[MAINT] Implement deprecation warnings-as-errors in prerelease test u…

…sing pytest fixture (#3936)

* Add fixture

* Add dependencies

* TODO

* Add monthly workflow config

* Numpy deprecation

* Update workflow

* Update

* Add to readme

.github/workflows/README.md

@@ -80,6 +80,14 @@ Artifacts hosting and deployment of development docs use CircleCI. See [.circlec
 On a pull request, only the "host" job is run. Then the artifacts can be accessed from the `host_and_deploy_doc` workflow seen under the checks list. Click on "Details" and then on the "host_docs" link on the page that opens. From there you can click on the artifacts tab to see all the html files. If you click on any of them you can then normally navigate the pages from there.
 With a merge on main, both "host" and "deploy" jobs are run.
 
+## DeprecationWarnings as errors
+
+### check_deprecations.yml
+
+Checks external core dependencies for deprecation warnings so they can be caught and resolved before causing a failure.
+Runs once a month and can be run manually from Github Actions.
+It works by calling pytest with an environment variable that will trigger a pytest fixture (``warnings_as_errors``) defined in [nilearn/conftest.py](/nilearn/conftest.py).
+
 ## Check spelling errors
 
 ### codespell.yml

.github/workflows/check_deprecations.yml

@@ -0,0 +1,59 @@
+---
+name: check deprecations
+
+# Runs once a month.
+# Checks for deprecations of core dependencies of nilearn
+# Turns deprecation warnings into errors so we can handle
+# them before an actual failure happens.
+
+on:
+
+# Uses the cron schedule for github actions
+#
+# https://docs.github.com/en/free-pro-team@latest/actions/reference/events-that-trigger-workflows#scheduled-events
+#
+#            ┌───────────── minute (0 - 59)
+#            │ ┌───────────── hour (0 - 23)
+#            │ │ ┌───────────── day of the month (1 - 31)
+#            │ │ │ ┌───────────── month (1 - 12 or JAN-DEC)
+#            │ │ │ │ ┌───────────── day of the week (0 - 6 or SUN-SAT)
+#            │ │ │ │ │
+#            │ │ │ │ │
+#            │ │ │ │ │
+#            * * * * *
+    schedule:
+    -   cron: 0 0 25 * * # on the 25th of every month
+
+  # Allows you to run this workflow manually from the Actions tab
+    workflow_dispatch:
+
+jobs:
+    deprecations:
+        if: github.repository == 'nilearn/nilearn'
+        runs-on: ubuntu-latest
+        env:
+            PIP_FLAGS: --pre
+            WARN_DEPRECATION_ERRORS: true
+
+        defaults:
+            run:
+                shell: bash
+        steps:
+        -   uses: actions/checkout@v4
+
+        -   name: Setup python
+            uses: actions/setup-python@v4
+            with:
+                python-version: 3.12
+
+        -   name: Display Python version
+            run: python -c "import sys; print(sys.version)"
+
+        -   name: Install dependencies
+            run: ./build_tools/github/dependencies.sh
+
+        -   name: Install nilearn
+            run: ./build_tools/github/install.sh
+
+        -   name: Run tests
+            run: python -m pytest --pyargs nilearn

nilearn/conftest.py

@@ -1,4 +1,7 @@
 """Configuration and extra fixtures for pytest."""
+import os
+import warnings
+
 import nibabel
 import numpy as np
 import pytest
@@ -79,6 +82,35 @@ def close_all():
         plt.close("all")  # takes < 1 us so just always do it
 
 
+@pytest.fixture(autouse=True)
+def warnings_as_errors():
+    """Raise errors on deprecations from external library prereleases."""
+    flag = os.environ.get("WARN_DEPRECATION_ERRORS")
+    if flag == "true":
+        with warnings.catch_warnings():
+            warnings.filterwarnings(
+                "error",
+                message=".*numpy.*|.*scipy.*|.*nibabel.*|"
+                ".*joblib.*|.*pandas.*|.*scikit-learn.*",
+                category=DeprecationWarning,
+            )
+            if matplotlib is not None:
+                warnings.filterwarnings(
+                    "error",
+                    category=matplotlib.MatplotlibDeprecationWarning,
+                )
+            # Ignore internal DeprecationWarnings that reference a dependency
+            pattern = '.*The "C" parameter.*'
+            warnings.filterwarnings(
+                "ignore",
+                message=pattern,
+                category=DeprecationWarning,
+            )
+            yield
+    else:
+        yield
+
+
 # ------------------------   RNG   ------------------------#
 
 

nilearn/mass_univariate/tests/utils.py

@@ -51,7 +51,7 @@ def get_tvalue_with_alternative_library(tested_vars, target_vars, covars=None):
                 current_tested_mask[j] = True
                 current_design_matrix = design_matrix[:, current_tested_mask]
                 ols_fit = OLS(current_target, current_design_matrix).fit()
-                t_values[i, j] = np.ravel(ols_fit.t_test(test_matrix).tvalue)
+                t_values[i, j] = np.squeeze(ols_fit.t_test(test_matrix).tvalue)
 
     except ImportError:  # use linalg if statsmodels is not available
         from numpy import linalg
@@ -83,7 +83,7 @@ def get_tvalue_with_alternative_library(tested_vars, target_vars, covars=None):
                     / float(n_samples - lost_dof)
                     * t_val_denom_aux
                 )
-                t_values[j, i] = np.ravel(t_val_num / t_val_denom)
+                t_values[j, i] = np.squeeze(t_val_num / t_val_denom)
 
     t_values = t_values.T
     assert t_values.shape == (n_regressors, n_descriptors)