Testing toolId=OSBv2_EXPANSE_0_7_3 & other fixes

.github/workflows/ci.yml

@@ -17,7 +17,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ["3.7", "3.9", "3.10", "3.11"]
+        python-version: ["3.8", "3.9", "3.10", "3.11", "3.12", "3.13"]
         runs-on: [ubuntu-latest, windows-latest, macos-latest]
 
     steps:

example/example_dir/example.py

@@ -7,16 +7,34 @@
 """
 
 
+from netpyne import specs
+from netpyne import sim
+from netpyne import __version__ as version
+from pyneuroml import pynml
+
 import sys
 import pkg_resources
 
-print("Running example script to list Python packages...")
+if __name__ == "__main__":
+    print("Running example script to list Python packages...")
+
+    with open("output.txt", "w") as f:
+        print(f"Python version is: {sys.version}", file=f)
+        print("Installed packages on NSG:", file=f)
+        dists = [str(d).replace(" ", "==") for d in pkg_resources.working_set]
+
+    # also check if netpyne/pyneuroml etc. cause importing matplotlib: we can't
+    # use matplotlib on NSG because the different mpi processes cause the same
+    # cache file to be read, which causes crashes
+    print("Checking if matplotlib loaded...")
+    print(f"Args are: {sys.argv}")
+    if sys.argv.count("-nogui") > 0:
+        print("nogui option found")
 
-with open("output.txt", "w") as f:
-    print(f"Python version is: {sys.version}", file=f)
-    print("Installed packages on NSG:", file=f)
-    dists = [str(d).replace(" ", "==") for d in pkg_resources.working_set]
     for i in dists:
         print(i, file=f)
+    for k in sys.modules.keys():
+        if "matplotlib" in k:
+            print(f"matplotlib still loaded: {k}")
 
-print("Done!")
+    print("Done!")

example/testParam.properties

@@ -1,7 +1,8 @@
-toolId=NEURON_EXPANSE
-number_cores_=1
-number_nodes_=1
-tasks_per_node_=1
+toolId=OSBv2_EXPANSE_0_7_3
+number_cores_=2
+number_nodes_=2
+tasks_per_node_=2
 runtime_=0.5
 nrnivmodl_o_=0
 filename_=example.py
+cmdlineopts_=-nogui

pynsgr/commands/nsgr_job.py

@@ -50,9 +50,9 @@ def nsgr_job(argv):
         nsgr_job -l
             list the user's jobs
         nsgr_job -j JOBHANDLE
-            shows status of the job whose jobhandle is JOBHANDLE
+            shows status of the job whose job handle is JOBHANDLE
         nsgr_job -j JOBHANDLE -d
-            download's results of the job whose jobhandle is JOBHANDLE
+            downloads results of the job whose job handle is JOBHANDLE
         nsgr_job -j JOBHANDLE -r
             cancel and remove the specified job.
     """

setup.cfg

@@ -1,6 +1,6 @@
 [metadata]
 name = pynsgr
-version = 1.0.3
+version = 1.0.4
 author = "Terry Schwartz, Padraig Gleeson"
 author_email = terri@sdsc.edu
 url = https://github.com/OpenSourceBrain/pynsgr
@@ -12,11 +12,12 @@ classifiers=
     License :: OSI Approved :: MIT License
     Natural Language :: English
     Operating System :: OS Independent
-    Programming Language :: Python :: 3.7
     Programming Language :: Python :: 3.8
     Programming Language :: Python :: 3.9
     Programming Language :: Python :: 3.10
     Programming Language :: Python :: 3.11
+    Programming Language :: Python :: 3.12
+    Programming Language :: Python :: 3.13
     Topic :: Scientific/Engineering
 
 [options]