Relax requirements (#22)

ghga-de · Jul 19, 2023 · fbbeafc · fbbeafc
1 parent 2432e5f
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diff --git a/.devcontainer/devcontainer.json b/.devcontainer/devcontainer.json
@@ -2,78 +2,80 @@
 // 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": "Data Steward scripts",
+	"name": "Data Steward Kit",
 	"dockerComposeFile": "docker-compose.yml",
 	"service": "app",
 	"workspaceFolder": "/workspace",
-	// Set *default* container specific settings.json values on container create.
-	"settings": {
-		"terminal.integrated.shell.linux": "/bin/bash",
-		"sqltools.connections": [
-			{
-				"name": "Container database",
-				"driver": "PostgreSQL",
-				"previewLimit": 50,
-				"server": "localhost",
-				"port": 5432,
-				"database": "postgres",
-				"username": "postgres",
-				"password": "postgres"
-			}
-		],
-		"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",
-		"editor.formatOnSave": true,
-		"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.unittestEnabled": false,
-		"python.testing.pytestEnabled": true,
-		"editor.renderWhitespace": "all",
-		"editor.rulers": [
-			88
-		],
-		"licenser.license": "AL2",
-		"licenser.author": "Universität Tübingen, DKFZ and EMBL\nfor the German Human Genome-Phenome Archive (GHGA)",
+	"customizations": {
+		"vscode": {
+			// Set *default* container specific settings.json values on container create.
+			"settings": {
+				"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.unittestEnabled": false,
+				"python.testing.pytestEnabled": true,
+				"editor.formatOnSave": true,
+				"editor.renderWhitespace": "all",
+				"editor.rulers": [
+					88
+				],
+				"licenser.license": "Custom",
+				"licenser.customHeaderFile": "/workspace/.devcontainer/license_header.txt"
+			},
+			// Add the IDs of extensions you want installed when the container is created.
+			"extensions": [
+				"mikestead.dotenv",
+				"ms-azuretools.vscode-docker",
+				"ms-python.black-formatter",
+				"ms-python.python",
+				"ms-python.isort",
+				"ms-python.vscode-pylance",
+				"ms-toolsai.jupyter",
+				"vtenentes.bdd",
+				"njpwerner.autodocstring",
+				"redhat.vscode-yaml",
+				"42crunch.vscode-openapi",
+				"arjun.swagger-viewer",
+				"eamodio.gitlens",
+				"github.vscode-pull-request-github",
+				"streetsidesoftware.code-spell-checker",
+				"yzhang.markdown-all-in-one",
+				"visualstudioexptteam.vscodeintellicode",
+				"ymotongpoo.licenser",
+				"editorconfig.editorconfig"
+			]
+		}
 	},
-	// Add the IDs of extensions you want installed when the container is created.
-	"extensions": [
-		"ms-python.python",
-		"ms-python.vscode-pylance",
-		"mtxr.sqltools",
-		"mtxr.sqltools-driver-pg",
-		"42crunch.vscode-openapi",
-		"eamodio.gitlens",
-		"formulahendry.terminal",
-		"tyriar.terminal-tabs",
-		"alexcvzz.vscode-sqlite",
-		"njpwerner.autodocstring",
-		"arjun.swagger-viewer",
-		"ms-toolsai.jupyter",
-		"redhat.vscode-yaml",
-		"ymotongpoo.licenser",
-		"ms-azuretools.vscode-docker",
-		"EditorConfig.EditorConfig"
-	],
 	// Use 'forwardPorts' to make a list of ports inside the container available locally.
 	// "forwardPorts": [5000, 5432],
 	// Use 'postCreateCommand' to run commands after the container is created.
 	"postCreateCommand": "dev_install",
 	// Comment out connect as root instead. More info: https://aka.ms/vscode-remote/containers/non-root.
 	"remoteUser": "vscode",
 	"features": {
-		"docker-in-docker": {
+		"ghcr.io/devcontainers/features/docker-in-docker:2": {
 			"version": "latest",
-			"moby": true
+			"enableNonRootDocker": "true",
+			"moby": true,
+			"azureDnsAutoDetection": false
 		}
 	}
 }
diff --git a/.devcontainer/docker-compose.yml b/.devcontainer/docker-compose.yml
@@ -27,54 +27,3 @@ services:
     user: vscode
     # Use "forwardPorts" in **devcontainer.json** to forward an app port locally.
     # (Adding the "ports" property to this file will not forward from a Codespace.)
-
-
-    # Please uncomment, add, or remove services as needed:
-
-    #   postgresql:
-    #     image: postgres:latest
-    #     restart: unless-stopped
-    #     volumes:
-    #       - postgres_fs:/var/lib/postgresql/data
-    #     environment:
-    #       POSTGRES_USER: postgres
-    #       POSTGRES_DB: postgres
-    #       POSTGRES_PASSWORD: postgres
-    #     # Add "forwardPorts": ["5432"] to **devcontainer.json** to forward PostgreSQL locally.
-    #     # (Adding the "ports" property to this file will not forward from a Codespace.)
-
-    #   rabbitmq:
-    #     image: rabbitmq:3-management
-    #     ports:
-    #       - 5672:5672
-    #       - 15672:15672
-
-    #   localstack:
-    #     image: localstack/localstack
-    #     ports:
-    #       - "4566:4566"
-    #     environment:
-    #       SERVICES: s3
-    #       DEFAULT_REGION: eu-west-1
-    #       AWS_DEFAULT_REGION: eu-west-1
-    #       # accessible at localhost
-    #       HOSTNAME_EXTERNAL: localhost
-    #       USE_SSL: "false"
-    #       DATA_DIR: /tmp/localstack/data
-    #       DEBUG: 1
-    #     volumes:
-    #       - type: volume
-    #         source: s3_fs
-    #         target: /tmp/localstack
-    #         volume:
-    #           nocopy: true
-    #   mongodb:
-    #     image: mongo:5.0.4
-    #     restart: unless-stopped
-    #     volumes:
-    #       - mongo_fs:/data/db
-
-    # volumes:
-    #   postgres_fs: {}
-    #   s3_fs: {}
-    #   mongo_fs: {}
diff --git a/.github/workflows/pypi_publish.yaml b/.github/workflows/pypi_publish.yaml
@@ -61,12 +61,12 @@ jobs:
           pytest .
 
       - name: Publish distribution package to PyPI (test)
-        uses: pypa/gh-action-pypi-publish@master
+        uses: pypa/gh-action-pypi-publish@release/v1
         with:
           password: ${{ secrets.TEST_PYPI_API_TOKEN }}
-          repository_url: https://test.pypi.org/legacy/
+          repository-url: https://test.pypi.org/legacy/
 
       - name: Publish distribution package to PyPI (production)
-        uses: pypa/gh-action-pypi-publish@master
+        uses: pypa/gh-action-pypi-publish@release/v1
         with:
           password: ${{ secrets.PYPI_API_TOKEN }}
diff --git a/ghga_datasteward_kit/__init__.py b/ghga_datasteward_kit/__init__.py
@@ -15,4 +15,4 @@
 
 """A utils package for GHGA data stewards."""
 
-__version__ = "0.4.4"
+__version__ = "0.4.5"
diff --git a/requirements-dev.txt b/requirements-dev.txt
@@ -2,5 +2,4 @@
 
 -r requirements-dev-common.txt
 
-# additional requirements can be listed here
-testcontainers[kafka,mongo,postgresql]==3.4.2
+testcontainers==3.4.1
diff --git a/setup.cfg b/setup.cfg
@@ -36,8 +36,8 @@ include_package_data = True
 packages = find:
 install_requires =
     crypt4gh==1.6
-    hexkit[mongodb,s3]==0.10.0
-    ghga-transpiler==1.0.3
+    hexkit[s3]>=0.10,<0.11
+    ghga-transpiler>=1.0.3,<1.1
     metldata==0.3.6
 
 python_requires = >= 3.9
Original file line number	Diff line number	Diff line change
Expand Up		@@ -15,4 +15,4 @@

		"""A utils package for GHGA data stewards."""

		__version__ = "0.4.4"
		__version__ = "0.4.5"