Merge pull request #196 from NeuralEnsemble/development

 Changes for NeuroML v2.3.1 release

Author: pgleeson

.github/workflows/ci.yml

@@ -14,14 +14,19 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ["3.7", "3.8", "3.9", "3.10", "3.11"]
+        python-version: ["3.8", "3.9", "3.10", "3.11", "3.12"]
         runs-on: [ubuntu-latest, windows-latest, macos-latest]
+        exclude:
+          - runs-on: macos-latest
+            python-version: "3.8"
+          - runs-on: macos-latest
+            python-version: "3.9"
 
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
 
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v4
+      uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
 
@@ -30,6 +35,11 @@ jobs:
         #sudo apt-get install libhdf5-serial-dev liblzo2-dev libgraphviz-dev -y
         python -m pip install --upgrade pip
 
+    - name: Install HDF5 for pytables on macos-latest
+      if: ${{ matrix.runs-on == 'macos-latest' }}
+      run: |
+        brew install hdf5
+
     - name: Build package
       run: |
         pip install .[full]
@@ -38,10 +48,9 @@ jobs:
       if: ${{ matrix.runs-on == 'ubuntu-latest' }}
       run: |
         # Just test on linux for now...
-        pytest -vs 
+        pytest -vs
 
     - name: Run examples
-      if: ${{ matrix.python-version != '3.7' || matrix.runs-on != 'macos-latest' }} # issue with _bz2 module...
       run: |
         cd neuroml/examples
         python run_all.py

.github/workflows/regenerate.yml

@@ -12,18 +12,19 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ["3.7", "3.8", "3.9", "3.10", "3.11"]
+        python-version: ["3.8", "3.9", "3.10", "3.11", "3.12"]
 
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
 
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v4
+      uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
 
     - name: Install dependencies
       run: |
+        sudo apt-get update -y
         sudo apt-get install libhdf5-serial-dev liblzo2-dev libgraphviz-dev -y
         python -m pip install --upgrade pip
         pip install .[dev]

.gitignore

@@ -55,3 +55,4 @@ neuroml/test/*.h5
 
 sed-script.txt
 /test.sh
+/*ken.sh

.pre-commit-config.yaml

@@ -0,0 +1,17 @@
+# See https://pre-commit.com for more information
+# See https://pre-commit.com/hooks.html for more hooks
+repos:
+-   repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.4.0
+    hooks:
+    -   id: trailing-whitespace
+        exclude: NeuroML.*xsd
+    -   id: end-of-file-fixer
+        exclude: NeuroML.*xsd
+    -   id: check-added-large-files
+- repo: https://github.com/astral-sh/ruff-pre-commit
+  rev: v0.4.1
+  hooks:
+    - id: ruff
+      args: [ "--select", "I", "--fix" ]
+    - id: ruff-format

CONTRIBUTING.md

@@ -0,0 +1,112 @@
+# Contributing
+
+Please open issues to discuss enhancements and bugs that you may encounter with
+libNeuroML. Pull requests with enhancements and bug fixes are welcome.
+
+## Virtual environments and editable installs
+
+It is best to use [virtual environments](https://docs.python.org/3/tutorial/venv.html) when developing Python packages.
+This ensures that one uses a clean environment that includes the necessary
+dependencies and does not affect the overall system installation.
+
+For quick development, consider using [editable installs](https://setuptools.pypa.io/en/latest/userguide/development_mode.html).
+The dependencies are broken down in the `setup.cfg` file. To get a complete development environment, one can run:
+
+
+    pip install -e .[dev]   # an editable install with all development dependecies installed
+
+
+## Code style
+
+1. The source code uses spaces, and each tab is equivalent to 4 spaces.
+
+2. We use the [reStructuredText (reST)
+   format](https://stackoverflow.com/a/24385103/375067) for Python docstrings.
+   Please document your code when opening pull requests.
+   All methods/functions/modules *must* include docstrings that explain the parameters.
+
+3. We use [ruff](https://pypi.org/project/ruff/) to format and lint our code. (See the section on pre-commit below.)
+
+4. Please use [type hints](https://docs.python.org/3/library/typing.html) wherever applicable.
+   You can set up type checkers such as [mypy](https://mypy.readthedocs.io/) to use type hints in your development environment/IDE.
+
+
+        pip install mypy
+
+
+### Pre-commit
+
+A number of [pre-commit](https://pre-commit.com/) hooks are used to improve code-quality.
+Please run the following code to set up the pre-commit hooks:
+
+    $ pre-commit install
+
+The hooks will be run at each `git commit`.
+Please see `.pre-commit-config.yaml` for information on what hooks we run.
+
+
+### Commit messages
+
+Writing good commit messages makes things easy to follow.
+Please see these posts:
+
+- [How to write a Git commit message](https://cbea.ms/git-commit/)
+- While not compulsory, we prefer [conventional commits](https://www.conventionalcommits.org/en/v1.0.0/)
+
+
+## Tests
+
+Bug fixes and new features should include unit tests to test for correctness.
+One can base new tests off the current ones included in the `tests/` directory.
+To see how tests are run, please see the [GitHub Actions configuration file](https://github.com/NeuralEnsemble/libNeuroML/blob/development/.github/workflows/ci.yml).
+
+We use [pytest](https://docs.pytest.org/) for unit testing.
+One can run it from the root of the repository:
+
+    pytest
+
+
+To run specific tests, one can use the `-k` flag:
+
+
+    pytest -k "..."
+
+
+## Pull Request Process
+
+1. Please contribute pull requests against the `development` branch.
+2. Please ensure that the automated build for your pull request passes.
+3. Please write good commit messages (see the section above).
+
+### Updating your pull request branch
+
+Over time, as pull requests are reviewed, the `development` branch continues to move on with other changes.
+Sometimes, it can be useful/necessary to pull in these changes to the pull request branch, using the following steps.
+
+Add the upstream libNeuroML repository as a remote:
+
+
+    git remote add upstream https://github.com/NeuralEnsemble/libNeuroML.git
+
+
+Update your local copy of the `development` branch, and the remote copy in your fork:
+
+
+    git checkout development
+    git pull upstream development
+    git push
+
+
+Pull in changes from development to your branch:
+
+
+    git checkout <feature branch being used for PR>
+    git merge development
+
+
+If there are merge conflicts, you will need to [resolve these](https://git-scm.com/book/en/v2/Git-Branching-Basic-Branching-and-Merging#_basic_merge_conflicts), since merging the feature branch in the pull request will also result in these.
+After any merge conflicts have been resolved (or if there aren't any), you can
+push your branch to your fork to update the pull request:
+
+
+    git push

README.md

@@ -41,6 +41,8 @@ See https://docs.neuroml.org/ for an overview of the various NeuroML libraries.
 
 ## Changelog
 
+See also https://github.com/NeuralEnsemble/libNeuroML/releases.
+
 ### version 0.5.8
 
 - drop py3.7, add py3,12

doc/component-list.json

@@ -0,0 +1 @@
+{"Cells": ["baseCell", "baseSpikingCell", "baseCellMembPot", "baseCellMembPotDL", "baseChannelPopulation", "channelPopulation", "channelPopulationNernst", "baseChannelDensity", "baseChannelDensityCond", "variableParameter", "inhomogeneousValue", "channelDensityNonUniform", "channelDensityNonUniformNernst", "channelDensityNonUniformGHK", "channelDensity", "channelDensityVShift", "channelDensityNernst", "channelDensityNernstCa2", "channelDensityGHK", "channelDensityGHK2", "pointCellCondBased", "pointCellCondBasedCa", "distal", "proximal", "parent", "segment", "segmentGroup", "member", "from", "to", "include", "path", "subTree", "inhomogeneousParameter", "proximalDetails", "distalDetails", "morphology", "specificCapacitance", "initMembPotential", "spikeThresh", "membraneProperties", "membraneProperties2CaPools", "biophysicalProperties", "biophysicalProperties2CaPools", "intracellularProperties", "intracellularProperties2CaPools", "resistivity", "concentrationModel", "decayingPoolConcentrationModel", "fixedFactorConcentrationModel", "fixedFactorConcentrationModelTraub", "species", "cell", "cell2CaPools", "baseCellMembPotCap", "baseIaf", "iafTauCell", "iafTauRefCell", "baseIafCapCell", "iafCell", "iafRefCell", "izhikevichCell", "izhikevich2007Cell", "adExIaFCell", "fitzHughNagumoCell", "pinskyRinzelCA3Cell", "hindmarshRose1984Cell"], "Synapses": ["baseSynapse", "baseVoltageDepSynapse", "baseSynapseDL", "baseCurrentBasedSynapse", "alphaCurrentSynapse", "baseConductanceBasedSynapse", "baseConductanceBasedSynapseTwo", "expOneSynapse", "alphaSynapse", "expTwoSynapse", "expThreeSynapse", "baseBlockMechanism", "voltageConcDepBlockMechanism", "basePlasticityMechanism", "tsodyksMarkramDepMechanism", "tsodyksMarkramDepFacMechanism", "blockingPlasticSynapse", "doubleSynapse", "stdpSynapse", "gapJunction", "baseGradedSynapse", "silentSynapse", "linearGradedSynapse", "gradedSynapse"], "Channels": ["baseVoltageDepRate", "baseVoltageConcDepRate", "baseHHRate", "HHExpRate", "HHSigmoidRate", "HHExpLinearRate", "baseVoltageDepVariable", "baseVoltageConcDepVariable", "baseHHVariable", "HHExpVariable", "HHSigmoidVariable", "HHExpLinearVariable", "baseVoltageDepTime", "baseVoltageConcDepTime", "fixedTimeCourse", "baseQ10Settings", "q10Fixed", "q10ExpTemp", "baseConductanceScaling", "q10ConductanceScaling", "baseConductanceScalingCaDependent", "baseGate", "gate", "gateHHrates", "gateHHtauInf", "gateHHInstantaneous", "gateHHratesTau", "gateHHratesInf", "gateHHratesTauInf", "gateFractional", "subGate", "baseIonChannel", "ionChannelPassive", "ionChannelHH", "ionChannel", "ionChannelVShift", "KSState", "closedState", "openState", "ionChannelKS", "KSTransition", "forwardTransition", "reverseTransition", "vHalfTransition", "tauInfTransition", "gateKS"], "Inputs": ["basePointCurrent", "baseVoltageDepPointCurrent", "baseVoltageDepPointCurrentSpiking", "basePointCurrentDL", "baseVoltageDepPointCurrentDL", "baseSpikeSource", "spikeGenerator", "spikeGeneratorRandom", "spikeGeneratorPoisson", "spikeGeneratorRefPoisson", "poissonFiringSynapse", "transientPoissonFiringSynapse", "timedSynapticInput", "spikeArray", "spike", "pulseGenerator", "compoundInput", "compoundInputDL", "pulseGeneratorDL", "sineGenerator", "sineGeneratorDL", "rampGenerator", "rampGeneratorDL", "voltageClamp", "voltageClampTriple"], "Networks": ["network", "networkWithTemperature", "basePopulation", "population", "populationList", "instance", "location", "region", "rectangularExtent", "projection", "explicitConnection", "connection", "synapticConnection", "synapticConnectionWD", "connectionWD", "electricalConnection", "electricalConnectionInstance", "electricalConnectionInstanceW", "electricalProjection", "continuousConnection", "continuousConnectionInstance", "continuousConnectionInstanceW", "continuousProjection", "explicitInput", "inputList", "input", "inputW"], "PyNN": ["basePyNNCell", "basePyNNIaFCell", "basePyNNIaFCondCell", "IF_curr_alpha", "IF_curr_exp", "IF_cond_alpha", "IF_cond_exp", "EIF_cond_exp_isfa_ista", "EIF_cond_alpha_isfa_ista", "HH_cond_exp", "basePynnSynapse", "expCondSynapse", "expCurrSynapse", "alphaCondSynapse", "alphaCurrSynapse", "SpikeSourcePoisson"], "NeuroMLCoreDimensions": [], "NeuroMLCoreCompTypes": ["notes", "annotation", "property", "baseStandalone", "rdf_RDF", "rdf_Description", "baseBqbiol", "bqbiol_encodes", "bqbiol_hasPart", "bqbiol_hasProperty", "bqbiol_hasVersion", "bqbiol_is", "bqbiol_isDescribedBy", "bqbiol_isEncodedBy", "bqbiol_isHomologTo", "bqbiol_isPartOf", "bqbiol_isPropertyOf", "bqbiol_isVersionOf", "bqbiol_occursIn", "bqbiol_hasTaxon", "bqmodel_is", "bqmodel_isDescribedBy", "bqmodel_isDerivedFrom", "rdf_Bag", "rdf:li", "point3DWithDiam"], "Simulation": ["Simulation", "Display", "Line", "OutputFile", "OutputColumn", "EventOutputFile", "EventSelection", "Meta"]}

doc/conf.py

@@ -11,8 +11,8 @@
 # All configuration values have a default; values that are commented out
 # serve to show the default.
 
-import sys
 import os
+import sys
 
 # If extensions (or modules to document with autodoc) are in another directory,
 # add these directories to sys.path here. If the directory is relative to the

doc/devdocs/index.rst

@@ -9,4 +9,3 @@ Contributing
    implementation_of_bindings
    meeting_june_2012
    nodes_segments_sections
-

doc/devdocs/meeting_june_2012.rst

@@ -109,7 +109,7 @@ Mike V was asked to add a clone method to a morphology.
 It was decided that fraction_along should be a property of segment.
 
 The syntax for segment groups should be as follows:
-group=morph.segment_groups['axon_group'] 
+group=morph.segment_groups['axon_group']
 (in connect merge groups should be false by default - throw an exception, tell the user setting merge_groups = True or rename group will fix this)
 
 This was a subject of great debate and has not been completely settled.