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* gn/packages/python.scm (python-enlighten): New variable.
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* gn/packages/python.scm (python-addict): New variable.
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* gn/packages/python.scm (python-typing-extensions-4.10): New
variable.
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python-rdflib-jsonld has been removed from upstream Guix.
* gn/packages/python.scm (python-rdflib-jsonld): New variable.
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* genenetwork3: Remove `yoyo-migrations` as a dependency
* gn-auth: Use the upstream `yoyo-migrations`
* Remove temporary local definition for yoyo-migrations.
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The package is broken, some of its inputs have been removed from
upstream Guix, and we no longer need this package. Restore it later if
necessary.
* gn/packages/python.scm (python-arvados-python-client): Delete
variable.
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* gn/packages/python.scm (python-mypy-0.981): Delete it.
* gn/packages/genenetwork.scm (genenetwork3)[native-inputs]: Replace
python-mypy-0.981 with upstream's python-mypy.
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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* 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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* 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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* gn/packages/python.scm (python-pytest-runner-4): New variable.
* gn/packages/bioinformatics.scm (python-pytest-runner-2): MOve to
python.scm
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* gn/packages/python.scm (python-pyshex): Downgrade to 0.7.14.
[arguments]: Disable tests. Add phase to fix compatibility with
rdflib-6. Adjust custom 'check phase.
[propagated-inputs]: Remove python-chardet. Replace python-pyshexc with
python-pyshexc-0.7, python-rdflib-shim with python-rdflib,
python-sparqlsluper with python-sparql-slurper.
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* gn/packages/python.scm (python-py-dateutil): New variable.
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* gn/packages/python.scm (python-pyshexc-0.7): New variable.
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* gn/packages/python.scm (python-pytest-5): New variable.
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* gn/packages/python.scm (python-arvados-python-client): Update to 2.5.0.
[source]: Add snippet to not limit the maximum version of pycurl.
[propagated-inputs]: Add python-google-api-core-1, python-google-auth-1,
python-protobuf, python-pyparsing-2.4.7, python-ruamel.yaml. Remove
python38-ruaml.yaml-0.15.76, python-setuptools, python-oauth2client,
python-uritemplate.
(python38-ruaml.yaml-0.15.76): Remove variable.
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* gn/packages/python.scm (python-shexjsg): Update to 0.8.2.
[arguments]: Remove custom 'patch-source phase. Update custom 'check
phase.
[propagated-inputs]: Remove python-antlr4-python3-runtime,
python-certifi, python-chardet, python-idna, python-isodate,
python-requests, python-urllib3.
[native-inputs]: Add python-rdflib-shim, python-requests. Remove
python-pyparsing, python-pyshexc, python-rdflib, python-rdflib-jsonld,
python-six, custom test-suite git checkout.
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* gn/packages/python.scm (python-sparqlslurper): New variable.
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* gn/packages/python.scm (python-rdflib-shim): New variable.
(python-rdflib-jsonld-0.6.1): New variable.
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* gn/packages/python.scm (python-pyshex): Update to 0.8.1.
[arguments]: Remove custom 'patch-source phase. Update custom 'check
phase.
[propagated-inputs]: Add python-chardet, python-rdflib-shim,
python-sparqlslurper. Remove python-rdflib, python-rdflib-jsonld,
python-pbr, python-sparql-slurper.
[native-inputs]: Add python-pbr, python-unitttest2.
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* gn/packages/python.scm (python-pyshexc): Update to 0.9.1.
[arguments]: Update custom 'check phase.
[propagated-inputs]: Add python-chardet, python-rdflib-shim,
python-shexjsg. Remove python-rdflib, python-rdflib-jsonld,
python-requests.
[native-inputs]: Add python-pbr, python-requests. Remove python-shexjsg,
custom test-suite git checkout.
(python-shexjsg-min): Remove variable.
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* gn/packages/python.scm (python-pyjsg): Update to 0.11.10.
[arguments]: Remove 'patch-source phase. Skip 1 set of tests in custom
'check phase.
[propagated-inputs]: Move python-requests ...
[native-inputs]: ... to here. Add python-unittest2. Remove test-suite
checkout.
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* gn/packages/python.scm (python-antlr4-python3-runtime): Update to
4.9.3.
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* gn/packages/python.scm (python-pytest-4)[native-inputs]: Add
python-atomicwrites.
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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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todo:
fix tests: https://github.com/NixOS/nixpkgs/blob/nixos-21.11/pkgs/development/python-modules/supervisor/default.nix#L16
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add more to description field
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* gn/packages/python.scm: New package.
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https://issues.guix.gnu.org/52177
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* gn/packages/python.scm (python-requirements-parser): New variable.
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python-sparqlwrapper has been upstreamed.
* gn/packages/python.scm (python-sparqlwrapper): Delete variable.
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python-flask-socketio has been upstreamed.
* gn/packages/python.scm (python-flask-socketio): Delete variable.
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* gn/packages/python.scm (python-webcolors): Delete variable.
* gn/packages/messaging.scm: Delete file.
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* gn/packages/python.scm (python-webcolors): New variable.
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* gn/packages/python.scm (python-flask-debugtoolbar): New variable.
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