Update VSC install script

Author: tovrstra

.gitignore

@@ -9,7 +9,7 @@ hints.txt
 .idea
 .vscode
 venvs
-setup/pip_inspect.json
+setup/pip-inspect.json
 slurm-*.*
 Untitled*.ipynb
 .virtual_documents

setup/extract_requirements.py

@@ -1,9 +1,14 @@
 #!/usr/bin/env python
+"""Extract Python packages installed in software modules.
+
+Run `pip inspect > pip-inspect.json` before calling this script.
+"""
+
 import json
 
 
 def main():
-    with open("pip_inspect.json") as fh:
+    with open("pip-inspect.json") as fh:
         data = json.load(fh)
 
     modules = {}
@@ -18,9 +23,9 @@ def main():
         module = "/".join(words)
         modules.setdefault(module, []).append(f"{name}=={version}")
 
-    for module, reqs in modules.items():
+    for module, reqs in sorted(modules.items()):
         print(f"# {module}")
-        for req in reqs:
+        for req in sorted(reqs):
             print(req)
         print()
 

setup/ipython_kernel_config.py

@@ -1,3 +1,3 @@
 # ruff: noqa: F821
-c.InteractiveShellApp.matplotlib = "widget"
+c.InteractiveShellApp.matplotlib = "inline"
 c.InlineBackend.figure_format = "svg"

setup/job_install_vsc.sh

@@ -8,7 +8,9 @@
 # the Tier-2 cluster in Ghent, on which OpenMM is already
 # installed.
 
+PYTHON_VERSION='3.13.1-GCCcore-14.2.0'
 MODULE_REQUIREMENTS="
+Python/${PYTHON_VERSION}
 matplotlib/3.10.3-gfbf-2025a
 MDTraj/1.11.0-foss-2025a
 nglview/3.1.4-foss-2025a
@@ -20,12 +22,10 @@ scikit-learn/1.7.0-gfbf-2025a
 SciPy-bundle/2025.06-gfbf-2025a
 tqdm/4.67.1-GCCcore-14.2.0
 "
-
 MODULE_REQUIREMENTS=$(tr '\n' ' ' <<< ${MODULE_REQUIREMENTS})
-PYTHON_VERSION='3.13.1-GCCcore-14.2.0'
 PYTHON_RELEASE=$(awk -F. '{print $1"."$2}' <<< ${PYTHON_VERSION})
 VSC_ARCH="${VSC_ARCH_LOCAL}${VSC_ARCH_SUFFIX}"
-PIP_TOOLS="pip==24.2 build==1.2.1 pip-tools==7.4.1 pyproject-hooks==1.1.0"
+PIP_TOOLS="pip==25.2 build==1.3.0 pip-tools==7.5.0 pyproject-hooks==1.2.0"
 ROOT=${VSC_DATA}/msbs
 VENV=${ROOT}/venvs/${VSC_ARCH}/${PYTHON_VERSION}
 
@@ -39,7 +39,7 @@ module load ${MODULE_REQUIREMENTS}
 echo "Modules loaded before installing:"
 module list
 
-python -m venv ${VENV} --system-site-packages
+python -m venv ${VENV} # --system-site-packages
 source ${VENV}/bin/activate
 pip install ${PIP_TOOLS}