MAINT: Update code credit [circle deploy] (#13038)

Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> Co-authored-by: Eric Larson <[email protected]> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
mne-tools · Dec 18, 2024 · 14938b9 · 14938b9
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Showing 11 changed files with 135 additions and 10 deletions.
diff --git a/azure-pipelines.yml b/azure-pipelines.yml
@@ -171,8 +171,7 @@ stages:
               python -m pip install --progress-bar off --upgrade pip
               python -m pip install --progress-bar off --upgrade --pre --only-binary=\"numpy,scipy,matplotlib,vtk\" numpy scipy matplotlib vtk
               python -c "import vtk"
-              # Bug on 2.5.13 https://github.com/openmeeg/openmeeg/issues/700
-              python -m pip install --progress-bar off --upgrade -ve .[full,test_extra] "openmeeg==2.5.12"
+              python -m pip install --progress-bar off --upgrade -ve .[full,test_extra]
             displayName: 'Install dependencies with pip'
           - bash: |
               set -e

diff --git a/doc/sphinxext/prs/13031.json b/doc/sphinxext/prs/13031.json
@@ -0,0 +1,35 @@
+{
+  "merge_commit_sha": "5b06ca4bb8f9138bf4af85ea3171d95df07462c5",
+  "authors": [
+    {
+      "n": "github-actions[bot]",
+      "e": "41898282+github-actions[bot]@users.noreply.github.com"
+    },
+    {
+      "n": "Eric Larson",
+      "e": "[email protected]"
+    }
+  ],
+  "changes": {
+    ".github/workflows/credit.yml": {
+      "a": 2,
+      "d": 2
+    },
+    "doc/documentation/cited.rst": {
+      "a": 3,
+      "d": 3
+    },
+    "doc/sphinxext/prs/13029.json": {
+      "a": 91,
+      "d": 0
+    },
+    "doc/sphinxext/prs/6915.json": {
+      "a": 43,
+      "d": 0
+    },
+    "tools/dev/update_credit_json.py": {
+      "a": 3,
+      "d": 1
+    }
+  }
+}
diff --git a/doc/sphinxext/prs/13032.json b/doc/sphinxext/prs/13032.json
@@ -0,0 +1,15 @@
+{
+  "merge_commit_sha": "b38385ef90d0fd8214d54b15c5fd91333c3bc032",
+  "authors": [
+    {
+      "n": "pre-commit-ci[bot]",
+      "e": "66853113+pre-commit-ci[bot]@users.noreply.github.com"
+    }
+  ],
+  "changes": {
+    ".pre-commit-config.yaml": {
+      "a": 2,
+      "d": 2
+    }
+  }
+}
diff --git a/doc/sphinxext/prs/13035.json b/doc/sphinxext/prs/13035.json
@@ -0,0 +1,51 @@
+{
+  "merge_commit_sha": "dcd26258c5fd83fd3974d73ba2b1e2773c33bc3d",
+  "authors": [
+    {
+      "n": "Mathieu Scheltienne",
+      "e": "[email protected]"
+    },
+    {
+      "n": "Eric Larson",
+      "e": "[email protected]"
+    }
+  ],
+  "changes": {
+    "environment.yml": {
+      "a": 1,
+      "d": 1
+    },
+    "mne/io/ant/ant.py": {
+      "a": 14,
+      "d": 12
+    },
+    "mne/io/ant/tests/test_ant.py": {
+      "a": 1,
+      "d": 1
+    },
+    "mne/preprocessing/tests/test_fine_cal.py": {
+      "a": 1,
+      "d": 1
+    },
+    "mne/utils/check.py": {
+      "a": 23,
+      "d": 24
+    },
+    "mne/utils/tests/test_check.py": {
+      "a": 7,
+      "d": 0
+    },
+    "pyproject.toml": {
+      "a": 1,
+      "d": 1
+    },
+    "tools/circleci_dependencies.sh": {
+      "a": 1,
+      "d": 6
+    },
+    "tutorials/intro/70_report.py": {
+      "a": 4,
+      "d": 5
+    }
+  }
+}
diff --git a/doc/sphinxext/prs/13036.json b/doc/sphinxext/prs/13036.json
@@ -0,0 +1,27 @@
+{
+  "merge_commit_sha": "41dbdd55eaff77314440ebc8700e0e58b1183113",
+  "authors": [
+    {
+      "n": "Daniel McCloy",
+      "e": null
+    },
+    {
+      "n": "autofix-ci[bot]",
+      "e": "114827586+autofix-ci[bot]@users.noreply.github.com"
+    }
+  ],
+  "changes": {
+    "doc/changes/devel/13036.bugfix.rst": {
+      "a": 1,
+      "d": 0
+    },
+    "mne/time_frequency/tests/test_spectrum.py": {
+      "a": 26,
+      "d": 0
+    },
+    "mne/viz/utils.py": {
+      "a": 3,
+      "d": 1
+    }
+  }
+}
diff --git a/environment.yml b/environment.yml
@@ -30,7 +30,7 @@ dependencies:
   - nilearn
   - numba
   - numpy >=1.23,<3
-  - openmeeg =2.5.12=*_1
+  - openmeeg >=2.5.5
   - packaging
   - pandas
   - pillow

diff --git a/mne/conftest.py b/mne/conftest.py
@@ -119,7 +119,7 @@ def pytest_configure(config):
     #   we should remove them from here.
     # - This list should also be considered alongside reset_warnings in
     #   doc/conf.py.
-    if os.getenv("MNE_IGNORE_WARNINGS_IN_TESTS", "") != "true":
+    if os.getenv("MNE_IGNORE_WARNINGS_IN_TESTS", "") not in ("true", "1"):
         first_kind = "error"
     else:
         first_kind = "always"
@@ -180,6 +180,8 @@ def pytest_configure(config):
     ignore:The 'copy' argument in Quantity is deprecated.*:
     # debugpy uses deprecated matplotlib API
     ignore:The (non_)?interactive_bk attribute was deprecated.*:
+    # SWIG (via OpenMEEG)
+    ignore:.*builtin type swigvarlink has no.*:DeprecationWarning
     """  # noqa: E501
     for warning_line in warning_lines.split("\n"):
         warning_line = warning_line.strip()

diff --git a/tools/azure_dependencies.sh b/tools/azure_dependencies.sh
@@ -5,7 +5,7 @@ SCRIPT_DIR=$( cd -- "$( dirname -- "${BASH_SOURCE[0]}" )" &> /dev/null && pwd )
 STD_ARGS="--progress-bar off --upgrade"
 python -m pip install $STD_ARGS pip setuptools wheel
 if [ "${TEST_MODE}" == "pip" ]; then
-	python -m pip install $STD_ARGS --only-binary="numba,llvmlite,numpy,scipy,vtk,dipy,openmeeg" -e .[test,full] "openmeeg==2.5.12"
+	python -m pip install $STD_ARGS --only-binary="numba,llvmlite,numpy,scipy,vtk,dipy,openmeeg" -e .[test,full]
 elif [ "${TEST_MODE}" == "pip-pre" ]; then
 	${SCRIPT_DIR}/install_pre_requirements.sh
 	python -m pip install $STD_ARGS --pre -e .[test_extra]

diff --git a/tools/circleci_dependencies.sh b/tools/circleci_dependencies.sh
@@ -8,7 +8,6 @@ python -m pip install --upgrade --progress-bar off \
     "git+https://github.com/sphinx-gallery/sphinx-gallery.git" \
     "git+https://github.com/mne-tools/mne-bids.git" \
     \
-    "openmeeg<2.5.13" \
     alphaCSC autoreject bycycle conpy emd fooof meggie \
     mne-ari mne-bids-pipeline mne-faster mne-features \
     mne-icalabel mne-lsl mne-microstates mne-nirs mne-rsa \

diff --git a/tools/hooks/update_environment_file.py b/tools/hooks/update_environment_file.py
@@ -56,9 +56,6 @@ def split_dep(dep):
     # `environment.yaml` breaks the solver
     if package_name == "PySide6":
         version_spec = version_spec.replace("!=6.7.0,", "")
-    # openmeeg 2.5.12=*_2 is broken, so pin to 2.5.12=*_1
-    if package_name == "openmeeg":
-        version_spec = "=2.5.12=*_1"
     # rstrip output line in case `version_spec` == ""
     line = f"  - {package_name} {version_spec}".rstrip()
     # use pip for packages needing e.g. `platform_system` or `python_version` triaging

diff --git a/tutorials/time-freq/50_ssvep.py b/tutorials/time-freq/50_ssvep.py
@@ -641,7 +641,7 @@ def snr_spectrum(psd, noise_n_neighbor_freqs=1, noise_skip_neighbor_freqs=1):
     ].mean(axis=1)
 
 fig, ax = plt.subplots(1)
-ax.boxplot(window_snrs, tick_labels=window_lengths, vert=True)
+ax.boxplot(window_snrs, tick_labels=window_lengths, orientation="vertical")
 ax.set(
     title="Effect of trial duration on 12 Hz SNR",
     ylabel="Average SNR",