From e30cf22953249eee1cba0579bd374e889deeac70 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Mon, 13 Oct 2025 19:15:36 +0000 Subject: [PATCH 1/2] Bump the python-packages group with 2 updates Bumps the python-packages group with 2 updates: [cloudpathlib](https://github.com/drivendataorg/cloudpathlib) and [botocore](https://github.com/boto/botocore). Updates `cloudpathlib` from 0.22.0 to 0.23.0 - [Release notes](https://github.com/drivendataorg/cloudpathlib/releases) - [Changelog](https://github.com/drivendataorg/cloudpathlib/blob/master/HISTORY.md) - [Commits](https://github.com/drivendataorg/cloudpathlib/compare/v0.22.0...v0.23.0) Updates `botocore` from 1.40.45 to 1.40.50 - [Commits](https://github.com/boto/botocore/compare/1.40.45...1.40.50) --- updated-dependencies: - dependency-name: cloudpathlib dependency-version: 0.23.0 dependency-type: direct:production update-type: version-update:semver-minor dependency-group: python-packages - dependency-name: botocore dependency-version: 1.40.50 dependency-type: direct:development update-type: version-update:semver-patch dependency-group: python-packages ... Signed-off-by: dependabot[bot] --- poetry.lock | 14 +++++++------- pyproject.toml | 2 +- 2 files changed, 8 insertions(+), 8 deletions(-) diff --git a/poetry.lock b/poetry.lock index 0cf8817c..768885ac 100644 --- a/poetry.lock +++ b/poetry.lock @@ -608,14 +608,14 @@ crt = ["botocore[crt] (>=1.21.0,<2.0a0)"] [[package]] name = "botocore" -version = "1.40.45" +version = "1.40.50" description = "Low-level, data-driven core of boto 3." optional = false python-versions = ">=3.9" groups = ["main", "dev"] files = [ - {file = "botocore-1.40.45-py3-none-any.whl", hash = "sha256:9abf473d8372ade8442c0d4634a9decb89c854d7862ffd5500574eb63ab8f240"}, - {file = "botocore-1.40.45.tar.gz", hash = "sha256:cf8b743527a2a7e108702d24d2f617e93c6dc7ae5eb09aadbe866f15481059df"}, + {file = "botocore-1.40.50-py3-none-any.whl", hash = "sha256:53126c153fae0670dc54f03d01c89b1af144acedb1020199b133dedb309e434d"}, + {file = "botocore-1.40.50.tar.gz", hash = "sha256:1d3d5b5759c9cb30202cd5ad231ec8afb1abe5be0c088a1707195c2cbae0e742"}, ] [package.dependencies] @@ -851,14 +851,14 @@ colorama = {version = "*", markers = "platform_system == \"Windows\""} [[package]] name = "cloudpathlib" -version = "0.22.0" +version = "0.23.0" description = "pathlib-style classes for cloud storage services." optional = false python-versions = ">=3.9" groups = ["main"] files = [ - {file = "cloudpathlib-0.22.0-py3-none-any.whl", hash = "sha256:2fdfaf5c4f85810ae8374d336d04dee371914d0e41a984695ae67308d7a5a009"}, - {file = "cloudpathlib-0.22.0.tar.gz", hash = "sha256:6c0cb0ceab4f66a3a05a84055f9318fb8316cae5e096819f3f8e4be64feab6e9"}, + {file = "cloudpathlib-0.23.0-py3-none-any.whl", hash = "sha256:8520b3b01468fee77de37ab5d50b1b524ea6b4a8731c35d1b7407ac0cd716002"}, + {file = "cloudpathlib-0.23.0.tar.gz", hash = "sha256:eb38a34c6b8a048ecfd2b2f60917f7cbad4a105b7c979196450c2f541f4d6b4b"}, ] [package.dependencies] @@ -5468,4 +5468,4 @@ test = ["big-O", "jaraco.functools", "jaraco.itertools", "jaraco.test", "more-it [metadata] lock-version = "2.1" python-versions = ">=3.9,<3.14" -content-hash = "df0306be2ea44627fabdae5894d1637d0ce01c24189b3e6322adfdb6766bd34d" +content-hash = "7d2ea3aa6f5938c14f0fa517072ed980839cfe15fb239633b15bf39e0e3ba211" diff --git a/pyproject.toml b/pyproject.toml index 1099a48e..453768a6 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -18,7 +18,7 @@ keywords = [ "python", "cellprofiler", "single-cell-analysis", "way-lab" ] [tool.poetry.dependencies] python = ">=3.9,<3.14" pyarrow = ">=13.0.0" -cloudpathlib = { extras = [ "all", "s3" ], version = ">=0.18,<0.23" } +cloudpathlib = { extras = [ "all", "s3" ], version = ">=0.18,<0.24" } duckdb = ">=0.8.0,!=0.10.0,>=0.10.1" parsl = ">=2023.9.25" numpy = [ From 8e9ff572d32c74af93c9dd97b5718ab018b05e15 Mon Sep 17 00:00:00 2001 From: d33bs Date: Mon, 13 Oct 2025 13:52:03 -0600 Subject: [PATCH 2/2] linting --- .pre-commit-config.yaml | 4 ++-- .pylintrc | 4 ---- .../in-carta/colas-lab/shrink_colas_lab_data_for_tests.py | 6 +++--- 3 files changed, 5 insertions(+), 9 deletions(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 3f824540..3324d3e2 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -56,7 +56,7 @@ repos: args: ["-c", "pyproject.toml"] additional_dependencies: ["bandit[toml]"] - repo: https://github.com/PyCQA/isort - rev: 6.1.0 + rev: 7.0.0 hooks: - id: isort - repo: https://github.com/jendrikseipp/vulture @@ -82,7 +82,7 @@ repos: hooks: - id: almanack-check - repo: https://github.com/PyCQA/pylint - rev: v3.3.9 + rev: v4.0.0 hooks: - id: pylint name: pylint diff --git a/.pylintrc b/.pylintrc index 19a310c3..ff8adac7 100644 --- a/.pylintrc +++ b/.pylintrc @@ -54,10 +54,6 @@ persistent=yes # the version used to run pylint. py-version=3.8 -# When enabled, pylint would attempt to guess common misconfiguration and emit -# user-friendly hints instead of false-positive error messages. -suggestion-mode=yes - # Allow loading of arbitrary C extensions. Extensions are imported into the # active Python interpreter and may run arbitrary code. unsafe-load-any-extension=no diff --git a/tests/data/in-carta/colas-lab/shrink_colas_lab_data_for_tests.py b/tests/data/in-carta/colas-lab/shrink_colas_lab_data_for_tests.py index 71425ae1..f5bc0d21 100644 --- a/tests/data/in-carta/colas-lab/shrink_colas_lab_data_for_tests.py +++ b/tests/data/in-carta/colas-lab/shrink_colas_lab_data_for_tests.py @@ -50,7 +50,7 @@ # as a pyarrow table then output to a new and # smaller csv for testing purposes. - OUTPUT_FILENAME = ( + output_filename = ( f"Test 0 Day{idx} Test Test_2024_Jan-0{idx+1}-{idx+12}-12-12_Test.csv" ) @@ -68,10 +68,10 @@ ).fetch_arrow_table(), # output the filtered data as a CSV to a new location output_file=( - f"{TARGET_DATA_DIR}/{OUTPUT_FILENAME}" + f"{TARGET_DATA_DIR}/{output_filename}" # For some files lowercase the first letter of the file # as a simulation of the source data. if idx < 3 - else f"{TARGET_DATA_DIR}/{OUTPUT_FILENAME[0].lower() + OUTPUT_FILENAME[1:]}" + else f"{TARGET_DATA_DIR}/{output_filename[0].lower() + output_filename[1:]}" ), )