Merge pull request #839 from SyneRBI/conda-libmamba-solver

revert to `conda` but with `libmamba` solver

CHANGES.md

@@ -12,6 +12,7 @@
     - The `devel` tag (for `DEVEL_BUILD=ON` with `master` versions of SIRF, STIR etc) is no longer pushed to DockerHub, and therefore will not be updated.
   - Docker images are now pushed to [DockerHub](https://hub.docker.com/r/synerbi/sirf/tags) and [GHCR](https://github.com/SyneRBI/SIRF-SuperBuild/pkgs/container/sirf)
   - added requirements.yml
+  - revert to `conda` but with `libmamba` solver
 - updated versions:
   - SIRF: v3.6.0
   - STIR: v6.0.0
@@ -41,7 +42,7 @@
 - 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.

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/user_demos.sh

@@ -22,11 +22,11 @@ if [ "$PYTHON" = "miniconda" ]; then
       # delete GPU deps
       sed -r -e '/^\s*- (astra-toolbox|tigre).*/d' -e '/^\s*- \S+.*#.*GPU/d' environment.yml > environment-sirf.yml
     fi
-    mamba env update --file environment-sirf.yml
+    conda env update --file environment-sirf.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.
       # This is handled by the install-sirf-exercises-dep.py script

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=$PYTHON_EXECUTABLE
 else
   PYTHON='miniconda'
@@ -26,16 +26,12 @@ fi
 # Python
 case "$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
   ;;
 *python*)
   # virtualenv
@@ -54,11 +50,11 @@ 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