[Fix] CuBIC, SPADE with scipy 1.14.0, deprecated .A attribute in `s…

…cipy.sparse` matrices` (NeuralEnsemble#636)

* fix deprecated .A attribute on coo_matrix
* make precision for cubic explicit
* ensure float64 precision for data when using scipy.stats.kstat

.github/workflows/CI.yml

@@ -131,22 +131,22 @@ jobs:
  fail-fast: false
  matrix:
  # OS [ubuntu-latest, macos-latest, windows-latest]
- os: [macos-11,macos-12]
+ os: [macos-12,macos-13]
  python-version: [3.11]
  steps:
  - name: Get current year-month
  id: date
  run: echo "date=$(date +'%Y-%m')" >> $GITHUB_OUTPUT
 
- - uses: actions/checkout@v3
+ - uses: actions/checkout@v4.1.6
 
  - name: Cache conda
  uses: actions/cache@v3
  with:
  path: ~/conda_pkgs_dir
  key: ${{ runner.os }}-conda-${{hashFiles('requirements/environment.yml') }}-${{ hashFiles('**/CI.yml') }}-${{ steps.date.outputs.date }}
 
- - uses: conda-incubator/setup-miniconda@030178870c779d9e5e1b4e563269f3aa69b04081 # corresponds to v3.0.3
+ - uses: conda-incubator/setup-miniconda@a4260408e20b96e80095f42ff7f1a15b27dd94ca # corresponds to v3.0.4
  with:
  auto-update-conda: true
  python-version: ${{ matrix.python-version }}

elephant/cubic.py

@@ -237,5 +237,6 @@ def _kstat(data):
  """
  if len(data) == 0:
  raise ValueError('The input data must be a non-empty array')
- moments = [scipy.stats.kstat(data, n=n) for n in [1, 2, 3]]
+ # Due to issues with precision, ensure float64 (default) is the precision of the data array. (scipy == 1.14.0)
+ moments = [scipy.stats.kstat(data.astype(np.float64), n=n) for n in [1, 2, 3]]
  return moments

elephant/spade.py

@@ -768,7 +768,7 @@ def _build_context(binary_matrix, winlen):
  (np.ones((len(windows_col)), dtype=bool),
  (windows_row, windows_col)),
  shape=(num_bins, winlen * num_neurons),
- dtype=bool).A
+ dtype=bool).toarray()
  # Array containing all the possible attributes (each spike is indexed by
  # a number equal to neu idx*winlen + bin_idx)
  attributes = np.array(