NeuroML · pgleeson · Aug 20, 2024 · May 20, 2024 · May 21, 2024 · May 21, 2024
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -39,6 +39,7 @@ jobs:
     - name: Upgrade pip, install deps
       run: |
         python -m pip install --upgrade pip
+        pip install 'numpy<2.0.0' # due to lingering issues with other modules
         pip install .[dev]
 
     - name: List packages so far

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
@@ -165,3 +165,19 @@ arm64
 /tests/plot/test_schematic_plot_2d_test_cell_nml_xz.png
 /tests/plot/test_schematic_plot_2d_test_cell_nml_yz.png
 /tests/analysis/*png
+*ken.sh
+/tests/plot/test_morphology*.png
+
+.vscode
+/tests/pyneuroml_20*
+/pyneuroml/xppaut/report.txt
+/examples/test_data/xppaut/fhn_2.ode
+/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/README.md b/README.md
@@ -77,7 +77,7 @@ Fedora users can install pyNeuroML using the following commands:
 This will also pull in all the necessary dependencies (Java, lxml, graphviz).
 Please see the [project documentation](https://docs.fedoraproject.org/en-US/neurofedora/copr/) for more information.
 
-### Installation from source
+### Installation from the source
 
 Clone the repository:
 

diff --git a/docs/source/index.rst b/docs/source/index.rst
@@ -11,16 +11,17 @@ Here you will find information on installing, using, and contributing to pyNeuro
 For more information on NeuroML standard, other tools in the NeuroML ecosystem, the NeuroML community and how to get in touch with us, please see the documentation at https://docs.neuroml.org.
 
 
+Contents
+---------
 
 .. toctree::
-   :maxdepth: 2
-   :caption: Contents:
+   :maxdepth: 1
 
    introduction
-   modules
+   pyneuroml
 
 Indices and tables
-==================
+------------------
 
 * :ref:`genindex`
 * :ref:`modindex`

diff --git a/docs/source/modules.rst b/docs/source/modules.rst
diff --git a/docs/source/pyneuroml.annotations.rst b/docs/source/pyneuroml.annotations.rst
@@ -0,0 +1,7 @@
+pyneuroml.annotations module
+=============================
+
+.. automodule:: pyneuroml.annotations
+   :members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/docs/source/pyneuroml.io.rst b/docs/source/pyneuroml.io.rst
@@ -0,0 +1,7 @@
+pyneuroml.io module
+======================
+
+.. automodule:: pyneuroml.io
+   :members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/docs/source/pyneuroml.modelgraphs.rst b/docs/source/pyneuroml.modelgraphs.rst
@@ -0,0 +1,7 @@
+pyneuroml.modelgraphs module
+=============================
+
+.. automodule:: pyneuroml.modelgraphs
+   :members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/docs/source/pyneuroml.nsgr.rst b/docs/source/pyneuroml.nsgr.rst
@@ -1,4 +1,4 @@
-pyneuroml.nsgr package
+pyneuroml.nsgr module
 ======================
 
 .. automodule:: pyneuroml.nsgr

diff --git a/docs/source/pyneuroml.plot.rst b/docs/source/pyneuroml.plot.rst
@@ -14,6 +14,14 @@ pyneuroml.plot.Plot module
    :undoc-members:
    :show-inheritance:
 
+pyneuroml.plot.PlotTimeSeries module
+--------------------------------------
+
+.. automodule:: pyneuroml.plot.PlotTimeSeries
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
 pyneuroml.plot.PlotSpikes module
 --------------------------------
 

diff --git a/docs/source/pyneuroml.pynml.rst b/docs/source/pyneuroml.pynml.rst
@@ -5,3 +5,5 @@ pyneuroml.pynml module
    :members:
    :undoc-members:
    :show-inheritance:
+   :imported-members:
+   :exclude-members: Cell, NeuroMLDocument, LEMSFileParser, Path, ZipFile, datetime, main
diff --git a/docs/source/pyneuroml.rst b/docs/source/pyneuroml.rst
@@ -1,26 +1,31 @@
-pyneuroml package
+API Documentation
 =================
 
 .. automodule:: pyneuroml
    :members:
    :undoc-members:
    :show-inheritance:
+   :exclude-members: print_v
 
-Subpackages
------------
+The PyNeuroML package includes the following sub-packages:
 
 .. toctree::
    :maxdepth: 1
 
-   pyneuroml.pynml
    pyneuroml.analysis
+   pyneuroml.annotations
    pyneuroml.archive
    pyneuroml.channelml
+   pyneuroml.io
    pyneuroml.lems
+   pyneuroml.modelgraphs
    pyneuroml.neuron
    pyneuroml.nsgr
+   pyneuroml.pynml
    pyneuroml.plot
    pyneuroml.povray
+   pyneuroml.runners
    pyneuroml.swc
+   pyneuroml.sbml
    pyneuroml.tune
    pyneuroml.utils
diff --git a/docs/source/pyneuroml.runners.rst b/docs/source/pyneuroml.runners.rst
@@ -0,0 +1,7 @@
+pyneuroml.runners module
+=========================
+
+.. automodule:: pyneuroml.runners
+   :members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/docs/source/pyneuroml.sbml.rst b/docs/source/pyneuroml.sbml.rst
@@ -0,0 +1,7 @@
+pyneuroml.sbml module
+======================
+
+.. automodule:: pyneuroml.sbml
+   :members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/docs/source/pyneuroml.swc.rst b/docs/source/pyneuroml.swc.rst
@@ -6,6 +6,14 @@ pyneuroml.swc package
    :undoc-members:
    :show-inheritance:
 
+pyneuroml.swc.LoadSWC module
+------------------------------
+
+.. automodule:: pyneuroml.swc.LoadSWC
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
 pyneuroml.swc.ExportSWC module
 ------------------------------
 

diff --git a/docs/source/pyneuroml.utils.rst b/docs/source/pyneuroml.utils.rst
@@ -6,3 +6,50 @@ pyneuroml.utils package
    :undoc-members:
    :show-inheritance:
 
+pyneuroml.utils.info module
+---------------------------
+
+.. automodule:: pyneuroml.utils.info
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+pyneuroml.utils.plot module
+---------------------------
+
+.. automodule:: pyneuroml.utils.plot
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+pyneuroml.utils.misc module
+---------------------------
+
+.. automodule:: pyneuroml.utils.misc
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+pyneuroml.utils.cli module
+---------------------------
+
+.. automodule:: pyneuroml.utils.cli
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+pyneuroml.utils.units module
+----------------------------
+
+.. automodule:: pyneuroml.utils.units
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+pyneuroml.utils.xml module
+----------------------------
+
+.. automodule:: pyneuroml.utils.xml
+   :members:
+   :undoc-members:
+   :show-inheritance:
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  v1.9.1
-         org.neuroml.model   v1.9.1
-         jLEMS               v0.10.8
+         org.neuroml.export  v1.10.1
+         org.neuroml.model   v1.10.1
+         jLEMS               v0.11.1
 
 ENDCOMMENT
 

diff --git a/examples/Vm_plot.py b/examples/Vm_plot.py
@@ -30,7 +30,6 @@ def generate_Vm_vs_time_plot(
     simulator="jNeuroML",
     include_included=True,
 ):
-
     ref = "Test"
     logger.info(
         "Generating Vm(mV) vs Time(ms) plot for cell %s in %s using %s (Inj %snA / %sms dur after %sms delay)"

diff --git a/examples/component_evaluation.py b/examples/component_evaluation.py
@@ -12,7 +12,6 @@ def main(args=None):
         nml_doc = pynml.read_neuroml2_file(f)
 
         for ct in nml_doc.ComponentType:
-
             ys = []
             for v in vs:
                 req_variables = {"v": "%sV" % v, "vShift": "10mV"}

diff --git a/examples/create_new_lems_file.py b/examples/create_new_lems_file.py
@@ -14,7 +14,6 @@
 
 
 if __name__ == "__main__":
-
     ############################################
     #  Create a LEMS file "manually"...
 

diff --git a/examples/generate_if_curve.py b/examples/generate_if_curve.py
@@ -16,5 +16,5 @@
     plot_voltage_traces=not nogui,
     plot_if=not nogui,
     plot_iv=not nogui,
-    save_if_data_to="if_data.dat"
+    save_if_data_to="if_data.dat",
 )
diff --git a/examples/generate_povray.py b/examples/generate_povray.py
@@ -1,6 +1,5 @@
-
 from pyneuroml.povray.NeuroML2ToPOVRay import generate_povray
 
-#generate_povray(neuroml_file='test_data/ca1/TestOLMNet.net.nml')
+# generate_povray(neuroml_file='test_data/ca1/TestOLMNet.net.nml')
 
-generate_povray(neuroml_file='test_data/Purk2M9s.nml', scalez=3)
+generate_povray(neuroml_file="test_data/Purk2M9s.nml", scalez=3)
diff --git a/examples/quick_plot.py b/examples/quick_plot.py
@@ -14,35 +14,35 @@
 siny = [math.sin(t / 10) for t in ts]
 cosey = [math.exp(t / -80) * math.cos(t / 5) for t in ts]
 
-if '-i' in sys.argv:
+if "-i" in sys.argv:
     from pyneuroml.plot.Plot import generate_interactive_plot
 
     # Generate a plot for this quickly with generate_interactive_plot
     ax = generate_interactive_plot(
         [ts, ts],  # Add 2 sets of x values
         [siny, cosey],  # Add 2 sets of y values
         "Some traces",  # Title
-        labels=['sin', 'cos'],
+        labels=["sin", "cos"],
         xaxis="Time (ms)",  # x axis legend
         yaxis="Arbitrary units...",  # y axis legend
         linewidths=[1, 3],  # Thicknesses of each trace
         save_figure_to="quick.png",
     )  # Save figure
 
 else:
-
     # Generate a plot for this quickly with generate_plot
     ax = generate_plot(
         [ts, ts],  # Add 2 sets of x values
         [siny, cosey],  # Add 2 sets of y values
         "Some traces",  # Title
-        labels=['sin', 'cos'],
+        labels=["sin", "cos"],
         xaxis="Time (ms)",  # x axis legend
         yaxis="Arbitrary units...",  # y axis legend
         linewidths=[1, 3],  # Thicknesses of each trace
         show_plot_already=False,  # Show or wait for plt.show()?
         font_size=10,  # Font
         bottom_left_spines_only=True,  # Box or just x & y axes
+        legend_position = "bottom center",
         save_figure_to="quick.png",
     )  # Save figure
 

diff --git a/examples/record_channel_currents.py b/examples/record_channel_currents.py
@@ -15,7 +15,6 @@
 
 
 if __name__ == "__main__":
-
     root_dir = "test_data/ca1"
     cell_file = "cells/olm.cell.nml"
     cell_comp = "olmcell"

diff --git a/examples/test_data/realtime.py b/examples/test_data/realtime.py
@@ -1,8 +1,8 @@
 from pyneuroml import pynml
 
 
-command = 'python snooze.py'
-run_dir = '.'
+command = "python snooze.py"
+run_dir = "."
 
 oo = pynml.execute_command_in_dir_with_realtime_output(command, run_dir, verbose=True)
Original file line number	Diff line number	Diff line change
Expand Up		@@ -14,7 +14,6 @@


		if __name__ == "__main__":

		############################################
		# Create a LEMS file "manually"...

Expand Down