Update template and dependencies (#70)

* template and dependency updates * further updates * Use new hexkit test fixture system Remove previous mongodb session fixture Apply pytestmark to files that need it and remove decorators * Remove pylint pragma statements * minor updates * licence headers are updated * version bump --------- Co-authored-by: TheByronHimes <TheByronHimes@gmail.com>
ghga-de · May 31, 2024 · d426dd1 · d426dd1
1 parent 37e51c9
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diff --git a/.devcontainer/Dockerfile b/.devcontainer/Dockerfile
@@ -1,4 +1,4 @@
-FROM mcr.microsoft.com/vscode/devcontainers/python:3.9-bullseye
+FROM mcr.microsoft.com/devcontainers/python:1-3.12-bookworm
 
 ENV PYTHONUNBUFFERED 1
 

diff --git a/.devcontainer/devcontainer.json b/.devcontainer/devcontainer.json
@@ -1,6 +1,5 @@
 // For format details, see https://aka.ms/devcontainer.json. For config options, see the README at:
 // https://github.com/microsoft/vscode-dev-containers/tree/v0.177.0/containers/python-3-postgres
-// Update the VARIANT arg in docker-compose.yml to pick a Python version: 3, 3.8, 3.7, 3.6
 {
 	"name": "${localWorkspaceFolderBasename}",
 	"dockerComposeFile": "docker-compose.yml",
@@ -20,13 +19,10 @@
 				"python.languageServer": "Pylance",
 				"python.analysis.typeCheckingMode": "basic",
 				"python.testing.pytestPath": "/usr/local/py-utils/bin/pytest",
-				"python.testing.pytestArgs": [
-					"--profile"
-				],
 				"python.testing.unittestEnabled": false,
 				"python.testing.pytestEnabled": true,
 				"editor.codeActionsOnSave": {
-					"source.organizeImports": true
+					"source.organizeImports": "explicit"
 				},
 				"editor.formatOnSave": true,
 				"editor.renderWhitespace": "all",
@@ -75,4 +71,4 @@
 		// details can be found here: https://github.com/devcontainers/features/tree/main/src/docker-outside-of-docker
 		"ghcr.io/devcontainers/features/docker-outside-of-docker:1": {}
 	}
-}
+}
diff --git a/.devcontainer/license_header.txt b/.devcontainer/license_header.txt
@@ -1,4 +1,4 @@
-Copyright 2021 - 2023 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
+Copyright 2021 - 2024 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
 for the German Human Genome-Phenome Archive (GHGA)
 
 Licensed under the Apache License, Version 2.0 (the "License");

diff --git a/.github/workflows/check_config_docs.yaml b/.github/workflows/check_config_docs.yaml
@@ -1,17 +1,24 @@
-name: Check if the config schema and the example are up to date.
+name: Check if the config schema and the example are up to date
 
 on: push
 
 jobs:
   static-code-analysis:
+    name: Check config schema and example
+
     runs-on: ubuntu-latest
+
     steps:
-      - uses: actions/checkout@v3
+      - name: Checkout repository
+        id: checkout
+        uses: actions/checkout@v4
 
-      - id: common
-        uses: ghga-de/gh-action-common@v4
+      - name: Common steps
+        id: common
+        uses: ghga-de/gh-action-common@v6
 
       - name: Check config docs
+        id: check-config-docs
         run: |
           export ${{ steps.common.outputs.CONFIG_YAML_ENV_VAR_NAME }}="${{ steps.common.outputs.CONFIG_YAML }}"
 

diff --git a/.github/workflows/check_pyproject.yaml b/.github/workflows/check_pyproject.yaml
@@ -1,16 +1,23 @@
-name: Check if the config schema and the example are up to date.
+name: Check if pyproject.toml file is up to date
 
 on: push
 
 jobs:
   static-code-analysis:
+    name: Check pyproject file
+
     runs-on: ubuntu-latest
+
     steps:
-      - uses: actions/checkout@v3
+      - name: Checkout repository
+        id: checkout
+        uses: actions/checkout@v4
 
-      - id: common
-        uses: ghga-de/gh-action-common@v4
+      - name: Common steps
+        id: common
+        uses: ghga-de/gh-action-common@v6
 
       - name: Check pyproject.toml
+        id: check-pyproject
         run: |
           ./scripts/update_pyproject.py --check
diff --git a/.github/workflows/check_readme.yaml b/.github/workflows/check_readme.yaml
@@ -1,16 +1,23 @@
-name: Check if the readme is up to date.
+name: Check if the README file is up to date
 
 on: push
 
 jobs:
   static-code-analysis:
+    name: Check README file
+
     runs-on: ubuntu-latest
+
     steps:
-      - uses: actions/checkout@v3
+      - name: Checkout repository
+        id: checkout
+        uses: actions/checkout@v4
 
-      - id: common
-        uses: ghga-de/gh-action-common@v4
+      - name: Common steps
+        id: common
+        uses: ghga-de/gh-action-common@v6
 
-      - name: Check readme
+      - name: Check README
+        id: check-readme
         run: |
           ./scripts/update_readme.py --check
diff --git a/.github/workflows/check_template_files.yaml b/.github/workflows/check_template_files.yaml
@@ -4,14 +4,23 @@ on: push
 
 jobs:
   check-template-files:
+    name: Check template files
+
     runs-on: ubuntu-latest
+
     steps:
-      - uses: actions/checkout@v3
-      - name: Set up Python 3.9
-        uses: actions/setup-python@v4
+      - name: Checkout repository
+        id: checkout
+        uses: actions/checkout@v4
+
+      - name: Set up Python 3.12
+        id: setup-python
+        uses: actions/setup-python@v5
         with:
-          python-version: 3.9
+          python-version: '3.12'
+
       - name: Check template files
+        id: check-template-files
         run: |
           if [ "${{ github.event.repository.name }}" == "microservice-repository-template" ]
           then

diff --git a/.github/workflows/ci_release.yaml b/.github/workflows/ci_release.yaml
@@ -6,7 +6,10 @@ on:
 
 jobs:
   push_to_docker_hub:
+    name: Push to Docker Hub
+
     runs-on: ubuntu-latest
+
     steps:
       - uses: ghga-de/gh-action-ci@v1
         with:

diff --git a/.github/workflows/ci_workflow_dispatch.yaml b/.github/workflows/ci_workflow_dispatch.yaml
@@ -11,6 +11,7 @@ on:
 
 jobs:
   fetch-tag:
+    name: Fetch Tag
     runs-on: ubuntu-latest
     if:  github.event_name == 'workflow_dispatch' || ( github.event.action != 'labeled' && contains(github.event.pull_request.labels.*.name, 'build') ) || ( github.event.action == 'labeled' && github.event.label.name == 'build' )
     steps:
@@ -20,6 +21,7 @@ jobs:
       latest_tag: ${{ steps.fetch-tag.outputs.latest_tag }}
 
   push_to_docker_hub:
+    name: Push to Docker Hub
     needs: fetch-tag
     runs-on: ubuntu-latest
     steps:

diff --git a/.github/workflows/static_code_analysis.yaml b/.github/workflows/static_code_analysis.yaml
@@ -4,24 +4,36 @@ on: push
 
 jobs:
   static-code-analysis:
-    runs-on: ubuntu-latest
     name: Static Code Analysis
+
+    runs-on: ubuntu-latest
+
     steps:
-      - uses: actions/checkout@v3
+      - name: Checkout repository
+        id: checkout
+        uses: actions/checkout@v4
 
-      - id: common
-        uses: ghga-de/gh-action-common@v4
+      - name: Common steps
+        id: common
+        uses: ghga-de/gh-action-common@v6
 
-      - uses: pre-commit/action@v3.0.0
+      - name: Run pre-commit
+        uses: pre-commit/action@v3.0.1
         env:
           SKIP: no-commit-to-branch
-      - name: ruff
+
+      - name: Run ruff
+        id: ruff
         run: |
           ruff check --output-format=github .
           ruff format --check .
-      - name: mypy
+
+      - name: Run mypy
+        id: mypy
         run: |
           mypy .
+
       - name: Check license header and file
+        id: license-checker
         run: |
-          ./scripts/license_checker.py
+          ./scripts/check_license.py
diff --git a/.github/workflows/tests.yaml b/.github/workflows/tests.yaml
@@ -1,19 +1,24 @@
-name: Tests
+name: Run test suite and measure coverage
 
 on: push
 
 jobs:
   tests:
+    name: Run test suite
+
     runs-on: ubuntu-latest
-    name: Tests
 
     steps:
-      - uses: actions/checkout@v3
+      - name: Checkout repository
+        id: checkout
+        uses: actions/checkout@v4
 
-      - id: common
-        uses: ghga-de/gh-action-common@v4
+      - name: Common steps
+        id: common
+        uses: ghga-de/gh-action-common@v6
 
-      - id: pytest
+      - name: Run tests
+        id: pytest
         run: |
           export ${{ steps.common.outputs.CONFIG_YAML_ENV_VAR_NAME }}="${{ steps.common.outputs.CONFIG_YAML }}"
 
@@ -22,8 +27,8 @@ jobs:
             --cov-report=xml \
             tests
 
-      - id: coveralls
-        name: Upload coverage to coveralls
+      - name: Upload coverage to coveralls
+        id: coveralls
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
         run: |

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -1,10 +1,7 @@
 # See https://pre-commit.com for more information
 # See https://pre-commit.com/hooks.html for more hooks
 
-default_language_version:
-  python: python3.9
-
-minimum_pre_commit_version: 3.0.0
+minimum_pre_commit_version: 3.7.0
 
 repos:
   - repo: local
@@ -48,13 +45,13 @@ repos:
       - id: no-commit-to-branch
         args: [--branch, dev, --branch, int, --branch, main]
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.3.3
+    rev: v0.4.5
     hooks:
       - id: ruff
         args: [--fix, --exit-non-zero-on-fix]
       - id: ruff-format
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v1.9.0
+    rev: v1.10.0
     hooks:
       - id: mypy
         args: [--no-warn-unused-ignores]
diff --git a/.pyproject_generation/README.md b/.pyproject_generation/README.md
@@ -1,5 +1,5 @@
 <!--
- Copyright 2021 - 2023 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
+ Copyright 2021 - 2024 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
  for the German Human Genome-Phenome Archive (GHGA)
 
  Licensed under the Apache License, Version 2.0 (the "License");

diff --git a/.pyproject_generation/pyproject_custom.toml b/.pyproject_generation/pyproject_custom.toml
@@ -1,12 +1,12 @@
 [project]
 name = "metldata"
-version = "1.2.1"
+version = "1.3.0"
 description = "metldata - A framework for handling metadata based on ETL, CQRS, and event sourcing."
 dependencies = [
-    "hexkit[akafka,mongodb] >=2.1.1, <3",
+    "hexkit[akafka,mongodb] >=3, <4",
     "ghga-service-commons[api,auth] >=3.1.1, <4",
     "ghga-event-schemas >=3.0.0, <4",
-    "typer~=0.9.0",
+    "typer>=0.12",
     "linkml==1.6.1",
     "linkml-runtime==1.6.0",
     "linkml-validator==0.4.5",

diff --git a/.pyproject_generation/pyproject_template.toml b/.pyproject_generation/pyproject_template.toml
@@ -1,20 +1,19 @@
 [build-system]
-requires = ["setuptools>=67.7.2"]
+requires = ["setuptools>=69"]
 build-backend = "setuptools.build_meta"
 
 [project]
 readme = "README.md"
 authors = [
     { name = "German Human Genome Phenome Archive (GHGA)", email = "contact@ghga.de" },
 ]
-requires-python = ">=3.9"
+requires-python = ">=3.12"
 license = { text = "Apache 2.0" }
 classifiers = [
     "Development Status :: 1 - Planning",
     "Operating System :: POSIX :: Linux",
-    "Programming Language :: Python :: 3.9",
-    "Programming Language :: Python :: 3.10",
-    "Programming Language :: Python :: 3.11",
+    "Programming Language :: Python :: 3",
+    "Programming Language :: Python :: 3.12",
     "License :: OSI Approved :: Apache Software License",
     "Topic :: Internet :: WWW/HTTP :: HTTP Servers",
     "Topic :: Software Development :: Libraries",
@@ -34,7 +33,7 @@ exclude = [
 ]
 line-length = 88
 src = ["src", "tests", "examples", "scripts"]
-target-version = "py39"
+target-version = "py312"
 
 [tool.ruff.lint]
 fixable = [
@@ -43,8 +42,9 @@ fixable = [
     "D", # pydocstyle
 ]
 ignore = [
-    "E", # pycodestyle errors
-    "W", # pycodestyle warnings - pycodestyle covered by black
+    "E111", # indentation with invalid multiple (for formatter)
+    "E114", # indentation with invalid multiple comment (for formatter)
+    "E116", # over indentation (for formatter)
     "PLW", # pylint warnings
     "RUF001", # ambiguous unicode character strings
     "RUF010", # explicit conversion to string or repr: !s or !r
@@ -56,8 +56,9 @@ ignore = [
     "D400", # first doc line ends in period
     "D401", # non-imperative-mood
     "D107", # missing docstring in __init__
-    "D206", # indent-with-spaces (ignored for formatter)
-    "D300", # triple-single-quotes (ignored for formatter)
+    "D206", # indent-with-spaces (for formatter)
+    "D300", # triple-single-quotes (for formatter)
+    "UP040", # type statement (not yet supported by mypy)
 ]
 select = [
     "C90", # McCabe Complexity
@@ -98,12 +99,12 @@ check_untyped_defs = true
 no_site_packages = false
 
 [tool.pytest.ini_options]
-minversion = "7.1"
+minversion = "8.0"
 asyncio_mode = "strict"
 
 [tool.coverage.paths]
 source = [
-  "src",
-  "/workspace/src",
-  "**/lib/python*/site-packages",
+    "src",
+    "/workspace/src",
+    "**/lib/python*/site-packages",
 ]