Fix/remove python 3.7 (#536)

* add python 3.11 to CI workflow
* drop support for python 3.7
* update the libstd for the CI runner to fix bugs related to newer scipy versions
* fix dtype error appearing with quantities 0.14.0

.github/workflows/CI.yml

@@ -1,4 +1,4 @@
-# This workflow will setup GitHub-hosted runners and install the required dependencies for elephant tests.
+# This workflow will set up GitHub-hosted runners and install the required dependencies for elephant tests.
 # On a pull requests and on pushes to master it will run different tests for elephant.
 
 name: tests
@@ -57,8 +57,8 @@ jobs:
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        # python versions for elephant: [3.7, 3.8, 3.9, "3.10"]
-        python-version: [3.7, 3.8, 3.9, "3.10"]
+        # python versions for elephant: [3.8, 3.9, "3.10", 3.11]
+        python-version: [3.8, 3.9, "3.10", 3.11]
         # OS [ubuntu-latest, macos-latest, windows-latest]
         os: [ubuntu-latest]
       # do not cancel all in-progress jobs if any matrix job fails
@@ -82,7 +82,7 @@ jobs:
       - name: Cache test_env
         uses: actions/cache@v3
         with:
-          path: ~/test_env
+          path: /home/runner/.cache/pip
           # Look to see if there is a cache hit for the corresponding requirements files
           # cache will be reset on changes to any requirements or every month
           key: ${{ runner.os }}-venv-${{ hashFiles('**/requirements.txt') }}-${{ hashFiles('**/requirements-tests.txt') }}
@@ -181,7 +181,7 @@ jobs:
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        # python versions for elephant: [3.6, 3.7, 3.8, 3.9]
+        # python versions for elephant: [3.8, 3.9, 3.10, 3.11]
         python-version: [3.8,]
         # OS [ubuntu-latest, macos-latest, windows-latest]
         os: [windows-latest]
@@ -243,7 +243,7 @@ jobs:
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        # python versions for elephant: [3.6, 3.7, 3.8, 3.9]
+        # python versions for elephant: [3.8, 3.9, 3.10, 3.11]
         python-version: [3.9]
         # OS [ubuntu-latest, macos-latest, windows-latest]
         os: [ubuntu-latest]
@@ -273,6 +273,7 @@ jobs:
 
       - name: Setup environment
         run: |
+          sudo apt-get update
           sudo apt install -y libopenmpi-dev openmpi-bin
 
           python -m pip install --upgrade pip
@@ -331,6 +332,7 @@ jobs:
         run: |
           conda config --add channels conda-forge # bugfix with scipy==1.8.1: libstdcxx-ng 12.1.0 required
           conda update conda
+          conda install -c conda-forge libstdcxx-ng=12 # fix libstdc++.so.6: version for new scipy versions > 1.9.1
           conda env update --file requirements/environment-tests.yml --name base
           activate base
           conda install -c conda-forge openmpi
@@ -387,6 +389,7 @@ jobs:
 
       - name: Install dependencies
         run: |
+          sudo apt-get update
           sudo apt install -y libopenmpi-dev openmpi-bin
           python -m pip install --upgrade pip
           pip install -r requirements/requirements-docs.txt

.github/workflows/build_wheels.yml

@@ -33,8 +33,8 @@ jobs:
       - name: Build wheels
         run: python -m cibuildwheel --output-dir wheelhouse
         env:
-          CIBW_SKIP: "cp27-* cp33-* cp34-* cp35-* cp36-* pp*"
-          CIBW_PROJECT_REQUIRES_PYTHON: ">=3.7"
+          CIBW_SKIP: "cp27-* cp33-* cp34-* cp35-* cp36-* cp37-* pp*"
+          CIBW_PROJECT_REQUIRES_PYTHON: ">=3.8"
           CIBW_ARCHS: "auto64"
 
       - uses: actions/upload-artifact@v3

doc/install.rst

@@ -14,7 +14,7 @@ Below is the explanation of how to proceed with these two steps.
 Prerequisites
 *************
 
-Elephant requires `Python <http://python.org/>`_ 3.7, 3.8, 3.9 or 3.10.
+Elephant requires `Python <http://python.org/>`_ 3.8, 3.9, 3.10 or 3.11.
 
 .. tabs::
 
@@ -25,7 +25,7 @@ Elephant requires `Python <http://python.org/>`_ 3.7, 3.8, 3.9 or 3.10.
 
            .. code-block:: sh
 
-              conda create --name elephant python=3.7 numpy scipy tqdm
+              conda create --name elephant python=3.8 numpy scipy tqdm
 
         2. Activate your environment:
 

elephant/cell_assembly_detection.py

@@ -440,7 +440,7 @@ def cell_assembly_detection(binned_spiketrain, max_lag, reference_lag=2,
         times = np.where(pattern['times'] > 0)[0] * bin_size + t_start
         pattern['times'] = times
         pattern['lags'] = pattern['lags'] * bin_size
-        pattern['signature'] = np.array(pattern['signature'], dtype=np.int32)
+        pattern['signature'] = np.array(pattern['signature'], dtype=int)
 
     # Give as output only the maximal groups
     if verbose:

elephant/test/test_conversion.py

@@ -510,8 +510,8 @@ def test_binned_spiketrain_n_bins_not_int(self):
     def test_to_array(self):
         x = cv.BinnedSpikeTrain(self.spiketrain_a, bin_size=1 * pq.s,
                                 n_bins=10, t_stop=10. * pq.s)
-        arr_float = x.to_array(dtype=np.float32)
-        assert_array_equal(arr_float, x.to_array().astype(np.float32))
+        arr_float = x.to_array(dtype=float)
+        assert_array_equal(arr_float, x.to_array().astype(float))
 
     # Test if error is raised when providing insufficient number of
     # parameters

elephant/test/test_spade.py

@@ -608,7 +608,7 @@ def test_spade_raise_error(self):
                           corr='invalid_key')
         # Test negative number of subset for stability
         self.assertRaises(ValueError, spade.approximate_stability, (),
-                          np.array([]), n_subsets=-3)
+                          np.ndarray([]), n_subsets=-3)
 
     def test_pattern_set_reduction(self):
         winlen = 6

elephant/test/test_statistics.py

@@ -410,7 +410,7 @@ def setUp(self):
     def test_lvr_with_quantities(self):
         seq = pq.Quantity(self.test_seq, units='ms')
         assert_array_almost_equal(statistics.lvr(seq), self.target, decimal=9)
-        seq = pq.Quantity(self.test_seq, units='ms').rescale('s')
+        seq = pq.Quantity(self.test_seq, units='ms').rescale('s', dtype=float)
         assert_array_almost_equal(statistics.lvr(seq), self.target, decimal=9)
 
     def test_lvr_with_plain_array(self):

elephant/test/test_unitary_event_analysis.py

@@ -319,6 +319,7 @@ def test__UE_surrogate(self):
                         item1))
 
     def test_jointJ_window_analysis(self):
+
         sts1 = self.sts1_neo
         sts2 = self.sts2_neo
 
@@ -498,6 +499,7 @@ def test_Riehle_et_al_97_UE(self):
 
     def test_multiple_neurons(self):
         np.random.seed(12)
+
         # Create a list of lists containing 3 Trials with 5 spiketrains
         spiketrains = \
             [StationaryPoissonProcess(

requirements/environment-docs.yml

@@ -4,7 +4,7 @@ channels:
   - conda-forge  # required for MPI
 
 dependencies:
-  - python>=3.7
+  - python>=3.8
 
   - mpi4py
   - numpy>=1.19.5

requirements/environment-tests.yml

@@ -4,7 +4,7 @@ channels:
   - conda-forge  # required for MPI
 
 dependencies:
-  - python>=3.7
+  - python>=3.8
 
   - mpi4py
   - numpy>=1.19.5

requirements/environment.yml

@@ -4,7 +4,7 @@ channels:
   - conda-forge  # required for MPI
 
 dependencies:
-  - python>=3.7
+  - python>=3.8
   - mpi4py
   - numpy>=1.19.5
   - scipy

setup.py

@@ -81,18 +81,18 @@
             "Documentation": "https://elephant.readthedocs.io/en/latest/",
             "Source Code": "https://github.com/NeuralEnsemble/elephant",
         },
-    "python_requires": ">=3.7",
+    "python_requires": ">=3.8",
     "classifiers": [
         'Development Status :: 5 - Production/Stable',
         'Intended Audience :: Science/Research',
         'License :: OSI Approved :: BSD License',
         'Natural Language :: English',
         'Operating System :: OS Independent',
         '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',
         'Programming Language :: Python :: 3 :: Only',
         'Topic :: Scientific/Engineering']
 }