Merge branch 'master' into old-git

Author: Nortamo

configs/lumi.yaml

@@ -12,7 +12,7 @@ defaults:
     composable: true
     # if this is not a thing which exist
     # I will do a singularity pull
-    container_src: 'docker://opensuse/leap:15.3'
+    container_src: 'docker://opensuse/leap:15.4'
     # name of the container image when on disk
     container_image: container.sif 
     sqfs_image: img.sqfs 

create_inst.sh

@@ -50,6 +50,9 @@ echo "export install_root=$CW_INSTALLATION_PATH" >> _extra_envs.sh
 echo "export install_root=$CW_INSTALLATION_PATH" >> _vars.sh
 export install_root=$CW_INSTALLATION_PATH
 
+
+
+
 if [[ "$CW_UPDATE_INSTALLATION" == "yes" ]];then
     _CONTAINER_EXEC="singularity --silent exec -B _deploy/$CW_SQFS_IMAGE:$CW_SOURCE_MOUNT_POINT:image-src=/ _deploy/$CW_CONTAINER_IMAGE"
     export SINGULARITY_BIND="$SINGULARITY_BIND,$PWD/_inst_dir:$CW_INSTALLATION_PATH,$_inst_path/_bin:$_inst_path/bin"
@@ -79,10 +82,28 @@ fi
 # There should be a separate folder so that removal is easier
 (cd _inst_dir && rm -f _vars.sh common_functions.sh  _sing_inst_script.sh _pre_install.sh _post_install.sh $CW_TEMPLATE_SCRIPT  _extra_user_envs.sh _extra_envs.sh )
 
+
 if [[ ! ${CW_NO_FIX_PERM+defined}  ]];then
     print_info "Fixing permissions within squashfs image" 2
     chmod -R ugo+rwX _inst_dir 
 fi
+
+# Save old configurations in separate folder so they are not overridden
+counter=0
+while true;do
+if [[ -e _inst_dir/previous_input/$counter ]]; then
+    counter=$((counter+1))
+else
+    mkdir -p _inst_dir/previous_input/$counter
+    break
+fi
+done
+for fp in "${CW_INSTALLATION_FILE_PATHS[@]}";do
+    n=$(basename $fp)
+    mv _inst_dir/$n _inst_dir/previous_input/$counter
+done
+####### 
+
 mksquashfs _inst_dir/ _deploy/$CW_SQFS_IMAGE -processors $_cpus $CW_SQFS_OPTIONS 
 
 # Check if we need to fix group permissions

post.sh

@@ -17,13 +17,11 @@ if [[ ${CW_UPDATE_INSTALLATION+defined } && "$CW_UPDATE_INSTALLATION" == "yes" ]
 fi
     cp -rd $CW_BUILD_TMPDIR/_deploy/* $CW_INSTALLATION_PREFIX/
     mkdir -p $CW_INSTALLATION_PREFIX/share
-    if [[ ${CW_INSTALLATION_FILE_PATHS+defined} ]]; then
-        for _fil in ${CW_INSTALLATION_FILE_PATHS[@]}; do
-            mv $CW_BUILD_TMPDIR/_inst_dir/$( basename $_fil ) $CW_INSTALLATION_PREFIX/share 
-        done
+    if [[ ${CW_INSTALLATION_FILE_PATHS+defined} ]];then
+        cp -r $CW_BUILD_TMPDIR/_inst_dir/previous_input* $CW_INSTALLATION_PREFIX/share
     fi
-    echo "tag: $(cd $SCRIPT_DIR; git describe --tags)" > $CW_INSTALLATION_PREFIX/share/VERSION.yml
-    echo "commit: $(cd $SCRIPT_DIR; git rev-parse --short HEAD )" >>  $CW_INSTALLATION_PREFIX/share/VERSION.yml
+    echo "tag: $(cd $SCRIPT_DIR; git describe --tags 2>/dev/null)" > $CW_INSTALLATION_PREFIX/share/VERSION.yml
+    echo "commit: $(cd $SCRIPT_DIR; git rev-parse --short HEAD 2>/dev/null )" >>  $CW_INSTALLATION_PREFIX/share/VERSION.yml
     echo "build-time: $(date)" >>  $CW_INSTALLATION_PREFIX/share/VERSION.yml 
 
     cp $CW_BUILD_TMPDIR/conf.yaml $CW_INSTALLATION_PREFIX/share

templates/conda_modify.sh

@@ -1,14 +1,19 @@
 #!/bin/bash
-cd $CW_INSTALLATION_PATH
+cd  $CW_BUILD_TMPDIR
 echo "export env_root=$CW_INSTALLATION_PATH/miniconda/envs/$CW_ENV_NAME/" >> _extra_envs.sh
 echo "export env_root=$CW_INSTALLATION_PATH/miniconda/envs/$CW_ENV_NAME/" >> _vars.sh
+cd $CW_INSTALLATION_PATH
 export env_root=$CW_INSTALLATION_PATH/miniconda/envs/$CW_ENV_NAME/
 eval "$($CW_INSTALLATION_PATH/miniconda/bin/conda shell.bash hook)"
 cd $CW_WORKDIR
 source $CW_INSTALLATION_PATH/_pre_install.sh
 conda activate $CW_ENV_NAME
 if [[ ${CW_REQUIREMENTS_FILE+defined}  ]];then
-    pip install -r $( basename "$CW_REQUIREMENTS_FILE" )
+    print_info "Installing requirements file" 1
+    pip install -r $( basename "$CW_REQUIREMENTS_FILE" )  > $CW_BUILD_TMPDIR/_pip.log &
+    bg_pid=$!
+    wait $bg_pid
+    follow_log $bg_pid $CW_BUILD_TMPDIR/_pip.log 10
 fi
 cd $CW_WORKDIR
 source $CW_INSTALLATION_PATH/_post_install.sh

templates/venv.sh

@@ -26,7 +26,10 @@ python3 -m venv $_SP $CW_ENV_NAME
 source $CW_INSTALLATION_PATH/$CW_ENV_NAME/bin/activate
 
 if [[ ${CW_REQUIREMENTS_FILE+defined}  ]];then
-    pip install --disable-pip-version-check -r "$( basename $CW_REQUIREMENTS_FILE)"  
+    pip install --disable-pip-version-check -r "$( basename $CW_REQUIREMENTS_FILE)" > $CW_BUILD_TMPDIR/_pip.log &
+    bg_pid=$!
+    wait $bg_pid
+    follow_log $bg_pid $CW_BUILD_TMPDIR/_pip.log 10
 fi
 cd $CW_WORKDIR
 print_info "Running user supplied commands" 1

templates/venv_modify.sh

@@ -17,7 +17,9 @@ source $CW_INSTALLATION_PATH/$CW_ENV_NAME/bin/activate
 if [[ ${CW_REQUIREMENTS_FILE+defined}  ]];then
     print_info "Installing requirements file" 1
     pip install --disable-pip-version-check -r "$( basename $CW_REQUIREMENTS_FILE)" > $CW_BUILD_TMPDIR/_pip.log &
-    follow_log $! $CW_BUILD_TMPDIR/_pip.log 10
+    bg_pid=$!
+    wait $bg_pid
+    follow_log $bg_pid $CW_BUILD_TMPDIR/_pip.log 10
 fi
 cd $CW_WORKDIR
 #print_info "Running user supplied commands" 1

tests/more_tests.sh

@@ -67,7 +67,7 @@ t_run "pip-containerize new --prefix subdir/PIP_INSTALL_DIR_3 subdir/req.txt" "P
 
 rm -fr PIP_INSTALL_DIR
 mkdir PIP_INSTALL_DIR
-t_run "wrap-container -w /usr/sbin/sln --prefix PIP_INSTALL_DIR test_container.sif" "wrap-container works with single target"
+t_run "wrap-container -w /usr/sbin/zdump --prefix PIP_INSTALL_DIR test_container.sif" "wrap-container works with single target"
 
 rm -fr PIP_INSTALL_DIR
 mkdir PIP_INSTALL_DIR

tests/tests.sh

@@ -85,20 +85,20 @@ t_run "test -z $rc_res" "User .condarc is ignored"
 export CW_ENABLE_CONDARC=1
 t_run "conda-containerize new --pre-install=pre.sh conda_base.yml --prefix CONDA_INSTALL_DIR  | grep -q $HOME/.conda/pkgs" "User .condarc can be enabled"
 unset CW_ENABLE_CONDARC
-t_run "conda-containerize new conda_base.yml -r req.txt --prefix CONDA_INSTALL_DIR &>/dev/null" "Basic installation works"
+t_run "conda-containerize new --mamba conda_base.yml -r req.txt --prefix CONDA_INSTALL_DIR &>/dev/null" "Basic installation works"
 t_run "CONDA_INSTALL_DIR/bin/python -m venv VE " "Virtual environment creation works"
 t_run "VE/bin/python -c 'import sys;sys.exit( sys.prefix == sys.base_prefix )'" "Virtual environment is correct"
 t_run "VE/bin/pip install requests" "pip works for a venv"
 t_run "VE/bin/python -c 'import requests;print(requests.__file__)' | grep -q VE " "Package is installed correctly to venv"
-CONDA_INSTALL_DIR/bin/_debug_exec bash -c "\$(dirname \$(readlink -f \$(which python)))/../../../bin/conda list --explicit" > explicit_env.txt 
+CONDA_INSTALL_DIR/bin/_debug_exec bash -c "\$(readlink -f \$env_root)/../../bin/conda list --explicit" > explicit_env.txt 
 t_run "CONDA_INSTALL_DIR/bin/python -c 'import yaml'" "Package added by -r is there"
 t_run "conda-containerize update CONDA_INSTALL_DIR --post-install post.sh" "Update works"
 t_run "CONDA_INSTALL_DIR/bin/python -c 'import requests'" "Package added by update is there"
 rm -fr CONDA_INSTALL_DIR && mkdir CONDA_INSTALL_DIR
-t_run "conda-containerize new explicit_env.txt --prefix CONDA_INSTALL_DIR &>/dev/null" "Explicit env file works"
+t_run "conda-containerize new --mamba explicit_env.txt --prefix CONDA_INSTALL_DIR &>/dev/null" "Explicit env file works"
 
 rm -fr CONDA_INSTALL_DIR && mkdir CONDA_INSTALL_DIR
-t_run "conda-containerize new dask_env.yaml --prefix CONDA_INSTALL_DIR &>/dev/null" "yaml ending is also supported"
+t_run "conda-containerize new --mamba dask_env.yaml --prefix CONDA_INSTALL_DIR &>/dev/null" "yaml ending is also supported"
 OLD_PATH=$PATH
 PATH="CONDA_INSTALL_DIR/bin:$PATH"
 t_run " \[  $(which python)==$(_debug_exec which python)  \] " "Which returns same in and out"