gnu: nss-certs: Relocate to (gnu packages nss).

This is made so that the source can be shared without introducing module
circular dependencies.

* gnu/packages/certs.scm (nss-certs)
(nss-certs-for-test): Move to...
* gnu/packages/nss.scm: ... here.

Adjust the module imports via:

  git grep -l '(gnu packages certs)' |
  xargs sed 's/(gnu packages certs)/(gnu packages nss)/' -i

Change-Id: I56d7bc52ddcdffbced8a162e8db8ea5071b0cb0f

gnu: python-lmdb: Switch to pyproject.

* gnu/packages/databases.scm (python-lmdb):
[source]: Improve style.
[build-system]: Switch to pyproject-build-system.
[arguments]<#:tests?>: Enable them.
<#:phases>: Refresh them.
[native-inputs]: Add python-pytest, python-setuptools, python-wheel.

Change-Id: Ic78cae77e77846d6bace552e1baf7839fafa1603
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>

gnu: python-alchemy-mock: Switch to pyproject.

* gnu/packages/databases.scm (python-alchemy-mock):
[source]: Switch to git-fetch.
[build-system]: Switch to pyproject-build-system.
[arguments]: Pass pytest options through <#:test-flags> rather than
<#:phases>.
[native-inputs]: Add python-setuptools, python-wheel.

Change-Id: I03ad45d452c11001b500b513682c338f3bff33e8
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>

gnu: python-mysqlclient: Update to 2.2.7.

* gnu/packages/databases.scm (python-mysqlclient): Upgrade to 2.2.7.

Change-Id: Ifa5a8f7c478a6823fd957b2788e9b52457c5713d
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>

gnu: aerich: Update to 0.8.1.

* gnu/packages/databases.scm (aerich): Update to 0.8.1.
[propagated-inputs]: Remove python-click, python-ddlparse, and
python-tomlkit; add python-asyncclick, python-pydantic, and
python-tomli-w.
[native-inputs]: Remove poetry, python-bandit, python-isort,
python-pydantic, and python-pytest-xdist; add python-poetry-core.

Change-Id: I685b79fdb6b1070ce86161d9f36064b84f4fe713

gnu: mariadb: Remove patch.

This was apparently merged in version 10.4 and does not apply anymore.

* gnu/packages/patches/mariadb-rocksdb-atomic-linking.patch: Remove file.
* gnu/local.mk (dist_patch_DATA): Unregister file.
* gnu/packages/databases.scm (mariadb)[arguments]<#:phases>{patch-source}:
Remove phase.
[native-inputs]: Remove patch and patch-file.

Change-Id: I6fcf4a1852d8abd1bdb29cd2a2fe96b19da602a9

gnu: go-github-com-olekukonko-tablewriter: Update to 1.0.7.

* gnu/packages/golang-xyz.scm (go-github-com-olekukonko-tablewriter): Update to 1.0.7.
[arguments] <go>: Use go-1.23.
[propagated-inputs]: Add go-github-com-fatih-color,
go-github-com-olekukonko-errors, and go-github-com-olekukonko-ll.
[native-inputs]: Add go-github-com-olekukonko-ts.
(go-csv2table) [arguments]: Inherit instead of overwrite.
[native-inputs]: Merge native and propagated inputs.
[propagated-inputs]: Drop all.
[inputs]: Drop all.
(go-github-com-olekukonko-tablewriter-0.0.5): New variable.
(go-github-com-charmbracelet-glamour-0.3) [propagated-inputs]: Remove
go-github-com-olekukonko-tablewriter; add
go-github-com-olekukonko-tablewriter-0.0.5.

* gnu/packages/golang-web.scm (go-github-com-jaytaylor-html2text,
go-github-com-yggdrasil-network-yggdrasil-go): [propagated-inputs]:
Remove go-github-com-olekukonko-tablewriter; add
go-github-com-olekukonko-tablewriter-0.0.5.

* gnu/packages/networking.scm (yggdrasil): Likewise.

* gnu/packages/check.scm (checkmake) [native-inputs]: Remove
go-github-com-olekukonko-tablewriter; add
go-github-com-olekukonko-tablewriter-0.0.5.

* gnu/packages/databases.scm (sqls): Likewise.

* gnu/packages/education.scm (cf-tool): Likewise.

* gnu/packages/textutils.scm (vale) [arguments] <go>: Use go-1.23.
[native-inputs]: Remove go-github-com-olekukonko-tablewriter; add
go-github-com-olekukonko-tablewriter-0.0.5.

Change-Id: Idefcb19961d22702de0cd6da912d9c964048fe8b

gnu: Pin some golang packages to use go-1.23.

After the defult Golang version was set to 1.24 some of the older
packages which had no fresh version started failing on the 'check phase,
this change pins them to go-1.23 helping to resolve the issue.

Go 1.24 requires non-constant format strings to be explicitly handled.

The errors might look like these:

    non-constant format string in call to (*testing.common).Errorf
    ExampleParseOptionsLifetime refers to unknown identifier: ParseOptionsLifetime

See <https://tip.golang.org/doc/go1.24#vet>.

Change-Id: Ife5093c4fd98af7cea59abf1a9a29351b66602bb

gnu: Remove #:go arguments using go-1.22, go-1.23 or go-1.24.

We are now building with go-1.24 by default.

Automated via:

  git grep -rl '#:go go-1.2' | xargs sed -i '/.*#:go go-1.2[234].*/d'

Change-Id: Ib821d96753619c7748a67ff58b95d8fa358839b7
Modified-by: Sharlatan Hellseher <sharlatanus@gmail.com>
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>

gnu: Add go-github-com-cockroachdb-pebble-v2.

* gnu/packages/databases.scm (go-github-com-cockroachdb-pebble-v2): New variable.

Change-Id: Ib0d7c31290a2009c8ed4495c8c77e93e3364c5dd

gnu: Add go-github-com-cockroachdb-pebble.

* gnu/packages/databases.scm (go-github-com-cockroachdb-pebble, pebble):
New variables.

Change-Id: I1ad3128d200786441c954609a36efadd49076947

gnu: virtuoso-ose: Update to 7.2.15.

* gnu/packages/databases.scm (virtuoso-ose): Update to 7.2.15.
[source]<patches>: Remove virtuoso-ose-remove-pre-built-jar-files.patch.
<snippet>: Update snippet to simply delete all prebuilt Java archives.
[arguments]<phases>: Remove the custom 'bootstrap phase.
<phases>: Update list of files in 'avoid-embedding-kernel-and-timestamps
phase.
[native-inputs]: Add python.
* gnu/packages/patches/virtuoso-ose-remove-pre-built-jar-files.patch: Delete.
* gnu/local.mk (dist_patch_DATA): Remove patch.

Change-Id: I35677732e80e17a9115a910c921f4f167b6d9b3b
Signed-off-by: Andreas Enge <andreas@enge.fr>

gnu: python-asyncmy: Update to 0.2.10.

* gnu/packages/databases.scm (python-asyncmy): Update to 0.2.10.
[source]: Switch to git-fetch.
[build-system]: Switch to pyproject-build-system.
[arguments]<#:tests?>: Disable them for now.
<#:phases>: Replace 'check phase. Add a 'cleanup phase.
[native-inputs]: Add mysql, python-poetry-core, python-pytest,
python-pytest-asyncio, python-setuptools, python-wheel.

Change-Id: I759a85d29372b0d50c2d8992ee303724b7462958
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>

gnu: mariadb-connector-c: Update to 3.4.5.

* gnu/packages/databases.scm (mariadb-connector-c): Update to 3.4.5.

Change-Id: I841a09573aa6776da1307044345d4e388b5cd17b

mariadb-connector-c: Update source URI.

* gnu/packages/databases.scm (mariadb-connector-c)[source]:
Update uri.

Change-Id: If439860ea58dbb5a5ab257f9fe5414ed1a684742
Signed-off-by: Andreas Enge <andreas@enge.fr>

gnu: apache-arrow: Update to 21.0.0.

* gnu/packages/databases.scm (apache-arrow): Update to 21.0.0.

Change-Id: Ide2fefee3c056c8384f311b8401a798ecd97bffb
Signed-off-by: Andreas Enge <andreas@enge.fr>

gnu: Remove apache-arrow-0.16.

* gnu/packages/databases.scm (apache-arrow-0.16): Delete variable.

Change-Id: I2ab52e27ff7bc7c05e9f315b8096087aba024a7d

gnu: Remove python-pyarrow-0.16.

* gnu/packages/databases.scm (python-pyarrow-0.16): Delete variable.

Change-Id: Ifcc22089497c205fc58906219d98ff7a909a819c

gnu: firebird: Update to 3.0.13.

* gnu/packages/databases.scm (firebird): Update to 3.0.13.
[inputs]: Remove icu4c-71; add icu4c-77.

Change-Id: I2fd54614d73ab8784884a260421093a14cbadd64

gnu: firebird: Use git-fetch.

* gnu/packages/databases.scm (source): Use git-fetch. Do not delete
files that are not in the git repository.
[native-inputs]: Set to autoconf, automake and libtool on all
architectures.

Change-Id: I667f6fb46b9ac70139f12bd492be5bfebae42995