Merge pull request #234 from NeuroML/chore/remove-deprecated-setup.py

Chore/remove deprecated setup.py

.github/workflows/ci.yml

@@ -36,27 +36,23 @@ jobs:
         echo "github.ref is: ${{ github.ref }}"
         echo "github.base_ref is: ${{ github.base_ref }}"
 
-    - name: Install deps from development
+    - name: Upgrade pip, install inspyred
+      run: |
+        python -m pip install --upgrade pip
+        pip install git+https://github.com/aarongarrett/inspyred.git@master#egg=inspyred
+        pip install .[all]
+
+    - name: Install package and development deps
       if: ${{ github.ref == 'refs/heads/development' || github.base_ref == 'development' }}
       run: |
         echo "Using deps from development for our repos"
-        cp -v requirements-development.txt requirements.txt
+        pip install .[dev]
 
-    - name: Install deps from experimental
+    - name: Install package and experimental deps
       if: ${{ github.ref == 'refs/heads/experimental' || github.base_ref == 'experimental' }}
       run: |
         echo "Using deps from experimental - assuming development in others"
-        cp -v requirements-experimental.txt requirements.txt
-
-    - name: Install package
-      run: |
-        python -m pip install --upgrade pip
-
-        # Ensure very latest inspyred (not on pypi) is installed
-        pip install git+https://github.com/aarongarrett/inspyred.git@master#egg=inspyred
-
-        pip install -r requirements.txt
-        pip install .
+        pip install .[experimental]
 
     - name: List packages so far
       run: |

.pre-commit-config.yaml

@@ -0,0 +1,13 @@
+# 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
+    -   id: end-of-file-fixer
+    -   id: check-added-large-files
+-   repo: https://github.com/psf/black
+    rev: 23.3.0
+    hooks:
+    -   id: black

.readthedocs.yaml

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

CONTRIBUTING.md

@@ -17,6 +17,14 @@ pyNeuroML. Pull requests with enhancements and bug fixes are welcome.
 
 ## Pull Request Process
 
-1. Please ensure that the automated build for your pull request passes.
-2. Please pay attention to the results from flake8 and make any modifications
+1. Please contribute pull requests against the `development` branch.
+2. Please ensure that the automated build for your pull request passes.
+3. Please pay attention to the results from flake8 and make any modifications
    to ensure a consistent code style.
+
+## 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

MANIFEST.in

@@ -1,3 +1,8 @@
 include README.md
+include CONTRIBUTING.md
 include LICENSE*
-include requirements.txt
+include *.sh
+recursive-include tests *
+recursive-include man *
+recursive-include examples *
+recursive-include docs *

README.md

@@ -59,16 +59,14 @@ Clone the repository:
 
 It should be possible to install pyNeuroML using just:
 
-    sudo pip install .
+    pip install .
 
-You **may** have to install lxml and the development version of [libNeuroML](https://github.com/NeuralEnsemble/libNeuroML) manually:
+To develop pyNeuroML, you can use the `dev` extra and the `development` branch:
 
-    apt-get install python-lxml
-    cd ..
-    git clone https://github.com/NeuralEnsemble/libNeuroML.git
-    cd libNeuroML
+    git clone https://github.com/NeuroML/pyNeuroML.git
+    cd pyNeuroML
     git checkout development
-    sudo python setup.py install
+    pip install .[dev]
 
 
 Current/planned features

pyneuroml/__init__.py

@@ -1,6 +1,12 @@
 import logging
 
-__version__ = "1.0.8"
+try:
+    import importlib.metadata
+    __version__ = importlib.metadata.version("pyNeuroML")
+except ImportError:
+    import importlib_metadata
+    __version__ = importlib_metadata.version("pyNeuroML")
+
 
 JNEUROML_VERSION = "0.12.2"
 

pyproject.toml

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

setup.cfg

@@ -1,2 +1,133 @@
+[metadata]
+name = pyNeuroML
+version = 1.0.8
+author = Padraig Gleeson
+author_email = p.gleeson@gmail.com
+url = https://github.com/NeuroML/pyNeuroML
+license = LGPL-3.0-only
+description = Python utilities for NeuroML
+long_description = file: README.md
+long_description_content_type = text/markdown
+classifiers=
+    Intended Audience :: Science/Research
+    License :: OSI Approved :: GNU Lesser General Public License v3 (LGPLv3)
+    Natural Language :: English
+    Operating System :: OS Independent
+    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
+
+[options]
+install_requires =
+    pylems>=0.5.7
+    airspeed>=0.5.5
+    neuromllite>=0.5.4
+    libNeuroML>=0.5.1
+    matplotlib
+    matplotlib-scalebar
+    graphviz
+    typing; python_version<"3.5"
+    lxml
+    pandas
+    argparse
+
+packages = find:
+
+[options.packages.find]
+where = .
+include = pyneuroml*
+
+[options.entry_points]
+console_scripts =
+    pynml                 = pyneuroml.pynml:main
+    pynml-archive         = pyneuroml.archive:main
+    pynml-channelanalysis = pyneuroml.analysis.NML2ChannelAnalysis:main
+    pynml-modchananalysis = pyneuroml.neuron.analysis.HHanalyse:main
+    pynml-povray          = pyneuroml.povray.NeuroML2ToPOVRay:main
+    pynml-tune            = pyneuroml.tune.NeuroMLTuner:main
+    pynml-summary         = pyneuroml.pynml:summary
+    pynml-plotspikes      = pyneuroml.plot.PlotSpikes:main
+    pynml-plotmorph       = pyneuroml.plot.PlotMorphology:main
+    pynml-channelml2nml   = pyneuroml.channelml:main
+    pynml-sonata          = neuromllite.SonataReader:main
+
+[options.package_data]
+* =
+        lib/*.jar
+        *.xml
+        *.html
+        *.md
+        *.xsl
+        *.hoc
+
+[options.extras_require]
+neuron =
+    NEURON
+    pyyaml
+
+brian =
+    Brian2
+
+netpyne =
+    netpyne
+
+povray =
+    opencv-python
+
+hdf5 =
+    tables
+
+analysis =
+    pyelectro
+
+tune =
+    neurotune>=0.2.6
+    ppft
+
+vispy =
+    vispy
+    pyqt5
+
+plotly =
+    plotly
+
+all =
+    pyNeuroML[neuron]
+    pyNeuroML[brian]
+    pyNeuroML[netpyne]
+    pyNeuroML[netpyne]
+    pyNeuroML[povray]
+    pyNeuroML[hdf5]
+    pyNeuroML[analysis]
+    pyNeuroML[tune]
+    pyNeuroML[vispy]
+    pyNeuroML[plotly]
+
+dev =
+    pyNeuroML[all]
+    airspeed>=0.5.5
+    modelspec @ git+https://github.com/ModECI/modelspec.git@development#egg=modelspec
+    libNeuroML @ git+https://github.com/NeuralEnsemble/libNeuroML.git@development#egg=libNeuroML
+    pylems @ git+https://github.com/LEMS/pylems.git@development#egg=pylems
+    pytest
+    pytest-cov
+    kaleido
+    pre-commit
+
+experimental =
+    pyNeuroML[dev]
+
+    modelspec @ git+https://github.com/ModECI/modelspec.git@development#egg=modelspec
+    libNeuroML @ git+https://github.com/NeuralEnsemble/libNeuroML.git@development#egg=libNeuroML
+    pylems @ git+https://github.com/LEMS/pylems.git@development#egg=pylems
+
+doc =
+    pyNeuroML[all]
+    sphinxcontrib-bibtex
+    pydata-sphinx-theme
+
 [flake8]
 ignore = E501, E502, F403, F405