Nima

Fix

- bump script
- Add class attribute docstring
- Try to fix the hatch run bump script

Build

- **deps**: update mypy requirement from <=1.10.0 to <=1.10.1 (635)
- **deps**: update scipy requirement from <=1.13.1 to <=1.14.0 (634)
- **pre-commit**: update hooks

Build

- **deps**: update sphinx-autodoc-typehints requirement (632)
- **deps**: update coverage[toml] requirement from <=7.5.3 to <=7.5.4 (631)
- **deps**: update ruff requirement from <=0.4.9 to <=0.4.10 (630)
- **deps**: update dask[distributed] requirement (629)
- **deps**: bump pip from 24.0 to 24.1 in /.github/workflows (628)
- **deps**: update dask[distributed] requirement (627)
- **deps**: update sphinx-autodoc-typehints requirement (626)
- **deps**: update tifffile requirement from <=2024.5.22 to <=2024.6.18 (625)
- **deps**: update scikit-image requirement from <=0.23.2 to <=0.24.0 (624)
- **pre-commit**: update hooks (622)
- **deps**: update dask[distributed] requirement (621)
- **deps**: update ruff requirement from <=0.4.8 to <=0.4.9 (620)
- **deps**: update numpy requirement from <=1.26.4 to <=2.0.0 (619)
- **deps**: bump codecov/codecov-action from 4.4.1 to 4.5.0 (618)
- **pre-commit**: update hooks (617)
- **deps**: update xdoctest requirement from <=1.1.4 to <=1.1.5 (616)
- **deps**: bump pooch from 1.8.1 to 1.8.2 (615)
- **deps**: update ruff requirement from <=0.4.7 to <=0.4.8 (614)
- **deps**: update pytest requirement from <=8.2.1 to <=8.2.2 (613)
- **deps**: update sphinx-autodoc-typehints requirement (612)
- **deps**: update pandas-stubs requirement (610)
- **pre-commit**: update hooks (609)
- **deps**: update ruff requirement from <=0.4.6 to <=0.4.7 (607)
- **deps**: update dask[distributed] requirement (606)
- **deps**: update xdoctest requirement from <=1.1.3 to <=1.1.4 (605)
- **deps**: bump hatch from 1.11.1 to 1.12.0 in /.github/workflows (604)
- **deps**: update pydata-sphinx-theme requirement (603)
- **deps**: update ruff requirement from <=0.4.5 to <=0.4.6 (602)
- **deps**: update coverage[toml] requirement from <=7.5.2 to <=7.5.3 (601)
- **pre-commit**: update hooks (600)
- **deps**: update zarr requirement from <=2.18.1 to <=2.18.2 (599)
- **deps**: update coverage[toml] requirement from <=7.5.1 to <=7.5.2 (598)
- **deps**: update tifffile requirement from <=2024.5.10 to <=2024.5.22 (597)
- **deps**: update scipy requirement from <=1.13.0 to <=1.13.1 (596)
- **deps**: bump hatch from 1.11.0 to 1.11.1 in /.github/workflows (595)
- **deps**: update commitizen requirement from <=3.26.1 to <=3.27.0 (594)
- **deps**: update ruff requirement from <=0.4.4 to <=0.4.5 (593)
- **deps**: bump jupyterlab-server from 2.27.1 to 2.27.2 (592)
- **pre-commit**: update hooks (589)
- **deps**: update commitizen requirement from <=3.25.0 to <=3.26.0 (588)
- **deps**: update dask[distributed] requirement (587)
- **deps**: update pytest requirement from <=8.2.0 to <=8.2.1 (586)
- **deps**: update zarr requirement from <=2.18.0 to <=2.18.1 (585)
- **deps**: update sphinx-click requirement from <=5.2.2 to <=6.0.0 (583)
- **deps**: update matplotlib requirement from <=3.8.4 to <=3.9.0 (582)
- **deps**: bump hatch from 1.10.0 to 1.11.0 in /.github/workflows (581)
- **deps**: bump codecov/codecov-action from 4.3.1 to 4.4.0 (580)
- **deps**: update pyarrow requirement from <=16.0.0 to <=16.1.0 (579)
- **deps**: update sphinx-click requirement from <=5.1.0 to <=5.2.2 (578)
- **deps**: update pandas-stubs requirement (577)
- **pre-commit**: update hooks (576)
- **deps**: update pre-commit requirement from <=3.7.0 to <=3.7.1 (575)
- **deps**: update tifffile requirement from <=2024.5.3 to <=2024.5.10 (574)
- **deps**: update ruff requirement from <=0.4.3 to <=0.4.4 (573)

Refactor

- Drop aicsimageio in favor of bioio-tifffile

Feat

- Add geometri mean filter

Fix

- gen_frame.clip(0) revealed fit_gaussian unstable with large sd
- iteratively_refine_background
- Improve BgParams with optional clip and erosion
- slow env create
- **docs**: Warning for main docstr with \*

Docs

- Compare methods for bg estimation
- Fix an import in usage

Style

- NDArray

Test

- Test PDF output without reference files

Build

- **deps**: update zarr requirement from <=2.17.2 to <=2.18.0 (572)
- **deps**: update nbsphinx requirement from <=0.9.3 to <=0.9.4 (571)
- **pre-commit**: update hooks (570)
- **deps**: update dask[distributed] requirement (569)
- **deps**: update ruff requirement from <=0.4.2 to <=0.4.3 (568)
- **deps**: update coverage[toml] requirement from <=7.5.0 to <=7.5.1 (567)
- **deps**: update tifffile requirement from <=2024.4.24 to <=2024.5.3 (566)
- **deps**: update pygments requirement from <=2.17.2 to <=2.18.0 (565)
- **deps**: bump hatch from 1.9.7 to 1.10.0 in /.github/workflows (564)
- **deps**: bump codecov/codecov-action from 4.3.0 to 4.3.1 (563)
- **deps**: update commitizen requirement from <=3.24.0 to <=3.25.0 (562)
- **pre-commit**: update hooks (561)
- **deps**: update pytest requirement from <=8.1.1 to <=8.2.0 (559)
- **deps**: update ruff requirement from <=0.4.1 to <=0.4.2 (558)
- **deps**: update tifffile requirement from <=2024.4.18 to <=2024.4.24 (557)
- **deps**: update mypy requirement from <=1.9.0 to <=1.10.0 (556)
- **deps**: bump hatch from 1.9.4 to 1.9.7 in /.github/workflows (555)
- **deps**: bump jupyterlab-server from 2.27.0 to 2.27.1 (554)
- **deps**: update coverage[toml] requirement from <=7.4.4 to <=7.5.0 (552)
- **deps**: bump questionary from 2.0.0 to 2.0.1 (550)
- Pin few indirect deps to speed up pip
- **deps**: update jupyterlab-server requirement (548)
- **deps**: update urllib3 requirement from <=1.26.18 to <=2.2.1 (547)
- **deps**: update ipython requirement from <=8.18.0 to <=8.23.0 (546)
- **deps**: update scikit-image requirement from <=0.23.1 to <=0.23.2 (544)
- **deps**: update pyarrow requirement from <=15.0.2 to <=16.0.0 (543)
- **deps**: update ruff requirement from <=0.4.0 to <=0.4.1 (542)
- **deps**: update sphinx requirement from <=7.3.6 to <=7.3.7 (541)
- **deps**: update dask[distributed] requirement (540)
- Move aicsimageio into deps
- Drop types-setuptools
- Drop typeguard test
- Update to py3.12
- Correct mypy configuration
- **deps**: update ruff requirement from <=0.3.7 to <=0.4.0 (539)
- **deps**: update tifffile requirement from <=2024.2.12 to <=2024.4.18 (538)
- **deps**: update commitizen requirement from <=3.22.0 to <=3.24.0 (537)
- **deps**: update sphinx requirement from <=7.3.4 to <=7.3.6 (536)
- **deps**: update sphinx-autodoc-typehints requirement (535)
- **deps**: update sphinx requirement from <=7.2.6 to <=7.3.4 (533)
- **deps**: bump codecov/codecov-action from 4.2.0 to 4.3.0 (524)
- **deps**: update types-setuptools requirement (532)
- **deps**: update ruff requirement from <=0.3.6 to <=0.3.7 (530)
- **deps**: update commitizen requirement from <=3.21.3 to <=3.22.0 (529)
- **deps**: update ruff requirement from <=0.3.5 to <=0.3.6 (528)
- **deps-dev**: update pandas requirement from <=2.2.1 to <=2.2.2 (527)
- **deps-dev**: update sphinx-autodoc-typehints requirement (526)
- **deps-dev**: update scikit-image requirement (525)
- **deps-dev**: update zarr requirement from <=2.17.1 to <=2.17.2 (522)
- **deps-dev**: update dask[distributed] requirement (521)
- **deps**: bump codecov/codecov-action from 4.1.1 to 4.2.0 (520)
- **deps-dev**: update matplotlib requirement from <=3.8.3 to <=3.8.4 (519)
- **deps-dev**: update scipy requirement from <=1.12.0 to <=1.13.0 (518)
- **deps-dev**: update ruff requirement from <=0.3.4 to <=0.3.5 (517)
- **deps-dev**: update dask[distributed] requirement (516)
- **deps-dev**: update commitizen requirement from <=3.20.0 to <=3.21.3 (514)
- **deps**: bump actions/configure-pages from 4 to 5 (513)

Refactor

- Add BgResult grouping dataclass
- Drop myhist()
- bg introducing BgParams
- generat for pylint
- To include pylint rule extract watershed function
- skimage import in nima; d_mask_label
- main cli
- read_tiff
- boolean traps
- exceptions
- Drop data-science-types
- **test**: Use consistently TESTS_PATH
- Add segmentation module
- **build**: From black to ruff format

chore

- Modify pre-commit update message
- update pre-commit hooks (545)

Fix

- **ci**: Add codecov token

Build

- **deps-dev**: update ipykernel requirement from <=6.29.3 to <=6.29.4 (512)

Feat

- Add utils and more temporary tutorials

Fix

- **ci**: TestPYPI upload
- tests after refactoring
- trivial type error
- commitizen version v3.13.0 from 3.12.0

Docs

- Cleaning tutorials
- Improve CLI doc strings
- Reorganize and update tutorials
- Fix tutorials
- Fix tutorials building
- Add ipynb tutorial
- Adopt github-pages-deploy-action

Style

- pyproject.toml

Build

- **deps**: bump codecov/codecov-action from 4.1.0 to 4.1.1 (511)
- **deps-dev**: update typeguard requirement from <=4.1.5 to <=4.2.1 (509)
- **deps-dev**: update pre-commit requirement from <=3.6.2 to <=3.7.0 (508)
- **deps-dev**: update ruff requirement from <=0.3.3 to <=0.3.4 (507)
- **deps-dev**: update commitizen requirement from <=3.18.4 to <=3.20.0 (506)
- **deps-dev**: update pyarrow requirement from <=15.0.1 to <=15.0.2 (505)
- **deps-dev**: update pandas-stubs requirement (503)
- **deps-dev**: update types-setuptools requirement (502)
- **deps-dev**: update ruff requirement from <=0.3.2 to <=0.3.3 (501)
- **deps-dev**: update dask[distributed] requirement (500)
- **deps-dev**: update coverage[toml] requirement (499)
- **deps-dev**: update commitizen requirement from <=3.18.3 to <=3.18.4 (498)
- **deps**: bump hatch from 1.9.3 to 1.9.4 in /.github/workflows (497)
- **deps-dev**: update dask[distributed] requirement (496)
- **deps-dev**: update commitizen requirement from <=3.18.0 to <=3.18.3 (494)
- **deps-dev**: update mypy requirement from <=1.8.0 to <=1.9.0 (493)
- **deps-dev**: update pytest requirement from <=8.1.0 to <=8.1.1 (492)
- **deps-dev**: update ruff requirement from <=0.3.1 to <=0.3.2 (491)
- **deps-dev**: update types-setuptools requirement (490)
- **deps-dev**: update types-setuptools requirement (489)
- **deps-dev**: update commitizen requirement from <=3.17.0 to <=3.18.0 (488)
- **deps-dev**: update pyarrow requirement from <=15.0.0 to <=15.0.1 (487)
- **deps-dev**: update ruff requirement from <=0.3.0 to <=0.3.1 (486)
- **deps-dev**: update zarr requirement from <=2.17.0 to <=2.17.1 (485)
- **deps-dev**: update commitizen requirement from <=3.16.0 to <=3.17.0 (484)
- **deps-dev**: update types-setuptools requirement (483)
- **deps-dev**: update pytest requirement from <=8.0.2 to <=8.1.0 (482)
- **deps-dev**: update types-setuptools requirement (481)
- **deps-dev**: update ruff requirement from <=0.2.2 to <=0.3.0 (480)
- **deps-dev**: update types-setuptools requirement (479)
- **deps**: bump codecov/codecov-action from 4.0.2 to 4.1.0 (478)
- **deps-dev**: update commitizen requirement from <=3.15.0 to <=3.16.0 (477)
- **deps-dev**: update ipykernel requirement from <=6.29.2 to <=6.29.3 (476)
- **deps-dev**: update pytest requirement from <=8.0.1 to <=8.0.2 (473)
- **deps**: bump codecov/codecov-action from 4.0.1 to 4.0.2 (475)
- **deps-dev**: update dask[distributed] requirement (474)
- **deps-dev**: update pandas requirement from <=2.2.0 to <=2.2.1 (472)
- **deps-dev**: update coverage[toml] requirement (471)
- **deps-dev**: update types-setuptools requirement (470)
- **deps-dev**: update coverage[toml] requirement (469)
- **deps-dev**: update commitizen requirement from <=3.14.1 to <=3.15.0 (464)
- **deps-dev**: update pytest requirement from <=8.0.0 to <=8.0.1 (466)
- **deps-dev**: update ruff requirement from <=0.2.1 to <=0.2.2 (465)
- **deps-dev**: update types-setuptools requirement (463)
- **deps-dev**: update pre-commit requirement from <=3.6.1 to <=3.6.2 (462)
- **deps-dev**: update pandas-stubs requirement (461)
- **deps-dev**: update matplotlib requirement from <=3.8.2 to <=3.8.3 (460)
- **deps-dev**: update zarr requirement from <=2.16.1 to <=2.17.0 (459)
- **deps-dev**: update types-setuptools requirement (458)
- **deps-dev**: update tifffile requirement (457)
- **deps-dev**: update pre-commit requirement from <=3.6.0 to <=3.6.1 (455)
- **deps-dev**: update dask[distributed] requirement (454)
- **deps-dev**: update ipykernel requirement from <=6.29.1 to <=6.29.2 (453)
- **deps-dev**: update sphinx-autodoc-typehints requirement (452)
- **deps-dev**: update ipykernel requirement from <=6.29.0 to <=6.29.1 (450)
- **deps-dev**: update numpy requirement from <=1.26.3 to <=1.26.4 (451)
- **deps-dev**: update ruff requirement from <=0.2.0 to <=0.2.1 (449)
- **deps**: bump pip from 23.3.2 to 24.0 in /.github/workflows (445)
- **deps-dev**: update commitizen requirement from <=3.14.0 to <=3.14.1 (444)
- **pre-commit**: Run autoupdate
- **pre-commit**: prettier v4.0.0-alpha.8
- **docs**: Drop darglint in favor of pydoclint; fix some docstring
- **deps-dev**: update tifffile requirement
- **deps**: bump codecov/codecov-action from 4.0.0 to 4.0.1 (442)
- **deps-dev**: update commitizen requirement from <=3.13.0 to <=3.14.0 (441)
- **deps-dev**: update ruff requirement from <=0.1.15 to <=0.2.0 (440)
- **deps**: bump codecov/codecov-action from 3.1.5 to 4.0.0 (439)
- **deps-dev**: update xdoctest requirement from <=1.1.2 to <=1.1.3 (438)
- **deps-dev**: update ruff requirement from <=0.1.14 to <=0.1.15 (435)
- **deps-dev**: update coverage[toml] requirement (434)
- **deps-dev**: update dask[distributed] requirement (433)
- **deps-dev**: update pytest requirement from <=7.4.4 to <=8.0.0 (432)
- **deps-dev**: update sphinx-autodoc-typehints requirement (431)
- **deps**: bump codecov/codecov-action from 3.1.4 to 3.1.5 (430)
- **deps**: bump hatch from 1.9.2 to 1.9.3 in /.github/workflows (429)
- **deps-dev**: update types-setuptools requirement (428)
- **deps**: bump hatch from 1.9.1 to 1.9.2 in /.github/workflows (427)
- **deps-dev**: update ruff requirement from <=0.1.13 to <=0.1.14 (426)
- **deps-dev**: update pandas requirement from <=2.1.4 to <=2.2.0 (425)
- **deps-dev**: update scipy requirement from <=1.11.4 to <=1.12.0 (424)
- **deps-dev**: update pydata-sphinx-theme requirement (423)
- **deps**: bump actions/cache from 3 to 4 (422)
- **deps-dev**: update ipykernel requirement from <=6.28.0 to <=6.29.0 (421)
- **deps-dev**: update ruff requirement from <=0.1.12 to <=0.1.13 (420)
- **deps-dev**: update types-setuptools requirement (419)
- **deps-dev**: update dask[distributed] requirement (418)
- **deps-dev**: update ruff requirement from <=0.1.11 to <=0.1.12 (417)
- **deps-dev**: update autodocsumm requirement (416)
- **deps-dev**: update types-setuptools requirement (415)
- **deps-dev**: update pydata-sphinx-theme requirement (414)
- **deps-dev**: update ruff requirement from <=0.1.9 to <=0.1.11 (413)
- **deps-dev**: update numpy requirement from <=1.26.2 to <=1.26.3 (412)
- **deps-dev**: update pytest requirement from <=7.4.3 to <=7.4.4 (411)
- **deps-dev**: update coverage[toml] requirement (410)
- **deps-dev**: update pandas-stubs requirement (409)
- **deps-dev**: update ipykernel requirement from <=6.27.1 to <=6.28.0 (408)
- **deps**: bump hatch from 1.9.0 to 1.9.1 in /.github/workflows (407)
- **deps-dev**: update ruff requirement from <=0.1.8 to <=0.1.9 (406)
- **deps-dev**: update mypy requirement from <=1.7.1 to <=1.8.0 (405)
- **deps-dev**: update coverage[toml] requirement (404)
- **deps**: bump hatch from 1.8.1 to 1.9.0 in /.github/workflows (400)
- **deps-dev**: update pandas-stubs requirement (399)
- **deps**: bump pip from 23.3.1 to 23.3.2 in /.github/workflows (398)
- **deps-dev**: update dask[distributed] requirement from <=2023.12.0 to <=2023.12.1 (397)
- **deps-dev**: update coverage[toml] requirement (396)
- **deps**: bump hatch from 1.8.0 to 1.8.1 in /.github/workflows (395)
- **deps**: bump actions/download-artifact from 3 to 4 (394)
- **deps-dev**: update ruff requirement from <=0.1.7 to <=0.1.8 (393)
- **deps**: bump hatch from 1.7.0 to 1.8.0 in /.github/workflows (392)
- **deps-dev**: update pandas requirement from <=2.1.3 to <=2.1.4 (391)
- **deps-dev**: update pre-commit requirement from <=3.5.0 to <=3.6.0 (390)
- **deps-dev**: update tifffile requirement (389)
- **deps**: bump actions/setup-python from 4 to 5 (388)
- **deps-dev**: update ruff requirement from <=0.1.6 to <=0.1.7 (387)
- **deps-dev**: update ipykernel requirement from <=6.27.0 to <=6.27.1 (386)
- **deps**: bump actions/configure-pages from 3 to 4 (385)
- **deps**: bump actions/deploy-pages from 2 to 3 (384)
- **deps-dev**: update dask[distributed] requirement (382)
- **deps-dev**: bump commitizen from 3.12.0 to 3.13.0
- **deps-dev**: bump types-setuptools from 68.2.0.2 to 69.0.0.0 (380)
- **deps-dev**: bump pydata-sphinx-theme from 0.14.3 to 0.14.4 (379)
- **deps-dev**: bump mypy from 1.7.0 to 1.7.1 (378)
- **deps-dev**: bump types-setuptools from 68.2.0.1 to 68.2.0.2 (377)

CI/CD

- Docs out of gh-pages

Refactor

- utils
- Improve generat module

chore

- Fix lint

Feat

- New bg kind `inverse_local_yen`

Fix

- Remove bokeh dep; generating win-py310 error
- warnings for not closing plots and entropy filter on 16-bit

Style

- Add type: ignore to all skimage function calls

Build

- **deps-dev**: bump sphinx-click from 5.0.1 to 5.1.0 (376)
- **deps-dev**: bump pygments from 2.17.1 to 2.17.2 (375)
- **deps-dev**: update scipy requirement from <1.11.4 to <1.11.5 (373)
- **deps-dev**: bump pygments from 2.16.1 to 2.17.1 (372)
- **deps-dev**: bump matplotlib from 3.8.1 to 3.8.2 (371)
- **deps-dev**: bump ruff from 0.1.5 to 0.1.6 (370)
- **deps-dev**: bump pandas from 2.1.2 to 2.1.3 (367)
- **deps-dev**: bump mypy from 1.6.1 to 1.7.0 (368)
- **deps-dev**: update dask[distributed] requirement (366)
- **deps-dev**: bump sphinx-autodoc-typehints from 1.25.0 to 1.25.2 (365)
- **deps-dev**: update numpy requirement from <1.26.2 to <1.26.3 (364)
- **deps-dev**: bump sphinx-autodoc-typehints from 1.24.1 to 1.25.0 (363)
- **deps-dev**: update bokeh requirement from <3.3.1 to <3.3.2 (362)
- **deps-dev**: bump types-setuptools from 68.2.0.0 to 68.2.0.1 (361)
- **deps-dev**: bump ruff from 0.1.4 to 0.1.5 (360)
- **deps-dev**: bump ruff from 0.1.3 to 0.1.4 (358)
- **deps-dev**: bump sphinx-autodoc-typehints from 1.24.0 to 1.24.1 (357)
- **deps-dev**: bump matplotlib from 3.8.0 to 3.8.1 (356)
- **deps-dev**: bump pydata-sphinx-theme from 0.14.2 to 0.14.3 (355)
- **deps-dev**: update dask[distributed] requirement (353)
- **deps-dev**: bump ruff from 0.1.2 to 0.1.3 (352)
- **deps-dev**: bump pandas from 2.1.1 to 2.1.2 (351)
- **deps-dev**: bump xdoctest from 1.1.1 to 1.1.2 (350)
- **deps-dev**: bump pydata-sphinx-theme from 0.14.1 to 0.14.2 (349)
- **deps-dev**: bump ruff from 0.1.1 to 0.1.2 (348)
- **deps-dev**: bump pytest from 7.4.2 to 7.4.3 (347)
- **deps**: bump pip from 23.3 to 23.3.1 in /.github/workflows (345)
- **deps-dev**: bump commitizen from 3.10.1 to 3.12.0 (342)
- **deps-dev**: bump ruff from 0.1.0 to 0.1.1 (344)
- **deps-dev**: bump mypy from 1.6.0 to 1.6.1 (343)
- **deps-dev**: bump ruff from 0.0.292 to 0.1.0 (341)
- **deps-dev**: bump commitizen from 3.10.0 to 3.10.1 (338)
- **deps**: bump pip from 23.2.1 to 23.3 in /.github/workflows (339)
- **deps-dev**: update numpy requirement from <1.26.1 to <1.26.2 (337)
- **deps-dev**: update dask[distributed] requirement (336)
- **deps-dev**: bump pre-commit from 3.4.0 to 3.5.0 (335)
- **deps-dev**: bump mypy from 1.5.1 to 1.6.0 (334)
- **deps-dev**: update bokeh requirement from <3.2.3 to <3.3.1 (333)
- **deps-dev**: bump scikit-image from 0.21.0 to 0.22.0
- **deps-dev**: bump coverage[toml] from 7.3.1 to 7.3.2 (329)
- **deps-dev**: bump ruff from 0.0.291 to 0.0.292 (328)
- **deps-dev**: update dask[distributed] requirement (327)
- **deps-dev**: bump pandas-stubs from 2.0.3.230814 to 2.1.1.230928 (326)
- **deps-dev**: update tifffile requirement (325)
- **deps-dev**: update scipy requirement from <1.11.3 to <1.11.4 (324)
- **deps-dev**: bump commitizen from 3.9.0 to 3.10.0 (322)
- **deps-dev**: bump ruff from 0.0.290 to 0.0.291 (321)
- **deps-dev**: bump pydata-sphinx-theme from 0.14.0 to 0.14.1 (320)
- **deps-dev**: bump pandas from 2.1.0 to 2.1.1 (319)
- **deps-dev**: update tifffile requirement (318)