Template updates (GSI613) (#18)

* Update template files

* Update tests

* Update all

* Use sync sleep

---------

Co-authored-by: TheByronHimes <[email protected]>

.devcontainer/.dev_config.yaml

@@ -1,6 +1,5 @@
 host: 127.0.0.1
 port: 8080
-log_level: info
 workers: 1
 auto_reload: true
 cors_allowed_origins: []

.devcontainer/dev_install

@@ -7,7 +7,7 @@ cd /workspace
 python -m pip install --upgrade pip
 
 # install or upgrade dependencies for development and testing
-pip install --no-deps -r requirements-dev.txt
+pip install --no-deps -r ./lock/requirements-dev.txt
 
 # install the package itself in edit mode:
 pip install --no-deps -e .

.github/workflows/check_config_docs.yaml

@@ -9,7 +9,7 @@ jobs:
       - uses: actions/checkout@v3
 
       - id: common
-        uses: ghga-de/gh-action-common@v3
+        uses: ghga-de/gh-action-common@v4
 
       - name: Check config docs
         run: |

.github/workflows/check_openapi_spec.yaml

@@ -10,7 +10,7 @@ jobs:
       - uses: actions/checkout@v3
 
       - id: common
-        uses: ghga-de/gh-action-common@v3
+        uses: ghga-de/gh-action-common@v4
 
       - name: Check if openapi.yaml is up to date
         run: |

.github/workflows/check_pyproject.yaml

@@ -0,0 +1,16 @@
+name: Check if the config schema and the example are up to date.
+
+on: push
+
+jobs:
+  static-code-analysis:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+
+      - id: common
+        uses: ghga-de/gh-action-common@v4
+
+      - name: Check pyproject.toml
+        run: |
+          ./scripts/update_pyproject.py --check

.github/workflows/check_readme.yaml

@@ -9,7 +9,7 @@ jobs:
       - uses: actions/checkout@v3
 
       - id: common
-        uses: ghga-de/gh-action-common@v3
+        uses: ghga-de/gh-action-common@v4
 
       - name: Check readme
         run: |

.github/workflows/ci_workflow_dispatch.yaml

@@ -12,7 +12,7 @@ on:
 jobs:
   fetch-tag:
     runs-on: ubuntu-latest
-    if: ( github.event.action != 'labeled' && contains(github.event.pull_request.labels.*.name, 'build') ) || ( github.event.action == 'labeled' && github.event.label.name == 'build' )
+    if: ( github.event.action == 'workflow_dispatch' || github.event.action != 'labeled' && contains(github.event.pull_request.labels.*.name, 'build') ) || ( github.event.action == 'labeled' && github.event.label.name == 'build' )
     steps:
       - id: fetch-tag
         uses: ghga-de/gh-action-fetch-tag@v1

.github/workflows/static_code_analysis.yaml

@@ -10,7 +10,7 @@ jobs:
       - uses: actions/checkout@v3
 
       - id: common
-        uses: ghga-de/gh-action-common@v3
+        uses: ghga-de/gh-action-common@v4
 
       - uses: pre-commit/[email protected]
         env:

.github/workflows/tests.yaml

@@ -11,7 +11,7 @@ jobs:
       - uses: actions/checkout@v3
 
       - id: common
-        uses: ghga-de/gh-action-common@v3
+        uses: ghga-de/gh-action-common@v4
 
       - id: pytest
         run: |

.pre-commit-config.yaml

@@ -51,13 +51,13 @@ repos:
       - id: debug-statements
       - id: debug-statements
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.1.7
+    rev: v0.2.1
     hooks:
       - id: ruff
         args: [--fix, --exit-non-zero-on-fix]
       - id: ruff-format
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v1.7.1
+    rev: v1.8.0
     hooks:
       - id: mypy
         args: [--no-warn-unused-ignores]

.pyproject_generation/README.md

@@ -0,0 +1,29 @@
+<!--
+ Copyright 2021 - 2023 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");
+ you may not use this file except in compliance with the License.
+ You may obtain a copy of the License at
+
+     http://www.apache.org/licenses/LICENSE-2.0
+
+ Unless required by applicable law or agreed to in writing, software
+ distributed under the License is distributed on an "AS IS" BASIS,
+ WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ See the License for the specific language governing permissions and
+ limitations under the License.
+
+-->
+
+# Generating the pyproject.toml
+
+The pyproject.toml of the service is generated by combining static configuration
+captured in [`./pyproject_template.toml`](./pyproject_template.toml) and custom
+package metadata specified in [`./pyproject_custom.toml`](./pyproject_custom.toml).
+
+The `./pyproject_template.toml` is managed by the template, please do not edit manually.
+
+You may specify properties in the `./pyproject_custom.toml` which are already specified
+in the `./pyproject_template.toml`. In that case, the `./pyproject_custom.toml` takes
+priority.

.pyproject_generation/pyproject_custom.toml

@@ -0,0 +1,16 @@
+[project]
+name = "wps"
+version = "1.0.1"
+description = "Work Package Service"
+dependencies = [
+    "ghga-event-schemas~=3.0.0",
+    "ghga-service-commons[api,auth,crypt]>=2, <3",
+    "hexkit[akafka,mongodb]>=2.1.0",
+    "typer>=0.9.0",
+]
+
+[project.urls]
+Repository = "https://github.com/ghga-de/work-package-service"
+
+[project.scripts]
+wps = "wps.__main__:cli"

.ruff.toml → .pyproject_generation/pyproject_template.toml

@@ -1,11 +1,37 @@
+[build-system]
+requires = ["setuptools>=67.7.2"]
+build-backend = "setuptools.build_meta"
+
+[project]
+readme = "README.md"
+authors = [
+    { name = "German Human Genome Phenome Archive (GHGA)", email = "[email protected]" },
+]
+requires-python = ">=3.9"
+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",
+    "License :: OSI Approved :: Apache Software License",
+    "Topic :: Internet :: WWW/HTTP :: HTTP Servers",
+    "Topic :: Software Development :: Libraries",
+    "Intended Audience :: Developers",
+]
+
+[tool.setuptools.packages.find]
+where = ["src"]
+
+[tool.ruff]
 exclude = [
     ".git",
     ".devcontainer",
     "__pycache__",
     "build",
     "dist",
 ]
-
 ignore = [
     "E", # pycodestyle errors
     "W", # pycodestyle warnings - pycodestyle covered by black
@@ -23,9 +49,7 @@ ignore = [
     "D206", # indent-with-spaces (ignored for formatter)
     "D300", # triple-single-quotes (ignored for formatter)
 ]
-
 line-length = 88
-
 select = [
     "C90", # McCabe Complexity
     "F", # pyflakes codes
@@ -39,26 +63,45 @@ select = [
     "SIM", # flake8-simplify
     "D", # pydocstyle
 ]
-
 fixable = [
     "UP", # e.g. List -> list
     "I", # sort imports
     "D", # pydocstyle
 ]
-
 src = ["src", "tests", "examples", "scripts"]
-
 target-version = "py39"
 
-[mccabe]
+[tool.ruff.mccabe]
 max-complexity = 10
 
-[per-file-ignores]
+[tool.ruff.per-file-ignores]
 "scripts/*" = ["PL", "S", "SIM", "D"]
 "tests/*" = ["S", "SIM", "PLR", "B011"]
 ".devcontainer/*" = ["S", "SIM", "D"]
 "examples/*" = ["S", "D"]
 "__init__.py" = ["D"]
 
-[pydocstyle]
+[tool.ruff.pydocstyle]
 convention = "pep257"
+
+[tool.mypy]
+disable_error_code = "import"
+show_error_codes = true
+exclude = [
+    'build/lib/',
+]
+warn_redundant_casts = true
+warn_unused_ignores = true
+check_untyped_defs = true
+no_site_packages = false
+
+[tool.pytest.ini_options]
+minversion = "7.1"
+asyncio_mode = "strict"
+
+[tool.coverage.paths]
+source = [
+  "src",
+  "/workspace/src",
+  "**/lib/python*/site-packages",
+]

readme_generation.md → .readme_generation/README.md

@@ -18,30 +18,30 @@
 
 # Readme Generation
 
-The README file is generated by collecting information from different sources as
+The Repository README is generated by collecting information from different sources as
 outlined in the following.
 
 - name: The full name of the package is derived from the remote origin Git repository.
 - title: A title case representation of the name.
 - shortname: An abbreviation of the full name. This is derived from the name mentioned
-  in the [`./pyproject.toml`](./pyproject.toml).
+  in the [`../pyproject.toml`](../pyproject.toml).
 - summary: A short 1-2 sentence summary derived from the description in the
-  [`./pyproject.toml`](./pyproject.toml).
+  [`../pyproject.toml`](../pyproject.toml).
 - version: The package version derived from the version specified in the
-  [`./pyproject.toml`](./pyproject.toml).
+  [`../pyproject.toml`](../pyproject.toml).
 - description: A markdown-formatted description of the features and use cases of this
-  service or package. Obtained from the [`./.description.md`](./.description.md).
+  service or package. Obtained from the [`./description.md`](./description.md).
 - design_description: A markdown-formatted description of the overall architecture and
-  design of the package. Obtained from the [`./.design.md`](./.design.md).
+  design of the package. Obtained from the [`./design.md`](./design.md).
 - config_description: A markdown-formatted description of all config parameters.
-  This is autogenerated from the [`./config_schema.json`](./config_schema.json).
+  This is autogenerated from the [`../config_schema.json`](../config_schema.json).
 - openapi_doc: A markdown-formatted description of the HTTP API. This is autogenerated
-  and links to the [`./openapi.yaml`](./openapi.yaml). If the openapi.yaml is not
+  and links to the [`../openapi.yaml`](../openapi.yaml). If the openapi.yaml is not
   this documentation is empty.
 
-The [`./.readme_template.md`](./.readme_template.md) serves as a template where the
+The [`./readme_template.md`](./readme_template.md) serves as a template where the
 above variable can be filled in using Pythons `string.Template` utility from the
 standard library.
 
-The [`./scripts/update_readme.py`] script can be used to collect all information and
-fill it into the template to generate the README file.
+The [`../scripts/update_readme.py`](../scripts/update_readme.py) script can be used to
+collect all information and fill it into the template to generate the README file.

.readme_template.md → .readme_generation/readme_template.md

@@ -1,6 +1,5 @@
-
-[![tests](https://github.com/ghga-de/$name/actions/workflows/tests.yaml/badge.svg)](https://github.com/ghga-de/$name/actions/workflows/tests.yaml)
-[![Coverage Status](https://coveralls.io/repos/github/ghga-de/$name/badge.svg?branch=main)](https://coveralls.io/github/ghga-de/$name?branch=main)
+[![tests](https://github.com/ghga-de/$repo_name/actions/workflows/tests.yaml/badge.svg)](https://github.com/ghga-de/$repo_name/actions/workflows/tests.yaml)
+[![Coverage Status](https://coveralls.io/repos/github/ghga-de/$repo_name/badge.svg?branch=main)](https://coveralls.io/github/ghga-de/$repo_name?branch=main)
 
 # $title
 

.template/README.md

@@ -0,0 +1,47 @@
+<!--
+ Copyright 2021 - 2023 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");
+ you may not use this file except in compliance with the License.
+ You may obtain a copy of the License at
+
+     http://www.apache.org/licenses/LICENSE-2.0
+
+ Unless required by applicable law or agreed to in writing, software
+ distributed under the License is distributed on an "AS IS" BASIS,
+ WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ See the License for the specific language governing permissions and
+ limitations under the License.
+
+-->
+
+# Template File Lists
+
+This directory contains multiple text files that are listing paths to other files
+of this repository. The listed files are affected in different ways by template updates
+as explained in the following.
+
+## `static_files.txt`
+The files listed here are synced with their counterparts in the template. They should
+never be modified manually.
+
+## `static_files_ignore.txt`
+To opt out of template updates just for individual files declared as static
+(e.g. because you would like manually modify them), you may add them to this list.
+
+## `mandatory_files.txt`
+The contents of the files listed here are not synced with the template, however, upon
+every template update it is checked that the files exist. You should modify them
+manually to the needs of your repository.
+
+## `mandatory_files_ignore.txt`
+To opt out of existence checks for individual files declared as mandatory, you may add
+them to this list.
+
+## `deprecated_files.txt`
+Files listed here must not exist in your repository and are automatically deleted upon
+a template update.
+
+## `deprecated_files_ignore.txt`
+If you would like to keep files declared as deprecated, you may add them to this list.