change install_alg to install. update user guide.

Author: lacava

Dockerfile

@@ -45,4 +45,4 @@ COPY --chown=$MAMBA_USER:$MAMBA_USER environment.yml /tmp/environment.yml
 RUN --mount=type=cache,target=/opt/conda/pkgs mamba env create -f /tmp/environment.yml 
 SHELL ["mamba", "run", "-n", "srbench", "/bin/bash", "-c"]
 COPY . .
-RUN bash install_algorithms.sh 
+RUN bash install.sh 

docs/user_guide.md

@@ -1,7 +1,12 @@
 # User Guide
 
+**NOTE**: if you are trying to reproduce the results from the 2022 Neurips Benchmark paper, you 
+should check out the [v2.0 release](https://github.com/cavalab/srbench/releases/tag/v2.0) version of this repo.  
+
 ## Installation
 
+### Local install
+
 We have provided a [conda environment](environment.yml), [configuration script](configure.sh) and [installation script](install.sh) that should make installation straightforward.
 We've currently tested this on Ubuntu and CentOS. 
 Steps:
@@ -20,7 +25,7 @@ conda env create -f environment.yml
 conda activate srbench
 ```
 
-2. Install the benchmark methods:
+2. Install the benchmark algorithms:
 
 ```bash
 bash install.sh
@@ -34,13 +39,17 @@ cd /path/to/pmlb
 git lfs pull
 ```
 
+### Docker install
+
 For Docker users,
 ```bash
 docker build --pull --rm -f "Dockerfile" -t srbench:latest "."
 ```
 
 ## Reproducing the benchmark results
 
+**NOTE**: these instructions are for the the [v2.0 release](https://github.com/cavalab/srbench/releases/tag/v2.0) version of this repo.  
+
 Experiments are launched from the `experiments/` folder via the script `analyze.py`.
 The script can be configured to run the experiment in parallel locally, on an LSF job scheduler, or on a SLURM job scheduler. 
 To see the full set of options, run `python analyze.py -h`. 

install.sh

@@ -1,53 +1,76 @@
-# note: make sure conda environment is installed 
-# and activated before running install. 
-# see configure.sh
-# or run this as: 
-#   conda run -n srbench bash install.sh
+# note: make sure conda srbench environment is installed 
+set -e
+
+if (($#==1)); #check if number of arguments is 1 
+then
+    subnames=($1)
+else
+    subnames=$(ls algorithms/)
+fi
 
 failed=()
 succeeded=()
 
 # install methods
 echo "////////////////////////////////////////"
-echo "installing SR methods from scripts..."
+echo "installing SR methods..."
+echo ${subnames}
 echo "////////////////////////////////////////"
 
-# move to methods folder
-cd experiment/methods/src/
-
 # install all methods
-for install_file in $(ls *.sh) ; do
+for SUBNAME in ${subnames[@]} ; do
+
     echo "vvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvv"
-    echo ".................... Running $install_file..."
-
-    name=${install_file%.sh}
-    # Option to redirect logs:
-    # bash ${install_file} > "${name}.log" 2> "${name}.err"
-    bash ${install_file} 
-
-    if [ $? -gt 0 ];
-    then
-        # failed+=("${install_file}")
-        failed+=("$name")
-        echo "!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! $install_file FAILED"
+    echo ".................... Installing $SUBNAME ..."
+
+    SUBFOLDER=algorithms/$SUBNAME
+    SUBENV=srbench-$SUBNAME
+    # install method
+    # cd $SUBFOLDER
+    pwd
+    echo "Installing dependencies for ${SUBNAME}"
+    echo "........................................"
+    echo "Copying base environment"
+    echo "........................................"
+    conda create --name $SUBENV --clone srbench
+    if test -f "environment.yml" ; then
+        echo "Update alg env from environment.yml"
+        echo "........................................"
+        mamba env update -n $SUBENV -f ${SUBFOLDER}/environment.yml
+    fi
+
+    if test -f "requirements.txt" ; then
+        echo "Update alg env from requirements.txt"
+        echo "........................................"
+        mamba run -n srbench-${SUBENV} pip install -r ${SUBFOLDER}/requirements.txt
+    fi
+
+    eval "$(conda shell.bash hook)"
+    conda init bash
+    conda activate $SUBENV
+    if test -f "install.sh" ; then
+        echo "running install.sh..."
+        echo "........................................"
+        cd $SUBFOLDER
+        bash install.sh
+        cd ../../
     else
-        succeeded+=("$install_file")
-        echo "........................................ $install_file complete"
+        echo "::warning::No install.sh file found in ${SUBFOLDER}."
+        echo " Assuming the method is a conda package specified in environment.yml."
     fi
-    echo "^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^"
-done
 
-echo "${#succeeded[@]} successful installs:"
-for s in ${succeeded[@]} ; do
-    echo "  "$s
-done
-echo "${#failed[@]} failed installs:"
-for f in ${failed[@]} ; do
-    echo "  "$f
-done
+    # Copy files and environment
+    # echo "Copying files and environment to experiment/methods ..."
+    # echo "........................................"
+    # cd ../../
+    mkdir -p experiment/methods/$SUBNAME
+    cp $SUBFOLDER/regressor.py experiment/methods/$SUBNAME/
+    cp $SUBFOLDER/metadata.yml experiment/methods/$SUBNAME/
+    touch experiment/methods/$SUBNAME/__init__.py
 
-if [ ${#failed[@]} -gt 0 ] ; then
-    exit 1
-else
-    echo "All installations completed successfully."
-fi
+    # export env
+    echo "Exporting environment"
+    # conda env export -n $SUBENV > $SUBFOLDER/environment.lock.yml
+    conda env export -n $SUBENV > $SUBFOLDER/environment.lock.yml
+    echo "^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^"
+done