CHANGELOG.md

Changelog

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.