[MAINT] add BIDS papers references in citation.cff

.codespellrc

@@ -1,5 +1,5 @@
 [codespell]
-skip = *.js,*.svg,*.eps,.git,node_modules,env,venv,.mypy_cache,package-lock.json,CITATION.cff,tools/new_contributors.tsv,./tools/schemacode/docs/build
+skip = *.js,*.svg,*.eps,.git,node_modules,env,venv,.mypy_cache,package-lock.json,CITATION.cff,tools/new_contributors.tsv,./tools/schemacode/docs/build,src/apa-6th-edition.csl,src/references.bib
 ignore-words-list = fo,te,als,Acknowledgements,acknowledgements,weill,bu,winn,manuel
 builtin = clear,rare,en-GB_to_en-US
 # this overloads default dictionaries and I have not yet figured out

CITATION.cff

@@ -28,6 +28,46 @@ identifiers:
   - description: PDFs of the BIDS specification for versions 1.0.0 to 1.8.0
     type: doi
     value: 10.5281/zenodo.3686061
+  # papers to inject in the how to cite section
+  # ### Original publication
+  - description: Original publication
+    type: doi
+    value: 10.1038/sdata.2016.44
+  # ### Datatype specific publications
+  - description: EEG
+    type: doi
+    value: 10.1038/s41597-019-0104-8
+  - description: iEEG
+    type: doi
+    value: 10.1038/s41597-019-0105-7
+  - description: MEG
+    type: doi
+    value: 10.1038/sdata.2018.110
+  - description: PET
+    type: doi
+    value: 10.1038/s41597-022-01164-1
+  - description: PET guidelines
+    type: doi
+    value: 10.1177/0271678X20905433
+  - description: Genetics
+    type: doi
+    value: 10.1093/gigascience/giaa104
+  - description: Microscopy
+    type: doi
+    value: 10.3389/fnins.2022.871228
+  - description: qMRI
+    type: doi
+    value: 10.1038/s41597-022-01571-4
+  - description: ASL
+    type: doi
+    value: 10.1038/s41597-022-01615-9
+  - description: NIRS
+    type: doi
+    value: 10.31219/osf.io/7nmcp
+  - description: Motion
+    type: doi
+    value: 10.31234/osf.io/w6z79
+
 
 keywords:
   - brain imaging data structure

environment.yml

@@ -0,0 +1,16 @@
+name: bids_spec
+channels:
+  - defaults
+dependencies:
+  - pip
+  - pypandoc
+  - numpy
+  - pip:
+    - tools/schemacode/[render]
+    - mkdocs>=1.1
+    - mkdocs-material>=5.4
+    - pymdown-extensions>=7.0.0
+    - mkdocs-branchcustomization-plugin~=0.1.3
+    - mkdocs-macros-plugin
+    - mkdocs-redirects
+    - mkdocs-bibtex

mkdocs.yml

@@ -103,6 +103,7 @@ markdown_extensions:
   - pymdownx.superfences
   - admonition
   - pymdownx.details
+  - footnotes
 plugins:
   - search
   - branchcustomization:
@@ -112,6 +113,10 @@ plugins:
             - css/watermark.css
   - macros:
       module_name: tools/mkdocs_macros_bids/main
+  - bibtex:
+      bib_file: "src/references.bib"
+      cite_inline: True
+      csl_file: src/apa-6th-edition.csl
   - redirects:
       redirect_maps:
         "01-introduction.md": "introduction.md"

readthedocs.yml

@@ -5,7 +5,8 @@ build:
   apt_packages:
     - jq
   tools:
-    python: "3.11"
+    python: "mambaforge-22.9"
+
   jobs:
     pre_build:
       - bst -v export --output src/schema.json
@@ -15,6 +16,9 @@ mkdocs:
   configuration: mkdocs.yml
   fail_on_warning: true
 
+conda:
+  environment: environment.yml
+
 python:
   install:
     - requirements: requirements.txt