From bbb094b6054935ee51044c597defeb08f188210f Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Thu, 14 May 2026 22:15:23 +0000 Subject: [PATCH] fix: bump copick from 1.23.4 to 1.24.1 Bumps [copick](https://github.com/copick/copick) from 1.23.4 to 1.24.1. - [Release notes](https://github.com/copick/copick/releases) - [Changelog](https://github.com/copick/copick/blob/main/CHANGELOG.md) - [Commits](https://github.com/copick/copick/compare/copick-v1.23.4...copick-v1.24.1) --- updated-dependencies: - dependency-name: copick dependency-version: 1.24.1 dependency-type: direct:production update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] --- uv.lock | 102 ++++++++++++++++++++++++++++++++++++++++++++++++++++++-- 1 file changed, 99 insertions(+), 3 deletions(-) diff --git a/uv.lock b/uv.lock index 12b1d5e..de9c03f 100644 --- a/uv.lock +++ b/uv.lock @@ -13,6 +13,15 @@ resolution-markers = [ "python_full_version < '3.12' and sys_platform != 'emscripten' and sys_platform != 'win32'", ] +[[package]] +name = "absl-py" +version = "2.4.0" +source = { registry = "https://pypi.org/simple" } +sdist = { url = "https://files.pythonhosted.org/packages/64/c7/8de93764ad66968d19329a7e0c147a2bb3c7054c554d4a119111b8f9440f/absl_py-2.4.0.tar.gz", hash = "sha256:8c6af82722b35cf71e0f4d1d47dcaebfff286e27110a99fc359349b247dfb5d4", size = 116543, upload-time = "2026-01-28T10:17:05.322Z" } +wheels = [ + { url = "https://files.pythonhosted.org/packages/18/a6/907a406bb7d359e6a63f99c313846d9eec4f7e6f7437809e03aa00fa3074/absl_py-2.4.0-py3-none-any.whl", hash = "sha256:88476fd881ca8aab94ffa78b7b6c632a782ab3ba1cd19c9bd423abc4fb4cd28d", size = 135750, upload-time = "2026-01-28T10:17:04.19Z" }, +] + [[package]] name = "acvl-utils" version = "0.2.6" @@ -364,6 +373,9 @@ dependencies = [ { name = "unittest2" }, ] sdist = { url = "https://files.pythonhosted.org/packages/9c/f8/bff7e5eaf85b064a85bf8827a6bda04e92e2ff4d2e908c45033344886b44/batchgenerators-0.25.1.tar.gz", hash = "sha256:4663a7f393bf1681d7675648362ba3f11b2a9474fb17228a92aac5d1ad28bb39", size = 76970, upload-time = "2024-11-07T06:56:32.595Z" } +wheels = [ + { url = "https://files.pythonhosted.org/packages/85/9b/80dd928c6a3a8873677d2aba70274cbe2e411c3f260d063396d50fd5ace4/batchgenerators-0.25.1-py3-none-any.whl", hash = "sha256:edaa428031692eeac06371e12d08f9895cd743d72dc0a33c53acc9d2aad7f74a", size = 100740, upload-time = "2026-05-12T06:56:06.509Z" }, +] [[package]] name = "batchgeneratorsv2" @@ -875,15 +887,17 @@ wheels = [ [[package]] name = "copick" -version = "1.23.4" +version = "1.24.1" source = { registry = "https://pypi.org/simple" } dependencies = [ + { name = "aiohttp" }, { name = "click" }, { name = "cryoet-data-portal" }, { name = "distinctipy" }, { name = "dynamotable" }, { name = "emfile" }, { name = "fsspec" }, + { name = "mlcroissant" }, { name = "mrcfile" }, { name = "numcodecs" }, { name = "numpy" }, @@ -903,9 +917,9 @@ dependencies = [ { name = "trimesh" }, { name = "zarr" }, ] -sdist = { url = "https://files.pythonhosted.org/packages/da/d5/7d17764c3569e0a9a24b26acf7ded98fcd20e74e8483330faba8f8ed5608/copick-1.23.4.tar.gz", hash = "sha256:d04afa15cd28c56575458ee633d61a06a882a9d1379c7b96c1d7ad2499db7137", size = 9357994, upload-time = "2026-04-10T20:08:00.996Z" } +sdist = { url = "https://files.pythonhosted.org/packages/97/b0/b51272bbb882241e6f45edcc1d8cf4256c69244616d4cabdbad10ec28284/copick-1.24.1.tar.gz", hash = "sha256:6197cc9b939c1d04e40d912b8f654ea639d534c23348ed1a86316ea6ec4832c1", size = 9426087, upload-time = "2026-05-05T03:27:28.617Z" } wheels = [ - { url = "https://files.pythonhosted.org/packages/4e/65/c43de08283e21a1904427d63688f1d2cac1df88895c8433d508ded933206/copick-1.23.4-py3-none-any.whl", hash = "sha256:a7523554acbd632038b3914d288c7b2688ab621f3fd4173c3243ae36a70d2f54", size = 156688, upload-time = "2026-04-10T20:07:59.537Z" }, + { url = "https://files.pythonhosted.org/packages/71/2c/1e80dda158f7a8178ec8d42e0fa2cc079e815fecb66c82dca4dc5f352f68/copick-1.24.1-py3-none-any.whl", hash = "sha256:e774f3a685cb9ce5dc8bcdbee922d48382c67275bcd2236f3842970b5262df6a", size = 197915, upload-time = "2026-05-05T03:27:26.636Z" }, ] [[package]] @@ -1432,6 +1446,22 @@ wheels = [ { url = "https://files.pythonhosted.org/packages/d9/51/482938baea53321ad0482544e9147905e96d9e7f29ab368d3a9c59b7e8f9/emfile-0.3.0-py3-none-any.whl", hash = "sha256:cda7eb08b74cacd9ce5b38d1e52abbf08092d7352ed5abe8b2ba50c54412eedf", size = 4787, upload-time = "2021-11-25T13:38:41.962Z" }, ] +[[package]] +name = "etils" +version = "1.14.0" +source = { registry = "https://pypi.org/simple" } +sdist = { url = "https://files.pythonhosted.org/packages/26/ce/6e067242fde898841922ac6fc82b0bb2fe35c38e995880bdffdfbe30182a/etils-1.14.0.tar.gz", hash = "sha256:8136e7f4c4173cd0af0ca5481c4475152f0b8686192951eefa60ee8711e1ede4", size = 108127, upload-time = "2026-03-04T17:41:36.291Z" } +wheels = [ + { url = "https://files.pythonhosted.org/packages/5a/3d/589663aeeacd59bb2f3e8596bfd3e81cf0fb18d70bb433199041f469771b/etils-1.14.0-py3-none-any.whl", hash = "sha256:b5df7341f54dbe1405a4450b2741207b4a8c279780402b45f87202b94dfc52b4", size = 172934, upload-time = "2026-03-04T17:41:35.01Z" }, +] + +[package.optional-dependencies] +epath = [ + { name = "fsspec" }, + { name = "typing-extensions" }, + { name = "zipp" }, +] + [[package]] name = "executing" version = "2.2.1" @@ -2088,6 +2118,17 @@ wheels = [ { url = "https://files.pythonhosted.org/packages/b8/42/cf027b4ac873b076189d935b135397675dac80cb29acb13e1ab86ad6c631/json5-0.14.0-py3-none-any.whl", hash = "sha256:56cf861bab076b1178eb8c92e1311d273a9b9acea2ccc82c276abf839ebaef3a", size = 36271, upload-time = "2026-03-27T22:50:47.073Z" }, ] +[[package]] +name = "jsonpath-rw" +version = "1.4.0" +source = { registry = "https://pypi.org/simple" } +dependencies = [ + { name = "decorator" }, + { name = "ply" }, + { name = "six" }, +] +sdist = { url = "https://files.pythonhosted.org/packages/71/7c/45001b1f19af8c4478489fbae4fc657b21c4c669d7a5a036a86882581d85/jsonpath-rw-1.4.0.tar.gz", hash = "sha256:05c471281c45ae113f6103d1268ec7a4831a2e96aa80de45edc89b11fac4fbec", size = 13814, upload-time = "2015-04-19T01:47:15.06Z" } + [[package]] name = "jsonpointer" version = "3.1.1" @@ -2835,6 +2876,28 @@ wheels = [ { url = "https://files.pythonhosted.org/packages/9b/f7/4a5e785ec9fbd65146a27b6b70b6cdc161a66f2024e4b04ac06a67f5578b/mistune-3.2.0-py3-none-any.whl", hash = "sha256:febdc629a3c78616b94393c6580551e0e34cc289987ec6c35ed3f4be42d0eee1", size = 53598, upload-time = "2025-12-23T11:36:33.211Z" }, ] +[[package]] +name = "mlcroissant" +version = "1.1.0" +source = { registry = "https://pypi.org/simple" } +dependencies = [ + { name = "absl-py" }, + { name = "etils", extra = ["epath"] }, + { name = "jsonpath-rw" }, + { name = "networkx" }, + { name = "pandas" }, + { name = "pandas-stubs" }, + { name = "python-dateutil" }, + { name = "rdflib" }, + { name = "requests" }, + { name = "scipy" }, + { name = "tqdm" }, +] +sdist = { url = "https://files.pythonhosted.org/packages/ad/94/67287557ad889c85d37700bed09b33f1be8b7a272a5d0dbb84f4a697e7b0/mlcroissant-1.1.0.tar.gz", hash = "sha256:fd4a5fc875fa1531fabe4c131acdf8aaf9428fd69583cc51a7a5c23262b48259", size = 111643, upload-time = "2026-04-16T13:18:44.302Z" } +wheels = [ + { url = "https://files.pythonhosted.org/packages/dd/f9/9d4602e4346e4d6625e67ddcfd1ebd8d7d13860025bde43c8ed8149758e5/mlcroissant-1.1.0-py2.py3-none-any.whl", hash = "sha256:46f9ab72fc193e1e3730dbbd872eb8cdf07ca16e854578c5c30c2aad2854423a", size = 155405, upload-time = "2026-04-16T13:18:42.718Z" }, +] + [[package]] name = "monai" version = "1.5.2" @@ -3668,6 +3731,18 @@ wheels = [ { url = "https://files.pythonhosted.org/packages/cb/2b/f8434233fab2bd66a02ec014febe4e5adced20e2693e0e90a07d118ed30e/pandas-3.0.2-cp314-cp314t-win_arm64.whl", hash = "sha256:5371b72c2d4d415d08765f32d689217a43227484e81b2305b52076e328f6f482", size = 9455341, upload-time = "2026-03-31T06:48:28.418Z" }, ] +[[package]] +name = "pandas-stubs" +version = "3.0.0.260204" +source = { registry = "https://pypi.org/simple" } +dependencies = [ + { name = "numpy" }, +] +sdist = { url = "https://files.pythonhosted.org/packages/27/1d/297ff2c7ea50a768a2247621d6451abb2a07c0e9be7ca6d36ebe371658e5/pandas_stubs-3.0.0.260204.tar.gz", hash = "sha256:bf9294b76352effcffa9cb85edf0bed1339a7ec0c30b8e1ac3d66b4228f1fbc3", size = 109383, upload-time = "2026-02-04T15:17:17.247Z" } +wheels = [ + { url = "https://files.pythonhosted.org/packages/7c/2f/f91e4eee21585ff548e83358332d5632ee49f6b2dcd96cb5dca4e0468951/pandas_stubs-3.0.0.260204-py3-none-any.whl", hash = "sha256:5ab9e4d55a6e2752e9720828564af40d48c4f709e6a2c69b743014a6fcb6c241", size = 168540, upload-time = "2026-02-04T15:17:15.615Z" }, +] + [[package]] name = "pandocfilters" version = "1.5.1" @@ -3825,6 +3900,15 @@ wheels = [ { url = "https://files.pythonhosted.org/packages/54/20/4d324d65cc6d9205fabedc306948156824eb9f0ee1633355a8f7ec5c66bf/pluggy-1.6.0-py3-none-any.whl", hash = "sha256:e920276dd6813095e9377c0bc5566d94c932c33b27a3e3945d8389c374dd4746", size = 20538, upload-time = "2025-05-15T12:30:06.134Z" }, ] +[[package]] +name = "ply" +version = "3.11" +source = { registry = "https://pypi.org/simple" } +sdist = { url = "https://files.pythonhosted.org/packages/e5/69/882ee5c9d017149285cab114ebeab373308ef0f874fcdac9beb90e0ac4da/ply-3.11.tar.gz", hash = "sha256:00c7c1aaa88358b9c765b6d3000c6eec0ba42abca5351b095321aef446081da3", size = 159130, upload-time = "2018-02-15T19:01:31.097Z" } +wheels = [ + { url = "https://files.pythonhosted.org/packages/a3/58/35da89ee790598a0700ea49b2a66594140f44dec458c07e8e3d4979137fc/ply-3.11-py2.py3-none-any.whl", hash = "sha256:096f9b8350b65ebd2fd1346b12452efe5b9607f7482813ffca50c22722a807ce", size = 49567, upload-time = "2018-02-15T19:01:27.172Z" }, +] + [[package]] name = "pre-commit" version = "4.5.1" @@ -4472,6 +4556,18 @@ wheels = [ { url = "https://files.pythonhosted.org/packages/01/1b/5dbe84eefc86f48473947e2f41711aded97eecef1231f4558f1f02713c12/pyzmq-27.1.0-pp311-pypy311_pp73-win_amd64.whl", hash = "sha256:c9f7f6e13dff2e44a6afeaf2cf54cee5929ad64afaf4d40b50f93c58fc687355", size = 544862, upload-time = "2025-09-08T23:09:56.509Z" }, ] +[[package]] +name = "rdflib" +version = "7.6.0" +source = { registry = "https://pypi.org/simple" } +dependencies = [ + { name = "pyparsing" }, +] +sdist = { url = "https://files.pythonhosted.org/packages/98/f5/18bb77b7af9526add0c727a3b2048959847dc5fb030913e2918bf384fec3/rdflib-7.6.0.tar.gz", hash = "sha256:6c831288d5e4a5a7ece85d0ccde9877d512a3d0f02d7c06455d00d6d0ea379df", size = 4943826, upload-time = "2026-02-13T07:15:55.938Z" } +wheels = [ + { url = "https://files.pythonhosted.org/packages/10/c2/6604a71269e0c1bd75656d5a001432d16f2cc5b8c057140ec797155c295e/rdflib-7.6.0-py3-none-any.whl", hash = "sha256:30c0a3ebf4c0e09215f066be7246794b6492e054e782d7ac2a34c9f70a15e0dd", size = 615416, upload-time = "2026-02-13T07:15:46.487Z" }, +] + [[package]] name = "referencing" version = "0.37.0"