sourmash

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`--from-file` vs pathlists - can we unify the way they work?

2

We have a few different issues around adding `--from-file` to new commands, e.g. https://github.com/sourmash-bio/sourmash/issues/1631. As I was implementing #1657 for a different reason, though, I realized that pathlists and `--from-file`...

ctb

loading signatures from pathlist fails confusingly if pathlist contains bad paths

3

below, if `pathlist.txt` contains a path that cannot be loaded, sourmash tells us that `pathlist.txt` can't be loaded instead of complaining about the specific file. ``` % sourmash sig fileinfo...

ctb

rationalize directory loading, directory traversal, and `--force`

1

we can force `sourmash` commands to load .sig/.sig.gz files from under a directory, and (with `-f`) we can ask sourmash to try to load other files that MIGHT be JSON...

ctb

pangenome investigation results

2

I wrote a script that calculates the distribution of hashes in collections of genomes. one goal is to generate some statistics for what the pangenome overlap is between genomes. It's...

ctb

Better conceptual definition on minhash/signature/query

12

I think we should separate `query`, `signature` and `minhash` better around the codebase. It's all pretty entangled, but they are different things! - MinHash: the low-level minhash object. Specific k,...

luizirber

Spread 'frozen' behavior through code base & document in dev docs

2

If `FrozenSourmashSignature` https://github.com/sourmash-bio/sourmash/pull/1610 goes in, we'll have a de facto documentation of everywhere in the code base where we modify signatures and sketches. This touches on a bunch of things...

ctb

summary: selectors are good, let's maybe have more of them.

2

This is an update of & replacement for https://github.com/dib-lab/sourmash/issues/1072, which introduced the idea of a `database.select(...)` function. This issue is being updated after the release of sourmash 4.1. --- In...

ctb

document that files in pathlists are relative to the cwd, not to the pathlist location.

2

currently, the file list returned by `load_file_list_of_signatures` is assumed to be relative to current working directory; an equally natural behavior would be to load relative paths based on the dirpath...

ctb

Currently `sig.select_sketch` in Rust only return sketches that match exactly a template. But... If there is a `scaled=10` sketch and the template is `scaled=100`, the sketch can be downsampled. There...

luizirber

Fix wasi tests in GitHub Actions

1

WASI tests [are breaking](https://github.com/dib-lab/sourmash/runs/1415524508?check_suite_focus=true#step:5:5) in GitHub Actions due to changes on the [`add-path` command](https://github.blog/changelog/2020-10-01-github-actions-deprecating-set-env-and-add-path-commands/). One way to fix is to check how the `wasmtime` CI [sets up](https://github.com/bytecodealliance/wasmtime-py/blob/784122b2e031baa2df10f6a1f025ecd85e3e5fc2/.github/workflows/main.yml#L47) the testing, and...

luizirber