revert to conda but with libmamaba solver

CHANGES.md

@@ -8,12 +8,13 @@
 - docker image updates
    - introduce `REMOVE_BUILD_FILES` variable. If set to 1 (which is the default),
      most build files will be removed in the docker image.
-   - introduce `RUN_CTESTS` variable. If set to 1 (which is the default),
+   - introduce `RUN_CTEST` variable. If set to 1 (which is the default),
      the CTests will be run while building the image.
    - remove obsolete copying of gadgetron.xml
    - Installing requirements for SIRF-Exercises uses its environment.yml or requirements.txt depending on settings.
-- Build Gadgetron master. Requires new Ubuntu packages: libdcmtk-dev, libpugixml-dev, libgflags-dev, 
-  libssl-dev, libcurl4-openssl-dev, pkg-config, golang, libboost-coroutine-dev, libboost-context-dev, libboost-random-dev. 
+   - revert to `conda` but with `libmamba` solver
+- Build Gadgetron master. Requires new Ubuntu packages: libdcmtk-dev, libpugixml-dev, libgflags-dev,
+  libssl-dev, libcurl4-openssl-dev, pkg-config, golang, libboost-coroutine-dev, libboost-context-dev, libboost-random-dev.
 - Added SuperBuild project dependencies for Gadgetron: range-v3, RocksDB, Date, mrd-storage-server
 - updated versions:
   - Gadgetron: 42f11bf14b77b16f1ca5bcfbfa435d5ee8cb22a6 (master)
@@ -25,7 +26,7 @@
   - CIL: 0ba2f8e2935db66ec3dfe8c88e407e8d0eb5609f
   - CCPi-Regularisation: v22.0.0
   - TomoPhantom: v2.0.0
-  
+
 ## v3.4.0
 - Removed CIL-ASTRA as it has been merged into CIL code base.
 - docker images updates
@@ -52,7 +53,7 @@
   - Boost: 1.78.0
 
 ## v3.3.1
-- VM: 
+- VM:
    - "update_VM.sh -s" (i.e. "UPDATE.sh -s") no longer runs configure_gnome.sh. If you have a very old VM, run it manually instead.
    - Updates to run using docker scripts
    - installs custom pip and all python prerequisites with pip
@@ -64,7 +65,7 @@
    - no longer force numpy<=1.20
 - CMake:
    - FindCython allows hints
-   
+
 ## v3.3.0
 - known problems:
    - VM and jupyterhub scripts need merging various fixes
@@ -78,7 +79,7 @@
 - docker:
    - fix problems with CUDA repo keys
    - minor fixes to scripts for use elsewhere (including preparation for more recent Ubuntu)
-- VM: 
+- VM:
   - set BUILD_CIL=ON
 - add CITATION.cff (and remove .zenodo.json)
 - added numba as dependency in docker files

docker/install-sirf-exercises-dep.py

@@ -4,7 +4,7 @@
 import functools
 
 def conda_install(package):
-    return f'mamba install -y -c conda-forge {package}'.rstrip()
+    return f'conda install -y -c conda-forge {package}'.rstrip()
 
 def pip_install(package):
     return f'pip install -U {package}'.rstrip()
@@ -30,18 +30,18 @@ def pip_install(package):
                     else:
                         print (f'Not on conda-forge: {line.rstrip()}')
                         install_by_pip.append(line.rstrip())
-    
+
     install_by_conda = functools.reduce(lambda x, y: x + ' ' + y, install_by_conda, '')
-    
+
 
     install_by_pip = functools.reduce(lambda x, y: x + ' ' + y, install_by_pip, '')
-    
+
 
     try:
         print ("Installing from conda-forge:", install_by_conda)
         subprocess.run(conda_install(install_by_conda), shell=True, check=True)
         print ("Installing from PyPI:", install_by_pip)
         subprocess.run([sys.executable,  "-m", pip_install(install_by_pip)], shell=True, check=True)
-        
+
     except subprocess.CalledProcessError as cpe:
-        print (cpe)
+        print (cpe)

docker/requirements.yml

@@ -5,7 +5,6 @@ channels:
   - ccpi
   - defaults
 dependencies:
-  - mamba
   - setuptools
   - wheel
   - pytest

docker/user_python-ubuntu.sh

@@ -1,17 +1,17 @@
 #!/usr/bin/env bash
 
-# User can pass 2 parameters to this script: 
+# User can pass 2 parameters to this script:
 # 1. PYTHON_EXECUTABLE which can be either the 'miniconda' string or the location of the Python executable
 # 2. PYTHON_INSTALL_DIR which points to the location where the user has their virtual environment installed
 #    The virtual environment can be either virtualenv or conda
 #
 # To pass these parameters the user needs to set (at least) temporary environment variables:
 # PYTHON_EXECUTABLE=python3 PYTHON_INSTALL_DIR="~/virtualenv" bash user_python-ubuntu.sh
-# For details see https://github.com/SyneRBI/SIRF-SuperBuild/pull/692#issuecomment-1102704682 
+# For details see https://github.com/SyneRBI/SIRF-SuperBuild/pull/692#issuecomment-1102704682
 [ -f .bashrc ] && . .bashrc
 set -exv
 
-if [ -n "${PYTHON_EXECUTABLE}" ]; then 
+if [ -n "${PYTHON_EXECUTABLE}" ]; then
   PYTHON=$PYTHON_EXECUTABLE
 else
   PYTHON='miniconda'
@@ -26,16 +26,14 @@ fi
 # Python
 case "$PYTHON" in
 miniconda)
-  #curl -L https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh > miniconda.sh
-  curl -L https://github.com/conda-forge/miniforge/releases/latest/download/Mambaforge-Linux-x86_64.sh > miniconda.sh
+  curl -L https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh > miniconda.sh
   echo -e "\nyes\n${INSTALL_DIR}\nno" | bash miniconda.sh
   rm miniconda.sh
   source "$INSTALL_DIR"/bin/activate
-  #conda config --add channels conda-forge
-  # https://github.com/conda/conda/issues/6030
-  #conda update -c conda-forge -y conda
-  # https://github.com/SyneRBI/SIRF-SuperBuild/issues/826
-  #conda install -c conda-forge -c defaults -y mamba
+  conda config --add channels conda-forge
+  conda update -c conda-forge -y conda
+  conda install conda-libmamba-solver
+  conda config --set solver libmamba
   ;;
 *python*)
   # virtualenv
@@ -54,11 +52,11 @@ esac
 
 if [ "$PYTHON" = "miniconda" ]; then
   if [ -f requirements.yml ]; then
-    # installs the required packages in the environment with requirements.yml. 
+    # installs the required packages in the environment with requirements.yml.
     # Notice that SciPy is set to 1.7.3 to prevent `GLIBCXX_3.4.30' not found
-    mamba env update --file requirements.yml 
+    conda env update --file requirements.yml
   fi
-  mamba clean -y --all
+  conda clean -y --all
 # Python (runtime)
 else
   if [ -f requirements.txt ]; then

docker/user_service-ubuntu.sh

@@ -2,7 +2,7 @@
 [ -f .bashrc ] && . .bashrc
 set -ev
 INSTALL_DIR="${1:-/opt}"
-if [ -n "${PYTHON_EXECUTABLE}" ]; then 
+if [ -n "${PYTHON_EXECUTABLE}" ]; then
   PYTHON=$PYTHON_EXECUTABLE
 else
   PYTHON='miniconda'
@@ -13,11 +13,11 @@ git clone https://github.com/SyneRBI/SIRF-Exercises --recursive -b master $INSTA
 
 if [ "$PYTHON" = "miniconda" ]; then
   if [ -f requirements-service.yml ]; then
-    # installs the required packages in the environment with requirements-service.yml. 
+    # installs the required packages in the environment with requirements-service.yml.
     # Notice that these requirements TEMPORARILY contains also the packages for SIRF-Exercises
-    mamba env update --file requirements-service.yml 
+    conda env update --file requirements-service.yml
   fi
-  mamba clean -y --all
+  conda clean -y --all
 
 # Python (runtime)
 else
@@ -30,13 +30,13 @@ fi
 cd $INSTALL_DIR/SIRF-Exercises
 if [ "$PYTHON" = "miniconda" ]; then
   if [ -f environment.yml ]; then
-    mamba env update --file environment.yml
+    conda env update --file environment.yml
   else
     if [ -f requirements.txt ]; then
       cat requirements.txt
-      # installing the requirements.txt with mamba requires some cleaning of the requirements.txt
+      # installing the requirements.txt with conda requires some cleaning of the requirements.txt
       # Also the requirements.txt contains some packages that are not found on conda-forge, i.e. brainweb
-      # Therefore, these need to be installed by pip. 
+      # Therefore, these need to be installed by pip.
       # This is handled by the install-sirf-exercises-dep.py script
       python ~/install-sirf-exercises-dep.py requirements.txt
     else
@@ -58,7 +58,7 @@ git config --global filter.nbstripout.extrakeys '
   metadata.language_info.pygments_lexer metadata.language_info.version'
 
 #install nbstripout in the SIRF-Exercises repo
-cd $INSTALL_DIR/SIRF-Exercises  
+cd $INSTALL_DIR/SIRF-Exercises
 nbstripout --install
 # jupyter labextension install @jupyter-widgets/jupyterlab-manager