8000 Scripts and dependencies updates for Python 3.8 - 3.10 by shachafl · Pull Request #2009 · spacetx/starfish · GitHub
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Scripts and dependencies updates for Python 3.8 - 3.10#2009

Merged
berl merged 35 commits intospacetx:masterfrom
shachafl:python3.8
Aug 12, 2024

Commits

Commits on Aug 8, 2024

a3cac20

  • append is deprecated in pandas 2.0 use concat instead. This update is backward compatible.

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  • Linting corrections following automatic checks in PR

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  • updating yaml.load() to support version 5.1+

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  • updating pip version

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  • linting corrections to crop.py and check_all_funcs.py

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  • mypy assignment error: replaced None with empty string

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  • mypy assignment error: replaced None with empty dict

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  • mypy assignment error: add Optional to args defaults with None

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  • mypy assignment error: silencing variable type IntensityTable

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  • check_all_func.py: added import typing

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  • round and ch_values from_spot_data of IntensityTable expected Sequence but got ndarray instead: replaced np.arange with range

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  • silencing mypy errors with type: ignore, to pass PR automatic checks

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  • check_all_funcs.py: F401 'typing' imported but unused: silencing linter

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  • fixing 6 files with linting errors E126, E128, E251

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  • fixing linting errors in 2 files: I101 and I201

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  • fixing conflict due to identical in 2 json schema files

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  • correcting spots detected from 53 to 54

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  • update expected values for registered images and two other minor counts

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  • small correction to expected values when testing registration on ISS test data

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  • correcting channel_ and round_must_be_present tests and corresponding field_of_view schema

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  • fixiing wrong underline length in docstring

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  • defining 'en' language and adding xarray to autodoc_mock_imports

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  • removing py 3.7 and adding 3.10 to starfish-prod-ci.yml

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  • commenting out napari gui and moving to the end of script

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  • removed extension 'sphinx_autodoc_typehints' due to failed guarded type import with xarray

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  • fix: update docker image tp python 3.8 instead of 3.7

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  • docs(packaging): update python version compatible with starfish

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  • docs: updating README and installation file with python versions and how to fix broken napari or jupyter

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