reimplement transform framework using schemapack (GSI-529) (#56)

- reimplemented functionality is added in a subpackage called "schemapack_" this allows the parallel evolution of
   the already existing code (much of which might be migrated at some point but not as part of this POC) and the 
   refactored code
- replaced terms "metadata" and "metadata_model" with simply "data" and "model"
- implemented a null transformation that return the input model and data unchanged
- used the null transformation for testing

.deprecated_files

@@ -10,6 +10,7 @@
 .github/workflows/check_mandatory_and_static_files.yaml
 .github/workflows/dev_cd.yaml
 .github/workflows/unit_and_int_tests.yaml
+.github/workflows/cd.yaml
 
 scripts/check_mandatory_and_static_files.py
 scripts/update_static_files.py

.devcontainer/devcontainer.json

@@ -25,12 +25,16 @@
 				],
 				"python.testing.unittestEnabled": false,
 				"python.testing.pytestEnabled": true,
+				"editor.codeActionsOnSave": {
+					"source.organizeImports": true
+				},
 				"editor.formatOnSave": true,
 				"editor.renderWhitespace": "all",
 				"editor.rulers": [
 					88
 				],
-				"editor.defaultFormatter": "ms-python.black-formatter",
+				"ruff.organizeImports": true,
+				"editor.defaultFormatter": "charliermarsh.ruff",
 				"licenser.license": "Custom",
 				"licenser.customHeaderFile": "/workspace/.devcontainer/license_header.txt"
 			},
@@ -52,7 +56,6 @@
 				"visualstudioexptteam.vscodeintellicode",
 				"ymotongpoo.licenser",
 				"charliermarsh.ruff",
-				"ms-python.black-formatter",
 				"ms-python.mypy-type-checker"
 			]
 		}

.github/workflows/ci_release.yaml

@@ -0,0 +1,15 @@
+name: CI on release
+
+on:
+  release:
+      types: [published]
+
+jobs:
+  push_to_docker_hub:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: ghga-de/gh-action-ci@v1
+        with:
+          tag: ${{ github.event.release.tag_name }}
+          dockerhub_username: ${{ secrets.DOCKERHUB_USERNAME }}
+          dockerhub_token: ${{ secrets.DOCKERHUB_TOKEN }}

.github/workflows/ci_workflow_dispatch.yaml

@@ -0,0 +1,30 @@
+name: Build on PR or dispatch
+
+on:
+  workflow_dispatch:
+  pull_request:
+    types:
+      - opened
+      - synchronize
+      - reopened
+      - labeled
+
+jobs:
+  fetch-tag:
+    runs-on: ubuntu-latest
+    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
+    outputs:
+      latest_tag: ${{ steps.fetch-tag.outputs.latest_tag }}
+
+  push_to_docker_hub:
+    needs: fetch-tag
+    runs-on: ubuntu-latest
+    steps:
+      - uses: ghga-de/gh-action-ci@v1
+        with:
+          tag: ${{ needs.fetch-tag.outputs.latest_tag }}-${{ github.sha }}
+          dockerhub_username: ${{ secrets.DOCKERHUB_USERNAME }}
+          dockerhub_token: ${{ secrets.DOCKERHUB_TOKEN }}

.github/workflows/static_code_analysis.yaml

@@ -16,10 +16,9 @@ jobs:
         env:
           SKIP: no-commit-to-branch
       - name: ruff
-        uses: chartboost/ruff-action@v1
-      - name: black
         run: |
-          black --check .
+          ruff check --output-format=github .
+          ruff format --check .
       - name: mypy
         run: |
           mypy .

.static_files

@@ -30,12 +30,13 @@ scripts/list_outdated_dependencies.py
 scripts/README.md
 
 .github/workflows/check_config_docs.yaml
+.github/workflows/check_openapi_spec.yaml
+.github/workflows/check_readme.yaml
 .github/workflows/check_template_files.yaml
+.github/workflows/ci_release.yaml
+.github/workflows/ci_workflow_dispatch.yaml
 .github/workflows/static_code_analysis.yaml
 .github/workflows/tests.yaml
-.github/workflows/check_openapi_spec.yaml
-.github/workflows/check_readme.yaml
-.github/workflows/cd.yaml
 
 example_data/README.md
 

pyproject.toml

@@ -28,6 +28,7 @@ dependencies = [
     "linkml==1.6.1",
     "linkml-runtime==1.6.0",
     "linkml-validator==0.4.5",
+    "schemapack<=1.0.0, <2.0.0"
 ]
 
 [project.license]

requirements-dev-common.in

@@ -13,8 +13,6 @@ mypy-extensions>=1.0.0
 
 ruff>=0.0.290
 
-black>=23.1.0
-
 click>=8.1.0
 typer>=0.7.0