Merge pull request #295 from Remi-Gau/maint

[MAINT] general maintenance

.github/dependabot.yml

@@ -1,13 +1,14 @@
+---
 # Documentation
 # https://docs.github.com/en/code-security/dependabot/dependabot-version-updates/configuration-options-for-the-dependabot.yml-file
 version: 2
 updates:
-  - package-ecosystem: 'github-actions'
-    directory: '/'
+-   package-ecosystem: github-actions
+    directory: /
     schedule:
-      interval: 'monthly'
+        interval: monthly
 
-  - package-ecosystem: 'gitsubmodule'
-    directory: '/'
+-   package-ecosystem: gitsubmodule
+    directory: /
     schedule:
-      interval: 'monthly'
+        interval: monthly

.github/workflows/check_md_links.yml

@@ -1,10 +1,11 @@
+---
 name: Check Markdown links
 
 on: push
 
 jobs:
-  markdown-link-check:
-    runs-on: ubuntu-latest
-    steps:
-    - uses: actions/checkout@v4
-    - uses: gaurav-nelson/github-action-markdown-link-check@v1
+    markdown-link-check:
+        runs-on: ubuntu-latest
+        steps:
+        -   uses: actions/checkout@v4
+        -   uses: gaurav-nelson/github-action-markdown-link-check@v1

.github/workflows/publishdocs.yaml

@@ -1,18 +1,19 @@
+---
 name: Publish docs via GitHub Pages
 on:
-  push:
-    branches:
-      - master
+    push:
+        branches:
+        -   master
 
 jobs:
-  build:
-    name: Deploy docs
-    runs-on: ubuntu-latest
-    steps:
-      - name: Checkout master
-        uses: actions/checkout@v4
+    build:
+        name: Deploy docs
+        runs-on: ubuntu-latest
+        steps:
+        -   name: Checkout master
+            uses: actions/checkout@v4
 
-      - name: Deploy docs
-        uses: mhausenblas/mkdocs-deploy-gh-pages@master
-        env:
-          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        -   name: Deploy docs
+            uses: mhausenblas/mkdocs-deploy-gh-pages@master
+            env:
+                GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}

.github/workflows/test_and_coverage.yml

@@ -1,3 +1,4 @@
+---
 name: Test and coverage
 
 # This workflow will install Python dependencies, run tests
@@ -13,36 +14,36 @@ on: [push, pull_request]
 
 jobs:
 
-  build:
+    build:
 
-    runs-on: ubuntu-latest
+        runs-on: ubuntu-latest
 
-    steps:
+        steps:
 
-    - name: Clone repo
-      uses: actions/checkout@v4
+        -   name: Clone repo
+            uses: actions/checkout@v4
 
-    - name: Set up Python
-      uses: actions/setup-python@v5
-      with:
-        python-version: 3.11
+        -   name: Set up Python
+            uses: actions/setup-python@v5
+            with:
+                python-version: 3.11
 
-    - name: Install dependencies
-      run: |
-        python -m pip install --upgrade pip setuptools
-        pip install -r python/requirements.txt
-        cd python && pip install -e . && cd ..
-        mkdir -p lib && git clone https://github.com/Remi-Gau/reproschema-py.git lib/reproschema-py
-        cd lib/reproschema-py && git checkout remi_schema_creator && pip install -e .
+        -   name: Install dependencies
+            run: |
+                python -m pip install --upgrade pip setuptools
+                pip install -r python/requirements.txt
+                cd python && pip install -e . && cd ..
+                mkdir -p lib && git clone https://github.com/Remi-Gau/reproschema-py.git lib/reproschema-py
+                cd lib/reproschema-py && git checkout remi_schema_creator && pip install -e .
 
-    - name: Run tests and generate coverage report
-      run: python -m pytest python/tests --cov=./ --cov-report=xml
+        -   name: Run tests and generate coverage report
+            run: python -m pytest python/tests --cov=./ --cov-report=xml
 
-    - name: Upload coverage to Codecov
-      uses: codecov/codecov-action@v4
-      with:
-        file: ./coverage.xml
-        flags: unittests
-        name: codecov-umbrella
-        fail_ci_if_error: true
-        verbose: true
+        -   name: Upload coverage to Codecov
+            uses: codecov/codecov-action@v4
+            with:
+                file: ./coverage.xml
+                flags: unittests
+                name: codecov-umbrella
+                fail_ci_if_error: true
+                verbose: true

.github/workflows/validate.yml

@@ -1,46 +1,47 @@
+---
 name: Validate eCobidas protocols and activities
 
 on:
     push:
-      branches: [master]
+        branches: [master]
     pull_request:
-      branches: "*"
+        branches: '*'
 
 jobs:
 
-  build:
+    build:
 
-    runs-on: ubuntu-latest
+        runs-on: ubuntu-latest
 
     # Steps represent a sequence of tasks that will be executed as part of the job
-    steps:
-      - name: Setup Node
-        uses: actions/setup-node@v4
-        with:
-          node-version: "12.x"
+        steps:
+        -   name: Setup Node
+            uses: actions/setup-node@v4
+            with:
+                node-version: 12.x
 
       # Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it
-      - uses: actions/checkout@v4
+        -   uses: actions/checkout@v4
 
       # Checks that our JSON are valid
-      - name: Check for syntax errors
-        run: |
-          npm install -g jsonlint
-          grep -r  "@context" activities | cut -d: -f1 | xargs -I fname jsonlint -q fname
-          grep -r  "@context" python/conversion/tests/data | cut -d: -f1 | xargs -I fname jsonlint -q fname
+        -   name: Check for syntax errors
+            run: |
+                npm install -g jsonlint
+                grep -r  "@context" activities | cut -d: -f1 | xargs -I fname jsonlint -q fname
+                grep -r  "@context" python/conversion/tests/data | cut -d: -f1 | xargs -I fname jsonlint -q fname
 
       # Checks that the schemas are valid
-      - name: Set up Python
-        uses: actions/setup-python@v5
-        with:
-          python-version: 3.8
-
-      - name: Install dependencies
-        run: |
-          python -m pip install --upgrade pip setuptools
-          pip install reproschema requests_cache
-
-      - name: Test with pyshacl
-        run: |
-          reproschema -l DEBUG validate python/tests/data/protocols
-          reproschema -l DEBUG validate python/tests/data/activities
+        -   name: Set up Python
+            uses: actions/setup-python@v5
+            with:
+                python-version: 3.8
+
+        -   name: Install dependencies
+            run: |
+                python -m pip install --upgrade pip setuptools
+                pip install reproschema requests_cache
+
+        -   name: Test with pyshacl
+            run: |
+                reproschema -l DEBUG validate python/tests/data/protocols
+                reproschema -l DEBUG validate python/tests/data/activities

.pre-commit-config.yaml

@@ -1,3 +1,4 @@
+---
 # See https://pre-commit.com for more information
 # See https://pre-commit.com/hooks.html for more hooks
 repos:
@@ -15,6 +16,13 @@ repos:
     -   id: black
 
 -   repo: https://github.com/ikamensh/flynt/
-    rev: '1.0.1'
+    rev: 1.0.1
     hooks:
     -   id: flynt
+
+
+-   repo: https://github.com/jumanjihouse/pre-commit-hook-yamlfmt
+    rev: 0.2.3
+    hooks:
+    -   id: yamlfmt
+        args: [--mapping, '4', --sequence, '4', --offset, '0']

mkdocs.yml

@@ -1,33 +1,34 @@
+---
 # Project information
-site_name: 'eCOBIDAS'
-repo_name: 'Remi-Gau/eCobidas'
-repo_url: 'https://github.com/Remi-Gau/eCobidas'
+site_name: eCOBIDAS
+repo_name: Remi-Gau/eCobidas
+repo_url: https://github.com/Remi-Gau/eCobidas
 # docs_dir: alternative_path # docs/ is the default folder
 
 # This will use Material them
 theme:
-  name: 'material'
-  language: 'en'
-  palette:
-    primary: 'light blue'
-    accent: 'light blue'
+    name: material
+    language: en
+    palette:
+        primary: light blue
+        accent: light blue
 
 # Pages
 nav:
-  - Welcome: "index.md"
-  - Motivations: "10-motivations.md"
-  - Goals:
-    - Short term goals: "21-short-term.md"
-    - Mid term goals: "22-mid-term.md"
-    - Long term goals: "23-long-term.md"
-  - General organization: "30-general-organization.md"
-  - Working with the spreadhseets: "40-spreadsheets.md"
-  - Viewing the checklist: "50-how-to-render-the-checklist.md"
-  - How to contribute: "80-how-to-contribute.md"
-  - Contributors: "90-contributors.md"
-  - References: "99-references.md"
+-   Welcome: index.md
+-   Motivations: 10-motivations.md
+-   Goals:
+    -   Short term goals: 21-short-term.md
+    -   Mid term goals: 22-mid-term.md
+    -   Long term goals: 23-long-term.md
+-   General organization: 30-general-organization.md
+-   Working with the spreadhseets: 40-spreadsheets.md
+-   Viewing the checklist: 50-how-to-render-the-checklist.md
+-   How to contribute: 80-how-to-contribute.md
+-   Contributors: 90-contributors.md
+-   References: 99-references.md
 
 # list of extension
 markdown_extensions:
-  - admonition
-  - pymdownx.details
+-   admonition
+-   pymdownx.details

mlc_config.json

@@ -8,6 +8,12 @@
         },
         {
             "pattern": "^https://static-content.springer.com"
+        },
+        {
+            "pattern": "^https://twitter.com/.*$"
+        },
+        {
+            "pattern": "^https://neurovault.org/.*$"
         }
     ]
 }