swancustomenvironments: Add support for pyproject.toml

Some constraints need to be taken into account:
- `pyproject.toml` does not use `-r` for installing its requirements. Instead, needs to be specified by its folder path.
  - For this reason, the `REQ_PATH` must be changed right before it is used for installation. Since it is also used for checking the presence of `nxcals` in it.
- The precedence must follow the following order:
  - `requirements.txt` -> `pyproject.toml` -> `requirements.in`
- One of the packages included in the environment is the project's package itself, which will point to its path during the installation process. However, as we later on move the project to `SWAN_projects`, the reference will still point to `/tmp/<project_name>`.
  - This represents a problem because after the first clone of the project, if the user generates a `requirements.txt` file, it will still be pointing to `/tmp`. And since the project is no longer there, the next creation of the environment will continuously fail.
  - For fixing this, the simplest way is to reinstall the requirements right after moving the project out of `/tmp`. Since all its dependencies are installed already, they will be automatically skipped and only the project package's reference will get updated, which makes this reinstallation process way faster
  - Example of a well referenced package `acc-py-example-package @ file:///eos/user/r/rhenriqu/SWAN_projects/python-package`

Author: rodrigo-sobral

SwanCustomEnvironments/swancustomenvironments/scripts/builders/accpy.sh

@@ -19,17 +19,24 @@ eval "${ACTIVATE_ENV_CMD}"
 # Use uv for better performance if environment is fully resolved;
 # Otherwise, use pip for resolution (more reliable long-term).
 _log "Installing packages from ${REQ_PATH}..."
+
+# If REQ_PATH points to a pyproject.toml, change it to the its parent folder
+# so pip doesn't get called with "-r pyproject.toml", which is invalid.
+if [[ "${REQ_PATH}" == *pyproject.toml ]]; then
+    REQ_PATH="$(dirname "${REQ_PATH}")"
+fi
+
 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)"
-    uv pip install ${ACCPY_PIP_CONF} -r "${REQ_PATH}" 2>&1
+    uv pip install ${ACCPY_PIP_CONF} ${R_FLAG} "${REQ_PATH}" 2>&1
     if [ $? -ne 0 ]; then
         return 1
     fi
     # Enforce installation of our version of ipykernel
     uv pip install ${ACCPY_PIP_CONF} ${IPYKERNEL} 2>&1
 else
-    pip install -r "${REQ_PATH}" 2>&1
+    pip install ${R_FLAG} "${REQ_PATH}" 2>&1
     if [ $? -ne 0 ]; then
         return 1
     fi

SwanCustomEnvironments/swancustomenvironments/scripts/builders/venv.sh

@@ -15,15 +15,21 @@ eval "${ACTIVATE_ENV_CMD}"
 # Use uv for better performance if environment is fully resolved;
 # Otherwise, use pip for resolution (more reliable long-term).
 _log "Installing packages from ${REQ_PATH}..."
+
+# If REQ_PATH points to a pyproject.toml, change it to the its parent folder
+# so pip doesn't get called with "-r pyproject.toml", which is invalid.
+if [[ "${REQ_PATH}" == *pyproject.toml ]]; then
+    REQ_PATH="$(dirname "${REQ_PATH}")"
+fi
 if [ "${RESOLVED_REQ}" = true ]; then
-    uv pip install -r "${REQ_PATH}" 2>&1
+    uv pip install ${R_FLAG} "${REQ_PATH}" 2>&1
     if [ $? -ne 0 ]; then
         return 1
     fi
     # Enforce installation of our version of ipykernel and its dependencies
     uv pip install ${IPYKERNEL} 2>&1
 else
-    pip install -r "${REQ_PATH}" 2>&1
+    pip install ${R_FLAG} "${REQ_PATH}" 2>&1
     if [ $? -ne 0 ]; then
         return 1
     fi

SwanCustomEnvironments/swancustomenvironments/scripts/makenv.sh

@@ -175,20 +175,27 @@ fi
 # --------------------------------------------------------------------------------------------
 # Create and set up the environment
 
+R_FLAG=""
 ENV_PATH="/home/$USER/${ENV_NAME}"
 IPYKERNEL="ipykernel==$(python -c 'import ipykernel; print(ipykernel.__version__)')"
 
 if [ -f "${TMP_REPO_PATH}/requirements.txt" ]; then
     # Fully resolved requirements (requirements.txt) take precedence
     RESOLVED_REQ=true
+    R_FLAG=-r
     REQ_PATH="${TMP_REPO_PATH}/requirements.txt"
+elif [ -f "${TMP_REPO_PATH}/pyproject.toml" ]; then
+    # Else if pyproject.toml is present, proceed with high-level requirements
+    RESOLVED_REQ=false
+    REQ_PATH="${TMP_REPO_PATH}/pyproject.toml"
 elif [ -f "${TMP_REPO_PATH}/requirements.in" ]; then
     # If only requirements.in is present, proceed with high-level requirements
     RESOLVED_REQ=false
+    R_FLAG=-r
     REQ_PATH="${TMP_REPO_PATH}/requirements.in"
 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
+    # There are no requirements files (neither requirements.txt, pyproject.toml nor requirements.in) in the repository
+    _log "ERROR: No requirements file found. You must provide a requirements.in, pyproject.toml, or requirements.txt file." && exit 1
 fi
 
 # Check if the requirements file contains the nxcals package, if the user activated the nxcals option
@@ -249,6 +256,13 @@ mv -f ${TMP_KERNEL} ${KERNEL_JSON} 2>&1
 if [ ! -d "${GIT_REPO_PATH}" ]; then
     mkdir -p ${GIT_HOME}
     mv ${TMP_REPO_PATH} ${GIT_HOME}
+    # If pyproject.toml was used, reinstall the package reference, because it was
+    # initially installed under /tmp (only if the repo was not previously cloned)
+    # So, when requirements.txt is generated, it will point to the actual path and not /tmp
+    if [ "${R_FLAG}" != "-r" ]; then
+        REQ_PATH="${GIT_REPO_PATH}"
+        pip install "${REQ_PATH}" 2>&1 # Use installed env pip
+    fi
 fi
 
 _log "REPO_PATH:${GIT_REPO_PATH#$HOME}"