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Prepare v0.3.0: New features and fixes
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Release Notes | ||
------------- | ||
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.. toctree:: | ||
:maxdepth: 2 | ||
:glob: | ||
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release_notes/release_notes_* |
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TACCO 0.3.0 (2024-01-10) | ||
======================== | ||
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Features | ||
-------- | ||
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- :func:`tacco.plots.subplots`: support for changing the dpi and forwarding kwargs to :func:`matplotlib.pyplot.subplots` | ||
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- :func:`tacco.plots.dotplot`: new swap_axes argument | ||
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- :func:`tacco.utils.split_spatial_samples`: more flexible and intuitive reimplementation for spatial splitting samples which can account explicitly for spatial correlations; deprecates the :func:`tacco.utils.spatial_split` function | ||
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- :func:`tacco.tools.setup_orthology_converter`, :func:`tacco.tools.run_orthology_converter`: orthology conversion between species | ||
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- :func:`tacco.get.get_data_from_key`: general getter to retrieve data from an anndata given a data path | ||
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- :func:`tacco.get.get_positions`: support for data paths | ||
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Fixes | ||
-------- | ||
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- :func:`tacco.tools.annotate`: reconstruction_key now honors max_annotation. So :func:`tacco.tools.split_observations` works with reconstruction_key as well. This fixes issue `#9 <https://github.com/simonwm/tacco/issues/9>`__ . | ||
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- :func:`tacco.tools.split_observations`: fixed map_obsm_keys parameter | ||
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- :func:`tacco.plots.significances`: fix using pre-supplied ax, fix not significant annotated but significance colored cells, fix future warning, work for data with enrichment and without depletion | ||
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- :func:`tacco.plots.dotplot`: catch edge case with gene-group combinations without a match in "marks" | ||
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- :func:`tacco.plots.co_occurrence`: fixed bug for multiple anndatas in the input | ||
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- :func:`tacco.plots.co_occurrence_matrix`: fixed bug for restrict_intervals=None | ||
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- :func:`tacco.tools.annotate`: multi_center=1 changed so it now behaves the same as multi_center=0/None, fix FutureWarning from kmeans | ||
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- :func:`tacco.tools.get_contributions`: fix FutureWarning from groupby | ||
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- :func:`tacco.plots.co_occurrence`, :func:`tacco.plots.co_occurrence_matrix`: coocurrence plots now follow the show_only and show_only_center order | ||
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Documentation | ||
------------- | ||
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- Add release notes | ||
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- Add visium example to address `#8 https://github.com/simonwm/tacco/issues/8`__ | ||
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Miscellaneous | ||
------------- | ||
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- Switch from setup.cfg to pyproject.toml | ||
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- Generalization of benchmarking to support conda-forge time | ||
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- Expanded testing | ||
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- Remove duplication in NOTICE.md |
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.. before release, ensure a correct date and version number here and in the name of the release_notes_a.b.c.rst file!!! | ||
.. and remove all the comments here... | ||
TACCO a.b.c (yyyy-mm-dd) | ||
======================== | ||
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.. all sections are optional: remove if empty | ||
.. link to issues/PRs/etc on github where applicable | ||
Features | ||
-------- | ||
.. include new and enhanced features here, as well as significant performance improvements | ||
- Add :func:`tacco.tools.new_func` to do new things. | ||
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- Add :func:`tacco.tools.other_new_func` to implement feature request. | ||
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Fixes | ||
-------- | ||
.. include resolution of bugs and very unintuitive behaviour here | ||
- Fix some issue `#9 <https://github.com/simonwm/tacco/issues/9>`__ | ||
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Documentation | ||
------------- | ||
.. include documentation updates here | ||
- Add example `#8 https://github.com/simonwm/tacco/issues/8`__ | ||
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Miscellaneous | ||
------------- | ||
.. include all the rest here | ||
- Deprecated old functionality | ||
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[build-system] | ||
requires = ["setuptools<=60", "wheel", "setuptools_scm>=6.2"] #for next release: could be relaxed, maybe to >61 | ||
requires = ["setuptools", "wheel", "setuptools_scm"] | ||
build-backend = "setuptools.build_meta" | ||
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[project] | ||
name = "tacco" | ||
description = "TACCO: Transfer of Annotations to Cells and their COmbinations" | ||
authors = [ | ||
{name = "Simon Mages"}, | ||
{name = "Noa Moriel"}, | ||
{name = "Jan Watter"}, | ||
] | ||
maintainers = [ | ||
{name = "Jan Watter", email = "[email protected]"}, | ||
{name = "Simon Mages", email = "[email protected]"}, | ||
] | ||
readme = "README.md" | ||
license = {file = "LICENCE.txt"} | ||
requires-python = ">=3.7" | ||
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classifiers = [ | ||
"License :: OSI Approved :: BSD License", | ||
"Intended Audience :: Developers", | ||
"Intended Audience :: Science/Research", | ||
"Natural Language :: English", | ||
"Programming Language :: Python :: 3", | ||
"Operating System :: OS Independent", | ||
"Topic :: Scientific/Engineering :: Bio-Informatics", | ||
"Topic :: Scientific/Engineering :: Visualization", | ||
] | ||
dynamic = ["version"] | ||
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@@ -31,14 +48,34 @@ dependencies = [ | |
"mkl_service", | ||
"scikit_learn", | ||
"threadpoolctl", | ||
"pyamg" | ||
"pyamg", | ||
] | ||
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[project.urls] | ||
documentation = "https://simonwm.github.io/tacco/index.html" | ||
Source = "https://github.com/simonwm/tacco" | ||
Documentation = "https://simonwm.github.io/tacco/index.html" | ||
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[tool.setuptools_scm] | ||
local_scheme = "no-local-version" | ||
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[tool.setuptools.dynamic] | ||
version = {attr = "tacco.VERSION"} | ||
[project.optional-dependencies] | ||
doc = [ | ||
"sphinx", | ||
"sphinx-rtd-theme", | ||
"pydata-sphinx-theme", | ||
"sphinx-autodoc-typehints", | ||
"nbsphinx", | ||
"ipython", | ||
"jupytext", | ||
"jupyter", | ||
] | ||
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benchmark = ["time"] | ||
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test = ["pytest"] | ||
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[tool.pytest.ini_options] | ||
testpaths = ["tests"] | ||
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[tool.setuptools] | ||
packages = ["tacco"] |
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