swancustomenvironments: New conda environment option

Conda (mamba) environments can now be built passing the argument `--conda` into the `makenv.sh` script.
Some logic and code flow modifications were needed in order to build them sameway as python-venv.

SwanCustomEnvironments/swancustomenvironments/scripts/builders/accpy.sh

@@ -0,0 +1,22 @@
+#!/bin/bash
+
+# Checks if the provided Acc-Py version is valid
+if [ ! -e "$ACCPY_PATH/base/$BUILDER_VERSION" ]; then
+    _error "Invalid Acc-Py version (${BUILDER_VERSION})."
+fi
+
+# Set up Acc-Py and create the environment
+source "${ACCPY_PATH}/base/${BUILDER_VERSION}/setup.sh"
+acc-py venv ${ENV_PATH} | tee -a ${LOG_PATH}
+
+# Activate the environment
+_log "Setting up the environment..."
+ACTIVATE_ENV_CMD="source ${ENV_PATH}/bin/activate"
+eval "${ACTIVATE_ENV_CMD}"
+
+# Install packages in the environment
+_log "Installing packages from ${REQ_PATH}..."
+pip install -r "${REQ_PATH}" | tee -a ${LOG_PATH}
+
+# Install the same ipykernel that the Jupyter server uses
+pip install ipykernel==${IPYKERNEL_VERSION} | tee -a ${LOG_FILE}

SwanCustomEnvironments/swancustomenvironments/scripts/builders/mamba.sh

@@ -0,0 +1,23 @@
+#!/bin/bash
+
+# Create the environment and install packages
+mamba create -p ${ENV_PATH} --file ${REQ_PATH} -y | tee -a ${LOG_PATH}
+
+# Activate the environment
+_log "Setting up the environment..."
+
+# Needed to use mamba activate without creating a new shell process
+MAMBADIR=$(mktemp -d)
+HOME=${MAMBADIR} mamba init
+ACTIVATE_MAMBA_CMD="source ${MAMBADIR}/.bashrc"
+eval "${ACTIVATE_MAMBA_CMD}"
+
+# Then activate the environment using mamba
+ACTIVATE_ENV_CMD="mamba activate ${ENV_PATH}"
+eval "${ACTIVATE_ENV_CMD}"
+
+# Install the same ipykernel that the Jupyter server uses
+mamba install "ipykernel==${IPYKERNEL_VERSION}" -y | tee -a ${LOG_PATH}
+
+# Source the mamba init script in the user's bash profile
+echo "${ACTIVATE_MAMBA_CMD}" >> /home/$USER/.bash_profile

SwanCustomEnvironments/swancustomenvironments/scripts/builders/venv.sh

@@ -0,0 +1,16 @@
+#!/bin/bash
+
+# Create the environment
+python3 -m venv ${ENV_PATH} | tee -a ${LOG_PATH}
+
+# Activate the environment
+_log "Setting up the environment..."
+ACTIVATE_ENV_CMD="source ${ENV_PATH}/bin/activate"
+eval "${ACTIVATE_ENV_CMD}"
+
+# Install packages in the environment
+_log "Installing packages from ${REQ_PATH}..."
+pip install -r "${REQ_PATH}" | tee -a ${LOG_PATH}
+
+# Install the same ipykernel that the Jupyter server uses
+pip install ipykernel==${IPYKERNEL_VERSION} | tee -a ${LOG_FILE}

SwanCustomEnvironments/swancustomenvironments/scripts/makenv.sh

@@ -33,11 +33,12 @@ define_repo_path() {
 
 # Function for printing the help page
 print_help() {
-    _log "Usage: makenv --repo/-r REPOSITORY [--repo_type TYPE] [--accpy ACCPY_VERSION] [--help/-h]"
+    _log "Usage: makenv --repo REPOSITORY --repo_type TYPE --builder BUILDER --builder_version VERSION [--help/-h]"
     _log "Options:"
-    _log "  -r, --repo REPOSITORY       Path or http link for a public repository (mandatory)"
-    _log "  --repo_type TYPE            Type of repository (git or eos) (mandatory)"
-    _log "  --accpy VERSION             Version of Acc-Py to be used"
+    _log "  --repo REPOSITORY           Path or http link for a public repository"
+    _log "  --repo_type TYPE            Type of repository (git or eos)"
+    _log "  --builder BUILDER           Builder to create the environment"
+    _log "  --builder_version VERSION   Version of the builder to use (optional)"
     _log "  -h, --help                  Print this help page"
 }
 
@@ -47,18 +48,47 @@ print_help() {
 while [ $# -gt 0 ]; do
     key="$1"
     case $key in
-        --repo|-r)
+        --repo)
             REPOSITORY=$2
+            # Check if a repository was provided
+            if [ -z "$REPOSITORY" ]; then
+                _log "ERROR: No repository provided." && log
+                print_help
+                exit 1
+            fi
             shift
             shift
             ;;
         --repo_type)
             REPO_TYPE=$2
+            # Check if a repository type was provided
+            if [ -z "$REPO_TYPE" ]; then
+                _log "ERROR: No repository type provided." && log
+                print_help
+                exit 1
+            fi
             shift
             shift
             ;;
-        --accpy)
-            ACCPY_VERSION=$2
+        --builder)
+            BUILDER=$2
+            BUILDER_PATH="$(dirname "$0")/builders/${BUILDER}.sh"
+            # Check if a builder was provided
+            if [ -z "$BUILDER" ]; then
+                _log "ERROR: No builder provided." && log
+                print_help
+                exit 1
+            # Check if is a valid builder
+            elif [ ! -f "${BUILDER_PATH}" ]; then
+                _log "ERROR: Invalid builder (${BUILDER})." && log
+                print_help
+                exit 1
+            fi
+            shift
+            shift
+            ;;
+        --builder_version)
+            BUILDER_VERSION=$2
             shift
             shift
             ;;
@@ -67,7 +97,7 @@ while [ $# -gt 0 ]; do
             exit 0
             ;;
         *)
-            _log "ERROR: Invalid argument: $1" && _log
+            _log "ERROR: Invalid argument: $1" && log
             print_help
             exit 1
             ;;
@@ -82,25 +112,8 @@ REPO_GIT_PATTERN='^https?:\/\/(github\.com|gitlab\.cern\.ch)\/([a-zA-Z0-9_-]+)\/
 # EOS path pattern: $CERNBOX_HOME/<folder1>/<folder2>/...(/?) or /eos/user/<lowercase_first_letter>/<username>/<folder1>?/<folder2>?/...(/?)
 REPO_EOS_PATTERN='^(\$CERNBOX_HOME(\/[^<>|\\:()&;,\/]+)*\/?|\/eos\/user\/[a-z](\/[^<>|\\:()&;,\/]+)+\/?)$'
 
-# Checks if the provided Acc-Py version is valid
-if [ -n "$ACCPY_VERSION" ] && [ ! -e "$ACCPY_PATH/base/$ACCPY_VERSION" ]; then
-    _log "ERROR: Invalid Acc-Py version (${ACCPY_VERSION})."
-    exit 1
-fi
-
-# Checks if a repository is provided
-if [ -z "$REPOSITORY" ]; then
-    _log "ERROR: No repository provided." && _log
-    print_help
-    exit 1
-
-elif [ -z "$REPO_TYPE" ]; then
-    _log "ERROR: No repository type provided." && _log
-    print_help
-    exit 1
-
 # Checks if the provided repository is a valid URL
-elif [[ "$REPO_TYPE" == "git" ]] && [[ "$REPOSITORY" =~ $REPO_GIT_PATTERN ]]; then
+if [[ "$REPO_TYPE" == "git" ]] && [[ "$REPOSITORY" =~ $REPO_GIT_PATTERN ]]; then
     # Extract the repository name
     repo_name=$(basename $REPOSITORY)
     repo_name=${repo_name%.*}
@@ -109,7 +122,7 @@ elif [[ "$REPO_TYPE" == "git" ]] && [[ "$REPOSITORY" =~ $REPO_GIT_PATTERN ]]; th
 
     # Clone the repository
     _log "Cloning the repository from ${REPOSITORY}..."
-    rm -rf "${REPO_PATH}" && git clone $REPOSITORY -q "${REPO_PATH}" || { _log "ERROR: Failed to clone repository"; exit 1; } | tee -a "${LOG_FILE}"
+    rm -rf "${REPO_PATH}" && git clone $REPOSITORY -q "${REPO_PATH}" || { _log "ERROR: Failed to clone repository"; exit 1; } | tee -a ${LOG_FILE}
     ENV_NAME="${repo_name}_env"
 
 # Checks if the provided local repository is an EOS path and actually exists
@@ -147,39 +160,25 @@ if [ ! -f "${REQ_PATH}" ]; then
     exit 1
 fi
 
+# Check if an environment already exists in the session, avoiding multiple environments
 CURRENT_ENV_NAME=$(find "/home/$USER" -type d -name "*_env" | head -n 1 | cut -d '/' -f4)
 CURRENT_REPO_PATH=$(tail -n 1 "/home/$USER/.bash_profile" | cut -d ' ' -f2)
-
-# Check if an environment already exists in the session
 if [ -n "${CURRENT_ENV_NAME}" ]; then
     _log "ENVIRONMENT_ALREADY_EXISTS:${CURRENT_ENV_NAME}"
     _log "REPO_PATH:${CURRENT_REPO_PATH#$HOME}"
     exit 1
 fi
 
-# Create environment (acc-py or generic)
-if [ -n "$ACCPY_VERSION" ]; then
-    source $ACCPY_PATH/base/${ACCPY_VERSION}/setup.sh
-    acc-py venv ${ENV_PATH} | tee -a "${LOG_FILE}"
+if [ -n "${BUILDER_VERSION}" ]; then
+    _log "Creating environment ${ENV_NAME} using ${BUILDER} (${BUILDER_VERSION})..."
 else
-    _log "Creating environment ${ENV_NAME} using Generic Python..."
-    python -m venv ${ENV_PATH} | tee -a "${LOG_FILE}"
+    _log "Creating environment ${ENV_NAME} using ${BUILDER}..."
 fi
-
-_log "ENV_NAME:${ENV_NAME}"
-
+source "${BUILDER_PATH}"
+
 # Make sure the Jupyter server finds the new environment kernel in /home/$USER/.local
 mkdir -p /home/$USER/.local/share/jupyter/kernels
-ln -f -s ${ENV_PATH}/share/jupyter/kernels/${ENV_NAME} /home/$USER/.local/share/jupyter/kernels/${ENV_NAME} | tee -a "${LOG_FILE}"
-
-# Activate the environment
-_log "Setting up the environment..."
-source ${ENV_PATH}/bin/activate
-
-# Install packages in the environment and the same ipykernel that the Jupyter server uses
-_log "Installing packages from ${REQ_PATH}..."
-pip install ipykernel==${IPYKERNEL_VERSION} | tee -a "${LOG_FILE}"
-pip install -r "${REQ_PATH}" | tee -a "${LOG_FILE}"
+ln -f -s ${ENV_PATH}/share/jupyter/kernels/${ENV_NAME} /home/$USER/.local/share/jupyter/kernels/${ENV_NAME} | tee -a ${LOG_FILE}
 
 if [[ ${REPO_TYPE} == "git" ]]; then
     # Move the repository from /tmp to the $CERNBOX_HOME/SWAN_projects folder
@@ -188,10 +187,11 @@ if [[ ${REPO_TYPE} == "git" ]]; then
     REPO_PATH="${GIT_HOME}/$(basename $REPO_PATH)"
 fi
 
+_log "ENV_NAME:${ENV_NAME}"
 _log "REPO_PATH:${REPO_PATH#$HOME}"
 
-# Install a Jupyter kernel for the environment
-python -m ipykernel install --name "${ENV_NAME}" --display-name "Python (${ENV_NAME})" --prefix "${ENV_PATH}" | tee -a "${LOG_FILE}"
+# Setting JUPYTER_PATH prevents ipykernel installation from complaining about non-found kernelspec
+JUPYTER_PATH=${ENV_PATH}/share/jupyter python -m ipykernel install --name "${ENV_NAME}" --display-name "Python (${ENV_NAME})" --prefix "${ENV_PATH}" | tee -a ${LOG_FILE}
 
 # Ensure the terminal loads the environment and cds into the repository path
-echo -e "source /home/$USER/${ENV_NAME}/bin/activate\ncd ${REPO_PATH}" > /home/$USER/.bash_profile
+echo -e "${ACTIVATE_ENV_CMD}\ncd ${REPO_PATH}" >> /home/$USER/.bash_profile

SwanCustomEnvironments/swancustomenvironments/serverextension.py

@@ -18,24 +18,24 @@ def get(self):
         """
         Gets the arguments from the query string and runs the makenv.sh script with them.
         repo (str): The git URL or absolute unix path to the repository.
-        accpy (str): The version of Accpy to be installed in the environment (optional).
+        repo_type (str): The type of repository (git or eos).
+        builder (str): The builder used for creating the environment.
+        builder_version (str): The version of the specified builder.
         """
         self.set_header("Content-Type", "text/event-stream")
 
         repository = self.get_query_argument("repo", default="")
-        repository_type = self.get_query_argument("repo_type", default="")
-        accpy_version = self.get_query_argument("accpy", default="")
-
-        arguments = ["--repo", repository, "--repo_type", repository_type]
-        if accpy_version:
-            arguments.extend(["--accpy", accpy_version])
+        repo_type = self.get_query_argument("repo_type", default="")
+        builder = self.get_query_argument("builder", default="")
+        builder_version = self.get_query_argument("builder_version", default="")
 
+        arguments = ["--repo", repository, "--repo_type", repo_type, "--builder", builder, "--builder_version", builder_version]
         makenv_process = subprocess.Popen([self.makenv_path, *arguments], stdout=subprocess.PIPE, stderr=subprocess.STDOUT)
 
         for line in iter(makenv_process.stdout.readline, b""):
             self.write(f"data: {line.decode('utf-8')}\n\n")
             self.flush()
-            
+
         self.finish("data: EOF\n\n")
 
 

SwanCustomEnvironments/swancustomenvironments/templates/customenvs.html

@@ -147,8 +147,9 @@ <h2 id="modal-title" style="text-align: left;"></h2>
 
     const urlParams = new URLSearchParams(window.location.search);
     var repository = urlParams.get('repo') || "";
-    var repository_type = urlParams.get('repo_type') || "";
-    var accpy_version = urlParams.get('accpy') || "";
+    var repo_type = urlParams.get('repo_type') || "";
+    var builder = urlParams.get('builder') || "";
+    var builder_version = urlParams.get('builder_version') || "";
     var file = `/${urlParams.get('file') || ""}`;
 
     // Environment creation elements
@@ -165,7 +166,7 @@ <h2 id="modal-title" style="text-align: left;"></h2>
     var modalJupyter = document.getElementById("modal-lab-button");
 
     // Create EventSource to listen for updates from the backend
-    var eventSource = new EventSource(`${base_url}api/customenvs?repo=${encodeURIComponent(repository)}&repo_type=${encodeURIComponent(repository_type)}&accpy=${encodeURIComponent(accpy_version)}`);
+    var eventSource = new EventSource(`${base_url}api/customenvs?repo=${encodeURIComponent(repository)}&repo_type=${encodeURIComponent(repo_type)}&builder=${encodeURIComponent(builder)}&builder_version=${encodeURIComponent(builder_version)}`);
 
     // Update UI every time a message is received
     eventSource.onmessage = (event) => {