diff --git a/.github/workflows/JOB_e2e.yml b/.github/workflows/JOB_e2e.yml index 9fc8d1705..5c1920b4d 100644 --- a/.github/workflows/JOB_e2e.yml +++ b/.github/workflows/JOB_e2e.yml @@ -26,7 +26,7 @@ jobs: strategy: fail-fast: false matrix: - python-version: ["3.10"] + python-version: ["3.11"] poetry-version: ["1.3.1"] os: [ubuntu-latest, windows-latest] runs-on: ${{ matrix.os }} diff --git a/.github/workflows/JOB_format.yml b/.github/workflows/JOB_format.yml index 0003c6d7b..6340a76fe 100644 --- a/.github/workflows/JOB_format.yml +++ b/.github/workflows/JOB_format.yml @@ -28,7 +28,7 @@ jobs: - name: Set up Python environment uses: actions/setup-python@39cd14951b08e74b54015e9e001cdefcf80e669f # v5.1.1 with: - python-version: "3.11" + python-version: "3.12" - name: Show filenames run: echo ${{ inputs.files }} diff --git a/.github/workflows/JOB_generate_documentation.yml b/.github/workflows/JOB_generate_documentation.yml index e9f43288a..51ec462ea 100644 --- a/.github/workflows/JOB_generate_documentation.yml +++ b/.github/workflows/JOB_generate_documentation.yml @@ -20,7 +20,7 @@ jobs: runs-on: ubuntu-latest strategy: matrix: - python-version: ["3.8", "3.9", "3.10", "3.11"] + python-version: ["3.9", "3.10", "3.11", "3.12", "3.13"] steps: - name: Harden Runner uses: step-security/harden-runner@5c7944e73c4c2a096b17a9cb74d65b6c2bbafbde # v2.9.1 diff --git a/.github/workflows/JOB_lint.yml b/.github/workflows/JOB_lint.yml index 3aa556782..f221cea5d 100644 --- a/.github/workflows/JOB_lint.yml +++ b/.github/workflows/JOB_lint.yml @@ -30,7 +30,7 @@ jobs: - name: Set up Python environment uses: actions/setup-python@39cd14951b08e74b54015e9e001cdefcf80e669f # v5.1.1 with: - python-version: "3.10" + python-version: "3.11" - name: Show filenames run: echo ${{ inputs.files }} diff --git a/.github/workflows/JOB_tests.yml b/.github/workflows/JOB_tests.yml index c057ab9b1..3616f1a47 100644 --- a/.github/workflows/JOB_tests.yml +++ b/.github/workflows/JOB_tests.yml @@ -14,15 +14,11 @@ jobs: strategy: matrix: os: [ubuntu-latest, macos-latest, windows-latest] - python-version: ["3.8", "3.9", "3.10", "3.11"] + python-version: ["3.9", "3.10", "3.11", "3.12", "3.13"] exclude: - - os: macos-latest - python-version: "3.8" - os: macos-latest python-version: "3.9" include: - - os: macos-13 - python-version: "3.8" - os: macos-13 python-version: "3.9" runs-on: ${{ matrix.os }} @@ -35,7 +31,10 @@ jobs: - uses: actions/checkout@692973e3d937129bcbf40652eb9f2f61becf3332 # v4.1.7 with: ref: ${{ github.head_ref || github.ref }} - + - name: Install Fortran Compiler (macOS) + if: runner.os == 'macOS' + run: | + brew install gcc - name: Install Python ${{ matrix.python-version }} uses: actions/setup-python@39cd14951b08e74b54015e9e001cdefcf80e669f # v5.1.1 with: diff --git a/.github/workflows/JOB_typecheck.yml b/.github/workflows/JOB_typecheck.yml index 11a5c77b6..22f841983 100644 --- a/.github/workflows/JOB_typecheck.yml +++ b/.github/workflows/JOB_typecheck.yml @@ -28,7 +28,7 @@ jobs: - name: Set up Python environment uses: actions/setup-python@39cd14951b08e74b54015e9e001cdefcf80e669f # v5.1.1 with: - python-version: "3.10" + python-version: "3.11" - name: Show filenames run: echo ${{ inputs.files }} diff --git a/darwin/importer/importer.py b/darwin/importer/importer.py index d630fbba4..4e16e51cc 100644 --- a/darwin/importer/importer.py +++ b/darwin/importer/importer.py @@ -499,9 +499,10 @@ def _import_properties( metadata_property_classes, metadata_item_props = _parse_metadata_file(metadata_path) # Get team properties - team_properties_annotation_lookup, team_item_properties_lookup = ( - _get_team_properties_annotation_lookup(client, dataset.team) - ) + ( + team_properties_annotation_lookup, + team_item_properties_lookup, + ) = _get_team_properties_annotation_lookup(client, dataset.team) # Build metadata lookups ( @@ -748,12 +749,13 @@ def _import_properties( ].add(t_prop_val.id) # Create/Update team item properties based on metadata - item_properties_to_create_from_metadata, item_properties_to_update_from_metadata = ( - _create_update_item_properties( - _normalize_item_properties(metadata_item_prop_lookup), - team_item_properties_lookup, - client, - ) + ( + item_properties_to_create_from_metadata, + item_properties_to_update_from_metadata, + ) = _create_update_item_properties( + _normalize_item_properties(metadata_item_prop_lookup), + team_item_properties_lookup, + client, ) console = Console(theme=_console_theme()) @@ -804,9 +806,10 @@ def _import_properties( updated_properties.append(prop) # get latest team properties - team_properties_annotation_lookup, team_item_properties_lookup = ( - _get_team_properties_annotation_lookup(client, dataset.team) - ) + ( + team_properties_annotation_lookup, + team_item_properties_lookup, + ) = _get_team_properties_annotation_lookup(client, dataset.team) # Update item-level properties from annotations _, item_properties_to_update_from_annotations = _create_update_item_properties( @@ -835,9 +838,10 @@ def _import_properties( updated_properties.append(prop) # get latest team properties - team_properties_annotation_lookup, team_item_properties_lookup = ( - _get_team_properties_annotation_lookup(client, dataset.team) - ) + ( + team_properties_annotation_lookup, + team_item_properties_lookup, + ) = _get_team_properties_annotation_lookup(client, dataset.team) # loop over metadata_cls_id_prop_lookup, and update additional metadata property values for (annotation_class_id, prop_name), m_prop in metadata_cls_id_prop_lookup.items(): @@ -987,7 +991,6 @@ def _create_update_item_properties( # If the property exists in the team, check that all values are present if item_prop_name in team_item_properties_lookup: - t_prop = team_item_properties_lookup[item_prop_name] # If the property is a text property it won't have predefined values, so continue if t_prop.type == "text": @@ -1014,7 +1017,6 @@ def _create_update_item_properties( # If the property does not exist in the team, create it else: - # If we've already planned to create this property, simply extend the property values for prop in create_properties: if prop.name == item_prop_name: @@ -1957,7 +1959,6 @@ def _overwrite_warning( files_with_item_properties_to_overwrite.append(local_file.full_path) if files_with_annotations_to_overwrite or files_with_item_properties_to_overwrite: - # Overwriting of annotations if files_with_annotations_to_overwrite: console.print( diff --git a/e2e_tests/cli/test_import.py b/e2e_tests/cli/test_import.py index d07f0a9dc..daccbf663 100644 --- a/e2e_tests/cli/test_import.py +++ b/e2e_tests/cli/test_import.py @@ -253,14 +253,15 @@ def compare_annotations_export( actual_filename = get_actual_annotation_filename( expected_filename, actual_annotation_files ) - 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"importlib-resources", "jaraco.functools", "jaraco.itertools", "jaraco.test", "more-itertools", "pytest (>=6,!=8.1.*)", "pytest-ignore-flaky"] +type = ["pytest-mypy"] [extras] dev = ["black", "debugpy", "isort", "mypy", "pytest", "pytest-rerunfailures", "responses", "ruff", "validate-pyproject"] @@ -2252,5 +2640,5 @@ test = ["pytest", "responses"] [metadata] lock-version = "2.0" -python-versions = ">=3.8.0,<3.12" -content-hash = "56a5bed4ed0b7d4d3a461d9fb7074fa1cb0855d9859434429a78a466cc6c65ac" +python-versions = ">=3.9,<3.14" +content-hash = "a843fbb1c7ba6d013a49847bfc1c915d7b10b6c04ae3724b4b5e1fbb26544dcf" diff --git a/pyproject.toml b/pyproject.toml index ffcfb2629..2bd42aa40 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -38,7 +38,6 @@ no_implicit_optional = true no_implicit_reexport = true plugins = ["pydantic.mypy"] pretty = true -python_version = "3.10" warn_redundant_casts = true warn_return_any = false warn_unreachable = true @@ -72,7 +71,7 @@ numpy = "^1.24.4" orjson = "^3.8.5" pillow = "^10.1.0" pydantic = "^2.0.0" -python = ">=3.8.0,<3.12" +python = ">=3.9,<3.14" pyyaml = "^6.0.1" requests = "^2.28.1" rich = "^13.0.1" @@ -81,7 +80,7 @@ tqdm = "^4.64.1" types-pyyaml = "^6.0.12.9" types-requests = "^2.28.11.8" upolygon = "0.1.11" -tenacity = "8.5.0" +tenacity = "^8.5.0" natsort = "^8.4.0" [tool.poetry.extras] @@ -100,7 +99,7 @@ darwin = "darwin.cli:main" [tool.poetry.dependencies.nibabel] optional = true -python = ">=3.8.1" +python = ">=3.9" version = "^5.0.0" [tool.poetry.dependencies.connected-components-3d] @@ -109,27 +108,26 @@ version = "^3.10.3" [tool.poetry.dependencies.scikit-learn] optional = true -python = ">=3.8.1,<3.12" -version = "^1.2.0" +python = ">=3.9,<3.14" +version = "^1.5.0" [tool.poetry.dependencies.scipy] optional = true -python = ">=3.8.1,<3.12" -version = "^1.10.1" +python = ">=3.9,<3.14" +version = "^1.13.1" [tool.poetry.dependencies.albumentations] optional = true -python = ">=3.8" -version = "^1.3.1" +python = ">=3.9,<3.14" +version = "^1.4.21" [tool.poetry.dependencies.torch] optional = true -version = "^2.0.0" +version = "^2.5.1" [tool.poetry.dependencies.torchvision] optional = true -version = "^0.15.0" - +version = "^0.20.1" [tool.poetry.dependencies.black] optional = true version = "^24.4.2" @@ -140,7 +138,7 @@ version = "^5.11.4" [tool.poetry.dependencies.mypy] optional = true -python = ">=3.8" +python = ">=3.9" version = "^1.5" [tool.poetry.dependencies.responses] @@ -159,7 +157,7 @@ version = "^1.8.1" version = "^2.7.0" [tool.poetry.dependencies.python-dotenv] -python = ">3.8" +python = ">3.9,<3.14" version = "^1.0.0" [tool.poetry.dependencies.opencv-python-headless] diff --git a/test.dcm b/test.dcm new file mode 100644 index 000000000..e69de29bb diff --git a/tests/darwin/dataset/upload_manager_test.py b/tests/darwin/dataset/upload_manager_test.py index 7640dfb39..9834e48f9 100644 --- a/tests/darwin/dataset/upload_manager_test.py +++ b/tests/darwin/dataset/upload_manager_test.py @@ -509,7 +509,6 @@ def test_default_value_for_handle_as_slices(): class TestUploadChunkSize: - def test_default_value_when_env_var_is_not_set(self): assert _upload_chunk_size() == 500 diff --git a/tests/darwin/importer/importer_test.py b/tests/darwin/importer/importer_test.py index 44603a144..fafe44fe2 100644 --- a/tests/darwin/importer/importer_test.py +++ b/tests/darwin/importer/importer_test.py @@ -1061,7 +1061,6 @@ def test_import_properties_creates_missing_item_level_properties_from_annotation ) as mock_get_team_props, patch( "darwin.importer.importer._create_update_item_properties" ) as mock_create_update_props: - metadata_path = False mock_get_team_props.side_effect = [ ({}, {}), @@ -1109,12 +1108,14 @@ def test_import_properties_creates_missing_item_level_properties_from_annotation dataset=mock_dataset, ) - create_properties_first_call, update_properties_first_call = ( - mock_create_update_props.call_args_list[0][0][0:2] - ) - create_properties_second_call, update_properties_second_call = ( - mock_create_update_props.call_args_list[1][0][0:2] - ) + ( + create_properties_first_call, + update_properties_first_call, + ) = mock_create_update_props.call_args_list[0][0][0:2] + ( + create_properties_second_call, + update_properties_second_call, + ) = mock_create_update_props.call_args_list[1][0][0:2] assert len(create_properties_first_call) == 0 assert len(update_properties_first_call) == 0 @@ -1158,7 +1159,6 @@ def test_import_properties_creates_missing_item_level_properties_from_manifest_n ) as mock_get_team_props, patch( "darwin.importer.importer._create_update_item_properties" ) as mock_create_update_props: - metadata_path = Path( "darwin/future/tests/data/.v7/metadata_with_item_level_properties.json" ) @@ -1238,12 +1238,14 @@ def test_import_properties_creates_missing_item_level_properties_from_manifest_n dataset=mock_dataset, ) - create_properties_first_call, update_properties_first_call = ( - mock_create_update_props.call_args_list[0][0][2:4] - ) - create_properties_second_call, update_properties_second_call = ( - mock_create_update_props.call_args_list[1][0][2:4] - ) + ( + create_properties_first_call, + update_properties_first_call, + ) = mock_create_update_props.call_args_list[0][0][2:4] + ( + create_properties_second_call, + update_properties_second_call, + ) = mock_create_update_props.call_args_list[1][0][2:4] assert len(create_properties_first_call) == 2 assert len(update_properties_first_call) == 0 @@ -1289,7 +1291,6 @@ def test_import_properties_creates_missing_item_level_properties_from_manifest_a ) as mock_get_team_props, patch( "darwin.importer.importer._create_update_item_properties" ) as mock_create_update_props: - metadata_path = Path( "darwin/future/tests/data/.v7/metadata_with_item_level_properties.json" ) @@ -1371,12 +1372,14 @@ def test_import_properties_creates_missing_item_level_properties_from_manifest_a dataset=mock_dataset, ) - create_properties_first_call, update_properties_first_call = ( - mock_create_update_props.call_args_list[0][0][2:4] - ) - create_properties_second_call, update_properties_second_call = ( - mock_create_update_props.call_args_list[1][0][2:4] - ) + ( + create_properties_first_call, + update_properties_first_call, + ) = mock_create_update_props.call_args_list[0][0][2:4] + ( + create_properties_second_call, + update_properties_second_call, + ) = mock_create_update_props.call_args_list[1][0][2:4] assert len(create_properties_first_call) == 2 assert len(update_properties_first_call) == 0 @@ -1432,7 +1435,6 @@ def test_import_properties_creates_missing_item_level_property_values_from_manif ) as mock_get_team_props, patch( "darwin.importer.importer._create_update_item_properties" ) as mock_create_update_props: - metadata_path = Path( "darwin/future/tests/data/.v7/metadata_with_item_level_properties.json" ) @@ -1571,12 +1573,14 @@ def test_import_properties_creates_missing_item_level_property_values_from_manif dataset=mock_dataset, ) - create_properties_first_call, update_properties_first_call = ( - mock_create_update_props.call_args_list[0][0][2:4] - ) - create_properties_second_call, update_properties_second_call = ( - mock_create_update_props.call_args_list[1][0][2:4] - ) + ( + create_properties_first_call, + update_properties_first_call, + ) = mock_create_update_props.call_args_list[0][0][2:4] + ( + create_properties_second_call, + update_properties_second_call, + ) = mock_create_update_props.call_args_list[1][0][2:4] assert len(create_properties_first_call) == 0 assert len(update_properties_first_call) == 2 @@ -1620,7 +1624,6 @@ def test_import_properties_creates_missing_item_level_property_values_from_annot ) as mock_get_team_props, patch( "darwin.importer.importer._create_update_item_properties" ) as mock_create_update_props: - metadata_path = False mock_get_team_props.side_effect = [ ( @@ -1761,12 +1764,14 @@ def test_import_properties_creates_missing_item_level_property_values_from_annot dataset=mock_dataset, ) - create_properties_first_call, update_properties_first_call = ( - mock_create_update_props.call_args_list[0][0][2:4] - ) - create_properties_second_call, update_properties_second_call = ( - mock_create_update_props.call_args_list[1][0][2:4] - ) + ( + create_properties_first_call, + update_properties_first_call, + ) = mock_create_update_props.call_args_list[0][0][2:4] + ( + create_properties_second_call, + update_properties_second_call, + ) = mock_create_update_props.call_args_list[1][0][2:4] assert len(create_properties_first_call) == 0 assert len(update_properties_first_call) == 0 @@ -1799,7 +1804,6 @@ def test_import_properties_creates_missing_item_level_property_values_from_manif ) as mock_get_team_props, patch( "darwin.importer.importer._create_update_item_properties" ) as mock_create_update_props: - metadata_path = Path( "darwin/future/tests/data/.v7/metadata_with_item_level_properties.json" ) @@ -1938,12 +1942,14 @@ def test_import_properties_creates_missing_item_level_property_values_from_manif dataset=mock_dataset, ) - create_properties_first_call, update_properties_first_call = ( - mock_create_update_props.call_args_list[0][0][2:4] - ) - create_properties_second_call, update_properties_second_call = ( - mock_create_update_props.call_args_list[1][0][2:4] - ) + ( + create_properties_first_call, + update_properties_first_call, + ) = mock_create_update_props.call_args_list[0][0][2:4] + ( + create_properties_second_call, + update_properties_second_call, + ) = mock_create_update_props.call_args_list[1][0][2:4] assert len(create_properties_first_call) == 0 assert len(update_properties_first_call) == 2