Refactor: Update rolling-ball-plugin to new plugin standards #429
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* New project structure
* Versioning
* Bump version: 1.0.2 → 1.1.0-dev0
* Switch from argparse to typer
* Update logging level
* Add CI tools
* Update tests
agerardin
requested review from
NHotaling,
Nicholas-Schaub and
hsidky
as code owners
nishaq503
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There are a couple of minor changes needed here. The main change though is that the tests should be updated to only use pytest and not the unittest module.
transforms/images/rolling-ball-plugin/src/polus/transforms/images/rolling_ball/__main__.py
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@agerardin Please have a look at my comments and let me know if you have questions
transforms/images/rolling-ball-plugin/tests/correctness_test.py
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transforms/images/rolling-ball-plugin/src/polus/transforms/images/rolling_ball/__main__.py
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transforms/images/rolling-ball-plugin/src/polus/transforms/images/rolling_ball/__main__.py
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transforms/images/rolling-ball-plugin/src/polus/transforms/images/rolling_ball/__main__.py
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transforms/images/rolling-ball-plugin/src/polus/transforms/images/rolling_ball/__main__.py
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…base. * refactor unit tests with pytests * add new tests for the client * add exceptions for bad plugin inputs * add a preview option
* add type info to method signature * better handle plugin parameters
nishaq503
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There are come more changes needed here:
- Update the email addresses of authors to the
nih.govdomain. - See my comments on the
pyproject.tomlfile. - This plugin needs a
filepatternargument as input and use it to filter input images.
| "title": "Rolling Ball", | ||
| "description": "A WIPP plugin to perform background subtraction using the rolling-ball algorithm.", | ||
| "author": "Najib Ishaq (najib.ishaq@axleinfo.com)", | ||
| "author": "Najib Ishaq (najib.ishaq@nih.gov), Antoine Gerardin (antoine.gerardin@gmail.com)", |
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Both email addresses should be in the nih.gov domain.
| name = "polus-plugins-transforms-images-rolling-ball" | ||
| version = "1.1.0-dev0" | ||
| description = "A WIPP plugin to perform background subtraction using the rolling-ball algorithm." | ||
| authors = ["Najib Ishaq <najib.ishaq@nih.gov>", "Antoine Gerardin <antoine,gerardin@gmail.com>"] |
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Email address here as well.
| packages = [{include = "polus", from = "src"}] | ||
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| [tool.poetry.dependencies] | ||
| python = "^3.9.15" |
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Specify this as ">=3.9,<3.12"
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| [tool.poetry.dependencies] | ||
| python = "^3.9.15" | ||
| bfio = "2.1.9" |
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Use all extras. bfio = { version = "2.1.9", extras = ["all]" }
| [[tool.poetry.source]] | ||
| name = "test" | ||
| url = "https://test.pypi.org/simple/" | ||
| default = false | ||
| secondary = true |
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Remove this and use the newest version of filepattern from pypi
| flake8 = "^6.0.0" | ||
| flake8-docstrings = "^1.7.0" |
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Remove flake8 and add ruff
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| @app.command() | ||
| def main( |
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Add an input argument for filepattern
| "-m", | ||
| "polus.plugins.transforms.images.rolling_ball" | ||
| ], | ||
| "inputs": [ |
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We need a filepattern input parameter.
4 participants
This PR updates the rolling ball plugin to the new plugin standard.
* New project structure
* Versioning
* Bump version: 1.0.2 → 1.1.0-dev0
* Switch from argparse to typer
* Update logging level
* Add CI tools
* Update tests