Initial commit

.github/ISSUE_TEMPLATE/publish_model.yml

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+---
+name: Publish model
+description: Update model with doi and publish
+title: "Publish model"
+labels: ["model published"]
+
+body:
+
+- type: input
+  id: doi
+  attributes:
+    label: -> doi
+    placeholder: "https://doi.org/10.47366/sabia.v5n1a3"
+    description: "Provide the doi of your published model"
+  validations:
+    required: true

.github/scripts/check_published.py

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+import os
+from github import Github, Auth
+
+# Environment variables
+token = os.environ.get("GITHUB_TOKEN")
+repo_name = os.environ.get("REPO_NAME")
+
+# Get repo
+auth = Auth.Token(token)
+g = Github(auth=auth)
+repo = g.get_repo(repo_name)
+
+# Find if any of the issues has the published label
+published = False
+
+for issue in repo.get_issues():
+    for label in issue.labels:
+        if 'published' in label.name:
+            published = True
+
+print(published)

.github/scripts/copy_files.py

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+import os
+import base64
+from github import Github, Auth
+
+# Environment variables
+token = os.environ.get("GITHUB_TOKEN")
+source_repo_owner = os.environ.get("SOURCE_REPO_OWNER")
+source_repo_name = os.environ.get("SOURCE_REPO_NAME")
+source_path = os.environ.get("SOURCE_PATH")
+target_repo_owner = os.environ.get("TARGET_REPO_OWNER")
+target_repo_name = os.environ.get("TARGET_REPO_NAME")
+target_branch_name = os.environ.get("TARGET_REPO_BRANCH")
+target_path = os.environ.get("TARGET_PATH")
+
+auth = Auth.Token(token)
+g = Github(auth=auth)
+source_repo = g.get_repo(f"{source_repo_owner}/{source_repo_name}")
+target_repo = g.get_repo(f"{target_repo_owner}/{target_repo_name}")
+
+def copy_files(contents, target_path):
+    for content in contents:
+        if content.type == "dir":
+            # Get the contents of the directory and copy recursively
+            copy_files(source_repo.get_contents(content.path), f"{target_path}/{content.name}")
+        else:
+            # Check if the file already exists in the target repo
+            try:
+                target_file = target_repo.get_contents(f"{target_path}/{content.name}", ref=target_branch_name)
+                # File exists, compare contents
+                if content.sha != target_file.sha:
+                    # Contents differ, update the file
+                    source_file_content = base64.b64decode(source_repo.get_git_blob(content.sha).content)
+                    target_repo.update_file(f"{target_path}/{content.name}",f"Updating {content.name}", source_file_content, target_file.sha, branch=target_branch_name)
+            except:
+                # Copy file to target repository
+                source_file_content = base64.b64decode(source_repo.get_git_blob(content.sha).content)
+                target_repo.create_file(f"{target_path}/{content.name}", f"Copying {content.name}", source_file_content, branch=target_branch_name)
+
+# Get contents of source directory
+source_contents = source_repo.get_contents(source_path)
+
+# Start copying files
+copy_files(source_contents, target_path)

.github/scripts/create_branch.py

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+import os
+from github import Github, Auth
+
+# Environment variables
+token = os.environ.get("GITHUB_TOKEN")
+repo_owner = os.environ.get("REPO_OWNER")
+repo_name = os.environ.get("REPO_NAME")
+branch_name = os.environ.get("BRANCH_NAME")
+
+auth = Auth.Token(token)
+g = Github(auth=auth)
+repo = g.get_repo(f"{repo_owner}/{repo_name}")
+
+# Check if the branch name already exists
+try:
+    assert repo.get_git_ref(f"heads/{branch_name}").ref is not None
+    print("Branch already exists")
+
+# Create new branch if it doesn't
+except:
+    base_ref = repo.get_git_ref(f"heads/{repo.default_branch}")
+
+    repo.create_git_ref(f"refs/heads/{branch_name}", base_ref.object.sha)

.github/scripts/file_utils.py

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+import json
+from ruamel.yaml import YAML
+import csv
+import os
+from io import StringIO
+
+def create_or_update_json_entry(rocrate, keys_path, new_value):
+    """
+    Create or update a nested JSON entry in a ro-crate structure.
+
+    Args:
+        rocrate (dict): The main ro-crate dictionary.
+        keys_path (str): Dot-separated path to the key that needs updating.
+        new_value (any): New value to be inserted or updated.
+    """
+    # Split the keys path into individual components
+    keys = keys_path.split('.')
+    prefix = ""
+    structure = rocrate
+
+    # Traverse through the nested structure using keys except the last one
+    for key in keys[:-1]:
+        key = prefix + key
+
+        # Handle potential './' prefix logic
+        if key == "":
+            prefix = "."
+            continue
+        else:
+            prefix = ""
+
+        if isinstance(structure, list):
+            # Find the item with matching '@id' key
+            for item in structure:
+                if item.get("@id") == key:
+                    structure = item
+                    break
+            else:
+                print(f"Key '{key}' not found.")
+                return
+        elif key in structure:
+            structure = structure[key]
+        else:
+            print(f"Key '{key}' not found.")
+            return
+
+    # The final key where the new value should be placed
+    last_key = keys[-1]
+
+    # Update the value at the final key
+    if last_key in structure:
+        if isinstance(structure[last_key], list):
+            # Prepend only if the new value is not already in the list
+            if new_value not in structure[last_key]:
+                structure[last_key].insert(0, new_value)
+        else:
+            # Convert existing non-list value to a list if needed
+            structure[last_key] = [new_value, structure[last_key]]
+    else:
+        # If the key doesn't exist, create a new list with the new value
+        structure[last_key] = [new_value]
+
+
+def navigate_and_assign(source, path, value):
+    """Navigate through a nested dictionary and assign a value to the specified path."""
+    keys = path.split('.')
+    for i, key in enumerate(keys[:-1]):
+        if key.isdigit():  # If the key is a digit, it's an index for a list
+            key = int(key)
+            while len(source) <= key:  # Extend the list if necessary
+                source.append({})
+            source = source[key]
+        else:
+            if i < len(keys) - 2 and keys[i + 1].isdigit():  # Next key is a digit, so ensure this key leads to a list
+                source = source.setdefault(key, [])
+            else:  # Otherwise, it leads to a dictionary
+                source = source.setdefault(key, {})
+    # Assign the value to the final key
+    if keys[-1].isdigit():  # If the final key is a digit, it's an index for a list
+        key = int(keys[-1])
+        while len(source) <= key:  # Extend the list if necessary
+            source.append(None)
+        source[key] = value
+    else:
+        source[keys[-1]] = value
+
+
+def read_yaml_with_header(file_path):
+    """
+    Read YAML content inside YAML header delimiters '---'
+    """
+
+    with open(file_path,'r') as file:
+        data = file.read()
+
+    yaml = YAML()
+    yaml_content = yaml.load(data.strip('---\n'))
+
+    return yaml_content
+
+def update_csv_content(file_path, field, value):
+    # Read the CSV file and update the field value
+    updated_rows = []
+    field_exists = False
+    with open(file_path, mode='r', newline='') as file:
+        reader = csv.reader(file)
+        for row in reader:
+            if row and row[0] == field:
+                row[1] = value
+                field_exists = True
+            updated_rows.append(row)
+
+    # If the field does not exist, add a new line
+    if not field_exists:
+        updated_rows.append([field, value])
+
+    # Convert the updated rows back into a CSV-formatted string
+    updated_csv_content = StringIO()
+    writer = csv.writer(updated_csv_content)
+    writer.writerows(updated_rows)
+    updated_csv_string = updated_csv_content.getvalue()
+
+    return updated_csv_string

.github/scripts/find_repos.py

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+import os
+import json
+import requests
+from github import Github, Auth
+
+# Environment variables
+token = os.environ.get("TOKEN")
+repo_name = os.environ.get("REPO")
+org = os.environ.get("ORG")
+
+repos = []
+
+# Get org
+auth = Auth.Token(token)
+g = Github(auth=auth)
+org = g.get_organization(org)
+
+# Find repos created from this template
+for repo in org.get_repos():
+    repo_json = requests.get(repo.url).json()
+    if 'template_repository' in repo_json:
+        if repo_json['template_repository']['name'] == repo_name:
+            repos.append(repo.name)
+
+print(json.dumps(repos))