| Age | Commit message (Expand) | Author |
|---|
| 2023-09-05 | gn: genenetwork: Update mypy and yoyo...* 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>
| Munyoki Kilyungi |
| 2023-09-05 | gn: python: Add python-mypy-0.981...* gn/packages/python.scm (python-mypy-0.981): New package.
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2023-09-05 | gn: python: Add yoyo-migrations-8.2.0...* 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>
| Munyoki Kilyungi |
| 2023-09-05 | Adjust how native/propagated inputs are defined for GN3...Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2023-09-04 | Revert "Pin python to python@3.8.5"...This reverts commit aaa6e53e7b623105d05e67e95186aba5b4671010.
| Munyoki Kilyungi |
| 2023-09-04 | Pin python to python@3.8.5...* gn/packages/genenetwork.scm: (genenetwork3, genenetwork2): Using
python@3.8.5
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2023-08-31 | Move gn-auth to (gn packages genenetwork). | Arun Isaac |
| 2023-08-30 | Replace `(...) with (list ...): Fixes "undefined gexp" failure....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
| Frederick Muriuki Muriithi |
| 2023-08-30 | Add missing `(guix gexp) module. Update package commit. | Frederick Muriuki Muriithi |
| 2023-08-25 | gn-auth: New package | Frederick Muriuki Muriithi |
| 2023-07-06 | Remove tissue....tissue is now in upstream Guix.
* gn/packages/gemini.scm: Delete file.
| Arun Isaac |
| 2023-07-05 | gn: genenetwork3: Update to 0.1.0-3.f52247c....* gn/packages/genenetwork.scm (genenetwork3): Update to
0.1.0-3.f52247c.
| Arun Isaac |
| 2023-07-05 | Run genenetwork3 tests using pytest....* gn/packages/genenetwork.scm (genenetwork3)[arguments]: Replace check
phase to use pytest.
| Arun Isaac |
| 2023-07-04 | Remove deprecated #:asd-files argument....* 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.
| Arun Isaac |
| 2023-06-29 | gn: gemma: Fix build using latest gcc | pjotrp |
| 2023-06-26 | Fix DirsAllowed parameter...* gn/services/databases.scm (virtuoso-shepherd-service): Remove square
brackets that sorround the DirsAllowed parameter.
| Munyoki Kilyungi |
| 2023-06-20 | Add dirs-allowed to virtuoso configs | Munyoki Kilyungi |
| 2023-06-18 | Remove unused twint from GN2 | pjotrp |
| 2023-06-15 | Uncommitted genome browser changes | Efraim Flashner |
| 2023-06-15 | Update pluto service and dependant julia packages | Efraim Flashner |
| 2023-06-14 | gn: genecup: Use correct python-h5py....* 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.
| Efraim Flashner |
| 2023-04-19 | gn: Update GN2 to 3.11-2.bfe557dc | Frederick Muriuki Muriithi |
| 2023-04-19 | gn: Update GN3 to 0.1.0-2.85610fc9 | Frederick Muriuki Muriithi |
| 2023-04-10 | vg: Use curl instead of curl-minimal....curl-minimal has been removed from upstream Guix.
* gn/packages/bioinformatics.scm (vg)[inputs]: Use curl instead of
curl-minimal.
| Arun Isaac |
| 2023-03-24 | Adding ruby-lmdb package | pjotrp |
| 2023-03-24 | Adding ruby-lmdb package | pjotrp |
| 2023-03-22 | bh20-seq-resource-container.scm updates | Efraim Flashner |
| 2023-03-22 | python-rdflib-shim: Build with upstream python-rdflib-jsonld....* 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.
| Efraim Flashner |
| 2023-03-22 | bh20-seq-resource: Add version without profile collisions....* gn/packages/bioinformatics.scm (bh20-seq-resource-for-service): New
variable.
* gn/services/bh20-seq-resource-container.scm
(covid19-pubseq-configuration): Use it by default.
| Efraim Flashner |
| 2023-03-22 | bh20-seq-resource: Patch reference to minimap2....* gn/packages/bioinformatics.scm (bh20-seq-resource)[arguments]: Add
phase to hardcode path to minimap2.
[inputs]: Add minimap2.
| Efraim Flashner |
| 2023-03-22 | bh20-seq-resource: Update to 1.0-4.2ae7191....* gn/packages/bioinformatics.scm (bh20-seq-resource): Update to
1.0-4.2ae7191.
[source]: Adjust snippet for changes in source.
[arguments]: Skip tests.
[propagated-inputs]: Add python-shexc-0.7. Remove python-dateutil,
python-flask, python-pycurl, python38-ruaml.yaml-0.15.76, clustalw,
python-twint.
[native-inputs]: Remove git, python-oauth2client, python-uritemplate.
Replace python-pytest-4 with python-pytest-5, python-pytest-runner-2
with python-pytest-runner-4.
| Efraim Flashner |
| 2023-03-22 | Add python-pytest-runner-4....* gn/packages/python.scm (python-pytest-runner-4): New variable.
* gn/packages/bioinformatics.scm (python-pytest-runner-2): MOve to
python.scm
| Efraim Flashner |
| 2023-03-22 | fixup python-pyshexc | Efraim Flashner |
| 2023-03-22 | python-pyshex: Downgrade to 0.7.14....* 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.
| Efraim Flashner |
| 2023-03-22 | Add python-py-dateutil....* gn/packages/python.scm (python-py-dateutil): New variable.
| Efraim Flashner |
| 2023-03-22 | Add python-pyshexc-0.7....* gn/packages/python.scm (python-pyshexc-0.7): New variable.
| Efraim Flashner |
| 2023-03-22 | Add python-pytest-5....* gn/packages/python.scm (python-pytest-5): New variable.
| Efraim Flashner |
| 2023-03-20 | python-arvados-python-client: Update to 2.5.0....* 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.
| Efraim Flashner |
| 2023-03-20 | python-shexjsg: Update to 0.8.2....* 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.
| Efraim Flashner |
| 2023-03-20 | Add python-sparqlslurper....* gn/packages/python.scm (python-sparqlslurper): New variable.
| Efraim Flashner |
| 2023-03-20 | Add python-rdflib-shim....* gn/packages/python.scm (python-rdflib-shim): New variable.
(python-rdflib-jsonld-0.6.1): New variable.
| Efraim Flashner |
| 2023-03-20 | python-pyshex: Update to 0.8.1....* 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.
| Efraim Flashner |
| 2023-03-20 | python-pyshexc: Update to 0.9.1....* 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.
| Efraim Flashner |
| 2023-03-19 | python-pyjsg: Update to 0.11.10....* 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.
| Efraim Flashner |
| 2023-03-19 | python-antlr4-python3-runtime: Update to 4.9.3....* gn/packages/python.scm (python-antlr4-python3-runtime): Update to
4.9.3.
| Efraim Flashner |
| 2023-03-19 | python-pytest-4: Add missing input....* gn/packages/python.scm (python-pytest-4)[native-inputs]: Add
python-atomicwrites.
| Efraim Flashner |
| 2023-03-19 | updates to julia packages | Efraim Flashner |
| 2023-03-08 | gn: genenetwork3: Add python-argon-cffi...As part of improving the security of passwords, this commit adds
python-argon-cffi that enables use of the better Argon2 password
hashing algorithm, rather than the dated bcrypt that is a tad
vulnerable to offline cracking.
| Frederick Muriuki Muriithi |
| 2023-03-02 | genenetwork3: New dependency (python-email-validator)...* gn/packages/genenetwork.scm: (python-email-validator): New
dependency
| Frederick Muriuki Muriithi |
| 2023-01-27 | gn: tissue: Update to 0.1.0....* gn/packages/gemini.scm: Import (gnu packages compression) and (guix
download).
(tissue): Update to 0.1.0.
[source]: Use url-fetch.
[native-inputs]: Add lzip.
| Arun Isaac |
