gnu: icedove-minimal: Add libotr support.

* gnu/packages/gnuzilla.scm (icedove-minimal)
[#:phases] {wrap-program}: Add $libotr/lib to LD_LIBRARY_PATH wrapper.
[inputs]: Add libotr.

Fixes: <https://bugs.gnu.org/79749>
Reported-by: "R.W.Flurando" <rw-flurando@inventati.org>
Change-Id: I00e96b3a09b5bc095990284d6971baa8d166181d

gnu: icedove: Update to 140.4.0 [security fixes].

Fixes CVE-2025-11708, CVE-2025-11709, CVE-2025-11710, CVE-2025-11711,
CVE-2025-11712, CVE-2025-11713, CVE-2025-11714 and CVE-2025-11715.

* gnu/packages/gnuzilla.scm (%icecat-140.3-source): Delete variable.
(icedove): Update to 140.4.0.
(%icedove-build-id): Bump to 20251111000000.
(%icedove-version): Bump to 140.4.0.
(thunderbird-comm-source): Update changeset/hash.
(icedove-source): Use icecat-source.

Change-Id: If339c9588295103c03afc6b002ca6f82e17d9ca1

gnu: python-rnc2rng: Update to 2.7.0.

* gnu/packages/python-xyz.scm (python-rnc2rng): Update to 2.7.0.
[source]: Switch to git-fetch.
[build-system]: Switch to pyproject-build-system.
[arguments]<#:test-backend, #:test-flags>: Set them.
[native-inputs]: Add python-setuptools.

Change-Id: If03ecdc1145c8c46c85a4df77e1b53e89e1d0210
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>

gnu: python-flufl-testing: Switch to pyproject.

* gnu/packages/python-xyz.scm (python-flufl-testing):
[source]: Switch to git-fetch.
[build-system]: Switch to pyproject-build-system.
[native-inputs]: Add python-setuptools.

Change-Id: I7371e7a4a5201419aa63fd82ff9cdcfdc43b62c7
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>

gnu: python-jinxed: Update to 1.3.0.

* gnu/packages/python-xyz.scm (python-jinxed): Update to 1.3.0.
[source]: Switch to git-fetch.
[build-system]: Switch to pyproject-build-system.
[arguments]: Improve style.
[native-inputs]: Add python-setuptools.

Change-Id: Ic4d9e4d07181df904d37f903ce0e49f430e62f67
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>

gnu: python-bashlex: Switch to pyproject.

* gnu/packages/python-xyz.scm (python-bashlex):
[source]: Switch to git-fetch.
[build-system]: Switch to pyproject-build-system.
[native-inputs]: Add python-pytest, python-setuptools.
[arguments, description]: Improve style.

Change-Id: Id449a9d2381b8bc29246e23690c1dae83f857aaa
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>

gnu: python-mujson: Switch to pyproject.

* gnu/packages/python-xyz.scm (python-mujson):
[source]: Switch to git-fetch.
[build-system]: Switch to pyproject-build-system.
[arguments]<#:tests?>: Disable them.
[native-inputs]: Add python-setuptools.
[description]: Improve style.

Change-Id: I945102d9215fcc24c0f04003f30304316afe0821
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>

gnu: python-pytidylib: Switch to pyproject.

* gnu/packages/python-xyz.scm (python-pytidylib):
[source]: Switch to git-fetch.
[build-system]: Switch to pyproject-build-system.
[native-inputs]: Add python-pytest, python-setuptools.

Change-Id: I1eeb1199d0be2746a927128bf165d8008e4694ed
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>

gnu: python-osc: Update to 1.9.3.

* gnu/packages/python-xyz.scm (python-osc): Update to 1.9.3.
[source]: Switch to git-fetch.  Remove snippet.
[build-system]: Switch to pyproject-build-system.
[native-inputs]: Add python-setuptools.

Change-Id: Ib68c0f0155b5177cef6c514488f75e79fcc6a2ac
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>

gnu: python-fastentrypoints: Update to 0.12-0.a3a26f3.

* gnu/packages/python-xyz.scm (python-fastentrypoints): Update to 0.12-0.a3a26f3.
[source]: Switch to git-fetch.
[build-system]: Switch to pyproject-build-system.
[arguments]<#:tests?, #:test-backend, #:test-flags>: Set them.
[native-inputs]: Add python-setuptools.
[synopsis]: Improve style.

Change-Id: I706cfdf597bb41faddd0cf3b577fee146c17a2da
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>

gnu: python-jsonplus: Update to 0.8.0-0.a4450ce.

* gnu/packages/python-xyz.scm (python-jsonplus): Update to 0.8.0-0.a4450ce.
[source]: Switch to git-fetch.
[build-system]: Switch to pyproject-build-system.
[arguments]<#:tests?>: Keep them disabled for now.
<#:phases>: Add phase 'chdir.
[native-inputs]: Add python-setuptools.

Change-Id: I200b09ff3b20f7a753407c9abe1fac02e52bfb23
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>

gnu: python-apscheduler: Update to 3.11.1.

* gnu/packages/python-xyz.scm (python-apscheduler): Update to 3.11.1.
[source]: Fix PyPI URI.
[arguments]: Deselect tests failing with latest python-pytest-asyncio.
[propagated-inputs]: Remove python-pytz and python-six.
[native-inputs]: Remove python-mock, python-pytest-cov,
python-pytest-tornado5, and python-wheel; add python-anyio, python-pytz,
and python-tornado.

Change-Id: Iaf52ba8dce6f2251810589157bc98b8da835e2c0
Modified-by: Sharlatan Hellseher <sharlatanus@gmail.com>
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>

gnu: reprotest: Update to 0.7.32.

* gnu/packages/diffoscope.scm (reprotest): Update to 0.7.32.

gnu: r-duckdb: Move to duckdb.

* gnu/packages/cran.scm (r-duckdb): Move from here ...
* gnu/packages/duckdb.scm: ... to here.

Change-Id: Ic735854106fd0b0e693105183b7408d447de882c

gnu: python-duckdb: Move to duckdb.

* gnu/packages/python-xyz.scm (python-duckdb): Move from here ...
* gnu/packages/duckdb.scm: ... to here.

* gnu/packages/python-science.scm: Add (gnu packages duckdb).

Change-Id: Ic8551cdd64f718e62a12576fbc1a38bf861d1644

gnu: duckdb: Update to 1.4.1.

* gnu/packages/duckdb.scm (duckdb): Update to 1.4.1.

Change-Id: Ib9640b2f39ff492404423373f9223f6c71c69f0c

gnu: duckdb: Move to duckdb.

* gnu/packages/databases.scm (duckdb): Move from here ...
* gnu/packages/duckdb.scm: ... to here.

Change-Id: Ie683a1d4d93d556d5d923830ca0132738463c0a8

gnu: Add (gnu packages duckdb) module.

* gnu/packages/duckdb.scm: New file.
* gnu/local.mk: Add to gnu/packages/duckdb.scm scope.

Change-Id: I5a6bbb0114ab588e25a42c8e98a1d2a475d28e0c

gnu: diffoscope: Update to 308.

* gnu/packages/diffoscope.scm (diffoscope): Update to 308.

gnu: gdcm: Fix reference in exported target.

* gnu/packages/bioinformatics.scm (gdcm)
[arguments]<#:phases>{refer-to-charls}: New phase.

Change-Id: I0671b71471c123b041156940640f0f745464052d
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>