Updates to requirements

.github/workflows/full-test.yml

@@ -16,10 +16,11 @@ jobs:
     strategy:
       fail-fast: true
       matrix:
-        python-version: ["3.8", "3.10", "3.12"]
+        python-version: ["3.9", "3.10", "3.12"]
         os: ["ubuntu-latest", "windows-latest"]
     steps:
     - uses: actions/checkout@v4
+    - uses: mpi4py/setup-mpi@v1
     - name: Set up Python ${{ matrix.python-version }}
       uses: actions/setup-python@v5
       with:
@@ -31,7 +32,7 @@ jobs:
     - name: Install basic Python dependencies
       run: |
         python -m pip install --upgrade pip
-        python -m pip install pytest pytest-cov coveralls flake8
+        python -m pip install pytest pytest-cov coveralls flake8 "setuptools<=75.8.2" "numpy<2"
     - name: Install Brian 2
       run: |
         python -m pip install brian2
@@ -52,13 +53,18 @@ jobs:
     - name: Install PyNN itself
       run: |
         pip install -e ".[test]"
-    - name: Test installation has worked
+    - name: Test installation has worked (Ubuntu)
       # this is needed because the PyNN tests are just skipped if the simulator
       # fails to install, so we need to catch import failures separately
+      if: startsWith(matrix.os, 'ubuntu')
       run: |
         python -c "import pyNN.nest"
         python -c "import pyNN.neuron"
         python -c "import pyNN.brian2"
+    - name: Test installation has worked (Windows)
+      if: startsWith(matrix.os, 'windows')
+      run: |
+        python -c "import pyNN.brian2"
     - name: Lint with flake8
       run: |
         # stop the build if there are Python syntax errors or undefined names

doc/developers/contributing.txt

@@ -70,7 +70,7 @@ We try to stay fairly close to PEP8_. Please note in particular:
     - some function/method names in PyNN use ``mixedCase``, but these will
       gradually be deprecated and replaced with ``lower_case_with_underscores``.
       Any new functions or methods should use the latter.
-    - we currently target versions 3.8+
+    - we currently target versions 3.9+
 
 
 Testing

doc/installation.txt

@@ -7,10 +7,10 @@ install and run PyNN on Windows, but this has not been tested.
 
 Installing PyNN requires:
 
-* Python (version 3.8+)
+* Python (version 3.9+)
 * a recent version of the NumPy_ package
 * the lazyarray_ package
-* the Neo_ package (>= 0.11.0)
+* the Neo_ package (>= 0.13.4)
 * at least one of the supported simulators: e.g. NEURON, NEST, Brian 2 or Arbor.
 
 Optional dependencies are:

pyNN/common/projections.py

@@ -443,7 +443,7 @@ def save(self, attribute_names, file, format='list', gather=True, with_address=T
         if attribute_names in ('all', 'connections'):
             attribute_names = self.synapse_type.get_parameter_names()
         if isinstance(file, str):
-            file = recording.files.StandardTextFile(file, mode='wb')
+            file = recording.files.StandardTextFile(file, mode='w')
         all_values = self.get(attribute_names, format=format,
                               gather=gather, with_address=with_address)
         if format == 'array':

pyNN/recording/files.py

@@ -28,17 +28,6 @@
 DEFAULT_BUFFER_SIZE = 10000
 
 
-def _savetxt(filename, data, format, delimiter):
-    """
-    Due to the lack of savetxt in older versions of numpy
-    we provide a cut-down version of that function.
-    """
-    f = open(filename, 'w')
-    for row in data:
-        f.write(delimiter.join([format % val for val in row]) + '\n')
-    f.close()
-
-
 def savez(file, *args, **kwds):
     import zipfile
     from numpy.lib import format
@@ -148,10 +137,9 @@ def write(self, data, metadata):
         # write header
         header_lines = ["# %s = %s" % item for item in metadata.items()]
         header = "\n".join(header_lines) + '\n'
-        self.fileobj.write(header.encode('utf-8'))
+        self.fileobj.write(header)
         # write data
-        savetxt = getattr(np, 'savetxt', _savetxt)
-        savetxt(self.fileobj, data, fmt='%r', delimiter='\t')
+        np.savetxt(self.fileobj, data, delimiter='\t')
         self.fileobj.close()
 
     def read(self):

pyproject.toml

@@ -3,7 +3,7 @@ name = "PyNN"
 version = "0.12.3"
 description = "A Python package for simulator-independent specification of neuronal network models"
 readme = "README.rst"
-requires-python = ">=3.8"
+requires-python = ">=3.9"
 license = {text = "CeCILL http://www.cecill.info"}
 authors = [
   {name = "The PyNN team", email = "pynn-maintainers@protonmail.com"}
@@ -20,19 +20,17 @@ classifiers = [
   "Natural Language :: English",
   "Operating System :: OS Independent",
   "Programming Language :: Python :: 3",
-  "Programming Language :: Python :: 3.8",
   "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 :: Education",
   "Topic :: Scientific/Engineering"
 ]
 dependencies = [
-  "numpy>=1.18.5",
   "lazyarray>=0.5.2",
-  "neo>=0.11.0",
-  "quantities>=0.12.1",
+  "neo>=0.13.4",
   "morphio"
 ]
 

test/system/test_neuron.py

@@ -28,11 +28,6 @@
     have_neuroml = False
 
 
-skip_ci = False
-if "JENKINS_SKIP_TESTS" in os.environ:
-    skip_ci = os.environ["JENKINS_SKIP_TESTS"] == "1"
-
-
 def test_ticket168():
     """
     Error setting firing rate of `SpikeSourcePoisson` after `reset()` in NEURON
@@ -131,8 +126,6 @@ class SimpleNeuronType(NativeCellType):
 
 def test_electrical_synapse():
     pytest.skip("Skipping test for now as it produces a segmentation fault")
-    if skip_ci:
-        pytest.skip("Skipping test on CI server as it produces a segmentation fault")
     p1 = pyNN.neuron.Population(4, pyNN.neuron.standardmodels.cells.HH_cond_exp())
     p2 = pyNN.neuron.Population(4, pyNN.neuron.standardmodels.cells.HH_cond_exp())
     syn = pyNN.neuron.ElectricalSynapse(weight=1.0)

test/unittests/test_connectors_parallel.py

@@ -448,7 +448,7 @@ def test_with_plastic_synapses_not_distributed(self, sim=sim):
             (2, 2, 0.4, 0.13, 130, 97),
             (0, 1, 0.5, 0.14, 140, 96),  # local
         ]
-        file = recording.files.StandardTextFile("test.connections.2", mode='wb')
+        file = recording.files.StandardTextFile("test.connections.2", mode='w')
         file.write(connection_list, {"columns": ["i", "j", "weight", "delay", "U", "tau_rec"]})
         C = connectors.FromFileConnector("test.connections.2", distributed=False)
         syn = sim.TsodyksMarkramSynapse(tau_facil=88.8)

test/unittests/test_connectors_serial.py

@@ -555,7 +555,7 @@ def test_with_plastic_synapses_not_distributed(self, sim=sim):
             (2, 2, 0.4, 0.13, 130, 97),
             (0, 1, 0.5, 0.14, 140, 96),  # local
         ]
-        file = recording.files.StandardTextFile("test.connections.2", mode='wb')
+        file = recording.files.StandardTextFile("test.connections.2", mode='w')
         file.write(connection_list, {"columns": ["i", "j", "weight", "delay", "U", "tau_rec"]})
         C = connectors.FromFileConnector("test.connections.2", distributed=False)
         syn = sim.TsodyksMarkramSynapse(tau_facil=88.8)

test/unittests/test_files.py

@@ -11,20 +11,6 @@
 builtin_open = open
 
 
-def test__savetxt():
-    mock_file = Mock()
-    files.open = Mock(return_value=mock_file)
-    files._savetxt(filename="dummy_file",
-                   data=[(0, 2.3), (1, 3.4), (2, 4.3)],
-                   format="%f",
-                   delimiter=" ")
-    target = [(('0.000000 2.300000\n',), {}),
-              (('1.000000 3.400000\n',), {}),
-              (('2.000000 4.300000\n',), {})]
-    assert mock_file.write.call_args_list == target
-    files.open = builtin_open
-
-
 def test_create_BaseFile():
     files.open = Mock()
     bf = files.BaseFile("filename", 'r')