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Author SHA1 Message Date
Maxim Cournoyer 2abde9b927
gnu: Remove python2-cov-core. 
* gnu/packages/check.scm (python2-cov-core): Delete variable.
 2022-05-31 14:52:21 -04:00
Maxim Cournoyer f9d31d90ec
gnu: Remove python2-discover. 
* gnu/packages/check.scm (python2-discover): Delete variable.
 2022-05-31 14:52:21 -04:00
Maxim Cournoyer 359a0b6c2e
gnu: Remove python2-flexmock. 
* gnu/packages/check.scm (python2-flexmock): Delete variable.
 2022-05-31 14:52:21 -04:00
Maxim Cournoyer ae2f3bed76
gnu: Remove python2-minimock. 
* gnu/packages/check.scm (python2-minimock): Delete variable.
 2022-05-31 14:52:20 -04:00
Maxim Cournoyer 2af19eb9b5
gnu: Remove python2-rednose. 
* gnu/packages/check.scm (python2-rednose): Delete variable.
 2022-05-31 14:52:20 -04:00
Maxim Cournoyer 4178b304ab
gnu: Remove python2-python-paramunittest. 
* gnu/packages/check.scm (python2-python-paramunittest): Delete variable.
 2022-05-31 14:52:20 -04:00
Maxim Cournoyer 099c5a90e4
gnu: Remove python2-pytest-capturelog. 
* gnu/packages/check.scm (python2-pytest-capturelog): Delete variable.
 2022-05-31 14:52:20 -04:00
Maxim Cournoyer 94447313e8
gnu: Remove python2-nose2. 
* gnu/packages/check.scm (python2-nose2): Delete variable.
 2022-05-31 14:52:20 -04:00
Maxim Cournoyer dc0da7e56f
gnu: Remove python2-testlib. 
* gnu/packages/check.scm (python2-testlib): Delete variable.
 2022-05-31 14:52:19 -04:00
Maxim Cournoyer dc612d54fd
gnu: Remove python2-pytest-catchlog. 
* gnu/packages/check.scm (python2-pytest-catchlog): Delete variable.
 2022-05-31 14:52:19 -04:00
Maxim Cournoyer 4746f9fc63
gnu: Remove python2-nose-timer. 
* gnu/packages/check.scm (python2-nose-timer): Delete variable.
 2022-05-31 14:52:19 -04:00
Maxim Cournoyer ddec4b81d6
gnu: Remove transmission-remote-cli. 
* gnu/packages/bittorrent.scm (transmission-remote-cli): Delete variable.
 2022-05-31 14:52:19 -04:00
Maxim Cournoyer c30ab2c0b4
gnu: Remove pyicoteo. 
* gnu/packages/bioinformatics.scm (pyicoteo): Delete variable.
 2022-05-31 14:52:19 -04:00
Maxim Cournoyer ba09192168
gnu: Remove python2-pbcore. 
* gnu/packages/bioinformatics.scm (python2-pbcore): Delete variable.
 2022-05-31 14:52:19 -04:00
Maxim Cournoyer 8287979669
gnu: Remove python2-pyfaidx. 
* gnu/packages/bioinformatics.scm (python2-pyfaidx): Delete variable.
 2022-05-31 14:52:18 -04:00
Maxim Cournoyer 850bd0c329
gnu: Remove python2-screed. 
* gnu/packages/bioinformatics.scm (python2-screed): Delete variable.
 2022-05-31 14:52:18 -04:00
Maxim Cournoyer a94bc7798a
gnu: Remove miso. 
* gnu/packages/bioinformatics.scm (miso): Delete variable.
 2022-05-31 14:52:18 -04:00
Maxim Cournoyer 23e133a907
gnu: Remove python2-warpedlmm. 
* gnu/packages/bioinformatics.scm (python2-warpedlmm): Delete variable.
 2022-05-31 14:52:18 -04:00
Maxim Cournoyer bb35b50adc
gnu: Remove poretools. 
* gnu/packages/bioinformatics.scm (poretools): Delete variable.
 2022-05-31 14:52:18 -04:00
Maxim Cournoyer bcdd45be6f
gnu: Remove python2-dendropy. 
* gnu/packages/bioinformatics.scm (python2-dendropy): Delete variable.
 2022-05-31 14:52:17 -04:00
Maxim Cournoyer d2c971e67b
gnu: Remove bamm. 
* gnu/packages/bioinformatics.scm (bamm): Delete variable.
 2022-05-31 14:52:17 -04:00
Maxim Cournoyer 1010c05800
gnu: Remove python2-pybedtools. 
* gnu/packages/bioinformatics.scm (python2-pybedtools): Delete variable.
 2022-05-31 14:52:17 -04:00
Maxim Cournoyer 725b562962
gnu: Remove python2-htseq. 
* gnu/packages/bioinformatics.scm (python2-htseq): Delete variable.
 2022-05-31 14:52:17 -04:00
Maxim Cournoyer 8bcb07d089
gnu: Remove pepr. 
* gnu/packages/bioinformatics.scm (pepr): Delete variable.
 2022-05-31 14:52:17 -04:00
Maxim Cournoyer 3d63c5f1ba
gnu: tetoolkit: Update to 2.2.1b. 
* gnu/packages/bioinformatics.scm (tetoolkit): Update to 2.2.1b.
[python]: Delete argument.
[phases]: Delete trailing #t.
{make-writable}: Delete phase.
{adjust-requirements}: New phase.
{patch-invocations}: Use search-input-file.
{wrap-program}: Use search-input-file.
[inputs]: Remove python2-argparse.  Replace python2-pysam with python-pysam.
[home-page]: Update URL.
 2022-05-31 14:52:16 -04:00
Maxim Cournoyer d29d50a556
gnu: Remove python2-pybigwig. 
* gnu/packages/bioinformatics.scm (python2-pybigwig): Delete variable.
 2022-05-31 14:52:16 -04:00
Maxim Cournoyer 98c4f97d18
gnu: Remove ribodiff. 
* gnu/packages/bioinformatics.scm (ribodiff): Delete variable.
 2022-05-31 14:52:16 -04:00
Maxim Cournoyer 9f4c958d62
gnu: Remove grit. 
* gnu/packages/bioinformatics.scm (grit): Delete variable.
 2022-05-31 14:52:16 -04:00
Maxim Cournoyer 7963e12568
gnu: Remove python2-fastalite. 
* gnu/packages/bioinformatics.scm (python2-fastalite): Delete variable.
 2022-05-31 14:52:16 -04:00
Maxim Cournoyer fd4668b111
gnu: Remove python2-pyaudio. 
* gnu/packages/audio.scm (python2-pyaudio): Delete variable.
 2022-05-31 14:52:15 -04:00
Maxim Cournoyer 1a60e11a98
gnu: Remove raul-devel. 
* gnu/packages/audio.scm (raul-devel): Delete variable.
 2022-05-31 14:52:15 -04:00
Maxim Cournoyer 94e8f2b9b5
gnu: Remove raul. 
* gnu/packages/audio.scm (raul): Delete variable.
 2022-05-31 14:52:15 -04:00
Maxim Cournoyer a5a84babb9
gnu: Remove ingen. 
* gnu/packages/music.scm (ingen): Delete variable.
 2022-05-31 14:52:15 -04:00
Maxim Cournoyer cfce386aba
gnu: Remove python2-pyalsaaudio. 
* gnu/packages/audio.scm (python2-pyalsaaudio): Delete variable.
 2022-05-31 14:52:15 -04:00
Maxim Cournoyer cd46c8c34b
gnu: Remove graphios. 
* gnu/packages/admin.scm (graphios): Delete variable.
 2022-05-31 14:52:14 -04:00
Maxim Cournoyer 74641c7f66
gnu: Remove python2-langkit. 
* gnu/packages/ada.scm (python2-langkit): Delete variable.
 2022-05-31 14:52:14 -04:00
Maxim Cournoyer 787a026f00
gnu: Remove python-pytest-runner-2. 
* gnu/packages/check.scm (python-pytest-runner-2): Delete variable.
(python2-pytest-runner): Likewise.
 2022-05-31 14:52:14 -04:00
Maxim Cournoyer 53cd5923ef
diagnostics: Fix typo about 0-indexed COL in location. 
* guix/diagnostics.scm (source-properties->location): The location column is
0-indexed, not 1-indexed (the same as in source-properties, so the code is
accurate).
 2022-05-31 14:52:14 -04:00
Maxim Cournoyer d7c4e7a0c2
utils: Add a %guix-source-root-directory procedure. 
* guix/utils.scm (%guix-source-root-directory): New procedure.
 2022-05-31 14:52:14 -04:00
Maxim Cournoyer 5bc1ede862
utils: Add a 'delete-expression' procedure. 
* guix/utils.scm: Fix copyright lines and order imports.
(edit-expression): Fix typo in doc.  Add a new 'include-trailing-newline?'
keyword argument.  Update doc.
(delete-expression): New procedure.
 2022-05-31 14:52:13 -04:00
Maxim Cournoyer 5e6efdfeec
etc/committer: Teach it how to commit package removal. 
* etc/committer.scm.in (hunk-types): New variable.
(<hunk>): Rename hunk-definition? getter to 'hunk-type'.
(diff-info): Mute a git warning by separating file names from arguments with
'--'.  Rename the 'definitions?' variable to 'type'.
Use the 'addition type when a new package addition is detected, 'removal when
removed else #f.
(add-commit-message): Re-indent.
(remove-commit-message): New procedure.
(main)[definitions]: Make commit message conditional depending on whether it
is an addition or removal.
[changes]: Adjust indentation.
 2022-05-31 14:52:13 -04:00
Maxim Cournoyer 6c956243bc
etc/committer: Prefix (sxml xpath) symbols to avoid name conflict. 
This avoids a naming conflict for 'filter', provided by both (srfi srfi-1)
and (sxml xpath).

* etc/committer.scm.in: Use 'use-modules' instead of 'import', and use a
prefix for the (sxml xpath) module.
(new-sexp): Adjust accordingly.
(change-commit-message): Likewise.
 2022-05-31 14:52:13 -04:00
Maxim Cournoyer 51b6715960
packages: Fix typo in package-superseded doc. 
* guix/packages.scm (package-superseded): Fix typo.
 2022-05-31 14:52:13 -04:00
Mark H Weaver 20432b839b
gnu: icecat: Update to 91.10.0-guix0-preview1 [security fixes]. 
Includes fixes for CVE-2022-31736, CVE-2022-31737, CVE-2022-31738,
CVE-2022-31739, CVE-2022-31740, CVE-2022-31741, CVE-2022-31742, and
CVE-2022-31747.

* gnu/packages/gnuzilla.scm (%icecat-version, %icecat-build-id): Update.
(icecat-source): Update gnuzilla commit, base version, and hashes.
 2022-05-31 14:12:31 -04:00
Marius Bakke be85c4d40f
gnu: ungoogled-chromium: Update to 102.0.5005.61-3. 
* gnu/packages/chromium.scm (%ungoogled-revision): Bump to latest.
(%ungoogled-origin): Update hash.
 2022-05-31 19:54:04 +02:00
Efraim Flashner 2c4c504272
gnu: python-sip-4: Update to 4.19.25. 
* gnu/packages/qt.scm (python-sip-4): Update to 4.19.25.
 2022-05-31 20:45:05 +03:00
Maxim Cournoyer d11d27e2e4
gnu: guile-ac-d-bus: Run test suite. 
* gnu/packages/patches/guile-ac-d-bus-fix-tests.patch: New patch.
* gnu/local.mk (dist_patch_DATA): Register it.
* gnu/packages/guile-xyz.scm (guile-ac-d-bus)
[source]: Apply patch.
[phases]{check}: New phase.
[native-inputs]: Add bash-minimal.
 2022-05-31 11:20:28 -04:00
Maxim Cournoyer 34c8558af2
gnu: guile-ac-d-bus: Build and install info manual. 
* gnu/packages/guile-xyz.scm (guile-ac-d-bus)
[arguments]: Use gexps.
[phases]{build-doc, install-doc}: New phases.
[native-inputs]: Add texinfo.
 2022-05-31 11:20:28 -04:00
Ricardo Wurmus 07909eb092
gnu: python-distributed: Update to 2022.05.2. 
* gnu/packages/python-science.scm (python-distributed): Update to 2022.05.2.
[arguments]: Remove 'sanity-check phase; adjust 'check phase.
[propagated-inputs]: Add python-urllib3.
[native-inputs]: Add python-pytest-timeout and python-flaky.
 2022-05-31 15:18:22 +02:00
Ricardo Wurmus 3d5144db5a
gnu: r-haven: Fix build. 
* gnu/packages/cran.scm (r-haven)[arguments]: Adjust 'unbundle-readstat phase.

Reported-by: Jonas Freimuth.
 2022-05-31 15:18:22 +02:00