template and dependency updates

ghga-de · Nov 16, 2023 · 31307b0 · 31307b0
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Showing 38 changed files with 479 additions and 257 deletions.
diff --git a/.deprecated_files b/.deprecated_files
@@ -21,3 +21,4 @@ setup.cfg
 
 .pylintrc
 .flake8
+.editorconfig
diff --git a/.devcontainer/devcontainer.json b/.devcontainer/devcontainer.json
@@ -2,41 +2,35 @@
 // 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": "metldata",
+	"name": "${localWorkspaceFolderBasename}",
 	"dockerComposeFile": "docker-compose.yml",
 	"service": "app",
 	"workspaceFolder": "/workspace",
 	"customizations": {
 		"vscode": {
 			// Set *default* container specific settings.json values on container create.
 			"settings": {
+				"files.eol": "\n",
 				"terminal.integrated.profiles.linux": {
 					"bash": {
 						"path": "/bin/bash"
 					}
 				},
 				"python.pythonPath": "/usr/local/bin/python",
 				"python.languageServer": "Pylance",
-				"python.linting.enabled": true,
-				"python.linting.pylintEnabled": true,
-				"python.formatting.autopep8Path": "/usr/local/py-utils/bin/autopep8",
-				"python.formatting.blackPath": "/usr/local/py-utils/bin/black",
-				"python.formatting.yapfPath": "/usr/local/py-utils/bin/yapf",
-				"python.formatting.provider": "black",
 				"python.analysis.typeCheckingMode": "basic",
-				"python.linting.banditPath": "/usr/local/py-utils/bin/bandit",
-				"python.linting.mypyPath": "/usr/local/py-utils/bin/mypy",
-				"python.linting.pycodestylePath": "/usr/local/py-utils/bin/pycodestyle",
-				"python.linting.pydocstylePath": "/usr/local/py-utils/bin/pydocstyle",
-				"python.linting.pylintPath": "/usr/local/py-utils/bin/pylint",
 				"python.testing.pytestPath": "/usr/local/py-utils/bin/pytest",
+				"python.testing.pytestArgs": [
+					"--profile"
+				],
 				"python.testing.unittestEnabled": false,
 				"python.testing.pytestEnabled": true,
 				"editor.formatOnSave": true,
 				"editor.renderWhitespace": "all",
 				"editor.rulers": [
 					88
 				],
+				"editor.defaultFormatter": "ms-python.black-formatter",
 				"licenser.license": "Custom",
 				"licenser.customHeaderFile": "/workspace/.devcontainer/license_header.txt"
 			},
@@ -45,7 +39,6 @@
 				"mikestead.dotenv",
 				"ms-azuretools.vscode-docker",
 				"ms-python.python",
-				"ms-python.isort",
 				"ms-python.vscode-pylance",
 				"ms-toolsai.jupyter",
 				"njpwerner.autodocstring",
@@ -58,7 +51,9 @@
 				"yzhang.markdown-all-in-one",
 				"visualstudioexptteam.vscodeintellicode",
 				"ymotongpoo.licenser",
-				"editorconfig.editorconfig"
+				"charliermarsh.ruff",
+				"ms-python.black-formatter",
+				"ms-python.mypy-type-checker"
 			]
 		}
 	},
@@ -68,12 +63,13 @@
 	"postCreateCommand": "dev_install",
 	// Comment out connect as root instead. More info: https://aka.ms/vscode-remote/containers/non-root.
 	"remoteUser": "vscode",
+	"containerEnv": {
+		// for testcontainers to connect to the docker host:
+		"TC_HOST": "host.docker.internal",
+		"DOCKER_HOST": "unix:///var/run/docker.sock"
+	},
 	"features": {
-		"ghcr.io/devcontainers/features/docker-in-docker:2": {
-			"version": "latest",
-			"enableNonRootDocker": "true",
-			"moby": true,
-			"azureDnsAutoDetection": false
-		}
+		// 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/.editorconfig b/.editorconfig
diff --git a/.gitignore b/.gitignore
@@ -133,6 +133,12 @@ dmypy.json
 # ignore VS Code settings:
 .vscode/
 
+# key stores
+*.key
+*.rnd
+.keystore
+.ssl/
+
 # desktop settings and thumbnails
 .DS_Store
 desktop.ini

diff --git a/.mandatory_files b/.mandatory_files
@@ -6,9 +6,7 @@
 # may differ from that of the template repository.
 
 .devcontainer/dev_launcher
-.devcontainer/devcontainer.json
 .devcontainer/docker-compose.yml
-.devcontainer/Dockerfile
 
 tests/__init__.py
 tests/fixtures/__init__.py

diff --git a/.readme_template.md b/.readme_template.md
@@ -1,5 +1,5 @@
 
-[![tests](https://github.com/ghga-de/$name/actions/workflows/unit_and_int_tests.yaml/badge.svg)](https://github.com/ghga-de/$name/actions/workflows/unit_and_int_tests.yaml)
+[![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)
 
 # $title
@@ -11,6 +11,7 @@ $summary
 $description
 
 ## Installation
+
 We recommend using the provided Docker container.
 
 A pre-build version is available at [docker hub](https://hub.docker.com/repository/docker/ghga/$name):
@@ -42,6 +43,7 @@ $shortname --help
 ```
 
 ## Configuration
+
 ### Parameters
 
 The service requires the following configuration parameters:
@@ -77,19 +79,20 @@ $openapi_doc
 $design_description
 
 ## Development
+
 For setting up the development environment, we rely on the
-[devcontainer feature](https://code.visualstudio.com/docs/remote/containers) of vscode
+[devcontainer feature](https://code.visualstudio.com/docs/remote/containers) of VS Code
 in combination with Docker Compose.
 
-To use it, you have to have Docker Compose as well as vscode with its "Remote - Containers"
+To use it, you have to have Docker Compose as well as VS Code with its "Remote - Containers"
 extension (`ms-vscode-remote.remote-containers`) installed.
-Then open this repository in vscode and run the command
-`Remote-Containers: Reopen in Container` from the vscode "Command Palette".
+Then open this repository in VS Code and run the command
+`Remote-Containers: Reopen in Container` from the VS Code "Command Palette".
 
 This will give you a full-fledged, pre-configured development environment including:
 - infrastructural dependencies of the service (databases, etc.)
-- all relevant vscode extensions pre-installed
-- pre-configured linting and auto-formating
+- all relevant VS Code extensions pre-installed
+- pre-configured linting and auto-formatting
 - a pre-configured debugger
 - automatic license-header insertion
 
@@ -101,9 +104,11 @@ if you update dependencies in the [`./pyproject.toml`](./pyproject.toml) or the
 [`./requirements-dev.txt`](./requirements-dev.txt), please run it again.
 
 ## License
+
 This repository is free to use and modify according to the
 [Apache 2.0 License](./LICENSE).
 
-## Readme Generation
-This readme is autogenerate, please see [`readme_generation.md`](./readme_generation.md)
+## README Generation
+
+This README file is auto-generated, please see [`readme_generation.md`](./readme_generation.md)
 for details.
diff --git a/.static_files b/.static_files
@@ -11,6 +11,7 @@
 .devcontainer/dev_install
 .devcontainer/license_header.txt
 .devcontainer/Dockerfile
+.devcontainer/devcontainer.json
 
 scripts/script_utils/__init__.py
 scripts/script_utils/cli.py
@@ -39,7 +40,6 @@ scripts/README.md
 example_data/README.md
 
 .coveragerc
-.editorconfig
 .gitattributes
 .gitignore
 .mypy.ini

diff --git a/pyproject.toml b/pyproject.toml
@@ -21,10 +21,10 @@ classifiers = [
     "Intended Audience :: Developers",
 ]
 dependencies = [
-    "hexkit[akafka,mongodb]>=0.10.2",
-    "ghga-service-commons[api,auth]>=0.5.0",
-    "ghga-event-schemas>=0.13.4",
-    "typer>=0.7.0",
+    "hexkit[akafka,mongodb]~=1.0.0",
+    "ghga-service-commons[api,auth]~=1.1.0",
+    "ghga-event-schemas~=1.0.0",
+    "typer~=0.9.0",
     "linkml==1.6.1",
     "linkml-runtime==1.6.0",
     "linkml-validator==0.4.5",
Original file line number	Diff line number	Diff line change
Expand Up		@@ -21,3 +21,4 @@ setup.cfg

		.pylintrc
		.flake8
		.editorconfig