Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Monorepo-wide fixes #62

Open
1 of 6 tasks
afermg opened this issue Jan 10, 2025 · 3 comments
Open
1 of 6 tasks

Monorepo-wide fixes #62

afermg opened this issue Jan 10, 2025 · 3 comments
Assignees
@afermg
Labels
documentation Improvements or additions to documentation maintenance Chores that improve the quality and sustainability of the codebase

Comments

@afermg
Copy link
Collaborator

afermg commented Jan 10, 2025 •
edited
Loading

Since most of the monorepo libraries are in a relatively stable status, it is worth cleaning up and documenting to ensure high quality. These are the main steps, but let me know if there is something else you think we should do @shntnu @leoank:

  • ruff formatting
  • ruff checks
    • All public functions documented
    • Typing defined

Lesser priority/require more work

  • CI for testing/checking
  • Docstrings contain valid examples
@afermg afermg self-assigned this Jan 10, 2025
@afermg afermg added documentation Improvements or additions to documentation maintenance Chores that improve the quality and sustainability of the codebase labels Jan 10, 2025
@afermg
Copy link
Collaborator Author

afermg commented Jan 10, 2025

Automated fixes applied on 63b80f5

@afermg
Copy link
Collaborator Author

afermg commented Jan 10, 2025 •
edited
Loading

Output of the "ruff check" on the root of the monorepo:

❯ ruff check --fix --ignore D212 --output-format concise
warning: `incorrect-blank-line-before-class` (D203) and `no-blank-line-before-class` (D211) are incompatible. Ignoring `incorrect-blank-line-before-class`.
libs/jump_babel/src/broad_babel/__init__.py:1:1: D104 Missing docstring in public package
libs/jump_babel/src/broad_babel/data.py:1:1: D100 Missing docstring in public module
libs/jump_babel/src/broad_babel/data.py:9:5: D103 Missing docstring in public function
libs/jump_babel/src/broad_babel/data.py:11:5: N806 Variable `METADATA_LOCATION` in function should be lowercase
libs/jump_babel/src/broad_babel/data.py:16:5: N806 Variable `METAFILE_HASH` in function should be lowercase
libs/jump_babel/src/broad_babel/query.py:1:1: D400 First line should end with a period
libs/jump_babel/src/broad_babel/query.py:1:1: D415 First line should end with a period, question mark, or exclamation point
libs/jump_babel/src/broad_babel/query.py:26:13: UP006 Use `dict` instead of `t.Dict` for type annotation
libs/jump_babel/src/broad_babel/query.py:35:89: E501 Line too long (125 > 88)
libs/jump_babel/src/broad_babel/query.py:39:89: E501 Line too long (89 > 88)
libs/jump_babel/src/broad_babel/query.py:47:89: E501 Line too long (109 > 88)
libs/jump_babel/src/broad_babel/query.py:63:49: UP031 Use format specifiers instead of percent format
libs/jump_babel/src/broad_babel/query.py:77:5: D205 1 blank line required between summary line and description
libs/jump_babel/src/broad_babel/query.py:77:5: D401 First line of docstring should be in imperative mood: "Convenience function to generate a mapper from a set of queries."
libs/jump_babel/src/broad_babel/query.py:88:89: E501 Line too long (91 > 88)
libs/jump_babel/src/broad_babel/query.py:112:5: D417 Missing argument description in the docstring for `broad_to_standard`: `query`
libs/jump_babel/src/broad_babel/query.py:112:37: UP006 Use `list` instead of `t.List` for type annotation
libs/jump_babel/src/broad_babel/query.py:112:60: UP006 Use `dict` instead of `t.Dict` for type annotation
libs/jump_babel/src/broad_babel/query.py:119:89: E501 Line too long (112 > 88)
libs/jump_babel/src/broad_babel/query.py:138:5: ANN201 Missing return type annotation for public function `export_csv`
libs/jump_babel/src/broad_babel/query.py:158:10: PTH123 `open()` should be replaced by `Path.open()`
libs/jump_babel/test/query_test.py:1:1: D100 Missing docstring in public module
libs/jump_babel/test/query_test.py:9:5: ANN201 Missing return type annotation for public function `test_export`
libs/jump_babel/test/query_test.py:9:5: D103 Missing docstring in public function
libs/jump_babel/test/query_test.py:31:5: ANN201 Missing return type annotation for public function `test_basic_query_broad`
libs/jump_babel/test/query_test.py:31:5: D103 Missing docstring in public function
libs/jump_babel/test/query_test.py:31:28: ANN001 Missing type annotation for function argument `query`
libs/jump_babel/test/query_test.py:31:35: ANN001 Missing type annotation for function argument `output_columns`
libs/jump_babel/test/query_test.py:45:5: ANN201 Missing return type annotation for public function `test_broad_to_standard`
libs/jump_babel/test/query_test.py:45:5: D103 Missing docstring in public function
libs/jump_babel/test/query_test.py:45:28: ANN001 Missing type annotation for function argument `query`
libs/jump_babel/test/query_test.py:53:5: ANN201 Missing return type annotation for public function `test_like_query`
libs/jump_babel/test/query_test.py:53:5: D103 Missing docstring in public function
libs/jump_babel/test/query_test.py:53:21: ANN001 Missing type annotation for function argument `query`
libs/jump_babel/tools/broad_babel_example.py:1:1: D100 Missing docstring in public module
libs/jump_babel/tools/gen_database.py:2:1: D400 First line should end with a period
libs/jump_babel/tools/gen_database.py:2:1: D415 First line should end with a period, question mark, or exclamation point
libs/jump_babel/tools/gen_database.py:19:5: ANN201 Missing return type annotation for public function `select_if_available`
libs/jump_babel/tools/gen_database.py:19:5: D103 Missing docstring in public function
libs/jump_babel/tools/gen_database.py:25:5: D103 Missing docstring in public function
libs/jump_babel/tools/numeric_entrez_to_gene_name.py:3:89: E501 Line too long (94 > 88)
libs/jump_babel/tools/numeric_entrez_to_gene_name.py:18:6: PTH123 `open()` should be replaced by `Path.open()`
libs/jump_portrait/src/jump_portrait/fetch.py:5:89: E501 Line too long (114 > 88)
libs/jump_portrait/src/jump_portrait/fetch.py:10:89: E501 Line too long (94 > 88)
libs/jump_portrait/src/jump_portrait/fetch.py:34:5: D401 First line of docstring should be in imperative mood: "Returns a formatted string for an S3 path to Cell Painting data."
libs/jump_portrait/src/jump_portrait/fetch.py:73:5: D401 First line of docstring should be in imperative mood: "Retrieves a sample of cell painting data from S3."
libs/jump_portrait/src/jump_portrait/fetch.py:102:5: D417 Missing argument descriptions in the docstring for `get_jump_image`: `compressed`, `staging`
libs/jump_portrait/src/jump_portrait/fetch.py:114:5: D205 1 blank line required between summary line and description
libs/jump_portrait/src/jump_portrait/fetch.py:114:5: D401 First line of docstring should be in imperative mood: "Main function to fetch a JUMP image for AWS."
libs/jump_portrait/src/jump_portrait/fetch.py:183:89: E501 Line too long (124 > 88)
libs/jump_portrait/src/jump_portrait/fetch.py:222:5: D205 1 blank line required between summary line and description
libs/jump_portrait/src/jump_portrait/fetch.py:244:89: E501 Line too long (136 > 88)
libs/jump_portrait/src/jump_portrait/fetch.py:248:89: E501 Line too long (113 > 88)
libs/jump_portrait/src/jump_portrait/fetch.py:275:5: D401 First line of docstring should be in imperative mood: "Filters a dataframe with well info. Loading and filtering happens in a threaded manner. Note that it does not check for whole row duplication."
libs/jump_portrait/src/jump_portrait/fetch.py:276:89: E501 Line too long (146 > 88)
libs/jump_portrait/src/jump_portrait/fetch.py:326:25: ANN001 Missing type annotation for function argument `s3_location_uri`
libs/jump_portrait/src/jump_portrait/fetch.py:327:5: D205 1 blank line required between summary line and description
libs/jump_portrait/src/jump_portrait/fetch.py:328:89: E501 Line too long (96 > 88)
libs/jump_portrait/src/jump_portrait/fetch.py:329:89: E501 Line too long (110 > 88)
libs/jump_portrait/src/jump_portrait/fetch.py:353:5: D417 Missing argument description in the docstring for `get_item_location_info`: `input_column`
libs/jump_portrait/src/jump_portrait/fetch.py:355:5: ANN001 Missing type annotation for function argument `input_column`
libs/jump_portrait/src/jump_portrait/fetch.py:357:5: D401 First line of docstring should be in imperative mood: "Wrapper to obtain a dataframe with locations of an item. It removes duplicate rows."
libs/jump_portrait/src/jump_portrait/fetch.py:383:89: E501 Line too long (90 > 88)
libs/jump_portrait/src/jump_portrait/fetch.py:393:5: D417 Missing argument descriptions in the docstring for `get_gene_images`: `channels`, `samples_per_plate`
libs/jump_portrait/src/jump_portrait/fetch.py:400:5: D205 1 blank line required between summary line and description
libs/jump_portrait/src/jump_portrait/fetch.py:400:5: D401 First line of docstring should be in imperative mood: "Returns a collage of images from a given gene. Returned matrices are arranged in two rows,"
libs/jump_portrait/src/jump_portrait/fetch.py:401:89: E501 Line too long (94 > 88)
libs/jump_portrait/src/jump_portrait/fetch.py:420:89: E501 Line too long (110 > 88)
libs/jump_portrait/src/jump_portrait/fetch.py:453:39: NPY002 Replace legacy `np.random.randint` call with `np.random.Generator`
libs/jump_portrait/src/jump_portrait/s3.py:1:1: D100 Missing docstring in public module
libs/jump_portrait/src/jump_portrait/s3.py:27:5: ANN201 Missing return type annotation for public function `s3client`
libs/jump_portrait/src/jump_portrait/s3.py:27:5: D103 Missing docstring in public function
libs/jump_portrait/src/jump_portrait/s3.py:54:5: D103 Missing docstring in public function
libs/jump_portrait/src/jump_portrait/s3.py:55:5: ANN001 Missing type annotation for function argument `s3_image_uri`
libs/jump_portrait/src/jump_portrait/s3.py:55:19: ANN001 Missing type annotation for function argument `bucket_name`
libs/jump_portrait/src/jump_portrait/s3.py:88:5: D417 Missing argument descriptions in the docstring for `get_corrected_image`: `apply_correction`, `channel`, `compressed`, `correction`, `images_location`, `staging`
libs/jump_portrait/src/jump_portrait/s3.py:97:89: E501 Line too long (125 > 88)
libs/jump_portrait/src/jump_portrait/s3.py:134:5: ANN201 Missing return type annotation for public function `keys`
libs/jump_portrait/src/jump_portrait/s3.py:134:5: D103 Missing docstring in public function
libs/jump_portrait/src/jump_portrait/s3.py:134:10: N803 Argument name `Bucket` should be lowercase
libs/jump_portrait/src/jump_portrait/s3.py:134:10: ANN001 Missing type annotation for function argument `Bucket`
libs/jump_portrait/src/jump_portrait/s3.py:134:18: N803 Argument name `Prefix` should be lowercase
libs/jump_portrait/src/jump_portrait/s3.py:134:18: ANN001 Missing type annotation for function argument `Prefix`
libs/jump_portrait/src/jump_portrait/s3.py:134:29: N803 Argument name `StartAfter` should be lowercase
libs/jump_portrait/src/jump_portrait/s3.py:134:29: ANN001 Missing type annotation for function argument `StartAfter`
libs/jump_portrait/src/jump_portrait/s3.py:134:44: N803 Argument name `Delimiter` should be lowercase
libs/jump_portrait/src/jump_portrait/s3.py:134:44: ANN001 Missing type annotation for function argument `Delimiter`
libs/jump_portrait/src/jump_portrait/s3.py:135:5: N806 Variable `Prefix` in function should be lowercase
libs/jump_portrait/src/jump_portrait/s3.py:139:13: N806 Variable `StartAfter` in function should be lowercase
libs/jump_portrait/src/jump_portrait/s3.py:157:5: D419 Docstring is empty
libs/jump_portrait/src/jump_portrait/s3.py:180:20: PTH122 `os.path.splitext()` should be replaced by `Path.suffix`, `Path.stem`, and `Path.parent`
libs/jump_portrait/src/jump_portrait/s3.py:197:5: ANN201 Missing return type annotation for public function `read_parquet_s3`
libs/jump_portrait/src/jump_portrait/save.py:2:1: D205 1 blank line required between summary line and description
libs/jump_portrait/src/jump_portrait/save.py:2:1: D400 First line should end with a period
libs/jump_portrait/src/jump_portrait/save.py:2:1: D415 First line should end with a period, question mark, or exclamation point
libs/jump_portrait/src/jump_portrait/save.py:24:5: D103 Missing docstring in public function
libs/jump_portrait/src/jump_portrait/save.py:50:5: ANN201 Missing return type annotation for public function `save_image`
libs/jump_portrait/src/jump_portrait/save.py:50:5: D103 Missing docstring in public function
libs/jump_portrait/src/jump_portrait/save.py:51:5: ANN001 Missing type annotation for function argument `row`
libs/jump_portrait/src/jump_portrait/save.py:58:5: F841 Local variable `s3_image_path` is assigned to but never used
libs/jump_portrait/src/jump_portrait/test_get_location_info.py:1:1: D100 Missing docstring in public module
libs/jump_portrait/src/jump_portrait/utils.py:1:1: D400 First line should end with a period
libs/jump_portrait/src/jump_portrait/utils.py:1:1: D415 First line should end with a period, question mark, or exclamation point
libs/jump_portrait/src/jump_portrait/utils.py:41:5: D417 Missing argument description in the docstring for `parallel`: `**kwargs`
libs/jump_portrait/src/jump_portrait/utils.py:91:5: ANN201 Missing return type annotation for public function `batch_processing`
libs/jump_portrait/src/jump_portrait/utils.py:91:5: D103 Missing docstring in public function
libs/jump_portrait/src/jump_portrait/utils.py:93:9: ANN202 Missing return type annotation for private function `batched_fn`
libs/jump_portrait/src/jump_portrait/utils.py:94:66: ANN002 Missing type annotation for `*args`
libs/jump_portrait/src/jump_portrait/utils.py:94:73: ANN003 Missing type annotation for `**kwargs`
libs/jump_portrait/src/jump_portrait/utils.py:112:5: ANN201 Missing return type annotation for public function `try_function`
libs/jump_portrait/src/jump_portrait/utils.py:112:5: D417 Missing argument description in the docstring for `try_function`: `f`
libs/jump_portrait/src/jump_portrait/utils.py:113:5: D205 1 blank line required between summary line and description
libs/jump_portrait/src/jump_portrait/utils.py:113:5: D400 First line should end with a period
libs/jump_portrait/src/jump_portrait/utils.py:113:5: D415 First line should end with a period, question mark, or exclamation point
libs/jump_portrait/src/jump_portrait/utils.py:129:9: ANN202 Missing return type annotation for private function `tryed_fn`
libs/jump_portrait/src/jump_portrait/utils.py:129:18: ANN002 Missing type annotation for `*item`
libs/jump_portrait/src/jump_portrait/utils.py:129:25: ANN003 Missing type annotation for `**kwargs`
libs/jump_portrait/src/jump_portrait/utils.py:133:9: E722 Do not use bare `except`
libs/jump_portrait/src/jump_portrait/workflow.py:2:1: D205 1 blank line required between summary line and description
libs/jump_portrait/src/jump_portrait/workflow.py:2:1: D400 First line should end with a period
libs/jump_portrait/src/jump_portrait/workflow.py:2:1: D415 First line should end with a period, question mark, or exclamation point
libs/jump_portrait/src/jump_portrait/workflow.py:33:1: E402 Module level import not at top of file
libs/jump_portrait/src/jump_portrait/workflow.py:34:1: E402 Module level import not at top of file
libs/jump_portrait/test/integration_tests.py:1:1: D100 Missing docstring in public module
libs/jump_portrait/test/integration_tests.py:24:5: ANN201 Missing return type annotation for public function `test_get_jump_image`
libs/jump_portrait/test/integration_tests.py:24:5: D103 Missing docstring in public function
libs/jump_portrait/test/integration_tests.py:25:5: ANN001 Missing type annotation for function argument `source`
libs/jump_portrait/test/integration_tests.py:26:5: ANN001 Missing type annotation for function argument `batch`
libs/jump_portrait/test/integration_tests.py:27:5: ANN001 Missing type annotation for function argument `plate`
libs/jump_portrait/test/integration_tests.py:28:5: ANN001 Missing type annotation for function argument `well`
libs/jump_portrait/test/integration_tests.py:29:5: ANN001 Missing type annotation for function argument `channel`
libs/jump_portrait/test/integration_tests.py:30:5: ANN001 Missing type annotation for function argument `site`
libs/jump_portrait/test/integration_tests.py:31:5: ANN001 Missing type annotation for function argument `correction`
libs/jump_portrait/test/integration_tests.py:32:5: ANN001 Missing type annotation for function argument `apply_correction`
libs/jump_portrait/test/integration_tests.py:33:5: ANN001 Missing type annotation for function argument `compressed`
libs/jump_portrait/test/integration_tests.py:34:5: ANN001 Missing type annotation for function argument `staging`
libs/jump_portrait/test/integration_tests.py:54:5: ANN201 Missing return type annotation for public function `test_get_corrected_image`
libs/jump_portrait/test/integration_tests.py:54:5: D103 Missing docstring in public function
libs/jump_portrait/test/integration_tests.py:59:5: ANN201 Missing return type annotation for public function `test_download_image`
libs/jump_portrait/test/integration_tests.py:59:5: D103 Missing docstring in public function
libs/jump_portrait/test/integration_tests.py:64:5: ANN201 Missing return type annotation for public function `test_negcon`
libs/jump_portrait/test/integration_tests.py:64:5: D103 Missing docstring in public function
libs/jump_portrait/test/integration_tests.py:66:5: F841 Local variable `tmp` is assigned to but never used
libs/jump_portrait/test/integration_tests.py:66:11: F821 Undefined name `get_item_location_info`
libs/jump_portrait/test/unit_test.py:1:1: D100 Missing docstring in public module
libs/jump_portrait/test/unit_test.py:12:5: ANN201 Missing return type annotation for public function `test_get_item_location`
libs/jump_portrait/test/unit_test.py:12:5: D103 Missing docstring in public function
libs/jump_portrait/test/unit_test.py:12:28: ANN001 Missing type annotation for function argument `gene`
libs/jump_portrait/test/unit_test.py:26:5: ANN201 Missing return type annotation for public function `test_get_image`
libs/jump_portrait/test/unit_test.py:26:5: D103 Missing docstring in public function
libs/jump_portrait/test/unit_test.py:26:20: ANN001 Missing type annotation for function argument `s3_image_uri`
libs/jump_portrait/test/unit_test.py:31:5: ANN201 Missing return type annotation for public function `get_metadata`
libs/jump_portrait/test/unit_test.py:31:5: D103 Missing docstring in public function
libs/jump_portrait/test/unit_test.py:45:5: ANN201 Missing return type annotation for public function `test_get_jump_image_batch`
libs/jump_portrait/test/unit_test.py:45:5: D103 Missing docstring in public function
libs/jump_portrait/test/unit_test.py:45:31: ANN001 Missing type annotation for function argument `get_metadata`
libs/jump_portrait/test/unit_test.py:45:45: ANN001 Missing type annotation for function argument `channel`
libs/jump_portrait/test/unit_test.py:45:54: ANN001 Missing type annotation for function argument `site`
libs/jump_portrait/test/unit_test.py:45:60: ANN001 Missing type annotation for function argument `correction`
libs/jump_portrait/test/unit_test.py:63:89: E501 Line too long (116 > 88)
libs/jump_portrait/test/unit_test.py:77:89: E501 Line too long (135 > 88)
libs/jump_portrait/test/unit_test.py:90:89: E501 Line too long (94 > 88)
libs/jump_rr/src/jump_rr/calculate_features.py:15:1: D205 1 blank line required between summary line and description
libs/jump_rr/src/jump_rr/calculate_features.py:83:89: E501 Line too long (114 > 88)
libs/jump_rr/src/jump_rr/calculate_matches.py:17:1: D205 1 blank line required between summary line and description
libs/jump_rr/src/jump_rr/concensus.py:2:1: D400 First line should end with a period
libs/jump_rr/src/jump_rr/concensus.py:2:1: D415 First line should end with a period, question mark, or exclamation point
libs/jump_rr/src/jump_rr/concensus.py:17:5: D205 1 blank line required between summary line and description
libs/jump_rr/src/jump_rr/concensus.py:17:5: D401 First line of docstring should be in imperative mood: "Returns the data frame as the aggregated median values, metadata and urls."
libs/jump_rr/src/jump_rr/concensus.py:19:89: E501 Line too long (108 > 88)
libs/jump_rr/src/jump_rr/concensus.py:34:5: ANN201 Missing return type annotation for public function `get_group_median`
libs/jump_rr/src/jump_rr/concensus.py:34:22: ANN001 Missing type annotation for function argument `med`
libs/jump_rr/src/jump_rr/concensus.py:35:5: D400 First line should end with a period
libs/jump_rr/src/jump_rr/concensus.py:35:5: D415 First line should end with a period, question mark, or exclamation point
libs/jump_rr/src/jump_rr/concensus.py:47:5: D205 1 blank line required between summary line and description
libs/jump_rr/src/jump_rr/concensus.py:47:5: D400 First line should end with a period
libs/jump_rr/src/jump_rr/concensus.py:47:5: D415 First line should end with a period, question mark, or exclamation point
libs/jump_rr/src/jump_rr/concensus.py:57:5: D103 Missing docstring in public function
libs/jump_rr/src/jump_rr/concensus.py:61:5: D103 Missing docstring in public function
libs/jump_rr/src/jump_rr/datasets.py:7:5: ANN201 Missing return type annotation for public function `get_dataset`
libs/jump_rr/src/jump_rr/datasets.py:7:5: D103 Missing docstring in public function
libs/jump_rr/src/jump_rr/datasets.py:16:89: E501 Line too long (99 > 88)
libs/jump_rr/src/jump_rr/datasets.py:17:89: E501 Line too long (96 > 88)
libs/jump_rr/src/jump_rr/feature_wide_correlations.py:14:1: D205 1 blank line required between summary line and description
libs/jump_rr/src/jump_rr/feature_wide_correlations.py:28:5: ANN201 Missing return type annotation for public function `map_back`
libs/jump_rr/src/jump_rr/feature_wide_correlations.py:28:5: D103 Missing docstring in public function
libs/jump_rr/src/jump_rr/feature_wide_correlations.py:28:14: ANN001 Missing type annotation for function argument `k`
libs/jump_rr/src/jump_rr/feature_wide_correlations.py:28:17: ANN001 Missing type annotation for function argument `n`
libs/jump_rr/src/jump_rr/formatters.py:1:1: D100 Missing docstring in public module
libs/jump_rr/src/jump_rr/formatters.py:9:5: D103 Missing docstring in public function
libs/jump_rr/src/jump_rr/formatters.py:14:89: E501 Line too long (89 > 88)
libs/jump_rr/src/jump_rr/formatters.py:22:5: D103 Missing docstring in public function
libs/jump_rr/src/jump_rr/galleries.py:40:5: ANN201 Missing return type annotation for public function `generate_gallery`
libs/jump_rr/src/jump_rr/galleries.py:40:5: D103 Missing docstring in public function
libs/jump_rr/src/jump_rr/index_selection.py:1:1: D100 Missing docstring in public module
libs/jump_rr/src/jump_rr/index_selection.py:6:5: D103 Missing docstring in public function
libs/jump_rr/src/jump_rr/index_selection.py:6:51: ANN001 Missing type annotation for function argument `skip_first`
libs/jump_rr/src/jump_rr/index_selection.py:20:5: D103 Missing docstring in public function
libs/jump_rr/src/jump_rr/metadata.py:1:1: D205 1 blank line required between summary line and description
libs/jump_rr/src/jump_rr/metadata.py:1:1: D400 First line should end with a period
libs/jump_rr/src/jump_rr/metadata.py:1:1: D415 First line should end with a period, question mark, or exclamation point
libs/jump_rr/src/jump_rr/metadata.py:20:89: E501 Line too long (156 > 88)
libs/jump_rr/src/jump_rr/metadata.py:21:89: E501 Line too long (126 > 88)
libs/jump_rr/src/jump_rr/metadata.py:22:89: E501 Line too long (196 > 88)
libs/jump_rr/src/jump_rr/metadata.py:23:89: E501 Line too long (182 > 88)
libs/jump_rr/src/jump_rr/metadata.py:24:89: E501 Line too long (149 > 88)
libs/jump_rr/src/jump_rr/metadata.py:25:89: E501 Line too long (227 > 88)
libs/jump_rr/src/jump_rr/metadata.py:26:89: E501 Line too long (136 > 88)
libs/jump_rr/src/jump_rr/metadata.py:27:89: E501 Line too long (107 > 88)
libs/jump_rr/src/jump_rr/metadata.py:28:89: E501 Line too long (102 > 88)
libs/jump_rr/src/jump_rr/metadata.py:29:89: E501 Line too long (228 > 88)
libs/jump_rr/src/jump_rr/metadata.py:30:89: E501 Line too long (123 > 88)
libs/jump_rr/src/jump_rr/metadata.py:31:89: E501 Line too long (98 > 88)
libs/jump_rr/src/jump_rr/metadata.py:32:89: E501 Line too long (149 > 88)
libs/jump_rr/src/jump_rr/metadata.py:33:89: E501 Line too long (224 > 88)
libs/jump_rr/src/jump_rr/metadata.py:35:89: E501 Line too long (333 > 88)
libs/jump_rr/src/jump_rr/metadata.py:36:89: E501 Line too long (299 > 88)
libs/jump_rr/src/jump_rr/metadata.py:37:89: E501 Line too long (149 > 88)
libs/jump_rr/src/jump_rr/metadata.py:38:89: E501 Line too long (116 > 88)
libs/jump_rr/src/jump_rr/metadata.py:39:89: E501 Line too long (319 > 88)
libs/jump_rr/src/jump_rr/metadata.py:67:5: ANN201 Missing return type annotation for public function `write_metadata`
libs/jump_rr/src/jump_rr/metadata.py:68:5: D401 First line of docstring should be in imperative mood: "Writes metadata file to customize Datasette."
libs/jump_rr/src/jump_rr/metadata.py:96:89: E501 Line too long (168 > 88)
libs/jump_rr/src/jump_rr/metadata.py:103:10: PTH123 `open()` should be replaced by `Path.open()`
libs/jump_rr/src/jump_rr/metadata.py:114:5: ANN201 Missing return type annotation for public function `table_type_to_suffix`
libs/jump_rr/src/jump_rr/parse_features.py:1:1: D100 Missing docstring in public module
libs/jump_rr/src/jump_rr/parse_features.py:12:5: D205 1 blank line required between summary line and description
libs/jump_rr/src/jump_rr/parse_features.py:12:5: D400 First line should end with a period
libs/jump_rr/src/jump_rr/parse_features.py:12:5: D415 First line should end with a period, question mark, or exclamation point
libs/jump_rr/src/jump_rr/replicability.py:2:89: E501 Line too long (121 > 88)
libs/jump_rr/src/jump_rr/replicability.py:9:5: D400 First line should end with a period
libs/jump_rr/src/jump_rr/replicability.py:9:5: D415 First line should end with a period, question mark, or exclamation point
libs/jump_rr/src/jump_rr/replicability.py:12:89: E501 Line too long (116 > 88)
libs/jump_rr/src/jump_rr/replicability.py:14:89: E501 Line too long (102 > 88)
libs/jump_rr/src/jump_rr/replicability.py:22:5: D103 Missing docstring in public function
libs/jump_rr/src/jump_rr/replicability.py:35:5: ANN003 Missing type annotation for `**kwargs`
libs/jump_rr/src/jump_rr/replicability.py:37:5: D205 1 blank line required between summary line and description
libs/jump_rr/src/jump_rr/replicability.py:38:89: E501 Line too long (114 > 88)
libs/jump_rr/src/jump_rr/replicability.py:39:89: E501 Line too long (112 > 88)
libs/jump_rr/src/jump_rr/replicability.py:40:89: E501 Line too long (99 > 88)
libs/jump_rr/src/jump_rr/significance.py:15:1: D205 1 blank line required between summary line and description
libs/jump_rr/src/jump_rr/significance.py:15:1: D400 First line should end with a period
libs/jump_rr/src/jump_rr/significance.py:15:1: D415 First line should end with a period, question mark, or exclamation point
libs/jump_rr/src/jump_rr/significance.py:20:89: E501 Line too long (156 > 88)
libs/jump_rr/src/jump_rr/significance.py:21:89: E501 Line too long (222 > 88)
libs/jump_rr/src/jump_rr/significance.py:55:89: E501 Line too long (92 > 88)
libs/jump_rr/src/jump_rr/significance.py:81:5: D103 Missing docstring in public function
libs/jump_rr/src/jump_rr/significance.py:100:5: D205 1 blank line required between summary line and description
libs/jump_rr/src/jump_rr/significance.py:159:5: ANN201 Missing return type annotation for public function `get_p_value`
libs/jump_rr/src/jump_rr/significance.py:159:17: ANN001 Missing type annotation for function argument `a`
libs/jump_rr/src/jump_rr/significance.py:159:20: ANN001 Missing type annotation for function argument `b`
libs/jump_rr/src/jump_rr/significance.py:160:5: D205 1 blank line required between summary line and description
libs/jump_rr/src/jump_rr/significance.py:160:5: D400 First line should end with a period
libs/jump_rr/src/jump_rr/significance.py:160:5: D415 First line should end with a period, question mark, or exclamation point
libs/jump_rr/src/jump_rr/significance.py:162:89: E501 Line too long (120 > 88)
libs/jump_rr/src/jump_rr/significance.py:190:5: ANN201 Missing return type annotation for public function `get_pvalue_mwu`
libs/jump_rr/src/jump_rr/significance.py:190:20: ANN001 Missing type annotation for function argument `a`
libs/jump_rr/src/jump_rr/significance.py:190:23: ANN001 Missing type annotation for function argument `b`
libs/jump_rr/src/jump_rr/significance.py:190:26: ANN001 Missing type annotation for function argument `axis`
libs/jump_rr/src/jump_rr/significance.py:191:5: D400 First line should end with a period
libs/jump_rr/src/jump_rr/significance.py:191:5: D401 First line of docstring should be in imperative mood: "Wrapper over scipy ttest_ind"
libs/jump_rr/src/jump_rr/significance.py:191:5: D415 First line should end with a period, question mark, or exclamation point
libs/jump_rr/src/jump_rr/significance.py:195:5: ANN201 Missing return type annotation for public function `calculate_mw`
libs/jump_rr/src/jump_rr/significance.py:200:5: D205 1 blank line required between summary line and description
libs/jump_rr/src/jump_rr/significance.py:200:5: D400 First line should end with a period
libs/jump_rr/src/jump_rr/significance.py:200:5: D415 First line should end with a period, question mark, or exclamation point
libs/jump_rr/src/jump_rr/significance.py:236:5: D205 1 blank line required between summary line and description
libs/jump_rr/src/jump_rr/significance.py:236:5: D400 First line should end with a period
libs/jump_rr/src/jump_rr/significance.py:236:5: D415 First line should end with a period, question mark, or exclamation point
libs/jump_rr/src/jump_rr/significance.py:241:89: E501 Line too long (93 > 88)
libs/jump_rr/src/jump_rr/significance.py:270:5: D205 1 blank line required between summary line and description
libs/jump_rr/src/jump_rr/significance.py:299:46: ANN002 Missing type annotation for `*args`
libs/jump_rr/src/jump_rr/significance.py:299:53: ANN003 Missing type annotation for `**kwargs`
libs/jump_rr/src/jump_rr/significance.py:300:5: D205 1 blank line required between summary line and description
libs/jump_rr/src/jump_rr/significance_feat_vs_pert.py:1:1: D100 Missing docstring in public module
libs/jump_rr/src/jump_rr/significance_feat_vs_pert.py:19:9: ANN201 Missing return type annotation for public function `wrapper_mwu`
libs/jump_rr/src/jump_rr/significance_feat_vs_pert.py:19:9: D103 Missing docstring in public function
libs/jump_rr/src/jump_rr/significance_feat_vs_pert.py:19:21: ANN001 Missing type annotation for function argument `jcp_pair`
libs/jump_rr/src/jump_rr/synonyms.py:9:5: ANN201 Missing return type annotation for public function `get_synonym_mapper`
libs/jump_rr/src/jump_rr/synonyms.py:9:5: D103 Missing docstring in public function
libs/jump_rr/src/jump_rr/test_matches.py:1:1: D100 Missing docstring in public module
libs/jump_rr/src/jump_rr/translate.py:1:1: D100 Missing docstring in public module
libs/jump_rr/src/jump_rr/translate.py:6:5: ANN201 Missing return type annotation for public function `get_mappers`
libs/jump_rr/src/jump_rr/translate.py:13:5: D205 1 blank line required between summary line and description
libs/trommel/src/trommel/core.py:131:9: B007 Loop control variable `i` not used within loop body
Found 285 errors.

@shntnu
Copy link
Contributor

shntnu commented Jan 10, 2025

These are the main steps, but let me know if there is something else you think we should do

Looks great!

I was going to suggest setting up precommit but then I saw this broadinstitute/carpenter-singh-lab-standards#4

So nothing further to add

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Assignees

@afermg afermg

Labels
documentation Improvements or additions to documentation maintenance Chores that improve the quality and sustainability of the codebase
Projects
None yet
Milestone
No milestone
Development

No branches or pull requests
2 participants
@shntnu @afermg