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command line interface#108

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yfukai wants to merge 179 commits intopeng-lab:devpeng-lab/BaSiCPy:devfrom yfukai:command_lineyfukai/BaSiCpy:command_lineCopy head branch name to clipboard

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Commits on Dec 20, 2021

• Add badges to README

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• Update .gitignore

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• Placeholder dct functions

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Commits on Dec 21, 2021

• Update gitignore

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• Add class for settings

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• Add docstring to settings class

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• Add validation to Settings input

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• Add gpu option to init

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Commits on Jan 12, 2022

• Update README formatting

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• Rename 'figures' folder to 'resources'

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• Move API from README to docs

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• Refactor, update docstrings

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• Change folder ExampleData to data

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• Remove environment file

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• API development

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• Read the docs config

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• Remove png from output formats

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• Update docstrings

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• Fix imports

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• Update workflow

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• Fix workflow

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• Fix workflows

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• Fix tests

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Commits on Jan 13, 2022

• Delete requirements.txt

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• Create VERSION

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• Update README.md

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• Settings becomes pydantic dataclass

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• Update types, variable names

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• Merge branch 'dev' of https://github.com/tdmorello/PyBaSiC into dev

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• Merge pull request #2 from tdmorello/dev

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• Rename variables

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• Add properties to Profile class

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• Add properties for getting/setting BaSiC settings

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• Add dct types to docs

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Commits on Jan 14, 2022

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• Add abstract base class for DCT

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Commits on Jan 15, 2022

• Feat/benchmarks (peng-lab#7)

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• Update pre-commit

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• Add dct backends and tests

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• Update setup.cfg

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• Quickfix for failing tests

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• Converted BaSiC to a pydantic class (peng-lab#23)

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• Merge branch 'dev' into dev

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Commits on Jan 16, 2022

• Added CLI parsing (peng-lab#26)

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• Check package installed before making DCT class

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• Merge HEAD, branches 'dev' and 'dev' of https://github.com/peng-lab/BaSiCPy into dev

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• Remove unused import

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Commits on Jan 17, 2022

• Added abstract base class for DCT (peng-lab#25)

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• Added predict method, does not include baseline estimation (peng-lab#29)

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• Implemented shading model fit algorithm from main branch (peng-lab#27)

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Commits on Jan 19, 2022

• Fix/fit (peng-lab#34)

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• Merge branch 'dev' of https://github.com/peng-lab/BaSiCPy into dev

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Commits on Jan 20, 2022

• Added caching to predict method (peng-lab#35)

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• Merge branch 'dev' of https://github.com/peng-lab/BaSiCPy into dev

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• Feat/autodoc pydantic (peng-lab#38)

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• Feat/cleanup (peng-lab#39)

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• Merge branch 'dev' of https://github.com/peng-lab/BaSiCPy into dev

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• Convert relative to absolute imports

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• Add pytest-benchmark

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• Update noxfile for pytest-benchmark

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Commits on Jan 25, 2022

• ignored python-version

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Commits on Jan 27, 2022

• Merge pull request peng-lab#41 from tdmorello/feat/absolute-imports

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• Update .gitignore

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Commits on Jan 28, 2022

• switched to commented line

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• Merge branch 'ignore_pyenv' of ssh://github.com/yfukai/BaSiCpy into ignore_pyenv

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• Merge branch 'dev' of git://github.com/peng-lab/BaSiCPy into ignore_pyenv

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• Merge pull request peng-lab#45 from yfukai/ignore_pyenv

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Commits on Mar 13, 2022

• refactor name to basicpy

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Commits on Mar 14, 2022

• further refactored...

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• changed dir name

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• refactor predict to transform

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Commits on Mar 17, 2022

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Commits on Mar 24, 2022

• Merge pull request peng-lab#42 from tdmorello/feat/pytest-benchmark

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Commits on May 17, 2022

• Implement logging (peng-lab#44)

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• Feat/jax dct (peng-lab#46)

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Commits on May 19, 2022

• Add save and load methods (peng-lab#43)

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• Update README.md (peng-lab#49)

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Commits on May 22, 2022

• fixed pydantic version lower bound to get test_basic_save_model

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Commits on May 25, 2022

• set the license to MIT

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• removed pydantic version

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• Merge pull request peng-lab#61 from yfukai/provide_license

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Commits on Jun 13, 2022

• Testing fit method with synthetic data (peng-lab#53)

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• Data in package (peng-lab#57)

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• Major update with LADMAP implementation (peng-lab#62)

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• Update contribution notes (peng-lab#66)

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Commits on Jun 14, 2022

• removed experimental_code reference

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Commits on Jun 21, 2022

• updated jaxlib version to avoid importerror (peng-lab#69)

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• Merge Yu's docs

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Commits on Jun 22, 2022

• deleting files not used at this point

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• enab

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• re-added autoflake and isort

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• Merge branch 'dev' of https://github.com/peng-lab/BaSiCPy into repository_cleanup

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• removed opencv

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• Feat/release (peng-lab#72)

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Commits on Jun 23, 2022

• Fix/release (peng-lab#75)

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• Merge branch 'dev' of https://github.com/peng-lab/BaSiCPy into repository_cleanup

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• 👥 Update @Nicholas-Schaub as a contributor

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• update readme

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• add tingying organizing meetings

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• Fix lambda flatfield bug (peng-lab#74)

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• fixed save bug for 3D images and added tests (peng-lab#77)

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Commits on Jun 24, 2022

• updated jaxlib dependency

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• updated notebooks

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• some update

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• fixed typos

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Commits on Jun 25, 2022

• fixed typos

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• changed default parameters

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• updated examples

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Commits on Jun 27, 2022

• compared lagrangian with the origin implementation

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• ifurther updated notebooks

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• Add contributing guide to docs

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• Add autoenum to docs

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• Merge pull request peng-lab#73 from tdmorello/feat/docs

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• Merge branch 'dev' of https://github.com/peng-lab/BaSiCPy into fix_jaxlib_import

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• updated notebooks

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• updated thumbnail data for docs

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• updated readme

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• fixed type

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• Merge pull request peng-lab#78 from yfukai/fix_jaxlib_import

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• Merge pull request peng-lab#70 from yfukai/repository_cleanup

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Commits on Jul 1, 2022

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Commits on Jul 2, 2022

• Merge branch 'dev' of https://github.com/peng-lab/BaSiCPy into update_readme

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• added windows instruction

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• fixed notebook folder

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• fixed typo

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Commits on Jul 3, 2022

• added macos and windows tests

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• test falling back to ubuntu

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• added jax installation in noxfile for windows

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• migrated contribution details to the docs

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• update badges

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• fixed badges

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• a bit more update...

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Commits on Jul 4, 2022

• Merge pull request peng-lab#79 from yfukai/update_defaults

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• Merge pull request peng-lab#82 from yfukai/update_readme

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• Merge pull request peng-lab#88 from yfukai/windows_support

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• fixed readme

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• Merge branch 'dev' of https://github.com/peng-lab/BaSiCPy into readme_fix

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• fixed badgee stype

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• further fix...

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Commits on Jul 29, 2022

• Timelapse option in transform (peng-lab#80)

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• Update example data (peng-lab#92)

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  Nicholas-Schaub

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• Fix fit bug for dask array inputs (peng-lab#93)

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  tdmorello

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Commits on Oct 27, 2022

• Update hashes (peng-lab#95)

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• Minor change before beta release (peng-lab#96)

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Commits on Nov 16, 2022

• DCT tools update (peng-lab#98)

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• Update coef definitions (peng-lab#103)

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Commits on Nov 23, 2022

• added click

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  2356ce0

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