Merge pull request #174 from NeuralEnsemble/experimental

To v0.5.3; uses setup.cfg; tested on mac & win too

.github/workflows/ci.yml

@@ -15,35 +15,33 @@ jobs:
       fail-fast: false
       matrix:
         python-version: ["3.7", "3.8", "3.9", "3.10", "3.11"]
-        runs-on: [ubuntu-latest]
+        runs-on: [ubuntu-latest, windows-latest, macos-latest]
 
     steps:
     - uses: actions/checkout@v3
 
-    - name: Start MongoDB
-      uses: supercharge/[email protected]
-
     - name: Set up Python ${{ matrix.python-version }}
       uses: actions/setup-python@v3
       with:
         python-version: ${{ matrix.python-version }}
 
     - name: Install dependencies
       run: |
-        sudo apt-get install libhdf5-serial-dev liblzo2-dev libgraphviz-dev -y
+        #sudo apt-get install libhdf5-serial-dev liblzo2-dev libgraphviz-dev -y
         python -m pip install --upgrade pip
-        if [ -f requirements-dev.txt ]; then pip install -r requirements-dev.txt; fi
-        if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
 
     - name: Build package
       run: |
         pip install .[full]
 
     - name: Test with pytest
+      if: ${{ matrix.runs-on == 'ubuntu-latest' }}
       run: |
-        pytest
+        # Just test on linux for now...
+        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
 
@@ -52,6 +50,7 @@ jobs:
           pip list
 
     - name: Lint with flake8
+      if: ${{ matrix.runs-on == 'ubuntu-latest' }}
       run: |
         # stop the build if there are Python syntax errors or undefined names
         flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics

.github/workflows/regenerate.yml

@@ -26,8 +26,7 @@ jobs:
       run: |
         sudo apt-get install libhdf5-serial-dev liblzo2-dev libgraphviz-dev -y
         python -m pip install --upgrade pip
-        if [ -f requirements-dev.txt ]; then pip install -r requirements-dev.txt; fi
-        if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
+        pip install .[dev]
 
     - name: Rebuild nml.py
       run: |

.readthedocs.yaml

@@ -12,4 +12,7 @@ sphinx:
 
 python:
   install:
-    - requirements: doc/requirements.txt
+    - method: pip
+      path: .
+      extra_requirements:
+        - doc

README.md

@@ -33,14 +33,14 @@ A related package, **[pyNeuroML](https://github.com/NeuroML/pyNeuroML)** builds
 
 pyNeuroML builds on: [libNeuroML](https://github.com/NeuralEnsemble/libNeuroML) & [PyLEMS](https://github.com/LEMS/pylems) and wraps functionality from [jNeuroML](https://github.com/NeuroML/jNeuroML).
 
-
 ## Development process for libNeuroML
 
 Most of the work happens in the [development branch](https://github.com/NeuralEnsemble/libNeuroML/tree/development).
 That branch is kept up to date with the development branches for [NeuroML 2](https://github.com/NeuroML/NeuroML2/tree/development) and related libraries.
 See https://docs.neuroml.org/ for an overview of the various NeuroML libraries.
 
 ## Changelog
+
 ### version 0.4.1
 
 - add multiple cell builder utility functions
@@ -128,6 +128,4 @@ See https://docs.neuroml.org/ for an overview of the various NeuroML libraries.
 - Schema validation utility
 - Improved documentation and documentation new look
 
-
 :copyright: Copyright 2023 by the libNeuroML team, see [AUTHORS](AUTHORS). Modified BSD License, see [LICENSE](LICENSE) for details.
-

doc/devdocs/how_to_contribute.rst

@@ -101,7 +101,7 @@ Release process
 libNeuroML is part of the official NeuroML release cycle.
 When a new libNeuroML release is ready the following needs to happen:
 
-- Update version number in setup.py
+- Update version number in setup.cfg
 - update version number in doc/conf.py
 - update release number in doc/conf.py (same as version number)
 - update changelog in README.md

doc/userdocs/install.rst

@@ -13,15 +13,13 @@ On most systems with a Python installation, libNeuroML can be installed using th
 It is recommended to use a `virtual environment <https://docs.python.org/3/tutorial/venv.html>`_ when installing Python packages using `pip` to prevent these from conflicting with other system libraries.
 
 This will support the default XML serialization.
-To install all of requirements to include the other serialisations, use
+Note that you may be required to install libhdf5 using your package manager because PyTables' wheels for python 3.7+ depend on the system libhdf5 to build.
 
 ::
 
     # On Ubuntu based systems
     sudo apt-get install libhdf5-dev
-    pip install libNeuroML[full]
-
-The ``apt`` line is required at time of writing because PyTables' wheels for python 3.7 depend on the system libhdf5.
+    pip install libNeuroML
 
 
 On Fedora based systems
@@ -51,14 +49,23 @@ To build and install libNeuroML, you can use the standard install method for Pyt
 
 ::
 
-    python setup.py install
+    pip install .
 
 To use the **latest development version of libNeuroML**, switch to the development branch:
 
 ::
 
     git checkout development
-    sudo python setup.py install
+    pip install .
+
+
+To install developer dependencies and other extras, use the extras declared in the `setup.cfg` file. E.g.:
+
+::
+
+    pip install .[dev]
+    pip install .[test]
+    pip install .[doc]
 
 
 Run an example

neuroml/__version__.py

@@ -7,7 +7,13 @@
 """
 
 
-__version__: str = "0.5.2"
+try:
+    import importlib.metadata
+    __version__ = importlib.metadata.version("libNeuroML")
+except ImportError:
+    import importlib_metadata
+    __version__ = importlib_metadata.version("libNeuroML")
+
 __version_info__: tuple = tuple(int(i) for i in __version__.split("."))
 
 

pyproject.toml

@@ -0,0 +1,3 @@
+[build-system]
+requires = ["setuptools"]
+build-backend = "setuptools.build_meta"

setup.cfg

@@ -1,3 +1,72 @@
+[metadata]
+name = libNeuroML
+version = 0.5.3
+author_email = [email protected], [email protected]
+author = libNeuroML authors and contributors
+description = A Python library for working with NeuroML descriptions of neuronal models
+long_description = file: README.md
+long_description_content_type=text/markdown
+url = http://libneuroml.readthedocs.org/en/latest/
+license = BSD-2-Clause
+classifiers =
+    Intended Audience :: Science/Research
+    License :: OSI Approved :: BSD License
+    Natural Language :: English
+    Operating System :: OS Independent
+    Development Status :: 5 - Production/Stable
+    Programming Language :: Python :: 3
+    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
+    Topic :: Scientific/Engineering :: Bio-Informatics
+    Topic :: Scientific/Engineering
+
+[options]
+install_requires =
+    lxml
+    six
+    networkx
+    numpy
+    tables>=3.3.0
+    typing; python_version<"3.5"
+
+packages = find:
+
+[options.packages.find]
+where = .
+include = neuroml*
+exclude = neuroml.test*
+
+[options.package_data]
+neuroml.nml =
+    *.xsd
+
+
+[options.extras_require]
+test =
+    pytest
+
+dev =
+    wheel
+    generateds >= 2.20a; python_version >= '3.0'
+    cython
+    numpy
+    networkx
+    flake8
+    pytest
+    black ; python_version >= '3.0'
+
+doc =
+    sphinxcontrib-bibtex
+    pydata-sphinx-theme
+
+full =
+    libNeuroML[test]
+    libNeuroML[dev]
+    libNeuroML[doc]
+
 [flake8]
 # ignore:
 # spacing around operators, comment blocks, in argument lists
@@ -8,3 +77,8 @@ exclude =
     neuroml/nml/helper_methods.py,
     doc,
     build
+
+[mypy]
+ignore_missing_imports = True
+follow_imports = silent
+exclude = (nml\.py|doc/|build/|helper_methods\.py|generateds_config\.py|examples/)