Merge branch 'main' into careamics-ci-script

bioimage-io · Nov 20, 2024 · 88a3285 · 88a3285
2 parents cd73ea8 + bf77257
commit 88a3285
Show file tree

Hide file tree

Showing 16 changed files with 74 additions and 337 deletions.
diff --git a/.github/workflows/request_changes_call.yaml b/.github/workflows/request_changes_call.yaml
@@ -30,7 +30,7 @@ jobs:
     steps:
       - name: reject reviewer id
         run: exit 1
-        if: (github.actor != 'bioimageiobot') && (format('github|{0}', github.actor_id)  != inputs.reviewer)
+        if: (github.actor != 'bioimageiobot') && (format('github|{0}', github.actor_id) != inputs.reviewer)
       - uses: actions/checkout@v4
       - uses: actions/setup-python@v5
         with:

diff --git a/bioimageio_collection_backoffice/__init__.py b/bioimageio_collection_backoffice/__init__.py
@@ -2,4 +2,6 @@
 .. include:: ../README.md
 """
 
-from ._backoffice import BackOffice as BackOffice
+from ._backoffice import BackOffice
+
+__all__ = ["BackOffice"]
diff --git a/bioimageio_collection_backoffice/_settings.py b/bioimageio_collection_backoffice/_settings.py
@@ -16,6 +16,9 @@ class Settings(BaseSettings, extra="ignore"):
     )
 
     github_output: Optional[str] = None
+    github_step_summary: Optional[str] = None
+    """see https://docs.github.com/en/actions/writing-workflows/choosing-what-your-workflow-does/workflow-commands-for-github-actions#adding-a-job-summary"""
+
     collection_config: str = (
         "https://raw.githubusercontent.com/bioimage-io/collection/main/bioimageio_collection_config.json"
     )

diff --git a/bioimageio_collection_backoffice/backup.py b/bioimageio_collection_backoffice/backup.py
@@ -16,15 +16,12 @@
 from bioimageio.spec.common import HttpUrl, RelativeFilePath
 from bioimageio.spec.utils import download
 from loguru import logger
-from ruyaml import YAML
 
 from ._settings import settings
 from .remote_collection import Record, RemoteCollection
 from .requests_utils import put_file, raise_for_status_discretely
 from .s3_client import Client
 
-yaml = YAML(typ="safe")
-
 
 class SkipForNow(NotImplementedError):
     pass

diff --git a/bioimageio_collection_backoffice/common.py b/bioimageio_collection_backoffice/common.py
@@ -1,4 +1,7 @@
 import pydantic
+from ruyaml import YAML
+
+yaml = YAML(typ="safe")
 
 
 class Node(

diff --git a/bioimageio_collection_backoffice/conda_env.py b/bioimageio_collection_backoffice/conda_env.py
diff --git a/bioimageio_collection_backoffice/db_structure/version_info.py b/bioimageio_collection_backoffice/db_structure/version_info.py
@@ -41,7 +41,7 @@ class UnpackingStatus(_DraftStatusBase, frozen=True):
 
 class UnpackedStatus(_DraftStatusBase, frozen=True):
     name: Literal["unpacked"] = "unpacked"
-    description: str = "staging was successful; awaiting automated tests to start ⏳"
+    description: str = "staging was successful; awaiting automated tests to start"
     step: Literal[2] = 2
     icon: str = "⏳"