ENH: Table sorting and ds004229 updates (#809)

mne-tools · Nov 4, 2023 · db45d21 · db45d21
1 parent 418a2e7
commit db45d21
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Showing 8 changed files with 19 additions and 9 deletions.
diff --git a/.circleci/config.yml b/.circleci/config.yml
@@ -265,15 +265,15 @@ jobs:
           at: ~/
       - restore_cache:
           keys:
-            - data-cache-ds004229-2
+            - data-cache-ds004229-103
       - bash_env
       - run:
           name: Get ds004229
           command: |
             $DOWNLOAD_DATA ds004229
       - codecov/upload
       - save_cache:
-          key: data-cache-ds004229-2
+          key: data-cache-ds004229-103
           paths:
             - ~/mne_data/ds004229
 
@@ -719,7 +719,7 @@ jobs:
       - bash_env
       - restore_cache:
           keys:
-            - data-cache-ds004229-2
+            - data-cache-ds004229-103
       - run:
           name: test ds004229
           command: $RUN_TESTS ds004229

diff --git a/docs/mkdocs.yml b/docs/mkdocs.yml
@@ -65,6 +65,10 @@ copyright: Copyright &copy; MNE-BIDS-Pipeline authors
 
 extra_css:
     - css/extra.css
+# https://squidfunk.github.io/mkdocs-material/reference/data-tables/
+extra_javascript:
+  - https://unpkg.com/tablesort@5.3.0/dist/tablesort.min.js
+  - javascripts/tablesort.js
 nav:
     - Home: index.md
     - Getting started:
@@ -172,6 +176,7 @@ markdown_extensions:
         repo_url_shorthand: true
         repo: mne-bids-pipeline
         user: mne-tools
+    - tables
     - toc:
         permalink: true  # Add paragraph symbol to link to current headline
     - pymdownx.tabbed:

diff --git a/docs/source/examples/gen_examples.py b/docs/source/examples/gen_examples.py
@@ -261,6 +261,7 @@ def _gen_demonstrated_funcs(example_config_path: Path) -> dict:
     demonstrated_funcs = _gen_demonstrated_funcs(config_path)
     all_demonstrated[dataset_name] = demonstrated_funcs
     del config, config_options
+    # Add the subsection and table header
     funcs = [
         "## Demonstrated features\n",
         "Feature | This example",
@@ -279,7 +280,7 @@ def _gen_demonstrated_funcs(example_config_path: Path) -> dict:
         f.write(config_str)
         f.write(report_str)
 
-# Finally, write our examples.html file
+# Finally, write our examples.html file with a table of examples
 
 _example_header = """\
 # Examples

diff --git a/docs/source/javascripts/tablesort.js b/docs/source/javascripts/tablesort.js
@@ -0,0 +1,6 @@
+document$.subscribe(function() {
+    var tables = document.querySelectorAll("article table:not([class])")
+    tables.forEach(function(table) {
+      new Tablesort(table)
+    })
+  })
diff --git a/docs/source/v1.5.md.inc b/docs/source/v1.5.md.inc
@@ -19,6 +19,7 @@ All users are encouraged to update.
   per-epochs basis; this can be enabled by setting [`reject`][mne_bids_pipeline._config.reject] to `"autoreject_local"`.
   The behavior can further be controlled via the new setting
   [`autoreject_n_interpolate`][mne_bids_pipeline._config.autoreject_n_interpolate]. (#807 by @hoechenberger)
+- Website documentation tables can now be sorted (e.g., to find examples that use a specific feature) (#808 by @larsoner)
 
 [//]: # (### :warning: Behavior changes)
 
@@ -38,6 +39,7 @@ All users are encouraged to update.
 - Enable [pre-commit.ci](https://pre-commit.ci) (#774 by @larsoner)
 - Use `pooch` for web downloads (#775 by @larsoner)
 - Ensure compatibility with MNE-Python 1.6 (#800 by @hoechenberger)
+- Updated testing dataset for ds004229 v1.0.3 (#808 by @larsoner)
 
 ### :bug: Bug fixes
 

diff --git a/mne_bids_pipeline/_config_utils.py b/mne_bids_pipeline/_config_utils.py
@@ -361,7 +361,7 @@ def get_mf_cal_fname(
             root=config.bids_root,
         ).meg_calibration_fpath
         if mf_cal_fpath is None:
-            raise ValueError("Could not find Maxwell Filter Calibration " "file.")
+            raise ValueError("Could not find Maxwell Filter Calibration file.")
     else:
         mf_cal_fpath = pathlib.Path(config.mf_cal_fname).expanduser().absolute()
         if not mf_cal_fpath.exists():

diff --git a/mne_bids_pipeline/tests/configs/config_ds004229.py b/mne_bids_pipeline/tests/configs/config_ds004229.py
@@ -16,8 +16,6 @@
 find_flat_channels_meg = True
 find_noisy_channels_meg = True
 use_maxwell_filter = True
-mf_cal_fname = bids_root + "/derivatives/meg_derivatives/sss_cal.dat"
-mf_ctc_fname = bids_root + "/derivatives/meg_derivatives/ct_sparse.fif"
 mf_destination = mne.transforms.translation(  # rotate backward and move up
     z=0.055,
 ) @ mne.transforms.rotation(x=np.deg2rad(-15))

diff --git a/mne_bids_pipeline/tests/datasets.py b/mne_bids_pipeline/tests/datasets.py
@@ -118,8 +118,6 @@ class DATASET_OPTIONS_T(TypedDict, total=False):
         "include": [
             "sub-102",
             "sub-emptyroom/ses-20000101",
-            "derivatives/meg_derivatives/ct_sparse.fif",
-            "derivatives/meg_derivatives/sss_cal.dat",
         ],
     },
 }