recommend (and test) 'standalone manifests' #235
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probably should link to https://sourmash.readthedocs.io/en/latest/databases-advanced.html in the docs here, as well. |
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The documentation is being significantly reworked in sourmash-bio/sourmash#3054 and sourmash-bio/sourmash#3027. Once those are merged, we can update here. In brief, we should recommend using |
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This PR: * fixes a minor nit in `sourmash sig collect` output where it said "loaded 0 signatures" * updates a lot of the documentation around standalone manifests to encourage their use * in tandem, modifies docs to discourage loading from pathlists/from-files and directory hierarchies TODO: - [x] look at TODO item re directories in sig collect - [x] think about adding #3023 information into docs about lazy loading; maybe in the advanced databases document? - [x] update `sig manifest` docs to point out that they do not generate standalone manifests - [x] revisit branchwater plugin documentation to, to either make issues or make changes - [x] update `sig check` and `sig collect` to tell people to expand their paths ref #3039 - [x] update docs more to recommend against pathlists and directories per #3040 Related issues: * sourmash-bio/sourmash_plugin_branchwater#235 * Fixes #3048 * Fixes #3009 by recommending `sig collect` and `sig check` instead of `sig manifest` for making standalone manifests * #3053 * Fixes #3023 * Fixes #3039 * Fixes #3040 --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Tessa Pierce Ward <bluegenes@users.noreply.github.com>
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Support for this is being added in #430. |
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related to sourmash-bio/sourmash#3023, I think we should proselytize the use of standalone manifests in certain circumstances.
We refer to 'manifest CSVs' in the current docs, but this is confusing, since it turns out manifest CSVs generated by
sig manifestdo not necessarily work as standalone manifests, while manifests generated bysig collectdo. Standalone manifests are (in my newspeak) files that can be loaded & used by sourmash as, well, standalone files - they are not tightly linked to a specific storage type.I'm going to work on the framing and documentation and tests a bit over in the sourmash repo, but one of the main goals is to get it straight for use in the branchwater plugin 😅 so I thought I'd create an issue here to make sure we update the docs appropriately (and make sure the functionality actually works).
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