Merge pull request #73 from LEMS/chore/remove-setup.py

feat: migrate away from deprecated setup.py

.github/workflows/ci.yml

@@ -14,7 +14,7 @@ jobs:
       fail-fast: false
       matrix:
         python-version: ["3.7", "3.9", "3.10", "3.11"]
-        runs-on: [ubuntu-latest, windows-latest]
+        runs-on: [ubuntu-latest, windows-latest, macos-latest]
 
     steps:
     - uses: actions/checkout@v3

.gitignore

@@ -14,6 +14,7 @@ doc/_build
 comp_*
 /lems/test/hhcell_resaved3.xml
 /lems/__init__$py.class
-/PyLEMS.egg-info
+*PyLEMS.egg-info
 /dist
 *ken.sh
+*.whl

MANIFEST.in

@@ -2,3 +2,4 @@ include README.md
 include examples/*.xml
 include examples/*.py
 include LICENSE.lesser
+recursive-include man *.1

Makefile

@@ -18,46 +18,46 @@ clean:
 	rm -rf doc/epydoc/*
 
 example1:
-	./pylems examples/example1.xml
+	pylems examples/example1.xml
 
 example2:
-	./pylems examples/example2.xml
+	pylems examples/example2.xml
 
 example3:
-	./pylems examples/example3.xml
+	pylems examples/example3.xml
 
 example4:
-	./pylems examples/example4.xml
+	pylems examples/example4.xml
 
 example5:
-	./pylems examples/example5.xml
+	pylems examples/example5.xml
 
 example6:
-	./pylems examples/example6.xml
+	pylems examples/example6.xml
 
 example7:
-	./pylems examples/example7.xml
+	pylems examples/example7.xml
 
 example8:
-	./pylems examples/example8.xml
+	pylems examples/example8.xml
 
 example9:
-	./pylems examples/example9.xml
+	pylems examples/example9.xml
 
 ex0:
-	./pylems examples/LEMS_NML2_Ex0.xml
+	pylems examples/LEMS_NML2_Ex0.xml
 
 nmlex0:
-	./pylems ../NeuroML2/NeuroML2CoreTypes/LEMS_NML2_Ex0_IaF.xml
+	pylems ../NeuroML2/NeuroML2CoreTypes/LEMS_NML2_Ex0_IaF.xml
 
 nmlex1:
-	./pylems ../NeuroML2/NeuroML2CoreTypes/LEMS_NML2_Ex1_HH.xml
+	pylems ../NeuroML2/NeuroML2CoreTypes/LEMS_NML2_Ex1_HH.xml
 
 nmlex2:
-	./pylems ../NeuroML2/NeuroML2CoreTypes/LEMS_NML2_Ex2_Izh.xml
+	pylems ../NeuroML2/NeuroML2CoreTypes/LEMS_NML2_Ex2_Izh.xml
 
 nmlex3:
-	./pylems ../NeuroML2/NeuroML2CoreTypes/LEMS_NML2_Ex3_Net.xml
+	pylems ../NeuroML2/NeuroML2CoreTypes/LEMS_NML2_Ex3_Net.xml
 
 run:	example1
 

README.md

@@ -28,16 +28,13 @@ A stable version of PyLEMS is [available on PyPI](https://pypi.python.org/pypi/P
 
     pip install pylems
 
-To install as root:
-
-    sudo pip install pylems
-
 Alternatively, you can obtain the latest version with
 
     git clone https://github.com/LEMS/pylems.git
     cd pylems
     git checkout development   # optional
-    sudo python setup.py install
+    pip install .
+
 
 ### Usage as a LEMS model simulator
 

ci/run-apitest.sh

@@ -12,6 +12,10 @@ python examples/loadtest.py
 
 # Update NeuroML2 path for CI
 if [ "$CI" = "true" ]; then
-    sed -i 's|../NeuroML2|./NeuroML2|g' lems/dlems/exportdlems.py
+    if [ "$RUNNER_OS" = "macOS" ]; then
+        sed -i '' 's|../NeuroML2|./NeuroML2|g' lems/dlems/exportdlems.py;
+    else
+        sed -i 's|../NeuroML2|./NeuroML2|g' lems/dlems/exportdlems.py;
+    fi
 fi
-python lems/dlems/exportdlems.py
+python lems/dlems/exportdlems.py

ci/run-examples-ghactions.sh

@@ -10,33 +10,33 @@ mkdir results
 
 ###      Try running "standard" LEMS examples
 echo "Running standard LEMS examples"
-./pylems examples/example1.xml -nogui
-./pylems examples/example2.xml -nogui
-./pylems examples/example3.xml -nogui
-#./pylems examples/example4.xml -nogui     # Not working (Unsupported in PyLEMS: KSChannel)
-#./pylems examples/example5.xml -nogui     # Not working (Unsupported in PyLEMS: KSChannel)
-./pylems examples/example6.xml -nogui
-./pylems examples/bounce-conditional.xml -nogui
+pylems examples/example1.xml -nogui
+pylems examples/example2.xml -nogui
+pylems examples/example3.xml -nogui
+#pylems examples/example4.xml -nogui     # Not working (Unsupported in PyLEMS: KSChannel)
+#pylems examples/example5.xml -nogui     # Not working (Unsupported in PyLEMS: KSChannel)
+pylems examples/example6.xml -nogui
+pylems examples/bounce-conditional.xml -nogui
 # Rest of examples require an update to the <Simulation> element, i.e. use <Simulation...> not <SimulationSet...>, to work in PyLEMS
 
 ###      Try running NeuroML 2 examples
 echo "Running NeuroML2 examples"
-./pylems -I NeuroML2/NeuroML2CoreTypes/ NeuroML2/LEMSexamples/LEMS_NML2_Ex0_IaF.xml -nogui
-./pylems -I NeuroML2/NeuroML2CoreTypes/ NeuroML2/LEMSexamples/LEMS_NML2_Ex1_HH.xml -nogui
-./pylems -I NeuroML2/NeuroML2CoreTypes/ NeuroML2/LEMSexamples/LEMS_NML2_Ex2_Izh.xml -nogui
-./pylems -I NeuroML2/NeuroML2CoreTypes/ NeuroML2/LEMSexamples/LEMS_NML2_Ex3_Net.xml -nogui
-#./pylems -I NeuroML2/NeuroML2CoreTypes/ NeuroML2/LEMSexamples/LEMS_NML2_Ex4_KS.xml -nogui  # Not working (Unsupported in PyLEMS: KSChannel)
-./pylems -I NeuroML2/NeuroML2CoreTypes/ NeuroML2/LEMSexamples/LEMS_NML2_Ex5_DetCell.xml -nogui
-./pylems -I NeuroML2/NeuroML2CoreTypes/ NeuroML2/LEMSexamples/LEMS_NML2_Ex6_NMDA.xml -nogui
-./pylems -I NeuroML2/NeuroML2CoreTypes/ NeuroML2/LEMSexamples/LEMS_NML2_Ex7_STP.xml -nogui
-./pylems -I NeuroML2/NeuroML2CoreTypes/ NeuroML2/LEMSexamples/LEMS_NML2_Ex8_AdEx.xml -nogui
-./pylems -I NeuroML2/NeuroML2CoreTypes/ NeuroML2/LEMSexamples/LEMS_NML2_Ex9_FN.xml -nogui
-#./pylems -I NeuroML2/NeuroML2CoreTypes/ NeuroML2/LEMSexamples/LEMS_NML2_Ex10_Q10.xml -nogui
-./pylems -I NeuroML2/NeuroML2CoreTypes/ NeuroML2/LEMSexamples/LEMS_NML2_Ex11_STDP.xml -nogui
+pylems -I NeuroML2/NeuroML2CoreTypes/ NeuroML2/LEMSexamples/LEMS_NML2_Ex0_IaF.xml -nogui
+pylems -I NeuroML2/NeuroML2CoreTypes/ NeuroML2/LEMSexamples/LEMS_NML2_Ex1_HH.xml -nogui
+pylems -I NeuroML2/NeuroML2CoreTypes/ NeuroML2/LEMSexamples/LEMS_NML2_Ex2_Izh.xml -nogui
+pylems -I NeuroML2/NeuroML2CoreTypes/ NeuroML2/LEMSexamples/LEMS_NML2_Ex3_Net.xml -nogui
+#pylems -I NeuroML2/NeuroML2CoreTypes/ NeuroML2/LEMSexamples/LEMS_NML2_Ex4_KS.xml -nogui  # Not working (Unsupported in PyLEMS: KSChannel)
+pylems -I NeuroML2/NeuroML2CoreTypes/ NeuroML2/LEMSexamples/LEMS_NML2_Ex5_DetCell.xml -nogui
+pylems -I NeuroML2/NeuroML2CoreTypes/ NeuroML2/LEMSexamples/LEMS_NML2_Ex6_NMDA.xml -nogui
+pylems -I NeuroML2/NeuroML2CoreTypes/ NeuroML2/LEMSexamples/LEMS_NML2_Ex7_STP.xml -nogui
+pylems -I NeuroML2/NeuroML2CoreTypes/ NeuroML2/LEMSexamples/LEMS_NML2_Ex8_AdEx.xml -nogui
+pylems -I NeuroML2/NeuroML2CoreTypes/ NeuroML2/LEMSexamples/LEMS_NML2_Ex9_FN.xml -nogui
+#pylems -I NeuroML2/NeuroML2CoreTypes/ NeuroML2/LEMSexamples/LEMS_NML2_Ex10_Q10.xml -nogui
+pylems -I NeuroML2/NeuroML2CoreTypes/ NeuroML2/LEMSexamples/LEMS_NML2_Ex11_STDP.xml -nogui
 
-./pylems -I NeuroML2/NeuroML2CoreTypes/ NeuroML2/LEMSexamples/LEMS_NML2_Ex13_Instances.xml -nogui
+pylems -I NeuroML2/NeuroML2CoreTypes/ NeuroML2/LEMSexamples/LEMS_NML2_Ex13_Instances.xml -nogui
 
-#./pylems -I NeuroML2/NeuroML2CoreTypes/ NeuroML2/LEMSexamples/LEMS_NML2_Ex15_CaDynamics.xml -nogui
+#pylems -I NeuroML2/NeuroML2CoreTypes/ NeuroML2/LEMSexamples/LEMS_NML2_Ex15_CaDynamics.xml -nogui
 
-#./pylems -I NeuroML2/NeuroML2CoreTypes/ NeuroML2/LEMSexamples/LEMS_NML2_Ex17_Tissue.xml -nogui
-#./pylems -I NeuroML2/NeuroML2CoreTypes/ NeuroML2/LEMSexamples/LEMS_NML2_Ex18_GHK.xml -nogui  # Mismatch...
+#pylems -I NeuroML2/NeuroML2CoreTypes/ NeuroML2/LEMSexamples/LEMS_NML2_Ex17_Tissue.xml -nogui
+#pylems -I NeuroML2/NeuroML2CoreTypes/ NeuroML2/LEMSexamples/LEMS_NML2_Ex18_GHK.xml -nogui  # Mismatch...

lems/__init__.py

@@ -4,11 +4,15 @@
 """
 
 import logging
+try:
+    import importlib.metadata
+    __version__ = importlib.metadata.version("PyLEMS")
+except ImportError:
+    import importlib_metadata
+    __version__ = importlib_metadata.version("PyLEMS")
 
 logger = logging.getLogger("LEMS")
 
-__version__ = "0.6.2"
-
 __schema_version__ = "0.7.6"
 __schema_branch__ = "development"
 __schema_location__ = (

pyproject.toml

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

setup.cfg

@@ -1,3 +1,42 @@
+[metadata]
+name = PyLEMS
+version = 0.6.3
+author = PyLEMS authors and contributors
+author_email = [email protected], [email protected]
+maintainer_email = [email protected]
+url = https://github.com/LEMS/pylems
+description = A Python library for working with the Low Entropy Model Specification language (LEMS)
+long_description = file: README.md, LICENSE.lesser
+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 :: 3.6
+    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
+license = LGPL-3.0-only
+
+[options]
+install_requires =
+    lxml
+    typing; python_version<"3.5"
+
+packages = find:
+
+[options.packages.find]
+where = .
+include = lems*
+
+[options.entry_points]
+console_scripts =
+    pylems = lems.run:main
+
+
 [flake8]
 # ignore:
 # spacing around operators, comment blocks, in argument lists