Remove numpy-pin, convert to pyproject

.github/workflows/ci.yml

@@ -13,7 +13,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ["3.8", "3.9", "3.10", "3.11"]
+        python-version: ["3.10", "3.11", "3.12", "3.13"]
     env:
       JNML_HOME: "/home/runner/work/NeuroMLlite/NeuroMLlite/jNeuroML"
       HDF5_DISABLE_VERSION_CHECK: 1
@@ -33,9 +33,7 @@ jobs:
     - name: Install NeuroMLlite and extra requirements
       run: |
           pip install .
-          pip install -r requirements-extra.txt
-
-          #pip install 'numpy<=1.23.0' # temp fix, see https://github.com/OpenSourceBrain/osb-model-validation/issues/91
+          pip install .[dev]
 
 
     - name: Lint with flake8
@@ -57,8 +55,7 @@ jobs:
         git clone https://github.com/NeuroML/pyNeuroML.git
         cd pyNeuroML
         git checkout $pynml_branch
-        pip install pandas==1.3.5
-        pip install NEURON==8.2.2 # Specify version of neuron - 8.2.1 fails
+        pip install "NEURON>=8.2.2" # Specify version of neuron - 8.2.1 fails
         #pip install -r requirements-dev.txt
         pip install .
         cd -
@@ -93,7 +90,7 @@ jobs:
 
     - name: Install some simulators for testing
       run: |
-        #pip install cython
+        pip install "cython<3.1.0" # for nest...
         omv install NEURON
         pip install NetPyNE  # strange issues on py3.7 with omv install...
         omv install PyNN

.pre-commit-config.yaml

@@ -0,0 +1,16 @@
+# 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
+      args: [ "--maxkb=5000"]
+- repo: https://github.com/astral-sh/ruff-pre-commit
+  rev: v0.4.1
+  hooks:
+    - id: ruff
+      args: [ "--select", "I", "--fix" ]
+    - id: ruff-format

README.md

@@ -14,7 +14,7 @@ NeuroMLlite is in active development. This will evolve into a framework for more
 
 For some more background to this package see here: https://github.com/NeuroML/NetworkShorthand.
 
-![Architecture](images/NetworkShorthand.png)
+![Architecture](images/NetworkShorthand.png) 
 
 
 ## Examples

pyproject.toml

@@ -0,0 +1,12 @@
+[build-system]
+requires = ["setuptools"]
+build-backend = "setuptools.build_meta"
+
+[tool.ruff]
+
+exclude = [
+    "examples",
+    ]
+
+[tool.ruff.lint]
+ignore = ["F403", "F405"]

setup.cfg

@@ -0,0 +1,85 @@
+[metadata]
+name = neuromllite
+version = 0.6.1
+author = Padraig Gleeson
+author_email = p.gleeson@gmail.com
+url = https://github.com/NeuroML/NeuroMLlit
+license = LGPL-3.0-only
+description = A common JSON/YAML based format for compact network specification, closely tied to NeuroML v2
+long_description = file: README.md
+long_description_content_type = text/markdown
+classifiers =
+    Intended Audience :: Science/Research
+    Natural Language :: English
+    Operating System :: OS Independent
+    Programming Language :: Python :: 3.9
+    Programming Language :: Python :: 3.10
+    Programming Language :: Python :: 3.11
+    Programming Language :: Python :: 3.12
+    Programming Language :: Python :: 3.13
+    Topic :: Scientific/Engineering
+
+[options]
+install_requires =
+    libNeuroML>=0.5.1
+    pyyaml
+    numpy
+    tables
+    h5py
+    modelspec>=0.2.6
+    ppft[dill]
+
+packages = find:
+
+[options.packages.find]
+include =
+    neuromllite
+    neuromllite.sweep
+    neuromllite.gui
+
+[options.entry_points]
+console_scripts =
+    nmllite-ui = neuromllite.gui.NMLliteUI:main
+
+[options.extras_require]
+extras =
+    pyNN
+    bmtk
+    matplotlib
+    PyQt5
+    pyneuroml
+    pyelectro
+    neuron
+    h5py
+    graphviz
+
+
+all =
+    neuromllite[extras]
+
+dev =
+    neuromllite[all]
+    neuromllite[doc]
+    pytest
+    pytest-xdist
+    pre-commit
+
+
+doc =
+    sphinxcontrib-bibtex
+    #pyNN
+    bmtk
+    matplotlib
+    PyQt5
+    pyneuroml
+    pyelectro
+    numpy
+    neuron
+    h5py
+    graphviz
+    pylems
+    tables
+    arbor==0.9.0
+
+[flake8]
+extend-ignore = E501, E502, F403, F405, W503, W504