swancustomenvironments: Remove swan middle layer

Due to the fact `venv-pack` (used by nxcals) can only ship one environment (user's), the packages installed in the middle layer won't be shipped, which leads to discrepancies in the results. For that reason, we remove this middle layer and ignore the extra packages installed by swan, ensuring they stay updated and reliable.
In spite of this, the requirements file must not be modified, which means a temporary and modified version of requirements.txt has to be created and used for the installation

SwanCustomEnvironments/swancustomenvironments/scripts/builders/accpy.sh

@@ -1,27 +1,10 @@
 #!/bin/bash
 
-# Create a middle layer for installing ipykernel, putting it apart from the user environment
-uv venv $SWAN_ENV --seed 2>&1
-source $SWAN_ENV/bin/activate
-uv pip install "ipykernel==${IPYKERNEL_VERSION}"
-SWAN_PACKAGES_PATH=$(python3 -c 'import sysconfig; print(sysconfig.get_paths()["purelib"])')
-deactivate
-
 # If using NXCALS, we need to also install the Spark packages and their dependencies in the SWAN environment
 if [ -n "${USE_NXCALS}" ]; then
     SPARKCONNECTOR="sparkconnector==$(python -c 'import sparkconnector; print(sparkconnector.__version__)')"
     SPARKMONITOR="sparkmonitor==$(python -c 'import sparkmonitor; print(sparkmonitor.__version__)')"
     SPARKCONNECTOR_DEPENDENCIES="swanportallocator requests" # TODO: Remove swanportallocator and requests installation when the SparkConnector package gets properly updated
-
-    # Activate the SWAN environment for installing the Spark packages
-    source $SWAN_ENV/bin/activate
-    uv pip install ${SPARKMONITOR} ${SPARKCONNECTOR_DEPENDENCIES} 2>&1
-
-    # -------------- HACK SECTION --------------
-    # Install SPARKCONNECTOR_DEPENDENCIES separately, install SparkConnector without its dependencies and change the configuration file
-    # TODO: Remove this when the SparkConnector package gets properly updated
-    uv pip install ${SPARKCONNECTOR} --no-deps 2>&1
-    wget https://raw.githubusercontent.com/swan-cern/jupyter-extensions/refs/heads/swan-on-tn/SparkConnector/sparkconnector/configuration.py -O ${SWAN_PACKAGES_PATH}/sparkconnector/configuration.py 2>&1
 fi
 
 # Set up Acc-Py and create the environment
@@ -36,7 +19,7 @@ eval "${ACTIVATE_ENV_CMD}"
 # Install user-requested packages in the environment.
 # Use uv for better performance if environment is fully resolved;
 # Otherwise, use pip for resolution (more reliable long-term).
-_log "Installing packages from ${REQ_PATH}..."
+_log "Installing packages from ${ORIGINAL_REQ_PATH}..."
 if [ "${RESOLVED_REQ}" = true ]; then
     # Use the same pip configuration as the Acc-Py default pip
     ACCPY_PIP_CONF="-i $(pip config get global.index-url) --allow-insecure-host $(pip config get global.trusted-host)"
@@ -48,8 +31,19 @@ if [ $? -ne 0 ]; then
     exit 1
 fi
 
-# Inject middle layer packages into the user environment by adding a .pth file to
-# the environment site-packages that contains the path to the middle layer site-packages
-USER_PACKAGES_PATH=$(python3 -c 'import sysconfig; print(sysconfig.get_paths()["purelib"])')
-echo ${SWAN_PACKAGES_PATH} > ${USER_PACKAGES_PATH}/$(basename $SWAN_ENV).pth
+if [ -n "${USE_NXCALS}" ]; then
+    # For NXCALS, install the Spark packages and their dependencies, using the according tool for its resolution
+    if [ "${RESOLVED_REQ}" = true ]; then
+        uv pip install ${ACCPY_PIP_CONF} ${SPARKMONITOR} ${SPARKCONNECTOR_DEPENDENCIES} 2>&1
+        uv pip install ${ACCPY_PIP_CONF} ${SPARKCONNECTOR} --no-deps 2>&1
+    else
+        pip install ${SPARKMONITOR} ${SPARKCONNECTOR_DEPENDENCIES} 2>&1
+        pip install ${SPARKCONNECTOR} --no-deps 2>&1
+    fi
 
+    # -------------- HACK SECTION --------------
+    # Install SPARKCONNECTOR_DEPENDENCIES separately, install SparkConnector without its dependencies and change the configuration file
+    # TODO: Remove this when the SparkConnector package gets properly updated
+    USER_PACKAGES_PATH=$(python3 -c 'import sysconfig; print(sysconfig.get_paths()["purelib"])')
+    wget https://raw.githubusercontent.com/swan-cern/jupyter-extensions/refs/heads/swan-on-tn/SparkConnector/sparkconnector/configuration.py -O ${USER_PACKAGES_PATH}/sparkconnector/configuration.py 2>&1
+fi

SwanCustomEnvironments/swancustomenvironments/scripts/builders/venv.sh

@@ -1,12 +1,5 @@
 #!/bin/bash
 
-# Create a middle layer for installing ipykernel, putting it apart from the user environment
-uv venv $SWAN_ENV --seed 2>&1
-source $SWAN_ENV/bin/activate
-uv pip install "ipykernel==${IPYKERNEL_VERSION}"
-SWAN_PACKAGES_PATH=$(python3 -c 'import sysconfig; print(sysconfig.get_paths()["purelib"])')
-deactivate
-
 if [ "${RESOLVED_REQ}" = true ]; then
     uv venv ${ENV_PATH} --seed 2>&1
 else
@@ -21,7 +14,7 @@ eval "${ACTIVATE_ENV_CMD}"
 # Install user-requested packages in the environment.
 # Use uv for better performance if environment is fully resolved;
 # Otherwise, use pip for resolution (more reliable long-term).
-_log "Installing packages from ${REQ_PATH}..."
+_log "Installing packages from ${ORIGINAL_REQ_PATH}..."
 if [ "${RESOLVED_REQ}" = true ]; then
     uv pip install -r "${REQ_PATH}" ${IPYKERNEL} 2>&1
 else
@@ -30,8 +23,3 @@ fi
 if [ $? -ne 0 ]; then
     exit 1
 fi
-
-# Inject middle layer packages into the user environment by adding a .pth file to
-# the environment site-packages that contains the path to the middle layer site-packages
-USER_PACKAGES_PATH=$(python3 -c 'import sysconfig; print(sysconfig.get_paths()["purelib"])')
-echo ${SWAN_PACKAGES_PATH} > ${USER_PACKAGES_PATH}/$(basename $SWAN_ENV).pth

SwanCustomEnvironments/swancustomenvironments/scripts/makenv.sh

@@ -162,19 +162,27 @@ IPYKERNEL="ipykernel==$(python -c 'import ipykernel; print(ipykernel.__version__
 if [ -f "${TMP_REPO_PATH}/requirements.txt" ]; then
     # Fully resolved requirements (requirements.txt) take precedence
     RESOLVED_REQ=true
-    REQ_PATH="${TMP_REPO_PATH}/requirements.txt"
+    ORIGINAL_REQ_PATH="${TMP_REPO_PATH}/requirements.txt"
+    REQ_PATH=$(mktemp)
+    if [ -n "${USE_NXCALS}" ]; then
+        grep -v -E "sparkmonitor|sparkconnector|swanportallocator|requests|ipykernel" ${ORIGINAL_REQ_PATH} > ${REQ_PATH}
+    else
+        grep -v -E "ipykernel" ${ORIGINAL_REQ_PATH} > ${REQ_PATH}
+
+    fi
 elif [ -f "${TMP_REPO_PATH}/requirements.in" ]; then
     # If only requirements.in is present, proceed with high-level requirements
     RESOLVED_REQ=false
-    REQ_PATH="${TMP_REPO_PATH}/requirements.in"
+    ORIGINAL_REQ_PATH="${TMP_REPO_PATH}/requirements.in"
+    REQ_PATH="${ORIGINAL_REQ_PATH}"
 else
     # There are no requirements files (neither requirements.txt nor requirements.in) in the repository
     _log "ERROR: No requirements file found. You must provide a requirements.in or requirements.txt file." && exit 1
 fi
 
 # Check if the requirements file contains the nxcals package, if the user activated the nxcals option
 if [ -n "${USE_NXCALS}" ] && ! grep -q "nxcals" "${REQ_PATH}"; then
-    _log "ERROR: The NXCALS cluster was selected but the requirements file (${REQ_PATH}) does not contain the nxcals package." && exit 1
+    _log "ERROR: The NXCALS cluster was selected but the requirements file (${ORIGINAL_REQ_PATH}) does not contain the nxcals package." && exit 1
 fi
 
 _log "Creating environment ${ENV_NAME} using ${BUILDER}${BUILDER_VERSION:+ (${BUILDER_VERSION})}..."