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Changelog

v0.3.12 (2024-08-21)

Build

  • deps: update xdoctest requirement from <=1.1.6 to <=1.2.0 (#250)
  • pre-commit: update hooks (#249)
  • deps: update nbsphinx requirement from <=0.9.4 to <=0.9.5 (#245)
  • deps: update ruff requirement from <=0.5.7 to <=0.6.1 (#248)
  • deps: update numpy requirement from <=2.0.1 to <=2.1.0 (#247)
  • deps: update matplotlib requirement from <=3.9.1.post1 to <=3.9.2 (#244)
  • pre-commit: update hooks (#243)
  • deps: update commitizen requirement from <=3.28.0 to <=3.29.0 (#242)
  • deps: update lxml requirement from <=5.2.2 to <=5.3.0 (#241)
  • deps: update ruff requirement from <=0.5.6 to <=0.5.7 (#240)
  • deps: update matplotlib requirement from <=3.9.1 to <=3.9.1.post1 (#239)
  • deps: update autodocsumm requirement from <=0.2.12 to <=0.2.13 (#238)
  • pre-commit: update hooks (#237)
  • deps: update ruff requirement from <=0.5.5 to <=0.5.6 (#236)
  • deps: update coverage[toml] requirement from <=7.6.0 to <=7.6.1 (#235)
  • deps: update bfio requirement from <=2.4.1 to <=2.4.2 (#234)
  • deps: update xdoctest requirement from <=1.1.5 to <=1.1.6 (#233)
  • deps: update mypy requirement from <=1.11.0 to <=1.11.1 (#232)
  • deps: update sphinx requirement from <=7.4.7 to <=8.0.2 (#231)
  • pre-commit: update hooks (#230)
  • deps: bump pip from 24.1.2 to 24.2 in /.github/workflows (#229)
  • deps: update pre-commit requirement from <=3.7.1 to <=3.8.0 (#228)
  • deps: update pytest requirement from <=8.3.1 to <=8.3.2 (#227)
  • deps: update ruff requirement from <=0.5.4 to <=0.5.5 (#226)
  • deps: update bfio requirement from <=2.4.0 to <=2.4.1 (#225)
  • deps: update bfio requirement from <=2.3.6 to <=2.4.0 (#224)
  • deps: update numpy requirement from <=2.0.0 to <=2.0.1 (#222)
  • pre-commit: update hooks (#223)
  • deps: update ruff requirement from <=0.5.3 to <=0.5.4 (#221)
  • deps: update sphinx requirement from <=7.4.6 to <=7.4.7 (#220)
  • deps: update pytest requirement from <=8.2.2 to <=8.3.1 (#219)
  • deps: update mypy requirement from <=1.10.1 to <=1.11.0 (#218)
  • deps: update sphinx requirement from <=7.4.5 to <=7.4.6 (#217)
  • deps: update ruff requirement from <=0.5.2 to <=0.5.3 (#216)
  • deps: update commitizen requirement from <=3.27.0 to <=3.28.0 (#215)
  • deps: update sphinx-autodoc-typehints requirement (#214)
  • deps: update sphinx requirement from <=7.4.4 to <=7.4.5 (#213)
  • deps: update sphinx requirement from <=7.3.7 to <=7.4.4 (#212)
  • pre-commit: update hooks (#211)
  • deps: update ruff requirement from <=0.5.1 to <=0.5.2 (#210)
  • deps: update coverage[toml] requirement from <=7.5.4 to <=7.6.0 (#209)
  • pre-commit: update hooks (#208)
  • deps: bump pip from 24.1.1 to 24.1.2 in /.github/workflows (#207)
  • deps: update ruff requirement from <=0.5.0 to <=0.5.1 (#206)
  • deps: update matplotlib requirement from <=3.9.0 to <=3.9.1 (#205)
  • pre-commit: update hooks (#204)
  • deps: update ruff requirement from <=0.4.10 to <=0.5.0 (#203)
  • deps: bump pip from 24.1 to 24.1.1 in /.github/workflows (#202)
  • deps: update pydata-sphinx-theme requirement (#201)
  • pre-commit: update hooks (#199)

CI/CD

  • Modify Lint job
  • Modify Lint job

v0.3.11 (2024-06-25)

Fix

  • bump
  • Drop of aicsimageio

v0.3.10 (2024-06-25)

Fix

  • Update pyproject

Build

  • deps: update mypy requirement from <=1.10.0 to <=1.10.1 (#200)
  • deps: update sphinx-autodoc-typehints requirement (#198)
  • deps: update coverage[toml] requirement from <=7.5.3 to <=7.5.4 (#197)
  • deps: update ruff requirement from <=0.4.9 to <=0.4.10 (#195)
  • deps: bump pip from 24.0 to 24.1 in /.github/workflows (#196)
  • deps: update sphinx-autodoc-typehints requirement (#194)
  • deps: update scikit-image requirement from <=0.23.2 to <=0.24.0 (#193)
  • pre-commit: update hooks (#192)
  • deps: update numpy requirement from <=1.26.4 to <=2.0.0 (#190)
  • deps: update ruff requirement from <=0.4.8 to <=0.4.9 (#191)
  • deps: bump codecov/codecov-action from 4.4.1 to 4.5.0 (#189)
  • deps: update scyjava requirement from <=1.9.1 to <=1.10.0 (#188)
  • deps: update pims requirement from <=0.6.1 to <=0.7 (#187)
  • pre-commit: update hooks (#186)
  • deps: update xdoctest requirement from <=1.1.4 to <=1.1.5 (#185)
  • deps: update ruff requirement from <=0.4.7 to <=0.4.8 (#184)
  • deps: update pytest requirement from <=8.2.1 to <=8.2.2 (#183)
  • deps: update sphinx-autodoc-typehints requirement (#182)
  • pre-commit: update hooks (#181)
  • deps: update ruff requirement from <=0.4.6 to <=0.4.7 (#180)
  • deps: update xdoctest requirement from <=1.1.3 to <=1.1.4 (#179)
  • deps: bump hatch from 1.11.1 to 1.12.0 in /.github/workflows (#178)
  • deps: update coverage[toml] requirement from <=7.5.2 to <=7.5.3 (#177)
  • deps: update ruff requirement from <=0.4.5 to <=0.4.6 (#176)
  • deps: update pydata-sphinx-theme requirement (#175)
  • pre-commit: update hooks (#174)
  • deps: update coverage[toml] requirement from <=7.5.1 to <=7.5.2 (#173)
  • deps: bump hatch from 1.11.0 to 1.11.1 in /.github/workflows (#172)
  • deps: update ruff requirement from <=0.4.4 to <=0.4.5 (#171)
  • deps: update sphinxcontrib-plantuml requirement (#170)
  • pre-commit: update hooks (#166)
  • deps: update dask-image requirement from <=2023.8.1 to <=2024.5.0 (#165)
  • deps: update commitizen requirement from <=3.25.0 to <=3.26.0 (#164)
  • deps: update pytest requirement from <=8.2.0 to <=8.2.1 (#163)
  • deps: update matplotlib requirement from <=3.8.4 to <=3.9.0 (#162)
  • deps: update sphinx-click requirement from <=5.2.2 to <=6.0.0 (#161)
  • deps: bump codecov/codecov-action from 4.3.1 to 4.4.0 (#160)
  • deps: bump hatch from 1.10.0 to 1.11.0 in /.github/workflows (#159)
  • deps: update sphinx-click requirement from <=5.1.0 to <=5.2.2 (#158)
  • deps: update lxml requirement from <=5.2.1 to <=5.2.2 (#157)
  • pre-commit: update hooks (#156)
  • deps: update pre-commit requirement from <=3.7.0 to <=3.7.1 (#155)
  • deps: update ruff requirement from <=0.4.3 to <=0.4.4 (#154)
  • deps: update nbsphinx requirement from <=0.9.3 to <=0.9.4 (#153)
  • pre-commit: update hooks (#152)
  • deps: update pygments requirement from <=2.17.2 to <=2.18.0 (#150)
  • deps: update ruff requirement from <=0.4.2 to <=0.4.3 (#151)
  • deps: update coverage[toml] requirement from <=7.5.0 to <=7.5.1 (#149)
  • deps: bump hatch from 1.9.7 to 1.10.0 in /.github/workflows (#148)
  • deps: bump codecov/codecov-action from 4.3.0 to 4.3.1 (#147)
  • deps: update commitizen requirement from <=3.24.0 to <=3.25.0 (#146)

v0.3.9 (2024-04-30)

Build

  • Update loci to 7.3.0
  • pre-commit: update hooks (#144)
  • deps: update pytest requirement from <=8.1.2 to <=8.2.0 (#143)
  • deps: update pytest requirement from <=8.1.1 to <=8.1.2 (#142)
  • deps: update ruff requirement from <=0.4.1 to <=0.4.2 (#141)
  • deps: update mypy requirement from <=1.9.0 to <=1.10.0 (#140)
  • deps: bump hatch from 1.9.4 to 1.9.7 in /.github/workflows (#139)
  • deps: update coverage[toml] requirement from <=7.4.4 to <=7.5.0 (#138)
  • deps: update scikit-image requirement from <=0.23.1 to <=0.23.2 (#136)
  • deps: update ruff requirement from <=0.4.0 to <=0.4.1 (#135)
  • deps: update sphinx requirement from <=7.3.6 to <=7.3.7 (#134)
  • deps: update commitizen requirement from <=3.22.0 to <=3.24.0 (#133)
  • deps: update ruff requirement from <=0.3.7 to <=0.4.0 (#132)
  • deps: update sphinx requirement from <=7.3.5 to <=7.3.6 (#131)
  • deps: update sphinx-autodoc-typehints requirement from <=2.0.1 to <=2.1.0 (#130)
  • deps: update sphinx requirement from <=7.2.6 to <=7.3.5 (#129)
  • deps: bump codecov/codecov-action from 4.2.0 to 4.3.0 (#119)
  • fix: message_template and prettier
  • deps: update ruff requirement from <=0.3.6 to <=0.3.7 (#124)
  • deps: update commitizen requirement from <=3.21.3 to <=3.22.0 (#123)
  • deps: update ruff requirement from <=0.3.5 to <=0.3.6 (#122)
  • deps-dev: update sphinx-autodoc-typehints requirement (#121)
  • deps-dev: update scikit-image requirement (#120)

CI/CD

  • rename pip caches
  • MacOS requires update of jdk from 8 to 11
  • Deploy pages also for pull request
  • Merge docs into ci
  • automerge fixes
  • Move auto_merge into ci workflow
  • fix: Add auto_merge workflow for dependabot labeled pr
  • fix: Add auto_merge workflow for dependabot labeled pr
  • Add auto_merge workflow for dependabot labeled pr

Refactor

  • cache pip

chore

  • Modify pre-commit update message
  • update pre-commit hooks (#137)
  • build: Adjust pre-commit config and pyproject.toml
  • update pre-commit hooks (#125)

v0.3.8 (2024-04-10)

Fix

  • license

v0.3.7 (2024-04-10)

Build

  • style: Adopt ruff format instead of black
  • docs: Update to the official upload-artifact action
  • deps-dev: update matplotlib requirement from <=3.8.3 to <=3.8.4 (#117)
  • deps: bump codecov/codecov-action from 4.1.1 to 4.2.0 (#116)
  • deps-dev: update lxml requirement from <=5.2.0 to <=5.2.1 (#115)
  • deps-dev: update ruff requirement from <=0.3.4 to <=0.3.5 (#114)
  • deps: bump actions/configure-pages from 4 to 5 (#112)
  • deps-dev: update commitizen requirement from <=3.20.0 to <=3.21.3 (#111)
  • deps-dev: update lxml requirement from <=5.1.0 to <=5.2.0 (#110)

chore

  • update pre-commit hooks (#118)
  • update pre-commit hooks (#113)

v0.3.6 (2024-03-28)

Fix

  • ci: Add codecov token

v0.3.5 (2024-03-28)

Fix

  • prettier-4.0.0-a8 in pre-commit

Build

  • deps: bump codecov/codecov-action from 4.1.0 to 4.1.1 (#109)
  • deps-dev: update pre-commit requirement from <=3.6.2 to <=3.7.0 (#107)
  • deps-dev: update ruff requirement from <=0.3.3 to <=0.3.4 (#106)
  • deps-dev: update commitizen requirement from <=3.18.4 to <=3.20.0 (#105)
  • deps-dev: update ruff requirement from <=0.3.2 to <=0.3.3 (#103)
  • deps-dev: update coverage[toml] requirement (#102)
  • deps-dev: update commitizen requirement from <=3.18.3 to <=3.18.4 (#101)
  • deps: bump hatch from 1.9.3 to 1.9.4 in /.github/workflows (#99)
  • deps-dev: update commitizen requirement from <=3.18.0 to <=3.18.3 (#98)
  • deps-dev: update mypy requirement from <=1.8.0 to <=1.9.0 (#97)
  • deps-dev: update pytest requirement from <=8.1.0 to <=8.1.1 (#96)
  • deps-dev: update sphinxcontrib-plantuml requirement (#95)
  • deps-dev: update ruff requirement from <=0.3.1 to <=0.3.2 (#94)
  • deps-dev: update commitizen requirement from <=3.17.0 to <=3.18.0 (#93)
  • deps-dev: update ruff requirement from <=0.3.0 to <=0.3.1 (#92)
  • deps-dev: update commitizen requirement from <=3.16.0 to <=3.17.0 (#91)
  • deps-dev: update pytest requirement from <=8.0.2 to <=8.1.0 (#90)
  • deps-dev: update ruff requirement from <=0.2.2 to <=0.3.0 (#89)
  • deps-dev: update commitizen requirement from <=3.15.0 to <=3.16.0 (#88)
  • deps: bump codecov/codecov-action from 4.0.2 to 4.1.0 (#87)
  • deps: bump codecov/codecov-action from 4.0.1 to 4.0.2 (#86)
  • deps-dev: update pytest requirement from <=8.0.1 to <=8.0.2 (#85)
  • deps-dev: update coverage[toml] requirement (#84)
  • deps-dev: update sphinxcontrib-plantuml requirement (#83)
  • deps-dev: update coverage[toml] requirement (#82)
  • deps-dev: update pre-commit requirement from <=3.6.1 to <=3.6.2 (#80)
  • deps-dev: update commitizen requirement from <=3.14.1 to <=3.15.0 (#79)
  • deps-dev: update ruff requirement from <=0.2.1 to <=0.2.2 (#78)
  • deps-dev: update pytest requirement from <=8.0.0 to <=8.0.1 (#77)
  • deps-dev: update matplotlib requirement from <=3.8.2 to <=3.8.3 (#76)
  • deps-dev: update bfio requirement from <=2.3.5 to <=2.3.6 (#75)
  • deps-dev: update pre-commit requirement from <=3.6.0 to <=3.6.1 (#73)
  • deps-dev: update sphinx-autodoc-typehints requirement (#72)
  • deps-dev: update ruff requirement from <=0.2.0 to <=0.2.1 (#71)
  • deps-dev: update numpy requirement from <=1.26.3 to <=1.26.4 (#70)
  • deps-dev: update bfio requirement from <=2.3.4 to <=2.3.5 (#69)
  • deps-dev: update commitizen requirement from <=3.14.0 to <=3.14.1 (#67)
  • deps-dev: update pyometiff requirement from <=0.0.13 to <=1.0.0 (#66)
  • deps: bump pip from 23.3.2 to 24.0 in /.github/workflows (#65)
  • deps-dev: update ruff requirement from <=0.1.15 to <=0.2.0 (#64)
  • deps: bump codecov/codecov-action from 4.0.0 to 4.0.1 (#63)
  • deps-dev: update commitizen requirement from <=3.13.0 to <=3.14.0 (#62)
  • deps-dev: update bfio requirement from <=2.3.3 to <=2.3.4 (#61)
  • deps: bump codecov/codecov-action from 3.1.5 to 4.0.0 (#60)
  • deps-dev: update xdoctest requirement from <=1.1.2 to <=1.1.3 (#59)
  • deps-dev: update ruff requirement from <=0.1.14 to <=0.1.15 (#57)
  • deps-dev: update coverage[toml] requirement (#56)
  • deps-dev: update pytest requirement from <=7.4.4 to <=8.0.0 (#55)
  • deps-dev: update sphinx-autodoc-typehints requirement (#54)
  • deps: bump codecov/codecov-action from 3.1.4 to 3.1.5 (#53)
  • deps: bump hatch from 1.9.2 to 1.9.3 in /.github/workflows (#52)
  • deps-dev: update ruff requirement from <=0.1.13 to <=0.1.14 (#51)
  • deps: bump hatch from 1.9.1 to 1.9.2 in /.github/workflows (#50)
  • deps-dev: update pydata-sphinx-theme requirement (#49)
  • deps: bump actions/cache from 3 to 4 (#48)

Refactor

  • build: Run pre-commit autoupdate; keep prettier

chore

  • update pre-commit hooks (#108)
  • update pre-commit hooks (#104)
  • update pre-commit hooks (#100)
  • update pre-commit hooks (#81)
  • update pre-commit hooks (#74)

v0.3.4 (2024-01-16)

Build

  • deps-dev: update ruff requirement from <=0.1.12 to <=0.1.13 (#47)

Refactor

  • Simplify get_md_dict function
  • Simplify stitch function
  • stitch
  • Remove redundant read_jpype

v0.3.3 (2024-01-12)

Fix

  • Overwrite log_miss logging file

Build

  • deps-dev: update ruff requirement from <=0.1.11 to <=0.1.12 (#46)

Refactor

  • Drop loci_tools in favor of bioformats_package
  • Remove download_loci start_jpype and their mock tests
  • Share JVM from scyjava

chore

  • Clean up toml from meaningless to do

v0.3.2 (2024-01-10)

Test

  • Improve coverage
  • Add monkey test for start_jpype
  • Add monkey test for download_loci

Refactor

  • Simplify get_md_dict
  • Simplify conversion from JavaField
  • Reduce complexity
  • Make boolean value keyword-only argument

v0.3.1 (2024-01-09)

Fix

  • read using jpype vs. scyjava

Style

  • Eradicate commented out code

Test

  • Add cli version checking
  • Add invalid file case to cli testing
  • Adopt CliRunner and fixture to test cli

Build

  • test: Remove xdist to fix missing coverage
  • deps-dev: update lxml requirement from <=5.0.0 to <=5.1.0 (#45)
  • Update to bioformats 7.1.0

CI/CD

  • Simplify gh actions and add macos runner

chore

  • Remove types.py
  • Remove unneeded annotations import from future

v0.3.0 (2024-01-06)

Feat

  • Adopt proper logging
  • Add parametrized fixture tests for the transition to CoreMetadata
  • Add CoreMetadata

Fix

  • Attenuation != 0.9 simplifying covert_value()
  • RtD missing maven

Docs

  • Add missing docstrings
  • Adopt github-pages-deploy-action

Build

  • deps-dev: update autodocsumm requirement (#44)
  • deps-dev: update pydata-sphinx-theme requirement (#43)
  • deps-dev: update numpy requirement from <=1.26.2 to <=1.26.3 (#42)
  • deps-dev: update ruff requirement from <=0.1.9 to <=0.1.11 (#41)
  • deps: update numpy requirement in /.github/workflows (#40)
  • Drop py3.8 and add py3.12
  • Remove the ci group
  • deps-dev: update lxml requirement from <=4.9.4 to <=5.0.0 (#39)
  • deps-dev: update pytest requirement from <=7.4.3 to <=7.4.4 (#38)
  • deps-dev: update coverage[toml] requirement (#37)
  • deps-dev: update jpype1 requirement from <=1.4.1 to <=1.5.0 (#36)
  • deps: bump hatch from 1.9.0 to 1.9.1 in /.github/workflows (#35)
  • deps-dev: update mypy requirement from <=1.7.1 to <=1.8.0 (#34)
  • deps-dev: update ruff requirement from <=0.1.8 to <=0.1.9 (#33)
  • deps-dev: update coverage[toml] requirement (#32)
  • deps-dev: update lxml requirement from <=4.9.3 to <=4.9.4 (#31)
  • deps: bump hatch from 1.8.1 to 1.9.0 in /.github/workflows (#30)
  • deps: bump pip from 23.3.1 to 23.3.2 in /.github/workflows (#27)
  • deps-dev: update coverage[toml] requirement (#26)
  • deps: bump hatch from 1.8.0 to 1.8.1 in /.github/workflows (#24)
  • deps-dev: update ruff requirement from <=0.1.7 to <=0.1.8 (#23)
  • deps: bump hatch from 1.7.0 to 1.8.0 in /.github/workflows (#22)

CI/CD

  • Docs out of gh-pages branch

Refactor

  • Add mypy and missing tests
  • Drop py3.9
  • Adopt pathlib
  • Remove outdated read functions
  • Transition from python-bioformats with javabridge to scyjava
  • Simplify jpype testing; update loci to 6.8.0
  • Drop javabridge read_jb and bioformats read_bf
  • Drop bftools showinf

chore

  • Again tutorials updating2
  • Again tutorials updating
  • Update Tutorials
  • Set max-complexity to 13
  • Fix few type annotations and pytest style
  • Clean up workflows

v0.2.0 (2023-12-13)

Feat

  • Download loci_tools.jar; fix tests.py3.10

Docs

  • RTD
  • Updating tutorials
  • Add docstrings and some type annotation

Style

  • Linted with pre-commit

Test

  • Separate module run with -k
  • Refactor TestDataItem for correct typing

Build

  • deps-dev: update pre-commit requirement from <=3.5.0 to <=3.6.0 (#21)
  • deps: bump actions/setup-python from 4 to 5 (#20)
  • deps-dev: bump ruff from 0.1.6 to 0.1.7 (#19)
  • deps: bump actions/deploy-pages from 2 to 3 (#18)
  • deps: bump actions/configure-pages from 3 to 4 (#17)
  • Switch from darglint to pydoclint
  • deps-dev: update commitizen requirement from <=3.12.0 to <=3.13.0 (#15)
  • deps-dev: bump pre-commit from 3.3.3 to 3.5.0 (#14)
  • deps: bump actions/cache from 2 to 3 (#13)
  • deps: bump actions/setup-java from 3 to 4 (#12)

CI/CD

  • Change caches and tests
  • Try to fix lint

Refactor

  • Add more type annotations
  • Add some typing and click test
  • Reformat code using ruff for improved consistency
  • ruff and precommit
  • Drop docopt in favor of click for imgdiff

chore

  • Refactor few variable names

v0.1.0 (2023-11-30)

Feat

  • Add jpype and pims; pytest markers for slow and jpype; blacken
  • Add read2 using new metadata (bit [0]*npar)

Build

  • Refactor from setup.py to pyproject.toml with hatch

Refactor

  • Renamed nima_io; Update up to py-3.10; Update deps
  • data test; jpype 30x faster md reading

v0.0.1 (2023-07-27)

  • Transferred from bitbucket.
  • Read all metadata from various data files

Available in TestPyPI:

pyenv virtualenv 3.8.18 test
pyenv activate test
pip install setuptools
pip install lxml==4.2.3
pip install javabridge==1.0.17
pip install python-bioformats==1.4.0
pip install -i https://test.pypi.org/simple/ imgread

Added

  • Project transferred from Bitbucket.
  • Implemented functionality to read all metadata from various data files.

Changed

This release marks the initial transfer of the project and introduces metadata reading capabilities for diverse data files.