adds yaml parsing and optional build argument to not start with a clone of the srbench base environment

Author: lacava

algorithms/feat/environment.yml

@@ -4,8 +4,8 @@ channels:
 dependencies:
     - python=3.10
     - cmake
-    - gcc
-    - gxx
+    # - gcc
+    # - gxx
     - ninja
     - eigen
     - shogun-cpp=6.1.4

algorithms/feat/metadata.yml

@@ -11,4 +11,9 @@ description: | # anything you'd like here to describe the method.
   ICLR 2019. arxiv:1807.0091
 
 url: http://cavalab.org/feat # a link to the project
+########################################
+# Option arguments for the build process. 
+# Unless you know what you are doing, do not change these.
+build:
+  clone_base_env: yes # 
 

configure.sh

@@ -1,5 +1,5 @@
-# install conda environment
-conda env create -f environment.yml
+# install base srbench environment
+conda env create -f base_environment.yml
 
 eval "$(conda shell.bash hook)"
 

install.sh

@@ -1,6 +1,39 @@
 # note: make sure conda srbench environment is installed 
 set -e
 
+# script to read yaml
+function parse_yaml {
+   local prefix=$2
+   local s='[[:space:]]*' w='[a-zA-Z0-9_]*' fs=$(echo @|tr @ '\034')
+   sed -ne "s|^\($s\):|\1|" \
+        -e "s|^\($s\)\($w\)$s:$s[\"']\(.*\)[\"']$s\$|\1$fs\2$fs\3|p" \
+        -e "s|^\($s\)\($w\)$s:$s\(.*\)$s\$|\1$fs\2$fs\3|p"  $1 |
+   awk -F$fs '{
+      indent = length($1)/2;
+      vname[indent] = $2;
+      for (i in vname) {if (i > indent) {delete vname[i]}}
+      if (length($3) > 0) {
+         vn=""; for (i=0; i<indent; i++) {vn=(vn)(vname[i])("_")}
+         printf("%s%s%s=\"%s\"\n", "'$prefix'",vn, $2, $3);
+      }
+   }'
+}
+
+# install base srbench environment if it doesn't exist
+if conda info --envs | grep srbench | grep -v "srbench-"; then 
+    echo "existing base srbench environment (not installing)"; 
+else 
+    echo "installing base srbench environment"
+
+    mamba env create -y -f base_environment.yml
+
+    eval "$(conda shell.bash hook)"
+
+    conda init bash
+fi
+
+
+
 if (($#==1)); #check if number of arguments is 1 
 then
     subnames=($1)
@@ -13,56 +46,76 @@ succeeded=()
 
 # install methods
 echo "////////////////////////////////////////"
-echo "installing SR methods..."
+echo "installing these SR methods:"
 echo ${subnames}
 echo "////////////////////////////////////////"
 
 # install all methods
 for SUBNAME in ${subnames[@]} ; do
 
+    build_clone_base_env="yes"
+
     echo "vvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvv"
     echo ".................... Installing $SUBNAME ..."
 
     SUBFOLDER=algorithms/$SUBNAME
     SUBENV=srbench-$SUBNAME
-    # install method
-    # cd $SUBFOLDER
-    pwd
-    echo "Installing dependencies for ${SUBNAME}"
-    echo "........................................"
-    echo "Making environment"
-    echo "........................................"
-    # conda create --name $SUBENV --clone srbench
-    mamba env create --name $SUBENV -f base_environment.yml -f ${SUBFOLDER}/environment.yml
-    # if test -f "environment.yml" ; then
-    #     echo "Update alg env from environment.yml"
-    #     echo "........................................"
-    #     mamba env update -n $SUBENV -f ${SUBFOLDER}/environment.yml
-    # fi
-
-    if test -f "requirements.txt" ; then
+
+    ########################################
+    # read yaml
+    eval $(parse_yaml $SUBFOLDER/metadata.yml)
+    ########################################
+
+    if [ "${build_clone_base_env}" == "yes" ] ; then
+        echo "$build_clone_base_env" is set to yes
+
+        echo "........................................"
+        echo "Cloning base environment"
+        echo "........................................"
+
+        if conda info --envs | grep -q $SUBENV ; then 
+            echo "not cloning base because ${SUBENV} already exists"
+        else
+            conda create --name $SUBENV --clone srbench
+            # update from base environment
+            if test -f "${SUBFOLDER}/environment.yml" ; then
+                echo "Update alg env from environment.yml"
+                echo "........................................"
+                mamba env update -n $SUBENV -f ${SUBFOLDER}/environment.yml
+            fi
+        fi
+    else
+
+        echo "........................................"
+        echo "Creating environment ${SUBENV} from scratch"
+        echo "........................................"
+        mamba create -n $SUBENV -f ${SUBFOLDER}/environment.yml
+    fi
+
+
+    if test -f "${SUBFOLDER}/requirements.txt" ; then
         echo "Update alg env from requirements.txt"
         echo "........................................"
         mamba run -n srbench-${SUBENV} pip install -r ${SUBFOLDER}/requirements.txt
     fi
 
-    eval "$(conda shell.bash hook)"
-    conda init bash
-    conda activate $SUBENV
+    # eval "$(conda shell.bash hook)"
+    # conda init bash
+    # conda activate $SUBENV
     cd $SUBFOLDER
     if test -f "install.sh" ; then
         echo "running install.sh..."
         echo "........................................"
-        bash install.sh
+        mamba run -n $SUBENV bash install.sh
     else
         echo "::warning::No install.sh file found in ${SUBFOLDER}."
         echo " Assuming the method is a conda package specified in environment.yml."
     fi
     cd ../../
 
     # Copy files and environment
-    # echo "Copying files and environment to experiment/methods ..."
-    # echo "........................................"
+    echo "Copying files and environment to experiment/methods ..."
+    echo "........................................"
     # cd ../../
     mkdir -p experiment/methods/$SUBNAME
     cp $SUBFOLDER/regressor.py experiment/methods/$SUBNAME/