From b928871c366e9b37485fea853a1c30fc122cd362 Mon Sep 17 00:00:00 2001 From: Travis Wrightsman Date: Mon, 5 May 2025 12:52:57 +0200 Subject: [PATCH] test: improve type checks and declare typing support * Migrate from mypy to pyrefly * Bump uv to avoid lock file churn * See https://github.com/astral-sh/uv/pull/13176 * Add py.typed to package root to signal it supports typing --- .github/workflows/ci.yml | 4 +- pyproject.toml | 5 +- src/grz_pydantic_models/pruefbericht/v0.py | 14 +- src/grz_pydantic_models/py.typed | 0 .../submission/metadata/v1.py | 14 +- uv.lock | 191 ++++++++---------- 6 files changed, 106 insertions(+), 122 deletions(-) create mode 100644 src/grz_pydantic_models/py.typed diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 6ec15d2..d575beb 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -26,7 +26,7 @@ jobs: uses: astral-sh/setup-uv@v5 with: # Install a specific version of uv and enable caching. - version: "0.6.2" + version: "0.7.2" enable-cache: true - name: Set up Python @@ -39,7 +39,7 @@ jobs: run: uv run ruff format --check - name: Run mypy - run: uv run mypy src + run: uv run pyrefly check - name: Run pytest run: uv run pytest diff --git a/pyproject.toml b/pyproject.toml index ac9cdd8..d0ade59 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -35,7 +35,7 @@ Changelog = "https://github.com/BfArM-MVH/grz-pydantic-models/commits/main" [dependency-groups] dev = [ "ruff >=0.11.0,<0.12", - "mypy >=1.13.0", + "pyrefly >=0.13.0,<0.14.0", "pytest == 8.*" ] @@ -52,3 +52,6 @@ fixable = [ select = [ "I" ] + +[tool.pyrefly] +search_path = ["src"] diff --git a/src/grz_pydantic_models/pruefbericht/v0.py b/src/grz_pydantic_models/pruefbericht/v0.py index 067345b..05e6023 100644 --- a/src/grz_pydantic_models/pruefbericht/v0.py +++ b/src/grz_pydantic_models/pruefbericht/v0.py @@ -22,18 +22,18 @@ class DataCategory(enum.StrEnum): """Type of submission.""" - clinical = enum.auto() - genomic = enum.auto() + clinical = "clinical" + genomic = "genomic" class LibraryType(enum.StrEnum): """Sequencing method, if applicable.""" - panel = enum.auto() - wes = enum.auto() - wgs = enum.auto() - wgs_lr = enum.auto() - none = enum.auto() + panel = "panel" + wes = "wes" + wgs = "wgs" + wgs_lr = "wgs_lr" + none = "none" class SubmittedCase(StrictBaseModel): diff --git a/src/grz_pydantic_models/py.typed b/src/grz_pydantic_models/py.typed new file mode 100644 index 0000000..e69de29 diff --git a/src/grz_pydantic_models/submission/metadata/v1.py b/src/grz_pydantic_models/submission/metadata/v1.py index 2b21720..d4095c9 100644 --- a/src/grz_pydantic_models/submission/metadata/v1.py +++ b/src/grz_pydantic_models/submission/metadata/v1.py @@ -727,7 +727,7 @@ class Donor(StrictBaseModel): @model_validator(mode="after") def warn_empty_sequence_data(self): for lab_datum in self.lab_data: - if not lab_datum.has_sequence_data(): + if lab_datum.sequence_data is None: log.warning( f"No sequence data found for lab datum '{lab_datum.lab_data_name}' in donor '{self.donor_pseudonym}'. " "Is this a submission without sequence data?" @@ -750,7 +750,7 @@ def validate_target_bed_files_exist(self): for lab_datum in self.lab_data: if ( - lab_datum.has_sequence_data() + lab_datum.sequence_data is not None and lab_datum.library_type in lib_types and not lab_datum.sequence_data.contains_files(FileType.bed) ): @@ -766,7 +766,7 @@ def validate_vcf_file_exists(self): Check if there is a VCF file """ for lab_datum in self.lab_data: - if lab_datum.has_sequence_data() and not lab_datum.sequence_data.contains_files(FileType.vcf): + if lab_datum.sequence_data is not None and not lab_datum.sequence_data.contains_files(FileType.vcf): raise ValueError( f"VCF file missing for lab datum '{lab_datum.lab_data_name}' in donor '{self.donor_pseudonym}'." ) @@ -779,7 +779,7 @@ def validate_sequencing_file_exists(self): # noqa: C901 Check if there is a FASTQ or BAM file (depending on library type) """ for lab_datum in self.lab_data: - if not lab_datum.has_sequence_data(): + if lab_datum.sequence_data is None: # Skip if no sequence data is present continue fastq_files = lab_datum.sequence_data.list_files(FileType.fastq) @@ -957,6 +957,7 @@ def validate_reference_genome_compatibility(self): (donor.donor_pseudonym, lab_datum.lab_data_name): lab_datum.sequence_data.reference_genome for donor in self.donors for lab_datum in donor.lab_data + if lab_datum.sequence_data is not None } unique_reference_genomes = set(reference_genomes.values()) if len(unique_reference_genomes) > 1: @@ -970,13 +971,12 @@ def validate_reference_genome_compatibility(self): def _check_thresholds(donor: Donor, lab_datum: LabDatum, thresholds: dict[str, Any]): - if not lab_datum.has_sequence_data(): + if lab_datum.sequence_data is None: # Skip if no sequence data is present; warning issues in the validator `warn_empty_sequence_data` of `Donor`. return pseudonym = donor.donor_pseudonym lab_data_name = lab_datum.lab_data_name - # mypy cannot reason about the `has_sequence_data` check - 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