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2025-04-08refactor: Explicity define no of cores for rqtl2 computation.Alexander_Kabui
2025-04-08feat: Append GN3 computation completion marker to log file.Alexander_Kabui
2025-04-08fix: Pylint fix for unused variable.Alexander_Kabui
2025-04-08refactor: Check for geno_tranposed and founder_geno_transposed.Alexander_Kabui
2025-04-07Remove debug logging: current_app.logger requires app context.Frederick Muriuki Muriithi
2025-04-07Log out debug messages separate from active statements.Frederick Muriuki Muriithi
2025-04-07Split the command if its a single, non-json-parseable string.Frederick Muriuki Muriithi
2025-03-27refactor: Temporary disable checking sex covariates in rqtl2.Alexander_Kabui
2025-03-27feat: Check for founder and covar file in rqtl2 metadata.Alexander_Kabui
2025-03-21Use HTTPS for LLM endpoint.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2025-03-18Order species by species id.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2025-03-07Merge pull request #218 from genenetwork/chores/refactor-qtl2-scriptAlexander Kabui
refactor rqtl2 script.
2025-03-07Demo CI in gn nairobi meet.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2025-03-07refactor function to process scan1 results.Alexander_Kabui
2025-03-07refactor: Construct map object from cross with columns (Marker, chr,cM, Mb).Alexander_Kabui
2025-03-07fix: Minor rqtl2 fixes.Alexander_Kabui
2025-03-07refactor rqtl2 script.Alexander_Kabui
2025-03-07Convert wikiId and versionId to ints.Munyoki Kilyungi
This fixes failing tests. * gn3/db/rdf/wiki.py (__sanitize_result): Convert versionId and wiki Id to ints. (get_wiki_entries_by_symbol): Get string representation of VersionId and the wikiId instead of the the URI. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2025-03-07Revert "fix: Replace file path fetching code in rqtl2.py with ↵Munyoki Kilyungi
current_app.root_path" This reverts commit e7baf1a4cf05a4e7794a6531c92d367fcd8f1651. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2025-03-04Revert "test: Add unit tests for fibonacci function in rqtl2 module"Munyoki Kilyungi
This reverts commit 9bad745abd94fd0eeb0b0dc6aba0d6a74db33f81.
2025-03-04Revert "docs: Add module and function docstrings for unit tests of fibonacci ↵Munyoki Kilyungi
function". This reverts commit 6a76e302f11c0a0aa0bc0ac8487ad250f8afb9bb.
2025-03-04Revert "feat: Add Python implementation of Fibonacci number calculation".Munyoki Kilyungi
This reverts commit 280c5e97d21501c03f672ed3576ae3eddfc76420.
2025-03-04Use self-holsted LLM API end-point.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2025-03-04docs: Add module and function docstrings for unit tests of fibonacci functionMunyoki Kilyungi (aider)
2025-03-04test: Add unit tests for fibonacci function in rqtl2 moduleMunyoki Kilyungi (aider)
2025-03-04feat: Add Python implementation of Fibonacci number calculationMunyoki Kilyungi (aider)
2025-03-04fix: Replace file path fetching code in rqtl2.py with current_app.root_pathMunyoki Kilyungi (aider)
2025-02-28Eliminate carriage-return and newline characters.Frederick Muriuki Muriithi
2025-02-28Print out the stack trace to help debug failures.Frederick Muriuki Muriithi
2025-02-28Fix issues caught by mypy.Frederick Muriuki Muriithi
2025-02-28Fix remaining linting error.Frederick Muriuki Muriithi
2025-02-28Fix linting errors.Frederick Muriuki Muriithi
2025-02-26feat: Add utility function for reading files and improve loggingAlexander_Kabui
* Add `read_file(file_path)` utility function to streamline file reading. * Updated `run_process()` to return log contents instead of just the log file path.
2025-02-25Comment out package causing build failure.Frederick Muriuki Muriithi
2025-02-25Make list of packages an actual list — add missing commas.Frederick Muriuki Muriithi
2025-02-25fix: handle extra columns in permutations CSV reader to prevent unpacking error.Alexander_Kabui
2025-02-24Fetch rscript from os env if it isn't set in the app's config.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2025-02-24Remove "generate_lod_plot" from rqtl2_wrapper.R.Munyoki Kilyungi
* scripts/rqtl2_wrapper.R (generate_lod_plot): Delete function. (output): Remove "lod_plot_path". Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2025-02-21Merge branch 'main' of https://github.com/genenetwork/genenetwork3Alexander_Kabui
2025-02-21feat: Temporary disable performing genome scan with covariates for RQTL2.Alexander_Kabui
2025-02-21Fix versioning of WIKI entries.Munyoki Kilyungi
* gn3/api/metadata_api/wiki.py (edit_wiki)[next_version]: Set to the latest+1 if a comment id exists. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2025-02-20refactor: Skip permutation test when NO_OF_PERMUTATION less than 0.Alexander_Kabui
2025-02-20refactor: Use p=0.63 in permutation summary for suggestive threshold.Alexander_Kabui
2025-02-19fix: Read and parse correct permutation file from R/qtl2.Alexander_Kabui
2025-02-19fix: Read and parse correct permutation file from R/qtl1Alexander_Kabui
2025-02-10feat: Add LMDB sample data retrieval API endpoint with testsMunyoki Kilyungi (aider)
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2025-02-10chore: Add version information to .gitignoreMunyoki Kilyungi (aider)
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2025-02-10chore: Update .gitignore to exclude .aider filesMunyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2025-02-07refactor: Add rqtl2 default method and update unittests.Alexander_Kabui
2025-02-07fix: pass the correct genome probabilites.Alexander_Kabui
generated by cgit-pink 1.4.1 (git 2.36.1) at 2025-11-22 06:03:50 +0000