gnu: go-github-com-onsi-gomega: Update to 1.33.1.

* gnu/packages/golang-check.scm (go-github-com-onsi-gomega): Update to 1.33.1.
[arguments] <#:go>: Swap to go-1.21.
[propagated-inputs]: Remove go-gopkg-in-yaml-v2; add go-gopkg-in-yaml-v3.

Change-Id: I910206fd44198550bdc7da1ebdaff3874d89f1ed

gnu: go-github-com-onsi-ginkgo-v2: Update to 2.18.0.

* gnu/packages/golang-check.scm (go-github-com-onsi-ginkgo-v2): Update to 2.18.0.
[propagated-inputs]: Remove go-github-com-go-task-slim-sprig; add
go-github-com-go-task-slim-sprig-v3 and go-github-com-google-pprof.

Change-Id: I3af9d36e1428745557173135fcaa1e4623d4f57f

gnu: Add go-github-com-go-task-slim-sprig-v3.

* gnu/packages/golang-xyz.scm (go-github-com-go-task-slim-sprig-v3): New
variable.

Change-Id: I46ef3728993556dfc2d6c9349da6962d747e2664

gnu: go-github-com-go-task-slim-sprig: Enable tests.

* gnu/packages/golang-xyz.scm (go-github-com-go-task-slim-sprig)
[arguments] <#:tests>: Enable it.
<#:phases>: Add 'remove-failing-tests phase.

Change-Id: I32424925a96defd69e2871dee079db8bef2861b2

gnu: go-github-com-go-task-slim-sprig: Move to golang-xyz.

* gnu/packages/golang.scm (go-github-com-go-task-slim-sprig): Move from
here ...
* gnu/packages/golang-xyz.scm: ... to here.

Change-Id: I540e4211e7e4006d654c7da40bba35e2bd577c78

gnu: Add go-go-uber-org-mock.

* gnu/packages/golang-check.scm (go-go-uber-org-mock): New variable.

Change-Id: I9028edc15f1acd3301fde3a49eae8cc28568c6a5

gnu: Add python-augeas.

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

Change-Id: I46d409debfbc358f0ff27c505fba089ceab4e195
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>

gnu: augeas: Update to 1.14.1.

* gnu/packages/augeas.scm (augeas): Update to 1.14.1.
  [source]: Use tarballs from GitHub.
  [inputs]: Change to "native-inputs".  Add readline.

Change-Id: I9ca46b8a50d11c75ff6d816f2f15e1f005877244
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>

gnu: Add r-tglkmeans.

* gnu/packages/cran.scm (r-tglkmeans): New variable.

Change-Id: I13aa0e8c4ab062993d84c99811971ebf6e9179bd

gnu: Add r-slanter.

* gnu/packages/cran.scm (r-slanter): New variable.

Change-Id: I3b6c76431940f5e6be6a86344029552dded54e54

gnu: Add r-shinydashboardplus.

* gnu/packages/cran.scm (r-shinydashboardplus): New variable.

Change-Id: Ie50bd8a0234af0fb5ea63377aa005655acad01bd

gnu: Add r-waiter.

* gnu/packages/cran.scm (r-waiter): New variable.

Change-Id: I98b27630eba86ab700ac30a361baf14a5d58dae8

gnu: Add esbuild-node.

* gnu/packages/web.scm (esbuild-node): New variable.

Change-Id: I5e1a353a13ef7b4018fcf4aef4832af25f3dabe2

gnu: ensembl-vep: Update to 112.

* gnu/packages/bioinformatics.scm (ensembl-vep): Update to 112.
[propagated-inputs]: Add perl-list-moreutils.
[native-inputs]: Add perl-test-deep and perl-test-warnings.

Change-Id: I8c7de9f3dbc8c6fe4d1383f9dc215aeba018af0d

gnu: Add r-chameleon.

* gnu/packages/cran.scm (r-chameleon): New variable.

Change-Id: I9e0f3c27e434bb802c86ef9e2877f4d810397158
Signed-off-by: Ricardo Wurmus <rekado@elephly.net>

doc: Make changes to the handling of branches.

Require that you create a "Request to merge" issue when you create a branch,
rather than when you wish to merge it.  This should help avoid this step being
missed.

Also, add information on how to manage these branches:

 1. Suggest creating the branch from patches, rather than having a stateful
 branch, since this should help to reduce complexity and avoid merges.

 2. Require that branches don't have unnecessary changes, since this increases
 the risks of conflicts with other branches.

 3. Suggest that the branch not be stateful, and it's just a combination of
 patches.

 4. Suggest avoiding merges since these create a more complicated Git history.

 5. Suggest that the branch be up to date before merging, as this helps avoid
 the combination of master plus the branch differing significantly from the
 branch alone.

 6. Document how to manage branches without commit access.

Finally, require that the branch be deleted once they're merged.  This
prepares for the branch being created again.

* doc/contributing.texi (Managing Patches and Branches): Make changes to the
handling of branches.

Change-Id: Ib9419c6df94f485475bd6f147e82ea254e76cec2

gnu: python-pandera: Update to 0.18.0, fix build.

* gnu/packages/python-science.scm (python-pandera): Update to 0.18.0.
[arguments] <#:test-flags>: Disable one more failing test.

Change-Id: I4d3f59dae8d90ea0afbe9cc932fc6163def282c9

gnu: python-pymysql: Propagate python-cryptography.

* gnu/packages/databases.scm (python-pymysql)
[inputs]: Swap to [propagated-inputs].
[propagated-inputs]: Add python-pynacl
(mycli, sqlcrush): Remove propagated python-cryptography.

Change-Id: I40ee51087cd14cb98bd2390095fa9f6f0d144b47

gnu: python-pymysql: Update to 1.1.1 [fixes CVE-2024-36039].

* gnu/packages/databases.scm (python-pymysql): Update to 1.1.1.
[source]: Refresh archive name as seen on
<https://pypi.org/project/PyMySQL/#files>.
[build-system]: Swap to pyproject-build-system.

Change-Id: I20d06f6d1d252f501df001120ee44520e6e5d785

gnu: schmutz: update to commit f8043e.

* gnu/packages/guile-xyz.scm (schmutz): Update to commit f8043e.
  [inputs]: Switch guile-2.2 to guile-3.0.

Change-Id: Ibd3e5a5074119e3d2a9affcd7c98f47cb9f1f677
Signed-off-by: Zheng Junjie <zhengjunjie@iscas.ac.cn>