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* gn/packages/genenetwork.scm: Import module crates-io.
(genenetwork3) [propagated-inputs]: Add gn-rust-correlations.
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* gn/packages/genenetwork.scm (commit): Update it.
(source): Update hash.
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* gn/packages/genenetwork.scm (commit): Update it.
(source): Update hash.
(propagated-inputs): Remove python-ipfshttpclient.
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* gn/packages/genenetwork.scm (python-seaborn-without-tests,
python-pingouin-with-working-python-seaborn): Delete variables.
(genenetwork3)[propagated-inputs]: Replace
python-pingouin-with-working-python-seaborn with upstream
python-pingouin.
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* gn/packages/genenetwork.scm (commit): Update it.
(source): Update hash.
(propagated-inputs): Add python-lmdb.
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- Genenetwork3 depends on diffutils
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* gn/packages/genenetwork.scm: Update commit and hash.
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GN2 on the testing branch relies on features in GN3 that are not
present in commit 16367dab9248d3aa2660e0b5cafdce25e8f7067c of
GN3. This commit thus updates the dependency to get the latest version
of GN3 that is building successfully.
Signed-off-by: BonfaceKilz <me@bonfacemunyoki.com>
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python-rpy2@3.4.5 has been upstreamed.
* gn/packages/python.scm (python-rpy2-next): Delete variable.
* gn/packages/genenetwork.scm (genenetwork2)[propagated-inputs]:
Replace python-rpy2-next with python-rpy2.
Signed-off-by: Arun Isaac <arunisaac@systemreboot.net>
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* gn/packages/genenetwork.scm (genenetwork3): Update to
0.1.0-2.16367da.
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These packages are required in the propagated-inputs so that they can be run
locally.
* gn/packages/genenetwork.scm (genenetwork)[native-inputs]: Move pytest and
pytest to...
[propagated-inputs]: here.
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* gn/packages/genenetwork.scm (genenetwork2) [native-inputs]: Add pytest and
pytest-mock
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* gn/packages/genenetwork.scm (genenetwork3)[native-inputs]: Add
python-pytest-mock.
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* gn/packages/genenetwork.scm (genenetwork2): Update to
3.11-2.17652b1.
[arguments]: Restore the default install phase.
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Guix now prefers inputs as a plain list instead of an association
list. Modernize.
* gn/packages/genenetwork.scm (genenetwork3)[propagated-inputs]: Use
plain list instead of association list.
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coreutils and diffutils are implicit inputs of the
python-build-system. They don't have to be included explicitly.
* gn/packages/genenetwork.scm (genenetwork3)[propagated-inputs]:
Remove coreutils and diffutils.
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* gn/packages/genenetwork.scm (genenetwork3): Update to
0.1.0-2.83a7aa7.
[arguments]: Enable tests.
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Test inputs are not required to actually run the built program. They
should therefore be in native-inputs. They should not be propagated.
* gn/packages/genenetwork.scm (genenetwork3)[propagated-inputs]: Move
python-mypy, python-mypy-extensions, python-pylint, python-hypothesis
and python-pytest to ...
[native-inputs]: ... here.
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In the effort to improve automated testing, this commit adds two
python modules that are useful for the tests.
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* gn/packages/genenetwork.scm (genenetwork2)[propagated-inputs]: Add
python-ijson.
Signed-off-by: Arun Isaac <arunisaac@systemreboot.net>
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* gn/packages/genenetwork.scm (genenetwork3)[propagated-inputs]: Add
r-ctl.
Signed-off-by: Arun Isaac <arunisaac@systemreboot.net>
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* gn/packages/genenetwork.scm (python-seaborn-without-tests,
python-pingouin-with-working-python-seaborn): New variables.
(genenetwork3)[propagated-inputs]: Replace python-pingouin with
python-pingouin-with-working-python-seaborn.
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* gn/packages/genenetwork.scm (genenetwork3)[propagated-inputs]:
Add diffutils.
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This reverts commit f7e876d53832cf1d5d4b19118266e910e6100ea9. Add an extra
dependency by running something like:
```
guix shell -L /home/bonface/projects/guix-bioinformatics \
-L /home/bonface/projects/guix-past/modules -C \
-D pudb -f guix.scm
```
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* gn/packages/genenetwork.scm (genenetwork3)[propagated-inputs]:
Add pudb for trouble-shooting purposes.
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* gn/packages/genenetwork.scm: Import (gnu packages textutils),
not (gn packages textutils).
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* gn/packages/genenetwork.scm (genenetwork2): Use updated version of csvdiff
from textutils.
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Also, semantic versioning starts from 0.1.0, not 0.0.1.
* gn/packages/genenetwork.scm (genenetwork3)[version]: Use
git-version.
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* gn/packages/genenetwork.scm (genenetwork3)[propagated-inputs]:
Remove python-sqlalchemy-stubs. Add python-sparqlwrapper and
rust-qtlreaper. Sort all inputs.
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javascript-xterm-addon-fit to genenetwork2
* gn/packages/genenetwork.scm(genenetwork2) [propagated-inputs]: Add javascript-xterm , javascript-xterm-style and javascript-xterm-addon-fit
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* gn/packages/genenetwork.scm (genenetwork3)[propagated-inputs]: Add
python-pingouin
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Only used when deemed necessary.
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* gn/packages/genenetwork.scm(genenetwork3) [propagated-inputs]: Add r-wgcna an r-rjson
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breaking the main genenetwork packages.
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This is already packaged upstream.
* gn/packages/genenetwork.scm: Remove "(gn packages golang)" import.
* gn/packages/golang.scm: Delete file.
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* gn/packages/genenetwork.scm (genenetwork2)[propagated-inputs]: Add
python-flask-debugtoolbar
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This fixes this error:
guix package: error: /home/bonface/projects/guix-bioinformatics/gn/packages/genenetwork.scm:295:4: package `genenetwork2@3.11-guix-84cbf35' has an invalid input: ("python" python-wrapper)
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