Merge pull request #42 from bioimage-io/replace-pyaml-with-ruyaml

fix: switched from pyyaml and ruamel to ruyaml, fixes #38

.github/scripts/upload_model_to_zenodo.py

@@ -10,15 +10,15 @@
 
 import requests  # type: ignore
 import spdx_license_list  # type: ignore
+
 from loguru import logger  # type: ignore
 from packaging.version import parse as parse_version
-from ruamel.yaml import YAML
+from ruyaml import YAML  # type: ignore
 from s3_client import create_client
 from update_status import update_status
 
 yaml = YAML(typ="safe")
 
-
 spdx_licenses = [item.id for item in spdx_license_list.LICENSES.values()]
 
 GOOD_STATUS_CODES = (

.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.resource_path }}" "Unzip and upload to ${{env.S3_HOST}}/${{env.S3_BUCKET}}/${{env.S3_FOLDER}}/${{inputs.resource_path}}/files" "1"

.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.resource_path }}" "Publishing to Zenodo" "5"