WIP: add Avro schema #1
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…ts new signature saving & loading mechanisms (#2428) Implement support for `load_from` and `save_to` plugins via `importlib.metadata` entry points. This supports a few of the plugins suggested in #1353 I am nominating this as an experimental feature that is not under semantic versioning/not public yet. Documentation page [here, in dev_plugins.html](https://sourmash--2428.org.readthedocs.build/en/2428/dev_plugins.html). A template repo for new plugins is at https://github.com/sourmash-bio/sourmash_plugin_template. ## Implementation/this PR This PR refactors the `_load_database` loading and `SaveSignaturesToLocation` saving code to build a prioritized list of functions to try in order, and then adds hooks in via the new `sourmash.plugins` module that insert additional loading/saving functions into that list. This PR also moves the current saving/loading functions out of `sourmash.sourmash_args` into the `sourmash.save_load` submodule, and simplifies the code a bit. ## Example plugins: - read JSON sigs and manifests from URLs: https://github.com/sourmash-bio/sourmash_plugin_load_urls - read and write signatures in Apache Avro: https://github.com/sourmash-bio/sourmash_plugin_avro - use extension `.avrosig` to write. Specific TODOs: - [x] provide a minimal "getting started" template repo - [x] add tests for multiple plugins & priorities - [ ] maybe try writing CSV export/import as a plugin? #1098 For later: - think about other kinds of plugins - new CLI entry points, picklist classes, tax loading, tax structure, ??. - work on getting avro support into rust over in luizirber/2021-02-11-sourmash-binary-format#1
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This PR adds Apache Avro as an output format.
The schema was copied over from a Python avro reader/writer plugin, here.
The tricky bit was the schema, which is defined here. The good news? It compiles! And, in Python, it seems to work! The bad news - more work needs to be done on the Rust side; when I do:
I get: