Upgrade cirro_api_client (#187)

* upgrade api client

* type -> type_

* remove mypy

Author: nathanthorpe

.github/workflows/lint.yml

@@ -15,30 +15,30 @@ jobs:
       contents: read
     strategy:
       matrix:
-        python-version: [ "3.9", "3.10", "3.11", "3.12" ]
+        python-version: [ "3.10", "3.11", "3.12", "3.13", "3.14" ]
 
     steps:
       # For SonarCloud scan
       - uses: actions/checkout@v4
-        if: matrix.python-version == '3.12'
+        if: matrix.python-version == '3.14'
         with:
           fetch-depth: 0
 
       - uses: actions/checkout@v4
-        if: matrix.python-version != '3.12'
+        if: matrix.python-version != '3.14'
 
       - name: Set up Python ${{ matrix.python-version }}
         uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
-      
+
       # for nextflow
       - name: Set up Java Runtime Environment
         uses: actions/setup-java@v4
         with:
           java-version: '21'
           distribution: 'temurin'
-      
+
       - name: Install Nextflow 25.04.2 (standalone)
         run: |
           curl -sL https://github.com/nextflow-io/nextflow/releases/download/v25.04.2/nextflow-25.04.2-dist -o nextflow
@@ -62,7 +62,7 @@ jobs:
 
       - name: SonarCloud Scan
         uses: sonarsource/sonarcloud-github-action@master
-        if: matrix.python-version == '3.12'  # Only run once
+        if: matrix.python-version == '3.14'  # Only run once
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-          SONAR_TOKEN: ${{ secrets.SONAR_TOKEN }}
+          SONAR_TOKEN: ${{ secrets.SONAR_TOKEN }}

.github/workflows/package.yml

@@ -20,10 +20,10 @@ jobs:
     steps:
       - uses: actions/checkout@v2
 
-      - name: Set up Python 3.12
+      - name: Set up Python 3.14
         uses: actions/setup-python@v2
         with:
-          python-version: "3.12"
+          python-version: "3.14"
 
       - name: Install deps
         run: |

cirro/sdk/project.py

@@ -134,7 +134,7 @@ def list_references(self, reference_type: str = None) -> DataPortalReferences:
                 for ref in self._client.references.get_for_project(
                     self.id
                 )
-                if reference_type is None or ref.type == reference_type
+                if reference_type is None or ref.type_ == reference_type
             ]
         )
 

cirro/sdk/reference.py

@@ -40,7 +40,7 @@ def name(self) -> str:
     @property
     def type(self) -> str:
         """Type of reference data (e.g. genome_fasta)"""
-        return self._data.type
+        return self._data.type_
 
     @property
     def absolute_path(self):

cirro/services/dataset.py

@@ -227,7 +227,7 @@ def get_assets_listing(self, project_id: str, dataset_id: str, file_limit: int =
         ]
         artifacts = [
             Artifact(
-                artifact_type=a.type,
+                artifact_type=a.type_,
                 file=File.from_file_entry(
                     FileEntry(a.path),
                     project_id=project_id,

poetry.lock

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "cirro"
-version = "1.9.5"
+version = "1.10.0"
 description = "CLI tool and SDK for interacting with the Cirro platform"
 authors = ["Cirro Bio <support@cirro.bio>"]
 license = "MIT"
@@ -11,7 +11,7 @@ packages = [{include = "cirro"}]
 [tool.poetry.dependencies]
 python = ">3.10.0,<4.0"
 attrs = ">=21.3.0"
-cirro_api_client = "1.2.2"
+cirro_api_client = "~1.3.0"
 click = "^8.1.3"
 boto3 = "~=1.41"
 questionary = "^2.0.1"