gnu: python-pecan: Update to 1.6.1.

* gnu/packages/python-web.scm (python-pecan): Update to 1.6.1.
[build-system]: Use pyproject-build-system.
[native-inputs]: Remove uwsgi.
[arguments]: Remove 'relax-requirements phase and custom 'check phase.

Change-Id: I94a09a56fa2f353d8df3a96cb38a5bd73d5b0c0b

gnu: python-dask-image: Update to 2024.5.3.

* gnu/packages/python-xyz.scm (python-dask-image): Update to 2024.5.3.
[arguments]: Add phase 'set-version.
[native-inputs]: Add python-coverage, python-flake8, python-pytest-cov,
python-pytest-timeout, python-setuptools, python-setuptools-scm, python-twine,
and python-wheel.

Change-Id: I2297cb6942f7c97a330847bda8e0c33c84266322

gnu: python-duckdb: Disable one more test.

* gnu/packages/python-xyz.scm (python-duckdb)[arguments]: Disable wrap
coverage test.

Change-Id: I625bc37c979d7c0fa3a2e67d35267993ae791b9e

gnu: python-pysam: Update to 0.23.0.

* gnu/packages/bioinformatics.scm (python-pysam): Update to 0.23.0.
[arguments]: Use #:test-flags instead of custom 'check phase; add 'pre-check
phase.

Change-Id: I92c715d5dfd5cbdbcf6dd61fc5e472f6c6ca977d

gnu: htscodecs: Update to 1.6.1.

* gnu/packages/bioinformatics.scm (htscodecs): Update to 1.6.1.

Change-Id: If5b4af407a8b639891d0b444056e81724cebac8c

gnu: bcftools: Update to 1.21.

* gnu/packages/bioinformatics.scm (bcftools): Update to 1.21.

Change-Id: I4a2a6c106f804a68c16074a6ce8ae449c299724e

gnu: htslib: Update to 1.21.

* gnu/packages/bioinformatics.scm (htslib): Update to 1.21.
(htslib-1.19): New variable.

Change-Id: If2a53871e69c606d3aebe820ee75bcc945d939b0

gnu: python-ratelimiter: Update to 1.2.0.post1.

* gnu/packages/python-xyz.scm (python-ratelimiter): Update to 1.2.0.post1.
[build-system]: Use pyproject-build-system.
[arguments]: Add phase 'pytest-compatibility.
[native-inputs]: Add python-pytest, python-pytest-asyncio, python-setuptools,
and python-wheel.

Change-Id: I9f7665feb4cf31e38185be7e0cd5ffe7691e26f7

gnu: snakemake-6: Disable one more test.

* gnu/packages/python-xyz.scm (snakemake)[arguments]: Disable test_lint test;
replace custom 'check phase with 'pre-check phase.

Change-Id: I9631383ab6160ee8a234145515bbf198b54b1e57

gnu: snakemake: Disable one more test.

* gnu/packages/python-xyz.scm (snakemake)[arguments]: Disable test_lint test.

Change-Id: I00d3e1e900c5d4dacb660d253a2a1839c7c7826a

gnu: python-yte: Update to 1.7.0.

* gnu/packages/python-xyz.scm (python-yte): Update to 1.7.0.
[build-system]: Use pyproject-build-system.
[arguments]: Replace 'check phase.
[propagated-inputs]: Add python-dpath.
[native-inputs]: Add python-numpy, python-poetry-core, and python-pytest.

Change-Id: If1d4e8e0289d9a36205353ad2c9bb345076e4ff7

gnu: python-dpath: Update to 2.2.0.

* gnu/packages/python-xyz.scm (python-dpath): Update to 2.2.0.
[build-system]: Use pyproject-build-system.
[arguments]: Remove custom 'check phase.
[native-inputs]: Remove python-mock and python-nose; add python-nose2,
python-setuptools, and python-wheel.

Change-Id: I30ca919712b03f868d3e9fed4802817e4602dcda

gnu: snakemake-7: Update to 7.32.4.

* gnu/packages/python-xyz.scm (snakemake-7): Update to 7.32.4.
[arguments]: Use #:test-flags instead of a custom 'check phase; remove
'tabulate-compatibility phase; add 'pre-check phase.
[propagated-inputs]: Add python-humanfriendly, python-reretry, and
python-throttler; remove python-ratelimiter.

Change-Id: Iea7f17559b19098ca5a589d164355f3918f4bb3e

gnu: python-toposort: Update to 1.10.

* gnu/packages/python-xyz.scm (python-toposort): Update to 1.10.
[build-system]: Use pyproject-build-system.
[arguments]: Replace 'check phase.
[native-inputs]: Add python-setuptools and python-wheel.

Change-Id: Ifde522ecba6331634c911856892c3b25098fbd88

gnu: Add python-reretry.

* gnu/packages/python-xyz.scm (python-reretry): New variable.

Change-Id: Ic54bdb5eee422b12d2c0e475abb6c4f142cad1e3

gnu: Add python-throttler.

* gnu/packages/python-xyz.scm (python-throttler): New variable.

Change-Id: I04a07281d4ba77d880d7c8176b1a3269713b9b63

gnu: zbar: Update to 0.23.93.

* gnu/packages/aidc.scm (zbar): Update to 0.23.93.

Change-Id: Id681057d67cfbd26d1b95a9450b2c9cace2545f6

gnu: python-glue-astronomy: Avoid deprecation failure in tests.

* gnu/packages/astronomy.scm (python-glue-astronomy) [arguments]
<test-flags>: Skip one failing test.

Change-Id: I4dd3d3e1d56b75cf8e6479bdeacf2c391d206e9c

gnu: python-sanic: Scip more tests, simplify.

* gnu/packages/python-web.scm (python-sanic) [arguments] <test-flags>:
Ignore all benchmark and typing tests. Skip more failing tests.
<phases>: Use default 'check.
[native-inputs]: Remove python-bandit, python-chardet, python-coverage,
python-cryptography, python-docutils, python-mypy, python-pygments,
python-pytest-benchmark, python-pytest-sanic, python-slotscheck,
python-towncrier, python-tox, and python-types-ujson; add
python-pytest-asyncio.

Change-Id: I8804114656fd76639939ba2fa50fb95d65b823ab

gnu: python-debug: Use G-Expressions.

* gnu/packages/python.scm (python-debug): Use G-Expressions, fix build.

Change-Id: I940ec4fddcea03a258659ca044b0dad4948c4ed5