diff --git a/.github/scripts/upload_model_to_zenodo.py b/.github/scripts/upload_model_to_zenodo.py index eedede8..ff3d55d 100644 --- a/.github/scripts/upload_model_to_zenodo.py +++ b/.github/scripts/upload_model_to_zenodo.py @@ -13,11 +13,13 @@ import requests # type: ignore from loguru import logger # type: ignore import spdx_license_list # type: ignore -import yaml # type: ignore +from ruyaml import YAML # type: ignore from update_status import update_status from s3_client import create_client +yaml=YAML(typ='safe') + spdx_licenses = [item.id for item in spdx_license_list.LICENSES.values()] GOOD_STATUS_CODES = ( @@ -103,7 +105,7 @@ def main(): bucket_url = deposition_info["links"]["bucket"] rdf_text = client.load_file(Path(s3_path, "rdf.yaml")) - rdf = yaml.safe_load(rdf_text) + rdf = yaml.load(rdf_text) if not isinstance(rdf, dict): raise Exception('Failed to load rdf.yaml from S3') diff --git a/.github/workflows/ci_runner.yaml b/.github/workflows/ci_runner.yaml index 72c8578..c9095c7 100644 --- a/.github/workflows/ci_runner.yaml +++ b/.github/workflows/ci_runner.yaml @@ -35,7 +35,7 @@ jobs: run: | echo "Installing workflow script dependencies" python -m pip install --upgrade pip - python -m pip install "minio==7.2.3" "ruamel.yaml==0.18.5" "bioimageio.spec==0.4.9.post5" "typer" + python -m pip install "minio==7.2.3" "ruyaml==0.91.0" "bioimageio.spec==0.4.9.post5" "typer" - name: Unzip model file run: | python .github/scripts/update_status.py "${{ inputs.model_nickname }}" "Unzipping package" "1" "6" diff --git a/.github/workflows/publish.yaml b/.github/workflows/publish.yaml index 2530135..2496641 100644 --- a/.github/workflows/publish.yaml +++ b/.github/workflows/publish.yaml @@ -30,7 +30,7 @@ jobs: run: | echo "Installing workflow script dependencies" python -m pip install --upgrade pip - python -m pip install "minio==7.2.3" "loguru==0.7.2" "packaging==23.2" "spdx-license-list==3.22" "ruamel.yaml==0.18.5" "typer" + python -m pip install "minio==7.2.3" "loguru==0.7.2" "packaging==23.2" "spdx-license-list==3.22" "ruyaml==0.91.0" "typer" - name: Publish to Zenodo run: | python .github/scripts/update_status.py "${{ inputs.model_nickname }}" "Publishing to Zenodo" "5" "6"