Anna (Anya) Parker

Debugger gets stuck - with Timeout after 2000 ms for 'terminate'

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Hi! I'm trying to debug a Julia package I'm maintaining (see test script: `https://github.com/PierreBarrat/TreeKnit.jl/blob/master/test/splitgraph/3solutions/test.jl`) When I run the debugger, it always gets stuck at the same function (`SplitGraph.sa_opt`), I also...

Is it possible to know more specifically on which branch/node this error occurs? That could be useful for debugging the tree! _Originally posted by @corneliusroemer in https://github.com/neherlab/treetime/pull/202#discussion_r943333323_

convolve_fft: convert to delta function if distributions too narrow

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## Issue https://github.com/nextstrain/augur/issues/1057 The monkey pox build has branches where the node distributions are much smaller than the branch distributions and the fft fails as the grid is not coarse...

New upper bound for inter1d objects

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After reproducing https://github.com/nextstrain/augur/issues/1032 @corneliusroemer and I found that the issue was during `_ml_t_joint`. An internal node was suggested time points that were out of bounds of pre-calculated interpolation objects (`integral_merger_rate`,...

Add CCHFV to nextclade_data.

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Using the https://github.com/neherlab/CCHFV repository and NCBI Virus I was able to create nextclade_data sets for CCHFV which can then be used by `nextclade run`. Auspice trees for the three segments...

Add simple influenza A H5N1 dataset with all segments

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Copy of the nextclade dataset created by @chaoran-chen in https://github.com/GenSpectrum/nextclade-datasets/tree/main/data/flu/h5n1. This dataset differs from https://github.com/nextstrain/nextclade_data/tree/master/data/community/moncla-lab/iav-h5/ha in that it includes all segments but does not do clade assignment. ### Alignment parameter...

Gff3 file: differences between nextclade datasets and augur ancestral

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Hi! I am not sure if this is a question for nextclade or augur. I am using `augur ancestral` as part of a pipeline to create a tree for use...

Update help docs for augur curate format-dates

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### Current Behavior Hi! I am running `augur curate format-dates`, but augur is unable to format any of the dates. ``` WARNING: Unable to format dates for the following (record,...

Unable to download all Orthomarburg marburgense virus sequences using datasets CLI

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**Describe the bug** I am using the most recent version ``` datasets --version datasets version: 16.33.0 ``` When I download taxonId 3052505 (Orthomarburg marburgense virus) using the datasets cli I...

Hi! Thank you for this great library! I am trying to use `pycountry` to curate data from the INSDC. I have the problem that subdivisions in the INSDC use the...