Merge branch 'main' of github.com:mne-tools/mne-bids-pipeline into types

.circleci/config.yml

@@ -1030,6 +1030,10 @@ jobs:
       - attach_workspace:
           at: ~/
       - bash_env
+      - run:
+          name: Install dependencies
+          command: |
+            pip install -ve .[docs]
       - run:
           name: Build documentation
           command: |
@@ -1058,6 +1062,10 @@ jobs:
           at: ~/
       - bash_env
       - gitconfig
+      - run:
+          name: Install dependencies
+          command: |
+            pip install -ve .[docs]
       - run:
           # This is a bit computationally inefficient, but it should be much
           # faster to "cp" directly on the machine rather than persist

.github/dependabot.yml

@@ -0,0 +1,15 @@
+# To get started with Dependabot version updates, you'll need to specify which
+# package ecosystems to update and where the package manifests are located.
+# Please see the documentation for all configuration options:
+# https://docs.github.com/code-security/dependabot/dependabot-version-updates/configuration-options-for-the-dependabot.yml-file
+
+version: 2
+updates:
+  - package-ecosystem: "github-actions"
+    directory: "/"
+    schedule:
+      interval: "weekly"
+    labels:
+      - "dependabot"
+    commit-message:
+      prefix: "[dependabot]"

.github/workflows/release.yml

@@ -18,9 +18,9 @@ jobs:
   package:
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
     - name: Set up Python
-      uses: actions/setup-python@v4
+      uses: actions/setup-python@v5
       with:
         python-version: '3.10'
     - name: Install dependencies
@@ -34,7 +34,7 @@ jobs:
     - name: Check env vars
       run: |
         echo "Triggered by: ${{ github.event_name }}"
-    - uses: actions/upload-artifact@v3
+    - uses: actions/upload-artifact@v4
       with:
         name: dist
         path: dist
@@ -45,7 +45,7 @@ jobs:
     runs-on: ubuntu-latest
     if: github.event_name == 'release'
     steps:
-    - uses: actions/download-artifact@v3
+    - uses: actions/download-artifact@v4
       with:
         name: dist
         path: dist

.github/workflows/run-tests.yml

@@ -13,15 +13,15 @@ jobs:
       run:
         shell: bash -l {0}
     steps:
-    - uses: actions/checkout@v3
-    - uses: actions/setup-python@v4
+    - uses: actions/checkout@v4
+    - uses: actions/setup-python@v5
       with:
         python-version: "3.11"
     - run: pip install --upgrade pip
     - run: pip install -ve .[tests] codespell tomli
     - run: make codespell-error
     - run: pytest mne_bids_pipeline -m "not dataset_test"
-    - uses: codecov/codecov-action@v3
+    - uses: codecov/codecov-action@v4
       if: success()
       name: 'Upload coverage to CodeCov'
   caching:
@@ -71,5 +71,5 @@ jobs:
       - run: pytest --cov-append -k ds003392 mne_bids_pipeline/
       - run: pytest --cov-append -k ds003392 mne_bids_pipeline/  # uses "mtime" method
         timeout-minutes: 1
-      - uses: codecov/codecov-action@v3
+      - uses: codecov/codecov-action@v4
         if: success()

.pre-commit-config.yaml

@@ -6,7 +6,7 @@ files: ^(.*\.(py|yaml))$
 exclude: ^(\.[^/]*cache/.*|.*/freesurfer/contrib/.*)$
 repos:
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.3.0
+    rev: v0.3.4
     hooks:
       - id: ruff
         args: ["--fix"]

CONTRIBUTING.md

@@ -1,9 +1,9 @@
-# Overview
+# Contributing to MNE-BIDS-Pipeline
 
 Contributors to MNE-BIDS-Pipeline are expected to follow our
 [Code of Conduct](https://github.com/mne-tools/.github/blob/main/CODE_OF_CONDUCT.md).
 
-# Installation
+## Installation
 
 First, you need to make sure you have MNE-Python installed and working on your
 system. See the [installation instructions](http://martinos.org/mne/stable/install_mne_python.html).
@@ -26,9 +26,9 @@ If you do not know how to use git, download the pipeline as a zip file
 Finally, for source analysis you'll also need `FreeSurfer`, follow the
 instructions on [their website](https://surfer.nmr.mgh.harvard.edu/).
 
-# Testing
+## Testing
 
-## Running the tests, and continuous integration
+### Running the tests, and continuous integration
 
 The tests are run using `pytest`. You can run them by calling
 `pytest mne_bids_pipeline` to run
@@ -42,17 +42,17 @@ For every pull request or merge into the `main` branch of the
 [CircleCI](https://circleci.com/gh/brainthemind/CogBrainDyn_MEG_Pipeline)
 will run tests as defined in `./circleci/config.yml`.
 
-## Debugging
+### Debugging
 
 To run the test in debugging mode, just pass `--pdb` to the `pytest` call
 as usual. This will place you in debugging mode on failure.
 See the
 [pdb help](https://docs.python.org/3/library/pdb.html#debugger-commands)
 for more commands.
 
-## Config files
+### Config files
 
-Nested in the `/tests` directory is a `/configs` directory, which contains
+Nested in the `tests` directory is a `configs` directory, which contains
 config files for specific test datasets. For example, the `config_ds001810.py`
 file specifies parameters only for the `ds001810` data, which should overwrite
 the more general parameters in the main `_config.py` file.