Merge pull request #298 from NeuroML/feat/add-method-to-generate-in-d…

…iff-dir Adds util method to generate simulation scripts in a different, clean directory
NeuroML · Feb 15, 2024 · 8ff9587 · 8ff9587
2 parents 3acf1b1 + e642371
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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.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 +1,30 @@
-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.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.utils.rst b/docs/source/pyneuroml.utils.rst
@@ -6,3 +6,42 @@ 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.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/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" "February 2024" "pynml-archive v1.1.13" "User Commands"
+.TH PYNML-ARCHIVE "1" "February 2024" "pynml-archive v1.2.0" "User Commands"
 .SH NAME
-pynml-archive \- manual page for pynml-archive v1.1.13
+pynml-archive \- manual page for pynml-archive v1.2.0
 .SH DESCRIPTION
 usage: pynml\-archive [\-h] [\-zipfileName <zip file name>]
 .TP
@@ -29,7 +29,7 @@ Extension to use for archive.
 Explicit list of files to create archive of.
 .SH ENVIRONMENT
 .PP
-pyNeuroML v1.1.13 (libNeuroML v0.5.8, jNeuroML v0.13.0)
+pyNeuroML v1.2.0 (libNeuroML v0.5.8, jNeuroML v0.13.0)
 .SH "SEE ALSO"
 .BR pynml (1),
 .BR pynml-channelanalysis (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" "February 2024" "pynml-channelanalysis v1.1.13" "User Commands"
+.TH PYNML-CHANNELANALYSIS "1" "February 2024" "pynml-channelanalysis v1.2.0" "User Commands"
 .SH NAME
-pynml-channelanalysis \- manual page for pynml-channelanalysis v1.1.13
+pynml-channelanalysis \- manual page for pynml-channelanalysis v1.2.0
 .SH DESCRIPTION
 usage: pynml\-channelanalysis [\-h] [\-v] [\-minV <min v>] [\-maxV <max v>]
 .TP
@@ -94,7 +94,7 @@ Save currents through voltage clamp at each level &
 plot current vs voltage for ion channel
 .SH ENVIRONMENT
 .PP
-pyNeuroML v1.1.13 (libNeuroML v0.5.8, jNeuroML v0.13.0)
+pyNeuroML v1.2.0 (libNeuroML v0.5.8, jNeuroML v0.13.0)
 .SH "SEE ALSO"
 .BR pynml (1),
 .BR pynml-channelanalysis (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" "February 2024" "pynml-channelml2nml v1.1.13" "User Commands"
+.TH PYNML-CHANNELML2NML "1" "February 2024" "pynml-channelml2nml v1.2.0" "User Commands"
 .SH NAME
-pynml-channelml2nml \- manual page for pynml-channelml2nml v1.1.13
+pynml-channelml2nml \- manual page for pynml-channelml2nml v1.2.0
 .SH DESCRIPTION
 usage: pynml\-channelml2nml [\-h] [\-xsltfile <XSLT file>]
 .TP
@@ -25,7 +25,7 @@ Path to the XSLT file
 Name of the outputfile file
 .SH ENVIRONMENT
 .PP
-pyNeuroML v1.1.13 (libNeuroML v0.5.8, jNeuroML v0.13.0)
+pyNeuroML v1.2.0 (libNeuroML v0.5.8, jNeuroML v0.13.0)
 .SH "SEE ALSO"
 .BR pynml (1),
 .BR pynml-channelanalysis (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" "February 2024" "pynml-modchananalysis v1.1.13" "User Commands"
+.TH PYNML-MODCHANANALYSIS "1" "February 2024" "pynml-modchananalysis v1.2.0" "User Commands"
 .SH NAME
-pynml-modchananalysis \- manual page for pynml-modchananalysis v1.1.13
+pynml-modchananalysis \- manual page for pynml-modchananalysis v1.2.0
 .SH DESCRIPTION
 usage: pynml\-modchananalysis [\-h] [\-v] [\-nogui] [\-minV <min v>]
 .TP
@@ -56,7 +56,7 @@ in mM)
 Name of the mod file containing the channel
 .SH ENVIRONMENT
 .PP
-pyNeuroML v1.1.13 (libNeuroML v0.5.8, jNeuroML v0.13.0)
+pyNeuroML v1.2.0 (libNeuroML v0.5.8, jNeuroML v0.13.0)
 .SH "SEE ALSO"
 .BR pynml (1),
 .BR pynml-channelanalysis (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" "February 2024" "pynml-plotchan v1.1.13" "User Commands"
+.TH PYNML-PLOTCHAN "1" "February 2024" "pynml-plotchan v1.2.0" "User Commands"
 .SH NAME
-pynml-plotchan \- manual page for pynml-plotchan v1.1.13
+pynml-plotchan \- manual page for pynml-plotchan v1.2.0
 .SH DESCRIPTION
 usage: pynml\-plotchan [\-h] [\-noDistancePlots] [\-nogui]
 .IP
@@ -25,7 +25,7 @@ Do not generate distance plots
 Do not show plots as they are generated
 .SH ENVIRONMENT
 .PP
-pyNeuroML v1.1.13 (libNeuroML v0.5.8, jNeuroML v0.13.0)
+pyNeuroML v1.2.0 (libNeuroML v0.5.8, jNeuroML v0.13.0)
 .SH "SEE ALSO"
 .BR pynml (1),
 .BR pynml-channelanalysis (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" "February 2024" "pynml-plotmorph v1.1.13" "User Commands"
+.TH PYNML-PLOTMORPH "1" "February 2024" "pynml-plotmorph v1.2.0" "User Commands"
 .SH NAME
-pynml-plotmorph \- manual page for pynml-plotmorph v1.1.13
+pynml-plotmorph \- manual page for pynml-plotmorph v1.2.0
 .SH DESCRIPTION
 usage: pynml\-plotmorph [\-h] [\-v] [\-nogui] [\-plane2d <plane, e.g. xy, yz, zx>]
 .TP
@@ -55,7 +55,7 @@ Scale axes so that image is approximately square, for
 2D plot
 .SH ENVIRONMENT
 .PP
-pyNeuroML v1.1.13 (libNeuroML v0.5.8, jNeuroML v0.13.0)
+pyNeuroML v1.2.0 (libNeuroML v0.5.8, jNeuroML v0.13.0)
 .SH "SEE ALSO"
 .BR pynml (1),
 .BR pynml-channelanalysis (1),

diff --git a/man/man1/pynml-plotspikes.1 b/man/man1/pynml-plotspikes.1
@@ -1,7 +1,7 @@
 .\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.49.3.
-.TH PYNML-PLOTSPIKES "1" "February 2024" "pynml-plotspikes v1.1.13" "User Commands"
+.TH PYNML-PLOTSPIKES "1" "February 2024" "pynml-plotspikes v1.2.0" "User Commands"
 .SH NAME
-pynml-plotspikes \- manual page for pynml-plotspikes v1.1.13
+pynml-plotspikes \- manual page for pynml-plotspikes v1.2.0
 .SH DESCRIPTION
 usage: pynml\-plotspikes [\-h] [\-format <format>] [\-rates] [\-showPlotsAlready]
 .TP
@@ -44,7 +44,7 @@ Window for rate calculation in ms
 Number of bins for rate histogram
 .SH ENVIRONMENT
 .PP
-pyNeuroML v1.1.13 (libNeuroML v0.5.8, jNeuroML v0.13.0)
+pyNeuroML v1.2.0 (libNeuroML v0.5.8, jNeuroML v0.13.0)
 .SH "SEE ALSO"
 .BR pynml (1),
 .BR pynml-channelanalysis (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" "February 2024" "pynml-povray v1.1.13" "User Commands"
+.TH PYNML-POVRAY "1" "February 2024" "pynml-povray v1.2.0" "User Commands"
 .SH NAME
-pynml-povray \- manual page for pynml-povray v1.1.13
+pynml-povray \- manual page for pynml-povray v1.2.0
 .SH DESCRIPTION
 usage: pynml\-povray [\-h] [\-split] [\-background <background colour>] [\-movie]
 .TP
@@ -96,7 +96,7 @@ cell/network
 Show segment ids
 .SH ENVIRONMENT
 .PP
-pyNeuroML v1.1.13 (libNeuroML v0.5.8, jNeuroML v0.13.0)
+pyNeuroML v1.2.0 (libNeuroML v0.5.8, jNeuroML v0.13.0)
 .SH "SEE ALSO"
 .BR pynml (1),
 .BR pynml-channelanalysis (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" "February 2024" "pynml-sonata v1.1.13" "User Commands"
+.TH PYNML-SONATA "1" "February 2024" "pynml-sonata v1.2.0" "User Commands"
 .SH NAME
-pynml-sonata \- manual page for pynml-sonata v1.1.13
+pynml-sonata \- manual page for pynml-sonata v1.2.0
 .SH DESCRIPTION
 usage: pynml\-sonata [\-h] [\-h5] [\-jnml] [\-neuron]
 .IP
@@ -34,7 +34,7 @@ Execute the generated LEMS/NeuroML2 model with
 jNeuroML_NEURON
 .SH ENVIRONMENT
 .PP
-pyNeuroML v1.1.13 (libNeuroML v0.5.8, jNeuroML v0.13.0)
+pyNeuroML v1.2.0 (libNeuroML v0.5.8, jNeuroML v0.13.0)
 .SH "SEE ALSO"
 .BR pynml (1),
 .BR pynml-channelanalysis (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" "February 2024" "pynml-summary v1.1.13" "User Commands"
+.TH PYNML-SUMMARY "1" "February 2024" "pynml-summary v1.2.0" "User Commands"
 .SH NAME
-pynml-summary \- manual page for pynml-summary v1.1.13
+pynml-summary \- manual page for pynml-summary v1.2.0
 .SH DESCRIPTION
 Usage:
 .PP
@@ -19,7 +19,7 @@ enable verbose mode
 print this help text and exit
 .SH ENVIRONMENT
 .PP
-pyNeuroML v1.1.13 (libNeuroML v0.5.8, jNeuroML v0.13.0)
+pyNeuroML v1.2.0 (libNeuroML v0.5.8, jNeuroML v0.13.0)
 .SH "SEE ALSO"
 .BR pynml (1),
 .BR pynml-channelanalysis (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" "February 2024" "pynml-tune v1.1.13" "User Commands"
+.TH PYNML-TUNE "1" "February 2024" "pynml-tune v1.2.0" "User Commands"
 .SH NAME
-pynml-tune \- manual page for pynml-tune v1.1.13
+pynml-tune \- manual page for pynml-tune v1.2.0
 .SH DESCRIPTION
 usage: pynml\-tune [\-h] [\-simTime <simTime>] [\-dt <dt>]
 .IP
@@ -132,7 +132,7 @@ Should (some) generated files, e.g. *.dat, be deleted
 as optimisation progresses?
 .SH ENVIRONMENT
 .PP
-pyNeuroML v1.1.13 (libNeuroML v0.5.8, jNeuroML v0.13.0)
+pyNeuroML v1.2.0 (libNeuroML v0.5.8, jNeuroML v0.13.0)
 .SH "SEE ALSO"
 .BR pynml (1),
 .BR pynml-channelanalysis (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" "February 2024" "pynml v1.1.13" "User Commands"
+.TH PYNML "1" "February 2024" "pynml v1.2.0" "User Commands"
 .SH NAME
-pynml \- manual page for pynml v1.1.13
+pynml \- manual page for pynml v1.2.0
 .SH DESCRIPTION
 usage: pynml [\-h|\-\-help] [<shared options>] <one of the mutually\-exclusive options>
 .PP
@@ -193,7 +193,7 @@ Validate SBML file(s), unit consistency failure generates an error
 Validate SEDML file(s)
 .SH ENVIRONMENT
 .PP
-pyNeuroML v1.1.13 (libNeuroML v0.5.8, jNeuroML v0.13.0)
+pyNeuroML v1.2.0 (libNeuroML v0.5.8, jNeuroML v0.13.0)
 .SH "SEE ALSO"
 .BR pynml (1),
 .BR pynml-channelanalysis (1),

diff --git a/man/man1/version.h2m b/man/man1/version.h2m
@@ -1,3 +1,3 @@
 [environment]
 .PP
-pyNeuroML v1.1.13 (libNeuroML v0.5.8, jNeuroML v0.13.0)
+pyNeuroML v1.2.0 (libNeuroML v0.5.8, jNeuroML v0.13.0)