Merge pull request #35 from wmvanvliet/update-workflows

Use newer versions of github actions
wmvanvliet · Oct 15, 2024 · a6fffe2 · a6fffe2
2 parents b88ab07 + 1483c47
commit a6fffe2
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Showing 5 changed files with 31 additions and 39 deletions.
diff --git a/.github/workflows/build-docs.yml b/.github/workflows/build-docs.yml
@@ -16,12 +16,12 @@ jobs:
           _MNE_BRAIN_TRACES_AUTO: false
 
       steps:
-        - uses: actions/checkout@v2
+        - uses: actions/checkout@v4
 
-        - name: Set up Python 3.11
-          uses: actions/setup-python@v2
+        - name: Set up Python 3.12
+          uses: actions/setup-python@v5
           with:
-            python-version: 3.11
+            python-version: 3.12
 
         - name: Merge with upstream
           run: |
@@ -49,7 +49,7 @@ jobs:
 
         - name: Cache Pip
           id: cache-pip
-          uses: actions/cache@v1
+          uses: actions/cache@v4
           with:
             path: ~/.cache/pip
             key: pip-cache
@@ -79,17 +79,8 @@ jobs:
             cd doc;
             make html;
 
-        # Save the outputs
-        #- store_artifacts:
-        #    path: doc/_build/html/
-        #    destination: dev
-
-        #- persist_to_workspace:
-        #    root: doc/_build
-        #    paths:
-        #      - html
         - name: Save HTML as artifact
-          uses: actions/upload-artifact@v1
+          uses: actions/upload-artifact@v4
           with:
             name: docs
             path: doc/_build/html
diff --git a/.github/workflows/unit-tests.yml b/.github/workflows/unit-tests.yml
@@ -15,11 +15,11 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-    - uses: actions/checkout@v2
-    - name: Set up Python 3.11
-      uses: actions/setup-python@v2
+    - uses: actions/checkout@v4
+    - name: Set up Python 3.12
+      uses: actions/setup-python@v5
       with:
-        python-version: 3.11
+        python-version: 3.12
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip

diff --git a/mne_rsa/rsa.py b/mne_rsa/rsa.py
@@ -76,7 +76,8 @@ def count_rank_tie(ranks):
 
 
 def _consolidate_masks(masks):
-    if type(masks[0]) == slice:
+    """Compute the union of multiple masks."""
+    if type(masks[0]) is slice:
         mask = slice(None)
     else:
         mask = masks[0]

diff --git a/mne_rsa/sensor_level.py b/mne_rsa/sensor_level.py
@@ -751,8 +751,8 @@ def rdm_epochs(
         ]
         for rdm in rdm_gen:
             rdm = distance.squareform(rdm)
-            rdm = np.insert(rdm, nan_locations, np.NaN, axis=0)
-            rdm = np.insert(rdm, nan_locations, np.NaN, axis=1)
+            rdm = np.insert(rdm, nan_locations, np.nan, axis=0)
+            rdm = np.insert(rdm, nan_locations, np.nan, axis=1)
             # Can't use squareform to convert back due to the NaNs.
             yield rdm[np.triu_indices(len(rdm), 1)]
 

diff --git a/tests/test_rsa.py b/tests/test_rsa.py
@@ -35,8 +35,8 @@ def test_spearman(self):
         model_rdm = np.array([2, 3, 3.5])
         assert next(rsa_gen(data_rdm, model_rdm, metric="spearman")) == 1.0
 
-        data_rdm = rdm_gen([[np.NaN, 2, 3, 4, 5]])
-        model_rdm = np.array([2, np.NaN, 3.5, 4, 5])
+        data_rdm = rdm_gen([[np.nan, 2, 3, 4, 5]])
+        model_rdm = np.array([2, np.nan, 3.5, 4, 5])
         assert (
             next(rsa_gen(data_rdm, model_rdm, metric="spearman", ignore_nan=True))
             == 1.0
@@ -48,8 +48,8 @@ def test_pearson(self):
         model_rdm = np.array([2, 3, 3.5])
         assert next(rsa_gen(data_rdm, model_rdm, metric="pearson")) < 1.0
 
-        data_rdm = rdm_gen([[np.NaN, 2, 3, 4, 5]])
-        model_rdm = np.array([2, np.NaN, 3.5, 4, 5])
+        data_rdm = rdm_gen([[np.nan, 2, 3, 4, 5]])
+        model_rdm = np.array([2, np.nan, 3.5, 4, 5])
         assert (
             next(rsa_gen(data_rdm, model_rdm, metric="pearson", ignore_nan=True)) < 1.0
         )
@@ -61,8 +61,8 @@ def test_kendall_tau_a(self):
         rsa_val = next(rsa_gen(data_rdm, model_rdm, metric="kendall-tau-a"))
         assert rsa_val == 2 / 3
 
-        data_rdm = rdm_gen([[1, np.NaN, 2, 3, 4]])
-        model_rdm = np.array([1, 2, 3, 3, np.NaN])
+        data_rdm = rdm_gen([[1, np.nan, 2, 3, 4]])
+        model_rdm = np.array([1, 2, 3, 3, np.nan])
         rsa_val = next(
             rsa_gen(data_rdm, model_rdm, metric="kendall-tau-a", ignore_nan=True)
         )
@@ -76,8 +76,8 @@ def test_regression(self):
         rsa_val = next(rsa_gen(data_rdm, [model_rdm1, model_rdm2], metric="regression"))
         assert_allclose(rsa_val, [3, 5])
 
-        model_rdm1 = np.array([-1, np.NaN, 0, 1, 1])
-        model_rdm2 = np.array([1, 3, -2, 1, np.NaN])
+        model_rdm1 = np.array([-1, np.nan, 0, 1, 1])
+        model_rdm2 = np.array([1, 3, -2, 1, np.nan])
         data_rdm = rdm_gen([3 * model_rdm1 + 5 * model_rdm2])
         rsa_val = next(
             rsa_gen(
@@ -95,9 +95,9 @@ def test_partial(self):
         rsa_val = next(rsa_gen(data_rdm, [model_rdm1, model_rdm2], metric="partial"))
         assert_allclose(rsa_val, [0.919145, 0.912871])
 
-        model_rdm1 = np.array([1, np.NaN, 2, 3, 4, 4])
-        model_rdm2 = np.array([0, 0, 0, 1, 1, np.NaN])
-        data_rdm = rdm_gen([[2, np.NaN, 4, 15, 20, np.NaN]])
+        model_rdm1 = np.array([1, np.nan, 2, 3, 4, 4])
+        model_rdm2 = np.array([0, 0, 0, 1, 1, np.nan])
+        data_rdm = rdm_gen([[2, np.nan, 4, 15, 20, np.nan]])
         rsa_val = next(
             rsa_gen(
                 data_rdm, [model_rdm1, model_rdm2], metric="partial", ignore_nan=True
@@ -116,9 +116,9 @@ def test_partial_spearman(self):
         )
         assert_allclose(rsa_val, [0, 2 / 3], atol=1e-15)
 
-        model_rdm1 = np.array([1, np.NaN, 2, 3, 4, 4])
-        model_rdm2 = np.array([0, 0, 0, 1, 1, np.NaN])
-        data_rdm = rdm_gen([[2, np.NaN, 4, 20, 15, np.NaN]])
+        model_rdm1 = np.array([1, np.nan, 2, 3, 4, 4])
+        model_rdm2 = np.array([0, 0, 0, 1, 1, np.nan])
+        data_rdm = rdm_gen([[2, np.nan, 4, 20, 15, np.nan]])
         rsa_val = next(
             rsa_gen(
                 data_rdm,
@@ -141,10 +141,10 @@ def test_invalid_metric(self):
             next(rsa_gen(rdm_gen([rdm()]), rdm(), metric="partial-spearman"))
 
     def test_nan(self):
-        """Test whether NaNs generate an error when appropriate."""
-        assert np.isnan(next(rsa_gen(rdm_gen([[1, 2, np.NaN, 4, 5, 6]]), rdm())))
+        """Test whether nans generate an error when appropriate."""
+        assert np.isnan(next(rsa_gen(rdm_gen([[1, 2, np.nan, 4, 5, 6]]), rdm())))
         assert_allclose(
-            next(rsa_gen(rdm_gen([[1, 2, np.NaN, 4, 5, 6]]), rdm(), ignore_nan=True)),
+            next(rsa_gen(rdm_gen([[1, 2, np.nan, 4, 5, 6]]), rdm(), ignore_nan=True)),
             1,
             atol=1e-15,
         )