Greg Hogan
2ddc161ff0
gnu: gdcm: Fix build.
...
* gnu/packages/bioinformatics.scm (gdcm)[arguments]
<#:configure-flags>: Move excluded tests ...
<#:excluded-tests>: ... to here.
Change-Id: I42cc96a9220e6e5aed1b4fe82ff10835789806e6
2025-08-04 04:11:33 +00:00
Greg Hogan
50c3fd729a
gnu: Remove BUILD_TESTING configuration flag.
...
* gnu/packages/assembly.scm (cpu-features),
* gnu/packages/astronomy.scm (casacore),
* gnu/packages/bioinformatics.scm (morpheus),
* gnu/packages/code.scm (rtags),
* gnu/packages/education.scm (gcompris-qt),
* gnu/packages/game-development.scm (libccd),
* gnu/packages/geo.scm (cloudcompare),
* gnu/packages/glib.scm (dbus-cxx),
* gnu/packages/graph.scm (faiss),
* gnu/packages/graphics.scm (f3d, mmg),
* gnu/packages/i2p.scm (i2pd),
* gnu/packages/image-processing.scm (vtk),
* gnu/packages/image.scm (openjpeg),
* gnu/packages/irc.scm (quassel),
* gnu/packages/jami.scm (jami),
* gnu/packages/kde.scm (kapptemplate, kdeconnect, kdenlive, krita),
* gnu/packages/kde-frameworks.scm (purpose, purpose-5),
* gnu/packages/kde-office.scm (calligra, ghostwriter),
* gnu/packages/linux.scm (bpftrace),
* gnu/packages/maths.scm (blitz, double-conversion, hpcombi, lapack,
vc),
* gnu/packages/messaging.scm (libsignal-protocol-c),
* gnu/packages/mold.scm (mold),
* gnu/packages/music.scm (sonivox),
* gnu/packages/networking.scm (dhtnet),
* gnu/packages/opencl.scm (opencl-clhpp),
* gnu/packages/openpgp.scm (rnp),
* gnu/packages/photo.scm (darktable),
* gnu/packages/popt.scm (gflags),
* gnu/packages/rdesktop.scm (freerdp),
* gnu/packages/security-token.scm (cppcodec),
* gnu/packages/terminals.scm (libtsm),
* gnu/packages/text-editors.scm (jucipp),
* gnu/packages/xdisorg.scm (xsettingsd)
[arguments]<#:configure-flags>: Remove BUILD_TESTING.
* gnu/packages/jupyter.scm (xeus)
[arguments]: Disable tests.
<#:configure-flags>: Remove BUILD_TESTING.
Change-Id: I6870720cdd2b10c7afacf0c6e7400cd1d73a1209
2025-08-04 04:11:23 +00:00
Greg Hogan
f4ce754028
gnu: Restore gnu-build-system phases.
...
* gnu/packages/bioinformatics.scm (bandage),
* gnu/packages/education.scm (openboard),
* gnu/packages/emulators.scm (qtmips),
* gnu/packages/games.scm (chessx),
* gnu/packages/kde-systemtools.scm (spectacle-ocr-screenshot),
* gnu/packages/qt.scm (pyotherside, qtwidgetanimationframework)
<#:phases>: Restore build phase.
* gnu/packages/admin.scm (wpa-supplicant-gui),
* gnu/packages/finance.scm (kitsas)
[arguments]<#:tests?>: Disable.
<#:phases>: Restore build phase.
* gnu/packages/engineering.scm (librecad)
[arguments]<#:test-target>: Delete.
<#:phases>: Restore build and check phases.
* gnu/packages/music.scm (samplebrain)
<#:phases>: Restore build, check, and install phases.
* gnu/packages/password-utils.scm (qtpass)
[arguments]<#:test-target>: Delete.
<#:phases>: Restore build, check, and install phases.
* gnu/packages/ebook.scm (inkbox),
* gnu/packages/engineering.scm (qelectrotech),
* gnu/packages/games.scm (doom-runner, moonlight-qt, pokerth,
qcheckers),
* gnu/packages/gps.scm (gpxsee),
* gnu/packages/hardware.scm (openrgb),
* gnu/packages/image-viewers.scm (qview),
* gnu/packages/pdf.scm (qpdfview),
* gnu/packages/qt.scm (signond),
* gnu/packages/radio.scm (dream)
<#:phases>: Restore build and install phases.
* gnu/packages/disk.scm (qdirstat),
* gnu/packages/pdf.scm (sioyek),
* gnu/packages/qt.scm (signon-plugin-oauth2),
* gnu/packages/radio.scm (qsstv, wfview),
* gnu/packages/security-token.scm (yubikey-manager-qt),
* gnu/packages/tex.scm (texmaker),
* gnu/packages/video.scm (smplayer)
[arguments]<#:tests?>: Disable.
<#:phases>: Restore build and install phases.
* gnu/packages/task-management.scm (timewarrior)
<#:phases>: Restore check phase.
* gnu/packages/audio.scm (supercollider)
<#:phases>: Restore install phase.
* gnu/packages/web.scm (libzim): Update to 9.3.0.
(kiwix-lib): Update to 14.0.0.
(kiwix-desktop): Update to 2.4.1.
[source](patches): Delete.
[arguments]<#:test-target>: Delete.
[arguments]<#:tests?>: Disable.
<#:phases>: Restore build and install phases.
(kiwix-tools): Update to 3.7.0.
* gnu/packages/patches/kiwix-desktop-newer-libkiwix.patch: Delete.
* gnu/local.mk: Update accordingly.
Change-Id: Ia5162ec190fc21334bbc516dcc01056d599f2891
2025-08-04 04:11:21 +00:00
Greg Hogan
5873967ce7
gnu: Pin CMake dependency.
...
* gnu/packages/emulators.scm (python-keystone-engine, unicorn),
* gnu/packages/freedesktop.scm (libdecor),
* gnu/packages/gnome.scm (raider, xffm+),
* gnu/packages/golang-xyz.scm (go-mvdan-cc-editorconfig),
* gnu/packages/hardware.scm (liblxi, lxi-tools),
* gnu/packages/mp3.scm (wavbreaker),
* gnu/packages/pantheon.scm (pantheon-calculator, pantheon-calendar),
* gnu/packages/plotutils.scm (asymptote),
* gnu/packages/photo.scm (entangle),
* gnu/packages/python-graphics.scm (python-pivy),
* gnu/packages/python-xyz.scm (python-awkward-cpp, python-contourpy,
python-symengine),
* gnu/packages/syndication.scm (syndication-domination)
* gnu/packages/qt.scm (soqt),
* gnu/packages/vnc.scm (tigervnc-server)
[native-inputs]: Change cmake to cmake-minimal.
* gnu/packages/bioinformatics.scm (trinityrnaseq)
[native-inputs]: Change cmake to cmake-minimal.
[arguments]<#:phases>[install]: Remove deletion of uncreated files.
Change-Id: I6ce8b737d9a21f83caad7b79b591e68a86f45fd0
2025-08-04 04:10:56 +00:00
Greg Hogan
364e883298
gnu: Remove #:test-target argument.
...
* gnu/packages/astronomy.scm (libsep),
* gnu/packages/bioinformatics.scm (megahit),
* gnu/packages/bittorrent.scm (qbittorrent),
* gnu/packages/calendar.scm (date),
* gnu/packages/check.scm (klee, trompeloeil),
* gnu/packages/compression.scm (zziplib),
* gnu/packages/cpp.scm (immer, lager, zug),
* gnu/packages/databases.scm (timescaledb),
* gnu/packages/emulators.scm (dolphin-emu),
* gnu/packages/fpga.scm (systemc),
* gnu/packages/game-development.scm (box2d),
* gnu/packages/games.scm (megaglest, openclonk, teeworld),
* gnu/packages/glib.scm (sdbus-c++),
* gnu/packages/gnucash.scm (gnucash),
* gnu/packages/graph.scm (igraph),
* gnu/packages/image.scm (exiv2),
* gnu/packages/inkscape.scm (inkscape),
* gnu/packages/instrumentation.scm (yactfr),
* gnu/packages/kde-multimedia.scm (elisa),
* gnu/packages/linux.scm (falcosecurity-libs),
* gnu/packages/llvm.scm (libcxx, libomp-15),
* gnu/packages/machine-learning.scm (ctranslate2, tvm),
* gnu/packages/maths.scm (blitz),
* gnu/packages/messaging.scm (libphonenumber),
* gnu/packages/music.scm (clementine, libdiscid, opustags, strawberry),
* gnu/packages/opencog.scm (atomspace, attention, cogserver, cogutil,
opencog),
* gnu/packages/python-xyz.scm (pybind11)
* gnu/packages/radio.scm (libfec, libcorrect),
* gnu/packages/serialization.scm (qtcsv),
* gnu/packages/shells.scm (fish),
* gnu/packages/tls.scm (aws-lc),
* gnu/packages/web.scm (wabt),
* gnu/packages/vulkan.com (spirv-llvm-translator)
[arguments]: Move #:test-target to ...
<#:phases>: ... 'check phase.
* gnu/packages/algebra.scm (xtensor),
* gnu/packages/astronomy (stellarium),
* gnu/packages/bioinformatics.scm (libsbml),
* gnu/packages/chemistry.scm (openbabel),
* gnu/packages/cpp.scm (xsimd, xtl),
* gnu/packages/documentation.scm (doxygen),
* gnu/packages/lua.scm (selene),
* gnu/packages/libftdi.scm (libftdi),
* gnu/packages/llvm.scm (cling, libomp@12, libomp@13),
* gnu/packages/hyperledger.scm (hyperledger-iroha),
* gnu/packages/markup.scm (cmark, cmark-gfm),
* gnu/packages/maths.scm (cryptominisat, double-conversion),
* gnu/packages/mp3.scm (chromaprint),
* gnu/packages/qt.scm (qtpromise)
* gnu/packages/rdf.scm (clucene),
* gnu/packages/sync.scm (lsyncd)
[arguments}: Remove #:test-target.
* gnu/packages/engineering.scm (libfive),
* gnu/packages/game-development.scm (box2d-3)
[arguments]: Remove #:test-target and disable tests.
Change-Id: I0a82091df1789980bbbac0c334b6f993c36f412a
2025-08-04 04:10:32 +00:00
Andreas Enge
10c29c4971
gnu: gemma: Update to v0.98.5.
...
* gnu/packages/bioinformatics.scm (gemma): Update to v0.98.5.
Change-Id: I911b18190de231934e05fe92375f581acfa3acb6
2025-08-01 22:07:26 +02:00
Andreas Enge
9351e06e3a
gnu: Remove r-r4rna.
...
This is a duplicate package with (gnu packages bioconductor) r-r4rna.
The only dependent package r-rnacrosslinkoo also builds with the
bioconductor version, which is at a higher release.
* gnu/packages/bioinformatics.scm (r-r4rna): Delete variable.
Reported-by: nomike@nomike.com
Change-Id: I4845e785eb1f6a3b2ff35c27ca86e23b2ea90aa5
2025-08-01 18:29:56 +02:00
Andreas Enge
e3bc81ffb8
gnu: imp: Update to 2.23.0.
...
* gnu/packages/bioinformatics.scm (imp): Update to 2.23.0.
[inputs]: Add cereal.
Change-Id: I8ceeeaa93aec0df69eda6d6193f9a87a0202bbad
2025-07-30 20:57:19 +02:00
Sharlatan Hellseher
036f2e66c3
gnu: python-pyrodigal: Update to 3.6.3.
...
* gnu/packages/bioinformatics.scm (python-pyrodigal): Update to 3.6.3.
Fix indentation.
[propagated-inputs]: Remove python-importlib-resources.
[arguments] <phases>: Add 'patch-pyproject; simplify custom 'check
phase.
[native-inputs]: Remove python-mock, python-unittest2, and
python-wheel; add cmake-minimal and python-scikit-build-core.
Change-Id: Id50fe9bd78c466d2dd5938c8a124d244c69da082
2025-07-24 16:18:07 +01:00
Janneke Nieuwenhuizen
035bc12055
gnu: python-pypairix: Update to 0.3.8 and fix build with gcc-14.
...
* gnu/packages/bioinformatics.scm (python-pypairix): Update to 0.3.8.
[arguments]: Use G-Expressions. Add phase "relax-gcc-14-strictness".
Change-Id: I5766c457da18ec7c9fedd83a583dc5e244f33dea
2025-07-18 20:17:22 +02:00
Janneke Nieuwenhuizen
baec3b1965
gnu: bedtools: Update to 2.31.1; fixes build with gcc-14.
...
* gnu/packages/bioinformatics.scm (bedtools): Update to 2.31.1.
Change-Id: I1576952e19449ad92aee3690c97d3f406df95321
2025-07-18 20:17:22 +02:00
Sharlatan Hellseher
c2861537a8
gnu: python-arboreto: Migrate to pyproject.
...
* gnu/packages/bioinformatics.scm (python-arboreto) [build-system]: Use
pyproject.
[native-inputs]: Add python-setuptools and python-wheel.
Change-Id: Id4b3de1b02537bbc15032d0978ef74d6c045d329
2025-07-06 18:44:04 +01:00
Nicolas Graves
7d1f5f950f
gnu: music: Add lint-hidden-cpe-vendors property.
...
* gnu/packages/bioinformatics.scm (music)[properties]: Add
lint-hidden-cpe-vendors property.
Signed-off-by: Zheng Junjie <z572@z572.online>
2025-06-23 12:32:51 +08:00
Nicolas Graves via Guix-patches via
a1dbf22d18
gnu: express: Add lint-hidden-cpe-vendors property.
...
* gnu/packages/bioinformatics.scm (express)[properties]: Add
lint-hidden-cpe-vendors property.
Signed-off-by: Zheng Junjie <z572@z572.online>
2025-06-23 12:31:14 +08:00
Kjartan Oli Agustsson
f731d71846
gnu: tetoolkit: Run guix style
...
* gnu/packages/bioinformatics.scm (tetoolkit): Run guix style.
Change-Id: I5f4c6a647a41a9d60e5bc1d2b4fbee045626dc12
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
2025-06-22 12:54:11 +01:00
Kjartan Oli Agustsson
09a3e09fa8
gnu: tetoolkit: Use pyproject-build-system.
...
* gnu/packages/bioinformatics.scm (tetoolkit): [build-system]: Use
pyproject.
[native-inputs]: Add python-setuptools and python-wheel.
Change-Id: I4fce644bee87c5d6c64a9a3cdf3581a1bae12909
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
2025-06-22 12:54:11 +01:00
Kjartan Oli Agustsson
825ceadb5f
gnu: tbsp: Run guix style
...
* gnu/packages/bioinformatics.scm (tbsp): Run guix style.
Change-Id: I3301f95963aac1f47b28e86a40374df2171732f8
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
2025-06-22 12:54:11 +01:00
Kjartan Oli Agustsson
8ed2fcd5aa
gnu: tbsp: Use pyproject-build-system.
...
* gnu/packages/bioinformatics.scm (tbsp): [build-system]: Use
pyproject.
[native-inputs]: Add python-setuptools and python-wheel.
Change-Id: I6d454d95050862378b7f06c09a42994efd9875a6
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
2025-06-22 12:54:11 +01:00
Kjartan Oli Agustsson
abeb7cd9fa
gnu: stpipeline: Run guix style
...
* gnu/packages/bioinformatics.scm (stpipeline): Run guix style.
Change-Id: I341e0b7adce82c079b1dcff94a2128d3e1773a4a
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
2025-06-22 12:54:10 +01:00
Kjartan Oli Agustsson
3bb992a357
gnu: stpipeline: Use pyproject-build-system.
...
* gnu/packages/bioinformatics.scm (stpipeline): [build-system]: Use
pyproject.
[native-inputs]: Add python-setuptools and python-wheel.
Change-Id: Ibfeea2feb08878d14becf15be5408689ba4c7c3f
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
2025-06-22 12:54:10 +01:00
Kjartan Oli Agustsson
18d5c62c6a
gnu: python-vireosnp: Run guix style
...
* gnu/packages/bioinformatics.scm (python-vireosnp): Run guix style.
Change-Id: I301322fbfa45b3ef7cb1c82eadc60aa1de33d442
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
2025-06-22 12:54:10 +01:00
Kjartan Oli Agustsson
b7ec773e5a
gnu: python-vireosnp: Use pyproject-build-system.
...
* gnu/packages/bioinformatics.scm (python-vireosnp): [build-system]: Use
pyproject.
[native-inputs]: Add python-setuptools and python-wheel.
Change-Id: Id49911001b3672402a17f0902a7e5a565168ab61
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
2025-06-22 12:54:10 +01:00
Kjartan Oli Agustsson
002d6e4109
gnu: python-velocyto: Run guix style
...
* gnu/packages/bioinformatics.scm (python-velocyto): Run guix style.
Change-Id: Ieda2b56cf13ae519e539ecef286ef63595532a7a
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
2025-06-22 12:54:10 +01:00
Kjartan Oli Agustsson
5853163fbf
gnu: python-velocyto: Use pyproject-build-system.
...
* gnu/packages/bioinformatics.scm (python-velocyto): [build-system]: Use
pyproject.
[native-inputs]: Add python-setuptools and python-wheel.
Change-Id: Ie5e605136a7eb7a1acd3850313f2796bf7c83c31
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
2025-06-22 12:54:10 +01:00
Kjartan Oli Agustsson
5eebea1b76
gnu: python-slamdunk: Run guix style
...
* gnu/packages/bioinformatics.scm (python-slamdunk): Run guix style.
Change-Id: I5235a49f7c2d128df6c903f35908fefe022fd50a
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
2025-06-22 12:54:10 +01:00
Kjartan Oli Agustsson
9aff205c4f
gnu: python-slamdunk: Use pyproject-build-system.
...
* gnu/packages/bioinformatics.scm (python-slamdunk): [build-system]: Use
pyproject.
[native-inputs]: Add python-setuptools and python-wheel.
Change-Id: I935dd9a0a7c08985dfb7ca989346783ebf024d50
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
2025-06-22 12:54:10 +01:00
Kjartan Oli Agustsson
15c4134067
gnu: python-scanorama: Run guix style
...
* gnu/packages/bioinformatics.scm (python-scanorama): Run guix style.
Change-Id: I43bfbe845f6e54dab94c6e0055ee811f70026ab4
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
2025-06-22 12:54:10 +01:00
Kjartan Oli Agustsson
492035dfa8
gnu: python-scanorama: Use pyproject-build-system.
...
* gnu/packages/bioinformatics.scm (python-scanorama): [build-system]: Use
pyproject.
[native-inputs]: Add python-setuptools and python-wheel.
Change-Id: Ie437414bff54c361ab61ee2e9baea670762c9ce5
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
2025-06-22 12:54:10 +01:00
Kjartan Oli Agustsson
673a485a6b
gnu: python-pyliftover: Run guix style
...
* gnu/packages/bioinformatics.scm (python-pyliftover): Run guix style.
Change-Id: I45bf0066db834fd99a2bbc1e64d4bc3e20e92cde
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
2025-06-22 12:54:09 +01:00
Kjartan Oli Agustsson
66ab4c5bc1
gnu: python-pyliftover: Use pyproject-build-system.
...
* gnu/packages/bioinformatics.scm (python-pyliftover): [build-system]: Use
pyproject.
[native-inputs]: Add python-setuptools and python-wheel.
Change-Id: Ifcdbfba497527edd82625a20e4baf6b2504f3f92
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
2025-06-22 12:54:09 +01:00
Kjartan Oli Agustsson
0809db9016
gnu: python-pyfit-sne: Use pyproject-build-system.
...
* gnu/packages/bioinformatics.scm (python-pyfit-sne): [build-system]: Use
pyproject.
[native-inputs]: Add python-setuptools and python-wheel.
Change-Id: I8f62f2dc30d2bd182a791830bb835adf778d2ecf
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
2025-06-22 12:54:09 +01:00
Kjartan Oli Agustsson
247afd63f2
gnu: python-ikarus: Run guix style
...
* gnu/packages/bioinformatics.scm (python-ikarus): Run guix style.
Change-Id: I493beb55986808a8ba27eadcc48d8a2a20b1678e
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
2025-06-22 12:54:09 +01:00
Kjartan Oli Agustsson
1ff6229402
gnu: python-ont-fast5-api: Use pyproject-build-system.
...
* gnu/packages/bioinformatics.scm (python-ont-fast5-api): [build-system]: Use
pyproject.
[native-inputs]: Add python-setuptools and python-wheel.
Change-Id: Idb3b5a65767998e232fcc31534cb923ea6f5fed8
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
2025-06-22 12:54:09 +01:00
Kjartan Oli Agustsson
7c405b8da9
gnu: python-ikarus: Use pyproject-build-system.
...
* gnu/packages/bioinformatics.scm (python-ikarus): [build-system]: Use
pyproject.
[native-inputs]: Add python-setuptools and python-wheel.
Change-Id: Idb3b5a65767998e232fcc31534cb923ea6f5fed8
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
2025-06-22 12:54:09 +01:00
Kjartan Oli Agustsson
78039c3e61
gnu: porechop: Use pyproject-build-system.
...
* gnu/packages/bioinformatics.scm (porechop): [build-system]: Use
pyproject.
[native-inputs]: Add python-setuptools, python-wheel, and python-pytest.
Change-Id: I77444786f3e64591c2dc526fb030cecdbb30a3c1
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
2025-06-22 12:54:09 +01:00
Kjartan Oli Agustsson
c1b7cf51dc
gnu: gdc-client: Run guix style
...
* gnu/packages/bioinformatics.scm (gdc-client): Run guix style.
Change-Id: I5dc3f65e622354a66ff71365f6dfd052da951297
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
2025-06-22 12:54:09 +01:00
Kjartan Oli Agustsson
81e55bc0d5
gnu: gdc-client: Use pyproject-build-system.
...
* gnu/packages/bioinformatics.scm (gdc-client): [build-system]: Use
pyproject.
[native-inputs]: Add python-setuptools and python-wheel.
Change-Id: Ifa6ddfab7ddfc90ecdc5838484b3763f1f653e81
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
2025-06-22 12:54:09 +01:00
Kjartan Oli Agustsson
50ece4e78f
gnu: crossmap: Run guix style
...
* gnu/packages/bioinformatics.scm (crossmap): Run guix style.
Change-Id: I56a0ba0e7f5fd24e02a5a769efa7b7e6bda5603b
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
2025-06-22 12:54:08 +01:00
Kjartan Oli Agustsson
1a5fa2c3b2
gnu: crossmap: Use pyproject-build-system.
...
* gnu/packages/bioinformatics.scm (crossmap): [build-system]: Use
pyproject.
[native-inputs]: Add python-setuptools and python-wheel.
Change-Id: I1750685ad8037d004fc1d5fc4f7f76613f257c17
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
2025-06-22 12:54:08 +01:00
Kjartan Oli Agustsson
313519348b
gnu: clipper-peak: Run guix style
...
* gnu/packages/bioinformatics.scm (clipper-peak): Run guix style.
Change-Id: I93c3aea922b1d493d004b401eb312cba63ae4d74
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
2025-06-22 12:54:08 +01:00
Kjartan Oli Agustsson
a694de3938
gnu: clipper-peak: Use pyproject-build-system.
...
* gnu/packages/bioinformatics.scm (clipper-peak): [build-system]: Use
pyproject.
[native-inputs]: Add python-setuptools and python-wheel.
Change-Id: I6cae7d463a412b6736413e80346e377ccb14c290
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
2025-06-22 12:54:08 +01:00
Kjartan Oli Agustsson
1eda883414
gnu: ciri-long: Run guix style
...
* gnu/packages/bioinformatics.scm (ciri-long): Run guix style.
Change-Id: I97e5bd025474ea4ba4f2781f523bc7f5c38fb8e8
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
2025-06-22 12:54:08 +01:00
Kjartan Oli Agustsson
dbfce79477
gnu: ciri-long: Use pyproject-build-system.
...
* gnu/packages/bioinformatics.scm (ciri-long): [build-system]: Use pyproject.
Change-Id: Ie4ff2f95cfe1988bb2b75eb78bda77b8c4259105
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
2025-06-22 12:54:08 +01:00
Kjartan Oli Agustsson
aeb5fd0a24
gnu: checkm: Use pyproject-build-system.
...
* gnu/packages/bioinformatics.scm (checkm): Run guix style.
[build-system]: Use pyproject.
[native-inputs]: Add python-setuptools and python-wheel.
Change-Id: I7d3214c29a7e2b3a6065336632f534a2c4cefbbc
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
2025-06-22 12:54:04 +01:00
Nicolas Graves
01ad0cf43e
gnu: ruby: Populating (gnu packages ruby-check/ruby-xyz).
...
* gnu/packages/ruby.scm: Move all packages except different versions
of ruby and mruby, to either (gnu packages ruby-check) or
(gnu packages ruby-xyz).
* gnu/packages/ruby-check.scm (bundler, ruby-builder, ruby-cucumber-ci-environment,
ruby-cucumber-compatibility-kit,
ruby-cucumber-compatibility-kit-bootstrap, ruby-cucumber-core,
ruby-cucumber-expressions, ruby-cucumber-gherkin,
ruby-cucumber-html-formatter, ruby-cucumber-messages,
ruby-cucumber-tag-expressions, ruby-cucumber-wire, ruby-diff-lcs,
ruby-docile, ruby-fivemat, ruby-given-core, ruby-hoe, ruby-hoe-3,
ruby-json, ruby-mime-types, ruby-mime-types-data, ruby-mini-portile,
ruby-mini-portile-2, ruby-minitest, ruby-minitest-bonus-assertions,
ruby-minitest-focus, ruby-minitest-hooks, ruby-minitest-moar,
ruby-multi-test, ruby-rake, ruby-rake-compiler,
ruby-rake-compiler-dock, ruby-rspec, ruby-rspec-2, ruby-rspec-core,
ruby-rspec-core-2, ruby-rspec-expectations, ruby-rspec-expectations-2,
ruby-rspec-mocks, ruby-rspec-mocks-2, ruby-rspec-support, ruby-sequel,
ruby-simplecov-json-formatter, ruby-simplecov, ruby-simplecov-html,
ruby-sorcerer, ruby-unindent): Moved from (gnu packages ruby).
(ruby-asciidoctor/minimal): New variable, to allow more minimal
import of only (gnu packages ruby-check) in a lot of modules.
(ruby-rubocop/minimal): New variable to build cucumber with a lot
less dependencies.
(cucumber-ruby-core)[native-inputs]: Replace ruby-rubocop by
ruby-rubocop/minimal. Remove ruby-coveralls.
* gnu/packages/ruby-xyz.scm: Move all other packages from
(gnu packages ruby).
* gnu/packages/admin.scm
* gnu/packages/bioinformatics.scm
* gnu/packages/databases.scm
* gnu/packages/emacs-xyz.scm
* gnu/packages/gnome-xyz.scm
* gnu/packages/gnome.scm
* gnu/packages/groff.scm
* gnu/packages/kde-systemtools.scm
* gnu/packages/libffi.scm
* gnu/packages/mail.scm
* gnu/packages/maths.scm
* gnu/packages/mpd.scm
* gnu/packages/ntp.scm
* gnu/packages/package-management.scm
* gnu/packages/plotutils.scm
* gnu/packages/protobuf.scm
* gnu/packages/rails.scm
* gnu/packages/ruby-check.scm
* gnu/packages/ruby-xyz.scm
* gnu/packages/ruby.scm
* gnu/packages/shellutils.scm
* gnu/packages/statistics.scm
* gnu/packages/tex.scm
* gnu/packages/virtualization.scm:
Adapt module imports accordingly.
* gnu/packages/backup.scm (btrbk):
* gnu/packages/ccache.scm (ccache):
* gnu/packages/cluster.scm (drbd-utils):
* gnu/packages/compton.scm (picom):
* gnu/packages/cryptsetup.scm (cryptsetup):
* gnu/packages/engineering.scm (kicad-doc):
* gnu/packages/games.scm (warzone2100):
* gnu/packages/irc.scm (open-adventure):
* gnu/packages/ntp.scm (weechat):
* gnu/packages/password-utils.scm (keepassxc):
* gnu/packages/radio.scm (wsjtx, jtdx):
* gnu/packages/syndication.scm (newsboat):
* gnu/packages/task-management.scm (timewarrior):
* gnu/packages/version-control.scm (git-lfs):
[native-inputs]: Replace ruby-asciidoctor by
ruby-asciidoctor/minimal. Adapt module imports accordingly.
* gnu/packages/text-editors.scm: Remove (gnu packages ruby) import.
Signed-off-by: Andreas Enge <andreas@enge.fr>
2025-06-20 20:40:02 +02:00
Sharlatan Hellseher
4db91aa852
gnu: packages: Remove redundant (gnu packages golang) from some modules.
...
* gnu/packages/android.scm: Remove redundant (gnu packages golang) from
used modules.
* gnu/packages/bioinformatics.scm: Likewise.
* gnu/packages/check.scm: Likewise.
* gnu/packages/configuration-management.scm: Likewise.
* gnu/packages/databases.scm: Likewise.
* gnu/packages/emacs-xyz.scm: Likewise.
* gnu/packages/file-systems.scm: Likewise.
* gnu/packages/golang-check.scm: Likewise.
* gnu/packages/hardware.scm: Likewise.
* gnu/packages/hyperledger.scm: Likewise.
* gnu/packages/irc.scm: Likewise.
* gnu/packages/mail.scm: Likewise.
* gnu/packages/messaging.scm: Likewise.
* gnu/packages/networking.scm: Likewise.
* gnu/packages/password-utils.scm: Likewise.
* gnu/packages/radio.scm: Likewise.
* gnu/packages/terminals.scm: Likewise.
* gnu/packages/tor-browsers.scm: Likewise.
* gnu/packages/video.scm: Likewise.
* gnu/packages/vpn.scm: Likewise.
Change-Id: I6bb92ac0f7c68644cc9b9cc16834aa54240d8fc9
2025-05-26 16:50:21 +01:00
nomike
8b84a2302c
gnu: Rename clipper to clipper-peak.
...
There's a naming conflict with cpp/bioinformatics clipper.
* gnu/packages/bioinformatics.scm
(clipper): Delete variable, rename to clipper-peak.
(clipper-peak): New variable, renamed from clipper.
Change-Id: I1411fe0eebf4ff322e4dadfbe53758feddc36599
Signed-off-by: Christopher Baines <mail@cbaines.net>
2025-05-26 16:00:25 +01:00
Ricardo Wurmus
b430cb1c78
gnu: r-anpan: Update to 0.3.0-1.efd4dc4.
...
* gnu/packages/bioinformatics.scm (r-anpan): Update to 0.3.0-1.efd4dc4.
[properties]: Record updater-extra-native-inputs.
[propagated-inputs]: Add r-cli; remove r-mass.
Change-Id: I60ea7dae8974df81b0188164568de2fe930d1fc4
2025-05-21 15:21:23 +02:00
Sergey Trofimov
380282f3f5
gnu: packages: Fix broken descriptions.
...
A few description mistakenly use @{foo} instead of @code{foo} which
results in broken formatting in guix search.
* gnu/packages/bioinformatics.scm (umi-tools),
* gnu/packages/cran.scm (r-ggside),
* gnu/packages/crates-apple.scm: (rust-commoncrypto-0.2),
* gnu/packages/crates-io.scm: (rust-ndarray-rand-0.15),
* gnu/packages/emacs-xyz.scm (emacs-load-relative, emacs-el-x)
(emacs-helm-org-ql, emacs-consult-lsp),
* gnu/packages/golang-xyz.scm (go-github-com-songmu-gitconfig),
* gnu/packages/haskell-xyz.scm (ghc-text-short, ghc-validation),
* gnu/packages/image.scm (imgp),
* gnu/packages/perl-check.scm (perl-test-file-contents),
* gnu/packages/perl-web.scm (perl-uri-db),
* gnu/packages/perl.scm (perl-clipboard, perl-module-refresh),
* gnu/packages/python-xyz.scm (python-ddlparse, python-black-macchiato)
(python-pysendfile),
* gnu/packages/qt.scm (qt5compat),
* gnu/packages/ruby.scm (ruby-ruby-engine, ruby-httpclient),
* gnu/packages/sagemath.scm (python-memory-allocator),
* gnu/packages/spreadsheet.scm (sc-im),
* gnu/packages/time.scm (python-pendulum):
[description]: Fix malformed macros.
Change-Id: I3ed755a54aecf40bf0c5c982f9e70b7cd3689de7
Signed-off-by: Greg Hogan <code@greghogan.com>
2025-05-13 16:35:45 +00:00
Ricardo Wurmus
8b2426a1a1
gnu: Add r-anglemania.
...
* gnu/packages/bioinformatics.scm (r-anglemania): New variable.
Change-Id: I14e8df223af809cb2a0bb2e569c9a6976de35e6b
2025-05-13 17:01:01 +02:00
