haplohub-cli 2.1.0__tar.gz → 2.3.0__tar.gz

{haplohub_cli-2.1.0 → haplohub_cli-2.3.0}/.github/workflows/on_pr.yml

@@ -13,15 +13,15 @@ jobs:
         python-version: ["3.8", "3.9", "3.10", "3.11", "3.12"]
 
     steps:
-      - uses: actions/checkout@v4
-      - uses: astral-sh/setup-uv@v5
+      - uses: actions/checkout@v6
+      - uses: astral-sh/setup-uv@v7
         with:
           python-version: ${{ matrix.python-version }}
       - name: Install dependencies
         run: uv sync --dev --no-sources
       - name: Lint and format with ruff
         run: |
-          ruff format --check .
-          ruff check .
+          uv run --no-sync ruff format --check .
+          uv run --no-sync ruff check .
       - name: Run tests
-        run: uv run pytest -v
+        run: uv run --no-sync pytest -v

{haplohub_cli-2.1.0 → haplohub_cli-2.3.0}/.github/workflows/on_push_main.yml

@@ -15,7 +15,7 @@ jobs:
     name: Build python package
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v6
         with:
           fetch-depth: 0
       - uses: hynek/build-and-inspect-python-package@v2
@@ -29,7 +29,7 @@ jobs:
     needs: build
     environment: testpypi
     steps:
-      - uses: actions/download-artifact@v4
+      - uses: actions/download-artifact@v8
         with:
           name: Packages
           path: dist
@@ -46,7 +46,7 @@ jobs:
     needs: build
     environment: pypi
     steps:
-      - uses: actions/download-artifact@v4
+      - uses: actions/download-artifact@v8
         with:
           name: Packages
           path: dist
@@ -60,12 +60,12 @@ jobs:
     runs-on: ubuntu-latest
     needs: publish-pypi
     steps:
-      - uses: actions/download-artifact@v4
+      - uses: actions/download-artifact@v8
         with:
           name: Packages
           path: dist
       - name: Sign the dists with Sigstore
-        uses: sigstore/gh-action-sigstore-python@v3.0.0
+        uses: sigstore/gh-action-sigstore-python@v3.3.0
         with:
           inputs: >-
             ./dist/*.tar.gz

{haplohub_cli-2.1.0 → haplohub_cli-2.3.0}/PKG-INFO

@@ -1,12 +1,12 @@
 Metadata-Version: 2.4
 Name: haplohub-cli
-Version: 2.1.0
+Version: 2.3.0
 Summary: HaploHub Command Line Interface
 Author-email: Mike Polcari <mike@haplotype-labs.com>, Ilya Khrustalev <ilya@haplotype-labs.com>
 Requires-Python: >=3.8
 Description-Content-Type: text/markdown
 Requires-Dist: click>=8.1.8
-Requires-Dist: haplohub>=2.1.0
+Requires-Dist: haplohub<3,>=2.2.0
 Requires-Dist: pendulum>=3.0.0
 Requires-Dist: requests>=2.32.0
 Requires-Dist: rich>=13.9.4

{haplohub_cli-2.1.0 → haplohub_cli-2.3.0}/haplohub_cli/_version.py

@@ -18,7 +18,7 @@ version_tuple: tuple[int | str, ...]
 commit_id: str | None
 __commit_id__: str | None
 
-__version__ = version = '2.1.0'
-__version_tuple__ = version_tuple = (2, 1, 0)
+__version__ = version = '2.3.0'
+__version_tuple__ = version_tuple = (2, 3, 0)
 
-__commit_id__ = commit_id = 'gf67752052'
+__commit_id__ = commit_id = 'g6d8dda047'

{haplohub_cli-2.1.0 → haplohub_cli-2.3.0}/haplohub_cli/commands/algorithm/result/__init__.py

@@ -31,26 +31,39 @@ def get(id):
 
 
 @result.command()
-@click.option("--algorithm-version", "-a", type=types.HAPLOHUB_ID, required=True, help="The ID of the algorithm version")
+@click.option("--algorithm", "-a", type=str, required=True, help="The algorithm name (e.g. pgsc_calc)")
+@click.option("--version", "-v", type=str, required=False, help="The algorithm version (defaults to the latest)")
 @click.option("--cohort", "-c", type=types.HAPLOHUB_ID, required=True, help="The ID of the cohort")
+@click.option("--member", "-m", type=types.HAPLOHUB_ID, required=False, help="The member id (its latest sample is scored)")
+@click.option("--sample", "-s", type=types.HAPLOHUB_ID, required=False, help="The sample id to run on")
 @click.option("--input-json", "-i", type=types.FILE_PATH, required=False, help="The input JSON")
 @click.option("--input-file", "-f", type=types.FILE_PATH, required=False, help="The input file")
-def create(algorithm_version: str, cohort: str, input_json: Optional[str] = None, input_file: Optional[str] = None):
-    if input_json is None and input_file is None:
-        raise click.ClickException("Either --input-json or --input-file must be provided")
-
+def create(
+    algorithm: str,
+    cohort: str,
+    version: Optional[str] = None,
+    member: Optional[str] = None,
+    sample: Optional[str] = None,
+    input_json: Optional[str] = None,
+    input_file: Optional[str] = None,
+):
     if input_json is not None and input_file is not None:
         raise click.ClickException("Only one of --input-json or --input-file can be provided")
 
     if input_json is not None:
         input_data = json.loads(input_json)
-    else:
+    elif input_file is not None:
         with open(input_file, "r") as f:
             input_data = json.load(f)
+    else:
+        input_data = {}
 
     request = CreateAlgorithmResultRequest(
-        algorithm_version_id=algorithm_version,
+        algorithm=algorithm,
+        version=version,
         cohort_id=cohort,
+        member_id=member,
+        sample_id=sample,
         input=input_data,
     )
 

{haplohub_cli-2.1.0 → haplohub_cli-2.3.0}/haplohub_cli/formatters/sample.py

@@ -13,10 +13,10 @@ from haplohub_cli.formatters.decorators import register
 def format_sample(data: SampleSchema):
     table = Table(title="Sample", caption=f"Id: {utils.format_id(data.id)}")
     table.add_column("Id")
-    table.add_column("Sample ID")
+    table.add_column("External ID")
     table.add_column("Member ID")
     table.add_column("Created")
-    table.add_row(utils.format_id(data.id), data.sample_id, utils.format_id(data.member_id), utils.format_dt(data.created))
+    table.add_row(utils.format_id(data.id), data.external_id, utils.format_id(data.member_id), utils.format_dt(data.created))
     return table
 
 
@@ -24,12 +24,14 @@ def format_sample(data: SampleSchema):
 def format_samples(data: PaginatedResponseSampleSchema):
     table = Table(title="Samples", caption=f"Total: {data.total_count}")
     table.add_column("Id")
-    table.add_column("Sample ID")
+    table.add_column("External ID")
     table.add_column("Member ID")
     table.add_column("Created")
 
     for item in data.items:
-        table.add_row(utils.format_id(item.id), item.sample_id, utils.format_id(item.member_id), utils.format_dt(item.created))
+        table.add_row(
+            utils.format_id(item.id), item.external_id, utils.format_id(item.member_id), utils.format_dt(item.created)
+        )
 
     return table
 

{haplohub_cli-2.1.0 → haplohub_cli-2.3.0}/haplohub_cli.egg-info/PKG-INFO

@@ -1,12 +1,12 @@
 Metadata-Version: 2.4
 Name: haplohub-cli
-Version: 2.1.0
+Version: 2.3.0
 Summary: HaploHub Command Line Interface
 Author-email: Mike Polcari <mike@haplotype-labs.com>, Ilya Khrustalev <ilya@haplotype-labs.com>
 Requires-Python: >=3.8
 Description-Content-Type: text/markdown
 Requires-Dist: click>=8.1.8
-Requires-Dist: haplohub>=2.1.0
+Requires-Dist: haplohub<3,>=2.2.0
 Requires-Dist: pendulum>=3.0.0
 Requires-Dist: requests>=2.32.0
 Requires-Dist: rich>=13.9.4

{haplohub_cli-2.1.0 → haplohub_cli-2.3.0}/haplohub_cli.egg-info/requires.txt

@@ -1,5 +1,5 @@
 click>=8.1.8
-haplohub>=2.1.0
+haplohub<3,>=2.2.0
 pendulum>=3.0.0
 requests>=2.32.0
 rich>=13.9.4

{haplohub_cli-2.1.0 → haplohub_cli-2.3.0}/pyproject.toml

@@ -10,7 +10,7 @@ requires-python = ">=3.8"
 dynamic = ["version"]
 dependencies = [
     "click>=8.1.8",
-    "haplohub>=2.1.0",
+    "haplohub>=2.2.0,<3",
     "pendulum>=3.0.0",
     "requests>=2.32.0",
     "rich>=13.9.4",