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base repository: malariagen/malariagen-data-python
base: v13.0.1
head repository: malariagen/malariagen-data-python
compare: master
Commits on Mar 26, 2024
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add plink converyt function, faff around with some tests
Tristan Dennis authored and Tristan Dennis committedMar 26, 2024 Loading Loading status checks…Configuration menu - View commit details
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Commits on Apr 11, 2024
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temp fix for avoiding error in mapping all-allele -> biallelic allele…
…s, avoids using dask
Tristan Dennis authored and Tristan Dennis committedApr 11, 2024 Configuration menu - View commit details
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updated plink converter to use biallelic_snp_calls with tmp. amended …
…variant_allele mapping
Tristan Dennis authored and Tristan Dennis committedApr 11, 2024 Configuration menu - View commit details
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Commits on Jun 21, 2024
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Commits on Aug 2, 2024
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Commits on Aug 8, 2024
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Added chunking of allele_mapping array so that da.map blocks works
Removed numba decorator for the apply_allele_mapping function, for now
Tristan Dennis authored and Tristan Dennis committedAug 8, 2024 Configuration menu - View commit details
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Tristan Dennis authored and Tristan Dennis committed
Aug 8, 2024 Configuration menu - View commit details
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Commits on Aug 9, 2024
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Tristan Dennis authored and Tristan Dennis committed
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Commits on Aug 14, 2024
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Commits on Aug 20, 2024
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Commits on Aug 27, 2024
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remove dud notebook, tidy up to_plink.py
Tristan Dennis authored and Tristan Dennis committedAug 27, 2024 Configuration menu - View commit details
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Commits on Aug 29, 2024
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Commits on Sep 2, 2024
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Commits on Sep 5, 2024
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Commits on Sep 16, 2024
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Removed some minor version options due to long list causing UI issues.
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Upgrade scikit-allel to resolve issues running large PCAs on a distri…
…buted cluster (#603) * upgrade scikit-allel * update lock file * fix broken poetry lock
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Commits on Sep 17, 2024
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Upgrade scikit-allel minimum version 1.3.13 to resolve issues with ru…
…nning large PCAs on a distributed cluster (#605) * upgrade scikit-allel minimum version * poetry update
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Commits on Sep 19, 2024
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Tristan Dennis authored and Tristan Dennis committed
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update plink converter test to include test for created files
Tristan Dennis authored and Tristan Dennis committedSep 19, 2024 Configuration menu - View commit details
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tidy, add tests, refactor snp_data call
Tristan Dennis authored and Tristan Dennis committedSep 19, 2024 Configuration menu - View commit details
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Merge pull request #602 from malariagen/update_switcher_2024-09-16
Update switcher.json
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Commits on Sep 20, 2024
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Handle dask distributed progress (#614)
* distributed progress * test local cluster
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More options for automatic sizing of chunks (#615)
* ndauto * typing * typing * fix typing * check it works * dunno
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* Fix typo in Af1.rst * Fix typo in Ag3.rst * Fix typo in Amin1.rst
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Add parameters to the Anopheles pca function to allow better handling…
… of outliers (#616) * add exclude_samples parameter to pca * add fit_exclude_samples parameter to pca * refine tests
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Commits on Sep 22, 2024
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Handle chunks parameter given as a size in memory; improve default ch…
…unks (#622) * Update util.py Add option for special handling of chunks parameter given as a size in memory (number of bytes). * Update base_params.py * refactor and pass through chunks * fix urls in notebooks * fix bucket names * fix directory names * add missing directories
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Commits on Sep 23, 2024
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Merge pull request #619 from malariagen/618-bad-random-value
Random error when performing tests
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Fix center and zoom map parameters to allow int or float values (#625)
* Upgrade center, zoom map params to floats * Explicitly allow either int, float for center, zoom map params
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Improve performance when accessing biallelic SNP calls (#623)
* fix bug with biallelic snp calls and variant_allele * optimisations, wip * massive thrash * comment * refactor * deal with strange performance issue in zarr and fsspec * poetry update * tweaks * revert silly mistake * avoid getattr pickle black hole of doom * fix gcs bucket * remove outputs * tweak test * tweak test
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Commits on Sep 24, 2024
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Further work on scalability for large biallelic genotype data computa…
…tions (#626) * back out usage of zarr * revert to native chunks for now * revert to native chunks for now
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Commits on Sep 26, 2024
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Commits on Sep 27, 2024
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