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2021-12-05gnu: python-bbknn: Add missing input.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-bbknn)[propagated-inputs]: Add python-scikit-learn.
2021-12-05gnu: velvet: Add missing TeX package.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (velvet)[native-inputs]: Add texlive-fonts-ec.
2021-12-05gnu: velvet: Remove trailing #T.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (velvet)[arguments]: Remove trailing #T from build phases.
2021-12-05gnu: python-bwapy: Remove pre-built object files.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-bwapy)[source]: Remove all .o files in a snippet.
2021-12-05gnu: metabat: Remove trailing #T.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (metabat)[arguments]: Remove trailing #T from build phases.
2021-12-05gnu: clapack: Pass -fcommon to compiler.Ricardo Wurmus
* gnu/packages/maths.scm (clapack)[arguments]: Set CFLAGS.
2021-12-05gnu: clapack: Remove trailing #T.Ricardo Wurmus
* gnu/packages/maths.scm (clapack)[arguments]: Remove trailing #T from build phases.
2021-12-05gnu: tla2tools: Remove remaining reference to %output.Ricardo Wurmus
This is a follow-up to commit 7e6ee16d498f48b7bb74fefe5d3d67c62b5baa9d. * gnu/packages/java.scm (tla2tools)[arguments]: Remove remaining reference to %output.
2021-12-05gnu: kraken2: Remove reference to %outputs.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (kraken2)[arguments]: Remove reference to %outputs by using a gexp.
2021-12-05gnu: methyldackel: Remove reference to %outputs.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (methyldackel)[arguments]: Remove reference to %outputs by using a gexp.
2021-12-05gnu: phast: Remove reference to %outputs.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (phast)[arguments]: Remove reference to %outputs by using a gexp.
2021-12-05gnu: libsbml: Remove references to %build-inputs.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (libsbml)[arguments]: Remove references to %build-inputs by using a gexp.
2021-12-05gnu: ataqv: Remove references to %outputs and %build-inputs.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (ataqv)[arguments]: Remove references to %outputs and %build-inputs by using a gexp.
2021-12-05gnu: adapterremoval: Remove reference to %outputs.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (adapterremoval)[arguments]: Remove reference to %outputs by using a gexp.
2021-12-05gnu: bbmap: Remove reference to %build-inputs.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (bbmap)[arguments]: Remove reference to %build-inputs by using a gexp.
2021-12-05gnu: intervaltree: Remove reference to %outputs.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (intervaltree)[arguments]: Remove reference to %outputs by using a gexp.
2021-12-05gnu: biobambam2: Remove reference to %build-inputs.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (biobambam2)[arguments]: Remove reference to %build-inputs by using a gexp.
2021-12-05gnu: sjcount: Remove reference to %build-inputs.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (sjcount)[arguments]: Remove reference to %build-inputs by using a gexp.
2021-12-05gnu: sjcount: Remove trailing #T.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (sjcount)[arguments]: Remove trailing #T from build phases.
2021-12-05gnu: dropseq-tools: Remove reference to %build-inputs.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (dropseq-tools)[arguments]: Remove reference to %build-inputs by using a gexp.
2021-12-05gnu: dropseq-tools: Remove trailing #T.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (dropseq-tools)[arguments]: Remove trailing #T from build phases... [source]: ...and from the snippet.
2021-12-05gnu: tbb: Update to 2021.4.0.Marius Bakke
* gnu/packages/tbb.scm (tbb): Update to 2021.4.0.
2021-12-05gnu: Adjust for python-build-system behavior change.Marius Bakke
Commit cb72f9a773e0931ee3758c851d96007ded034e4c changed the semantics of SITE-PACKAGES, but did not adjust all callers. * gnu/packages/bioinformatics.scm (python-pyvcf)[arguments]: Adjust for missing trailing slash. * gnu/packages/maths.scm (nomad-optimizer)[arguments]: Likewise. * gnu/packages/patchutils.scm (patchwork)[arguments]: Likewise.
2021-12-05gnu: python-pyvcf: Fix bytecode compilation.Marius Bakke
* gnu/packages/bioinformatics.scm (python-pyvcf)[arguments]: Add phase to patch sample script.
2021-12-05gnu: python-whisper: Update to 1.1.8.Marius Bakke
* gnu/packages/monitoring.scm (python-whisper): Update to 1.1.8.
2021-12-05gnu: python-mailman-hyperkitty: Update to 1.2.0.Marius Bakke
* gnu/packages/mail.scm (python-mailman-hyperkitty): Update to 1.2.0. [source](patches): Remove.
2021-12-05gnu: python-hyperkitty: Update to 1.3.5.Marius Bakke
* gnu/packages/mail.scm (python-hyperkitty): Update to 1.3.5. [arguments]: Add pythonpath in test invokation. [propagated-inputs]: Add PYTHON-MISTUNE-NEXT. Change from PYTHON-DJANGO-2.2 to PYTHON-DJANGO. [native-inputs]: Add PYTHON-LXML.
2021-12-05gnu: Add python-mistune-next.Marius Bakke
* gnu/packages/python-xyz.scm (python-mistune-next): New variable.
2021-12-05gnu: python-django-haystack: Update to 3.1.1.Marius Bakke
* gnu/packages/django.scm (python-django-haystack): Update to 3.1.1. [arguments]: Adjust substitution.
2021-12-05gnu: python-alembic: Update to 1.7.5.Marius Bakke
* gnu/packages/databases.scm (python-alembic): Update to 1.7.5. [propagated-inputs]: Remove PYTHON-IMPORTLIB-RESOURCES.
2021-12-05gnu: ganeti: Add the output directory on GUIX_PYTHONPATH.Marius Bakke
This is a follow-up to commit 1ed567c8721ec2810fdb70f1c6fc8396a705d503. * gnu/packages/virtualization.scm (ganeti)[arguments]: Adjust wrap phase to include Ganetis own site-packages on $GUIX_PYTHONPATH.
2021-12-05gnu: python-webassets: Patch for Python 3.9.Marius Bakke
* gnu/packages/python-web.scm (python-webassets)[arguments]: Add substitution.
2021-12-05gnu: python-django-mailman3: Update to 1.3.7.Marius Bakke
* gnu/packages/mail.scm (python-django-mailman3): Update to 1.3.7.
2021-12-05gnu: python-mailmanclient: Update to 3.3.3.Marius Bakke
* gnu/packages/mail.scm (python-mailmanclient): Update to 3.3.3.
2021-12-05gnu: python-django-url-filter: Adjust phase order.Marius Bakke
* gnu/packages/django.scm (python-django-url-filter)[arguments]: Move substitution to after the unpack phase, so that it does not end up in the egg info.
2021-12-05gnu: python-django-netfields: Propagate psycopg2.Marius Bakke
* gnu/packages/django.scm (python-django-netfields)[propagated-inputs]: Add PYTHON-PSYCOPG2.
2021-12-05gnu: python-django-logging-json: Disable sanity check.Marius Bakke
* gnu/packages/django.scm (python-django-logging-json)[arguments]: Add #:phases.
2021-12-05gnu: python-django-appconf: Fix tests.Marius Bakke
* gnu/packages/django.scm (python-django-appconf): Invoke django-admin with custom pythonpath.
2021-12-05gnu: python-django-pipeline: Fix tests.Marius Bakke
* gnu/packages/django.scm (python-django-pipeline): Provide pythonpath to django-admin.
2021-12-05gnu: python-django-sortedm2m: Fix tests.Marius Bakke
This is a follow-up to commit 283d5ac97f2f7663b788bd2fc3b9a27a3d82c7d5. * gnu/packages/django.scm (python-django-sortedm2m): Invoke django-admin with pythonpath and test settings.
2021-12-05gnu: python-django-contact-form: Update to 1.9.Marius Bakke
* gnu/packages/django.scm (python-django-contact-form): Update to 1.9.
2021-12-05gnu: python-django-jinja: Update to 2.9.1.Marius Bakke
* gnu/packages/django.scm (python-django-jinja): Update to 2.9.1.
2021-12-05gnu: python-django-haystack: Disable sanity check.Marius Bakke
* gnu/packages/django.scm (python-django-haystack)[arguments]: Delete one phase. While at it, remove trailing #t's.
2021-12-05gnu: python-fakeredis: Update to 1.7.0.Marius Bakke
* gnu/packages/databases.scm (python-fakeredis): Update to 1.7.0.
2021-12-05gnu: Django packages propagate Django, after all.Marius Bakke
This reverts commit d7922f488b658b1adb5aff09f04a9bed0221aee1. Mainly to placate the new 'sanity-check' phase, and because --with-input and friends makes it easy to override. * gnu/packages/django.scm (python-django-extensions, python-django-simple-math-captcha, python-django-taggit, python-easy-thumbnails, python-django-haystack, python-django-allauth, python-django-debug-toolbar, python-django-debug-toolbar-alchemy, python-django-assets, python-django-jinja, python-django-picklefield, python-django-bulk-update, python-django-contact-form, python-django-contrib-comments, python-django-pipeline, python-django-redis, python-django-rq, python-django-q, python-django-sortedm2m, python-django-appconf, python-django-statici18n, python-djangorestframework, python-django-sekizai, python-django-crispy-forms, python-django-override-storage, python-django-auth-ldap, python-django-logging-json, python-django-netfields, python-django-url-filter)[propagated-inputs]: Add PYTHON-DJANGO. [native-inputs]: Remove it.
2021-12-05gnu: evolution: Build with libsoup 2.Vivien Kraus
* gnu/packages/gnome.scm (evolution) [phase adjust-webkitgtk-version]: Remove it. [inputs]: Depend on webkitgtk-with-libsoup2 instead of webkitgtk. Signed-off-by: Mathieu Othacehe <othacehe@gnu.org>
2021-12-05gnu: tla2tools: Remove reference to %output.Ricardo Wurmus
* gnu/packages/java.scm (tla2tools)[arguments]: Bind OUTPUTS in build phase 'install to remove reference to %output.
2021-12-05gnu: java-log4j-core: Remove reference to %outputs.Ricardo Wurmus
* gnu/packages/java.scm (java-log4j-core)[arguments]: Remove reference to %outputs by using a gexp.
2021-12-05gnu: java-log4j-api: Remove reference to %outputs.Ricardo Wurmus
* gnu/packages/java.scm (java-log4j-api)[arguments]: Remove reference to %outputs by using a gexp.
2021-12-05gnu: java-native-access: Use older GCC.Ricardo Wurmus
* gnu/packages/java.scm (java-native-access)[native-inputs]: Add gcc-7 to fix the build.
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