Multi barcode decoder#4
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otherwise multiple local maxima are returned even within the distance if their values are identical. This lead to lots of over-segmentation. In particular, multiple perfectly contigous nuclei were split in half.
* Add min_distance parameter to peak_local_max call otherwise multiple local maxima are returned even within the distance if their values are identical. This lead to lots of over-segmentation. In particular, multiple perfectly contigous nuclei were split in half. Related spacetx#2006 * Fix iss test adjust assumption on number of detected cells * Fix docker build the docker build was failing, because botocore needs urllib3 to be in a certain version range. Pinning urllib3 to that range fixes the issue.
* multichannel replaced with channel_axis in scikit-image ver 0.19 * in scikit-image 0.20 watershed was moved from morphology module to segmentation * in scikit-image 0.20 selem was changed to footprint selsm was replaced with footprint in scikit-image 0.20 * updates due to scikit-image 0.21.0 prefix GeometricTransform with _ * updating napari version and removing anisotropy in spot sizes * fix(requirements): edit Makefile and update REQUIREMENTS.txt to generate all req files updating requirements files to support sphinx's make html * numpy.float is deprecated in ver 1.20 * append is deprecated in pandas 2.0 use concat instead. This update is backward compatible. * Linting corrections following automatic checks in PR * updating yaml.load() to support version 5.1+ * updating pip version * linting corrections to crop.py and check_all_funcs.py * mypy assignment error: replaced None with empty string * mypy assignment error: replaced None with empty dict * mypy assignment error: add Optional to args defaults with None added: from typing import Optional * mypy assignment error: silencing variable type IntensityTable * check_all_func.py: added import typing * round and ch_values from_spot_data of IntensityTable expected Sequence but got ndarray instead: replaced np.arange with range * silencing mypy errors with type: ignore, to pass PR automatic checks * check_all_funcs.py: F401 'typing' imported but unused: silencing linter * fixing 6 files with linting errors E126, E128, E251 * fixing linting errors in 2 files: I101 and I201 * fixing conflict due to identical in 2 json schema files * correcting spots detected from 53 to 54 * update expected values for registered images and two other minor counts * small correction to expected values when testing registration on ISS test data * correcting channel_ and round_must_be_present tests and corresponding field_of_view schema * fixiing wrong underline length in docstring * defining 'en' language and adding xarray to autodoc_mock_imports * removing py 3.7 and adding 3.10 to starfish-prod-ci.yml * commenting out napari gui and moving to the end of script * removed extension 'sphinx_autodoc_typehints' due to failed guarded type import with xarray * fix: update docker image tp python 3.8 instead of 3.7 * docs(packaging): update python version compatible with starfish docs(packaging): minor syntax correction * docs: updating README and installation file with python versions and how to fix broken napari or jupyter
* Update readthedocs.yml make readthedocs config compatible with latest requirements
…acetx#2018) * removing support for python 3.8 * upgrading setuptools as older ver is part of venv * dropping python 3.8 and adding tests for 3.11
* np.product is deprecated in numpy 1.25. Use np.prod instead. * np.NINF is deprecated in numpy 2.0. Use -np.inf instead. * updating requirements files for numpy==1.26.4 * Updating tests as quicksort (default) is not stable for columns with same values
* updating CHANGELOG.md for release 0.3.0 * scikit-image version issue: replacing selem with footprint * adding symbolic link to data folder for osm pipeline example * skipping starmap pipeline example due to high memory requirements (>32Gb) * correcting Operating System classifier in setup.cfg
* updating versioneer and add python 3.12 to setup files * add python 3.12 to CI * fix: python 3.12 flake8 linting error * removing backslash sequences that raise SyntaxWarning in python 3.12+ when using sphinx-gallery to convert reST to markdown * add python 3.12 support to docs * docs: fixes to README.rst loading on PyPI project description (spacetx#2029)
* updating CHANGELOG.md for release 0.3.1
Bumps [lxml-html-clean](https://github.com/fedora-python/lxml_html_clean) from 0.3.1 to 0.4.0. - [Changelog](https://github.com/fedora-python/lxml_html_clean/blob/main/CHANGES.rst) - [Commits](fedora-python/lxml_html_clean@0.3.1...0.4.0) --- updated-dependencies: - dependency-name: lxml-html-clean dependency-type: direct:production ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Will automatically open PR to update: actions/cache actions/checkout actions/setup-python https://docs.github.com/en/code-security/dependabot/working-with-dependabot/keeping-your-actions-up-to-date-with-dependabot
Bumps [tornado](https://github.com/tornadoweb/tornado) from 6.4.1 to 6.4.2. - [Changelog](https://github.com/tornadoweb/tornado/blob/v6.4.2/docs/releases.rst) - [Commits](tornadoweb/tornado@v6.4.1...v6.4.2) --- updated-dependencies: - dependency-name: tornado dependency-type: direct:production ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
* Create dependabot.yml to update Actions version Will automatically open PR to update: actions/cache actions/checkout actions/setup-python https://docs.github.com/en/code-security/dependabot/working-with-dependabot/keeping-your-actions-up-to-date-with-dependabot * moving dependabot.yml to .github/ folder
Bumps [actions/checkout](https://github.com/actions/checkout) from 2 to 4. - [Release notes](https://github.com/actions/checkout/releases) - [Changelog](https://github.com/actions/checkout/blob/main/CHANGELOG.md) - [Commits](actions/checkout@v2...v4) --- updated-dependencies: - dependency-name: actions/checkout dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Bumps [actions/cache](https://github.com/actions/cache) from 2 to 4. - [Release notes](https://github.com/actions/cache/releases) - [Changelog](https://github.com/actions/cache/blob/main/RELEASES.md) - [Commits](actions/cache@v2...v4) --- updated-dependencies: - dependency-name: actions/cache dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Bumps [actions/setup-python](https://github.com/actions/setup-python) from 2 to 5. - [Release notes](https://github.com/actions/setup-python/releases) - [Commits](actions/setup-python@v2...v5) --- updated-dependencies: - dependency-name: actions/setup-python dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Tried to delete and remove dependabot.yml file from the wrong folder, but this didn't register in PR spacetx#2039
* replaced deprecated python setup.py sdist with python -m build * adding package build to requirements files * adding pyproject.toml and removing setup.cfg
Bumps [jinja2](https://github.com/pallets/jinja) from 3.1.4 to 3.1.5. - [Release notes](https://github.com/pallets/jinja/releases) - [Changelog](https://github.com/pallets/jinja/blob/main/CHANGES.rst) - [Commits](pallets/jinja@3.1.4...3.1.5) --- updated-dependencies: - dependency-name: jinja2 dependency-type: direct:production ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
* changed importing of img_as_float32() to skimage.util * silencing mypy error due to dynamic function call * removing stale code and loading match_histograms from skimage.exposure * output parameter in gaussian() is replaced by out * replacing _GeometricTransform with SimilarityTransform * updating requirements files
…h navbar logo and sub-menus (spacetx#2050)
Bumps [cryptography](https://github.com/pyca/cryptography) from 44.0.0 to 44.0.1. - [Changelog](https://github.com/pyca/cryptography/blob/main/CHANGELOG.rst) - [Commits](pyca/cryptography@44.0.0...44.0.1) --- updated-dependencies: - dependency-name: cryptography dependency-type: direct:production ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Bumps [jinja2](https://github.com/pallets/jinja) from 3.1.5 to 3.1.6. - [Release notes](https://github.com/pallets/jinja/releases) - [Changelog](https://github.com/pallets/jinja/blob/main/CHANGES.rst) - [Commits](pallets/jinja@3.1.5...3.1.6) --- updated-dependencies: - dependency-name: jinja2 dependency-type: direct:production ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
…ther requirements files (spacetx#2054)
…lity (spacetx#2066) * updating REQUIREMENTS-JUPYTER.txt to resolve h11 dependency vulnerability * updating pip version in Makefile due to failed workflow run with GitHub actions/cache@v4
… value None (spacetx#2063) * Update tests for normalization parameter * Add normalization parameter Fix spacetx#2062 * Update documentation for normalization parameter * Revert changes to registration tests from 02c654f * Fix expectation
…i-barcode-decoder
Multi barcode decoder
added the quality decoder to __init__.py
improved the codebook_comb generation
…er' into multi-barcode-decoder merge changes from quality-barcode-decoder
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fixed the runtime issue in the quality decoder