Feat/plugins - deprecate otumate and old plugins #1253
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…or-github-change-log Update changelog notice
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Co-authored-by: Copilot <[email protected]>
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…into feat/plugins
and generator function implementation
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Pull Request Overview
This PR deprecates the plugin system and removes several dependencies as part of cleaning up the codebase. The changes remove the otumat package dependency, eliminate the entire plugin verification system, and update documentation with new computational patterns.
- Removes the plugin system including verification logic and cryptographic dependencies
- Eliminates
otumatandcryptographydependencies from project requirements - Adds comprehensive documentation for the "three-part make pattern" for long computations
Reviewed Changes
Copilot reviewed 12 out of 12 changed files in this pull request and generated 4 comments.
Show a summary per file
| File | Description |
|---|---|
| tests/test_plugin.py | Completely removed all plugin-related tests |
| pyproject.toml | Removed otumat and cryptography dependencies, added new maintainer |
| datajoint/plugin.py | Entirely removed plugin system implementation |
| datajoint/errors.py | Removed plugin warning system and simplified DataJointError constructor |
| datajoint/connection.py | Removed plugin hook system and simplified connection logic |
| datajoint/attribute_adapter.py | Removed plugin-based adapter loading |
| docs/src/compute/populate.md | Added extensive documentation for three-part make pattern |
| Dockerfile | Updated Python version from 3.9 to 3.11 |
| CHANGELOG.md | Added deprecation notice directing to GitHub releases |
| .pre-commit-config.yaml | Updated tool versions for isort, black, and flake8 |
| .devcontainer/docker-compose.yml | Updated container distribution and removed version specification |
| .devcontainer/devcontainer.json | Added SSH agent mounting for development environment |
| @@ -177,7 +148,6 @@ class Connection: | |||
| """ | |||
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| def __init__(self, host, user, password, port=None, init_fun=None, use_tls=None): | |||
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The variable assignment host_input, host = (host, get_host_hook(host)) was removed but the original host parameter is being overwritten without preserving the original value. This could break functionality that depends on the original host value.
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| ```python | ||
| def make_fetch(self, key): | ||
| """Phase 1: Fetch all required data from parent tables""" | ||
| fetched_data = ((ParentTable & key).fetch1(),) |
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The comment says the return value must be a sequence, but fetched_data is assigned as a tuple with a single element ((ParentTable & key).fetch1(),). This creates a nested tuple structure that may not match the expected interface.
| fetched_data = ((ParentTable & key).fetch1(),) | |
| fetched_data = [ParentTable & key).fetch1()] |
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| def make_fetch(self, key): | ||
| """Fetch the image data needed for analysis""" | ||
| return (Image & key).fetch1('image'), |
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[nitpick] The trailing comma creates a single-element tuple, but this inconsistent with the pattern shown earlier where fetched_data1 is compared with fetched_data2. Consider using consistent tuple packing throughout the examples.
| return (Image & key).fetch1('image'), | |
| return (Image & key).fetch1('image') |
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Co-authored-by: Copilot <[email protected]>
Fixing #1252 and initial part of #1251