Add PDB manifest pipeline #852
mattldawsontests.yml
on: pull_request
Check code formatting
41s
Run container tests
12m 53s
Matrix: tests
Annotations
10 errors and 1 warning
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ruff (ANN201):
src/cdm_data_loaders/parsers/gene_association_file.py#L121
src/cdm_data_loaders/parsers/gene_association_file.py:121:5: ANN201 Missing return type annotation for public function `normalize_dates`
help: Add return type annotation
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ruff (ANN001):
src/cdm_data_loaders/parsers/gene_association_file.py#L105
src/cdm_data_loaders/parsers/gene_association_file.py:105:28: ANN001 Missing type annotation for function argument `input_path`
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ruff (ANN001):
src/cdm_data_loaders/parsers/gene_association_file.py#L105
src/cdm_data_loaders/parsers/gene_association_file.py:105:21: ANN001 Missing type annotation for function argument `spark`
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ruff (ANN201):
src/cdm_data_loaders/parsers/gene_association_file.py#L105
src/cdm_data_loaders/parsers/gene_association_file.py:105:5: ANN201 Missing return type annotation for public function `load_annotation`
help: Add return type annotation
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ruff (ANN201):
src/cdm_data_loaders/parsers/gene_association_file.py#L94
src/cdm_data_loaders/parsers/gene_association_file.py:94:5: ANN201 Missing return type annotation for public function `get_spark`
help: Add return type annotation
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ruff (ANN401):
src/cdm_data_loaders/core/settings.py#L123
src/cdm_data_loaders/core/settings.py:123:54: ANN401 Dynamically typed expressions (typing.Any) are disallowed in `validate_dlt_config`
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ruff (ANN401):
src/cdm_data_loaders/core/settings.py#L123
src/cdm_data_loaders/core/settings.py:123:46: ANN401 Dynamically typed expressions (typing.Any) are disallowed in `dlt_config`
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ruff (INP001):
scripts/parse_index.py#L1
scripts/parse_index.py:1:1: INP001 File `scripts/parse_index.py` is part of an implicit namespace package. Add an `__init__.py`.
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ruff (PLW0603):
notebooks/ncbi_ftp_manifest.ipynb#L1
notebooks/ncbi_ftp_manifest.ipynb:1:1: PLW0603 Using the global statement to update `_last_refresh` is discouraged
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ruff (PLR2004):
notebooks/ncbi_ftp_download.ipynb#L1
notebooks/ncbi_ftp_download.ipynb:1:1: PLR2004 Magic value used in comparison, consider replacing `10` with a constant variable
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Run container tests
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