Merge branch 'main' into brendt/iso-tv-norm

.github/workflows/pytest_macos.yml

@@ -59,11 +59,13 @@ jobs:
           pip install pytest-split
           pip install -r requirements.txt
           pip install -r dev_requirements.txt
+          mamba install -c conda-forge svmbir>=0.3.3
           mamba install -c astra-toolbox astra-toolbox
           mamba install -c conda-forge pyyaml
           pip install --upgrade --force-reinstall scipy>=1.6.0  # Temporary fix for GLIBCXX_3.4.30 not found in conda forge version
+          pip install bm3d>=4.0.0
           pip install bm4d>=4.0.0
-          pip install "ray[tune]>=2.0.0"
+          pip install "ray[tune]>=2.5.0"
           pip install hyperopt
       # Install package to be tested
       - name: Install package to be tested

.github/workflows/pytest_ubuntu.yml

@@ -62,12 +62,13 @@ jobs:
           pip install pytest-split
           pip install -r requirements.txt
           pip install -r dev_requirements.txt
+          mamba install -c conda-forge svmbir>=0.3.3
           mamba install -c astra-toolbox astra-toolbox
           mamba install -c conda-forge pyyaml
           pip install --upgrade --force-reinstall scipy>=1.6.0  # Temporary fix for GLIBCXX_3.4.30 not found in conda forge version
           pip install bm3d>=4.0.0
           pip install bm4d>=4.2.2
-          pip install "ray[tune]>=2.0.0"
+          pip install "ray[tune]>=2.5.0"
           pip install hyperopt
       # Install package to be tested
       - name: Install package to be tested

CHANGES.rst

@@ -3,7 +3,14 @@ SCICO Release Notes
 ===================
 
 
-Version 0.0.5   (unreleased)
+Version 0.0.6   (unreleased)
+----------------------------
+
+• No significant changes.
+
+
+
+Version 0.0.5   (2023-12-18)
 ----------------------------
 
 • New functionals ``functional.AnisotropicTVNorm``,
@@ -18,7 +25,7 @@ Version 0.0.5   (unreleased)
 • Rename ``solver.ATADSolver`` to ``solver.MatrixATADSolver``.
 • Rename some ``__init__`` parameters of ``linop.DiagonalStack`` and
   ``linop.VerticalStack``.
-• Support ``jaxlib`` and ``jax`` versions 0.4.3 to 0.4.21.
+• Support ``jaxlib`` and ``jax`` versions 0.4.3 to 0.4.23.
 • Support ``flax`` versions up to 0.7.5.
 • Use ``orbax`` for checkpointing ``flax`` models.
 

conftest.py

@@ -27,8 +27,25 @@ def pytest_addoption(parser, pluginmanager):
     Level definitions:
       1  Critical tests only
       2  Skip tests that do have a significant impact on coverage
-      3  All tests
+      3  All standard tests
+      4  Run all tests, including those marked as slow to run
     """
     parser.addoption(
         "--level", action="store", default=3, type=int, help="Set test level to be run"
     )
+
+
+def pytest_configure(config):
+    """Add marker description."""
+    config.addinivalue_line("markers", "slow: mark test as slow to run")
+
+
+def pytest_collection_modifyitems(config, items):
+    """Skip slow tests depending on selected testing level."""
+    if config.getoption("--level") >= 4:
+        # don't skip tests at level 4 or higher
+        return
+    level_skip = pytest.mark.skip(reason="test not appropriate for selected level")
+    for item in items:
+        if "slow" in item.keywords:
+            item.add_marker(level_skip)

dev_requirements.txt

@@ -1,3 +1,4 @@
+-r requirements.txt
 pylint
 pytest>=7.3.0
 pytest-runner

docs/source/install.rst

@@ -54,26 +54,32 @@ GPU Support
 The instructions above install a CPU-only version of SCICO. To install
 a version with GPU support:
 
-1. Follow the CPU only instructions, above
+1. Follow the CPU-only instructions, above
 
 2. Install the version of jaxlib with GPU support, as described in the `JAX installation
-   instructions  <https://github.com/google/jax#installation>`_.
+   instructions  <https://jax.readthedocs.io/en/latest/installation.html>`_.
    In the simplest case, the appropriate command is
 
    ::
 
-      pip install --upgrade "jax[cuda]" -f https://storage.googleapis.com/jax-releases/jax_cuda_releases.html
+      pip install --upgrade "jax[cuda11]"
 
+   for CUDA 11, or
 
-   but it may be necessary to explicitly specify the ``jaxlib``
-   version if the most recent release is not yet supported by SCICO
-   (as specified in the ``requirements.txt`` file), or if using a
-   version of CUDA older than 11.4, or CuDNN older than 8.2, in which
-   case the command would be of the form ::
+   ::
+
+      pip install --upgrade "jax[cuda12]"
+
+   for CUDA 12, but it may be necessary to explicitly specify the
+   ``jaxlib`` version if the most recent release is not yet supported
+   by SCICO (as specified in the ``requirements.txt`` file), or if
+   using a version of CUDA older than 11.4, or CuDNN older than 8.2,
+   in which case the command would be of the form ::
 
       pip install --upgrade "jaxlib==0.4.2+cuda11.cudnn82" -f https://storage.googleapis.com/jax-releases/jax_cuda_releases.html
 
-   with appropriate substitution of ``jaxlib``, CUDA, and CuDNN version numbers.
+   with appropriate substitution of ``jaxlib``, CUDA, and CuDNN version
+   numbers.
 
 
 

examples/examples_requirements.txt

@@ -1,5 +1,8 @@
-astra-toolbox
+-r ../requirements.txt
+tifffile
 colour_demosaicing
+svmbir>=0.3.3
+astra-toolbox
 xdesign>=0.5.5
 ray[tune,train]>=2.5.0
 hyperopt

examples/notebooks_requirements.txt

@@ -1,7 +1,7 @@
+-r examples-requirements.txt
 nbformat
 nbconvert
 nb_conda_kernels
 psutil
 py2jn
 pypandoc
-ray[tune]

examples/scriptcheck.sh

@@ -97,7 +97,7 @@ for f in $SCRIPTPATH/scripts/*.py; do
     sed -E -e "$re1$re2$re3$re4$re5$re6$re7$re8" $f > $g
 
     # Run temporary script and print status message.
-    if output=$(timeout 60s python $g 2>&1); then
+    if output=$(timeout 180s python $g 2>&1); then
         printf "%s\n" succeeded
     else
         printf "%s\n" FAILED

misc/conda/make_conda_env.sh

@@ -25,13 +25,17 @@ REPOPATH=$(realpath $(dirname $0))
 USAGE=$(cat <<-EOF
 Usage: $SCRIPT [-h] [-y] [-g] [-p python_version] [-e env_name]
           [-h] Display usage information
+          [-v] Verbose operation
+          [-t] Display actions that would be taken but do nothing
           [-y] Do not ask for confirmation
           [-p python_version] Specify Python version (e.g. 3.9)
           [-e env_name] Specify conda environment name
 EOF
 )
 
 AGREE=no
+VERBOSE=no
+TEST=no
 PYVER="3.9"
 ENVNM=py$(echo $PYVER | sed -e 's/\.//g')
 
@@ -46,13 +50,13 @@ EOF
 )
 # Requirements that cannot be installed via conda (i.e. have to use pip)
 NOCONDA=$(cat <<-EOF
-flax bm3d bm4d faculty-sphinx-theme py2jn colour_demosaicing ray[tune]
+flax bm3d bm4d py2jn colour_demosaicing ray[tune,train]
 EOF
 )
 
 
 OPTIND=1
-while getopts ":hyp:e:" opt; do
+while getopts ":hvtyp:e:" opt; do
     case $opt in
 	p|e) if [ -z "$OPTARG" ] || [ "${OPTARG:0:1}" = "-" ] ; then
 		     echo "Error: option -$opt requires an argument" >&2
@@ -61,6 +65,8 @@ while getopts ":hyp:e:" opt; do
 		 fi
 		 ;;&
 	h) echo "$USAGE"; exit 0;;
+	t) VERBOSE=yes;TEST=yes;;
+	v) VERBOSE=yes;;
 	y) AGREE=yes;;
 	p) PYVER=$OPTARG;;
 	e) ENVNM=$OPTARG;;
@@ -125,31 +131,6 @@ JLVER=$($SED -n 's/^jaxlib>=.*<=\([0-9\.]*\).*/\1/p' \
 JXVER=$($SED -n 's/^jax>=.*<=\([0-9\.]*\).*/\1/p' \
 	     $REPOPATH/../../requirements.txt)
 
-CONDAHOME=$(conda info --base)
-ENVDIR=$CONDAHOME/envs/$ENVNM
-if [ -d "$ENVDIR" ]; then
-    echo "Error: environment $ENVNM already exists"
-    exit 9
-fi
-
-if [ "$AGREE" == "no" ]; then
-    RSTR="Confirm creation of conda environment $ENVNM with Python $PYVER"
-    RSTR="$RSTR [y/N] "
-    read -r -p "$RSTR" CNFRM
-    if [ "$CNFRM" != 'y' ] && [ "$CNFRM" != 'Y' ]; then
-	echo "Cancelling environment creation"
-	exit 10
-    fi
-else
-    echo "Creating conda environment $ENVNM with Python $PYVER"
-fi
-
-if [ "$AGREE" == "yes" ]; then
-    CONDA_FLAGS="-y"
-else
-    CONDA_FLAGS=""
-fi
-
 # Construct merged list of all requirements
 if [ "$OS" == "Darwin" ]; then
     ALLREQUIRE=$(/usr/bin/mktemp -t condaenv)
@@ -177,15 +158,56 @@ sort $ALLREQUIRE | uniq | $SED -E 's/(>|<|\|)/\\\1/g' \
     | $SED -E 's/\#.*$//g' \
     | $SED -E '/^-r.*|^jaxlib.*|^jax.*/d' > $FLTREQUIRE
 # Remove requirements that cannot be installed via conda
+PIPREQ=""
 for nc in $NOCONDA; do
     # Escape [ and ] for use in regex
-    nc=$(echo $nc | sed -E 's/(\[|\])/\\\1/g')
+    nc=$(echo $nc | $SED -E 's/(\[|\])/\\\1/g')
+    # Add package to pip package list
+    PIPREQ="$PIPREQ "$(grep "$nc" $FLTREQUIRE | $SED 's/\\//g')
     # Remove package $nc from conda package list
     $SED -i "/^$nc.*\$/d" $FLTREQUIRE
 done
 # Get list of requirements to be installed via conda
 CONDAREQ=$(cat $FLTREQUIRE | xargs)
 
+if [ "$VERBOSE" == "yes" ]; then
+    echo "Create python $PYVER environment $ENVNM in conda installation"
+    echo "    $CONDAHOME"
+    echo "Packages to be installed via conda:"
+    echo "    $CONDAREQ" | fmt -w 79
+    echo "Packages to be installed via pip:"
+    echo "    jaxlib==$JLVER jax==$JXVER $PIPREQ" | fmt -w 79
+    if [ "$TEST" == "yes" ]; then
+	exit 0
+    fi
+fi
+
+CONDAHOME=$(conda info --base)
+ENVDIR=$CONDAHOME/envs/$ENVNM
+if [ -d "$ENVDIR" ]; then
+    echo "Error: environment $ENVNM already exists"
+    exit 9
+fi
+
+if [ "$AGREE" == "no" ]; then
+    RSTR="Confirm creation of conda environment $ENVNM with Python $PYVER"
+    RSTR="$RSTR [y/N] "
+    read -r -p "$RSTR" CNFRM
+    if [ "$CNFRM" != 'y' ] && [ "$CNFRM" != 'Y' ]; then
+	echo "Cancelling environment creation"
+	exit 10
+    fi
+else
+    echo "Creating conda environment $ENVNM with Python $PYVER"
+fi
+
+if [ "$AGREE" == "yes" ]; then
+    CONDA_FLAGS="-y"
+else
+    CONDA_FLAGS=""
+fi
+
+
 # Update conda, create new environment, and activate it
 conda update $CONDA_FLAGS -n base conda
 conda create $CONDA_FLAGS -n $ENVNM python=$PYVER
@@ -215,7 +237,7 @@ fi
 pip install --upgrade jaxlib==$JLVER jax==$JXVER
 
 # Install other packages that require installation via pip
-pip install $NOCONDA
+pip install $PIPREQ
 
 # Warn if libopenblas-dev not installed on debian/ubuntu
 if [ "$(which dpkg 2>/dev/null)" ]; then
@@ -233,13 +255,12 @@ echo "  conda activate $ENVNM"
 echo "The environment can be deactivated with the command"
 echo "  conda deactivate"
 echo
-echo "Jax installed without GPU support. To avoid warning messages,"
-echo "add the following to your .bashrc or .bash_aliases file"
-echo "  export JAX_PLATFORM_NAME=cpu"
-echo "To include GPU support, reinstall the astra-toolbox conda"
-echo "package on a host with GPUs, and see the instructions at"
-echo "   https://github.com/google/jax#pip-installation-gpu-cuda"
-echo "for additional steps required after running this script and"
-echo "activating the environment created by it."
+echo "JAX installed without GPU support. To enable GPU support, install a"
+echo "version of jaxlib with CUDA support following the instructions at"
+echo "   https://jax.readthedocs.io/en/latest/installation.html#nvidia-gpu"
+echo "ASTRA Toolbox installed without GPU support if this script was"
+echo "run on a host without CUDA drivers installed. To enable GPU support,"
+echo "uninstall and then reinstall the astra-toolbox conda package on a"
+echo "host with CUDA drivers installed."
 
 exit 0

requirements.txt

@@ -1,10 +1,10 @@
+typing_extensions
 numpy>=1.20.0
 scipy>=1.6.0
-tifffile
 imageio>=2.17
 matplotlib
-jaxlib>=0.4.3,<=0.4.21
-jax>=0.4.3,<=0.4.21
+jaxlib>=0.4.3,<=0.4.23
+jax>=0.4.3,<=0.4.23
+orbax-checkpoint
 flax>=0.6.1,<=0.7.5
-svmbir>=0.3.3
 pyabel>=0.9.0

scico/__init__.py

@@ -8,7 +8,7 @@
 solving the inverse problems that arise in scientific imaging applications.
 """
 
-__version__ = "0.0.5.dev0"
+__version__ = "0.0.6.dev0"
 
 import logging
 import sys

scico/_version.py

@@ -96,7 +96,8 @@ def package_version(split: bool = False) -> Union[str, Tuple[str, str]]:  # prag
         Package version string or tuple of strings.
     """
     version = init_variable_assign_value("__version_")
-    if re.match(r"^[0-9\.]+$", version):  # don't extend purely numeric version numbers
+    # don't extend purely numeric version numbers, possibly ending with post<n>
+    if re.match(r"^[0-9\.]+(post[0-9]+)?$", version):
         git_hash = None
     else:
         git_hash = current_git_hash()