From f21f6b8f1b4377fddee179f9c706413823262059 Mon Sep 17 00:00:00 2001 From: "pre-commit-ci[bot]" <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Mon, 16 Dec 2024 16:27:36 +0000 Subject: [PATCH 1/3] [pre-commit.ci] pre-commit autoupdate MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit updates: - [github.com/astral-sh/ruff-pre-commit: v0.7.0 → v0.8.3](https://github.com/astral-sh/ruff-pre-commit/compare/v0.7.0...v0.8.3) --- .pre-commit-config.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 7773f40..a003802 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -10,7 +10,7 @@ repos: - id: check-case-conflict - repo: https://github.com/astral-sh/ruff-pre-commit - rev: v0.7.0 + rev: v0.8.3 hooks: - id: ruff args: [--fix, --show-fixes, --exit-non-zero-on-fix] From fa8c2518e20bd7955e281796aa251a3797561eed Mon Sep 17 00:00:00 2001 From: "pre-commit-ci[bot]" <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Mon, 16 Dec 2024 16:27:49 +0000 Subject: [PATCH 2/3] [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci --- docs/make_cli_rst.py | 2 +- src/cooler/__init__.py | 18 +++++++++--------- src/cooler/_reduce.py | 2 +- src/cooler/_typing.py | 2 +- src/cooler/cli/zoomify.py | 2 +- src/cooler/core/__init__.py | 4 ++-- src/cooler/create/__init__.py | 30 +++++++++++++++--------------- src/cooler/fileops.py | 2 +- src/cooler/parallel.py | 2 +- 9 files changed, 32 insertions(+), 32 deletions(-) diff --git a/docs/make_cli_rst.py b/docs/make_cli_rst.py index bf7b86b..3d9145c 100644 --- a/docs/make_cli_rst.py +++ b/docs/make_cli_rst.py @@ -60,7 +60,7 @@ def _write_opts(opts): if opt.required: extra.append("required") if extra: - help = "{}[{}]".format(help and help + " " or "", "; ".join(extra)) + help = "{}[{}]".format((help and help + " ") or "", "; ".join(extra)) return ", ".join(rv), help diff --git a/src/cooler/__init__.py b/src/cooler/__init__.py index 86ef07f..4753e6d 100644 --- a/src/cooler/__init__.py +++ b/src/cooler/__init__.py @@ -19,21 +19,21 @@ __all__ = [ "Cooler", + "__format_version__", + "__version__", "annotate", "balance_cooler", + "binnify", + "coarsen_cooler", "create_cooler", "create_scool", - "rename_chroms", - "coarsen_cooler", - "merge_coolers", - "zoomify_cooler", + "fetch_chromsizes", "fileops", + "get_verbosity_level", + "merge_coolers", "parallel", - "binnify", - "fetch_chromsizes", "read_chromsizes", - "get_verbosity_level", + "rename_chroms", "set_verbosity_level", - "__version__", - "__format_version__", + "zoomify_cooler", ] diff --git a/src/cooler/_reduce.py b/src/cooler/_reduce.py index be7ce3b..1117531 100644 --- a/src/cooler/_reduce.py +++ b/src/cooler/_reduce.py @@ -19,7 +19,7 @@ from .parallel import lock from .util import GenomeSegmentation, parse_cooler_uri -__all__ = ["merge_coolers", "coarsen_cooler", "zoomify_cooler"] +__all__ = ["coarsen_cooler", "merge_coolers", "zoomify_cooler"] logger = get_logger(__name__) diff --git a/src/cooler/_typing.py b/src/cooler/_typing.py index be36e25..7802200 100644 --- a/src/cooler/_typing.py +++ b/src/cooler/_typing.py @@ -12,4 +12,4 @@ GenomicRangeTuple = Tuple[str, int, int] Tabular = Union[pd.DataFrame, Dict[str, np.ndarray]] -__all__ = ["MapFunctor", "GenomicRangeSpecifier", "GenomicRangeTuple", "Tabular"] +__all__ = ["GenomicRangeSpecifier", "GenomicRangeTuple", "MapFunctor", "Tabular"] diff --git a/src/cooler/cli/zoomify.py b/src/cooler/cli/zoomify.py index ba245e4..9dfded9 100644 --- a/src/cooler/cli/zoomify.py +++ b/src/cooler/cli/zoomify.py @@ -194,7 +194,7 @@ def zoomify( # Parse and expand user-provided resolutions resolutions, rstring = [], resolutions for res in [s.strip().lower() for s in rstring.split(",")]: - if "n" in res or "b" in res and maxres < curres: + if "n" in res or ("b" in res and maxres < curres): warnings.warn( "Map is already < 256 x 256. Provide resolutions " "explicitly if you want to coarsen more.", diff --git a/src/cooler/core/__init__.py b/src/cooler/core/__init__.py index 21d4fa4..fc8c39d 100644 --- a/src/cooler/core/__init__.py +++ b/src/cooler/core/__init__.py @@ -14,9 +14,9 @@ "FillLowerRangeQuery2D", "RangeSelector1D", "RangeSelector2D", - "region_to_extent", - "region_to_offset", "delete", "get", "put", + "region_to_extent", + "region_to_offset", ] diff --git a/src/cooler/create/__init__.py b/src/cooler/create/__init__.py index e0a832d..ef760e1 100644 --- a/src/cooler/create/__init__.py +++ b/src/cooler/create/__init__.py @@ -36,26 +36,20 @@ ) __all__ = [ - "MAGIC", - "MAGIC_SCOOL", - "MAGIC_MCOOL", - "URL", - "CHROM_DTYPE", + "BIN1OFFSET_DTYPE", + "BIN_DTYPE", "CHROMID_DTYPE", + "CHROMOFFSET_DTYPE", "CHROMSIZE_DTYPE", + "CHROM_DTYPE", "COORD_DTYPE", - "BIN_DTYPE", "COUNT_DTYPE", - "CHROMOFFSET_DTYPE", - "BIN1OFFSET_DTYPE", - "PIXEL_FIELDS", + "MAGIC", + "MAGIC_MCOOL", + "MAGIC_SCOOL", "PIXEL_DTYPES", - "append", - "create", - "create_cooler", - "create_from_unordered", - "create_scool", - "rename_chroms", + "PIXEL_FIELDS", + "URL", "ArrayLoader", "BadInputError", "ContactBinner", @@ -63,6 +57,12 @@ "PairixAggregator", "TabixAggregator", "aggregate_records", + "append", + "create", + "create_cooler", + "create_from_unordered", + "create_scool", + "rename_chroms", "sanitize_pixels", "sanitize_records", "validate_pixels", diff --git a/src/cooler/fileops.py b/src/cooler/fileops.py index e6dfd94..cdc42f6 100644 --- a/src/cooler/fileops.py +++ b/src/cooler/fileops.py @@ -24,7 +24,7 @@ from .create import MAGIC, MAGIC_SCOOL from .util import natsorted, parse_cooler_uri -__all__ = ["is_cooler", "is_multires_file", "list_coolers", "cp", "mv", "ln"] +__all__ = ["cp", "is_cooler", "is_multires_file", "list_coolers", "ln", "mv"] def json_dumps(o: object) -> str: diff --git a/src/cooler/parallel.py b/src/cooler/parallel.py index abdd707..9bcbecd 100644 --- a/src/cooler/parallel.py +++ b/src/cooler/parallel.py @@ -15,7 +15,7 @@ from .core import get from .util import partition -__all__ = ["partition", "split", "lock"] +__all__ = ["lock", "partition", "split"] """ Two possible reasons for using a lock From 750028f029441eed8d5f056b2c358e028db22eb6 Mon Sep 17 00:00:00 2001 From: Nezar Abdennur Date: Thu, 19 Dec 2024 06:30:44 -0600 Subject: [PATCH 3/3] Fix grouping --- src/cooler/cli/zoomify.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/cooler/cli/zoomify.py b/src/cooler/cli/zoomify.py index 9dfded9..5192146 100644 --- a/src/cooler/cli/zoomify.py +++ b/src/cooler/cli/zoomify.py @@ -194,7 +194,7 @@ def zoomify( # Parse and expand user-provided resolutions resolutions, rstring = [], resolutions for res in [s.strip().lower() for s in rstring.split(",")]: - if "n" in res or ("b" in res and maxres < curres): + if ("n" in res or "b" in res) and maxres < curres: warnings.warn( "Map is already < 256 x 256. Provide resolutions " "explicitly if you want to coarsen more.",