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Author SHA1 Message Date
Ricardo Wurmus
4202f4d58a
gnu: python-bbknn: Fix sanity-check phase. 
* gnu/packages/bioinformatics.scm (python-bbknn)[arguments]: Add phase
'do-not-fail-to-find-sklearn, which prevents the 'sanity-check phase from
failing.
 2021-12-05 17:33:17 +01:00
Ricardo Wurmus
b1bd997d50
gnu: python-bbknn: Add missing input. 
* gnu/packages/bioinformatics.scm (python-bbknn)[propagated-inputs]: Add
python-scikit-learn.
 2021-12-05 17:32:50 +01:00
Ricardo Wurmus
19f6b770dc
gnu: velvet: Add missing TeX package. 
* gnu/packages/bioinformatics.scm (velvet)[native-inputs]: Add
texlive-fonts-ec.
 2021-12-05 17:22:11 +01:00
Ricardo Wurmus
fe0f8c627a
gnu: velvet: Remove trailing #T. 
* gnu/packages/bioinformatics.scm (velvet)[arguments]: Remove trailing #T from
build phases.
 2021-12-05 17:21:39 +01:00
Ricardo Wurmus
f2b99e3aaf
gnu: python-bwapy: Remove pre-built object files. 
* gnu/packages/bioinformatics.scm (python-bwapy)[source]: Remove all .o files
in a snippet.
 2021-12-05 15:04:05 +01:00
Ricardo Wurmus
57f278ffc4
gnu: metabat: Remove trailing #T. 
* gnu/packages/bioinformatics.scm (metabat)[arguments]: Remove trailing #T
from build phases.
 2021-12-05 15:04:05 +01:00
Ricardo Wurmus
c13046cb68
gnu: clapack: Pass -fcommon to compiler. 
* gnu/packages/maths.scm (clapack)[arguments]: Set CFLAGS.
 2021-12-05 15:04:04 +01:00
Ricardo Wurmus
ae0acf6b6d
gnu: clapack: Remove trailing #T. 
* gnu/packages/maths.scm (clapack)[arguments]: Remove trailing #T from build
phases.
 2021-12-05 15:04:04 +01:00
Ricardo Wurmus
1d53c697b3
gnu: tla2tools: Remove remaining reference to %output. 
This is a follow-up to commit 7e6ee16d49.

* gnu/packages/java.scm (tla2tools)[arguments]: Remove remaining reference to
%output.
 2021-12-05 15:04:04 +01:00
Ricardo Wurmus
8ae33d6844
gnu: kraken2: Remove reference to %outputs. 
* gnu/packages/bioinformatics.scm (kraken2)[arguments]: Remove reference to
%outputs by using a gexp.
 2021-12-05 15:04:04 +01:00
Ricardo Wurmus
c973107a25
gnu: methyldackel: Remove reference to %outputs. 
* gnu/packages/bioinformatics.scm (methyldackel)[arguments]: Remove reference
to %outputs by using a gexp.
 2021-12-05 15:04:04 +01:00
Ricardo Wurmus
d531dc6761
gnu: phast: Remove reference to %outputs. 
* gnu/packages/bioinformatics.scm (phast)[arguments]: Remove reference to
%outputs by using a gexp.
 2021-12-05 15:04:03 +01:00
Ricardo Wurmus
2b1e53850f
gnu: libsbml: Remove references to %build-inputs. 
* gnu/packages/bioinformatics.scm (libsbml)[arguments]: Remove references to
%build-inputs by using a gexp.
 2021-12-05 15:04:03 +01:00
Ricardo Wurmus
dc4b4d4d95
gnu: ataqv: Remove references to %outputs and %build-inputs. 
* gnu/packages/bioinformatics.scm (ataqv)[arguments]: Remove references to
%outputs and %build-inputs by using a gexp.
 2021-12-05 15:04:03 +01:00
Ricardo Wurmus
03ca627b09
gnu: adapterremoval: Remove reference to %outputs. 
* gnu/packages/bioinformatics.scm (adapterremoval)[arguments]: Remove
reference to %outputs by using a gexp.
 2021-12-05 15:04:03 +01:00
Ricardo Wurmus
fac4c98699
gnu: bbmap: Remove reference to %build-inputs. 
* gnu/packages/bioinformatics.scm (bbmap)[arguments]: Remove reference to
%build-inputs by using a gexp.
 2021-12-05 15:04:03 +01:00
Ricardo Wurmus
b798d90bee
gnu: intervaltree: Remove reference to %outputs. 
* gnu/packages/bioinformatics.scm (intervaltree)[arguments]: Remove reference
to %outputs by using a gexp.
 2021-12-05 15:04:03 +01:00
Ricardo Wurmus
c9892edceb
gnu: biobambam2: Remove reference to %build-inputs. 
* gnu/packages/bioinformatics.scm (biobambam2)[arguments]: Remove reference to
%build-inputs by using a gexp.
 2021-12-05 15:04:02 +01:00
Ricardo Wurmus
a8b60bd475
gnu: sjcount: Remove reference to %build-inputs. 
* gnu/packages/bioinformatics.scm (sjcount)[arguments]: Remove reference to
%build-inputs by using a gexp.
 2021-12-05 15:04:02 +01:00
Ricardo Wurmus
4c6cb448fd
gnu: sjcount: Remove trailing #T. 
* gnu/packages/bioinformatics.scm (sjcount)[arguments]: Remove trailing #T
from build phases.
 2021-12-05 15:04:02 +01:00
Ricardo Wurmus
c1fe074915
gnu: dropseq-tools: Remove reference to %build-inputs. 
* gnu/packages/bioinformatics.scm (dropseq-tools)[arguments]: Remove reference
to %build-inputs by using a gexp.
 2021-12-05 15:04:02 +01:00
Ricardo Wurmus
1462e5c919
gnu: dropseq-tools: Remove trailing #T. 
* gnu/packages/bioinformatics.scm (dropseq-tools)[arguments]: Remove
trailing #T from build phases...
[source]: ...and from the snippet.
 2021-12-05 15:04:02 +01:00
Marius Bakke
10554e0a57
gnu: python-django-netfields: Update to 1.2.4. 
* gnu/packages/django.scm (python-django-netfields): Update to 1.2.4.
 2021-12-05 14:40:08 +01:00
Marius Bakke
50fff94b5a
gnu: python-django: Update to 3.2.9. 
* gnu/packages/django.scm (python-django): Update to 3.2.9.
 2021-12-05 14:40:08 +01:00
Marius Bakke
f63fb61d0c
import: PyPI: Validate GPG signatures when applicable. 
* guix/import/pypi.scm (<distribution>): Fix funny typo.
(latest-release): When the distribution has a cryptographic signature, pass it
along to UPSTREAM-SOURCE.
 2021-12-05 14:40:08 +01:00
Marius Bakke
e166e6acf6
gnu: drbd-utils: Update to 9.19.1. 
* gnu/packages/cluster.scm (drbd-utils): Update to 9.19.1.
 2021-12-05 14:40:07 +01:00
Nicolas Goaziou
21e2be5968
gnu: emacs-peg: Update to 0.10.3. 
* gnu/packages/emacs-xyz.scm (emacs-peg): Update to 0.10.3.
 2021-12-05 14:20:16 +01:00
Marius Bakke
c61e49aa94
gnu: tbb: Update to 2021.4.0. 
* gnu/packages/tbb.scm (tbb): Update to 2021.4.0.
 2021-12-05 14:02:10 +01:00
Marius Bakke
db5646d957
gnu: Adjust for python-build-system behavior change. 
Commit cb72f9a773 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.
 2021-12-05 14:02:10 +01:00
Marius Bakke
b507cc49ab
gnu: python-pyvcf: Fix bytecode compilation. 
* gnu/packages/bioinformatics.scm (python-pyvcf)[arguments]: Add phase to
patch sample script.
 2021-12-05 14:02:10 +01:00
Marius Bakke
a2584a08be
gnu: python-whisper: Update to 1.1.8. 
* gnu/packages/monitoring.scm (python-whisper): Update to 1.1.8.
 2021-12-05 14:02:10 +01:00
Marius Bakke
0d196ab9bd
gnu: python-mailman-hyperkitty: Update to 1.2.0. 
* gnu/packages/mail.scm (python-mailman-hyperkitty): Update to 1.2.0.
[source](patches): Remove.
 2021-12-05 14:02:10 +01:00
Marius Bakke
3f9d122dcb
gnu: python-hyperkitty: Update to 1.3.5. 
* 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.
 2021-12-05 14:02:10 +01:00
Marius Bakke
b0ce8bdb39
gnu: Add python-mistune-next. 
* gnu/packages/python-xyz.scm (python-mistune-next): New variable.
 2021-12-05 14:02:09 +01:00
Marius Bakke
f457fb19dd
gnu: python-django-haystack: Update to 3.1.1. 
* gnu/packages/django.scm (python-django-haystack): Update to 3.1.1.
[arguments]: Adjust substitution.
 2021-12-05 14:02:09 +01:00
Marius Bakke
eb8619a5a6
gnu: python-alembic: Update to 1.7.5. 
* gnu/packages/databases.scm (python-alembic): Update to 1.7.5.
[propagated-inputs]: Remove PYTHON-IMPORTLIB-RESOURCES.
 2021-12-05 14:02:09 +01:00
Marius Bakke
d801827b84
gnu: ganeti: Add the output directory on GUIX_PYTHONPATH. 
This is a follow-up to commit 1ed567c872.

* gnu/packages/virtualization.scm (ganeti)[arguments]: Adjust wrap phase to
include Ganetis own site-packages on $GUIX_PYTHONPATH.
 2021-12-05 14:02:09 +01:00
Marius Bakke
846bd3d083
gnu: python-webassets: Patch for Python 3.9. 
* gnu/packages/python-web.scm (python-webassets)[arguments]: Add
substitution.
 2021-12-05 14:02:09 +01:00
Marius Bakke
9f5b9d18d8
gnu: python-django-mailman3: Update to 1.3.7. 
* gnu/packages/mail.scm (python-django-mailman3): Update to 1.3.7.
 2021-12-05 14:02:09 +01:00
Marius Bakke
837688e505
gnu: python-mailmanclient: Update to 3.3.3. 
* gnu/packages/mail.scm (python-mailmanclient): Update to 3.3.3.
 2021-12-05 14:02:09 +01:00
Marius Bakke
97edcf2e63
gnu: python-django-url-filter: Adjust phase order. 
* 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.
 2021-12-05 14:02:09 +01:00
Marius Bakke
458e972484
gnu: python-django-netfields: Propagate psycopg2. 
* gnu/packages/django.scm (python-django-netfields)[propagated-inputs]: Add
PYTHON-PSYCOPG2.
 2021-12-05 14:02:09 +01:00
Marius Bakke
63975ea51c
gnu: python-django-logging-json: Disable sanity check. 
* gnu/packages/django.scm (python-django-logging-json)[arguments]: Add
 #:phases.
 2021-12-05 14:02:09 +01:00
Marius Bakke
19520996f0
gnu: python-django-appconf: Fix tests. 
* gnu/packages/django.scm (python-django-appconf): Invoke django-admin with
custom pythonpath.
 2021-12-05 14:02:09 +01:00
Marius Bakke
88e9e9e697
gnu: python-django-pipeline: Fix tests. 
* gnu/packages/django.scm (python-django-pipeline): Provide pythonpath to
django-admin.
 2021-12-05 14:02:09 +01:00
Marius Bakke
e73f565445
gnu: python-django-sortedm2m: Fix tests. 
This is a follow-up to commit 283d5ac97f.

* gnu/packages/django.scm (python-django-sortedm2m): Invoke django-admin with
pythonpath and test settings.
 2021-12-05 14:02:08 +01:00
Marius Bakke
ddea9e32e7
gnu: python-django-contact-form: Update to 1.9. 
* gnu/packages/django.scm (python-django-contact-form): Update to 1.9.
 2021-12-05 14:02:08 +01:00
Marius Bakke
6b458747da
gnu: python-django-jinja: Update to 2.9.1. 
* gnu/packages/django.scm (python-django-jinja): Update to 2.9.1.
 2021-12-05 14:02:08 +01:00
Marius Bakke
de5a8b26f2
gnu: python-django-haystack: Disable sanity check. 
* gnu/packages/django.scm (python-django-haystack)[arguments]: Delete one
phase.  While at it, remove trailing #t's.
 2021-12-05 14:02:08 +01:00
Marius Bakke
acbc01940b
gnu: python-fakeredis: Update to 1.7.0. 
* gnu/packages/databases.scm (python-fakeredis): Update to 1.7.0.
 2021-12-05 14:02:08 +01:00