gnu: python-strict-rfc3339: Disable more tests on 32-bit platforms.

* gnu/packages/python-xyz.scm (python-strict-rfc3339)[arguments]:
Conditionally ignore the TestTimestampToRFC3339UTCOffset tests on 32-bit
platforms due to the size of the time_t type.

Change-Id: I2c9844c6a022946d9ec917bb3a6b06777b0fc260

gnu: python-werkzeug-1.0: Do not abort on warnings.

* gnu/packages/python-web.scm (python-werkzeug-1.0)[arguments]: Remove custom
'check phase; do not raise errors when warnings are printed.

Change-Id: Ia13e63f6504e5254e35625528ad3ed8e00355528

gnu: python-flask-oidc: Update to 2.3.1.

* gnu/packages/python-web.scm (python-flask-oidc): Update to 2.3.1.
[build-system]: Use pyproject-build-system.
[propagated-inputs]: Remove python-itsdangerous, python-oauth2client, and
python-six; add python-authlib, python-blinker, python-requests, and
python-responses.
[native-inputs]: Add python-pytest and python-poetry-core; remove python-nose
and python-mock.

Change-Id: I5658d420c49626fd72c7c8a4e7fff13eaaee6276

gnu: Add python-authlib.

* gnu/packages/python-web.scm (python-authlib): New variable.

Change-Id: Ia19965ca2e6b26d40740a6fb96a2a03d7842d364

gnu: make-llvm: Remove dynamic linker cache phase also with version 15.0.

On i686-linux the 'make-dynamic-linker-cache fails also when building llvm@15.

* gnu/packages/llvm.scm (make-llvm)[arguments]: Remove
'make-dynamic-linker-cache phase on i686-linux also when version is 15.0.

Change-Id: Iedbe8ce684aae5d8dc07e3c11e696e1b425b9652

gnu: python-numpy: Disable test on 32 bit systems.

* gnu/packages/python-xyz.scm (python-numpy)[arguments]: Conditionally disable
failing test_int test.

Change-Id: I12b25b4019ff8a06b311decdcd2eafe68854b241

gnu: tensorflow: Fix build.

* gnu/packages/machine-learning.scm (tensorflow)[arguments]: Rename phase
'python3.10-compatibility to 'python3.11-compatibility; update it to deal with
removals in Python 3.11; add phase 'numpy-compatibility.

Change-Id: I6c08b7b03cb01223fe9d62545f6687e9440b2011

gnu: Remove python-anyio/without-dataclasses.

* gnu/packages/python-xyz.scm (python-anyio/without-dataclasses): Remove
variable.
* gnu/packages/jupyter.scm (python-jupyter-server)[propagated-inputs]: Replace
python-anyio/without-dataclasses with python-anyio.

Change-Id: I81433128fc3ed2f098bd84f1f89555e9dda62d6d

gnu: bedtools: Update to 2.31.1.

* gnu/packages/bioinformatics.scm (bedtools): Update to 2.31.1.

Change-Id: I9f104d68fbdc2040fee41f1565d48a40999bc219

gnu: ams-lv2: Make compatible with Python 3.11.

* gnu/packages/music.scm (ams-lv2)[arguments]: Add phase 'python3.11-compatibility.

Change-Id: Iaa2709495e24d586a7d9f75dda7e527ca920e127

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