cstar-ocean 0.0.0__tar.gz

cstar_ocean-0.0.0/.github/PULL_RELEASE_TEMPLATE.md

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+<!-- Feel free to remove check-list items aren't relevant to your change -->
+
+- [ ] Closes #xxxx
+- [ ] Tests added
+- [ ] Tests passing
+- [ ] Full type hint coverage
+- [ ] Changes are documented in `docs/releases.rst`
+- [ ] New functions/methods are listed in `api.rst`
+- [ ] New functionality has documentation

cstar_ocean-0.0.0/.github/workflows/close_jira_ticket.yaml

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+name: Close Jira Ticket on Issue Close
+
+on:
+  issues:
+    types: [closed]
+
+jobs:
+  close-jira-ticket:
+    runs-on: ubuntu-latest
+    if: contains(github.event.issue.labels.*.name, 'jira-story')
+    steps:
+      - name: Extract Jira Story Key from Issue Comment
+        id: extract_story_key
+        uses: actions/github-script@v6
+        with:
+          script: |
+            // Fetch all comments on the closed issue
+            const { data: comments } = await github.rest.issues.listComments({
+              owner: context.repo.owner,
+              repo: context.repo.repo,
+              issue_number: context.issue.number
+            });
+            
+            // Find the comment containing the Jira link
+            const jiraComment = comments.find(comment => comment.body.includes('This issue has been linked to Jira story'));
+            if (!jiraComment) {
+              core.setFailed("No Jira comment found with story key.");
+              return;
+            }
+
+            // Extract the Jira story key from the comment
+            const match = jiraComment.body.match(/\[(.*?)\]\(https:\/\/cworthy\.atlassian\.net\/browse\/.*?\)/);
+            if (!match || match.length < 2) {
+              core.setFailed("Jira story key not found in the comment.");
+              return;
+            }
+            const storyKey = match[1];
+
+            // Print the extracted story key
+            console.log("Extracted STORY_KEY:", storyKey);
+
+            core.setOutput("story_key", storyKey);
+            
+      - name: Close Jira Ticket
+        env:
+          JIRA_API_TOKEN: ${{ secrets.JIRA_API_TOKEN_DAFYDD }}
+          JIRA_EMAIL: ${{ secrets.JIRA_EMAIL_DAFYDD }}
+          STORY_KEY: ${{ steps.extract_story_key.outputs.story_key }}
+        run: |
+          story_key="${{ steps.extract_story_key.outputs.story_key }}"
+          jira_domain="https://cworthy.atlassian.net"
+
+          curl -s -w "%{http_code}" -o response.json -X POST -u "$JIRA_EMAIL:$JIRA_API_TOKEN" \
+            -H "Content-Type: application/json" \
+            --data '{"transition": {"id": "31"}}' \
+            "$jira_domain/rest/api/3/issue/$story_key/transitions"

cstar_ocean-0.0.0/.github/workflows/create_jira_tickets.sh

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+#!/bin/bash
+
+######################################
+# FORMAT THE TICKET SUMMARY:
+
+# Escape double quotes in ISSUE_TITLE
+ESCAPED_TITLE="${ISSUE_TITLE//\"/\\\"}"
+
+##############################
+# FORMAT THE TICKET DESCRIPTION:
+
+## Escape double quotes and newlines in ISSUE_BODY
+ESCAPED_BODY="${ISSUE_BODY//\"/\\\"}"
+
+## This is literally the only way to replace newlines with spaces that the Jira API accepts:
+IFS=' ' read -r -d '' ESCAPED_BODY <<<"$ESCAPED_BODY"
+
+## Add link back to original GitHub URL
+ESCAPED_BODY="${ESCAPED_BODY} --- [View the original GitHub issue|$GITHUB_ISSUE_URL]"
+
+##############################
+# DETERMINE ASSIGNEES
+
+# Trim and set GITHUB_ASSIGNEE_USERNAME if needed
+GITHUB_ASSIGNEE_USERNAME=$(echo "$GITHUB_ASSIGNEE_USERNAME" | xargs)
+
+# Map GitHub username to Jira account ID directly
+declare -A JIRA_IDS=(
+  ["TomNicholas"]="712020:035c37ae-65d0-49c2-aa10-89ecfde5257a"
+  ["NoraLoose"]="712020:383dc845-6121-46b3-a5f9-3b90a54478a5"
+  ["dafyddstephenson"]="712020:41094963-a473-4408-9c16-c445f195fd65"
+)
+
+JIRA_ASSIGNEE_ID="${JIRA_IDS[$GITHUB_ASSIGNEE_USERNAME]}"
+
+##############################
+# CREATE THE STORY
+
+# Create the JSON payload, adding assignee if there is one
+if [[ -n "$JIRA_ASSIGNEE_ID" ]]; then
+  cat > payload.json <<EOF
+{
+  "fields": {
+    "project": { "key": "CW" },
+    "summary": "$ESCAPED_TITLE",
+    "description": "$ESCAPED_BODY",
+    "issuetype": { "name": "Story" },
+    "assignee": { "accountId": "$JIRA_ASSIGNEE_ID" }
+  }
+}
+EOF
+else
+  cat > payload.json <<EOF
+{
+  "fields": {
+    "project": { "key": "CW" },
+    "summary": "$ESCAPED_TITLE",
+    "description": "$ESCAPED_BODY",
+    "issuetype": { "name": "Story" }
+  }
+}
+EOF
+fi
+
+# Display the JSON content for verification
+echo "Generated JSON payload:"
+cat payload.json
+
+# Make the API request to create the main story
+RESPONSE=$(curl -s -w "%{http_code}" -o response.json -X POST -u "$JIRA_EMAIL_DAFYDD:$JIRA_API_TOKEN_DAFYDD" \
+  -H "Content-Type: application/json" \
+  -d @payload.json \
+  "https://cworthy.atlassian.net/rest/api/2/issue")
+
+echo "Jira response (Code $RESPONSE):"
+cat response.json
+
+# Check if curl was successful
+if [[ $? -ne 0 || "$RESPONSE" -ne 201 ]]; then
+    echo "Error: Failed to make a request to Jira API."
+  exit 1
+fi
+
+##############################
+# FORMAT SUBTASKS:
+
+# Extract the ID of the story created above
+STORY_ID=$(jq -r '.key' response.json)
+
+# Verify STORY_ID is not empty
+if [[ -z "$STORY_ID" ]]; then
+  echo "Error: STORY_ID is empty. Failed to retrieve a valid story ID."
+  exit 1
+fi
+
+# Use readarray to populate TASKS array directly from matching lines in ISSUE_BODY
+readarray -t TASKS < <(echo "$ISSUE_BODY" | grep -E '^- \[[ x]\] ')
+
+# If there are tasks, create subtasks
+if [[ ${#TASKS[@]} -gt 0 ]]; then
+  echo "Creating subtasks for tasks found in the issue..."
+
+  for TASK in "${TASKS[@]}"; do
+    # Remove the `- [ ]` or `- [x]` prefix from each TASK
+    CLEANED_TASK=$(echo "$TASK" | sed 's/^- \[[ x]\] //')
+    
+    # Check for presence of colon and split based on that
+    if [[ "$CLEANED_TASK" == *:* ]]; then
+      # Split into summary and description based on the first colon
+      TASK_SUMMARY="${CLEANED_TASK%%:*}"
+      TASK_DESCRIPTION="${CLEANED_TASK#*:}"
+    else
+      # If no colon, treat the whole line as the summary and leave description empty
+      TASK_SUMMARY="$CLEANED_TASK"
+      TASK_DESCRIPTION=""
+    fi
+
+
+    ## Trim any extra whitespace or newlines in summary and description
+    TASK_SUMMARY=$(echo "$TASK_SUMMARY" | tr -d '\n' | tr -d '\r' | xargs)
+    TASK_DESCRIPTION=$(echo "$TASK_DESCRIPTION" | tr -d '\n' | tr -d '\r' | xargs)
+    
+    ## Escape double quotes in the summary and description
+    ESCAPED_TASK_SUMMARY="${TASK_SUMMARY//\"/\\\"}"
+    ESCAPED_TASK_DESCRIPTION="${TASK_DESCRIPTION//\"/\\\"}"
+    ESCAPED_TASK_SUMMARY="${ESCAPED_TASK_SUMMARY//$'\n'/ }"
+    ESCAPED_TASK_DESCRIPTION="${ESCAPED_TASK_DESCRIPTION//$'\n'/ }"
+    
+    # Create JSON payload for each subtask with summary and description
+    # issuetype id 10009 corresponds to subtask
+
+
+    if [[ -n "$JIRA_ASSIGNEE_ID" ]]; then	
+	cat > subtask.json <<EOF
+{
+  "fields": {
+    "project": { "key": "CW" },
+    "summary": "$ESCAPED_TASK_SUMMARY",
+    "description": "$ESCAPED_TASK_DESCRIPTION",
+    "issuetype": { "id": "10009" },
+    "parent": { "key": "$STORY_ID" },
+    "assignee": { "accountId": "$JIRA_ASSIGNEE_ID" }
+  }
+}
+EOF
+    else
+	cat > subtask.json <<EOF
+{
+  "fields": {
+    "project": { "key": "CW" },
+    "summary": "$ESCAPED_TASK_SUMMARY",
+    "description": "$ESCAPED_TASK_DESCRIPTION",
+    "issuetype": { "id": "10009" },
+    "parent": { "key": "$STORY_ID" }
+  }
+}
+EOF
+    fi	
+    echo "Generated JSON payload for subtask:"
+    cat subtask.json
+
+    # Make the API request to create each subtask
+    SUBTASK_RESPONSE=$(curl -s -w "%{http_code}" -o subtask_response.json -X POST -u "$JIRA_EMAIL_DAFYDD:$JIRA_API_TOKEN_DAFYDD" \
+      -H "Content-Type: application/json" \
+      -d @subtask.json \
+      "https://cworthy.atlassian.net/rest/api/2/issue")
+
+    # Check if subtask creation was successful
+    if [[ $? -ne 0 || "$SUBTASK_RESPONSE" -ne 201 ]]; then
+      echo "Error: Failed to create subtask for '$TASK_SUMMARY'. Response:"
+      cat subtask_response.json
+      exit 1
+    else
+      echo "Subtask created successfully for '$TASK_SUMMARY'."
+      cat subtask_response.json
+    fi
+  done
+else
+  echo "No tasks found in the issue body. No subtasks created."
+fi

cstar_ocean-0.0.0/.github/workflows/integration_tests.yaml

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+name: integration_tests
+
+on:
+  push:
+    branches:
+      - '*'
+  pull_request:
+    branches:
+      - '*'
+
+jobs:
+
+  test:
+    name: integration-${{ matrix.python-version }}
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ["3.12",]
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Create conda environment
+        uses: mamba-org/setup-micromamba@v1
+        with:
+          cache-downloads: true
+          cache-environment: true
+          micromamba-version: 'latest'
+          environment-file: ci/environment.yml
+          create-args: |
+            python=${{ matrix.python-version }}
+
+      - name: Environment info
+        shell: micromamba-shell {0}                
+        run: |
+          conda info
+          printenv
+
+      - name: Install C-Star
+        shell: micromamba-shell {0}
+        run: |
+           python - V
+           python -m pip install -e . --force-reinstall
+
+      - name: Running Tests
+        shell: micromamba-shell {0}        
+        run: |
+           python -V
+           coverage run --rcfile=coverage.toml -m pytest -s --verbose cstar/tests/integration_tests/*
+           
+      - name: Get coverage report
+        shell: micromamba-shell {0}                
+        run: |
+          coverage report -m ; coverage xml
+
+      - name: Upload coverage reports to Codecov
+        uses: codecov/codecov-action@v4.0.1
+        with:
+          token: ${{ secrets.CODECOV_TOKEN }}
+          files: ./coverage.xml

cstar_ocean-0.0.0/.github/workflows/open_jira_ticket.yaml

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+name: Create Jira Ticket on Label
+
+on:
+  issues:
+    types: [labeled]
+
+jobs:
+  create_jira_ticket:
+    if: contains(github.event.label.name, 'jira-story')
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout Repository
+        uses: actions/checkout@v2
+
+      - name: Run Jira Ticket Creation Script
+        env:
+          JIRA_EMAIL_DAFYDD: ${{ secrets.JIRA_EMAIL_DAFYDD }}
+          JIRA_API_TOKEN_DAFYDD: ${{ secrets.JIRA_API_TOKEN_DAFYDD }}
+          ISSUE_TITLE: "${{ github.event.issue.title }}"
+          ISSUE_BODY: "${{ github.event.issue.body }}"
+          GITHUB_ISSUE_URL: "https://github.com/${{ github.repository }}/issues/${{ github.event.issue.number }}"
+          GITHUB_ASSIGNEE_USERNAME: "${{ github.event.issue.assignee.login }}"          
+        run: |
+          .github/workflows/create_jira_tickets.sh
+          STORY_KEY=$(jq -r '.key' response.json)
+          echo "STORY_KEY=$STORY_KEY" >> $GITHUB_ENV
+      - name: Comment on GitHub Issue
+        run: |
+          # Comment on the GitHub issue with the Jira story key
+          COMMENT_BODY="This issue has been linked to Jira story [$STORY_KEY](https://cworthy.atlassian.net/browse/$STORY_KEY)."
+          curl -X POST -H "Authorization: token ${{ secrets.GITHUB_TOKEN }}" \
+          -H "Accept: application/vnd.github.v3+json" \
+          -d "{\"body\": \"$COMMENT_BODY\"}" \
+          "https://api.github.com/repos/${{ github.repository }}/issues/${{ github.event.issue.number }}/comments"

cstar_ocean-0.0.0/.github/workflows/pre-commit.yaml

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+name: pre-commit
+
+on:
+  pull_request:
+  push:
+    branches: [main]
+
+jobs:
+  pre-commit:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v4
+      - name: Install specific pre-commit version
+        run: pip install pre-commit==3.8.0
+      - uses: pre-commit/action@v3.0.1
+        with:
+          extra_args: --all-files

cstar_ocean-0.0.0/.github/workflows/pypipublish.yaml

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+name: Build distribution
+on:
+  release:
+    types:
+      - published
+  push:
+    branches:
+      - main
+  pull_request:
+    branches:
+      - main
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  build-artifacts:
+    runs-on: ubuntu-latest
+    if: github.repository == 'CWorthy-ocean/C-Star'
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+      - uses: actions/setup-python@v4
+        name: Install Python
+        with:
+          python-version: 3.13
+
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          python -m pip install build
+
+      - name: Build tarball and wheels
+        run: |
+          git clean -xdf
+          git restore -SW .
+          python -m build --sdist --wheel .
+
+      - uses: actions/upload-artifact@v4
+        with:
+          name: releases
+          path: dist
+
+  test-built-dist:
+    needs: build-artifacts
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/setup-python@v4
+        name: Install Python
+        with:
+          python-version: '3.13'
+      - uses: actions/download-artifact@v4
+        with:
+          name: releases
+          path: dist
+      - name: List contents of built dist
+        run: |
+          ls -ltrh
+          ls -ltrh dist
+      - name: Verify the built dist/wheel is valid
+        run: |
+          python -m pip install --upgrade pip
+          python -m pip install dist/cstar*.whl
+          python -c "import cstar; print(cstar.__version__)"
+
+  upload-to-pypi:
+    needs: test-built-dist
+    if: github.event_name == 'release'
+    runs-on: ubuntu-latest
+    environment:
+      name: pypi
+      url: https://pypi.org/p/cstar-ocean
+    permissions:
+      id-token: write
+    steps:
+      - uses: actions/download-artifact@v4
+        with:
+          name: releases
+          path: dist
+      - name: Publish package to PyPI
+        uses: pypa/gh-action-pypi-publish@v1.8.10

cstar_ocean-0.0.0/.github/workflows/sphinx.yaml

@@ -0,0 +1,30 @@
+
+name: Build Documentation
+on:
+  pull_request:
+    branches:
+      - "*"
+
+jobs:
+  docs:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - name: Create conda environment
+        uses: mamba-org/setup-micromamba@v1
+        with:
+          cache-downloads: true
+          cache-environment: true
+          micromamba-version: 'latest'
+          environment-file: ci/environment.yml
+          create-args: |
+            python=${{ matrix.python-version }}
+      - name: Install C-Star
+        shell: micromamba-shell {0}
+        run: |
+           python - V
+           python -m pip install -e . --force-reinstall
+      - name: Build Docs
+        shell: bash -l {0}
+        run: |
+          cd docs ; make fresh; make html

cstar_ocean-0.0.0/.github/workflows/unit_tests.yaml

@@ -0,0 +1,58 @@
+name: unit_tests
+
+on:
+  push:
+    branches:
+      - '*'
+  pull_request:
+    branches:
+      - '*'
+
+jobs:
+  test:
+    name: unit-${{ matrix.python-version }}
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ["3.12",]
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Create conda environment
+        uses: mamba-org/setup-micromamba@v1
+        with:
+          cache-downloads: true
+          cache-environment: true
+          micromamba-version: 'latest'
+          environment-file: ci/environment.yml
+          create-args: |
+            python=${{ matrix.python-version }}
+
+      - name: Environment info
+        shell: micromamba-shell {0}                
+        run: |
+          conda info
+          printenv
+
+      - name: Install C-Star
+        shell: micromamba-shell {0}
+        run: |
+           python - V
+           python -m pip install -e . --force-reinstall
+
+      - name: Running Tests
+        shell: micromamba-shell {0}        
+        run: |
+           python -V
+           coverage run --rcfile=coverage.toml -m pytest -s --verbose cstar/tests/unit_tests/*
+           
+      - name: Get coverage report
+        shell: micromamba-shell {0}                
+        run: |
+          coverage report -m ; coverage xml
+
+      - name: Upload coverage reports to Codecov
+        uses: codecov/codecov-action@v4.0.1
+        with:
+          token: ${{ secrets.CODECOV_TOKEN }}
+          files: ./coverage.xml

cstar_ocean-0.0.0/.gitignore

@@ -0,0 +1,135 @@
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+pip-wheel-metadata/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+.python-version
+
+# pipenv
+#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+#   However, in case of collaboration, if having platform-specific dependencies or dependencies
+#   having no cross-platform support, pipenv may install dependencies that don't work, or not
+#   install all needed dependencies.
+#Pipfile.lock
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/
+
+# Dask
+dask-worker-space/
+
+# Vscode
+.vscode/