Merge branch 'development' of https://github.com/NeuroML/pyNeuroML in…

…to development
AdityaBITMESRA · Jun 18, 2024 · 67f7319 · 67f7319
2 parents 31bc91d + 9c89227
commit 67f7319
Show file tree

Hide file tree

Showing 60 changed files with 754 additions and 495 deletions.
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -7,7 +7,7 @@ on:
       - development
       - experimental
       - 'test*'
-  pull_request:
+  pull_request_target:
     branches:
       - master
       - development
@@ -18,6 +18,8 @@ jobs:
   build:
 
     runs-on: ubuntu-latest
+    permissions:
+      pull-requests: write
     strategy:
       matrix:
         python-version: ["3.8", "3.9", "3.10", "3.11", "3.12"]
@@ -51,7 +53,23 @@ jobs:
 
         ./test-ghactions.sh -neuron
 
-    - name: Lint with ruff
-      run: |
-        pip install ruff
-        ruff . --exit-zero --show-source
+    - name: Code Coverage Summary
+      uses: irongut/[email protected]
+      if: ${{ matrix.python-version == '3.12' }}
+      with:
+        output: both
+        filename: coverage.xml
+        badge: true
+        format: markdown
+        indicators: true
+        fail_below_min: false
+        hide_complexity: true
+        hide_branch_rate: true
+        thresholds: '50 75'
+
+    - name: Add Coverage PR Comment
+      uses: marocchino/sticky-pull-request-comment@v2
+      if: ${{ github.event_name == 'pull_request_target' && matrix.python-version == '3.12' }}
+      with:
+        recreate: true
+        path: code-coverage-results.md
diff --git a/.github/workflows/ruff.yml b/.github/workflows/ruff.yml
@@ -0,0 +1,16 @@
+name: Ruff
+on:
+  pull_request:
+    branches:
+      - master
+      - development
+      - experimental
+      - 'test*'
+jobs:
+  ruff:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - uses: chartboost/ruff-action@v1
+        with:
+          changed-files: 'true'
diff --git a/.gitignore b/.gitignore
@@ -175,3 +175,9 @@ arm64
 /examples/test_data/xppaut/fhn_brain.py
 /examples/test_data/xppaut/nca_2.ode
 /examples/test_data/xppaut/wc_2.ode
+
+coverage.xml
+/examples/LEMS_NML2_Ex5_DetCell.sedml.omex
+/examples/hhcell.swc
+/examples/metadata.rdf
+/tests/utils/test_translation.net.nml
diff --git a/examples/LeakConductance.mod b/examples/LeakConductance.mod
@@ -3,9 +3,9 @@ TITLE Mod file for component: Component(id=LeakConductance type=ionChannelHH)
 COMMENT
 
     This NEURON file has been generated by org.neuroml.export (see https://github.com/NeuroML/org.neuroml.export)
-         org.neuroml.export  v1.10.0
-         org.neuroml.model   v1.10.0
-         jLEMS               v0.11.0
+         org.neuroml.export  v1.10.1
+         org.neuroml.model   v1.10.1
+         jLEMS               v0.11.1
 
 ENDCOMMENT
 

diff --git a/man/man1/pynml-archive.1 b/man/man1/pynml-archive.1
@@ -1,7 +1,7 @@
 .\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.49.3.
-.TH PYNML-ARCHIVE "1" "May 2024" "pynml-archive v1.2.15" "User Commands"
+.TH PYNML-ARCHIVE "1" "June 2024" "pynml-archive v1.3.1" "User Commands"
 .SH NAME
-pynml-archive \- manual page for pynml-archive v1.2.15
+pynml-archive \- manual page for pynml-archive v1.3.1
 .SH DESCRIPTION
 usage: pynml\-archive [\-h] [\-zipfileName <zip file name>]
 .TP
@@ -51,4 +51,4 @@ master file.
 Please see https://docs.neuroml.org for complete documentation on the NeuroML standard and the software ecosystem.
 .SH ENVIRONMENT
 .PP
-pyNeuroML v1.2.15 (libNeuroML v0.5.9, jNeuroML v0.13.0)
+pyNeuroML v1.3.1 (libNeuroML v0.6.2, jNeuroML v0.13.1)
diff --git a/man/man1/pynml-channelanalysis.1 b/man/man1/pynml-channelanalysis.1
@@ -1,7 +1,7 @@
 .\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.49.3.
-.TH PYNML-CHANNELANALYSIS "1" "May 2024" "pynml-channelanalysis v1.2.15" "User Commands"
+.TH PYNML-CHANNELANALYSIS "1" "June 2024" "pynml-channelanalysis v1.3.1" "User Commands"
 .SH NAME
-pynml-channelanalysis \- manual page for pynml-channelanalysis v1.2.15
+pynml-channelanalysis \- manual page for pynml-channelanalysis v1.3.1
 .SH DESCRIPTION
 usage: pynml\-channelanalysis [\-h] [\-v] [\-minV <min v>] [\-maxV <max v>]
 .TP
@@ -111,4 +111,4 @@ plot current vs voltage for ion channel
 Please see https://docs.neuroml.org for complete documentation on the NeuroML standard and the software ecosystem.
 .SH ENVIRONMENT
 .PP
-pyNeuroML v1.2.15 (libNeuroML v0.5.9, jNeuroML v0.13.0)
+pyNeuroML v1.3.1 (libNeuroML v0.6.2, jNeuroML v0.13.1)
diff --git a/man/man1/pynml-channelml2nml.1 b/man/man1/pynml-channelml2nml.1
@@ -1,7 +1,7 @@
 .\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.49.3.
-.TH PYNML-CHANNELML2NML "1" "May 2024" "pynml-channelml2nml v1.2.15" "User Commands"
+.TH PYNML-CHANNELML2NML "1" "June 2024" "pynml-channelml2nml v1.3.1" "User Commands"
 .SH NAME
-pynml-channelml2nml \- manual page for pynml-channelml2nml v1.2.15
+pynml-channelml2nml \- manual page for pynml-channelml2nml v1.3.1
 .SH DESCRIPTION
 usage: pynml\-channelml2nml [\-h] [\-xsltfile <XSLT file>]
 .TP
@@ -42,4 +42,4 @@ Name of the outputfile file
 Please see https://docs.neuroml.org for complete documentation on the NeuroML standard and the software ecosystem.
 .SH ENVIRONMENT
 .PP
-pyNeuroML v1.2.15 (libNeuroML v0.5.9, jNeuroML v0.13.0)
+pyNeuroML v1.3.1 (libNeuroML v0.6.2, jNeuroML v0.13.1)
diff --git a/man/man1/pynml-modchananalysis.1 b/man/man1/pynml-modchananalysis.1
@@ -1,7 +1,7 @@
 .\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.49.3.
-.TH PYNML-MODCHANANALYSIS "1" "May 2024" "pynml-modchananalysis v1.2.15" "User Commands"
+.TH PYNML-MODCHANANALYSIS "1" "June 2024" "pynml-modchananalysis v1.3.1" "User Commands"
 .SH NAME
-pynml-modchananalysis \- manual page for pynml-modchananalysis v1.2.15
+pynml-modchananalysis \- manual page for pynml-modchananalysis v1.3.1
 .SH DESCRIPTION
 usage: pynml\-modchananalysis [\-h] [\-v] [\-nogui] [\-savePlots] [\-minV <min v>]
 .TP
@@ -76,4 +76,4 @@ Name of the mod file containing the channel
 Please see https://docs.neuroml.org for complete documentation on the NeuroML standard and the software ecosystem.
 .SH ENVIRONMENT
 .PP
-pyNeuroML v1.2.15 (libNeuroML v0.5.9, jNeuroML v0.13.0)
+pyNeuroML v1.3.1 (libNeuroML v0.6.2, jNeuroML v0.13.1)
diff --git a/man/man1/pynml-plotchan.1 b/man/man1/pynml-plotchan.1
@@ -1,7 +1,7 @@
 .\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.49.3.
-.TH PYNML-PLOTCHAN "1" "May 2024" "pynml-plotchan v1.2.15" "User Commands"
+.TH PYNML-PLOTCHAN "1" "June 2024" "pynml-plotchan v1.3.1" "User Commands"
 .SH NAME
-pynml-plotchan \- manual page for pynml-plotchan v1.2.15
+pynml-plotchan \- manual page for pynml-plotchan v1.3.1
 .SH DESCRIPTION
 usage: pynml\-plotchan [\-h] [\-noDistancePlots] [\-nogui]
 .IP
@@ -42,4 +42,4 @@ Do not show plots as they are generated
 Please see https://docs.neuroml.org for complete documentation on the NeuroML standard and the software ecosystem.
 .SH ENVIRONMENT
 .PP
-pyNeuroML v1.2.15 (libNeuroML v0.5.9, jNeuroML v0.13.0)
+pyNeuroML v1.3.1 (libNeuroML v0.6.2, jNeuroML v0.13.1)
diff --git a/man/man1/pynml-plotmorph.1 b/man/man1/pynml-plotmorph.1
@@ -1,7 +1,7 @@
 .\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.49.3.
-.TH PYNML-PLOTMORPH "1" "May 2024" "pynml-plotmorph v1.2.15" "User Commands"
+.TH PYNML-PLOTMORPH "1" "June 2024" "pynml-plotmorph v1.3.1" "User Commands"
 .SH NAME
-pynml-plotmorph \- manual page for pynml-plotmorph v1.2.15
+pynml-plotmorph \- manual page for pynml-plotmorph v1.3.1
 .SH DESCRIPTION
 usage: pynml\-plotmorph [\-h] [\-v] [\-nogui] [\-plane2d <plane, e.g. xy, yz, zx>]
 .TP
@@ -72,4 +72,4 @@ Scale axes so that image is approximately square, for
 Please see https://docs.neuroml.org for complete documentation on the NeuroML standard and the software ecosystem.
 .SH ENVIRONMENT
 .PP
-pyNeuroML v1.2.15 (libNeuroML v0.5.9, jNeuroML v0.13.0)
+pyNeuroML v1.3.1 (libNeuroML v0.6.2, jNeuroML v0.13.1)
diff --git a/man/man1/pynml-plotspikes.1 b/man/man1/pynml-plotspikes.1
@@ -1,10 +1,11 @@
 .\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.49.3.
-.TH PYNML-PLOTSPIKES "1" "May 2024" "pynml-plotspikes v1.2.15" "User Commands"
+.TH PYNML-PLOTSPIKES "1" "June 2024" "pynml-plotspikes v1.3.1" "User Commands"
 .SH NAME
-pynml-plotspikes \- manual page for pynml-plotspikes v1.2.15
+pynml-plotspikes \- manual page for pynml-plotspikes v1.3.1
 .SH DESCRIPTION
-usage: pynml\-plotspikes [\-h] [\-format <format>] [\-rates] [\-showPlotsAlready]
+usage: pynml\-plotspikes [\-h] [\-format <format>] [\-offset] [\-rates]
 .TP
+[\-showPlotsAlready]
 [\-saveSpikePlotTo <spiketime plot filename>]
 [\-rateWindow <rate window>] [\-rateBins <rate bins>]
 <spiketime file> [<spiketime file> ...]
@@ -20,13 +21,15 @@ List of text file containing spike times
 show this help message and exit
 .TP
 \fB\-format\fR <format>
-How the spiketimes are represented on each line of
-file: id_t: id of cell, space(s) / tab(s), time of
-spike (default); id_t_nest_dat: id of cell, space(s) /
-tab(s), time of spike, allowing NEST dat file
-comments/metadata; t_id: time of spike, space(s) /
-tab(s), id of cell; sonata: SONATA format HDF5 file
-containing spike times
+How the spiketimes are represented on each line of file:
+.TP
+\- id_t: id of cell, space(s) / tab(s), time of spike (default);
+\- id_t_nest_dat: id of cell, space(s) / tab(s), time of spike, allowing NEST dat file comments/metadata
+\- t_id: time of spike, space(s) / tab(s), id of cell
+\- sonata: SONATA format HDF5 file containing spike times
+.TP
+\fB\-offset\fR
+Toggle whether plots are overlaid or offset
 .TP
 \fB\-rates\fR
 Show a plot of rates
@@ -61,4 +64,4 @@ Number of bins for rate histogram
 Please see https://docs.neuroml.org for complete documentation on the NeuroML standard and the software ecosystem.
 .SH ENVIRONMENT
 .PP
-pyNeuroML v1.2.15 (libNeuroML v0.5.9, jNeuroML v0.13.0)
+pyNeuroML v1.3.1 (libNeuroML v0.6.2, jNeuroML v0.13.1)
diff --git a/man/man1/pynml-plottimeseries.1 b/man/man1/pynml-plottimeseries.1
@@ -1,7 +1,7 @@
 .\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.49.3.
-.TH PYNML-PLOTTIMESERIES "1" "May 2024" "pynml-plottimeseries v1.2.15" "User Commands"
+.TH PYNML-PLOTTIMESERIES "1" "June 2024" "pynml-plottimeseries v1.3.1" "User Commands"
 .SH NAME
-pynml-plottimeseries \- manual page for pynml-plottimeseries v1.2.15
+pynml-plottimeseries \- manual page for pynml-plottimeseries v1.3.1
 .SH DESCRIPTION
 usage: pynml\-plottimeseries [\-h] [\-offset] [\-saveToFile <Image file name>]
 .IP
@@ -42,4 +42,4 @@ Name of the image file to save plot to
 Please see https://docs.neuroml.org for complete documentation on the NeuroML standard and the software ecosystem.
 .SH ENVIRONMENT
 .PP
-pyNeuroML v1.2.15 (libNeuroML v0.5.9, jNeuroML v0.13.0)
+pyNeuroML v1.3.1 (libNeuroML v0.6.2, jNeuroML v0.13.1)
diff --git a/man/man1/pynml-povray.1 b/man/man1/pynml-povray.1
@@ -1,7 +1,7 @@
 .\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.49.3.
-.TH PYNML-POVRAY "1" "May 2024" "pynml-povray v1.2.15" "User Commands"
+.TH PYNML-POVRAY "1" "June 2024" "pynml-povray v1.3.1" "User Commands"
 .SH NAME
-pynml-povray \- manual page for pynml-povray v1.2.15
+pynml-povray \- manual page for pynml-povray v1.3.1
 .SH DESCRIPTION
 usage: pynml\-povray [\-h] [\-split] [\-background <background colour>] [\-movie]
 .TP
@@ -113,4 +113,4 @@ Show segment ids
 Please see https://docs.neuroml.org for complete documentation on the NeuroML standard and the software ecosystem.
 .SH ENVIRONMENT
 .PP
-pyNeuroML v1.2.15 (libNeuroML v0.5.9, jNeuroML v0.13.0)
+pyNeuroML v1.3.1 (libNeuroML v0.6.2, jNeuroML v0.13.1)
diff --git a/man/man1/pynml-sonata.1 b/man/man1/pynml-sonata.1
@@ -1,7 +1,7 @@
 .\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.49.3.
-.TH PYNML-SONATA "1" "May 2024" "pynml-sonata v1.2.15" "User Commands"
+.TH PYNML-SONATA "1" "June 2024" "pynml-sonata v1.3.1" "User Commands"
 .SH NAME
-pynml-sonata \- manual page for pynml-sonata v1.2.15
+pynml-sonata \- manual page for pynml-sonata v1.3.1
 .SH DESCRIPTION
 usage: pynml\-sonata [\-h] [\-h5] [\-jnml] [\-neuron]
 .IP
@@ -51,4 +51,4 @@ jNeuroML_NEURON
 Please see https://docs.neuroml.org for complete documentation on the NeuroML standard and the software ecosystem.
 .SH ENVIRONMENT
 .PP
-pyNeuroML v1.2.15 (libNeuroML v0.5.9, jNeuroML v0.13.0)
+pyNeuroML v1.3.1 (libNeuroML v0.6.2, jNeuroML v0.13.1)
diff --git a/man/man1/pynml-summary.1 b/man/man1/pynml-summary.1
@@ -1,7 +1,7 @@
 .\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.49.3.
-.TH PYNML-SUMMARY "1" "May 2024" "pynml-summary v1.2.15" "User Commands"
+.TH PYNML-SUMMARY "1" "June 2024" "pynml-summary v1.3.1" "User Commands"
 .SH NAME
-pynml-summary \- manual page for pynml-summary v1.2.15
+pynml-summary \- manual page for pynml-summary v1.3.1
 .SH DESCRIPTION
 Usage:
 .PP
@@ -36,4 +36,4 @@ print this help text and exit
 Please see https://docs.neuroml.org for complete documentation on the NeuroML standard and the software ecosystem.
 .SH ENVIRONMENT
 .PP
-pyNeuroML v1.2.15 (libNeuroML v0.5.9, jNeuroML v0.13.0)
+pyNeuroML v1.3.1 (libNeuroML v0.6.2, jNeuroML v0.13.1)
diff --git a/man/man1/pynml-tune.1 b/man/man1/pynml-tune.1
@@ -1,7 +1,7 @@
 .\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.49.3.
-.TH PYNML-TUNE "1" "May 2024" "pynml-tune v1.2.15" "User Commands"
+.TH PYNML-TUNE "1" "June 2024" "pynml-tune v1.3.1" "User Commands"
 .SH NAME
-pynml-tune \- manual page for pynml-tune v1.2.15
+pynml-tune \- manual page for pynml-tune v1.3.1
 .SH DESCRIPTION
 usage: pynml\-tune [\-h] [\-simTime <simTime>] [\-dt <dt>]
 .IP
@@ -149,4 +149,4 @@ as optimisation progresses?
 Please see https://docs.neuroml.org for complete documentation on the NeuroML standard and the software ecosystem.
 .SH ENVIRONMENT
 .PP
-pyNeuroML v1.2.15 (libNeuroML v0.5.9, jNeuroML v0.13.0)
+pyNeuroML v1.3.1 (libNeuroML v0.6.2, jNeuroML v0.13.1)
diff --git a/man/man1/pynml-xpp.1 b/man/man1/pynml-xpp.1
@@ -1,7 +1,7 @@
 .\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.49.3.
-.TH PYNML-XPP "1" "May 2024" "pynml-xpp v1.2.15" "User Commands"
+.TH PYNML-XPP "1" "June 2024" "pynml-xpp v1.3.1" "User Commands"
 .SH NAME
-pynml-xpp \- manual page for pynml-xpp v1.2.15
+pynml-xpp \- manual page for pynml-xpp v1.3.1
 .SH DESCRIPTION
 usage: pynml\-xpp [\-h] [\-xpp] [\-lems] [\-brian2] [\-run] [\-plot]
 .IP
@@ -51,4 +51,4 @@ Plot saved variables
 Please see https://docs.neuroml.org for complete documentation on the NeuroML standard and the software ecosystem.
 .SH ENVIRONMENT
 .PP
-pyNeuroML v1.2.15 (libNeuroML v0.5.9, jNeuroML v0.13.0)
+pyNeuroML v1.3.1 (libNeuroML v0.6.2, jNeuroML v0.13.1)
diff --git a/man/man1/pynml.1 b/man/man1/pynml.1
@@ -1,7 +1,7 @@
 .\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.49.3.
-.TH PYNML "1" "May 2024" "pynml v1.2.15" "User Commands"
+.TH PYNML "1" "June 2024" "pynml v1.3.1" "User Commands"
 .SH NAME
-pynml \- manual page for pynml v1.2.15
+pynml \- manual page for pynml v1.3.1
 .SH DESCRIPTION
 usage: pynml [\-h|\-\-help] [<shared options>] <one of the mutually\-exclusive options>
 .PP
@@ -225,4 +225,4 @@ Load NeuroML file(s), and convert it to swc format
 Please see https://docs.neuroml.org for complete documentation on the NeuroML standard and the software ecosystem.
 .SH ENVIRONMENT
 .PP
-pyNeuroML v1.2.15 (libNeuroML v0.5.9, jNeuroML v0.13.0)
+pyNeuroML v1.3.1 (libNeuroML v0.6.2, jNeuroML v0.13.1)
diff --git a/man/man1/version.h2m b/man/man1/version.h2m
@@ -1,3 +1,3 @@
 [environment]
 .PP
-pyNeuroML v1.2.15 (libNeuroML v0.5.9, jNeuroML v0.13.0)
+pyNeuroML v1.3.1 (libNeuroML v0.6.2, jNeuroML v0.13.1)
diff --git a/pyneuroml/__init__.py b/pyneuroml/__init__.py
@@ -12,7 +12,7 @@
     __version__ = importlib_metadata.version("pyNeuroML")
 
 
-JNEUROML_VERSION = "0.13.0"
+JNEUROML_VERSION = "0.13.1"
 
 # Define a logger for the package
 logging.basicConfig(
@@ -39,8 +39,8 @@ def print_v(msg):
 except KeyError:
     java_max_memory = "400M"
 
-DEFAULTS = {
+DEFAULTS: typing.Dict[str, typing.Any] = {
     "v": False,
     "default_java_max_memory": java_max_memory,
     "nogui": False,
-}  # type: dict[str, typing.Any]
+}