for numpy 2

.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"]
+        python-version: ["3.8", "3.9", "3.10", "3.11", "3.12", "3.13"]
       fail-fast: true
 
     steps:
@@ -46,11 +46,22 @@ jobs:
         rm "${{ github.workspace }}\hdf\HDF5-1.10.7-win64.msi"
         rm "${{ github.workspace }}\msi.log"
         }
-    - name: Install HDF5 (macOS)
+    - name: Install HDF5 and CVXOPT (macOS)
       if: ${{ runner.os == 'macOS' }}
+      env:
+        # see https://github.com/cvxopt/cvxopt/blob/master/.github/workflows/macos_build.yml
+        CVXOPT_SUITESPARSE_LIB_DIR: /opt/homebrew/lib
+        CVXOPT_SUITESPARSE_INC_DIR: /opt/homebrew/include/suitesparse
+        CVXOPT_BLAS_LIB_DIR: /opt/homebrew/opt/openblas/lib
+        CVXOPT_BLAS_LIB: openblas
+        CVXOPT_LAPACK_LIB: openblas
+        LDFLAGS: -L/opt/homebrew/opt/openblas/lib
+        CPPFLAGS: -I/opt/homebrew/opt/openblas/include
       run: |
-        brew update
-        brew install hdf5
+        brew --prefix
+        brew install hdf5 openblas gsl fftw suite-sparse glpk
+        python -m pip install --upgrade pip
+        python -m pip install cvxopt
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip

README.md

@@ -9,7 +9,7 @@ An attempt to rewrite the project documentation is available as a [separate proj
 
 ## Installation
 
-You will need Python >= 3.6.
+You will need Python >= 3.8.
 
 ### Windows users
 
@@ -26,10 +26,10 @@ pip install tramway
 Note that the HDF5 library can usually be installed using any OS' package manager.
 Only Windows users may have to [manually download and install the HDF5 library](https://tramway.readthedocs.io/en/latest/libhdf5.html), if they do not wish to use Conda instead of pip.
 
-Several installation targets are available, including `full`, that install optional dependencies:
+Several installation targets are available; they install optional dependencies. For example (recommended):
 
 ```
-pip install tramway[full]
+pip install tramway[roi,animate]
 ```
 
 Most of the functionalities and code examples described in the documentation will run without optional dependencies.

containers/available_images.md

@@ -189,3 +189,80 @@ 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
+
+  *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.
+  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 # py == 3.8
+contourpy==1.3.0 # py == 3.9
+contourpy==1.3.1 # py >= 3.10
+cvxopt==1.3.2
+cycler==0.12.1
+dbus-python==1.2.16
+fonttools==4.55.5
+h5py==3.11.0 # py == 3.8
+h5py==3.12.1 # py >= 3.9
+idna==2.8
+imageio==2.35.1 # py == 3.8
+imageio==2.37.0 # py >= 3.9
+importlib_resources==6.4.5 # py == 3.8
+importlib_resources==6.5.2 # py == 3.9
+joblib==1.4.2
+kiwisolver==1.4.7 # py <= 3.9
+kiwisolver==1.4.8 # py >= 3.10
+lazy_loader==0.4
+matplotlib==3.7.5 # py == 3.8
+matplotlib==3.9.4 # py == 3.9
+matplotlib==3.10.0 # py >= 3.10
+networkx==3.1 # py == 3.8
+networkx==3.2.1 # py == 3.9
+networkx==3.4.2 # py >= 3.10
+numpy==1.24.4 # py == 3.8
+numpy==2.0.2 # py == 3.9
+numpy==2.2.2 # py >= 3.10
+opencv-python==4.11.0.86
+packaging==24.2
+pandas==2.0.3 # py == 3.8
+pandas==2.2.3 # py >= 3.9
+pillow==10.4.0 # py == 3.8
+pillow==11.1.0 # py >= 3.9
+polytope==0.2.5
+PyGObject==3.36.0
+pyparsing==3.1.4 # py == 3.8
+pyparsing==3.2.1 # py >= 3.9
+python-apt==2.0.1+ubuntu0.20.4.1
+python-dateutil==2.9.0.post0
+pytz==2024.2
+requests==2.22.0
+requests-unixsocket==0.2.0
+rwa-python==0.9.5
+scikit-image==0.21.0 # py == 3.8
+scikit-image==0.24.0 # py == 3.9
+scikit-image==0.25.0 # py >= 3.10
+scikit-learn==1.3.2 # py == 3.8
+scikit-learn==1.6.1 # py >= 3.9
+scipy==1.10.1 # py == 3.8
+scipy==1.13.1 # py == 3.9
+scipy==1.15.1 # py >= 3.10
+setuptools==75.8.0 # py >= 3.11
+six==1.17.0
+stopit==1.1.2
+threadpoolctl==3.5.0
+tifffile==2023.7.10 # py == 3.8
+tifffile==2024.8.30 # py == 3.9
+tifffile==2025.1.10 # py >= 3.10
+tqdm==4.67.1
+tzdata==2025.1
+urllib3==1.25.8
+zipp==3.20.2 # py == 3.8
+zipp==3.21.0 # py == 3.9
+```
+

containers/container-pip-freeze.sh

@@ -9,13 +9,17 @@ CONTAINER=$1
 shift
 
 if [ -z $1 ]; then
-  SINGULARITY="singularity"
+  SINGULARITY="singularity exec"
 else
-  SINGULARITY=$1
+  SINGULARITY="$1 exec"
 fi
 
-PYTHON=$($SINGULARITY exec "$CONTAINER" ./detect_python.sh)
+if [ -d /pasteur ]; then
+  SINGULARITY="$SINGULARITY -B /pasteur"
+fi
+
+PYTHON=$($SINGULARITY "$CONTAINER" ./detect_python.sh)
 echo $PYTHON
 
-$SINGULARITY exec "$CONTAINER" $PYTHON -s -m pip freeze
+$SINGULARITY "$CONTAINER" $PYTHON -s -m pip freeze
 

containers/detect_python.sh

@@ -1,22 +1,21 @@
 #!/bin/bash
 
-for ((minor=12;6<=minor;minor--)); do
+for ((minor=13;6<=minor;minor--)); do
 py=python3.$minor
-if [ -x "$(command -v $py)" ]; then
-if [ -z "$($py -m pip show -q tramway 2>&1)" ]; then
+if command -v $py &>/dev/null; then
+if $py -m pip freeze | grep tramway &>/dev/null; then
 echo $py
 exit 0
 fi
 fi
 done
 
 py=python2.7
-if [ -x "$(command -v $py)" ]; then
+if command -v $py &>/dev/null; then
 if [ -z "$($py -m pip show -q tramway 2>&1)" ]; then
 echo $py
 exit 0
 fi
 fi
 
 exit 1
-

containers/tramway-hpc-py313

@@ -0,0 +1,74 @@
+Bootstrap: docker
+From: ubuntu:focal
+
+%help
+TRamWAy is available in the python3.13 environment:
+    python3.13 -m tramway
+The container OS is Ubuntu Focal Fossa.
+
+%setup
+
+    #echo "fr_FR.UTF-8 UTF-8" > ${SINGULARITY_ROOTFS}/etc/locale.gen
+    echo "en_GB.UTF-8 UTF-8" > ${SINGULARITY_ROOTFS}/etc/locale.gen
+    if ! [ -f ${SINGULARITY_ROOTFS}/root/get-pip.py ]; then
+        wget -P ${SINGULARITY_ROOTFS}/root/ -- https://bootstrap.pypa.io/get-pip.py
+    fi
+
+    # TRamWAy can be installed in any of the following 3 ways:
+    # 1. using `pip install tramway` (stable release)
+    # 2. using `git clone`+`pip install .` (git version, default)
+    # 3. copying your own copy of TRamWAy into the container (local version)
+
+    # (3.) test local changes that have not been committed yet:
+    LOCAL=/path/to/local/TRamWAy
+    if [ -d $LOCAL ]; then
+       CONTAINED=${SINGULARITY_ROOTFS}/root/TRamWAy
+       mkdir -p ${CONTAINED}
+       cp -u  -t ${CONTAINED}/ ${LOCAL}/setup.py ${LOCAL}/requirements.txt ${LOCAL}/README.md
+       cp -ru -t ${CONTAINED}/ ${LOCAL}/tramway ${LOCAL}/scripts
+    fi
+
+%post
+
+    ln -sf /usr/share/zoneinfo/Europe/Paris /etc/localtime
+    apt-get update -y
+    apt-get install -y --no-install-recommends locales
+    locale-gen
+    apt-get install -y --no-install-recommends libhdf5-103 ffmpeg \
+        build-essential git software-properties-common libopenblas0 glpk-utils
+
+    # Python 3.13
+    add-apt-repository -y ppa:deadsnakes/ppa
+    apt-get update -y
+    apt-get install -y --no-install-recommends python3.13 python3.13-venv
+    rm -rf /var/lib/apt/lists/*
+    python3.13 /root/get-pip.py
+    export LC_ALL=C
+    #pip3.13 install --upgrade pip
+    pip3.13 uninstall -qy tramway || true
+
+    # (2.) and (3.)
+    cd /root
+    if ! [ -d TRamWAy ]; then
+        git clone https://github.com/DecBayComp/TRamWAy -b dev --single-branch --depth 1 --no-tags
+    fi
+    cd TRamWAy
+    pip3.13 install .[hpc-minimal,animate]
+
+    # (1.)
+    #pip3.13 install tramway[hpc-minimal,animate]
+
+    pip3.13 install scikit-learn
+
+    mkdir -p /pasteur
+
+%runscript
+
+    cmd="tramway"
+    python="python3.13"
+    if [ -n "$1" -a "$1" = "-s" ]; then
+       cmd="${python} -s -m tramway"
+       shift
+    fi
+    exec $cmd $@
+

doc/conf.py

@@ -21,7 +21,7 @@
 sys.path.insert(0, os.path.abspath('..'))
 
 
-# mocking out rwa (and hopefully h5py) for readthedocs to successfully compile the project and 
+# mocking out rwa (and hopefully h5py) for readthedocs to successfully compile the project and
 # generate the doc
 mock_ok = True
 try:
@@ -75,7 +75,7 @@ def __getattr__(cls, name):
 
 # General information about the project.
 project = u'TRamWAy'
-copyright = u'2017-2021, Institut Pasteur'
+copyright = u'2017-2025, Institut Pasteur'
 author = u'François Laurent'
 
 # The version info for the project you're documenting, acts as replacement for
@@ -85,7 +85,7 @@ def __getattr__(cls, name):
 # The short X.Y version.
 version = u'0.6'
 # The full version, including alpha/beta/rc tags.
-release = u'0.6.3'
+release = u'0.6.9'
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.

doc/installation.rst

@@ -3,7 +3,7 @@
 Installation
 ============
 
-You will need Python >= 3.6.
+You will need Python >= 3.8.
 
 Windows users
 -------------
@@ -22,9 +22,9 @@ From PyPI
 Note that the HDF5 library can usually be installed using any OS' package manager.
 Only Windows users may have to :ref:`manually download and install the HDF5 library <hdf5_install>`, if they do not wish to use Conda instead of pip.
 
-Several installation targets are available, including ``full``, that install optional dependencies::
+Several installation targets are available; they install optional dependencies. For example (recommended)::
 
-        pip install tramway[full]
+        pip install tramway[roi,animate]
 
 Most of the functionalities and code examples described in this documentation will run without the optional dependencies this target installs in addition to the required dependencies.
 It is safe to first install |tramway| with minimal requirements and then ``pip install`` the missing dependencies as you hit ``ImportError`` while using |tramway|.
@@ -47,7 +47,7 @@ Initial install::
 
 	git clone https://github.com/DecBayComp/TRamWAy
 	cd TRamWAy
-	pip install -e .
+	pip install -e .[roi,animate]
 
 Can be updated with ``git pull`` run in the local repository.
 
@@ -63,9 +63,3 @@ The generated documentation will be available at ``_build/html/index.html`` from
 
 Building the documentation requires Sphinx.
 
-
-OS and version specific notes
------------------------------
-
-Some modules require *Python>=3.7*.
-These are *bayes_factor* for force “detection” based on Bayesian statistics, *snr* that extracts signal-to-noise ratios required by the *bayes_factor* module, and *d.conj_prior* which estimates the diffusion similarly to *ddrift* with no regularization but with additional confidence intervals.

notebooks/RWAnalyzer tour.ipynb

@@ -102789,23 +102789,37 @@
      "output_type": "stream",
      "text": [
       "Traceback (most recent call last):\n",
-      "  File \"<stdin>\", line 2, in <module>\n",
-      "ModuleNotFoundError: No module named 'tramway'\n"
+      "  File \"...\", line 11, in <module>\n",
+      "    a.spt_data     = spt_data.from_dataframe(df)\n",
+      "    ^^^^^^^^^^\n",
+      "  File \".../tramway/analyzer/__init__.py\", line 577, in __setattr__\n",
+      "    warnings.warn(\n",
+      "    ~~~~~~~~~~~~~^\n",
+      "        \"attribute '{}' is already initialized; side effects may occur\".format(\n",
+      "        ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n",
+      "    ...<2 lines>...\n",
+      "        SideEffectWarning,\n",
+      "        ^^^^^^^^^^^^^^^^^^\n",
+      "    )\n",
+      "    ^\n",
+      "tramway.core.exceptions.SideEffectWarning: attribute 'spt_data' is already initialized; side effects may occur"
      ]
     }
    ],
    "source": [
-    "%%script python3 --no-raise-error\n",
-    "\n",
     "from tramway.analyzer import *\n",
+    "import traceback\n",
     "\n",
     "a              = RWAnalyzer()\n",
     "a.spt_data     = spt_data.from_ascii_file('data-examples/demo1.txt')\n",
     "\n",
     "df             = a.spt_data.dataframe\n",
     "\n",
-    "# not allowed!\n",
-    "a.spt_data     = spt_data.from_dataframe(df)"
+    "try:\n",
+    "    # not allowed!\n",
+    "    a.spt_data = spt_data.from_dataframe(df)\n",
+    "except:\n",
+    "    traceback.print_exc()"
    ]
   },
   {

pyproject.toml

@@ -1,16 +1,16 @@
 [tool.poetry]
 name = "tramway"
-version = "0.6.8"
+version = "0.6.9"
 description = ""
 authors = ["François Laurent <francois.laurent@pasteur.fr>"]
 license = "CECILL-2.1"
 readme = "README.md"
 
 [tool.poetry.dependencies]
-python = ">=3.8,<3.13"
+python = ">=3.8,<4"
 setuptools = ">=69.1.0,<99"
 six = ">=1.16,<2"
-numpy = ">=1.24.3,<2"
+numpy = ">=1.24.3,<3"
 scipy = ">=1.9.1,<2"
 pandas = ">=2.0.2,<3"
 matplotlib = ">=3.7.1,<4"