gnu: cnvkit: Update to 0.9.12-0.52f367b. * gnu/packages/bioinformatics.scm (cnvkit): Update to 52f367bd0edbf55cabaaa2fbcf68c8742dc97b4c commit. [native-inputs]: Remove python-wheel. Change-Id: I1d26ac113414b0d6428678b61acefa058d0af6f7 Signed-off-by: Rutherther <rutherther@ditigal.xyz>
gnu: python-pyfaidx: Update to 0.9.0.3. * gnu/packages/bioinformatics.scm (python-pyfaidx): Update to 0.9.0.3. [arguments] <tests?>: Disable for now. <phases>: Remove 'fix-version; add 'set-version. [propagated-inputs]: Remove python-setuptools; add python-packaging. [native-inputs]: Remove libc-utf8-locales-for-target; add python-biopython, python-fsspec, python-numpy, python-pytest, python-setuptools, and python-setuptools-scm. Change-Id: I49e95f8e1b19a181d4d1b2e344cf1a00b055eefd Signed-off-by: Rutherther <rutherther@ditigal.xyz>
gnu: python-pomegranate: Move to machine-learning. * gnu/packages/python-xyz.scm (python-pomegranate): Move from here ... * gnu/packages/machine-learning.scm: ... to here. Change-Id: I1ef53f52439c0cae22e96ec381ecff3e2f616d71 Signed-off-by: Rutherther <rutherther@ditigal.xyz>
gnu: python-pomegranate: Update to 1.1.0. * gnu/packages/python-xyz.scm (python-pomegranate): Update to 1.1.0. [source]: Switch to git-fetch providing tests. [arguments] <tests?, test-flags>: Enable them. [propagated-inputs]: Remove python-joblib and python-pyyaml; add python-apricot-select, python-scikit-learn, and python-pytorch. [native-inputs]: Remove python-pandas and python-wheel; add python-pytest. Change-Id: Idf53aff2124c98fd7dc1172a31028a57347d2a4b Signed-off-by: Rutherther <rutherther@ditigal.xyz>
gnu: Add python-apricot-select. * gnu/packages/machine-learning.scm (python-apricot-select): New variable. Change-Id: Ib4e7b76e4025870e73a52d67277f8bc302740d01 Signed-off-by: Rutherther <rutherther@ditigal.xyz>
gnu: python-presto: Improve package, fix tests. * gnu/packages/bioinformatics.scm (python-presto): Refresh package style. [arguments] <test-flags>: Skip 3 tests. [native-inputs]: Remove python-wheel. Change-Id: I5992e127fd653aa04711647cf0a458586029b3d4 Signed-off-by: Rutherther <rutherther@ditigal.xyz>
gnu: python-brian2: Update to 2.10.1. * gnu/packages/machine-learning.scm (python-brian2): Update to 2.10.1. [arguments] <test-flags>: Run portion of tests. <phases>: Use default 'check; add 'relax-requirements. [propagated-inputs]: Remove python-py-cpuinfo; add python-packaging. [native-inputs]: Remove python-wheel; add python-pytest-timeout and python-setuptools-scm. Fixes: guix/guix#2568 Change-Id: Iad4d1bc211069fccbec7eb9b0082bf2ea73c8e41 Signed-off-by: Rutherther <rutherther@ditigal.xyz>
gnu: macs-3: Update to 3.0.3. * gnu/packages/bioinformatics.scm (macs-3): Update to 3.0.3. [arguments, properties]: Drop all. [native-inputs]: Remove python-wheel. Change-Id: Ida52036ce3305d1db67f27f98cbc0d48c1f9650a Signed-off-by: Rutherther <rutherther@ditigal.xyz>
gnu: python-cellbender: Update to 0.3.2. * gnu/packages/bioinformatics.scm (python-cellbender): Update to 0.3.2. [arguments] <phases>: Add 'relax-requirements. [propagated-inputs]: Remove python-scikit-learn, python-sphinx, python-sphinx-argparse, python-sphinx-autodoc-typehints, python-sphinx-rtd-theme, and python-sphinxcontrib-programoutput; add python-loompy, python-lxml-html-clean, python-nbconvert, python-notebook, python-psutil, and python-pytorch. [native-inputs]: Add python-setuptools. Change-Id: I79473da4ca33b648fd9bd19f21dc91edb4a12cc3 Signed-off-by: Rutherther <rutherther@ditigal.xyz>
gnu: python-captum: Update to 0.8.0-0.4fade3a. * gnu/packages/machine-learning.scm (python-captum): Update to 4fade3af8dc398c1f96b193c969565aad23aedf5 commit. [propagated-inputs]: Add python-openai. Change-Id: Ic51de929ac28f565244b7aec93b9b2be7211fb02 Signed-off-by: Rutherther <rutherther@ditigal.xyz>
gnu: mageck: Use python-numpy@1. * gnu/packages/bioinformatics.scm (mageck): [inputs]: Remove python-numpy; add python-numpy-1. [native-inputs]: Remove python-wheel; add python-setuptools. Change-Id: If26cf31016b769b01d502c33b97c5579873337b6 Signed-off-by: Rutherther <rutherther@ditigal.xyz>
gnu: idr: Fix build. * gnu/packages/bioinformatics.scm (idr): [propagated-inputs]: Use python-numpy-1. [native-inputs]: Use python-cython-0. Change-Id: Ic1fabb53311a74db3872f50c2f67f8e1310be204 Signed-off-by: Rutherther <rutherther@ditigal.xyz>
gnu: python-cnmf: Update to 1.7.0. * gnu/packages/bioinformatics.scm (python-cnmf): Update to 1.7.0. [arguments] <tests?, test-flags>: Enable them. [native-inputs]: Remove python-wheel; add python-pytest. Change-Id: I927b10045e563cc81bcb077f3af9ba3312869280 Signed-off-by: Rutherther <rutherther@ditigal.xyz>
gnu: python-cooltools: Update to 0.7.1. * gnu/packages/bioinformatics.scm (python-cooltools): Update to 0.7.1. [arguments] <phases>: Add 'fix-pytest-config. [native-inputs]: Add python-setuptools. Change-Id: I1a5c03cc626c1401f1a6b34f7af13d2a259e74a3 Signed-off-by: Rutherther <rutherther@ditigal.xyz>
gnu: python-magic-impute: Update to 3.0.0. * gnu/packages/bioinformatics.scm (python-magic-impute): Update to 3.0.0. [arguments] <tests?, test-flags>: Enable them. [native-inputs]: Add python-pytest and python-setuptools. [propagated-inputs]: Add python-scprep. Change-Id: I4e1567fc6b5b32ee77f13d801042ea321f33dfa8 Signed-off-by: Rutherther <rutherther@ditigal.xyz>
gnu: Add python-scprep. * gnu/packages/bioinformatics.scm (python-scprep): New variable. Change-Id: I61674e690bf798c17e84806b606673f84bd07636 Signed-off-by: Rutherther <rutherther@ditigal.xyz>
gnu: python-fcsparser: Use python-numpy@1. * gnu/packages/bioinformatics.scm (python-fcsparser): [propagated-inputs]: Remove python-numpy; add python-numpy-1. Change-Id: I2a069293821b769aa981c15ccbc5c96cde5a497a Signed-off-by: Rutherther <rutherther@ditigal.xyz>
gnu: python-graphtools: Update to 2.1.0. * gnu/packages/graph.scm (python-graphtools): Update to 2.1.0. [arguments]<phases>: Remove 'patch-tets; use default 'check; add 'fix-pytest-config. [native-inputs]: Remove util-linux, python-pynose, and python-nose2; add python-pytest and python-setuptools. Change-Id: If5561d5c4de1a9c78e7d4baa7011bd0ad622c4ef Signed-off-by: Rutherther <rutherther@ditigal.xyz>
gnu: python-pygsp: Update to 0.6.0. * gnu/packages/graph.scm (python-pygsp): Update to 0.6.0. [source] <pypi-uri>: Fix name. [arguments] <test-flags>: Rework skipped tests. <phases>: Remove 'disable-doctets. [propagated-inputs]: Remove python-scikit-image. [native-inputs]: Remove python-coverage, python-coveralls, and python-flake8; add python-matplotlib, python-pyunlocbox, python-scikit-image, and python-setuptools. Change-Id: Ic2ef43e47967897e2d7df7e628a8d02ff7684360 Signed-off-by: Rutherther <rutherther@ditigal.xyz>
gnu: Add python-pyunlocbox. * gnu/packages/graph.scm (python-pyunlocbox): New variable. Change-Id: I0281d2e1cfa4ad61a64e168f2c70344afd96ad3a Signed-off-by: Rutherther <rutherther@ditigal.xyz>