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Diffstat (limited to 'tasks/bonfacem.gmi')
| -rw-r--r-- | tasks/bonfacem.gmi | 76 |
1 files changed, 55 insertions, 21 deletions
diff --git a/tasks/bonfacem.gmi b/tasks/bonfacem.gmi index 03848f1..2d56e72 100644 --- a/tasks/bonfacem.gmi +++ b/tasks/bonfacem.gmi @@ -4,41 +4,46 @@ * kanban: bonfacem * assigned: bonfacem -* status: in progress ## Tasks ### Note -- GN-auth dashboard fixes. Follow up with Fred. -- Case-attributes used in co-variates. -- Encourage FahamuAI to be open. +* Don't lose metadata. Have an array of disabled snips. +* Store by snip (rows). Storage by marker. 2 different files. +* gn-auth: + have wrappers around gn-auth (draw-back: folk may forget). + use Nginx as a MTM (re-routing calls). How to add handler in Nginx and to work with tokens. +* GN-auth dashboard fixes. Follow up with Fred. +* Case-attributes used in co-variates. + +### PhD Work + +* Concept note/ideas: Add all metadata in GN to an LLM that enriches GnQA. +* Use mapping output as full vectors for gpt/transformers. Integrate this work into GN. +* Share PhD concept note with PJ for polishing ### This week -* [+] Case Attributes (Do a diagnostic and delegate) -* - Git blame. Add tests. -* - Error when checking the history. -* - Reach out to Zach. -* - Disable diff in the UI. -* [ ] Distinct admin and dev user. -* [ ] Adapter to LMDB into a cross object. +* [] Look at deep-seek/anthropic (also really doc deployment in balg01). Run in debian machine. +* [~] Adapter to LMDB into a cross object. * - Try computations with R/qtl2. * - Look at R LMDB libraries. * - Look at functions that read the files. * - PJ: LMDB adapter in R and cross-type files. -* [ ] Send Arun an e-mail on how to go about upgrading shepherd. -* [ ] Dump all genotypes from production to LMDB. +* [~] gn-guile webhook. +* [~] Dump all genotypes from tux02 to LMDB. * - PJ sync tux01 genotypes with tux02/04. +* - Yet to set-up 2FA on new device + +### Later +* [ ] Generate RDF docs using AI. +* [ ] Editing genotype metadata +* [ ] Look at XAPIAN search for gene alias. +* [ ] Add GeneNetwork abstracts to XAPIAN search. * [+] Correlations hash. * - Add dataset count to RDF. * [ ] Spam + LLMs * - RateLimiting for Rif Editing. -* - Honep Pot approach. -* [+] Help Alex with SSL certification container error. -* - Put the changes in the actual scm files. -* [X] Python Fahamu. -* [X] Memvid - brief look. - -### Later +* - Honepot approach. * [ ] Dockerise GN container. For Harm. * [ ] Send emails when job fail. * [ ] Look at updating gn-auth/gn-libs to PYTHONPATH for gn2/3. @@ -92,7 +97,8 @@ Currently closed issues are: * [X] lmdb publishdata output and share with Pjotr and Johannes ## Done - +* [X] Updated Penguin2 with cuda drivers. Cuda no longer supports K80s +* [X] Provided Johannes anthropic tokens * [X] Add lmdb output hashes with index and export LMDB_DATA_DIRECTORY * [X] Share small database with @pjotrp and @felixl * [X] With Alex get rqtl2 demo going in CD (for BXD) @@ -131,3 +137,31 @@ Currently closed issues are: * - Simplify (focus on small files). Don't over-rely on Numpy. * [X] Assess adding GeneRIF to LLM. * [X] Referrer headers -- a way of preventing bots beyond rate-limiting. +* [X] Python Fahamu. +* [X] Memvid - brief look. +* [X] Encourage FahamuAI to be open. +* Another paper with his group should be out this month +* [X] Help Alex with SSL certification container error. +* - Fix SSL issues in local container. +* [X] Send Arun an e-mail on how to go about upgrading shepherd. +* [X] Case Attributes. +* - Git blame. Add tests. Fred. +* - NOTE: Fixed the diffs. But there's an edge-case with BXD longevity (I haven't checked. Shared scripts) +* - NOTE: Elpy broke. Eglot/lspemacs doesn't work. +* - NOTE: Moved away from storing diffs in files to LMDB. +* - Error when checking the history. Fixed by fixing the diffs. +* - Reach out to Zach. NOTE: Timing differences. +* - Disable diff in the UI - unnecessary. +* [X] Added LMDB_PATH to dev container. Updated old commits. +* [X] Merged no-login AI work that Alex did. +* [X] Talk to Fred and hand over case-attributes. +* [X] Distinct admin and dev user. [w/ Fred] +* - Extra fluff to grant dev user access to everything. +* [X] Merged rate-limiter. +* [X] Look at slow running CD (look at issue tracker and be systematic). +* [X] Fix CD. Build guix against a recent pinned profile. +* [X] Fix CD tests. +* [X] Look at different provider(s) for LLMs. +* [X] Install OpenCL in Penguin2 and try LLM script. Check differences between OpenCL and CUDA. PJ installed CUDA in balg01. +* [X] Look at container work. Look at permissions issue. +* [X] Set-up wolfshead: Resolving dependency conflicts in Python. Using DSPY |