Merge pf7 package updates to master - #2
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Drop cohorts columns below min cohort size when computing frequencies
…rovide more clarity
* try out an approach to sample_query * adds query to snp freqs * tests * Update malariagen_data/ag3.py Co-authored-by: Alistair Miles <alimanfoo@googlemail.com> * Update malariagen_data/ag3.py Co-authored-by: Alistair Miles <alimanfoo@googlemail.com> * Update malariagen_data/ag3.py Co-authored-by: Alistair Miles <alimanfoo@googlemail.com> * fixes tests Co-authored-by: chris <kai.clarkson@gmail.com> Co-authored-by: Chris Clarkson <cclarkson@users.noreply.github.com>
* new plotly based style method * allow multi-index * update toml to required version of plotly * cohort label x axis * Update malariagen_data/ag3.py Co-authored-by: Alistair Miles <alimanfoo@googlemail.com> * Update malariagen_data/ag3.py Co-authored-by: Alistair Miles <alimanfoo@googlemail.com> * Update malariagen_data/ag3.py Co-authored-by: Alistair Miles <alimanfoo@googlemail.com> * Update malariagen_data/ag3.py Co-authored-by: Alistair Miles <alimanfoo@googlemail.com> * Update malariagen_data/ag3.py Co-authored-by: Alistair Miles <alimanfoo@googlemail.com> * Update malariagen_data/ag3.py Co-authored-by: Alistair Miles <alimanfoo@googlemail.com> * AMs comments * try to simplify * AMs changes working * demo notebook * fixes cnv_freq nans and adds index=None to the plotter * tests fixed * Update malariagen_data/ag3.py Co-authored-by: Alistair Miles <alimanfoo@googlemail.com> * adds index tests * fixes test * more fixin tests Co-authored-by: Alistair Miles <alimanfoo@googlemail.com>
* drop support for python 3.6 * deal with zarr 2.11 * fix bug * fix test failures * add comments
* update release notes for v1 * add missing v1 release note * a few more release notes
* wip refactor region support * amin1 tests passing * wip bug fixes * wip optimise and fix * wip haplotypes optimise and support region * tweaks * fix test locate region
… specifically that the path can be overridden
Co-authored-by: Alistair Miles <alimanfoo@googlemail.com>
Co-authored-by: Alistair Miles <alimanfoo@googlemail.com>
Co-authored-by: Alistair Miles <alimanfoo@googlemail.com>
Co-authored-by: Alistair Miles <alimanfoo@googlemail.com>
Add pf7 module
…ease Update version for pf7 pre-release
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Update master branch to keep synced with malariagen repo