doc(mkdocs): use mkdocs-github-admonitions-plugin

Author: WillForan

.github/workflows/ci.yml

@@ -20,5 +20,5 @@ jobs:
           path: .cache
           restore-keys: |
             mkdocs-material-
-      - run: pip install mkdocs-material 
+      - run: pip install mkdocs-material mkdocs-github-admonitions-plugin
       - run: mkdocs gh-deploy --force

Makefile

@@ -1,4 +1,4 @@
-.PHONY: docker check experiments coverage docker-test install depends install-make install-shell
+.PHONY: docker check experiments coverage docker-test install depends install-make install-shell mkdocs
 check: .make/check
 docker-test:  .make/docker-test
 docker: .make/docker
@@ -39,6 +39,9 @@ dryrun.exe: src/dryrun.c
 .make/:
 	mkdir -p $@
 
+mkdocs:
+	uv tool run --with mkdocs-material --with mkdocs-github-admonitions-plugin  mkdocs serve
+
 ## make install
 # move all exec files in top level to install directory (/usr/bin)
 # exclude those not useful outside of lncd server rhea

docs/tat2.md

@@ -71,10 +71,10 @@ Imagine a somewhat pathological file organization like
 
 ```
 sub_ses="sub-01/ses-01"
-censor_regex='s/.*func\/(.*)-preproc_bold.nii.gz/censor_files\/\1\/preproc_censor-fd0.3.1D/'
+censor_regex='s/.*func\/(.*)_desc-preproc_bold.nii.gz/censor_files\/\1\/preproc_censor-fd0.3.1D/'
 tat2 \
     -output "deriv/$sub_ses/func/${sub_ses//\//_}_space-MNI152NLin2009cAsym_tat2.nii.gz" \
-    -mask_rel 's/preproc_bold.nii.gz/brain_mask.nii.gz/' \
+    -mask_rel 's/desc-preproc_bold.nii.gz/brain_mask.nii.gz/' \
     -censor_rel "$censor_regex" \
     -median_time \
     -median_vol \
@@ -83,14 +83,22 @@ tat2 \
     deriv/$sub_ses/func/*space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz
 ```
 
-* sibling mask files are matched using `-mask_rel 's/preproc_bold.nii.gz/brain_mask.nii.gz/'` 
-   1. searches each input file for `preproc_bold.nii.gz`
-   2. and replaces that with `brain_maks.nii.gz`
-* to match censor files across directories, `censor_regex` uses `s/.*func\/(.*)-preproc_bold.nii.gz/censor_files\/\1\/preproc_censor-fd0.3.1D/`). Also see https://regex101.com/r/bM6p7X/1
-  1.  searches each input file for  `.*func\/(.*)-preproc_bold.nii.gz`, where
-    * `\/` "escapes" the directory slash, escape to distinguish it from the search-replace deliminator in `s///`
-    *  where `(.*)` captures the matching part to reuse as `\\1`  in
-  3. the replacement like `censor_files\/\1\/preproc_censor-fd0.3.1D`
+  * sibling mask files are matched using `-mask_rel 's/desc-preproc_bold.nii.gz/brain_mask.nii.gz/'` 
+   ```
+   func/sub-1_ses-2_run-1_desc-preproc_bold.nii.gz  # becomes
+   func/sub-1_ses-2_run-1_desc-brain_mask.nii.gz
+   ```
+    1. searches each input file for `desc-preproc_bold.nii.gz`
+    2. and replaces that with `brain_maks.nii.gz`
+  * to match censor files across directories, `censor_regex` uses `s/.*func\/(.*)_desc-preproc_bold.nii.gz/censor_files\/\1\/preproc_censor-fd0.3.1D/`). Also see https://regex101.com/r/bM6p7X/1
+   ```
+   func/sub-1_ses-2_run-1_desc-preproc_bold.nii.gz        # becomes
+   censor_files/sub-1_ses-2_run-1/preproc_censor-fd0.3.1D
+   ```
+    1.  searches each input file for  `.*func\/(.*)_desc-preproc_bold.nii.gz`, where
+        * `\/` "escapes" the directory slash, escape to distinguish it from the search-replace deliminator in `s///`
+      *  where `(.*)` captures the matching part to reuse as `\\1`  in
+    3. the replacement like `censor_files\/\1\/preproc_censor-fd0.3.1D`
 
 Also see [issue#5](https://github.com/lncd/lncdtools/issues/5).
 

mkdocs.yml

@@ -17,3 +17,5 @@ markdown_extensions:
       pygments_lang_class: true
   - pymdownx.inlinehilite
 
+plugins:
+  - gh-admonitions