Set up virtual environment for cluster users

.github/workflows/testsuite.yml

@@ -20,12 +20,15 @@ jobs:
       - name: Install dependencies
         run: |
           module load ESPResSo/4.2.1-foss-2023a
-          python3 -m pip install --user -r requirements.txt
+          python3 -m venv --system-site-packages pymbe
+          source pymbe/bin/activate
+          python3 maintainer/configure_venv.py
+          python3 -m pip install -r requirements.txt
+          deactivate
       - name: Run testsuite
         run: |
           module load ESPResSo/4.2.1-foss-2023a
-          export OLD_PYTHONPATH="${PYTHONPATH}"
-          export PYTHONPATH="$(realpath .)${PYTHONPATH:+:$PYTHONPATH}"
+          source pymbe/bin/activate
           make testsuite
-          export PYTHONPATH="${OLD_PYTHONPATH}"
+          deactivate
         shell: bash

README.md

@@ -52,12 +52,30 @@ the path to the ESPResSo build folder:
 ```sh
 python3 -m venv pymbe
 source pymbe/bin/activate
-python3 maintainer/configure_venv.py /home/user/Documents/espresso/build # adapt this
+python3 maintainer/configure_venv.py --espresso_path=~/espresso/build # adapt path
 python3 -m pip install -r requirements.txt
 deactivate
 ```
 
-We highlight that the path `/home/user/Documents/espresso/build` is just an example of a possible absolute path to the ESPResSo build folder. The user should change this path to match the local path were ESPResSo was installed.
+We highlight that the path `~/espresso/build` is just an example of a possible
+path to the ESPResSo build folder. The user should change this path to match
+the local path were ESPResSo was installed.
+
+Cluster users who rely on module files to load dependencies should opt for the
+following alternative:
+
+```sh
+module load ESPResSo/4.2.1-foss-2022a # adapt module name
+python3 -m venv --system-site-packages pymbe
+source pymbe/bin/activate
+python3 maintainer/configure_venv.py
+python3 -m pip install -r requirements.txt
+deactivate
+module purge
+```
+
+We highlight that the module files need to be loaded before every activation
+of the virtual environment.
 
 Now you can use pyMBE and ESPResSo by activating the virtual environment:
 

maintainer/configure_venv.py

@@ -1,6 +1,11 @@
 import os
 import argparse
 import sysconfig
+try:
+    import espressomd
+    espressomd_found = True
+except ModuleNotFoundError:
+    espressomd_found = False
 
 
 def make_pth(name, path):
@@ -12,11 +17,13 @@ def make_pth(name, path):
 
 
 parser = argparse.ArgumentParser(description="Configure pyBME and ESPResSo module paths")
-parser.add_argument("espresso_build_path", type=str, help="Path to the ESPResSo build folder")
+parser.add_argument("--espresso_path", type=str, required=not espressomd_found,
+                    help="Path to the ESPResSo build folder")
 args = parser.parse_args()
 
 if not os.environ.get("VIRTUAL_ENV"):
     raise RuntimeError("This script should be run in a virtual environment")
 
+if not espressomd_found:
+    make_pth("espresso", os.path.join(args.espresso_path, "src", "python"))
 make_pth("pymbe", os.path.dirname(os.path.dirname(__file__)))
-make_pth("espresso", os.path.join(args.espresso_build_path, "src", "python"))