[FIX] fix CI (#309)

* fixes

* use RTD

* check in ci

* update CI

* do not run on PR

* add tmp script

* add folder tree

* remove tree

.github/workflows/update_spreadsheets.yml

@@ -4,6 +4,7 @@ name: Update spreadsheet
 on:
     push:
         branches: [main]
+
     # to trigger update manually from the Action tab in github
     workflow_dispatch:
         inputs:
@@ -35,6 +36,7 @@ jobs:
         -   name: Update TSVs
             run: tox run -e update
         -   name: Clean up
+            continue-on-error: true
             run: |
                 pre-commit install
                 pre-commit run --all-files --show-diff-on-failure

.readthedocs.yaml

@@ -0,0 +1,18 @@
+---
+version: 2
+
+build:
+    os: ubuntu-22.04
+    tools:
+        python: '3.11'
+
+submodules:
+    include: all
+    recursive: true
+
+mkdocs:
+    configuration: mkdocs.yml
+
+python:
+    install:
+    -   requirements: requirements.txt

docs/contributing/general-organization.md

@@ -55,6 +55,55 @@ methods and results reporting in (f)MRI, (i)EEG, MEG.
 By extension, this workflow can also be used on other types of guidelines (like
 the ones for PET imaging and eyetracking).
 
+```bash
+📂
+┣━━ 📂 docs
+┣━━ 📂 ecobidas
+┃   ┣━━ 📂 inputs
+┃   ┃   ┣━━ 📂 core
+┃   ┃   ┣━━ 📂 eyetracking
+┃   ┃   ┣━━ 📂 meeg
+┃   ┃   ┣━━ 📂 mri
+┃   ┃   ┣━━ 📂 neurovault
+┃   ┃   ┣━━ 📂 pet
+┃   ┃   ┣━━ 📂 reexecution
+┃   ┃   ┣━━ 📂 response_options
+┃   ┃   ┣━━ 📄 data-dictionary.json
+┃   ┃   ┗━━ 📄 spreadsheet_google_id.yml
+┃   ┣━━ 📂 templates
+┃   ┣━━ 🐍 __init__.py
+┃   ┣━━ 🐍 cli.py
+┃   ┣━━ 🐍 create_schema.py
+┃   ┣━━ 🐍 download_tsv.py
+┃   ┣━━ 🐍 generate_landing_page.py
+┃   ┣━━ 🐍 item.py
+┃   ┣━━ 🐍 macros.py
+┃   ┣━━ 🐍 parsers.py
+┃   ┣━━ 🐍 serve.py
+┃   ┣━━ 🐍 template_manager.py
+┃   ┗━━ 🐍 utils.py
+┣━━ 📂 inputs
+┃   ┣━━ 📂 bids_template
+┃   ┗━━ 📂 boilerplate
+┣━━ 📂 macros
+┣━━ 📂 schema # (1)
+┣━━ 📂 tests
+┣━━ 📄 CITATION.cff
+┣━━ 📄 LICENSE
+┣━━ 📄 Makefile
+┣━━ 📄 mkdocs.yml
+┣━━ 📄 pyproject.toml
+┣━━ 📄 README.md
+┣━━ 📄 requirements.txt
+┗━━ 📄 tox.ini
+```
+
+1.  :man_raising_hand: I'm an annotation! I can contain `code`, __formatted
+    text__, images, ... basically anything that can be expressed in Markdown.
+
+
+
+
 ```text
 .
 ├── .github           <-- continuous integration "scripts"

ecobidas/macros.py

@@ -37,7 +37,7 @@ def main(output_dir: Path | None = None) -> None:
     with open(output_dir / "spreadsheets_table.md", "w") as out:
         out.write(f"{table_spreadsheets()}")
 
-    with open(output_dir / "data_dcitionary_table.md", "w") as out:
+    with open(output_dir / "data_dictionary_table.md", "w") as out:
         out.write(f"{table_data_dictionary()}")
 
 

ecobidas/utils.py

@@ -55,7 +55,7 @@ def get_landing_page(schema_info: dict[str, str]) -> str:
     if schema_info["landing_page"]:
         return schema_info["landing_page"]
     else:
-        return "README_eCOBIDAS-en.md"
+        return "../README_eCOBIDAS-en.md"
 
 
 def get_schema_info(this_schema: str | Path) -> dict[str, str]:

mkdocs.yml

@@ -31,6 +31,7 @@ theme:
     features:
         -   announce.dismiss
         -   content.action.edit
+        -   content.code.annotate
         -   content.tooltips
         -   footnotes
         -   header.autohide
@@ -114,3 +115,5 @@ extra:
     #     link: https://mattermost.brainhack.org/brainhack/channels/cobidas_checklist
     -   icon: fontawesome/brands/google
         link: https://groups.google.com/d/forum/cobidas-checklist
+    annotate:
+        json: [.s2]

tests/data/protocols/test_schema.jsonld

@@ -9,7 +9,7 @@
     "schemaVersion": "1.0.0-rc4",
     "version": "0.0.1",
     "landingPage": {
-        "@id": "https://raw.githubusercontent.com/ohbm/cobidas_schema/master/landing_pages/README_eCOBIDAS-en.md",
+        "@id": "../README_eCOBIDAS-en.md",
         "inLanguage": "en"
     },
     "preamble": {