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 d49648f2..13a8edac 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -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"
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
[](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/poetry.lock b/poetry.lock
index 6ae0a141..b4447b18 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -1,4 +1,4 @@
-# This file is automatically @generated by Poetry 2.4.1 and should not be changed by hand.
+# This file is automatically @generated by Poetry 2.2.1 and should not be changed by hand.
[[package]]
name = "agate"
@@ -332,13 +332,13 @@ scipy = ">1.8"
[package.extras]
cu11 = ["cupy-cuda11x"]
cu12 = ["cupy-cuda12x"]
-dask = ["dask[array] (>=2022.9.2,<2024.8.dev0 || >=2024.10.dev0)"]
+dask = ["dask[array] (>=2022.09.2,<2024.8.dev0 || >=2024.10.dev0)"]
dev = ["pytest-xdist", "setuptools-scm", "towncrier (>=24.8.0)"]
dev-doc = ["towncrier (>=24.8.0)"]
dev-test = ["pytest-xdist"]
doc = ["awkward (>=2.3)", "ipython", "myst-parser", "nbsphinx", "readthedocs-sphinx-search", "scanpydoc[theme,typehints] (>=0.14.1)", "sphinx (>=7.4.6)", "sphinx-autodoc-typehints (>=2.2.0)", "sphinx-book-theme (>=1.1.0)", "sphinx-copybutton", "sphinx-design (>=0.5.0)", "sphinx-issues", "sphinx-toolbox (>=3.8.0)", "sphinxext-opengraph", "towncrier (>=24.8.0)", "zarr (<3)"]
gpu = ["cupy"]
-test = ["awkward (>=2.3)", "boltons", "dask[array] (>=2022.9.2,<2024.8.dev0 || >=2024.10.dev0)", "dask[distributed]", "httpx", "joblib", "loompy (>=3.0.5)", "matplotlib", "openpyxl", "pyarrow", "pytest (>=8.2,<8.3.4)", "pytest-cov (>=2.10)", "pytest-memray", "pytest-mock", "scanpy (>=1.9.8)", "scikit-learn", "zarr (<3)"]
+test = ["awkward (>=2.3)", "boltons", "dask[array] (>=2022.09.2,<2024.8.dev0 || >=2024.10.dev0)", "dask[distributed]", "httpx", "joblib", "loompy (>=3.0.5)", "matplotlib", "openpyxl", "pyarrow", "pytest (>=8.2,<8.3.4)", "pytest-cov (>=2.10)", "pytest-memray", "pytest-mock", "scanpy (>=1.9.8)", "scikit-learn", "zarr (<3)"]
[[package]]
name = "anndata"
@@ -372,8 +372,8 @@ dev = ["hatch-vcs", "towncrier (>=24.8.0)"]
dev-doc = ["towncrier (>=24.8.0)"]
doc = ["awkward (>=2.3)", "dask[array] (>=2023.5.1,<2024.8.dev0 || >=2024.10.dev0,<2025.2.0)", "ipython", "myst-nb", "myst-parser", "scanpydoc[theme,typehints] (>=0.15.3)", "sphinx (>=8.2.1)", "sphinx-autodoc-typehints (>=2.2.0)", "sphinx-book-theme (>=1.1.0)", "sphinx-copybutton", "sphinx-design (>=0.5.0)", "sphinx-issues (>=5.0.1)", "sphinx-toolbox (>=3.8.0)", "sphinxext-opengraph", "towncrier (>=24.8.0)"]
gpu = ["cupy"]
-lazy = ["aiohttp", "dask[array] (>=2023.5.1,<2024.8.dev0 || >=2024.10.dev0,<2025.2.0)", "requests", "xarray (>=2025.6.1)"]
-test = ["aiohttp", "awkward (>=2.3.2)", "boltons", "dask[array] (>=2023.5.1,<2024.8.dev0 || >=2024.10.dev0,<2025.2.0)", "dask[distributed]", "filelock", "httpx (<1.0)", "joblib", "loompy (>=3.0.5)", "matplotlib", "openpyxl", "pyarrow (<21)", "pytest (>=8.2,<8.3.4)", "pytest-cov", "pytest-memray", "pytest-mock", "pytest-randomly", "pytest-xdist[psutil]", "requests", "scanpy (>=1.10)", "scikit-learn", "xarray (>=2025.6.1)"]
+lazy = ["aiohttp", "dask[array] (>=2023.5.1,<2024.8.dev0 || >=2024.10.dev0,<2025.2.0)", "requests", "xarray (>=2025.06.1)"]
+test = ["aiohttp", "awkward (>=2.3.2)", "boltons", "dask[array] (>=2023.5.1,<2024.8.dev0 || >=2024.10.dev0,<2025.2.0)", "dask[distributed]", "filelock", "httpx (<1.0)", "joblib", "loompy (>=3.0.5)", "matplotlib", "openpyxl", "pyarrow (<21)", "pytest (>=8.2,<8.3.4)", "pytest-cov", "pytest-memray", "pytest-mock", "pytest-randomly", "pytest-xdist[psutil]", "requests", "scanpy (>=1.10)", "scikit-learn", "xarray (>=2025.06.1)"]
test-min = ["awkward (>=2.3.2)", "boltons", "dask[array] (>=2023.5.1,<2024.8.dev0 || >=2024.10.dev0,<2025.2.0)", "dask[distributed]", "filelock", "httpx (<1.0)", "joblib", "loompy (>=3.0.5)", "matplotlib", "openpyxl", "pyarrow (<21)", "pytest (>=8.2,<8.3.4)", "pytest-cov", "pytest-memray", "pytest-mock", "pytest-randomly", "pytest-xdist[psutil]", "scanpy (>=1.10)", "scikit-learn"]
[[package]]
@@ -828,39 +828,39 @@ test = ["coverage (>=5.1)", "dask[array,distributed] (>=2021.4.1)", "pytest (>=5
[[package]]
name = "black"
-version = "26.5.1"
+version = "26.3.1"
description = "The uncompromising code formatter."
optional = false
python-versions = ">=3.10"
groups = ["docs"]
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[package.dependencies]
@@ -1726,7 +1726,7 @@ files = [
click = ">=8.1"
cloudpickle = ">=3.0.0"
distributed = {version = ">=2026.1.2,<2026.1.3", optional = true, markers = "extra == \"distributed\""}
-fsspec = ">=2021.9.0"
+fsspec = ">=2021.09.0"
importlib_metadata = {version = ">=4.13.0", markers = "python_version < \"3.12\""}
numpy = {version = ">=1.24", optional = true, markers = "extra == \"array\""}
packaging = ">=20.0"
@@ -1894,47 +1894,47 @@ test = ["cloudpickle", "pytest"]
[[package]]
name = "duckdb"
-version = "1.5.3"
+version = "1.5.2"
description = "DuckDB in-process database"
optional = false
python-versions = ">=3.10.0"
groups = ["main"]
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[[package]]
name = "google-cloud-storage"
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google-resumable-media = ">=2.6.0"
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[[package]]
name = "google-crc32c"
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name = "googleapis-common-protos"
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python-versions = ">=3.9"
groups = ["dev", "docs"]
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isoduration = {version = "*", optional = true, markers = "extra == \"format-nongpl\""}
jsonpointer = {version = ">1.13", optional = true, markers = "extra == \"format-nongpl\""}
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rfc3339-validator = {version = "*", optional = true, markers = "extra == \"format-nongpl\""}
rfc3986-validator = {version = ">0.1.0", optional = true, markers = "extra == \"format-nongpl\""}
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python-versions = ">=3.9"
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]
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{version = ">=0.25", optional = true, markers = "python_version >= \"3.13\" and extra == \"pint\""},
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pydantic-core = {version = ">=2.20.0", markers = "python_version >= \"3.13\""}
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{version = ">=1.26.0", markers = "python_version >= \"3.12\""},
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python-dateutil = ">=2.8.2"
pytz = ">=2020.1"
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description = "Simple data dependent workflows in Python"
optional = false
python-versions = ">=3.10.0"
groups = ["main"]
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[[package]]
@@ -8650,7 +8627,7 @@ files = [
]
[package.extras]
-cffi = ["cffi (>=1.17,<2.0) ; platform_python_implementation != \"PyPy\" and python_version < \"3.14\"", "cffi (>=2.0.0b0) ; platform_python_implementation != \"PyPy\" and python_version >= \"3.14\""]
+cffi = ["cffi (>=1.17,<2.0) ; platform_python_implementation != \"PyPy\" and python_version < \"3.14\"", "cffi (>=2.0.0b) ; platform_python_implementation != \"PyPy\" and python_version >= \"3.14\""]
[extras]
iceberg = ["pyiceberg"]