gnu: python-deeptools: Update to 3.5.6.

* gnu/packages/bioinformatics.scm (python-deeptools): Update to 3.5.6.
[arguments] <test-flags>: Skip one test.
<phases>: Remove 'fix-test.
[native-inputs]: Remove python-wheel.

Change-Id: I233b272ee06ab6c290c11a6875961de0fe52b8e8
Signed-off-by: Rutherther <rutherther@ditigal.xyz>

gnu: python-deepdish: Use python-numpy@1.

* gnu/packages/python-science.scm (python-deepdish):
[propagated-inputs]: Remove python-numpy; add python-numpy-1.
[native-inputs]: Remove python-wheel.

Change-Id: I8c4e2bd6538411df0f33d05b80fe178690fcc4d8
Signed-off-by: Rutherther <rutherther@ditigal.xyz>

gnu: python-tdda: Skip one more test.

* gnu/packages/python-science.scm (python-tdda):
[arguments] <test-flags>: Skip one more test.
[native-inputs]: Remove python-wheel.

Change-Id: I1bcb5223627945d580d64e911cd73cf2da06287a
Signed-off-by: Rutherther <rutherther@ditigal.xyz>

gnu: piglit: Use python-numpy@1.

* gnu/packages/gl.scm (piglit):
[inputs]: Remove python-numpy; add python-numpy-1.

Change-Id: I9d8975ebaff57e56fe293b7f2c6f5c86aa181115
Signed-off-by: Rutherther <rutherther@ditigal.xyz>

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>