Updated seqFISH Decoding Method: CheckAll Decoder

REQUIREMENTS.txt

@@ -16,7 +16,7 @@ semantic_version
 # 0.16.[012] are excluded because https://github.com/scikit-image/scikit-image/pull/3984 introduced
 # a bug into max peak finder.  0.16.3 presumably will have the fix from
 # https://github.com/scikit-image/scikit-image/pull/4263.
-scikit-image >= 0.14.0, != 0.16.0.*, != 0.16.1.*, != 0.16.2.*, != 0.17.1.*, != 0.17.2.*
+scikit-image >= 0.14.0, != 0.16.0.*, != 0.16.1.*, != 0.16.2.*, != 0.17.1.*, != 0.17.2.*, < 0.19.0
 scikit-learn
 scipy
 showit >= 1.1.4
@@ -26,4 +26,4 @@ tqdm
 trackpy
 validators
 xarray >= 0.14.1
-ipywidgets
+ipywidgets

requirements/REQUIREMENTS-CI.txt

@@ -116,7 +116,7 @@ slicedimage==4.1.1
 snowballstemmer==2.1.0
 Sphinx==4.1.2
 sphinx-autodoc-typehints==1.12.0
-sphinx-bootstrap-theme==0.7.1
+sphinx-bootstrap-theme==0.8.1
 sphinx-gallery==0.9.0
 sphinx-rtd-theme==0.5.2
 sphinxcontrib-applehelp==1.0.2
@@ -147,5 +147,4 @@ wcwidth==0.2.5
 webencodings==0.5.1
 widgetsnbextension==3.5.1
 xarray==0.19.0
-zipp==3.5.0
-
+zipp==3.5.0

requirements/REQUIREMENTS-CI.txt.in

@@ -22,4 +22,4 @@ sphinx_bootstrap_theme
 sphinxcontrib-programoutput
 sphinx-gallery
 sphinx_rtd_theme
-twine
+twine

requirements/REQUIREMENTS-NAPARI-CI.txt

@@ -1,142 +1,160 @@
 # You should not edit this file directly.  Instead, you should edit one of the following files (requirements/REQUIREMENTS-NAPARI-CI.txt.in) and run make requirements/REQUIREMENTS-NAPARI-CI.txt
 alabaster==0.7.12
 appdirs==1.4.4
-argon2-cffi==21.1.0
-attrs==21.2.0
-Babel==2.9.1
+argon2-cffi==21.3.0
+argon2-cffi-bindings==21.2.0
+asttokens==2.0.5
+attrs==21.4.0
+Babel==2.10.3
 backcall==0.2.0
-bleach==4.1.0
-boto3==1.18.37
-botocore==1.21.37
+beautifulsoup4==4.11.1
+bleach==5.0.0
+boto3==1.24.14
+botocore==1.27.14
+build==0.8.0
 cachey==0.2.1
-certifi==2021.5.30
-cffi==1.14.6
-charset-normalizer==2.0.4
-click==8.0.1
-cloudpickle==1.6.0
-cycler==0.10.0
-dask==2021.10.0
+certifi==2022.6.15
+cffi==1.15.0
+charset-normalizer==2.0.12
+click==8.1.3
+cloudpickle==2.1.0
+cycler==0.11.0
+dask==2022.6.0
 dataclasses==0.6
-debugpy==1.4.1
+debugpy==1.6.0
 decorator==4.4.2
 defusedxml==0.7.1
-diskcache==5.2.1
-docstring-parser==0.10
-docutils==0.17.1
-entrypoints==0.3
-freetype-py==2.2.0
-fsspec==2021.8.1
-h5py==3.4.0
+diskcache==5.4.0
+docstring-parser==0.14.1
+docutils==0.18.1
+entrypoints==0.4
+executing==0.8.3
+fastjsonschema==2.15.3
+fonttools==4.33.3
+freetype-py==2.3.0
+fsspec==2022.5.0
+h5py==3.7.0
 HeapDict==1.0.1
-hsluv==5.0.2
-idna==3.2
-imageio==2.9.0
-imagesize==1.2.0
+hsluv==5.0.3
+idna==3.3
+imageio==2.19.3
+imagesize==1.3.0
+importlib-metadata==4.11.4
 iniconfig==1.1.1
-ipykernel==6.3.1
-ipython==7.27.0
+ipykernel==6.15.0
+ipython==8.4.0
 ipython-genutils==0.2.0
-ipywidgets==7.6.4
-jedi==0.18.0
-Jinja2==3.0.1
-jmespath==0.10.0
-joblib==1.0.1
-jsonschema==3.2.0
-jupyter-client==7.0.2
-jupyter-core==4.7.1
-jupyterlab-pygments==0.1.2
-jupyterlab-widgets==1.0.1
-kiwisolver==1.3.2
-locket==0.2.1
-magicgui==0.2.10
-MarkupSafe==2.0.1
-matplotlib==3.4.3
+ipywidgets==7.7.1
+jedi==0.18.1
+Jinja2==3.1.2
+jmespath==1.0.1
+joblib==1.1.0
+jsonschema==4.6.0
+jupyter-client==7.3.4
+jupyter-core==4.10.0
+jupyterlab-pygments==0.2.2
+jupyterlab-widgets==1.1.1
+kiwisolver==1.4.3
+locket==1.0.0
+magicgui==0.5.1
+MarkupSafe==2.1.1
+matplotlib==3.5.2
 matplotlib-inline==0.1.3
 mistune==0.8.4
 mpmath==1.2.1
-napari==0.4.11
+napari==0.4.16
 napari-console==0.0.4
-napari-plugin-engine==0.1.9
-napari-svg==0.1.5
-nbclient==0.5.4
-nbconvert==6.1.0
-nbformat==5.1.3
-nest-asyncio==1.5.1
-networkx==2.6.2
-notebook==6.4.3
-numpy==1.21.2
-numpydoc==1.1.0
-packaging==21.0
-pandas==1.3.2
-pandocfilters==1.4.3
-parso==0.8.2
+napari-plugin-engine==0.2.0
+napari-svg==0.1.6
+nbclient==0.6.4
+nbconvert==6.5.0
+nbformat==5.4.0
+nest-asyncio==1.5.5
+networkx==2.8.4
+notebook==6.4.12
+npe2==0.5.0
+numpy==1.22.4
+numpydoc==1.4.0
+packaging==21.3
+pandas==1.4.2
+pandocfilters==1.5.0
+parso==0.8.3
 partd==1.2.0
+pep517==0.12.0
 pexpect==4.8.0
 pickleshare==0.7.5
-Pillow==8.3.2
-Pint==0.17
+Pillow==9.1.1
+Pint==0.19.2
 pluggy==1.0.0
-prometheus-client==0.11.0
-prompt-toolkit==3.0.20
-psutil==5.8.0
+prometheus-client==0.14.1
+prompt-toolkit==3.0.29
+psutil==5.9.1
+psygnal==0.3.5
 ptyprocess==0.7.0
-py==1.10.0
-pycparser==2.20
-pydantic==1.8.2
-Pygments==2.10.0
-PyOpenGL==3.1.5
-pyparsing==2.4.7
+pure-eval==0.2.2
+py==1.11.0
+pycparser==2.21
+pydantic==1.9.1
+Pygments==2.12.0
+PyOpenGL==3.1.6
+pyparsing==3.0.9
 PyQt5==5.14.2
-PyQt5-sip==12.9.0
-pyrsistent==0.18.0
-pytest==6.2.5
+PyQt5-sip==12.11.0
+pyrsistent==0.18.1
+pytest==7.1.2
 pytest-qt==4.0.2
 python-dateutil==2.8.2
-pytz==2021.1
-PyWavelets==1.1.1
-PyYAML==5.4.1
-pyzmq==22.2.1
-qtconsole==5.1.1
-QtPy==1.11.0
+pytomlpp==1.0.11
+pytz==2022.1
+PyWavelets==1.3.0
+PyYAML==6.0
+pyzmq==23.2.0
+qtconsole==5.3.1
+QtPy==2.1.0
 read-roi==1.6.0
 regional==1.1.2
-requests==2.26.0
-s3transfer==0.5.0
+requests==2.28.0
+s3transfer==0.6.0
 scikit-image==0.18.3
-scikit-learn==0.24.2
-scipy==1.7.1
-semantic-version==2.8.5
+scikit-learn==1.1.1
+scipy==1.8.1
+semantic-version==2.10.0
 Send2Trash==1.8.0
-setuptools==56.0.0
+setuptools==58.1.0
 showit==1.1.4
 six==1.16.0
 slicedimage==4.1.1
-snowballstemmer==2.1.0
-Sphinx==4.1.2
+snowballstemmer==2.2.0
+soupsieve==2.3.2.post1
+Sphinx==5.0.2
+sphinx-bootstrap-theme==0.8.1
 sphinxcontrib-applehelp==1.0.2
 sphinxcontrib-devhelp==1.0.2
 sphinxcontrib-htmlhelp==2.0.0
 sphinxcontrib-jsmath==1.0.1
 sphinxcontrib-qthelp==1.0.3
 sphinxcontrib-serializinghtml==1.1.5
-superqt==0.2.3
+stack-data==0.3.0
+superqt==0.3.2
 sympy==1.5.1
-terminado==0.12.1
-testpath==0.5.0
-threadpoolctl==2.2.0
-tifffile==2021.8.30
-toml==0.10.2
-toolz==0.11.1
+terminado==0.15.0
+threadpoolctl==3.1.0
+tifffile==2022.5.4
+tinycss2==1.1.1
+tomli==2.0.1
+toolz==0.11.2
 tornado==6.1
-tqdm==4.62.2
+tqdm==4.64.0
 trackpy==0.5.0
-traitlets==5.1.0
-typing-extensions==3.10.0.2
-urllib3==1.26.6
-validators==0.18.2
-vispy==0.8.1
+traitlets==5.3.0
+typer==0.4.1
+typing_extensions==4.2.0
+urllib3==1.26.9
+validators==0.20.0
+vispy==0.10.0
 wcwidth==0.2.5
 webencodings==0.5.1
-widgetsnbextension==3.5.1
-wrapt==1.12.1
-xarray==0.19.0
+widgetsnbextension==3.6.1
+wrapt==1.14.1
+xarray==2022.3.0
+zipp==3.8.0