merging master

.codespellrc

@@ -0,0 +1,4 @@
+[codespell]
+skip = env,venv,*.svg
+ignore-words-list = HSI
+builtin = clear,rare

.github/dependabot.yml

@@ -0,0 +1,9 @@
+---
+# 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: /
+    schedule:
+        interval: monthly

.github/workflows/check_md_links.yml

@@ -0,0 +1,28 @@
+---
+name: Check Markdown links
+
+# checking for any dead links in markdown files
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+on:
+  push:
+    branches:
+    - master
+  pull_request:
+    branches: ['*']
+
+jobs:
+  markdown-link-check:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v4
+    - uses: gaurav-nelson/github-action-markdown-link-check@v1
+      with:
+        config-file: ./mlc_config.json
+        folder-path: ./docs/
+        use-verbose-mode: yes
+        max-depth: -1
+        file-path: ./README.md,

.github/workflows/publishdocs.yaml

@@ -10,7 +10,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Checkout master
-        uses: actions/checkout@v1
+        uses: actions/checkout@v4
 
       - name: Deploy docs
         uses: mhausenblas/mkdocs-deploy-gh-pages@master

.github/workflows/pythonpackage.yml

@@ -15,9 +15,9 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v4
     - name: Set up Python 3.10
-      uses: actions/setup-python@v2
+      uses: actions/setup-python@v5
       with:
         python-version: "3.10"
     - name: Install dependencies

.github/workflows/run_precommit.yml

@@ -0,0 +1,15 @@
+---
+name: pre-commit
+
+on:
+    pull_request:
+    push:
+        branches: [master]
+
+jobs:
+    pre-commit:
+        runs-on: ubuntu-latest
+        steps:
+        -   uses: actions/checkout@v4
+        -   uses: actions/setup-python@v5
+        -   uses: pre-commit/[email protected]

.github/workflows/update_precommit_hooks.yml

@@ -0,0 +1,53 @@
+---
+name: Update precommit hooks
+
+
+on:
+
+# Uses the cron schedule for github actions
+#
+# https://docs.github.com/en/free-pro-team@latest/actions/reference/events-that-trigger-workflows#scheduled-events
+#
+#            ┌───────────── minute (0 - 59)
+#            │ ┌───────────── hour (0 - 23)
+#            │ │ ┌───────────── day of the month (1 - 31)
+#            │ │ │ ┌───────────── month (1 - 12 or JAN-DEC)
+#            │ │ │ │ ┌───────────── day of the week (0 - 6 or SUN-SAT)
+#            │ │ │ │ │
+#            │ │ │ │ │
+#            │ │ │ │ │
+#            * * * * *
+    schedule:
+    -   cron: 0 0 * 1,7 * # january and july
+
+  # Allows you to run this workflow manually from the Actions tab
+    workflow_dispatch:
+
+jobs:
+    update_precommit_hooks:
+
+    # only run on upstream repo
+        if: github.repository_owner == 'SIMEXP'
+
+        runs-on: ubuntu-latest
+        steps:
+        -   name: Checkout repo
+            uses: actions/checkout@v4
+        -   name: Set up Python
+            uses: actions/setup-python@v5
+            with:
+                python-version: '3.12'
+                allow-prereleases: false
+        -   name: Install pre-commit
+            run: pip install pre-commit
+        -   name: Update pre-commit hooks
+            run: pre-commit autoupdate
+        -   name: Create Pull Request
+            uses: peter-evans/create-pull-request@v6
+            with:
+                commit-message: pre-commit hooks auto-update
+                base: main
+                token: ${{ secrets.GITHUB_TOKEN }}
+                delete-branch: true
+                title: '[BOT] update pre-commit hooks'
+                body: done via this [GitHub Action](https://github.com/${{ github.repository_owner }}/reproschema /blob/main/.github/workflows/update_precommit_hooks.yml)

.github/workflows/validation.yml

@@ -0,0 +1,22 @@
+---
+name: validation
+
+on:
+  pull_request:
+  push:
+    branches: [master]
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+jobs:
+
+  validate_cff:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v4
+    - name: Check whether the citation metadata from CITATION.cff is valid
+      uses: citation-file-format/[email protected]
+      with:
+        args: --validate

.gitignore

@@ -1,6 +1,11 @@
 .DS_Store
-.idea/
 activities/.DS_Store
 protocols/.DS_Store
+
+.idea/
+
 node_modules
 local_data
+
+package-lock.json
+package.json

.pre-commit-config.yaml

@@ -2,13 +2,20 @@
 # See https://pre-commit.com/hooks.html for more hooks
 repos:
 -   repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v2.0.0
+    rev: v4.5.0
     hooks:
     -   id: trailing-whitespace
     -   id: end-of-file-fixer
     -   id: check-yaml
+    -   id: check-json
+    -   id: check-ast
     -   id: check-added-large-files
+    -   id: check-merge-conflict
 -   repo: https://github.com/psf/black
-    rev: 19.3b0
+    rev: 24.3.0
     hooks:
     -   id: black
+-   repo: https://github.com/codespell-project/codespell
+    rev: v2.2.6
+    hooks:
+    -   id: codespell

.remarkrc

@@ -0,0 +1,18 @@
+{
+  "plugins": [
+    "preset-lint-markdown-style-guide",
+    "preset-lint-recommended",
+    "remark-gfm",
+    ["lint-no-duplicate-headings", false],
+    ["lint-list-item-indent", "tab-size"],
+    ["lint-emphasis-marker", "consistent"],
+    ["lint-maximum-line-length", 500],
+    ["lint-maximum-heading-length", false],
+    ["lint-no-shortcut-reference-link", false],
+    ["remark-lint-unordered-list-marker-style", "-"],
+    ["lint-no-trailing-spaces"],
+    ["remark-lint-code-block-style", false],
+    ["lint-no-undefined-references", false],
+    ["remark-lint-heading-style", false]
+  ]
+}

CITATION.cff

@@ -0,0 +1,33 @@
+# schema: https://github.com/citation-file-format/citation-file-format/blob/main/schema-guide.md
+
+cff-version: 1.2.0
+
+title: reproschema
+
+abstract: >-
+  A standardized form generation and data collection schema to harmonize results by design across projects.
+
+version: 1.0.0-rc4
+
+license: CC-BY-4.0
+
+repository-code: https://github.com/ReproNim/reproschema.git
+
+message: >-
+  To cite the reproschema, please follow the instructions here:
+  https://zenodo.org/doi/10.5281/zenodo.4064939
+
+identifiers:
+  - description: PDFs of the BIDS specification for versions 1.9.0 and above
+    type: doi
+    value: 10.5281/zenodo.4064939
+
+keywords:
+    - "schema"
+    - "assessment"
+    - "jsonld"
+    - "rdf"
+    - "repronim"
+
+authors:
+  - family-names: Reproschema Contributors

README.md

@@ -39,7 +39,7 @@ following libraries via pip
 
 To make a new release:
 
-```
+```bash
 python scripts/makeRelease.py <version>
 python scripts/editProperties.py <version>
 ```