update yaml

.pre-commit-config.yaml

@@ -0,0 +1,20 @@
+# See https://pre-commit.com for more information
+# See https://pre-commit.com/hooks.html for more hooks
+repos:
+-   repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.6.0
+    hooks:
+    -   id: trailing-whitespace
+    -   id: end-of-file-fixer
+    -   id: check-yaml
+    -   id: check-json
+    -   id: check-ast
+    -   id: check-added-large-files
+-   repo: https://github.com/psf/black
+    rev: 24.4.2
+    hooks:
+    -   id: black
+-   repo: https://github.com/codespell-project/codespell
+    rev: v2.2.6
+    hooks:
+    -   id: codespell

README.md

@@ -14,16 +14,16 @@ You can find a demo protocol [here](https://github.com/ReproNim/reproschema-demo
 The following are required and recommended tools for using this cookiecutter and the ReproSchema protocol it generates. This is all a one-time setup, so if you have already done it, skip to the [next section](#creating-a-new-project)!
 
   * **pipx**
-  
+
     pipx is a tool for managing isolated Python-based applications. It is the recommended way to install Poetry and cruft. To install `pipx` follow the instructions here: https://pypa.github.io/pipx/installation/
-  
+
   * **cruft**
 
     cruft is a tool for generating projects based on a cookiecutter (like this one!) and keeping those projects updated if the original cookiecutter changes. Install it with `pipx` by running:
     ```shell
     pipx install cruft
     ```
-    You may also choose to not have a persistent installation of cruft, in which case you would replace any calls to the `cruft` command below with `pipx run cruft`. 
+    You may also choose to not have a persistent installation of cruft, in which case you would replace any calls to the `cruft` command below with `pipx run cruft`.
 
 ## Creating a new protocol
 
@@ -71,21 +71,21 @@ make setup
    git branch -M main
    git push -u origin main
    ```
-3. Create the gh-pages branch 
-    - Fetch the latest changes from your repository (if any): 
-        ```bash 
-        git fetch origin 
-        ``` 
-    - Create and switch to the new gh-pages branch: 
-        ```bash 
-        git checkout -b gh-pages 
-        ``` 
+3. Create the gh-pages branch
+    - Fetch the latest changes from your repository (if any):
+        ```bash
+        git fetch origin
+        ```
+    - Create and switch to the new gh-pages branch:
+        ```bash
+        git checkout -b gh-pages
+        ```
     - Push the gh-pages branch to remote:
         ```bash
         git push --set-upstream origin gh-pages
         ```
-    This branch allows you to deploy your ReproSchema UI publicly. 
-    
+    This branch allows you to deploy your ReproSchema UI publicly.
+
 ## Keeping your project up to date
 
 To be up-to-date with the template, first check if there is a mismatch

hooks/post_gen_project.py

@@ -2,65 +2,88 @@
 import os
 import shutil
 import requests
+import subprocess
+
 
 def get_pref_label(activity_path):
     try:
-        with open(activity_path, 'r') as file:
+        with open(activity_path, "r") as file:
             activity_schema = json.load(file)
         return activity_schema.get("prefLabel", "Unknown Activity")
     except (FileNotFoundError, json.JSONDecodeError):
         return "Unknown Activity"
 
+
 def update_json_schema(activities, base_path):
-    schema_file = os.path.join(base_path, '{{ cookiecutter.__protocol_slug }}/{{ cookiecutter.__protocol_slug }}_schema')
-    with open(schema_file, 'r') as file:
+    schema_file = os.path.join(
+        base_path,
+        "{{ cookiecutter.__protocol_slug }}/{{ cookiecutter.__protocol_slug }}_schema",
+    )
+    with open(schema_file, "r") as file:
         schema = json.load(file)
 
-    schema['ui']['addProperties'] = []
-    schema['ui']['order'] = []
+    schema["ui"]["addProperties"] = []
+    schema["ui"]["order"] = []
 
     for activity in activities:
-        activity_schema_path = os.path.join(base_path, f'activities/{activity}/{activity}_schema')
+        activity_schema_path = os.path.join(
+            base_path, f"activities/{activity}/{activity}_schema"
+        )
         pref_label = get_pref_label(activity_schema_path)
         activity_path = f"../activities/{activity}/{activity}_schema"
 
-        schema['ui']['addProperties'].append({
-            "isAbout": activity_path,
-            "variableName": f"{activity}_schema",
-            "prefLabel": pref_label
-        })
-        schema['ui']['order'].append(activity_path)
+        schema["ui"]["addProperties"].append(
+            {
+                "isAbout": activity_path,
+                "variableName": f"{activity}_schema",
+                "prefLabel": pref_label,
+            }
+        )
+        schema["ui"]["order"].append(activity_path)
 
-    with open(schema_file, 'w') as file:
+    with open(schema_file, "w") as file:
         json.dump(schema, file, indent=4)
 
+
 def fetch_latest_checksum(base_path):
     try:
         # Using Python requests to fetch and parse JSON
-        response = requests.get("https://api.github.com/repos/ReproNim/reproschema-ui/commits/master")
+        response = requests.get(
+            "https://api.github.com/repos/ReproNim/reproschema-ui/commits/master"
+        )
         response.raise_for_status()  # Raises an HTTPError if the HTTP request returned an unsuccessful status code
-        latest_hash = response.json()['sha']
+        latest_hash = response.json()["sha"]
 
-        config_path = os.path.join(base_path, 'config.env')
-        with open(config_path, 'w') as file:
+        config_path = os.path.join(base_path, "config.env")
+        with open(config_path, "w") as file:
             file.write(f"REPROSCHEMA_UI_CHECKSUM={latest_hash}\n")
 
         print("Latest checksum fetched and saved in config.env.")
 
     except Exception as e:
         print(f"Error fetching checksum: {e}")
 
+
+def setup_pre_commit():
+    try:
+        subprocess.check_call([sys.executable, "-m", "pip", "install", "pre-commit"])
+        subprocess.check_call(["pre-commit", "install"])
+        print("Pre-commit hooks set up successfully.")
+    except subprocess.CalledProcessError as e:
+        print(f"Failed to set up pre-commit hooks: {e}")
+
+
 def main():
     base_path = os.getcwd()
-    init_flag_path = os.path.join(base_path, '.initialized')
+    init_flag_path = os.path.join(base_path, ".initialized")
 
     # Check if the project has been initialized before
     if not os.path.exists(init_flag_path):
         # Project initialization logic
-        activities_path = os.path.join(base_path, 'activities')
+        activities_path = os.path.join(base_path, "activities")
 
         try:
-            with open('selected_activities.json') as f:
+            with open("selected_activities.json") as f:
                 selected_activities = json.load(f)
         except (FileNotFoundError, json.JSONDecodeError):
             print("Error reading selected activities.")
@@ -71,22 +94,35 @@ def main():
             if not os.path.exists(activity_dir):
                 os.makedirs(activity_dir)
 
-        all_activities = ['Activity1', 'Activity2', 'Activity3', 'selectActivity', 'voiceActivity']
+        all_activities = [
+            "Activity1",
+            "Activity2",
+            "Activity3",
+            "selectActivity",
+            "voiceActivity",
+        ]
         for activity in all_activities:
             if activity not in selected_activities:
                 activity_dir = os.path.join(activities_path, activity)
                 if os.path.exists(activity_dir):
                     shutil.rmtree(activity_dir)
 
-        activities = [activity for activity in selected_activities if os.path.exists(os.path.join(activities_path, activity))]
+        activities = [
+            activity
+            for activity in selected_activities
+            if os.path.exists(os.path.join(activities_path, activity))
+        ]
         update_json_schema(activities, base_path)
 
         # Mark initialization as complete
-        with open(init_flag_path, 'w') as f:
-            f.write('initialized')
+        with open(init_flag_path, "w") as f:
+            f.write("initialized")
 
     # Fetch and save the latest checksum
     fetch_latest_checksum(base_path)
 
+    setup_pre_commit()
+
+
 if __name__ == "__main__":
-    main()
+    main()

hooks/pre_gen_project.py

@@ -3,13 +3,21 @@
 import sys
 import json
 
+
 def select_activities(n):
-    all_activities = ['Activity1', 'Activity2', 'Activity3', 'selectActivity', 'voiceActivity']
+    all_activities = [
+        "Activity1",
+        "Activity2",
+        "Activity3",
+        "selectActivity",
+        "voiceActivity",
+    ]
     return random.sample(all_activities, n)
 
+
 def main():
     # Read the number of activities from the Cookiecutter context
-    num_activities_str = '{{ cookiecutter.number_of_activities }}'
+    num_activities_str = "{{ cookiecutter.number_of_activities }}"
 
     try:
         num_activities = int(num_activities_str)
@@ -23,8 +31,9 @@ def main():
     print(f"Selected activities: {', '.join(selected_activities)}")
 
     # Write the selected activities to a file
-    with open('selected_activities.json', 'w') as f:
+    with open("selected_activities.json", "w") as f:
         json.dump(selected_activities, f)
 
+
 if __name__ == "__main__":
-    main()
+    main()

update_schema_version.py

@@ -1,21 +1,27 @@
 import os
 import re
 
-latest_release = os.environ['LATEST_RELEASE']
+latest_release = os.environ["LATEST_RELEASE"]
+
 
 def update_file(file_path, version):
-    with open(file_path, 'r') as file:
+    with open(file_path, "r") as file:
         content = file.read()
 
-    content = re.sub(r'"@context": "https://raw\.githubusercontent\.com/ReproNim/reproschema/.+?/contexts/generic"',
-                     f'"@context": "https://raw.githubusercontent.com/ReproNim/reproschema/{version}/contexts/generic"',
-                     content)
-    content = re.sub(r'"schemaVersion": ".+?"', f'"schemaVersion": "{version}"', content)
+    content = re.sub(
+        r'"@context": "https://raw\.githubusercontent\.com/ReproNim/reproschema/.+?/contexts/generic"',
+        f'"@context": "https://raw.githubusercontent.com/ReproNim/reproschema/{version}/contexts/generic"',
+        content,
+    )
+    content = re.sub(
+        r'"schemaVersion": ".+?"', f'"schemaVersion": "{version}"', content
+    )
 
-    with open(file_path, 'w') as file:
+    with open(file_path, "w") as file:
         file.write(content)
 
-for root, dirs, files in os.walk('.'):
+
+for root, dirs, files in os.walk("."):
     for file in files:
-        if file.endswith('_schema') or file.endswith('_item') or '_item_' in file:
+        if file.endswith("_schema") or file.endswith("_item") or "_item_" in file:
             update_file(os.path.join(root, file), latest_release)

{{cookiecutter.protocol_name}}/.github/workflows/build_deploy.yaml

@@ -14,11 +14,11 @@ jobs:
     - name: Set Environment Variable
       run: |
         echo "PROTOCOL_SLUG={{cookiecutter.__protocol_slug}}" >> $GITHUB_ENV
-    
+
     - name: Echo Environment Variable
       run: |
-        echo "PROTOCOL_SLUG is set to $PROTOCOL_SLUG"    
-    
+        echo "PROTOCOL_SLUG is set to $PROTOCOL_SLUG"
+
     - name: Check out repository
       uses: actions/checkout@v3
       with:
@@ -53,7 +53,7 @@ jobs:
       run: |
         python -m pip install --upgrade pip setuptools
         pip install reproschema requests_cache pre-commit
-    
+
     - name: Test with pyshacl
       run: |
         reproschema -l DEBUG validate activities
@@ -76,6 +76,6 @@ jobs:
       if: github.ref == 'refs/heads/main'
       uses: JamesIves/github-pages-deploy-action@v4
       with:
-        token: {% raw %}${{ secrets.GITHUB_TOKEN }}{% endraw %}
+        token: "{% raw %}${{ secrets.GITHUB_TOKEN }}{% endraw %}"
         branch: gh-pages
         folder: ui/dist

{{cookiecutter.protocol_name}}/.gitignore

@@ -1 +1 @@
-*.DS_Store
+*.DS_Store

{{cookiecutter.protocol_name}}/.pre-commit-config.yaml

@@ -0,0 +1,20 @@
+# See https://pre-commit.com for more information
+# See https://pre-commit.com/hooks.html for more hooks
+repos:
+-   repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.6.0
+    hooks:
+    -   id: trailing-whitespace
+    -   id: end-of-file-fixer
+    -   id: check-yaml
+    -   id: check-json
+    -   id: check-ast
+    -   id: check-added-large-files
+-   repo: https://github.com/psf/black
+    rev: 24.4.2
+    hooks:
+    -   id: black
+-   repo: https://github.com/codespell-project/codespell
+    rev: v2.2.6
+    hooks:
+    -   id: codespell

{{cookiecutter.protocol_name}}/Makefile

@@ -49,4 +49,4 @@ cruft-check:
 
 # Update the project from the Cookiecutter template
 cruft-update:
-	cruft update
+	cruft update

{{cookiecutter.protocol_name}}/activities/Activity1/activity1_schema

@@ -29,4 +29,4 @@
 			"reproschema:AllowExport"
 		]
     }
-}
+}

{{cookiecutter.protocol_name}}/activities/Activity1/items/document_upload_item

@@ -13,4 +13,4 @@
     "responseOptions": {
         "valueType": "DigitalDocument"
     }
-}
+}

{{cookiecutter.protocol_name}}/activities/Activity2/Activity2_schema

@@ -67,4 +67,4 @@
 			"reproschema:AllowExport"
 		]
     }
-}
+}

{{cookiecutter.protocol_name}}/activities/Activity2/items/date_item

@@ -13,4 +13,4 @@
     "responseOptions": {
         "valueType": "xsd:date"
     }
-}
+}

{{cookiecutter.protocol_name}}/activities/Activity2/items/time_range_item

@@ -13,4 +13,4 @@
     "responseOptions": {
         "valueType": "xsd:datetime"
     }
-}
+}