From a336d6cb0f18055d0371c566691ea64795a43d98 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Mon, 1 Jun 2026 18:54:05 +0000 Subject: [PATCH 1/5] Bump the pre-commit-hooks group with 10 updates Bumps the pre-commit-hooks group with 10 updates: | Package | From | To | | --- | --- | --- | | [https://github.com/tox-dev/pyproject-fmt](https://github.com/tox-dev/pyproject-fmt) | `v2.12.1` | `2.21.2` | | [https://github.com/executablebooks/mdformat](https://github.com/executablebooks/mdformat) | `0.7.18` | `1.0.0` | | [https://github.com/citation-file-format/cffconvert](https://github.com/citation-file-format/cffconvert) | `5295f87c0e261da61a7b919fc754e3a77edd98a7` | `b6045d78aac9e02b039703b030588d54d53262ac` | | cloudpathlib | `0.13.0` | `0.24.0` | | pyarrow | `13.0.0` | `24.0.0` | | pytest | `7.2.0` | `9.0.3` | | moto | `4.0.0` | `5.2.1` | | duckdb | `0.8.0` | `1.5.3` | | parsl | `2023.4.24` | `2026.5.18` | | pycytominer | `1.2.4` | `1.5.0` | Updates `https://github.com/tox-dev/pyproject-fmt` from v2.12.1 to 2.21.2 - [Release notes](https://github.com/tox-dev/pyproject-fmt/releases) - [Commits](https://github.com/tox-dev/pyproject-fmt/compare/v2.12.1...v2.21.2) Updates `https://github.com/executablebooks/mdformat` from 0.7.18 to 1.0.0 - [Commits](https://github.com/executablebooks/mdformat/compare/0.7.18...1.0.0) Updates `https://github.com/citation-file-format/cffconvert` from 5295f87c0e261da61a7b919fc754e3a77edd98a7 to b6045d78aac9e02b039703b030588d54d53262ac - [Release notes](https://github.com/citation-file-format/cffconvert/releases) - [Changelog](https://github.com/citation-file-format/cffconvert/blob/main/CHANGELOG.md) - [Commits](https://github.com/citation-file-format/cffconvert/compare/5295f87c0e261da61a7b919fc754e3a77edd98a7...b6045d78aac9e02b039703b030588d54d53262ac) Updates `cloudpathlib` from 0.13.0 to 0.24.0 Updates `pyarrow` from 13.0.0 to 24.0.0 Updates `pytest` from 7.2.0 to 9.0.3 Updates `moto` from 4.0.0 to 5.2.1 Updates `duckdb` from 0.8.0 to 1.5.3 Updates `parsl` from 2023.4.24 to 2026.5.18 Updates `pycytominer` from 1.2.4 to 1.5.0 --- updated-dependencies: - dependency-name: https://github.com/tox-dev/pyproject-fmt dependency-version: 2.21.2 dependency-type: direct:production dependency-group: pre-commit-hooks - dependency-name: https://github.com/executablebooks/mdformat dependency-version: 1.0.0 dependency-type: direct:production update-type: version-update:semver-major dependency-group: pre-commit-hooks - dependency-name: https://github.com/citation-file-format/cffconvert dependency-version: b6045d78aac9e02b039703b030588d54d53262ac dependency-type: direct:production dependency-group: pre-commit-hooks - dependency-name: cloudpathlib dependency-version: 0.24.0 dependency-type: direct:production update-type: version-update:semver-minor dependency-group: pre-commit-hooks - dependency-name: pyarrow dependency-version: 24.0.0 dependency-type: direct:production update-type: version-update:semver-major dependency-group: pre-commit-hooks - dependency-name: pytest dependency-version: 9.0.3 dependency-type: direct:production update-type: version-update:semver-major dependency-group: pre-commit-hooks - dependency-name: moto dependency-version: 5.2.1 dependency-type: direct:production update-type: version-update:semver-major dependency-group: pre-commit-hooks - dependency-name: duckdb dependency-version: 1.5.3 dependency-type: direct:production update-type: version-update:semver-major dependency-group: pre-commit-hooks - dependency-name: parsl dependency-version: 2026.5.18 dependency-type: direct:production update-type: version-update:semver-major dependency-group: pre-commit-hooks - dependency-name: pycytominer dependency-version: 1.5.0 dependency-type: direct:production update-type: version-update:semver-minor dependency-group: pre-commit-hooks ... Signed-off-by: dependabot[bot] --- .pre-commit-config.yaml | 20 ++++++++++---------- 1 file changed, 10 insertions(+), 10 deletions(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index d49648f2..108508a3 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -15,7 +15,7 @@ repos: hooks: - id: poetry-check - repo: https://github.com/tox-dev/pyproject-fmt - rev: "v2.12.1" + rev: "v2.21.2" hooks: - id: pyproject-fmt - repo: https://github.com/codespell-project/codespell @@ -29,7 +29,7 @@ repos: additional_dependencies: - tomli - repo: https://github.com/executablebooks/mdformat - rev: 0.7.18 + rev: 1.0.0 hooks: - id: mdformat additional_dependencies: @@ -73,7 +73,7 @@ repos: cytotable_from_the_cloud\.py$ ) - repo: https://github.com/citation-file-format/cffconvert - rev: 5295f87c0e261da61a7b919fc754e3a77edd98a7 + rev: b6045d78aac9e02b039703b030588d54d53262ac hooks: - id: validate-cff - repo: https://github.com/software-gardening/almanack @@ -98,11 +98,11 @@ repos: # pylint due to it's dynamic analysis capabilities # and the way pre-commit references virtual environments. additional_dependencies: - - "cloudpathlib[all]>=0.13.0" - - "pyarrow>=13.0.0" - - "pytest>=7.2.0" - - "moto[server,s3]>=4.0.0,<5.0.0" - - "duckdb>=0.8.0" - - "parsl>=2023.4.24" - - "pycytominer>=1.2.4" + - "cloudpathlib[all]>=0.24.0" + - "pyarrow>=24.0.0" + - "pytest>=9.0.3" + - "moto[server,s3]>=5.2.1,<6.0.0" + - "duckdb>=1.5.3" + - "parsl>=2026.5.18" + - "pycytominer>=1.5.0" - "anndata" From 60eace50c6e1d023cba2b8a085995b9c6e487b41 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Tue, 2 Jun 2026 22:11:31 +0000 Subject: [PATCH 2/5] Bump the pre-commit-hooks group across 1 directory with 10 updates Bumps the pre-commit-hooks group with 10 updates in the / directory: | Package | From | To | | --- | --- | --- | | [https://github.com/tox-dev/pyproject-fmt](https://github.com/tox-dev/pyproject-fmt) | `v2.12.1` | `2.21.2` | | [https://github.com/executablebooks/mdformat](https://github.com/executablebooks/mdformat) | `0.7.18` | `1.0.0` | | [https://github.com/citation-file-format/cffconvert](https://github.com/citation-file-format/cffconvert) | `5295f87c0e261da61a7b919fc754e3a77edd98a7` | `b6045d78aac9e02b039703b030588d54d53262ac` | | cloudpathlib | `0.13.0` | `0.24.0` | | pyarrow | `13.0.0` | `24.0.0` | | pytest | `7.2.0` | `9.0.3` | | moto | `4.0.0` | `5.2.1` | | duckdb | `0.8.0` | `1.5.3` | | parsl | `2023.4.24` | `2026.5.25` | | pycytominer | `1.2.4` | `1.5.0` | Updates `https://github.com/tox-dev/pyproject-fmt` from v2.12.1 to 2.21.2 - [Release notes](https://github.com/tox-dev/pyproject-fmt/releases) - [Commits](https://github.com/tox-dev/pyproject-fmt/compare/v2.12.1...v2.21.2) Updates `https://github.com/executablebooks/mdformat` from 0.7.18 to 1.0.0 - [Commits](https://github.com/executablebooks/mdformat/compare/0.7.18...1.0.0) Updates `https://github.com/citation-file-format/cffconvert` from 5295f87c0e261da61a7b919fc754e3a77edd98a7 to b6045d78aac9e02b039703b030588d54d53262ac - [Release notes](https://github.com/citation-file-format/cffconvert/releases) - [Changelog](https://github.com/citation-file-format/cffconvert/blob/main/CHANGELOG.md) - [Commits](https://github.com/citation-file-format/cffconvert/compare/5295f87c0e261da61a7b919fc754e3a77edd98a7...b6045d78aac9e02b039703b030588d54d53262ac) Updates `cloudpathlib` from 0.13.0 to 0.24.0 Updates `pyarrow` from 13.0.0 to 24.0.0 Updates `pytest` from 7.2.0 to 9.0.3 Updates `moto` from 4.0.0 to 5.2.1 Updates `duckdb` from 0.8.0 to 1.5.3 Updates `parsl` from 2023.4.24 to 2026.5.25 Updates `pycytominer` from 1.2.4 to 1.5.0 --- updated-dependencies: - dependency-name: cloudpathlib dependency-version: 0.24.0 dependency-type: direct:production update-type: version-update:semver-minor dependency-group: pre-commit-hooks - dependency-name: duckdb dependency-version: 1.5.3 dependency-type: direct:production update-type: version-update:semver-major dependency-group: pre-commit-hooks - dependency-name: https://github.com/citation-file-format/cffconvert dependency-version: b6045d78aac9e02b039703b030588d54d53262ac dependency-type: direct:production dependency-group: pre-commit-hooks - dependency-name: https://github.com/executablebooks/mdformat dependency-version: 1.0.0 dependency-type: direct:production update-type: version-update:semver-major dependency-group: pre-commit-hooks - dependency-name: https://github.com/tox-dev/pyproject-fmt dependency-version: 2.21.2 dependency-type: direct:production dependency-group: pre-commit-hooks - dependency-name: moto dependency-version: 5.2.1 dependency-type: direct:production update-type: version-update:semver-major dependency-group: pre-commit-hooks - dependency-name: parsl dependency-version: 2026.5.18 dependency-type: direct:production update-type: version-update:semver-major dependency-group: pre-commit-hooks - dependency-name: pyarrow dependency-version: 24.0.0 dependency-type: direct:production update-type: version-update:semver-major dependency-group: pre-commit-hooks - dependency-name: pycytominer dependency-version: 1.5.0 dependency-type: direct:production update-type: version-update:semver-minor dependency-group: pre-commit-hooks - dependency-name: pytest dependency-version: 9.0.3 dependency-type: direct:production update-type: version-update:semver-major dependency-group: pre-commit-hooks ... Signed-off-by: dependabot[bot] --- .pre-commit-config.yaml | 20 ++++++++++---------- 1 file changed, 10 insertions(+), 10 deletions(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index d49648f2..cb71302b 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -15,7 +15,7 @@ repos: hooks: - id: poetry-check - repo: https://github.com/tox-dev/pyproject-fmt - rev: "v2.12.1" + rev: "v2.21.2" hooks: - id: pyproject-fmt - repo: https://github.com/codespell-project/codespell @@ -29,7 +29,7 @@ repos: additional_dependencies: - tomli - repo: https://github.com/executablebooks/mdformat - rev: 0.7.18 + rev: 1.0.0 hooks: - id: mdformat additional_dependencies: @@ -73,7 +73,7 @@ repos: cytotable_from_the_cloud\.py$ ) - repo: https://github.com/citation-file-format/cffconvert - rev: 5295f87c0e261da61a7b919fc754e3a77edd98a7 + rev: b6045d78aac9e02b039703b030588d54d53262ac hooks: - id: validate-cff - repo: https://github.com/software-gardening/almanack @@ -98,11 +98,11 @@ repos: # pylint due to it's dynamic analysis capabilities # and the way pre-commit references virtual environments. additional_dependencies: - - "cloudpathlib[all]>=0.13.0" - - "pyarrow>=13.0.0" - - "pytest>=7.2.0" - - "moto[server,s3]>=4.0.0,<5.0.0" - - "duckdb>=0.8.0" - - "parsl>=2023.4.24" - - "pycytominer>=1.2.4" + - "cloudpathlib[all]>=0.24.0" + - "pyarrow>=24.0.0" + - "pytest>=9.0.3" + - "moto[server,s3]>=5.2.1,<6.0.0" + - "duckdb>=1.5.3" + - "parsl>=2026.5.25" + - "pycytominer>=1.5.0" - "anndata" From 0ece7033a16cbe2f6c1ea026633a3183d6c45162 Mon Sep 17 00:00:00 2001 From: "pre-commit-ci-lite[bot]" <117423508+pre-commit-ci-lite[bot]@users.noreply.github.com> Date: Tue, 2 Jun 2026 22:25:21 +0000 Subject: [PATCH 3/5] [pre-commit.ci lite] apply automatic fixes --- docs/source/presentations.md | 2 +- pyproject.toml | 93 +++++++++++++++++------------------- 2 files changed, 44 insertions(+), 51 deletions(-) diff --git a/docs/source/presentations.md b/docs/source/presentations.md index 8b2fb4b0..60ef42ce 100644 --- a/docs/source/presentations.md +++ b/docs/source/presentations.md @@ -15,7 +15,7 @@ We presented these slides for a lightning talk at [ParslFest 2025](https://parsl [![Poster DOI badge](https://img.shields.io/badge/Poster_DOI-10.5281/zenodo.16945320-blue)](https://doi.org/10.5281/zenodo.16945320) -We presented this poster at [SBI2](https://sbi2.org/) 2023 in Boston, MA. +We presented this poster at [SBI2](https://sbi2.org/) 2023 in Boston, MA. diff --git a/pyproject.toml b/pyproject.toml index 61332057..f4359761 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -6,7 +6,10 @@ requires = [ "poetry-core>=1", "poetry-dynamic-versioning>=1,<2" ] name = "CytoTable" # note: version data is maintained by poetry-dynamic-versioning (do not edit) version = "0.0.0" -description = "Transform CellProfiler and DeepProfiler data for processing image-based profiling readouts with Pycytominer and other Cytomining tools." +description = """\ + Transform CellProfiler and DeepProfiler data for processing image-based profiling readouts with Pycytominer and \ + other Cytomining tools.\ + """ authors = [ "Cytomining Community" ] license = "BSD-3-Clause License" packages = [ { include = "cytotable" } ] @@ -14,64 +17,54 @@ readme = "readme.md" repository = "https://github.com/cytomining/CytoTable" documentation = "https://cytomining.github.io/CytoTable/" keywords = [ "python", "cellprofiler", "single-cell-analysis", "way-lab" ] - -[tool.poetry.dependencies] -python = ">=3.10,<3.15" -pyarrow = ">=13.0.0" -cloudpathlib = { extras = [ "all", "s3" ], version = ">=0.18,<0.25" } -duckdb = ">=0.8.0,!=0.10.0,>=0.10.1" -parsl = ">=2023.9.25" -pyiceberg = { version = ">=0.11,<0.12", optional = true } -ome-arrow = [ +dependencies.python = ">=3.10,<3.15" +dependencies.pyarrow = ">=13.0.0" +dependencies.cloudpathlib = { extras = [ "all", "s3" ], version = ">=0.18,<0.25" } +dependencies.duckdb = ">=0.8.0,!=0.10.0,>=0.10.1" +dependencies.parsl = ">=2023.9.25" +dependencies.pyiceberg = { version = ">=0.11,<0.12", optional = true } +dependencies.ome-arrow = [ { version = ">=0.0.8,<0.1", optional = true, python = ">=3.11" }, ] -numpy = [ +dependencies.numpy = [ { version = "<=1.24.4", python = "<3.11" }, { version = ">=1.26.0", python = ">=3.11" }, ] -scipy = [ +dependencies.scipy = [ { version = "<1.12.0", python = "<3.9" }, { version = "^1.12.0", python = ">=3.9" }, ] -anndata = [ +dependencies.anndata = [ { version = "<0.12.2", python = "<3.11" }, { version = ">=0.12.2", python = ">=3.11" }, ] # Explicit zarr dependency for # anndata <0.12.2 and Python <3.11 -zarr = [ +dependencies.zarr = [ { version = "<3.1.1", python = "<3.11" }, { version = ">=3.1.1", python = ">=3.11" }, ] -botocore = "^1.34.133" - -[tool.poetry.extras] -iceberg = [ "pyiceberg" ] -images = [ "ome-arrow" ] -iceberg-images = [ "pyiceberg", "ome-arrow" ] - -[tool.poetry.group.dev.dependencies] -pytest = ">=7.4,<10.0" -pytest-cov = ">=4.1,<8.0" -cytominer-database = "^0.3.4" -pycytominer = "^1.1.0" -dunamai = "^1.19.0" -pillow = ">=11.3,<13.0" # added to help visualize images within examples - -[tool.poetry.group.docs.dependencies] -jupyterlab = "^4.4.3" -jupyterlab-code-formatter = "^3.0.2" -black = ">=25.1,<27.0" -isort = ">=6.0.1,<9.0.0" -jupytext = "^1.17.1" -Sphinx = ">=6,<9" -myst-parser = ">=2,<5" -sphinxcontrib-mermaid = ">=0.9,<2.1" -myst-nb = "^1.2.0" -typing-extensions = "^4.14.0" - -[tool.poetry.requires-plugins] -poetry-dynamic-versioning = { version = ">=1.0.0,<2.0.0", extras = [ "plugin" ] } +dependencies.botocore = "^1.34.133" +extras.iceberg = [ "pyiceberg" ] +extras.images = [ "ome-arrow" ] +extras.iceberg-images = [ "pyiceberg", "ome-arrow" ] +group.dev.dependencies.pytest = ">=7.4,<10.0" +group.dev.dependencies.pytest-cov = ">=4.1,<8.0" +group.dev.dependencies.cytominer-database = "^0.3.4" +group.dev.dependencies.pycytominer = "^1.1.0" +group.dev.dependencies.dunamai = "^1.19.0" +group.dev.dependencies.pillow = ">=11.3,<13.0" # added to help visualize images within examples +group.docs.dependencies.jupyterlab = "^4.4.3" +group.docs.dependencies.jupyterlab-code-formatter = "^3.0.2" +group.docs.dependencies.black = ">=25.1,<27.0" +group.docs.dependencies.isort = ">=6.0.1,<9.0.0" +group.docs.dependencies.jupytext = "^1.17.1" +group.docs.dependencies.Sphinx = ">=6,<9" +group.docs.dependencies.myst-parser = ">=2,<5" +group.docs.dependencies.sphinxcontrib-mermaid = ">=0.9,<2.1" +group.docs.dependencies.myst-nb = "^1.2.0" +group.docs.dependencies.typing-extensions = "^4.14.0" +requires-plugins.poetry-dynamic-versioning = { version = ">=1.0.0,<2.0.0", extras = [ "plugin" ] } [tool.poetry-dynamic-versioning] enable = true @@ -87,12 +80,16 @@ profile = "black" [tool.codespell] ignore-words = ".codespell-ignore" -[tool.pytest.ini_options] -filterwarnings = [ +[tool.bandit] +exclude_dirs = [ "tests" ] +skips = [ "B608" ] + +[tool.pytest] +ini_options.filterwarnings = [ "ignore::DeprecationWarning:pkg_resources", "ignore::DeprecationWarning:cytominer_database", ] -markers = [ +ini_options.markers = [ "large_data_tests: tests which involve the use of large data.", ] @@ -104,7 +101,3 @@ min_confidence = 80 paths = [ "cytotable" ] sort_by_size = true verbose = true - -[tool.bandit] -exclude_dirs = [ "tests" ] -skips = [ "B608" ] From 56c9e5912c4f07d654e0af0d7b524c5bda28ba5b Mon Sep 17 00:00:00 2001 From: d33bs Date: Tue, 2 Jun 2026 16:50:14 -0600 Subject: [PATCH 4/5] linting and constraint for pyproject fmting --- .github/dependabot.yml | 2 ++ .pre-commit-config.yaml | 2 +- docs/source/presentations.md | 2 +- 3 files changed, 4 insertions(+), 2 deletions(-) diff --git a/.github/dependabot.yml b/.github/dependabot.yml index 5e3c87f6..d42da458 100644 --- a/.github/dependabot.yml +++ b/.github/dependabot.yml @@ -36,6 +36,8 @@ updates: interval: "monthly" cooldown: default-days: 7 + ignore: + - dependency-name: "https://github.com/tox-dev/pyproject-fmt" groups: pre-commit-hooks: patterns: diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 108508a3..13a8edac 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -15,7 +15,7 @@ repos: hooks: - id: poetry-check - repo: https://github.com/tox-dev/pyproject-fmt - rev: "v2.21.2" + rev: "v2.12.1" hooks: - id: pyproject-fmt - repo: https://github.com/codespell-project/codespell diff --git a/docs/source/presentations.md b/docs/source/presentations.md index 8b2fb4b0..60ef42ce 100644 --- a/docs/source/presentations.md +++ b/docs/source/presentations.md @@ -15,7 +15,7 @@ We presented these slides for a lightning talk at [ParslFest 2025](https://parsl [![Poster DOI badge](https://img.shields.io/badge/Poster_DOI-10.5281/zenodo.16945320-blue)](https://doi.org/10.5281/zenodo.16945320) -We presented this poster at [SBI2](https://sbi2.org/) 2023 in Boston, MA. +We presented this poster at [SBI2](https://sbi2.org/) 2023 in Boston, MA. From 2ade2fc4615cac18f7da9dcd2f389f41e1d7641a Mon Sep 17 00:00:00 2001 From: d33bs Date: Tue, 2 Jun 2026 16:55:22 -0600 Subject: [PATCH 5/5] Update pyproject.toml --- pyproject.toml | 93 +++++++++++++++++++++++++++----------------------- 1 file changed, 50 insertions(+), 43 deletions(-) diff --git a/pyproject.toml b/pyproject.toml index f4359761..61332057 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -6,10 +6,7 @@ requires = [ "poetry-core>=1", "poetry-dynamic-versioning>=1,<2" ] name = "CytoTable" # note: version data is maintained by poetry-dynamic-versioning (do not edit) version = "0.0.0" -description = """\ - Transform CellProfiler and DeepProfiler data for processing image-based profiling readouts with Pycytominer and \ - other Cytomining tools.\ - """ +description = "Transform CellProfiler and DeepProfiler data for processing image-based profiling readouts with Pycytominer and other Cytomining tools." authors = [ "Cytomining Community" ] license = "BSD-3-Clause License" packages = [ { include = "cytotable" } ] @@ -17,54 +14,64 @@ readme = "readme.md" repository = "https://github.com/cytomining/CytoTable" documentation = "https://cytomining.github.io/CytoTable/" keywords = [ "python", "cellprofiler", "single-cell-analysis", "way-lab" ] -dependencies.python = ">=3.10,<3.15" -dependencies.pyarrow = ">=13.0.0" -dependencies.cloudpathlib = { extras = [ "all", "s3" ], version = ">=0.18,<0.25" } -dependencies.duckdb = ">=0.8.0,!=0.10.0,>=0.10.1" -dependencies.parsl = ">=2023.9.25" -dependencies.pyiceberg = { version = ">=0.11,<0.12", optional = true } -dependencies.ome-arrow = [ + +[tool.poetry.dependencies] +python = ">=3.10,<3.15" +pyarrow = ">=13.0.0" +cloudpathlib = { extras = [ "all", "s3" ], version = ">=0.18,<0.25" } +duckdb = ">=0.8.0,!=0.10.0,>=0.10.1" +parsl = ">=2023.9.25" +pyiceberg = { version = ">=0.11,<0.12", optional = true } +ome-arrow = [ { version = ">=0.0.8,<0.1", optional = true, python = ">=3.11" }, ] -dependencies.numpy = [ +numpy = [ { version = "<=1.24.4", python = "<3.11" }, { version = ">=1.26.0", python = ">=3.11" }, ] -dependencies.scipy = [ +scipy = [ { version = "<1.12.0", python = "<3.9" }, { version = "^1.12.0", python = ">=3.9" }, ] -dependencies.anndata = [ +anndata = [ { version = "<0.12.2", python = "<3.11" }, { version = ">=0.12.2", python = ">=3.11" }, ] # Explicit zarr dependency for # anndata <0.12.2 and Python <3.11 -dependencies.zarr = [ +zarr = [ { version = "<3.1.1", python = "<3.11" }, { version = ">=3.1.1", python = ">=3.11" }, ] -dependencies.botocore = "^1.34.133" -extras.iceberg = [ "pyiceberg" ] -extras.images = [ "ome-arrow" ] -extras.iceberg-images = [ "pyiceberg", "ome-arrow" ] -group.dev.dependencies.pytest = ">=7.4,<10.0" -group.dev.dependencies.pytest-cov = ">=4.1,<8.0" -group.dev.dependencies.cytominer-database = "^0.3.4" -group.dev.dependencies.pycytominer = "^1.1.0" -group.dev.dependencies.dunamai = "^1.19.0" -group.dev.dependencies.pillow = ">=11.3,<13.0" # added to help visualize images within examples -group.docs.dependencies.jupyterlab = "^4.4.3" -group.docs.dependencies.jupyterlab-code-formatter = "^3.0.2" -group.docs.dependencies.black = ">=25.1,<27.0" -group.docs.dependencies.isort = ">=6.0.1,<9.0.0" -group.docs.dependencies.jupytext = "^1.17.1" -group.docs.dependencies.Sphinx = ">=6,<9" -group.docs.dependencies.myst-parser = ">=2,<5" -group.docs.dependencies.sphinxcontrib-mermaid = ">=0.9,<2.1" -group.docs.dependencies.myst-nb = "^1.2.0" -group.docs.dependencies.typing-extensions = "^4.14.0" -requires-plugins.poetry-dynamic-versioning = { version = ">=1.0.0,<2.0.0", extras = [ "plugin" ] } +botocore = "^1.34.133" + +[tool.poetry.extras] +iceberg = [ "pyiceberg" ] +images = [ "ome-arrow" ] +iceberg-images = [ "pyiceberg", "ome-arrow" ] + +[tool.poetry.group.dev.dependencies] +pytest = ">=7.4,<10.0" +pytest-cov = ">=4.1,<8.0" +cytominer-database = "^0.3.4" +pycytominer = "^1.1.0" +dunamai = "^1.19.0" +pillow = ">=11.3,<13.0" # added to help visualize images within examples + +[tool.poetry.group.docs.dependencies] +jupyterlab = "^4.4.3" +jupyterlab-code-formatter = "^3.0.2" +black = ">=25.1,<27.0" +isort = ">=6.0.1,<9.0.0" +jupytext = "^1.17.1" +Sphinx = ">=6,<9" +myst-parser = ">=2,<5" +sphinxcontrib-mermaid = ">=0.9,<2.1" +myst-nb = "^1.2.0" +typing-extensions = "^4.14.0" + +[tool.poetry.requires-plugins] +poetry-dynamic-versioning = { version = ">=1.0.0,<2.0.0", extras = [ "plugin" ] } [tool.poetry-dynamic-versioning] enable = true @@ -80,16 +87,12 @@ profile = "black" [tool.codespell] ignore-words = ".codespell-ignore" -[tool.bandit] -exclude_dirs = [ "tests" ] -skips = [ "B608" ] - -[tool.pytest] -ini_options.filterwarnings = [ +[tool.pytest.ini_options] +filterwarnings = [ "ignore::DeprecationWarning:pkg_resources", "ignore::DeprecationWarning:cytominer_database", ] -ini_options.markers = [ +markers = [ "large_data_tests: tests which involve the use of large data.", ] @@ -101,3 +104,7 @@ min_confidence = 80 paths = [ "cytotable" ] sort_by_size = true verbose = true + +[tool.bandit] +exclude_dirs = [ "tests" ] +skips = [ "B608" ]