remove pypi release action

.github/workflows/release_ci.yml

@@ -35,35 +35,4 @@ jobs:
           context: ./
           file: ./Dockerfile
           push: true
-          tags: "clinicalgenomics/arnold:${{github.event.release.tag_name}}, clinicalgenomics/arnold:latest"
-
-  build-n-publish:
-    name: Build and publish Python distribution to PyPI
-    runs-on: ubuntu-latest
-    steps:
-      - name: Check out git repository
-        uses: actions/checkout@v2
-
-      - name: Set up Python 3.8
-        uses: actions/setup-python@v2
-        with:
-          python-version: 3.8
-
-      - name: Install build tools
-        run: >-
-          python -m
-          pip install
-          wheel
-          twine
-          --user
-      - name: Build a binary wheel and a source tarball
-        run: >-
-          python
-          setup.py
-          sdist
-          bdist_wheel
-      - name: Publish distribution 📦 to PyPI
-        uses: pypa/gh-action-pypi-publish@release/v1
-        with:
-          user: __token__
-          password: ${{ secrets.pypi_password }}
+          tags: "clinicalgenomics/arnold:${{github.event.release.tag_name}}, clinicalgenomics/arnold:latest"

arnold/api/api_v1/endpoints/flow_cell.py

@@ -41,7 +41,8 @@ def create_flow_cell(
 ) -> JSONResponse:
     if find_flow_cell(flow_cell_id=flow_cell.flow_cell_id, adapter=adapter):
         return JSONResponse(
-            status_code=status.HTTP_405_METHOD_NOT_ALLOWED, content="flow_cell already in database"
+            status_code=status.HTTP_405_METHOD_NOT_ALLOWED,
+            content="flow_cell already in database",
         )
     try:
         create.create_flow_cell(adapter=adapter, flow_cell=flow_cell)
@@ -52,5 +53,6 @@ def create_flow_cell(
         )
 
     return JSONResponse(
-        status_code=status.HTTP_200_OK, content=f"flow_cell {flow_cell.flow_cell_id} inserted to db"
+        status_code=status.HTTP_200_OK,
+        content=f"flow_cell {flow_cell.flow_cell_id} inserted to db",
     )

arnold/api/api_v1/endpoints/plots.py

@@ -25,7 +25,11 @@ class ReceivedPlotModel(BaseModel):
     datapoints: List[ReceivedPlotDatapointsModel]
 
 
-@router.get("/received", response_model=List[ReceivedPlotModel], response_model_exclude_none=True)
+@router.get(
+    "/received",
+    response_model=List[ReceivedPlotModel],
+    response_model_exclude_none=True,
+)
 def received(
     adapter: ArnoldAdapter = Depends(get_arnold_adapter),
     date_min: Optional[dt.date] = dt.date.min,
@@ -53,7 +57,11 @@ def received(
             },
             {
                 "$group": {
-                    "_id": {"tag": "$tag", "year": "$received_year", "month": "$received_month"},
+                    "_id": {
+                        "tag": "$tag",
+                        "year": "$received_year",
+                        "month": "$received_month",
+                    },
                     "total": {"$sum": 1},
                 }
             },
@@ -96,7 +104,11 @@ def received(
     return list(samples)
 
 
-@router.get("/turnaround", response_model=List[ReceivedPlotModel], response_model_exclude_none=True)
+@router.get(
+    "/turnaround",
+    response_model=List[ReceivedPlotModel],
+    response_model_exclude_none=True,
+)
 def turnaround(
     adapter: ArnoldAdapter = Depends(get_arnold_adapter),
     date_min: Optional[dt.date] = dt.date.min,
@@ -124,7 +136,10 @@ def turnaround(
                     "received_month": {"$month": "$received_date"},
                     "priority": "$priority",
                     "turnaround_time": {
-                        "$divide": [{"$subtract": ["$delivery_date", "$received_date"]}, 86400000]
+                        "$divide": [
+                            {"$subtract": ["$delivery_date", "$received_date"]},
+                            86400000,
+                        ]
                     },
                 }
             },

arnold/api/api_v1/endpoints/sample.py

@@ -49,7 +49,8 @@ def create_sample(
 ) -> JSONResponse:
     if arnold.crud.read.sample.find_sample(sample_id=sample.sample_id, adapter=adapter):
         return JSONResponse(
-            status_code=status.HTTP_405_METHOD_NOT_ALLOWED, content="Sample already in database"
+            status_code=status.HTTP_405_METHOD_NOT_ALLOWED,
+            content="Sample already in database",
         )
     try:
         create.create_sample(adapter=adapter, sample=sample)
@@ -60,7 +61,8 @@ def create_sample(
         )
 
     return JSONResponse(
-        status_code=status.HTTP_200_OK, content=f"Sample {sample.sample_id} inserted to db"
+        status_code=status.HTTP_200_OK,
+        content=f"Sample {sample.sample_id} inserted to db",
     )
 
 
@@ -75,7 +77,9 @@ def create_samples(
             status_code=status.HTTP_405_METHOD_NOT_ALLOWED,
             content=f"exception {e} ",
         )
-    return JSONResponse(status_code=status.HTTP_200_OK, content="Samples inserted to db")
+    return JSONResponse(
+        status_code=status.HTTP_200_OK, content="Samples inserted to db"
+    )
 
 
 @router.put("/sample/")
@@ -92,7 +96,8 @@ def update_sample(
         )
 
     return JSONResponse(
-        status_code=status.HTTP_200_OK, content=f"Sample {sample.sample_id} inserted to db"
+        status_code=status.HTTP_200_OK,
+        content=f"Sample {sample.sample_id} inserted to db",
     )
 
 
@@ -108,4 +113,6 @@ def update_samples(
             status_code=status.HTTP_405_METHOD_NOT_ALLOWED,
             content=f"exception {e} ",
         )
-    return JSONResponse(status_code=status.HTTP_200_OK, content="Samples inserted to db")
+    return JSONResponse(
+        status_code=status.HTTP_200_OK, content="Samples inserted to db"
+    )

arnold/api/api_v1/endpoints/step.py

@@ -17,7 +17,12 @@
 from arnold.models.database.step import Step
 import logging
 
-from arnold.models.api_models import WorkflowResponce, StepFilters, StepFiltersBase, Pagination
+from arnold.models.api_models import (
+    WorkflowResponce,
+    StepFilters,
+    StepFiltersBase,
+    Pagination,
+)
 from arnold.settings import get_arnold_adapter
 import arnold.crud.read.step
 
@@ -87,10 +92,13 @@ def get_steps(
 
 
 @router.post("/step/")
-def create_step(step: Step, adapter: ArnoldAdapter = Depends(get_arnold_adapter)) -> JSONResponse:
+def create_step(
+    step: Step, adapter: ArnoldAdapter = Depends(get_arnold_adapter)
+) -> JSONResponse:
     if arnold.crud.read.step.find_step(step_id=step.step_id, adapter=adapter):
         return JSONResponse(
-            status_code=status.HTTP_405_METHOD_NOT_ALLOWED, content="step already in database"
+            status_code=status.HTTP_405_METHOD_NOT_ALLOWED,
+            content="step already in database",
         )
     try:
         create.create_step(adapter=adapter, step=step)
@@ -120,7 +128,9 @@ def create_steps(
 
 
 @router.put("/step/")
-def update_step(step: Step, adapter: ArnoldAdapter = Depends(get_arnold_adapter)) -> JSONResponse:
+def update_step(
+    step: Step, adapter: ArnoldAdapter = Depends(get_arnold_adapter)
+) -> JSONResponse:
 
     try:
         update.update_step(adapter=adapter, step=step)

arnold/api/api_v1/endpoints/trends.py

@@ -41,7 +41,12 @@ def get_dynamic_udfs_over_time(
 ):
     """Endpoint for trending step udf fields over time. Possible to group by sample fields"""
     return trend_step_fields(
-        adapter=adapter, step_type=step_type, workflow=workflow, field=field, group=group, year=year
+        adapter=adapter,
+        step_type=step_type,
+        workflow=workflow,
+        field=field,
+        group=group,
+        year=year,
     )
 
 

arnold/commands/base.py

@@ -25,7 +25,9 @@ def cli(context: click.Context):
 
 
 @cli.command(name="serve")
-@click.option("--version", default="v1", type=click.Choice(["v1", "v2"]), show_default=True)
+@click.option(
+    "--version", default="v1", type=click.Choice(["v1", "v2"]), show_default=True
+)
 @click.option("--reload", is_flag=True)
 def serve_command(reload: bool, version: str):
     """Serve the arnold app for testing purpose."""

arnold/crud/read/flow_cell.py

@@ -9,7 +9,9 @@
 def find_flow_cell(adapter: ArnoldAdapter, flow_cell_id: str) -> Optional[FlowCell]:
     """Find one flow_cell from the flow_cell collection"""
 
-    raw_flow_cell = adapter.flow_cell_collection.find_one({"flow_cell_id": flow_cell_id})
+    raw_flow_cell = adapter.flow_cell_collection.find_one(
+        {"flow_cell_id": flow_cell_id}
+    )
     if not raw_flow_cell:
         return None
     return FlowCell(**raw_flow_cell)

arnold/crud/read/plot/format_plot_data.py

@@ -23,6 +23,10 @@ def format_grouped_plot_data(plot_data: list, group_field, trend_field):
             grouped_plottdata[group][trend_field].append(trend_value)
             grouped_plottdata[group]["month"].append(month)
             continue
-        grouped_plottdata[group] = {trend_field: [trend_value], "month": [month], "group": group}
+        grouped_plottdata[group] = {
+            trend_field: [trend_value],
+            "month": [month],
+            "group": group,
+        }
 
     return [value for group, value in grouped_plottdata.items()]

arnold/crud/read/plot/trend_nr_recieved_samples.py

@@ -1,7 +1,10 @@
 from typing import Optional
 
 from arnold.adapter import ArnoldAdapter
-from arnold.crud.read.plot.format_plot_data import format_grouped_plot_data, format_plot_data
+from arnold.crud.read.plot.format_plot_data import (
+    format_grouped_plot_data,
+    format_plot_data,
+)
 
 
 def trend_nr_samples_per_month(
@@ -37,7 +40,9 @@ def trend_nr_samples_per_month(
     pipe = [match, project, match_year, group_by]
     data = list(adapter.sample_collection.aggregate(pipe))
     return (
-        format_grouped_plot_data(plot_data=data, group_field=group, trend_field="nr_samples")
+        format_grouped_plot_data(
+            plot_data=data, group_field=group, trend_field="nr_samples"
+        )
         if group
         else format_plot_data(plot_data=data, trend_field="nr_samples")
     )

arnold/crud/read/plot/trend_step_fields.py

@@ -1,7 +1,10 @@
 from typing import Optional
 
 from arnold.adapter import ArnoldAdapter
-from arnold.crud.read.plot.format_plot_data import format_grouped_plot_data, format_plot_data
+from arnold.crud.read.plot.format_plot_data import (
+    format_grouped_plot_data,
+    format_plot_data,
+)
 
 
 def trend_step_fields(
@@ -46,7 +49,9 @@ def trend_step_fields(
         }
     }
     add_average = {
-        "$addFields": {f"average_{field_replaced_dot}": {"$avg": f"${field_replaced_dot}"}}
+        "$addFields": {
+            f"average_{field_replaced_dot}": {"$avg": f"${field_replaced_dot}"}
+        }
     }
 
     if group:
@@ -59,8 +64,12 @@ def trend_step_fields(
     data = list(adapter.step_collection.aggregate(pipe))
     return (
         format_grouped_plot_data(
-            plot_data=data, group_field=group, trend_field=f"average_{field_replaced_dot}"
+            plot_data=data,
+            group_field=group,
+            trend_field=f"average_{field_replaced_dot}",
         )
         if group
-        else format_plot_data(plot_data=data, trend_field=f"average_{field_replaced_dot}")
+        else format_plot_data(
+            plot_data=data, trend_field=f"average_{field_replaced_dot}"
+        )
     )

arnold/crud/read/plot/trend_turn_around_times.py

@@ -1,7 +1,10 @@
 from typing import Optional
 
 from arnold.adapter import ArnoldAdapter
-from arnold.crud.read.plot.format_plot_data import format_grouped_plot_data, format_plot_data
+from arnold.crud.read.plot.format_plot_data import (
+    format_grouped_plot_data,
+    format_plot_data,
+)
 
 
 def trend_turn_around_times(

arnold/crud/read/step.py

@@ -40,7 +40,11 @@ def join_udf_rules(udf_filters: Optional[list[UDFFilter]]) -> list:
             except:
                 pass
         udf_queries.append(
-            {f"{udf_filter.udf_type}_udfs.{udf_filter.udf_name}": {udf_filter.udf_rule: udf_value}}
+            {
+                f"{udf_filter.udf_type}_udfs.{udf_filter.udf_name}": {
+                    udf_filter.udf_rule: udf_value
+                }
+            }
         )
     return udf_queries
 
@@ -114,7 +118,9 @@ def find_step_type_artifact_udfs(
 ) -> List[ArtifactUDF]:
     """Getting available artifact udfs from specific step type within specific workflow"""
 
-    pipe = find_step_type_udfs_pipe(workflow=workflow, step_type=step_type, udf_from="artifact")
+    pipe = find_step_type_udfs_pipe(
+        workflow=workflow, step_type=step_type, udf_from="artifact"
+    )
     try:
         aggregation_result = list(adapter.step_collection.aggregate(pipe))
         return parse_obj_as(List[ArtifactUDF], aggregation_result[0].get("all_udfs"))
@@ -127,7 +133,9 @@ def find_step_type_process_udfs(
 ) -> List[ProcessUDF]:
     """Getting available artifact udfs from specific step type within specific workflow"""
 
-    pipe = find_step_type_udfs_pipe(workflow=workflow, step_type=step_type, udf_from="process")
+    pipe = find_step_type_udfs_pipe(
+        workflow=workflow, step_type=step_type, udf_from="process"
+    )
     try:
         aggregation_result = list(adapter.step_collection.aggregate(pipe))
         return parse_obj_as(List[ProcessUDF], aggregation_result[0].get("all_udfs"))

arnold/crud/update.py

@@ -34,7 +34,9 @@ def update_step(adapter: ArnoldAdapter, step: Step) -> str:
 
     step_id = step.step_id
     result: UpdateResult = adapter.step_collection.update_one(
-        {"_id": step_id}, {"$set": step.dict(by_alias=True, exclude_none=True)}, upsert=True
+        {"_id": step_id},
+        {"$set": step.dict(by_alias=True, exclude_none=True)},
+        upsert=True,
     )
     if result.raw_result.get("updatedExisting"):
         LOG.info("Updated step %s", step_id)

tests/api/test_post_sample.py

@@ -39,7 +39,9 @@ def test_post_sample_already_in_db(mocker, fast_app_client, valid_sample):
 def test_post_sample_create_sample_failing(mocker, fast_app_client, valid_sample):
     # GIVEN that the sample is not in the database but the create_sample fails
     mocker.patch("arnold.crud.read.sample.find_sample", return_value=False)
-    mocker.patch("arnold.crud.create.create_sample", side_effect=Exception("mocked error"))
+    mocker.patch(
+        "arnold.crud.create.create_sample", side_effect=Exception("mocked error")
+    )
 
     # WHEN running the sample request with data
     response = fast_app_client.post("/api/v1/sample/", json=valid_sample.dict())
@@ -69,7 +71,9 @@ def test_post_invalid_samples(fast_app_client, invalid_samples):
 
 def test_post_sample_create_samples_failing(mocker, fast_app_client, valid_samples):
     # GIVEN that the create_samples fails
-    mocker.patch("arnold.crud.create.create_samples", side_effect=Exception("mocked error"))
+    mocker.patch(
+        "arnold.crud.create.create_samples", side_effect=Exception("mocked error")
+    )
 
     # WHEN running the samples request with data
     response = fast_app_client.post("/api/v1/samples/", json=valid_samples)

tests/api/test_post_step.py

@@ -39,7 +39,9 @@ def test_post_step_already_in_db(mocker, fast_app_client, valid_step):
 def test_post_step_create_step_failing(mocker, fast_app_client, valid_step):
     # GIVEN that the step is not in the database but the create_step fails
     mocker.patch("arnold.crud.read.step.find_step", return_value=False)
-    mocker.patch("arnold.crud.create.create_step", side_effect=Exception("mocked error"))
+    mocker.patch(
+        "arnold.crud.create.create_step", side_effect=Exception("mocked error")
+    )
 
     # WHEN running the step request with data
     response = fast_app_client.post("/api/v1/step/", json=valid_step.dict())