~ruther/guix-local: gnu/packages/bioinformatics.scm 28d63cb66b42e14f964d33f866c3a4eb1a3de24d

cbad86a9 — Sharlatan Hellseher 6 months ago

gnu: python-cython-3: Mark as deprecated.

This is a followup to 941b6ff1c11be3ba73e4e67bc661bd0eed3e9d58 commit.

Replace all python-cython-3 occurrences with python-cython.

* gnu/packages/python-xyz.scm (python-cython-3): Deprecate variable.

* gnu/packages/algebra.scm (python-fpylll, python-flint)[native-inputs]:
Remove python-cython-3; add python-cython.

* gnu/packages/astronomy.scm (python-astropy, python-astroscrappy,
python-halotools, python-healpy, python-libstempo, python-lofar-h5plot,
python-losoto, python-photutils, python-pyxsim, python-regions,
python-reproject, python-sncosmo, python-sndata, python-stcal,
python-yt)[native-inputs]: Remove python-cython-3; add python-cython.

* gnu/packages/bioinformatics.scm (macs-3, python-pyrodigal):
[native-inputs]: Remove python-cython-3; add python-cython.

* gnu/packages/build-tools.scm (meson-python)[propagated-inputs]: Remove
python-cython-3; add python-cython.
[native-inputs]: Remove python-cython-3; add python-cython.

* gnu/packages/databases.scm: (python-adbc-driver-manager,
python-psycopg, python-pyarrow)[native-inputs]: Remove
python-cython-3; add python-cython.

* gnu/packages/finance.scm (python-ta-lib)[native-inputs]: Remove
python-cython-3; add python-cython.

* gnu/packages/game-development.scm (python-pygame-ce)[native-inputs]:
Remove python-cython-3; add python-cython.

* gnu/packages/geo.scm (python-pyogrio, python-cf-units)[native-inputs]:
Remove python-cython-3; add python-cython.

* gnu/packages/machine-learning.scm: (python-scikit-learn,
python-opentsne)[native-inputs]: Remove python-cython-3; add
python-cython.

* gnu/packages/maths.scm: (python-cylp, python-petsc4py,
python-primecountpy, python-slepc4py)[native-inputs]: Remove
python-cython-3; add python-cython.

* gnu/packages/python-check.scm (python-line-profiler)[native-inputs]:
Remove python-cython-3; add python-cython.

* gnu/packages/python-compression.scm (python-blosc2)[native-inputs]:
Remove python-cython-3; add python-cython.

* gnu/packages/python-graphics.scm (python-vispy)[native-inputs]:
Remove python-cython-3; add python-cython.

* gnu/packages/python-science.scm: (python-pykdtree, python-qutip,
python-scikit-misc, python-scikit-surprise, python-pandas-2,
python-vaex-core)[native-inputs]: Remove python-cython-3; add
python-cython.

* gnu/packages/python-web.scm: (python-aiohttp, python-falcon,
python-yarl, python-uvloop)[native-inputs]: Remove python-cython-3; add
python-cython.

* gnu/packages/python-xyz.scm: (python-logbook, python-netcdf4,
python-pyyaml, python-propcache, python-pywavelets, python-symengine,
python-cysignals, python-pyemd, python-rbfly)[native-inputs]: Remove
python-cython-3; add python-cython.

* gnu/packages/sagemath.scm: (python-cypari2, python-pplpy, sage)
[native-inputs]: Remove python-cython-3; add python-cython.

* gnu/packages/sphinx.scm (python-sphinx)[native-inputs]: Remove
python-cython-3; add python-cython.

* gnu/packages/statistics.scm: (python-statsmodels, python-pyreadstat):
[native-inputs]: Remove python-cython-3; add python-cython.

* gnu/packages/tor.scm (onionshare-cli)[native-inputs]: Remove
python-cython-3; add python-cython.

* gnu/packages/xorg.scm (xpra)[native-inputs]: Remove python-cython-3;
add python-cython.

Change-Id: I38038d2ab18e6a7b549070083d6e4c5beb8b0293

225193d5 — Andreas Enge 6 months ago

gnu: stringtie: Update to 3.0.2.

* gnu/packages/bioinformatics.scm (stringtie): Update to 3.0.2.

Change-Id: Ie35084c70ad6c91b9e03b09ec6fe4f825bd39dcd

56d3b81e — Andreas Enge 6 months ago

gnu: Remove htslib-1.12.

* gnu/packages/bioinformatics.scm (htslib-1.12): Delete variable.

Change-Id: Id1fd05bddc1b40be0e3186c0e5848a1a0f343ce3

ff6b3eb2 — Andreas Enge 6 months ago

gnu: Remove htslib-for-stringtie.

* gnu/packages/bioinformatics.scm (htslib-for-stringtie): Delete variable.
* gnu/packages/patches/htslib-for-stringtie.patch: Remove file.
* gnu/local.mk (dist_patch_DATA): Unregister file.

Change-Id: Idbf3fa982895baed97913e08650cbff6947e8182

a3f9fd26 — Andreas Enge 6 months ago

gnu: stringtie: Update input.

* gnu/packages/bioinformatics.scm (stringtie)[inputs]:
Replace htslib-for-stringtie by htslib.

Change-Id: I8f197b461ee5f0a0e1b1e1201437d3c7667c2685

f8eb0eb0 — Andreas Enge 6 months ago

gnu: python-doubletdetection: Corrected deprecated input.

* gnu/packages/bioinformatics.scm (python-doubletdetection)[inputs]:
Replace python-vtraag-louvain by python-louvain-igraph.

Change-Id: I27c87906c44bd536d67938c0315e40ca7ee82bf5

50591e81 — Andreas Enge 6 months ago

gnu: Remove htslib-1.19.

* gnu/packages/bioinformatics.scm (htslib-1.19): Delete variable.

Change-Id: I7804d3ae403dbdf149e3012922f7ac9a382288d7

71d60494 — Andreas Enge 6 months ago

gnu: Remove samtools-1.14.

* gnu/packages/bioinformatics.scm (samtools-1.14): Delete variable.

Change-Id: I68e8e3ad05841d300897d830f9bcd7fa73c68adc

c5121e08 — Andreas Enge 6 months ago

gnu: Remove bcftools-1.12.

* gnu/packages/bioinformatics.scm (bcftools-1.12): Delete variable.

Change-Id: I805ec24f6eb47d37b2158b85f9d03d5a36999695

cb2dc11b — Andreas Enge 6 months ago

gnu: Remove samtools-1.12.

* gnu/packages/bioinformatics.scm (samtools-1.12): Delete variable.

Change-Id: Ibd80f3fb79efab17193f82b4f713ff1f2cbd2470

666d490b — Andreas Enge 6 months ago

gnu: Remove htslib-1.10.

* gnu/packages/bioinformatics.scm (htslib-1.10): Delete variable.

Change-Id: I9d1bd86e580de2b9b7fe096e7f86b3a96e6df4d1

00fa458a — Andreas Enge 6 months ago

gnu: Remove bcftools-1.10.

* gnu/packages/bioinformatics.scm (bcftools-1.10): Delete variable.

Change-Id: I41d5a65b6857debf3586b3d3716bb7a2693645cb

44dfc987 — Andreas Enge 6 months ago

gnu: Remove samtools-1.10.

* gnu/packages/bioinformatics.scm (samtools-1.10): Delete variable.

Change-Id: If3ef93c3473c4fe9c21f062fe619d883fbafb2ec

87b90f04 — Andreas Enge 6 months ago

gnu: Remove htslib-for-samtools-1.2.

* gnu/packages/bioinformatics.scm (htslib-for-samtools-1.2):
Delete variable.

Change-Id: I62c8525d27321acd7fea32e25623e5cbd7e74c33

788513d4 — Andreas Enge 6 months ago

gnu: Remove samtools-1.2.

* gnu/packages/bioinformatics.scm (samtools-1.2): Delete variable.

Change-Id: I38effe41c32349b5b72754da07fe6696d2f21669

9fcfb939 — Ludovic Courtès 6 months ago

gnu: Use ‘define-deprecated-package’ for deprecated packages.

Use ‘define-deprecated-package’ instead of (define x (deprecated-package …))
throughout gnu/packages/*.scm.

Change-Id: I4e176da9ac660327489dab256ca4d12c4e78fe8d

7dfdf10f — Andreas Enge 6 months ago

gnu: Remove python-velocyto.

* gnu/packages/bioinformatics.scm (python-velocyto): Delete variable.

Fixes: guix/guix#2922
Change-Id: Ifcc556de612ee596019b4164e9f5b33e76bf67a3

08392478 — Andreas Enge 6 months ago

gnu: Remove python-plastid.

* gnu/packages/bioinformatics.scm (python-plastid): Delete variable.

Fixes: guix/guix#2897
Change-Id: I72a38912c7c89997add49d08a01f8522acaa46d1

5571db77 — Sharlatan Hellseher 6 months ago

gnu: instrain: Update to 1.10.0-0.6180be7.

* gnu/packages/bioinformatics.scm (instrain): Update to
6180be7b49a61b7e1ffe9f1489da5c6aa2ff9ac3 commit.
[arguments]: Use G-Expressions.
<phases>: Add 'relax-requirements.
[native-inputs]: Remove python-boto3, python-pytest, and python-wheel.

Change-Id: I5cf37e5128a962007aa9d4e8a8ffa3da474e7c6f

df7c77aa — Andreas Enge 6 months ago

gnu: libsbml: Update to 5.20.5.

* gnu/packages/bioinformatics.scm (libsbml): Update to 5.20.5.
[source]: Switch to git-fetch.

Change-Id: Idee7f2826c8c863482b048ab5500526e6c10e0f5