Merge pull request #12 from bioimage-io/improve_datastructures

Improve datastructures

.github/workflows/publish.yaml

@@ -7,8 +7,8 @@ on:
         description: "Bioimageio ID of the resource - to be used to access the resource on S3"
         required: true
         type: string
-      stage_nr:
-        description: stage nr to publish
+      stage_number:
+        description: stage number to publish
         required: true
         type: number
 
@@ -28,7 +28,7 @@ jobs:
     uses: ./.github/workflows/publish_call.yaml
     with:
       resource_id: ${{inputs.resource_id}}
-      stage_nr: ${{inputs.stage_nr}}
+      stage_number: ${{inputs.stage_number}}
       S3_HOST: ${{vars.S3_HOST}}
       S3_BUCKET: ${{vars.S3_BUCKET}}
       S3_FOLDER: ${{vars.S3_FOLDER}}

.github/workflows/publish_call.yaml

@@ -7,8 +7,8 @@ on:
         description: "Bioimageio ID of the resource - to be used to access the resource on S3"
         required: true
         type: string
-      stage_nr:
-        description: stage nr to publish
+      stage_number:
+        description: stage number to publish
         required: true
         type: number
       S3_HOST:
@@ -45,7 +45,7 @@ jobs:
           python-version: "3.12"
           cache: "pip" # caching pip dependencies
       - run: pip install .
-      - run: backoffice publish "${{ inputs.resource_id }}" "${{ inputs.stage_nr }}"
+      - run: backoffice publish "${{ inputs.resource_id }}" "${{ inputs.stage_number }}"
       # - name: Publish to Zenodo
       #   run: |
       #     python .github/scripts/update_status.py "${{ inputs.resource_path }}" "Publishing to Zenodo" "5"

.github/workflows/request_changes.yaml

@@ -0,0 +1,41 @@
+name: request changes
+
+on:
+  workflow_dispatch:
+    inputs:
+      resource_id:
+        description: "Bioimageio ID of the resource - to be used to access the resource on S3"
+        required: true
+        type: string
+      stage_number:
+        description: stage number
+        required: true
+        type: number
+      reason:
+        description: Why are changes required? What needs changing?
+        required: true
+        type: string
+
+concurrency: ${{inputs.resource_id}}
+
+env:
+  S3_HOST: ${{vars.S3_HOST}}
+  S3_BUCKET: ${{vars.S3_BUCKET}}
+  S3_FOLDER: ${{vars.S3_FOLDER}}
+  S3_ACCESS_KEY_ID: ${{secrets.S3_ACCESS_KEY_ID}}
+  S3_SECRET_ACCESS_KEY: ${{secrets.S3_SECRET_ACCESS_KEY}}
+  ZENODO_URL: ${{vars.ZENODO_URL}}
+  ZENODO_API_ACCESS_TOKEN: ${{secrets.ZENODO_API_ACCESS_TOKEN}}
+
+jobs:
+  call:
+    uses: ./.github/workflows/request_changes_call.yaml
+    with:
+      resource_id: ${{inputs.resource_id}}
+      stage_number: ${{inputs.stage_number}}
+      reason: ${{inputs.reason}}
+      S3_HOST: ${{vars.S3_HOST}}
+      S3_BUCKET: ${{vars.S3_BUCKET}}
+      S3_FOLDER: ${{vars.S3_FOLDER}}
+      ZENODO_URL: ${{vars.ZENODO_URL}}
+    secrets: inherit

.github/workflows/request_changes_call.yaml

@@ -0,0 +1,52 @@
+name: request changes call
+
+on:
+  workflow_call:
+    inputs:
+      resource_id:
+        description: "Bioimageio ID of the resource - to be used to access the resource on S3"
+        required: true
+        type: string
+      stage_number:
+        description: stage number
+        required: true
+        type: number
+      reason:
+        description: Why are changes required? What needs changing?
+        required: true
+        type: string
+      S3_HOST:
+        required: true
+        type: string
+      S3_BUCKET:
+        required: true
+        type: string
+      S3_FOLDER:
+        required: true
+        type: string
+      ZENODO_URL:
+        required: true
+        type: string
+
+concurrency: ${{inputs.resource_id}}-call
+
+env:
+  S3_HOST: ${{inputs.S3_HOST}}
+  S3_BUCKET: ${{inputs.S3_BUCKET}}
+  S3_FOLDER: ${{inputs.S3_FOLDER}}
+  ZENODO_URL: ${{inputs.ZENODO_URL}}
+  S3_ACCESS_KEY_ID: ${{secrets.S3_ACCESS_KEY_ID}}
+  S3_SECRET_ACCESS_KEY: ${{secrets.S3_SECRET_ACCESS_KEY}}
+  ZENODO_API_ACCESS_TOKEN: ${{secrets.ZENODO_API_ACCESS_TOKEN}}
+
+jobs:
+  request-changes:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
+        with:
+          python-version: "3.12"
+          cache: "pip" # caching pip dependencies
+      - run: pip install .
+      - run: backoffice request-changes "${{ inputs.resource_id }}" "${{ inputs.stage_number }}" "${{ inputs.reason }}"

.github/workflows/test.yaml

@@ -49,7 +49,7 @@ jobs:
     uses: ./.github/workflows/publish_call.yaml
     with:
       resource_id: ${{vars.TEST_PACKAGE_ID}} # testing!
-      stage_nr: 1
+      stage_number: 1
       S3_HOST: ${{vars.S3_HOST}}
       S3_BUCKET: ${{vars.S3_TEST_BUCKET}} # testing!
       S3_FOLDER: ${{vars.S3_TEST_FOLDER}}/ci # testing!

backoffice/_backoffice.py

@@ -5,13 +5,14 @@
 from dotenv import load_dotenv
 
 from backoffice.backup import backup
-from backoffice.run_dynamic_tests import run_dynamic_tests
-from backoffice.utils.remote_resource import (
+from backoffice.remote_resource import (
     PublishedVersion,
     RemoteResource,
     StagedVersion,
 )
-from backoffice.utils.s3_client import Client
+from backoffice.run_dynamic_tests import run_dynamic_tests
+from backoffice.s3_client import Client
+from backoffice.s3_structure.versions import StageNumber
 from backoffice.validate_format import validate_format
 
 _ = load_dotenv()
@@ -44,23 +45,27 @@ def stage(self, resource_id: str, package_url: str):
     def test(
         self,
         resource_id: str,
-        stage_nr: int,
+        stage_number: StageNumber,
         weight_format: Optional[Union[WeightsFormat, Literal[""]]] = None,
         create_env_outcome: Literal["success", ""] = "success",
     ):
-        staged = StagedVersion(self.client, resource_id, stage_nr)
+        staged = StagedVersion(self.client, resource_id, stage_number)
         run_dynamic_tests(
             staged=staged,
             weight_format=weight_format or None,
             create_env_outcome=create_env_outcome,
         )
 
-    def await_review(self, resource_id: str, stage_nr: int):
-        staged = StagedVersion(self.client, resource_id, stage_nr)
+    def await_review(self, resource_id: str, stage_number: StageNumber):
+        staged = StagedVersion(self.client, resource_id, stage_number)
         staged.await_review()
 
-    def publish(self, resource_id: str, stage_nr: int):
-        staged = StagedVersion(self.client, resource_id, stage_nr)
+    def request_changes(self, resource_id: str, stage_number: StageNumber, reason: str):
+        staged = StagedVersion(self.client, resource_id, stage_number)
+        staged.request_changes(reason=reason)
+
+    def publish(self, resource_id: str, stage_number: StageNumber):
+        staged = StagedVersion(self.client, resource_id, stage_number)
         published = staged.publish()
         assert isinstance(published, PublishedVersion)
 

backoffice/backup.py

@@ -1,7 +1,7 @@
 from dotenv import load_dotenv
 from loguru import logger
 
-from backoffice.utils.s3_client import Client
+from backoffice.s3_client import Client
 
 _ = load_dotenv()