Merge pull request #1 from yarikoptic/enh-codespell

Add codespell support (config, workflow) and make it fix some typos

.codespellrc

@@ -0,0 +1,6 @@
+[codespell]
+# Ref: https://github.com/codespell-project/codespell#using-a-config-file
+skip = .git*,.codespellrc
+check-hidden = true
+# ignore-regex = 
+# ignore-words-list =

.github/workflows/codespell.yml

@@ -0,0 +1,23 @@
+# Codespell configuration is within .codespellrc
+---
+name: Codespell
+
+on:
+  push:
+    branches: [main]
+  pull_request:
+    branches: [main]
+
+permissions:
+  contents: read
+
+jobs:
+  codespell:
+    name: Check for spelling errors
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+      - name: Codespell
+        uses: codespell-project/actions-codespell@v2

00_dcm-rewrite-from-xlsx.py

@@ -18,7 +18,7 @@
     ):
         continue
 
-    # final protocol wont save out derivatives (e.g. moco, tenesorFA)
+    # final protocol won't save out derivatives (e.g. moco, tenesorFA)
     # skip to save space and time
     if re.search('deriv|dwi.*_desc-',row["new_name"]):
         print(f'# skipping derivative {row["new_name"]}')

entity_ux/index.html

@@ -110,7 +110,7 @@
 }
 function datatype_update_suffix(){
   var dt = document.getElementById('datatype');
-  // clear even if empyt -- any change is worth reseting things
+  // clear even if empyt -- any change is worth resetting things
   var sel = document.getElementById('suffix');
   sel.innerHTML = "<option value=''> </option>";
 

entity_ux/make_json.py

@@ -17,7 +17,7 @@ def write_json(fname, data):
 
 
 """
-build a table indexed by datatype. with list of suffix poperties (display_name, description, entities)
+build a table indexed by datatype. with list of suffix properties (display_name, description, entities)
 >>> table.keys()
 dict_keys(['anat', 'dwi', 'fmap', 'func', 'perf', 'pet'])
 >>> table['anat'][0].keys()

readme.md

@@ -1,5 +1,5 @@
 # Namer
-[`entity_ux/`](entity_ux/) contains a web app to guide naming sequences as an alternative to the [ReproIn Creator Spreedsheet](./ReproIn-creator.xlsx).
+[`entity_ux/`](entity_ux/) contains a web app to guide naming sequences as an alternative to the [ReproIn Creator Spreadsheet](./ReproIn-creator.xlsx).
 
 It's live on https://NPACore.github.io/reproin-namer (via github pages w/ `doc/` symlink)
 
@@ -9,7 +9,7 @@ It's live on https://NPACore.github.io/reproin-namer (via github pages w/ `doc/`
 * [ReproIn](https://dbic-handbook.readthedocs.io/en/latest/mri/reproin.html) sequence name convention/standard
   * Siemens' scanner `Dot Cockpit` and `Exam Card` setup [walk through](https://github.com/ReproNim/reproin/blob/master/docs/walkthrough-1.md) (with screenshots)
   * automation implemented by [heudiconv](https://github.com/nipy/heudiconv/). See [reproin.py](https://github.com/nipy/heudiconv/blob/master/heudiconv/heuristics/reproin.py)
-  * [ReproIn Creator Spreedsheet](./ReproIn-creator.xlsx): MRRC template to ReproIn using a formula with per column BIDS key-value pairs. ![sheet with dropdown](ReproInCreator.png)
+  * [ReproIn Creator Spreadsheet](./ReproIn-creator.xlsx): MRRC template to ReproIn using a formula with per column BIDS key-value pairs. ![sheet with dropdown](ReproInCreator.png)
   * [Flywheel Study Design Sheet](https://docs.google.com/spreadsheets/d/1Yd74ewWAk4roA-IBfrQuOSMNR4DPxhB9/edit#gid=1495259008) (cf. [gitlab template folder](https://gitlab.com/flywheel-io/public/bids-client/-/tree/master/flywheel_bids/templates))
 * goal is near automated [BIDS](https://bids-specification.readthedocs.io/en/stable/#the-brain-imaging-data-structure) Brain Imaging Data Structure conforming scanner dicom to nifti image+json sidecar name conversion.
    * Ideal for input in [fmriprep](https://fmriprep.org/en/stable/)
@@ -47,7 +47,7 @@ See [`output-filelist.txt`](txt/output-filelist.txt) for full list.
 | [`validate.txt`](txt/validate.txt)          | `bids-validator` output, using [.bidsignore](bidsignore)|
 
 # Issues
-* path `SPA_Luna/20231103lunapilotspa2/sub-20231103lunapilotspa2` has redudant ID folder. Should be `SPA_Luna/sub-20231103lunapilotspa2`?
+* path `SPA_Luna/20231103lunapilotspa2/sub-20231103lunapilotspa2` has redundant ID folder. Should be `SPA_Luna/sub-20231103lunapilotspa2`?
 * Does not pass bids validation. see [`validate.txt`](txt/validate.txt).
   * multiple echos as e.g. `_heudiconv323_e5` instead of `_echo-5` 
   * no `.json` files!? (see missing in [`output-filelist.txt`](txt/output-filelist.txt))

requirements.txt

@@ -1,4 +1,4 @@
-# for 01_dcm-bids.sh and imporant to be > than debian12 version 0.13
+# for 01_dcm-bids.sh and important to be > than debian12 version 0.13
 heudiconv >= 1.0.1
 
 # for 00_dcm-rewrite-from-xlsx.py. but system versions okay