| Age | Commit message (Expand) | Author |
|---|
| 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 |
| 2023-01-22 | genecup: Update to 1.8. | Efraim Flashner |
| 2023-01-20 | Upgrade guix channel to 2491a60. | Arun Isaac |
| 2023-01-20 | gn: tissue: Use latest guile-xapian....* gn/packages/gemini.scm (guile-xapian-latest): New variable.
(tissue): Use guile-xapian-latest.
| Arun Isaac |
| 2023-01-12 | gn: genecup: Update to 1.7. | Efraim Flashner |
| 2022-12-28 | gn: (genenetwork2): Add python-authlib as a dependency...* gn/packages/genenetwork.scm: (python-authlib): New dependency
| Frederick Muriuki Muriithi |
| 2022-12-28 | gn: (genenetwork2): Add flask-session as a dependency...Flask session already handles a lot of the house-keeping involved with
server-side sessions: this commit adds it as a dependency to avoid
having to do the house-keeping manually.
* gn/packages/genenetwork.scm: (python-flask-session): New dependency
| Frederick Muriuki Muriithi |
| 2022-12-24 | Update README | Pjotr Prins |
| 2022-12-23 | Disable pingouin tests | Pjotr Prins |
| 2022-12-23 | Making the build work for genenetwork | Pjotr Prins |
| 2022-12-23 | Add key for tux02 subsitute server | Pjotr Prins |
| 2022-12-20 | gn: (genenetwork3): Add dependency...* gn/packages/genenetwork.scm (genenetwork3): Add python-authlib as a
dependency to genenetwork3
| Frederick Muriuki Muriithi |
| 2022-12-16 | gn: (python-authlib): New package...* gn/packages/python-web.scm: (python-authlib): New package.
| Frederick Muriuki Muriithi |
| 2022-12-11 | gn: Fix building genenetwork1 | Efraim Flashner |
| 2022-12-11 | Revert "gn: rust-quick-csv-0.1: remove duplicated package"...This reverts commit fb631515ccf985e6e89c6cb03a86833aa3b963c6.
rust-quick-csv-0.1 isn't actually in Guix yet.
| Efraim Flashner |
| 2022-12-08 | Minor fixes aiming for genenetwork1 | Pjotr Prins |
| 2022-12-06 | gn: (rust-clap-4): Update dependency...* gn/packages/crates-io.scm (rust-clap-4): Change from
rust-terminal-size-0.2 which is undefined to rust-terminal-size-0.1
| Frederick Muriuki Muriithi |
| 2022-12-06 | gn: (julia-visuals): Slurp expressions to fix package definition...* gn/packages/julia.scm (julia-visuals): slurp in sexps to fix the
package definition.
| Frederick Muriuki Muriithi |
| 2022-12-06 | gn: rust-quick-csv-0.1: remove duplicated package...* gn/packages/crates-io.scm (rust-quick-csv-0.1): Remove package that
is also defined in mainline guix
| Frederick Muriuki Muriithi |
| 2022-12-06 | gn: (genenetwork3): Update to 0.1.0-2.e781996...* gn/packages/genenetwork.scm (genenetwork3): Update to version
0.1.0-2.e781996
| Frederick Muriuki Muriithi |
| 2022-12-05 | Commented Julia inputs that no longer work | pjotrp |
| 2022-12-04 | gn: Replace IPFS links in python24 and python with GN file server | Pjotr Prins |
| 2022-11-30 | gn: Remove upstreamed packages | Efraim Flashner |
| 2022-11-29 | gn: (gn-rust-correlation): Update to 0.1.4-0.a22381e...* gn/packages/crates-io.scm (gn-rust-correlation): 0.1.4--0.a22381e
| AlexanderKabui |
| 2022-11-27 | gn: Fix guix pull. | Efraim Flashner |
| 2022-11-16 | gn: Add graph-genotyper and dependent packages | Efraim Flashner |
| 2022-11-13 | gn: pgr-tk: Unbundle agc. | Efraim Flashner |
