From fd7421ed9385debba4f22b01157807d88de0817c Mon Sep 17 00:00:00 2001 From: "Ali R. Khan" Date: Thu, 29 Oct 2026 18:55:16 -0400 Subject: [PATCH 1/2] update snakemake to fix logger groups bug --- pixi.lock | 81 +++++++++++++++++++++++++++++++------------------------ 1 file changed, 46 insertions(+), 35 deletions(-) diff --git a/pixi.lock b/pixi.lock index de93ebc..08f315c 100644 --- a/pixi.lock +++ b/pixi.lock @@ -23,16 +23,16 @@ environments: packages: linux-64: - conda: https://conda.anaconda.org/bioconda/noarch/snakebids-0.15.0-pyhdfd78af_0.conda - - conda: https://conda.anaconda.org/bioconda/noarch/snakemake-9.22.0-hdfd78af_0.conda + - conda: https://conda.anaconda.org/bioconda/noarch/snakemake-9.27.1-hdfd78af_0.conda - conda: https://conda.anaconda.org/bioconda/noarch/snakemake-executor-plugin-slurm-1.9.2-pyhdfd78af_0.conda - conda: https://conda.anaconda.org/bioconda/noarch/snakemake-executor-plugin-slurm-jobstep-0.3.0-pyhdfd78af_0.tar.bz2 - - conda: https://conda.anaconda.org/bioconda/noarch/snakemake-interface-common-1.24.0-pyhdfd78af_0.conda + - conda: https://conda.anaconda.org/bioconda/noarch/snakemake-interface-common-1.23.1-pyhdfd78af_0.conda - conda: https://conda.anaconda.org/bioconda/noarch/snakemake-interface-executor-plugins-9.4.0-pyh84498cf_0.conda - conda: https://conda.anaconda.org/bioconda/noarch/snakemake-interface-logger-plugins-2.1.0-pyhdfd78af_0.conda - conda: https://conda.anaconda.org/bioconda/noarch/snakemake-interface-report-plugins-1.3.0-pyhd4c3c12_0.conda - conda: https://conda.anaconda.org/bioconda/noarch/snakemake-interface-scheduler-plugins-2.0.2-pyhd4c3c12_0.conda - conda: https://conda.anaconda.org/bioconda/noarch/snakemake-interface-storage-plugins-4.4.1-pyh84498cf_0.conda - - conda: https://conda.anaconda.org/bioconda/noarch/snakemake-minimal-9.22.0-pyhdfd78af_0.conda + - conda: https://conda.anaconda.org/bioconda/noarch/snakemake-minimal-9.27.1-pyhdfd78af_0.conda - conda: https://conda.anaconda.org/bioconda/noarch/snakemake-storage-plugin-cached-http-0.3-pyhdfd78af_0.conda - conda: https://conda.anaconda.org/bioconda/noarch/snakemake-storage-plugin-fs-1.1.3-pyhdfd78af_0.conda - conda: https://conda.anaconda.org/bioconda/noarch/snakemake-storage-plugin-gcs-1.1.4-pyhdfd78af_0.tar.bz2 @@ -533,7 +533,7 @@ environments: - conda: https://conda.anaconda.org/conda-forge/noarch/ome-zarr-0.21.0-pyhd8ed1ab_0.conda - conda: https://conda.anaconda.org/conda-forge/noarch/ome-zarr-models-1.8.1-pyhc364b38_0.conda - conda: https://conda.anaconda.org/conda-forge/noarch/omegaconf-2.3.1-pyhd8ed1ab_1.conda - - conda: https://conda.anaconda.org/conda-forge/noarch/packaging-26.3-pyhc364b38_0.conda + - conda: https://conda.anaconda.org/conda-forge/noarch/packaging-25.0-pyh29332c3_1.conda - conda: https://conda.anaconda.org/conda-forge/noarch/partd-1.4.2-pyhd8ed1ab_0.conda - conda: https://conda.anaconda.org/conda-forge/noarch/pathspec-1.1.1-pyhd8ed1ab_0.conda - conda: https://conda.anaconda.org/conda-forge/noarch/patsy-1.0.3-pyhcf101f3_0.conda @@ -651,16 +651,16 @@ environments: linux-64: - conda: https://conda.anaconda.org/bioconda/noarch/snakebids-0.15.0-pyhdfd78af_0.conda - conda: https://conda.anaconda.org/bioconda/noarch/snakefmt-2.1.0-pyhdfd78af_0.conda - - conda: https://conda.anaconda.org/bioconda/noarch/snakemake-9.22.0-hdfd78af_0.conda + - conda: https://conda.anaconda.org/bioconda/noarch/snakemake-9.27.1-hdfd78af_0.conda - conda: https://conda.anaconda.org/bioconda/noarch/snakemake-executor-plugin-slurm-1.9.2-pyhdfd78af_0.conda - conda: https://conda.anaconda.org/bioconda/noarch/snakemake-executor-plugin-slurm-jobstep-0.3.0-pyhdfd78af_0.tar.bz2 - - conda: https://conda.anaconda.org/bioconda/noarch/snakemake-interface-common-1.24.0-pyhdfd78af_0.conda + - conda: https://conda.anaconda.org/bioconda/noarch/snakemake-interface-common-1.23.1-pyhdfd78af_0.conda - conda: https://conda.anaconda.org/bioconda/noarch/snakemake-interface-executor-plugins-9.4.0-pyh84498cf_0.conda - conda: https://conda.anaconda.org/bioconda/noarch/snakemake-interface-logger-plugins-2.1.0-pyhdfd78af_0.conda - conda: https://conda.anaconda.org/bioconda/noarch/snakemake-interface-report-plugins-1.3.0-pyhd4c3c12_0.conda - conda: https://conda.anaconda.org/bioconda/noarch/snakemake-interface-scheduler-plugins-2.0.2-pyhd4c3c12_0.conda - conda: https://conda.anaconda.org/bioconda/noarch/snakemake-interface-storage-plugins-4.4.1-pyh84498cf_0.conda - - conda: https://conda.anaconda.org/bioconda/noarch/snakemake-minimal-9.22.0-pyhdfd78af_0.conda + - conda: https://conda.anaconda.org/bioconda/noarch/snakemake-minimal-9.27.1-pyhdfd78af_0.conda - conda: https://conda.anaconda.org/bioconda/noarch/snakemake-storage-plugin-cached-http-0.3-pyhdfd78af_0.conda - conda: https://conda.anaconda.org/bioconda/noarch/snakemake-storage-plugin-fs-1.1.3-pyhdfd78af_0.conda - conda: https://conda.anaconda.org/bioconda/noarch/snakemake-storage-plugin-gcs-1.1.4-pyhdfd78af_0.tar.bz2 @@ -1268,7 +1268,7 @@ environments: - conda: https://conda.anaconda.org/conda-forge/noarch/ome-zarr-models-1.8.1-pyhc364b38_0.conda - conda: https://conda.anaconda.org/conda-forge/noarch/omegaconf-2.3.1-pyhd8ed1ab_1.conda - conda: https://conda.anaconda.org/conda-forge/noarch/overrides-7.7.0-pyhd8ed1ab_1.conda - - conda: https://conda.anaconda.org/conda-forge/noarch/packaging-26.3-pyhc364b38_0.conda + - conda: https://conda.anaconda.org/conda-forge/noarch/packaging-25.0-pyh29332c3_1.conda - conda: https://conda.anaconda.org/conda-forge/noarch/pandocfilters-1.5.1-pyh5ded981_0.conda - conda: https://conda.anaconda.org/conda-forge/noarch/parso-0.8.7-pyhcf101f3_0.conda - conda: https://conda.anaconda.org/conda-forge/noarch/partd-1.4.2-pyhd8ed1ab_0.conda @@ -1596,16 +1596,16 @@ environments: packages: linux-64-cuda: - conda: https://conda.anaconda.org/bioconda/noarch/snakebids-0.15.0-pyhdfd78af_0.conda - - conda: https://conda.anaconda.org/bioconda/noarch/snakemake-9.22.0-hdfd78af_0.conda + - conda: https://conda.anaconda.org/bioconda/noarch/snakemake-9.27.1-hdfd78af_0.conda - conda: https://conda.anaconda.org/bioconda/noarch/snakemake-executor-plugin-slurm-1.9.2-pyhdfd78af_0.conda - conda: https://conda.anaconda.org/bioconda/noarch/snakemake-executor-plugin-slurm-jobstep-0.3.0-pyhdfd78af_0.tar.bz2 - - conda: https://conda.anaconda.org/bioconda/noarch/snakemake-interface-common-1.24.0-pyhdfd78af_0.conda + - conda: https://conda.anaconda.org/bioconda/noarch/snakemake-interface-common-1.23.1-pyhdfd78af_0.conda - conda: https://conda.anaconda.org/bioconda/noarch/snakemake-interface-executor-plugins-9.4.0-pyh84498cf_0.conda - conda: https://conda.anaconda.org/bioconda/noarch/snakemake-interface-logger-plugins-2.1.0-pyhdfd78af_0.conda - conda: https://conda.anaconda.org/bioconda/noarch/snakemake-interface-report-plugins-1.3.0-pyhd4c3c12_0.conda - conda: https://conda.anaconda.org/bioconda/noarch/snakemake-interface-scheduler-plugins-2.0.2-pyhd4c3c12_0.conda - conda: https://conda.anaconda.org/bioconda/noarch/snakemake-interface-storage-plugins-4.4.1-pyh84498cf_0.conda - - conda: https://conda.anaconda.org/bioconda/noarch/snakemake-minimal-9.22.0-pyhdfd78af_0.conda + - conda: https://conda.anaconda.org/bioconda/noarch/snakemake-minimal-9.27.1-pyhdfd78af_0.conda - conda: https://conda.anaconda.org/bioconda/noarch/snakemake-storage-plugin-cached-http-0.3-pyhdfd78af_0.conda - conda: https://conda.anaconda.org/bioconda/noarch/snakemake-storage-plugin-fs-1.1.3-pyhdfd78af_0.conda - conda: https://conda.anaconda.org/bioconda/noarch/snakemake-storage-plugin-gcs-1.1.4-pyhdfd78af_0.tar.bz2 @@ -2135,7 +2135,7 @@ environments: - conda: https://conda.anaconda.org/conda-forge/noarch/ome-zarr-0.21.0-pyhd8ed1ab_0.conda - conda: https://conda.anaconda.org/conda-forge/noarch/ome-zarr-models-1.8.1-pyhc364b38_0.conda - conda: https://conda.anaconda.org/conda-forge/noarch/omegaconf-2.3.1-pyhd8ed1ab_1.conda - - conda: https://conda.anaconda.org/conda-forge/noarch/packaging-26.3-pyhc364b38_0.conda + - conda: https://conda.anaconda.org/conda-forge/noarch/packaging-25.0-pyh29332c3_1.conda - conda: https://conda.anaconda.org/conda-forge/noarch/partd-1.4.2-pyhd8ed1ab_0.conda - conda: https://conda.anaconda.org/conda-forge/noarch/pathspec-1.1.1-pyhd8ed1ab_0.conda - conda: https://conda.anaconda.org/conda-forge/noarch/patsy-1.0.3-pyhcf101f3_0.conda @@ -2292,23 +2292,23 @@ packages: - snakefmt >=2.1.0,<2.2.0a0 size: 51142 timestamp: 1791956837135 -- conda: https://conda.anaconda.org/bioconda/noarch/snakemake-9.22.0-hdfd78af_0.conda - sha256: 113a7939e2ee7eb4eda146fb0ed268a1b91fda68955f6561c19ec35c9ec1e590 - md5: 687021acde26bc5e47918f8bf804fcf0 +- conda: https://conda.anaconda.org/bioconda/noarch/snakemake-9.27.1-hdfd78af_0.conda + sha256: 86750ea69be7b6fd47b791996911deb4541b88bfbb5162a6dbfa85991e9c1fa0 + md5: b03e785852a302c6a0ea7107aedf7da8 depends: - eido - pandas <3 - peppy - pygments - slack_sdk - - snakemake-minimal 9.22.0.* + - snakemake-minimal 9.27.1.* license: MIT license_family: MIT run_exports: weak: - - snakemake >=9.22.0,<10.0a0 - size: 11265 - timestamp: 1780342023407 + - snakemake >=9.27.1,<10.0a0 + size: 11373 + timestamp: 1792575136089 - conda: https://conda.anaconda.org/bioconda/noarch/snakemake-executor-plugin-slurm-1.9.2-pyhdfd78af_0.conda sha256: 69a7bf42dae2f6e14294602af237444b7deb03c387e31db79bb30fab744420ef md5: d154a174a811bf42513b2d7636ce0a5f @@ -2340,21 +2340,21 @@ packages: - snakemake-executor-plugin-slurm-jobstep >=0.3.0,<1.0a0 size: 12881 timestamp: 1739611671448 -- conda: https://conda.anaconda.org/bioconda/noarch/snakemake-interface-common-1.24.0-pyhdfd78af_0.conda - sha256: 3f06df134ffc8cc9c00bf47dbcdf78339bb6f21e9464ff0c86151c482daa1613 - md5: fe896f0986228a408b1df7bc99b28a8a +- conda: https://conda.anaconda.org/bioconda/noarch/snakemake-interface-common-1.23.1-pyhdfd78af_0.conda + sha256: 6c00ad64aba26fa72a49a4e8f1664dba53f75fe5852425c4a5f1bd676960ccfa + md5: 3d6d8846f3e486d2c39882b1ea912020 depends: - argparse-dataclass >=2.0.0 - configargparse >=1.7 - - packaging >=26.1 + - packaging >=24.0 - python >=3.8 license: MIT license_family: MIT run_exports: weak: - - snakemake-interface-common >=1.24.0,<2.0a0 - size: 22795 - timestamp: 1791749052204 + - snakemake-interface-common >=1.23.1,<2.0a0 + size: 22734 + timestamp: 1788762587812 - conda: https://conda.anaconda.org/bioconda/noarch/snakemake-interface-executor-plugins-9.4.0-pyh84498cf_0.conda sha256: 16c8e1ba64837b10460459e710e2578e8b0be5d1ed9501cfcf27b2ba316e5ad2 md5: 0d8bbf1699b16ac225031ae0c73729f8 @@ -2423,9 +2423,9 @@ packages: - snakemake-interface-storage-plugins >=4.4.1,<5.0a0 size: 22783 timestamp: 1773699846635 -- conda: https://conda.anaconda.org/bioconda/noarch/snakemake-minimal-9.22.0-pyhdfd78af_0.conda - sha256: cd80ed5caf6405af8b55788057862e386dc3b1e49ac483dc151639d03e7dfde1 - md5: 11ba597632bcb10e10350e55e930627b +- conda: https://conda.anaconda.org/bioconda/noarch/snakemake-minimal-9.27.1-pyhdfd78af_0.conda + sha256: 04593158837013f35cc731bb03d9611dd61db722cd2efe06dd165bbde9b33b98 + md5: f8a5e6198c343169c33cc24f554872ba depends: - conda-inject >=1.3.1,<2.0 - configargparse @@ -2438,11 +2438,11 @@ packages: - jinja2 >=3.0,<4.0 - jsonschema - nbformat - - packaging >=24.0 + - packaging >=24.0,<26 - platformdirs - psutil - pulp >=2.3.1,<3.4 - - python >=3.11,<3.14 + - python >=3.11 - pyyaml - referencing - requests >=2.8.1,<3.0 @@ -2452,7 +2452,7 @@ packages: - snakemake-interface-logger-plugins >=1.1.0,<3.0.0 - snakemake-interface-report-plugins >=1.2.0,<2.0.0 - snakemake-interface-scheduler-plugins >=2.0.0,<3.0.0 - - snakemake-interface-storage-plugins >=4.3.2,<5.0 + - snakemake-interface-storage-plugins >=4.4.1,<5.0 - sqlmodel >=0.0.37,<0.0.38 - tabulate - tenacity >=9.1.4,<10.0 @@ -2463,9 +2463,9 @@ packages: license_family: MIT run_exports: weak: - - snakemake-minimal >=9.22.0,<10.0a0 - size: 888285 - timestamp: 1780342021389 + - snakemake-minimal >=9.27.1,<10.0a0 + size: 890511 + timestamp: 1792575133103 - conda: https://conda.anaconda.org/bioconda/noarch/snakemake-storage-plugin-cached-http-0.3-pyhdfd78af_0.conda sha256: bfeb67de43a70a563567d4a5f200e24481e1b72eefc0ccc43e445f4f8c177b5a md5: 15fe83cb157467c0c85c375f56abf199 @@ -12737,6 +12737,17 @@ packages: run_exports: {} size: 30139 timestamp: 1734587755455 +- conda: https://conda.anaconda.org/conda-forge/noarch/packaging-25.0-pyh29332c3_1.conda + sha256: 289861ed0c13a15d7bbb408796af4de72c2fe67e2bcb0de98f4c3fce259d7991 + md5: 58335b26c38bf4a20f399384c33cbcf9 + depends: + - python >=3.8 + - python + license: Apache-2.0 + license_family: APACHE + run_exports: {} + size: 62477 + timestamp: 1745345660407 - conda: https://conda.anaconda.org/conda-forge/noarch/packaging-26.3-pyhc364b38_0.conda sha256: c432626b16768b8dab228bfb706f7060c2d462a21c516d240f68f2f902b5a044 md5: 936687ed80f295a1f5dbcf8bd34c252c From 0644173e619835feeb3fdf06d38a23e7516c2863 Mon Sep 17 00:00:00 2001 From: "Ali R. Khan" Date: Thu, 29 Oct 2026 18:55:31 -0400 Subject: [PATCH 2/2] minor resource update --- spimquant/workflow/rules/templatereg.smk | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/spimquant/workflow/rules/templatereg.smk b/spimquant/workflow/rules/templatereg.smk index 85ca292..9613fcf 100644 --- a/spimquant/workflow/rules/templatereg.smk +++ b/spimquant/workflow/rules/templatereg.smk @@ -514,7 +514,7 @@ rule deform_spim_nii_to_template_nii: "../envs/ants.yaml" threads: 8 resources: - mem_mb=scaled_mem_mb(4000, 21000), + mem_mb=scaled_mem_mb(8000, 32000), runtime=10, shell: "ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS={threads} "