write scripts as backoffice package

.github/workflows/test.yaml

@@ -1,4 +1,4 @@
-name: test stage call
+name: test and build docs
 
 on: push
 

README.md

@@ -1,2 +1,3 @@
 # collection
+
 Maintains the resources displayed on bioimage.io (Successor to collection-bioimage-io)

backoffice/VERSION

@@ -0,0 +1,3 @@
+{
+    "version": "0.1.0"
+}

backoffice/__main__.py

@@ -0,0 +1,55 @@
+import os
+from typing import Literal, Optional
+
+import fire
+from bioimageio.spec.model.v0_5 import WeightsFormat
+from dotenv import load_dotenv
+
+from .backup import backup
+from .run_dynamic_tests import run_dynamic_tests
+from .utils.remote_resource import PublishedVersion, RemoteResource, StagedVersion
+from .utils.s3_client import Client
+from .validate_format import validate_format
+
+_ = load_dotenv()
+
+
+class BackOffice:
+    def __init__(self) -> None:
+        super().__init__()
+        self.client = Client()
+
+    def stage(self, resource_id: str, package_url: str):
+        resource = RemoteResource(client=Client(), id=resource_id)
+        staged = resource.stage_new_version(package_url)
+        validate_format(staged)
+
+    def test(
+        self,
+        resource_id: str,
+        version: int,
+        weight_format: Optional[WeightsFormat] = None,
+        create_env_outcome: Literal["success", ""] = "success",
+    ):
+        staged = StagedVersion(self.client, resource_id, version)
+        run_dynamic_tests(
+            staged=staged,
+            weight_format=weight_format,
+            create_env_outcome=create_env_outcome,
+        )
+
+    def await_review(self, resource_id: str, version: int):
+        staged = StagedVersion(self.client, resource_id, version)
+        staged.await_review()
+
+    def publish(self, resource_id: str, stage_nr: int):
+        staged = StagedVersion(client=self.client, id=resource_id, version=stage_nr)
+        published = staged.publish()
+        assert isinstance(published, PublishedVersion)
+
+    def backup(self):
+        _ = backup(self.client, os.environ["ZENODO_URL"])
+
+
+if __name__ == "__main__":
+    fire.Fire(BackOffice)

scripts/backup.py → backoffice/backup.py

@@ -1,25 +1,19 @@
 import os
 
-import typer
 from dotenv import load_dotenv
 from loguru import logger
-from utils.s3_client import Client
+
+from backoffice.utils.s3_client import Client
 
 _ = load_dotenv()
 
 
-def backup():
+def backup(client: Client, destination: str):
     """backup collection
 
     Returns:
         list of folders and file names backed up
     """
-    client = Client()
     content_to_backup = list(client.ls(""))
-    destination = os.environ["ZENODO_URL"]
-    logger.error("Backup to '{}': {}", destination, content_to_backup)
+    logger.error("Not implemented: Backup to '{}': {}", destination, content_to_backup)
     return content_to_backup
-
-
-if __name__ == "__main__":
-    typer.run(backup)

scripts/run_dynamic_tests.py → backoffice/run_dynamic_tests.py

@@ -5,7 +5,6 @@
 
 import bioimageio.core
 import bioimageio.spec
-import typer
 from bioimageio.spec.model.v0_5 import WeightsFormat
 from bioimageio.spec.summary import (
     ErrorEntry,
@@ -14,8 +13,8 @@
     ValidationSummary,
 )
 from ruyaml import YAML
-from utils.remote_resource import StagedVersion
-from utils.s3_client import Client
+
+from backoffice.utils.remote_resource import StagedVersion
 
 try:
     from tqdm import tqdm
@@ -44,14 +43,10 @@ def get_summary_detail_from_exception(name: str, exception: Exception):
 
 
 def run_dynamic_tests(
-    resource_id: str,
-    version: int,
-    weight_format: Optional[WeightsFormat] = typer.Argument(
-        ..., help="weight format to test model with."
-    ),
-    create_env_outcome: str = "success",
+    staged: StagedVersion,
+    weight_format: Optional[WeightsFormat],  # "weight format to test model with."
+    create_env_outcome: str,
 ):
-    staged = StagedVersion(client=Client(), id=resource_id, version=version)
     staged.set_status(
         "testing",
         "Testing" + ("" if weight_format is None else f" {weight_format} weights"),
@@ -124,7 +119,3 @@ def run_dynamic_tests(
         )
 
     staged.add_log_entry("bioimageio.core", summary.model_dump(mode="json"))
-
-
-if __name__ == "__main__":
-    typer.run(run_dynamic_tests)

scripts/upload_model_to_zenodo.py → backoffice/upload_model_to_zenodo.py

@@ -15,7 +15,7 @@
 from packaging.version import parse as parse_version
 from ruyaml import YAML
 
-# from utils.s3_client import create_client, version_from_resource_path_or_s3
+# from backoffice.utils.s3_client import create_client, version_from_resource_path_or_s3
 
 yaml = YAML(typ="safe")
 

scripts/utils/remote_resource.py → backoffice/utils/remote_resource.py

@@ -184,6 +184,12 @@ def _set_log(self, log: Log) -> None:
 class StagedVersion(_RemoteResourceVersion):
     version_prefix: ClassVar[str] = "staged/"
 
+    def await_review(self):
+        self.set_status(
+            "awaiting review",
+            description="Thank you for your contribution! Our bioimage.io maintainers will take a look soon.",
+        )
+
     def publish(self) -> PublishedVersion:
         # get next version and update versions.json
         versions_path = f"{self.id}/versions.json"

scripts/utils/validate_format.py → backoffice/validate_format.py

@@ -11,7 +11,7 @@
 from packaging.version import Version
 from ruyaml import YAML
 
-from .remote_resource import StagedVersion
+from backoffice.utils.remote_resource import StagedVersion
 
 yaml = YAML(typ="safe")
 

pyproject.toml

@@ -2,7 +2,7 @@
 target-version = ["py312"]
 
 [tool.pyright]
-include = ["scripts"]
+include = ["backoffice", "tests"]
 pythonPlatform = "All"
 pythonVersion = "3.12"
 reportIncompatibleMethodOverride = true
@@ -20,4 +20,4 @@ useLibraryCodeForTypes = true
 
 [tool.pytest.ini_options]
 addopts = "--capture=no --doctest-modules --failed-first"
-testpaths = ["scripts", "tests"]
+testpaths = ["backoffice", "tests"]

setup.py

@@ -0,0 +1,50 @@
+import json
+from pathlib import Path
+
+from setuptools import find_packages, setup
+
+# Get the long description from the README file
+ROOT_DIR = Path(__file__).parent.resolve()
+long_description = (ROOT_DIR / "README.md").read_text(encoding="utf-8")
+VERSION_FILE = ROOT_DIR / "backoffice" / "VERSION"
+VERSION = json.loads(VERSION_FILE.read_text(encoding="utf-8"))["version"]
+
+
+setup(
+    name="backoffice",
+    version=VERSION,
+    description="backoffice to control bioimage.io collection",
+    long_description=long_description,
+    long_description_content_type="text/markdown",
+    url="https://github.com/bioimage-io/collection",
+    author="bioimage.io Team",
+    classifiers=[
+        "Development Status :: 3 - Alpha",
+        "Intended Audience :: Developers",
+        "Programming Language :: Python :: 3.12",
+    ],
+    packages=find_packages(exclude=["tests"]),
+    install_requires=[
+        "bioimageio.core @ git+https://github.com/bioimage-io/core-bioimage-io-python@3a7875b5debc2d52b2fc87f6579afe217e1c7280",  # TODO: change to released version
+        "bioimageio.spec @ git+https://github.com/bioimage-io/spec-bioimage-io@19105665ad779014e03c7b311c0b4003ab08f752",  # TODO: change to released version
+        "fire",
+        "loguru",
+        "minio==7.2.3",
+        "ruyaml",
+        "tqdm",
+    ],
+    extras_require={
+        "dev": [
+            "black",
+            "pdoc",
+            "pre-commit",
+            "pyright",
+            "pytest",
+        ]
+    },
+    entry_points={"console_scripts": ["backoffice = backoffice.__main__"]},
+    project_urls={
+        "Bug Reports": "https://github.com/bioimage-io/collection/issues",
+        "Source": "https://github.com/bioimage-io/collection",
+    },
+)

tests/test_scripts/test_utils/test_remote_resource.py → tests/test_utils/test_remote_resource.py

@@ -1,19 +1,17 @@
-from typing import TYPE_CHECKING
+import os
 
-if TYPE_CHECKING:
-    from scripts.utils.s3_client import Client
+from backoffice.backup import backup
+from backoffice.utils.remote_resource import (
+    PublishedVersion,
+    RemoteResource,
+    StagedVersion,
+)
+from backoffice.utils.s3_client import Client
 
 
 def test_lifecycle(
-    client: "Client", package_url: str, package_id: str, s3_test_folder_url: str
+    client: Client, package_url: str, package_id: str, s3_test_folder_url: str
 ):
-    from scripts.backup import backup
-    from scripts.utils.remote_resource import (
-        PublishedVersion,
-        RemoteResource,
-        StagedVersion,
-    )
-
     resource = RemoteResource(client=client, id=package_id)
     staged = resource.stage_new_version(package_url)
     assert isinstance(staged, StagedVersion)
@@ -29,5 +27,5 @@ def test_lifecycle(
         published_rdf_url == f"{s3_test_folder_url}frank-water-buffalo/1/files/rdf.yaml"
     )
 
-    backed_up = backup()
+    backed_up = backup(client, os.environ["ZENODO_TEST"])
     assert backed_up == ["frank-water-buffalo"]

tests/test_scripts/test_utils/test_s3client.py → tests/test_utils/test_s3client.py

@@ -1,10 +1,7 @@
-from typing import TYPE_CHECKING
+from backoffice.utils.s3_client import Client
 
-if TYPE_CHECKING:
-    from scripts.utils.s3_client import Client
 
-
-def test_client(client: "Client"):
+def test_client(client: Client):
     assert client.prefix.startswith("sandbox")
     client.put_json("test/test1.json", "test")
     client.put_json("test/dir/test2.json", "test")