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path: root/gn/packages/genenetwork.scm
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2022-04-13Update GN3 to latest commitFrederick Muriuki Muriithi
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>
2022-04-12gn: python-rpy2-next: Remove package.Alexander
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>
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.
generated by cgit v1.2.3 (git 2.44.0) at 2024-11-05 13:47:36 +0000