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2022-03-16gn: genenetwork3: Update to 0.1.0-2.16367da.BonfaceKilz
* gn/packages/genenetwork.scm (genenetwork3): Update to 0.1.0-2.16367da.
2022-03-16gn: genenetwork2: Move pytest and pytest-mock to propagated-inputsBonfaceKilz
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.
2022-03-16gn: genenetwork2: Add pytest and pytest-mockBonfaceKilz
* gn/packages/genenetwork.scm (genenetwork2) [native-inputs]: Add pytest and pytest-mock
2022-03-03gn: genenetwork3: Add python-pytest-mockBonfaceKilz
* gn/packages/genenetwork.scm (genenetwork3)[native-inputs]: Add python-pytest-mock.
2022-02-18gn: genenetwork2: Update to 3.11-2.17652b1.Arun Isaac
* gn/packages/genenetwork.scm (genenetwork2): Update to 3.11-2.17652b1. [arguments]: Restore the default install phase.
2022-02-18gn: genenetwork3: List propagated inputs in plain list.Arun Isaac
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.
2022-02-18gn: genenetwork3: Remove implicit inputs.Arun Isaac
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.
2022-02-18gn: genenetwork3: Update to 0.1.0-2.83a7aa7.Arun Isaac
* gn/packages/genenetwork.scm (genenetwork3): Update to 0.1.0-2.83a7aa7. [arguments]: Enable tests.
2022-02-18gn: genenetwork3: Move test inputs to native inputs.Arun Isaac
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.
2022-02-14Add pytest and hypothesis for automated testingFrederick Muriuki Muriithi
In the effort to improve automated testing, this commit adds two python modules that are useful for the tests.
2022-02-09gn: genenetwork2: Add python-ijson.Alexander Kabui
* gn/packages/genenetwork.scm (genenetwork2)[propagated-inputs]: Add python-ijson. Signed-off-by: Arun Isaac <arunisaac@systemreboot.net>
2022-02-09gn: genenetwork3: Add r-ctl.Alexander Kabui
* gn/packages/genenetwork.scm (genenetwork3)[propagated-inputs]: Add r-ctl. Signed-off-by: Arun Isaac <arunisaac@systemreboot.net>
2022-01-26gn: genenetwork: Disable tests on python-seaborn.Arun Isaac
* 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.
2022-01-06gn: genenetwork: Add diffutilsBonfaceKilz
* gn/packages/genenetwork.scm (genenetwork3)[propagated-inputs]: Add diffutils.
2022-01-05Revert "gn: genenetwork: Add pudb"BonfaceKilz
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 ```
2022-01-05gn: genenetwork: Add pudbBonfaceKilz
* gn/packages/genenetwork.scm (genenetwork3)[propagated-inputs]: Add pudb for trouble-shooting purposes.
2022-01-01genenetwork3: updated and disabled testsPjotr Prins
2022-01-01genenetwork2: put a hack in to fix failing build. Please amendPjotr Prins
2021-12-29Fix typo in import of (gnu packages textutils).Arun Isaac
* gn/packages/genenetwork.scm: Import (gnu packages textutils), not (gn packages textutils).
2021-12-21gn/packages/genenetwork.scm: Use csvdiff from textutils.BonfaceKilz
* gn/packages/genenetwork.scm (genenetwork2): Use updated version of csvdiff from textutils.
2021-12-09gn: genenetwork: Define version using git-version.Arun Isaac
Also, semantic versioning starts from 0.1.0, not 0.0.1. * gn/packages/genenetwork.scm (genenetwork3)[version]: Use git-version.
2021-12-09gn: genenetwork: Reorganize inputs.Arun Isaac
* gn/packages/genenetwork.scm (genenetwork3)[propagated-inputs]: Remove python-sqlalchemy-stubs. Add python-sparqlwrapper and rust-qtlreaper. Sort all inputs.
2021-11-17gn: genenetwork: Add javascript-xterm , javascript-xterm-style, ↵Alexander Kabui
javascript-xterm-addon-fit to genenetwork2 * gn/packages/genenetwork.scm(genenetwork2) [propagated-inputs]: Add javascript-xterm , javascript-xterm-style and javascript-xterm-addon-fit
2021-11-05gn: genenetwork: Remove unused package inputsBonfaceKilz
2021-11-05gn: genenetwork: Delete dead commentsBonfaceKilz
2021-11-04gn: Update genenetwork3 to 0.0.1-guix-9e0fa5fBonfaceKilz
2021-11-01gn: Add python-pingouinBonfaceKilz
* gn/packages/genenetwork.scm (genenetwork3)[propagated-inputs]: Add python-pingouin
2021-10-27gn: genenetwork: Add python-deprecatedBonfaceKilz
Only used when deemed necessary.
2021-10-06gn: Update genenetwork3 to 0.0.1-guix-77c274bBonfaceKilz
2021-09-29gn: Add r-wgcna, r-rjson to genenetwork3.Alexander Kabui
* gn/packages/genenetwork.scm(genenetwork3) [propagated-inputs]: Add r-wgcna an r-rjson
2021-08-28Moved packages into past/genenetwork1 and packages/pangenome to reduce chance ofpjotrp
breaking the main genenetwork packages.
2021-08-28Remove golang module loaderpjotrp
2021-08-24genenetwork[23]: updated git checkout and commented out DAG generationPjotr Prins
2021-08-20gn: Add missing importEfraim Flashner
2021-08-18Remove csv-diff from channel.BonfaceKilz
This is already packaged upstream. * gn/packages/genenetwork.scm: Remove "(gn packages golang)" import. * gn/packages/golang.scm: Delete file.
2021-08-16gn: Add toolbar overlay for debugging genenetwork2BonfaceKilz
* gn/packages/genenetwork.scm (genenetwork2)[propagated-inputs]: Add python-flask-debugtoolbar
2021-08-16gn: start moving calculated files to build separatelyEfraim Flashner
2021-08-15gn: genenetwork2: Don't hardcode python version.Efraim Flashner
2021-08-12gn: genenetwork: Remove "#:python ,python-wrapper" from "arguments"BonfaceKilz
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)
2021-08-11gn: fix genenetwork2 package definitionEfraim Flashner
2021-08-11fixup genenetwork2Efraim Flashner
2021-08-09gn: Adjust genenetwork2 for removal of python2-genenetwork2Efraim Flashner
2021-08-07python2-genenetwork2: remove unused Python2 version of genenetworkpjotrp
2021-08-05gn: Update genenetwork3 to 0.0.1-guix-487e50eBonfaceKilz
2021-08-03gn: genenetwork3: Add csvdiff as a propagated inputBonfaceKilz
2021-08-02gn: code updatesEfraim Flashner
2021-07-12gn: Update genenetwork3 to 0.0.1-guix-7d22039BonfaceKilz
2021-07-11gn: Add python24-direct.Efraim Flashner
* gn/packages/python24.scm (python24-direct): New variable. * gn/packages/genenetwork.scm (genenetwork1)[propagated-inputs]: Add python24-direct.
2021-07-11Added GNU parallel to genenetwork2pjotrp
2021-06-07gn: Update genenetwork3 to 0.0.1-guix-3881b50BonfaceKilz
generated by cgit v1.2.3 (git 2.44.0) at 2024-11-05 13:40:12 +0000