Merge pull request #200 from effigies/ci/fix_test_config

CI: Update test workflow with narrower job spec, more Python versions, concurrency

Author: arokem

.github/workflows/test.yml

@@ -1,6 +1,19 @@
 name: Test suite
 
-on: [push, pull_request]
+on:
+  push:
+    branches:
+      - master
+    tags:
+      - "*"
+  pull_request:
+    branches:
+      - master
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
 
 jobs:
   build:
@@ -9,13 +22,13 @@ jobs:
     strategy:
       max-parallel: 4
       matrix:
-        python-version: [3.7, 3.8]
+        python-version: ['3.7', '3.8', '3.9', '3.10', '3.11']
 
     steps:
     - name: Checkout repo
-      uses: actions/checkout@v1
+      uses: actions/checkout@v3
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v1
+      uses: actions/setup-python@v4
       with:
         python-version: ${{ matrix.python-version }}
     - name: Install
@@ -26,7 +39,7 @@ jobs:
         python -m pip install .
     - name: Lint
       run: |
-        flake8 --ignore N802,N806,W504 --select W503 `find . -name \*.py | grep -v setup.py | grep -v version.py | grep -v __init__.py | grep -v /docs/`
+        pipx run flake8 --ignore N802,N806,W504 --select W503 nitime/ tools/
     - name: Test
       run: |
         cd && mkdir for_test && cd for_test && pytest --pyargs nitime --cov-report term-missing --cov=AFQ

nitime/algorithms/cohere.py

@@ -1005,7 +1005,7 @@ def cache_fft(time_series, ij, lb=0, ub=None,
     FFT_conj_slices = {}
 
     for i_channel in all_channels:
-        Slices = np.zeros((n_slices, n_freqs), dtype=np.complex)
+        Slices = np.zeros((n_slices, n_freqs), dtype=complex)
         for iSlice in range(n_slices):
             thisSlice = time_series[i_channel,
                                     i_times[iSlice]:i_times[iSlice] + NFFT]
@@ -1161,7 +1161,7 @@ def cache_to_relative_phase(cache, ij):
     channels_i = max(1, max(ij_array[:, 0]) + 1)
     channels_j = max(1, max(ij_array[:, 1]) + 1)
     # Pre-allocate for speed:
-    Phi_xy = np.zeros((channels_i, channels_j, freqs), dtype=np.complex)
+    Phi_xy = np.zeros((channels_i, channels_j, freqs), dtype=complex)
 
     # These checks take time, so do them up front, not in every iteration:
     if list(FFT_slices.items())[0][1].shape[0] > 1:
@@ -1221,7 +1221,7 @@ def cache_to_coherency(cache, ij):
 
     channels_i = max(1, max(ij_array[:, 0]) + 1)
     channels_j = max(1, max(ij_array[:, 1]) + 1)
-    Cxy = np.zeros((channels_i, channels_j, freqs), dtype=np.complex)
+    Cxy = np.zeros((channels_i, channels_j, freqs), dtype=complex)
 
     #These checks take time, so do them up front, not in every iteration:
     if list(FFT_slices.items())[0][1].shape[0] > 1:

nitime/analysis/coherence.py

@@ -653,10 +653,10 @@ def coherency(self):
         if len(self.seed.shape) > 1:
             Cxy = np.empty((self.seed.data.shape[0],
                             self.target.data.shape[0],
-                            self.frequencies.shape[0]), dtype=np.complex)
+                            self.frequencies.shape[0]), dtype=complex)
         else:
             Cxy = np.empty((self.target.data.shape[0],
-                            self.frequencies.shape[0]), dtype=np.complex)
+                            self.frequencies.shape[0]), dtype=complex)
 
         #Get the fft window cache for the target time-series:
         cache = self.target_cache

nitime/analysis/correlation.py

@@ -147,7 +147,7 @@ def corrcoef(self):
 
             # Preallocate results
             Cxy = np.empty((self.seed.data.shape[0],
-                            self.target.data.shape[0]), dtype=np.float)
+                            self.target.data.shape[0]), dtype=float)
 
             for seed_idx, this_seed in enumerate(self.seed.data):
 

nitime/analysis/spectral.py

@@ -418,8 +418,8 @@ def iir(self):
 
             wp = [lb_frac, ub_frac]
 
-            ws = [np.max([lb_frac - 0.1, 0]),
-                  np.min([ub_frac + 0.1, 1.0])]
+            ws = [np.max([lb_frac - 0.1, 0.001]),
+                  np.min([ub_frac + 0.1, 0.999])]
 
         # For the lowpass:
         elif lb_frac == 0:

nitime/fmri/io.py

@@ -88,7 +88,7 @@ def time_series_from_file(nifti_files, coords=None, TR=None, normalize=None,
         if verbose:
             print("Reading %s" % nifti_files)
         im = load(nifti_files)
-        data = im.get_data()
+        data = im.get_fdata()
         # If coordinates are provided as input, read data only from these coordinates:
         if coords is not None:
             #If the input is the coords of several ROIs
@@ -118,7 +118,7 @@ def time_series_from_file(nifti_files, coords=None, TR=None, normalize=None,
             if verbose:
                 print("Reading %s" % f)
             im = load(f)
-            data = im.get_data()
+            data = im.get_fdata()
             if coords is not None:
                 #If the input is the coords of several ROIs
                 if isinstance(coords, tuple) or isinstance(coords, list):

nitime/fmri/tests/test_io.py

@@ -65,7 +65,7 @@ def test_time_series_from_file():
     npt.assert_equal(t4.sampling_interval,nitime.TimeArray(1.35))
 
     # Test the default behavior:
-    data = io.load(fmri_file1).get_data()
+    data = io.load(fmri_file1).get_fdata()
     t5 = ts_ff(fmri_file1)
     npt.assert_equal(t5.shape, data.shape)
     npt.assert_equal(t5.sampling_interval, ts.TimeArray(1, time_unit='s'))

nitime/tests/test_algorithms.py

@@ -145,11 +145,11 @@ def test_psd_matlab():
     ts = np.loadtxt(os.path.join(test_dir_path, 'tseries12.txt'))
 
     #Complex signal!
-    ts0 = ts[1] + ts[0] * np.complex(0, 1)
+    ts0 = ts[1] + ts[0] * complex(0, 1)
 
     NFFT = 256
     Fs = 1.0
-    noverlap = NFFT / 2
+    noverlap = NFFT // 2
 
     fxx, f = mlab.psd(ts0, NFFT=NFFT, Fs=Fs, noverlap=noverlap,
                       scale_by_freq=True)

requirements-dev.txt

@@ -3,4 +3,3 @@ pytest
 pytest-cov
 nibabel
 networkx
-flake8