ENH: Report along the way

.circleci/setup_bash.sh

@@ -68,6 +68,7 @@ echo "export DOWNLOAD_DATA=\"python -m mne_bids_pipeline._download\"" >> $BASH_E
 # Similar CircleCI setup to mne-python (Xvfb, venv, minimal commands, env vars)
 wget -q https://raw.githubusercontent.com/mne-tools/mne-python/main/tools/setup_xvfb.sh
 bash setup_xvfb.sh
+sudo apt update
 sudo apt install -qq tcsh git-annex-standalone python3.10-venv python3-venv libxft2
 python3.10 -m venv ~/python_env
 wget -q https://raw.githubusercontent.com/mne-tools/mne-python/main/tools/get_minimal_commands.sh

docs/mkdocs.yml

@@ -59,8 +59,6 @@ nav:
             - BEM surface: settings/source/bem.md
             - Source space & forward solution: settings/source/forward.md
             - Inverse solution: settings/source/inverse.md
-        - Report:
-            - HTML Report: settings/report/report.md
     - Examples:
         - Examples Gallery: examples/examples.md
         - examples/ds003392.md
@@ -95,6 +93,7 @@ plugins:
                     show_root_heading: true
                     show_root_full_path: false
                     separate_signature: true
+                    line_length: 80  # needed for long param entries
                     show_bases: false
                 selection:
                     docstring_style: numpy

docs/source/changes.md

@@ -202,6 +202,9 @@ authors:
   ({{ gh(647) }} by {{ authors.larsoner }})
 - A template configuration file can now be created via `mne_bids_pipeline --create-config`
   ({{ gh(653) }} by {{ authors.hoechenberger }})
+- Make report generation happen within relevant steps instead of at the end
+  of all steps
+  ({{ gh(652) }} by {{ authors.larsoner }})
 
 ### Behavior changes
 

docs/source/getting_started/basic_usage.md

@@ -93,11 +93,6 @@ Run the pipeline
     mne_bids_pipeline --config=/path/to/your/custom_config.py --steps=source
     ```
 
-    Only generate the report:
-    ```shell
-    mne_bids_pipeline --config=/path/to/your/custom_config.py --steps=report
-    ```
-
     (Re-)run ICA:
     ```shell
     mne_bids_pipeline --config=/path/to/your/custom_config.py --steps=preprocessing/ica

docs/source/settings/sensor/statistics.md

@@ -1,4 +1,5 @@
 ::: mne_bids_pipeline._config.contrasts
+::: mne_bids_pipeline._config.report_evoked_n_time_points
 ::: mne_bids_pipeline._config.decode
 ::: mne_bids_pipeline._config.decoding_metric
 ::: mne_bids_pipeline._config.decoding_n_splits

docs/source/settings/source/inverse.md

@@ -4,3 +4,4 @@
 ::: mne_bids_pipeline._config.noise_cov
 ::: mne_bids_pipeline._config.source_info_path_update
 ::: mne_bids_pipeline._config.inverse_targets
+::: mne_bids_pipeline._config.report_stc_n_time_points