numpy deprecations

.github/workflows/ci.yml

@@ -20,7 +20,7 @@ jobs:
           - ubuntu-latest
           - macos-latest
           - windows-latest
-        python-version: ["3.8", "3.9", "3.10", "3.11"]
+        python-version: ["3.8", "3.9", "3.10", "3.11", "3.12", "3.13"]
       fail-fast: true
 
     steps:

containers/rwa-jammy

@@ -11,20 +11,13 @@ RWA-python is available in multiple Python environments:
     python3.9
     python3.10 (alias python3)
     python3.11
+    python3.12
+    python3.13
 The container OS is Ubuntu Jammy.
 
 %setup
 
     echo "fr_FR.UTF-8 UTF-8" > ${SINGULARITY_ROOTFS}/etc/locale.gen
-    for OLD in 2.7 3.5 3.6; do
-        if ! [ -f ${SINGULARITY_ROOTFS}/root/get-pip$OLD.py ]; then
-            wget -P ${SINGULARITY_ROOTFS}/root/ -- https://bootstrap.pypa.io/pip/$OLD/get-pip.py
-            mv ${SINGULARITY_ROOTFS}/root/get-pip.py ${SINGULARITY_ROOTFS}/root/get-pip$OLD.py
-        fi
-    done
-    if ! [ -f ${SINGULARITY_ROOTFS}/root/get-pip.py ]; then
-        wget -P ${SINGULARITY_ROOTFS}/root/ -- https://bootstrap.pypa.io/get-pip.py
-    fi
 
     # test local changes that have not been committed yet;
     # to be run from any subdirectory in the RWA-python directory, e.g. containers, tests...
@@ -45,26 +38,52 @@ The container OS is Ubuntu Jammy.
     locale-gen
 
     apt-get install -y --no-install-recommends libhdf5-openmpi-dev \
-        build-essential git software-properties-common pkg-config
+        build-essential git software-properties-common pkg-config \
+        gpg-agent wget curl libssl-dev zlib1g-dev libbz2-dev \
+        libreadline-dev libsqlite3-dev libncursesw5-dev xz-utils \
+        tk-dev libxml2-dev libxmlsec1-dev libffi-dev liblzma-dev
+
+    curl -fsSL https://pyenv.run | bash #&>/dev/null
+    export PYENV_ROOT=/root/.pyenv
+    for VER in 3.5 3.6; do
+      /root/.pyenv/bin/pyenv install $VER
+      cat <<EOF >/root/python$VER
+#!/bin/bash
+PYTHON=\$(ls /root/.pyenv/versions/$VER*/bin/python)
+eval "\$PYTHON \$@"
+EOF
+      chmod a+x /root/python$VER
+    done
 
     add-apt-repository -y ppa:deadsnakes/ppa
     apt-get update  -y
     apt-get install -y --no-install-recommends \
         python2.7 python2.7-dev \
-        python3.5 python3.5-dev \
-        python3.6 python3.6-dev python3.6-distutils \
         python3.7 python3.7-dev python3.7-distutils \
         python3.8 python3.8-dev python3.8-venv \
-        python3.9 python3.9-dev \
-        python3.10 python3.10-dev python3.10-venv \
-        python3.11 python3.11-dev python3.11-venv
+        python3.9 python3.9-dev python3.9-distutils \
+        python3.10-dev python3.10-venv \
+        python3.11 python3.11-dev python3.11-venv \
+        python3.12 python3.12-dev python3.12-venv \
+        python3.13 python3.13-dev python3.13-venv
+        #python3.5 python3.5-dev \
+        #python3.6 python3.6-dev python3.6-distutils \
 
     # python 3.8 and 3.10 won't work with get-pip.py without package venv
 
-    for OLD in 2.7 3.5 3.6; do
-        python$OLD /root/get-pip$OLD.py
+    for OLD in 2.7 3.7; do
+        if ! [ -f /root/get-pip$OLD.py ]; then
+            wget -P /root/ -- https://bootstrap.pypa.io/pip/$OLD/get-pip.py
+            mv /root/get-pip.py ${SINGULARITY_ROOTFS}/root/get-pip$OLD.py
+        fi
+        if command -v python$OLD &>/dev/null; then
+          python$OLD /root/get-pip$OLD.py
+        fi
     done
-    for VER in 3.7 3.8 3.9 3.10 3.11; do
+    if ! [ -f /root/get-pip.py ]; then
+        wget -P /root/ -- https://bootstrap.pypa.io/get-pip.py
+    fi
+    for VER in 3.8 3.9 3.10 3.11 3.12 3.13; do
         python$VER /root/get-pip.py
     done
 
@@ -85,15 +104,20 @@ The container OS is Ubuntu Jammy.
     cd $cur
 
     export LC_ALL=C
-    for version in 2.7 3.5 3.6 3.7 3.8 3.9 3.10 3.11; do
+    for version in 2.7 3.6 3.7 3.8 3.9 3.10 3.11 3.12 3.13; do
         python="python${version}"
+        if [ "$version" = "3.5" -o "$version" = "3.6" ]; then
+          python="/root/$python"
+        elif ! command -v $python $>/dev/null; then
+          continue
+        fi
         pip="$python -m pip"
         pip_install="$pip install -U"
-        if [ "$version" = "3.6" -o "$version" = "3.7" -o "$version" = "3.8" -o "$version" = "3.9" -o "$version" = "3.10" -o "$version" = "3.11" ]; then
+        if [ "$version" = "3.6" -o "$version" = "3.7" -o "$version" = "3.8" -o "$version" = "3.9" -o "$version" = "3.10" -o "$version" = "3.11" -o "$version" = "3.12" -o "$version" = "3.13" ]; then
             $pip_install --force-reinstall setuptools
             $pip_install pytest
         fi
-        if [ "$version" = "3.8" -o "$version" = "3.9" -o "$version" = "3.10" -o "$version" = "3.11" ]; then
+        if [ "$version" = "3.8" -o "$version" = "3.9" -o "$version" = "3.10" -o "$version" = "3.11" -o "$version" = "3.12" -o "$version" = "3.13" ]; then
             $pip_install mpi4py
             #$pip_install --no-binary=h5py h5py
         fi
@@ -112,16 +136,16 @@ The container OS is Ubuntu Jammy.
 
 %runscript
 
-    python="python2.7"
+    python="python3"
     if [ -n "$1" ]; then
         if [ "$1" = "-2" -o "$1" = "-27" ]; then
-            # nothing to do
+            python="python2.7"
             shift
-        elif [ "$1" = "-3" -o "$1" = "-35" ]; then
-            python="python3.5"
+        elif [ "$1" = "-35" ]; then
+            python="/root/python3.5"
             shift
         elif [ "$1" = "-36" ]; then
-            python="python3.6"
+            python="/root/python3.6"
             shift
         elif [ "$1" = "-37" ]; then
             python="python3.7"
@@ -132,12 +156,18 @@ The container OS is Ubuntu Jammy.
         elif [ "$1" = "-39" ]; then
             python="python3.9"
             shift
-        elif [ "$1" = "-310" ]; then
+        elif [ "$1" = "-3" -o "$1" = "-310" ]; then
             python="python3.10"
             shift
         elif [ "$1" = "-311" ]; then
             python="python3.11"
             shift
+        elif [ "$1" = "-312" ]; then
+            python="python3.12"
+            shift
+        elif [ "$1" = "-313" ]; then
+            python="python3.13"
+            shift
         fi
     fi
     exec $python $@

pyproject.toml

@@ -1,13 +1,13 @@
 [tool.poetry]
 name = "rwa"
-version = "0.9.3"
+version = "0.9.4"
 description = "HDF5-based serialization library for Python datatypes"
 authors = ["François Laurent <francois.laurent@pasteur.fr>"]
 license = "Apache 2.0"
 readme = "README.md"
 
 [tool.poetry.dependencies]
-python = ">=3.8,<3.12"
+python = ">=3.8,<3.14"
 six = "^1.16.0"
 numpy = ">=0"
 scipy = ">=0"

rwa/generic.py

@@ -1110,13 +1110,26 @@ def namedtuple_storable(namedtuple, *args, **kwargs):
 except ImportError:
     numpy_storables = []
 else:
-    numpy_basic_types = (
+    numpy_basic_types = [
         numpy.bool_, numpy.int_, numpy.intc, numpy.intp,
         numpy.int8, numpy.int16, numpy.int32, numpy.int64,
         numpy.uint8, numpy.uint16, numpy.uint32, numpy.uint64,
-        numpy.float_, numpy.float16, numpy.float32, numpy.float64,
-        numpy.complex_, numpy.complex64, numpy.complex128,
-        )
+    ]
+    try:
+        numpy_basic_types.append(numpy.float_)
+    except AttributeError:
+        pass
+    numpy_basic_types.extend([
+        numpy.float16, numpy.float32, numpy.float64,
+    ])
+    try:
+        numpy_basic_types.append(numpy.complex_)
+    except AttributeError:
+        pass
+    numpy_basic_types.extend([
+        numpy.complex64, numpy.complex128,
+    ])
+    numpy_basic_types = tuple(numpy_basic_types)
 
     # numpy.dtype
     numpy_storables = [\

rwa/hdf5.py

@@ -28,7 +28,7 @@
 def to_binary(s):
     if isinstance(s, six.text_type):
         s = s.encode('utf-8')
-    return numpy.string_(s)
+    return numpy.bytes_(s)
 
 if six.PY3:
     def from_unicode(s): return s
@@ -45,7 +45,7 @@ def from_unicode(s):
     def from_bytes(b): return b
     to_str = str
 
-to_attr = numpy.string_
+to_attr = numpy.bytes_
 from_attr = from_bytes
 
 def native_poke(service, objname, obj, container, *args, **kargs):

setup.py

@@ -24,7 +24,7 @@
 
 setup(
     name = 'rwa-python',
-    version = '0.9.3',
+    version = '0.9.4',
     description = 'HDF5-based serialization library for Python datatypes',
     long_description = long_description,
     url = 'https://github.com/DecBayComp/RWA-python',
@@ -41,6 +41,8 @@
         'Programming Language :: Python :: 3.9',
         'Programming Language :: Python :: 3.10',
         'Programming Language :: Python :: 3.11',
+        'Programming Language :: Python :: 3.12',
+        'Programming Language :: Python :: 3.13',
     ],
     packages = ['rwa'],
     install_requires = install_requires,

tests/multi-py_compat.sh

@@ -1,7 +1,6 @@
 #!/bin/sh
 
-versions="3.5 3.6 3.7 3.8 3.9 3.10 3.11"
-#versions="3.6 2.7"
+versions="3.6 3.7 3.8 3.9 3.10 3.11 3.12 3.13"
 
 if [ "$(pwd | rev | cut -d/ -f1 | rev)" = "tests" ]; then
     container="$(pwd)/../containers/rwa-openmpi-dev.sif"
@@ -17,22 +16,23 @@ fi
 if ! [ -f "$container" -o -h "$container" ]; then
     cd ../containers # if this crashes, $0 is not run from the tests directory as it should be
     echo "No container found; building one..."
-    if [ -z "$(which apptainer)" ]; then
-    echo "singularity build --fakeroot rwa-openmpi-dev.sif rwa-focal"
-    singularity build --fakeroot rwa-openmpi-dev.sif rwa-focal || exit
-    else
+    if command -v apptainer &>/dev/null; then
     echo "apptainer build rwa-openmpi-dev.sif rwa-jammy"
     apptainer build rwa-openmpi-dev.sif rwa-jammy || exit
+    else
+    echo "singularity build --fakeroot rwa-openmpi-dev.sif rwa-focal"
+    singularity build --fakeroot rwa-openmpi-dev.sif rwa-focal || exit
     fi
     echo "======================================"
     echo "Container ready; starting the tests..."
     echo "======================================"
     cd ../tests
 fi
 
-hdf5_file=$(mktemp) || exit
-poke_script=$(mktemp) || exit
-peek_script=$(mktemp) || exit
+tmpdir=$(mktemp -d -p .) || exit
+hdf5_file=$(mktemp -p $tmpdir) || exit
+poke_script=$(mktemp -p $tmpdir) || exit
+peek_script=$(mktemp -p $tmpdir) || exit
 
 trap "rm -f -- '$hdf_file' '$poke_script' '$peek_script'" EXIT
 
@@ -90,7 +90,7 @@ done
 done
 
 
-rm -f -- '$hdf_file' '$poke_script' '$peek_script'
+rm -rf -- '$tmpdir'
 trap - EXIT
 exit
 

tests/test_native_hdf5.py

@@ -44,7 +44,7 @@ def test_base_types(self, tmpdir):
             for _type in store.store:
                 val = store.peek(_type)
                 # the assertion immediately below is redundant but helps debug when numpy hides its base types
-                assert not isinstance(val, (np.bool_, np.int_, np.float_))
+                assert not isinstance(val, (np.bool_, np.int_, np.float32, np.float64))
                 assert type(val) is type(value[_type])
         finally:
             store.close()