FEA: Add initial example service

.github/workflows/add-issues-to-octue-board.yml

@@ -0,0 +1,15 @@
+name: add-issues-to-octue-board
+
+on:
+  issues:
+    types: [opened, reopened, transferred]
+
+jobs:
+  add-issues-to-octue-board:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Add to Board
+        uses: actions/add-to-project@v0.5.0
+        with:
+          project-url: https://github.com/orgs/octue/projects/22
+          github-token: ${{ secrets.OCTUE_PROJECT_ISSUES_TOKEN }}

.github/workflows/codeql.yml

@@ -0,0 +1,80 @@
+# For most projects, this workflow file will not need changing; you simply need
+# to commit it to your repository.
+#
+# You may wish to alter this file to override the set of languages analyzed,
+# or to provide custom queries or build logic.
+#
+# ******** NOTE ********
+# We have attempted to detect the languages in your repository. Please check
+# the `language` matrix defined below to confirm you have the correct set of
+# supported CodeQL languages.
+#
+name: "CodeQL"
+
+on:
+  push:
+    branches: [ "main" ]
+
+jobs:
+  analyze:
+    name: Analyze
+    # Runner size impacts CodeQL analysis time. To learn more, please see:
+    #   - https://gh.io/recommended-hardware-resources-for-running-codeql
+    #   - https://gh.io/supported-runners-and-hardware-resources
+    #   - https://gh.io/using-larger-runners
+    # Consider using larger runners for possible analysis time improvements.
+    runs-on: 'ubuntu-latest'
+
+    permissions:
+      # required for all workflows
+      security-events: write
+
+      # only required for workflows in private repositories
+      actions: read
+      contents: read
+
+    strategy:
+      fail-fast: false
+      matrix:
+        language: [ 'python' ]
+        # CodeQL supports [ 'c-cpp', 'csharp', 'go', 'java-kotlin', 'javascript-typescript', 'python', 'ruby', 'swift' ]
+        # Use only 'java-kotlin' to analyze code written in Java, Kotlin or both
+        # Use only 'javascript-typescript' to analyze code written in JavaScript, TypeScript or both
+        # Learn more about CodeQL language support at https://aka.ms/codeql-docs/language-support
+
+    steps:
+    - name: Checkout repository
+      uses: actions/checkout@v4
+
+    # Initializes the CodeQL tools for scanning.
+    - name: Initialize CodeQL
+      uses: github/codeql-action/init@v3
+      with:
+        languages: ${{ matrix.language }}
+        # If you wish to specify custom queries, you can do so here or in a config file.
+        # By default, queries listed here will override any specified in a config file.
+        # Prefix the list here with "+" to use these queries and those in the config file.
+
+        # For more details on CodeQL's query packs, refer to: https://docs.github.com/en/code-security/code-scanning/automatically-scanning-your-code-for-vulnerabilities-and-errors/configuring-code-scanning#using-queries-in-ql-packs
+        # queries: security-extended,security-and-quality
+
+
+    # Autobuild attempts to build any compiled languages (C/C++, C#, Go, Java, or Swift).
+    # If this step fails, then you should remove it and run the build manually (see below)
+    - name: Autobuild
+      uses: github/codeql-action/autobuild@v3
+
+    # ℹ️ Command-line programs to run using the OS shell.
+    # 📚 See https://docs.github.com/en/actions/using-workflows/workflow-syntax-for-github-actions#jobsjob_idstepsrun
+
+    #   If the Autobuild fails above, remove it and uncomment the following three lines.
+    #   modify them (or add more) to build your code if your project, please refer to the EXAMPLE below for guidance.
+
+    # - run: |
+    #     echo "Run, Build Application using script"
+    #     ./location_of_script_within_repo/buildscript.sh
+
+    - name: Perform CodeQL Analysis
+      uses: github/codeql-action/analyze@v3
+      with:
+        category: "/language:${{matrix.language}}"

.github/workflows/release.yml

@@ -0,0 +1,34 @@
+name: Release the package on merge into main
+
+# Only trigger when a pull request into main branch is closed.
+on:
+  pull_request:
+    types: [closed]
+    branches:
+      - main
+
+jobs:
+  release:
+    # This job will only run if the PR has been merged (and not closed without merging).
+    if: "github.event.pull_request.merged == true && !contains(github.event.pull_request.head.message, 'skipci')"
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Install Poetry
+        uses: snok/install-poetry@v1.3.2
+
+      - name: Get package version
+        id: get-package-version
+        run: echo "PACKAGE_VERSION=$(poetry version -s)" >> $GITHUB_OUTPUT
+
+      - name: Create Release
+        uses: actions/create-release@v1
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} # This token is provided by Actions, no need to create your own.
+        with:
+          tag_name: ${{ steps.get-package-version.outputs.PACKAGE_VERSION }}
+          release_name: ${{ github.event.pull_request.title }}
+          body: ${{ github.event.pull_request.body }}
+          draft: false
+          prerelease: false

.github/workflows/semantic.yml

@@ -0,0 +1,14 @@
+name: semantic
+
+on:
+  push:
+    branches-ignore:
+      - main
+
+jobs:
+  check-semantic-version:
+    if: "!contains(github.event.head_commit.message, 'skipci')"
+    uses: octue/workflows/.github/workflows/check-semantic-version.yml@main
+    with:
+      path: pyproject.toml
+      breaking_change_indicated_by: minor

.github/workflows/update-pull-request.yml

@@ -0,0 +1,18 @@
+# This workflow updates the pull request description with an auto-generated section containing the categorised commit
+# message headers of the commits since the last pull request merged into main. The auto generated section is enveloped
+# between two comments: "<!--- START AUTOGENERATED NOTES --->" and "<!--- END AUTOGENERATED NOTES --->". Anything
+# outside these in the description is left untouched. Auto-generated updates can be skipped for a commit if
+# "<!--- SKIP AUTOGENERATED NOTES --->" is added to the pull request description.
+
+name: update-pull-request
+
+on: [pull_request]
+
+jobs:
+  description:
+    uses: octue/workflows/.github/workflows/generate-pull-request-description.yml@main
+    secrets:
+      token: ${{ secrets.GITHUB_TOKEN }}
+    permissions:
+      contents: read
+      pull-requests: write

.gitignore

@@ -20,6 +20,7 @@ parts/
 sdist/
 var/
 wheels/
+pip-wheel-metadata/
 share/python-wheels/
 *.egg-info/
 .installed.cfg
@@ -49,7 +50,6 @@ coverage.xml
 *.py,cover
 .hypothesis/
 .pytest_cache/
-cover/
 
 # Translations
 *.mo
@@ -72,7 +72,6 @@ instance/
 docs/_build/
 
 # PyBuilder
-.pybuilder/
 target/
 
 # Jupyter Notebook
@@ -83,9 +82,7 @@ profile_default/
 ipython_config.py
 
 # pyenv
-#   For a library or package, you might want to ignore these files since the code is
-#   intended to run in multiple environments; otherwise, check them in:
-# .python-version
+.python-version
 
 # pipenv
 #   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
@@ -94,30 +91,7 @@ ipython_config.py
 #   install all needed dependencies.
 #Pipfile.lock
 
-# UV
-#   Similar to Pipfile.lock, it is generally recommended to include uv.lock in version control.
-#   This is especially recommended for binary packages to ensure reproducibility, and is more
-#   commonly ignored for libraries.
-#uv.lock
-
-# poetry
-#   Similar to Pipfile.lock, it is generally recommended to include poetry.lock in version control.
-#   This is especially recommended for binary packages to ensure reproducibility, and is more
-#   commonly ignored for libraries.
-#   https://python-poetry.org/docs/basic-usage/#commit-your-poetrylock-file-to-version-control
-#poetry.lock
-
-# pdm
-#   Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control.
-#pdm.lock
-#   pdm stores project-wide configurations in .pdm.toml, but it is recommended to not include it
-#   in version control.
-#   https://pdm.fming.dev/latest/usage/project/#working-with-version-control
-.pdm.toml
-.pdm-python
-.pdm-build/
-
-# PEP 582; used by e.g. github.com/David-OConnor/pyflow and github.com/pdm-project/pdm
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow
 __pypackages__/
 
 # Celery stuff
@@ -154,18 +128,5 @@ dmypy.json
 # Pyre type checker
 .pyre/
 
-# pytype static type analyzer
-.pytype/
-
-# Cython debug symbols
-cython_debug/
-
-# PyCharm
-#  JetBrains specific template is maintained in a separate JetBrains.gitignore that can
-#  be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore
-#  and can be added to the global gitignore or merged into this file.  For a more nuclear
-#  option (not recommended) you can uncomment the following to ignore the entire idea folder.
-#.idea/
-
-# PyPI configuration file
-.pypirc
+.idea
+.DS_store

.pre-commit-config.yaml

@@ -0,0 +1,58 @@
+exclude: "build|.git/|.tox|dist|octue.egg-info"
+default_stages: [commit]
+fail_fast: true
+default_language_version:
+  python: python3 # force all unspecified python hooks to run python3
+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.3.0
+    hooks:
+      - id: trailing-whitespace
+      - id: end-of-file-fixer
+      - id: check-yaml
+      - id: check-added-large-files
+
+  - repo: https://github.com/PyCQA/isort
+    rev: 5.10.1
+    hooks:
+      - id: isort
+
+  - repo: https://github.com/psf/black
+    rev: 22.6.0
+    hooks:
+      - id: black
+        args: ["--line-length", "120"]
+
+  - repo: https://github.com/pycqa/flake8
+    rev: 6.0.0
+    hooks:
+      - id: flake8
+        language_version: python3
+        additional_dependencies:
+          - "pep8-naming"
+        args:
+          - --ignore-names=setUp,tearDown,setUpClass,tearDownClass,asyncSetUp,asyncTearDown,setUpTestData,failureException,longMessage,maxDiff,startTestRun,stopTestRun
+
+  - repo: https://github.com/pre-commit/mirrors-prettier
+    rev: v2.7.1
+    hooks:
+      - id: prettier
+
+  - repo: https://github.com/pycqa/pydocstyle
+    rev: 6.1.1
+    hooks:
+      - id: pydocstyle
+
+  - repo: https://github.com/windpioneers/pre-commit-hooks
+    rev: 0.0.5
+    hooks:
+      - id: check-branch-name
+        args:
+          - "^main$"
+          - "^([a-z][a-z0-9]*)(-[a-z0-9]+)*$"
+
+  - repo: https://github.com/octue/conventional-commits
+    rev: 0.9.0
+    hooks:
+      - id: check-commit-message-is-conventional
+        stages: [commit-msg]

app_configuration.json

@@ -0,0 +1,3 @@
+{
+  "output_location": "gs://octue-sdk-python-test-bucket/example-service-kueue/outputs"
+}

example_service_kueue/app.py

@@ -0,0 +1,28 @@
+import logging
+import os
+import tempfile
+import time
+
+from octue.resources import Datafile, Dataset
+
+from example_service_kueue.submodule import do_something
+
+
+logger = logging.getLogger(__name__)
+
+
+def run(analysis):
+    logger.info("Started example analysis.")
+    do_something()
+    time.sleep(2)
+    analysis.output_values = [1, 2, 3, 4, 5]
+
+    with tempfile.TemporaryDirectory() as temporary_directory:
+
+        with Datafile(os.path.join(temporary_directory, "output.dat"), mode="w") as (datafile, f):
+            f.write("This is some example service output.")
+
+        analysis.output_manifest.datasets["example_dataset"] = Dataset(path=temporary_directory, files={datafile})
+        analysis.finalise(upload_output_datasets_to=analysis.output_location)
+
+    logger.info("Finished example analysis.")

example_service_kueue/submodule.py

@@ -0,0 +1,8 @@
+import logging
+
+
+logger = logging.getLogger(__name__)
+
+
+def do_something():
+    logger.info("Submodules are included in logging.")

octue.yaml

@@ -0,0 +1,6 @@
+services:
+  - namespace: octue
+    name: example-service-kueue
+    app_source_path: example_service_kueue
+    app_configuration_path: app_configuration.json
+    event_store_table_id: octue_sdk_python_test_dataset.service-events