Age | Commit message (Collapse) | Author |
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There is a `rust-clap-4` package upstream.
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Update yoyo and mypy to allow the use of Python-3.10
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* gn/packages/genenetwork.scm: Import (guix packages).
(genenetwork3): Use yoyo-migrations v8.2.0 and python-mypy v0.981.
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
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* gn/packages/python.scm (python-mypy-0.981): New package.
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
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* gn/packages/python.scm: Import (gnu packages databases) and (guix
hg-download).
(yoyo-migrations-8.2.0): New package.
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
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Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
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.guix-channel: Use guix at commit
8d70ff3a49f7cdf0eab93b3a1c54ec2f016afc4a.
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
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This reverts commit aaa6e53e7b623105d05e67e95186aba5b4671010.
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Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
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Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
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Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
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Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
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Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
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Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
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* .guix-channel: Add guix-forge.
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
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* gn/packages/genenetwork.scm: (genenetwork3, genenetwork2): Using
python@3.8.5
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
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This reverts commit 0d743eb249bbdb67009d23ee53b2ee0ae881f725.
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A number of GeneNetwork services/applications will not run with
Python-3.10. This commit pins guix-bioinformatics to a specific commit
to allow use of the older Python-3.10 before we are able to update
everything needed to get them running on Python-3.10
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Replace the backquoted expression in the (arguments ...) section of
the package definition to fix the error where the build could not find
the variable gexp
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tissue is now in upstream Guix.
* gn/packages/gemini.scm: Delete file.
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* gn/packages/genenetwork.scm (genenetwork3): Update to
0.1.0-3.f52247c.
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* gn/packages/genenetwork.scm (genenetwork3)[arguments]: Replace check
phase to use pytest.
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* gn/packages/lisp.scm (sbcl-defstar, sbcl-2am, sbcl-fare-memoization,
sbcl-meta, sbcl-scribble), gn/packages/notebooks.scm (sbcl-nb),
gn/packages/quality-control.scm (sbcl-qc): Remove #:asd-files
argument.
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* gn/services/databases.scm (virtuoso-shepherd-service): Remove square
brackets that sorround the DirsAllowed parameter.
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Add dirs-allowed to virtuoso configs
See merge request genenetwork/guix-bioinformatics!24
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* .guix-channel: Fix indentation.
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* .guix-channel: Update how channel dependencies are defined to match:
https://guix.gnu.org/manual/en/html_node/Declaring-Channel-Dependencies.html
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* gn/packages/python.scm (python-h5py-2): New variable.
* gn/packages/machine-learning.scm (tensorflow-native): Remove comments.
* gn/packages/ratspub.scm (use-corrected-inputs): New procedure.
(genecup-with-tensorflow-native, genecup-latest-with-tensorflow-native):
Use use-corrected-inputs.
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curl-minimal has been removed from upstream Guix.
* gn/packages/bioinformatics.scm (vg)[inputs]: Use curl instead of
curl-minimal.
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* gn/packages/python.scm (python-rdflib-shim)[source]: Add snippet to
use any version of python-rdflib-jsonld.
[propagated-inputs]: Replace python-rdflib-jsonld-0.6.1 with
python-rdflib-jsonld.
(python-rdflib-jsonld-0.6.1): Remove variable.
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