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| author | Pjotr Prins | 2023-07-13 04:05:54 -0500 |
|---|---|---|
| committer | Pjotr Prins | 2023-07-13 04:15:55 -0500 |
| commit | 6a0e96e12b001e90e154df400e06ab5cb29997b2 (patch) | |
| tree | effa1b9bf5711a451769bf3e75efe51759e2f140 | |
| parent | 6107c0ab3aa2d3fa2814fe67d47225fdb4dc8b55 (diff) | |
| download | gn-gemtext-6a0e96e12b001e90e154df400e06ab5cb29997b2.tar.gz | |
GN SoC progress
| -rw-r--r-- | topics/biohackathon/GNGSoC2023.gmi | 31 | ||||
| -rw-r--r-- | topics/systems/ci-cd.gmi | 2 |
2 files changed, 32 insertions, 1 deletions
diff --git a/topics/biohackathon/GNGSoC2023.gmi b/topics/biohackathon/GNGSoC2023.gmi index f1377a7..8fe7310 100644 --- a/topics/biohackathon/GNGSoC2023.gmi +++ b/topics/biohackathon/GNGSoC2023.gmi @@ -39,6 +39,16 @@ git repo genenetwork-machines, guix-bioinformatics * guix-bioinformatics now has CI! * ~700 packages, 240 are broken ;) +### Week 3 + +* Arun gives a presentation on laminar using guix-forge: slides: +=> https://issues.genenetwork.org/topics/ci-rethink-slides +* New system is simpler and has reproducibility issues +* Efraim is doing channels for GN2 and GN3 +* Sarthak will try to run guix-forge + +### More + => https://ci.genenetwork.org/jobs/guix-bioinformatics * CI/CD is up and running again (and broken) @@ -73,6 +83,10 @@ git repo genenetwork3 * Fred is running SPARQL queries * Alex is adding lmdb phenotype API endpoints +### Week 3 + +* Bonface demoes new documentation & code + ## LLMs & metadata (RDF) * lead: Shelby @@ -95,6 +109,13 @@ git repo genenetwork3 * Shelby is integrating into a Flask interface for GeneNetwork * Using a pubmed UI style +### Week 3 + +* Shelby shows code +* Plan to host +* Priscilla is working on SLA and document acquisition +* Hosting GN Q&A + ## API to access data from GN * lead: Rupert @@ -127,6 +148,12 @@ git repo gn-docs & genenetwork3 & SPARQL * Flavia added questions in gn-doc - e.g. for synteny search => https://issues.genenetwork.org/topics/xapian-search-queries Examples for synteny +### Week 3 + +* Rupert proposes endpoints and metadata traversing + +=> https://github.com/genenetwork/gn-docs/blob/master/api/alternative-API-structure.md + ## Editing data * lead: Fred @@ -160,6 +187,10 @@ git repo gn-docs & genenetwork3 & SPARQL * Looking into GeneNetwork3 service * Enumerated types +### Week 3 + +* Preparing for BLOG on S-exp + ## Links * Matrix room is GNSoC2023 diff --git a/topics/systems/ci-cd.gmi b/topics/systems/ci-cd.gmi index 9db9885..e9a24a3 100644 --- a/topics/systems/ci-cd.gmi +++ b/topics/systems/ci-cd.gmi @@ -26,7 +26,7 @@ periodically, say, once an hour/day): * CI: run unit tests * CD: rebuild and redeploy a container running GN3 -Arun has figured out the CI part. It runs a suitably configured laminar CI service in a Guix container created with `guix system container'. A cron job periodically triggers the laminar CI job. +Arun has figured out the CI part. It runs a suitably configured laminar CI service in a Guix container created with `guix system container'. A cron job periodically triggers the laminar CI job (note: this is no longer true). => https://git.systemreboot.net/guix-forge/about/ |