Merge pull request #1 from Ganymede-Bio/add-staging-prod-gh-action

Add staging prod gh action

.github/workflows/publish-package-prod.yaml

@@ -0,0 +1,34 @@
+name: Publish Packages to Prod
+on:
+  push:
+    branches:
+      - 'main'
+
+jobs:
+  Publish:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout source
+        uses: actions/checkout@v3
+      - name: Install dependencies
+        run: |
+          python -m pip install twine build
+          python -m pip install keyrings.google-artifactregistry-auth
+      - name: Capture build tag
+        run: |
+          echo "COMMIT_TAG=$(git rev-parse --short  HEAD)"  >> $GITHUB_ENV
+
+      - name: Make dists
+        run: |
+          python -m build
+      - name: Show output
+        run: tree .
+      - name: Setup gcloud
+        uses: google-github-actions/[email protected]
+        with:
+          service_account_key: ${{ secrets.GCP_SA_KEY_PROD }}
+          project_id: ganymede-core
+          export_default_credentials: true
+      - name: Publish package
+        run: |
+          python3 -m twine upload --verbose --repository-url https://us-central1-python.pkg.dev/ganymede-core/ganymede-py/ dist/*

.github/workflows/publish-package-staging.yaml

@@ -0,0 +1,34 @@
+name: Publish Packages to Staging
+on:
+  push:
+    branches:
+      - 'main'
+
+jobs:
+  Publish:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout source
+        uses: actions/checkout@v3
+      - name: Install dependencies
+        run: |
+          python -m pip install twine build
+          python -m pip install keyrings.google-artifactregistry-auth
+      - name: Capture build tag
+        run: |
+          echo "COMMIT_TAG=$(git rev-parse --short  HEAD)"  >> $GITHUB_ENV
+
+      - name: Make dists
+        run: |
+          python -m build
+      - name: Show output
+        run: tree .
+      - name: Setup gcloud
+        uses: google-github-actions/[email protected]
+        with:
+          service_account_key: ${{ secrets.GCP_SA_KEY_STAGING}}
+          project_id: ganymede-core-staging
+          export_default_credentials: true
+      - name: Publish package
+        run: |
+          python3 -m twine upload --verbose --repository-url https://us-central1-python.pkg.dev/ganymede-core-staging/ganymede-py/ dist/*

.github/workflows/test.yml

@@ -5,8 +5,6 @@ name: test
 on:
   push:
     branches: [ main ]
-  pull_request:
-    types: [opened, edited, synchronize]
 
 permissions:
   contents: read

.vscode/settings.json

@@ -12,27 +12,19 @@
       "editor.autoIndent": "keep"
     },
 
-    // Use flake8, not pylint
-    "python.linting.pylintEnabled": false,
-    "python.linting.flake8Enabled": true,
-    "python.linting.mypyEnabled": true,
     // Disable Python tests for now.
     "python.testing.pytestEnabled": false,
     "python.testing.unittestEnabled": false,
-    // isort
-    "isort.path": ["ruff"],
-    "isort.args": ["--quiet"],
-    // Use Black for formatting
-    "python.formatting.provider": "black",
-    "python.formatting.blackArgs": ["--config", "${workspaceRoot}/pyproject.toml"],
+
     "[python]": {
       "editor.formatOnPaste": false,
       "editor.formatOnSave": true,
       "editor.codeActionsOnSave": {
         "source.organizeImports": "explicit"
-      }
+      },
+      "editor.defaultFormatter": "ms-python.black-formatter"
     },
+    "black-formatter.args": ["--line-length", "110"],
 
     "search.useIgnoreFiles": true,
-    "python.linting.enabled": true,
   }

src/allotropy/allotrope/models/cell_counting_benchling_2023_09_cell_counting.py

@@ -102,18 +102,14 @@ class ProcessedDataDocument:
     viability__cell_counter_: TQuantityValuePercent
     viable_cell_density__cell_counter_: TQuantityValueMillionCellsPerMilliliter
     total_cell_count: TQuantityValueCell
-    total_cell_density__cell_counter_: TQuantityValueMillionCellsPerMilliliter | None = (
-        None
-    )
+    total_cell_density__cell_counter_: TQuantityValueMillionCellsPerMilliliter | None = None
     dead_cell_density__cell_counter_: TQuantityValueMillionCellsPerMilliliter | None = (
         None
     )
     average_total_cell_diameter: TQuantityValueMicrometer | None = None
     average_live_cell_diameter__cell_counter_: TQuantityValueMicrometer | None = None
     average_dead_cell_diameter__cell_counter_: TQuantityValueMicrometer | None = None
-    total_cell_diameter_distribution_data_cube: TotalCellDiameterDistributionDataCube | None = (
-        None
-    )
+    total_cell_diameter_distribution_data_cube: TotalCellDiameterDistributionDataCube | None = None
     viable_cell_count: TQuantityValueCell | None = None
     dead_cell_count: TQuantityValueCell | None = None
     average_total_cell_circularity: TQuantityValueUnitless | None = None

src/allotropy/allotrope/models/cell_counting_benchling_2023_11_cell_counting.py

@@ -318,9 +318,7 @@ class ProcessedDataDocumentItem1:
     data_processing_document: DataProcessingDocument | None = None
     data_source_aggregate_document: DataSourceAggregateDocument | None = None
     processed_data_identifier: TStringValue | None = None
-    fluorescent_tag_positive_cell_density: TQuantityValueMillionCellsPerMilliliter | None = (
-        None
-    )
+    fluorescent_tag_positive_cell_density: TQuantityValueMillionCellsPerMilliliter | None = None
     fluorescent_tag_positive_percentage: TQuantityValuePercent | None = None
     field_index: int | None = None
 
@@ -429,9 +427,7 @@ class ProcessedDataDocumentItem:
     data_processing_document: DataProcessingDocument | None = None
     data_source_aggregate_document: DataSourceAggregateDocument | None = None
     processed_data_identifier: TStringValue | None = None
-    total_cell_density__cell_counter_: TQuantityValueMillionCellsPerMilliliter | None = (
-        None
-    )
+    total_cell_density__cell_counter_: TQuantityValueMillionCellsPerMilliliter | None = None
     dead_cell_density__cell_counter_: TQuantityValueMillionCellsPerMilliliter | None = (
         None
     )

src/allotropy/allotrope/models/cell_culture_analyzer_benchling_2023_09_cell_culture_analyzer.py

@@ -43,9 +43,7 @@ class SampleDocument:
 @dataclass
 class AnalyteDocumentItem:
     analyte_name: TStringValue
-    molar_concentration: TNullableQuantityValueMillimolePerLiter | TNullableQuantityValueGramPerLiter | TNullableQuantityValueUnitPerLiter | None = (
-        None
-    )
+    molar_concentration: TNullableQuantityValueMillimolePerLiter | TNullableQuantityValueGramPerLiter | TNullableQuantityValueUnitPerLiter | None = None
 
 
 @dataclass
@@ -66,21 +64,11 @@ class MeasurementDocumentItem:
     pH: TNullableQuantityValuePH | None = None
     osmolality: TNullableQuantityValueMilliOsmolesPerKilogram | None = None
     viability__cell_counter_: TNullableQuantityValuePercent | None = None
-    total_cell_density__cell_counter_: TNullableQuantityValueMillionCellsPerMilliliter | None = (
-        None
-    )
-    viable_cell_density__cell_counter_: TNullableQuantityValueMillionCellsPerMilliliter | None = (
-        None
-    )
-    average_live_cell_diameter__cell_counter_: TNullableQuantityValueMicrometer | None = (
-        None
-    )
-    average_total_cell_diameter__cell_counter_: TNullableQuantityValueMicrometer | None = (
-        None
-    )
-    total_cell_diameter_distribution__cell_counter_: TNullableQuantityValueTODO | None = (
-        None
-    )
+    total_cell_density__cell_counter_: TNullableQuantityValueMillionCellsPerMilliliter | None = None
+    viable_cell_density__cell_counter_: TNullableQuantityValueMillionCellsPerMilliliter | None = None
+    average_live_cell_diameter__cell_counter_: TNullableQuantityValueMicrometer | None = None
+    average_total_cell_diameter__cell_counter_: TNullableQuantityValueMicrometer | None = None
+    total_cell_diameter_distribution__cell_counter_: TNullableQuantityValueTODO | None = None
     viable_cell_count__cell_counter_: TNullableQuantityValueCell | None = None
     total_cell_count__cell_counter_: TNullableQuantityValueCell | None = None
 

src/allotropy/allotrope/models/liquid_chromatography_rec_2023_03_liquid_chromatography.py

@@ -68,12 +68,8 @@ class DeviceControlDocumentItem:
     detection_type: TStringValue | None = None
     electronic_absorbance_wavelength_setting: TQuantityValueNanometer | None = None
     electronic_absorbance_bandwidth_setting: TQuantityValueNanometer | None = None
-    electronic_absorbance_reference_bandwidth_setting: TQuantityValueNanometer | None = (
-        None
-    )
-    electronic_absorbance_reference_wavelength_setting: TQuantityValueNanometer | None = (
-        None
-    )
+    electronic_absorbance_reference_bandwidth_setting: TQuantityValueNanometer | None = None
+    electronic_absorbance_reference_wavelength_setting: TQuantityValueNanometer | None = None
     detector_offset_setting: TQuantityValue | None = None
     detector_sampling_rate_setting: TQuantityValueHertz | None = None
     field_index: int | None = None
@@ -148,7 +144,5 @@ class LiquidChromatographyAggregateDocument:
 
 @dataclass
 class Model:
-    liquid_chromatography_aggregate_document: LiquidChromatographyAggregateDocument | None = (
-        None
-    )
+    liquid_chromatography_aggregate_document: LiquidChromatographyAggregateDocument | None = None
     manifest: str = "http://purl.allotrope.org/manifests/liquid-chromatography/REC/2023/03/liquid-chromatography.manifest"

src/allotropy/allotrope/models/multi_analyte_profiling_benchling_2024_01_multi_analyte_profiling.py

@@ -234,6 +234,4 @@ class MultiAnalyteProfilingAggregateDocument:
 @dataclass
 class Model(Asm):
     field_asm_manifest: str | Manifest
-    multi_analyte_profiling_aggregate_document: MultiAnalyteProfilingAggregateDocument | None = (
-        None
-    )
+    multi_analyte_profiling_aggregate_document: MultiAnalyteProfilingAggregateDocument | None = None

src/allotropy/allotrope/models/plate_reader_benchling_2023_09_plate_reader.py

@@ -423,12 +423,8 @@ class UltravioletAbsorbancePointDetectionDeviceControlDocumentItem(
     detector_bandwidth_setting: TQuantityValueNanometer | None = None
     electronic_absorbance_wavelength_setting: TQuantityValueNanometer | None = None
     electronic_absorbance_bandwidth_setting: TQuantityValueNanometer | None = None
-    electronic_absorbance_reference_bandwidth_setting: TQuantityValueNanometer | None = (
-        None
-    )
-    electronic_absorbance_reference_wavelength_setting: TQuantityValueNanometer | None = (
-        None
-    )
+    electronic_absorbance_reference_bandwidth_setting: TQuantityValueNanometer | None = None
+    electronic_absorbance_reference_wavelength_setting: TQuantityValueNanometer | None = None
     field_index: int | None = None
 
 

src/allotropy/allotrope/models/shared/components/liquid_chromatography.py

@@ -51,35 +51,17 @@ class PeakItem:
     chromatographic_peak_asymmetry_factor: TQuantityValueUnitless | None = None
     asymmetry_factor_measured_at_baseline: TQuantityValueUnitless | None = None
     chromatographic_peak_resolution: TQuantityValueUnitless | None = None
-    chromatographic_peak_resolution_using_baseline_peak_widths: TQuantityValueUnitless | None = (
-        None
-    )
-    chromatographic_peak_resolution_using_peak_width_at_half_height: TQuantityValueUnitless | None = (
-        None
-    )
-    chromatographic_peak_resolution_using_statistical_moments: TQuantityValueUnitless | None = (
-        None
-    )
+    chromatographic_peak_resolution_using_baseline_peak_widths: TQuantityValueUnitless | None = None
+    chromatographic_peak_resolution_using_peak_width_at_half_height: TQuantityValueUnitless | None = None
+    chromatographic_peak_resolution_using_statistical_moments: TQuantityValueUnitless | None = None
     number_of_theoretical_plates__chromatography_: TQuantityValueUnitless | None = None
-    number_of_theoretical_plates_measured_at_60_7___of_peak_height: TQuantityValueUnitless | None = (
-        None
-    )
-    number_of_theoretical_plates_measured_at_32_4___of_peak_height: TQuantityValueUnitless | None = (
-        None
-    )
-    number_of_theoretical_plates_measured_at_13_4___of_peak_height: TQuantityValueUnitless | None = (
-        None
-    )
-    number_of_theoretical_plates_measured_at_4_4___of_peak_height: TQuantityValueUnitless | None = (
-        None
-    )
+    number_of_theoretical_plates_measured_at_60_7___of_peak_height: TQuantityValueUnitless | None = None
+    number_of_theoretical_plates_measured_at_32_4___of_peak_height: TQuantityValueUnitless | None = None
+    number_of_theoretical_plates_measured_at_13_4___of_peak_height: TQuantityValueUnitless | None = None
+    number_of_theoretical_plates_measured_at_4_4___of_peak_height: TQuantityValueUnitless | None = None
     number_of_theoretical_plates_by_tangent_method: TQuantityValueUnitless | None = None
-    number_of_theoretical_plates_by_peak_width_at_half_height: TQuantityValueUnitless | None = (
-        None
-    )
-    number_of_theoretical_plates_by_peak_width_at_half_height__JP14_: TQuantityValueUnitless | None = (
-        None
-    )
+    number_of_theoretical_plates_by_peak_width_at_half_height: TQuantityValueUnitless | None = None
+    number_of_theoretical_plates_by_peak_width_at_half_height__JP14_: TQuantityValueUnitless | None = None
 
     def __post_init__(self) -> None:
         any_of_keys = [

src/allotropy/allotrope/models/shared/definitions/definitions.py

@@ -2,7 +2,6 @@
 
 from dataclasses import dataclass
 from enum import Enum
-from typing import Union
 
 from allotropy.exceptions import AllotropeConversionError
 
@@ -27,16 +26,16 @@ class TStringValueItem:
 
 TBooleanArray = list[bool]
 TBooleanOrNullArray = list[bool | None]
-TBooleanValue = Union[bool, TBooleanValueItem]
+TBooleanValue = bool | TBooleanValueItem
 TClass = str
-TDateTimeValue = Union[str, TDateTimeValueItem]
+TDateTimeValue = str | TDateTimeValueItem
 # TODO(brian): inline this
 TDateTimeStampValue = TDateTimeValue
 TNumberArray = list[float]
 TNumberOrNullArray = list[float | None]
 TStringArray = list[str]
 TStringOrNullArray = list[str | None]
-TStringValue = Union[str, TStringValueItem]
+TStringValue = str | TStringValueItem
 TTupleData = list[float | bool | str | None]
 TUnit = str
 
@@ -62,7 +61,7 @@ class InvalidJsonFloat(Enum):
     field_Infinity_1 = "-Infinity"
 
 
-JsonFloat = Union[float, InvalidJsonFloat]
+JsonFloat = float | InvalidJsonFloat
 
 
 @dataclass
@@ -125,10 +124,10 @@ class TDatacubeComponent:
     field_asm_fill_value: str | float | int | bool | None = None
 
 
-TDimensionArray = Union[TNumberArray, TBooleanArray, TStringArray]
+TDimensionArray = TNumberArray | TBooleanArray | TStringArray
 
 
-TMeasureArray = Union[TNumberOrNullArray, TBooleanOrNullArray, TStringOrNullArray]
+TMeasureArray = TNumberOrNullArray | TBooleanOrNullArray | TStringOrNullArray
 
 
 @dataclass

src/allotropy/allotrope/models/spectrophotometry_benchling_2023_12_spectrophotometry.py

@@ -356,9 +356,7 @@ class ProcessedDataDocumentItem:
     data_processing_document: DataProcessingDocument | None = None
     data_source_aggregate_document: DataSourceAggregateDocument | None = None
     processed_data_identifier: TStringValue | None = None
-    mass_concentration: TQuantityValueNanogramPerMicroliter | TQuantityValueMicrogramPerMicroliter | TQuantityValuePicogramPerMilliliter | TQuantityValueNanogramPerMilliliter | TQuantityValueMicrogramPerMilliliter | TQuantityValueMilligramPerMilliliter | None = (
-        None
-    )
+    mass_concentration: TQuantityValueNanogramPerMicroliter | TQuantityValueMicrogramPerMicroliter | TQuantityValuePicogramPerMilliliter | TQuantityValueNanogramPerMilliliter | TQuantityValueMicrogramPerMilliliter | TQuantityValueMilligramPerMilliliter | None = None
     field_index: int | None = None
 
 
@@ -393,12 +391,8 @@ class UltravioletAbsorbancePointDetectionDeviceControlDocumentItem(
     detector_bandwidth_setting: TQuantityValueNanometer | None = None
     electronic_absorbance_wavelength_setting: TQuantityValueNanometer | None = None
     electronic_absorbance_bandwidth_setting: TQuantityValueNanometer | None = None
-    electronic_absorbance_reference_bandwidth_setting: TQuantityValueNanometer | None = (
-        None
-    )
-    electronic_absorbance_reference_wavelength_setting: TQuantityValueNanometer | None = (
-        None
-    )
+    electronic_absorbance_reference_bandwidth_setting: TQuantityValueNanometer | None = None
+    electronic_absorbance_reference_wavelength_setting: TQuantityValueNanometer | None = None
     field_index: int | None = None
 
 

src/allotropy/allotrope/schema_parser/backup_manager.py

@@ -3,9 +3,8 @@
 from itertools import zip_longest
 from pathlib import Path
 import shutil
-from typing import Union
 
-PathType = Union[Path, str]
+PathType = Path | str
 
 
 def _files_equal(path1: PathType, path2: PathType) -> bool:

src/allotropy/allotrope/schema_parser/generate_schemas.py

@@ -55,10 +55,14 @@ def lint_file(model_path: str) -> None:
     )
     # The second call to ruff checks for additional rules.
     subprocess.check_call(
-        f"ruff {model_path} --fix", shell=True, stdout=subprocess.DEVNULL  # noqa: S602
+        f"ruff {model_path} --fix",
+        shell=True,  # noqa: S602
+        stdout=subprocess.DEVNULL,
     )
     subprocess.check_call(
-        f"black {model_path}", shell=True, stderr=subprocess.DEVNULL  # noqa: S602
+        f"black {model_path}",
+        shell=True,  # noqa: S602
+        stderr=subprocess.DEVNULL,
     )