From dcfbf9470c62f0a4465878924a8d9febf6e44483 Mon Sep 17 00:00:00 2001
From: Padraig Gleeson <p.gleeson@gmail.com>
Date: Wed, 20 Sep 2023 21:49:24 +0100
Subject: [PATCH 1/7] Test OSBv2_EXPANSE_0.7.3

---
 example/testParam.properties | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/example/testParam.properties b/example/testParam.properties
index 388298c..a4a55c7 100644
--- a/example/testParam.properties
+++ b/example/testParam.properties
@@ -1,4 +1,4 @@
-toolId=NEURON_EXPANSE
+toolId=OSBv2_EXPANSE_0.7.3
 number_cores_=1
 number_nodes_=1
 tasks_per_node_=1

From 52d6a9fb8ed5e2b82d3fb9752b9591c0fa044ef2 Mon Sep 17 00:00:00 2001
From: pgleeson <p.gleeson@gmail.com>
Date: Thu, 21 Sep 2023 16:42:54 +0100
Subject: [PATCH 2/7] To v1.0.4; testing toolId=OSBv2_EXPANSE_0_7_3

---
 example/testParam.properties | 2 +-
 setup.cfg                    | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/example/testParam.properties b/example/testParam.properties
index a4a55c7..885f985 100644
--- a/example/testParam.properties
+++ b/example/testParam.properties
@@ -1,4 +1,4 @@
-toolId=OSBv2_EXPANSE_0.7.3
+toolId=OSBv2_EXPANSE_0_7_3
 number_cores_=1
 number_nodes_=1
 tasks_per_node_=1
diff --git a/setup.cfg b/setup.cfg
index 240a3c6..5991710 100644
--- a/setup.cfg
+++ b/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

From 5ed2997eaefc30aaf5d22c6d33951e0404b684fe Mon Sep 17 00:00:00 2001
From: "Ankur Sinha (Ankur Sinha Gmail)" <sanjay.ankur@gmail.com>
Date: Wed, 1 Nov 2023 18:25:54 +0000
Subject: [PATCH 3/7] debug: netpyne

---
 example/example.zip            | Bin 629 -> 713 bytes
 example/example_dir/example.py |  21 +++++++++++++--------
 example/testParam.properties   |   5 +++--
 3 files changed, 16 insertions(+), 10 deletions(-)

diff --git a/example/example.zip b/example/example.zip
index e39fd0e84c958c784994224faff9f91d5b1b3212..cebaa23109b2ad21a49bcbd8d56fd37206708d4c 100644
GIT binary patch
literal 713
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zHIciz4cu#DqrYt8eOoBOa&?)kqM2$yNO1Ct-Tt0)mT0f)R_Xfl^W*euQFr(3Fy!MX
zoD{0y!TVc7fzd*E%7OmlyV;lK{cZ3*P`j>ka?o`}zc;_99yt2*X!wtx6|BAriT|gl
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literal 629
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zzg;A2&0csR^@D<FaL5IQJJlY&&woBXGlTur9g#aLwiX&ZGdt3_GFHoHo!a#eM*ADJ
zDpG&FFx?>GbMM#%E4Hu+j(zucWQo5~`4VGksAg1ow%}T||2|u_If*4IT<eu%bXJGn
zwAy$rDep{M38$jf{KOZg-?B<qS8(n)DC5<bmZh-QaM8i$lgpDAhIlUfF!jKjg&*gt
z&EArB@kx5}k0-9D*A;)w|MgJoa{Vu>MlO*LYNsOSMwe~W)}F5TW<r;ep=sknwomo_
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zMj$IB0?`5+Vj`~SgO~`6NrokjZfGVVM<&p0P-J45&B_LH2NMvk1JWBo1~C8tKcLvf

diff --git a/example/example_dir/example.py b/example/example_dir/example.py
index 57c2c22..3bded64 100644
--- a/example/example_dir/example.py
+++ b/example/example_dir/example.py
@@ -7,16 +7,21 @@
 """
 
 
+from netpyne import specs
 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]
-    for i in dists:
-        print(i, file=f)
+    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)
 
-print("Done!")
\ No newline at end of file
+    print(f"Args are: {sys.argv}")
+    if sys.argv.count("-nogui") > 0:
+        print("nogui found")
+    print("Done!")
diff --git a/example/testParam.properties b/example/testParam.properties
index 885f985..5397125 100644
--- a/example/testParam.properties
+++ b/example/testParam.properties
@@ -1,7 +1,8 @@
 toolId=OSBv2_EXPANSE_0_7_3
-number_cores_=1
+number_cores_=2
 number_nodes_=1
-tasks_per_node_=1
+tasks_per_node_=2
 runtime_=0.5
 nrnivmodl_o_=0
 filename_=example.py
+cmdlineopts_=-nogui

From 2baf02706e6ad55c44dbed14538ee21831c02d7f Mon Sep 17 00:00:00 2001
From: "Ankur Sinha (Ankur Sinha Gmail)" <sanjay.ankur@gmail.com>
Date: Thu, 2 Nov 2023 08:11:56 +0000
Subject: [PATCH 4/7] feat: add netpyne reproducer

---
 example/example_dir/example.py | 7 +++++++
 1 file changed, 7 insertions(+)

diff --git a/example/example_dir/example.py b/example/example_dir/example.py
index 3bded64..9791994 100644
--- a/example/example_dir/example.py
+++ b/example/example_dir/example.py
@@ -8,6 +8,9 @@
 
 
 from netpyne import specs
+from netpyne import sim
+from netpyne import __version__ as version
+
 import sys
 import pkg_resources
 
@@ -21,6 +24,10 @@
         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(f"Args are: {sys.argv}")
     if sys.argv.count("-nogui") > 0:
         print("nogui found")

From 0fb52603f2aeec0e8c14664f509a237f9616812f Mon Sep 17 00:00:00 2001
From: "Ankur Sinha (Ankur Sinha Gmail)" <sanjay.ankur@gmail.com>
Date: Mon, 6 Nov 2023 09:42:16 +0000
Subject: [PATCH 5/7] ci(example): update to test pyneuroml/netpyne imports

to ensure that matplotlib is not also imported
---
 example/example.zip            | Bin 713 -> 894 bytes
 example/example_dir/example.py |  16 +++++++++++-----
 example/testParam.properties   |   2 +-
 3 files changed, 12 insertions(+), 6 deletions(-)

diff --git a/example/example.zip b/example/example.zip
index cebaa23109b2ad21a49bcbd8d56fd37206708d4c..86de20e018134b770a0c99e772c5aadf315bc3d5 100644
GIT binary patch
literal 894
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zFf%ZKi2$G}B0zl{U{hqaZRb&8Vql16VPFtLGX-j*UO^??Jdl}a=H&)?_g^*;*!Mh~
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J!2H3$001E3S3Up$

delta 527
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z&_A&{WA-@j((sy9yI;kw+_zjMPhx}Zq%+s_>{n!RS2Ri0sXug$mON&$gH2p&TSaN?
zk6i~YG%f#cYdrhF>!dbcjrzW#+cEpk-hDZ5nbpIe!p&9I@6F!{TO6zOIsW(a>U+i0
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d85lW}|1in$p+?(eHD-OVR0OjE8!Hni{sC>0-`4;D

diff --git a/example/example_dir/example.py b/example/example_dir/example.py
index 9791994..3ccb572 100644
--- a/example/example_dir/example.py
+++ b/example/example_dir/example.py
@@ -10,6 +10,7 @@
 from netpyne import specs
 from netpyne import sim
 from netpyne import __version__ as version
+from pyneuroml import pynml
 
 import sys
 import pkg_resources
@@ -21,14 +22,19 @@
         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)
 
+    # 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")
+
+    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(f"Args are: {sys.argv}")
-    if sys.argv.count("-nogui") > 0:
-        print("nogui found")
     print("Done!")
diff --git a/example/testParam.properties b/example/testParam.properties
index 5397125..edaff50 100644
--- a/example/testParam.properties
+++ b/example/testParam.properties
@@ -1,6 +1,6 @@
 toolId=OSBv2_EXPANSE_0_7_3
 number_cores_=2
-number_nodes_=1
+number_nodes_=2
 tasks_per_node_=2
 runtime_=0.5
 nrnivmodl_o_=0

From 9c92f117a7fce6b27c2f4c73b967947e3421ff7a Mon Sep 17 00:00:00 2001
From: "Ankur Sinha (Ankur Sinha Gmail)" <sanjay.ankur@gmail.com>
Date: Wed, 23 Oct 2024 16:43:52 +0100
Subject: [PATCH 6/7] feat: support py3.8 - py3.13

---
 .github/workflows/ci.yml | 2 +-
 setup.cfg                | 3 ++-
 2 files changed, 3 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 9b75d92..9e8c593 100644
--- a/.github/workflows/ci.yml
+++ b/.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:
diff --git a/setup.cfg b/setup.cfg
index 5991710..fe96572 100644
--- a/setup.cfg
+++ b/setup.cfg
@@ -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]

From 0748b56dda7b2a457bfcd2ea4e3ef9a98bc2f76e Mon Sep 17 00:00:00 2001
From: Padraig Gleeson <p.gleeson@gmail.com>
Date: Tue, 22 Apr 2025 12:22:21 +0100
Subject: [PATCH 7/7] minor typos

---
 pynsgr/commands/nsgr_job.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/pynsgr/commands/nsgr_job.py b/pynsgr/commands/nsgr_job.py
index 29da93a..e86fd4d 100644
--- a/pynsgr/commands/nsgr_job.py
+++ b/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.
     """