Merge branch 'bep-016' into tensor_as_representation

.circleci/config.yml

@@ -2,7 +2,7 @@ version: 2.1
 jobs:
   build_docs:
     docker:
-      - image: cimg/python:3.8
+      - image: cimg/python:3.12-node
     steps:
       # checkout code to default ~/project
       - checkout
@@ -21,14 +21,15 @@ jobs:
       - persist_to_workspace:
           # the mkdocs build outputs are in ~/project/site
           root: ~/project
-          paths: site
+          paths:
+            - site
       - store_artifacts:
           path: ~/project/site/
           destination: dev_docs
 
   check_links:
     docker:
-      - image: cimg/python:3.8
+      - image: cimg/python:3.12
     steps:
       # checkout code to default ~/project
       - checkout
@@ -66,14 +67,16 @@ jobs:
 
   build_docs_pdf:
     docker:
-      - image: danteev/texlive:latest
+      - image: texlive/texlive:latest
     steps:
       # checkout code to default ~/project
       - checkout
       - run:
           name: install dependencies
           command: |
-            apt-get update && apt install -y python3-pip
+            apt-get update && apt install -y python3-pip python3-venv pandoc
+            python3 -m venv .venv
+            source .venv/bin/activate
             python3 -m pip install --upgrade pip
             python3 -m pip install -r  ~/project/requirements.txt
             python3 -m pip install ~/project/tools/schemacode/[render]
@@ -83,6 +86,7 @@ jobs:
       - run:
           name: generate pdf version docs
           command: |
+            source .venv/bin/activate
             cd ~/project/pdf_build_src
             bash build_pdf.sh
             mv ~/project/pdf_build_src/bids-spec.pdf ~/project/bids-spec.pdf
@@ -128,7 +132,8 @@ jobs:
       - persist_to_workspace:
           # raw generated changelog in ~/changelog_build/CHANGES.md
           root: ~/.
-          paths: changelog_build
+          paths:
+            - changelog_build
 
   # Lint and fix the auto generated changes.md file
   lint_generated_changelog:
@@ -161,7 +166,8 @@ jobs:
       - persist_to_workspace:
           # linted and fixed changelog in ~/changelog_build/CHANGES.md
           root: ~/.
-          paths: changelog_build
+          paths:
+            - changelog_build
 
   # Push built changelog to repo
   commit_generated_changelog:
@@ -175,7 +181,7 @@ jobs:
       - attach_workspace:
           # fixed+linted changelog in ~/changelog_build/CHANGES.md
           at: ~/.
-      - deploy:
+      - run:
           name: Changelog deployment
           # $CHANGE_TOKEN is generated via the GitHub web UI, and then securely stored within CircleCI web UI
           command: |
@@ -194,7 +200,6 @@ jobs:
             fi
 
 workflows:
-  version: 2
   search_build:
     jobs:
       - build_docs

.codecov.yml

@@ -1,4 +1,5 @@
 ignore:
-    - "*/*/tests/*"
-    - "**/tests/*"
-
+  - "*/*/tests/*"
+  - "**/tests/*"
+codecov:
+  token: 7e84a7fb-8f7e-45f5-8dcc-9f5219fa3855

.codespell_dict

@@ -0,0 +1,11 @@
+sub-directory->subdirectory
+Sub-directory->Subdirectory
+sub-directories->subdirectories
+Sub-directories->Subdirectories
+file name->filename
+File name->Filename
+file names->filenames
+File names->Filenames
+folder->directory
+Folder->Directory
+Folders->Directories

.codespellrc

@@ -0,0 +1,8 @@
+[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
+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
+# how to have multiple https://github.com/codespell-project/codespell/issues/2727
+# dictionary = .codespell_dict
+exclude-file = src/CHANGES.md

.github/labeler.yml

@@ -0,0 +1,27 @@
+# labeler "full" schema
+# https://github.com/marketplace/actions/auto-labeler
+
+# enable labeler on issues, prs, or both.
+enable:
+  issues: false
+  prs: true
+# comments object allows you to specify a different message for issues and prs
+
+comments:
+  prs: |
+    I have applied any labels matching special text in your title and description.
+
+    Please review the labels and make any necessary changes.
+
+# Labels is an object where:
+# - keys are labels
+# - values are objects of { include: [ pattern ], exclude: [ pattern ] }
+#    - pattern must be a valid regex, and is applied globally to
+#      title + description of issues and/or prs (see enabled config above)
+#    - 'include' patterns will associate a label if any of these patterns match
+#    - 'exclude' patterns will ignore this label if any of these patterns match
+labels:
+  exclude-from-changelog:
+    include:
+      - 'pre-commit\.ci'
+    exclude: []

.github/workflows/labeler.yml

@@ -0,0 +1,21 @@
+name: "Label PRs"
+# See https://github.com/marketplace/actions/auto-labeler
+
+on:
+
+  pull_request_target:
+    types: [opened]
+
+jobs:
+
+  labeler:
+    runs-on: ubuntu-latest
+
+    if: github.repository_owner == 'bids-standard'
+
+    steps:
+    - name: Check Labels
+      id: labeler
+      uses: jimschubert/labeler-action@v2
+      with:
+        GITHUB_TOKEN: ${{secrets.GITHUB_TOKEN}}

.github/workflows/redirect_circleci_artifacts.yml

@@ -1,13 +1,18 @@
 on: [status]
+
 jobs:
   circleci_artifacts_redirector_job:
     runs-on: ubuntu-latest
+    if: "${{ startsWith(github.event.context, 'ci/circleci: build_docs_pdf') }}"
+    permissions:
+      statuses: write
     name: Run CircleCI artifacts redirector
     steps:
       - name: GitHub Action step
         uses: larsoner/circleci-artifacts-redirector-action@master
         with:
           repo-token: ${{ secrets.GITHUB_TOKEN }}
+          api-token: ${{ secrets.CIRCLECI_TOKEN }}
           artifact-path: 0/bids-spec.pdf
           circleci-jobs: build_docs_pdf
           job-title: Check the rendered PDF version here!