Part of #11992.
These were all the things that seemed pretty straight-forward. It's actually a bit bulky but should still be easy to review, hopefully.
LabelPropagation converges much slower than LabelSpreading. The default
of max_iter=30 works well for LabelSpreading but not for
LabelPropagation.
This was extracted from #5893.
* Files for my dev environment with Docker
* Fixing label clamping (alpha=0 for hard clamping)
* Deprecating alpha, fixing its value to zero
* Correct way to deprecate alpha for LabelPropagation
The previous way was breaking the test
sklearn.tests.test_common.test_all_estimators
* Detailed info for LabelSpreading's alpha parameter
Based on the original paper.
* Minor changes in the deprecation message
* Improving "deprecated" doc string and raising DeprecationWarning
* Using a local "alpha" in "fit" to deprecate LabelPropagation's alpha
This solution isn't great, but it sets the correct value for alpha
without violating the restrictions imposed by the tests.
* Removal of my development files
* Using sphinx's "deprecated" tag (jnothman's suggestion)
* Deprecation warning: stating that the alpha's value will be ignored
* Use __init__ with alpha=None
* Update what's new
* Try fix RuntimeWarning in test_alpha_deprecation
* DOC Indent deprecation details
* DOC wording
* Update docs
* Change to the one true implementation.
* Add sanity-checked impl. of Label{Propagation,Spreading}
* Raise ValueError if alpha is invalid in LabelSpreading.
* Add a normalizing step before clamping to LabelPropagation.
* Fix flake8 errors.
* Remove duplicate imports.
* DOC Update What's New.
* Specify alpha's value in the error.
* Tidy up tests.
Add a test and add references, where needed.
* Add comment to non-regression test.
* Fix documentation.
* Move check for alpha into fit from __init__.
* Fix corner case of LabelSpreading with alpha=None.
* alpha -> self.variant
* Make Whats_new more explicit.
* Simplify impl. of Label{Propagation,Spreading}.
* variant -> _variant.
* use less nose.tools import to simplify future transition to activly developing test suites/runners
* assert_equal -> assert_array_equal in test_feature_hasher_pairs_with_string_values
and one missed ImportError that should be replaced with AttributeError
* test for py2.6 compat with except AttributeError
* fix importing of SkipTest
* force using nose in python2.6 for now
* there was no assert_dict_equal in py2.6. but we can use assert_equal
although failed test will look a little bit ugly
* remove nose imports from doc/datasets
Update kneighbors_graph()
Add n_job attribute.
Update Isomap
Add n_job attribute to Isomap.__init__ method.
Conform isomap.py to pep8.
Conform graph.py to pep8.
Update dbscan_.py
Add n_jobs parameter to dbscan function and DBSCAN.__init__ method.
Refactor DBSCAN.__init__ documentation.
Update mean_shift_.py
Add n_jobs parameter to estimate_bandwidth function.
Propagate existing n_jobs parameter in mean_shift to estimate_bandwidth and NearestNeighbors.
Conform mean_shift_.py to pep8.
Conform locally_linear.py to pep8.
Add n_jobs parameter to SpectralClustering.__init__ method.
Add n_jobs parameter to SpectralEmbedding.__init__ method.
Update usage of barycenter_kneighbors_graph function.
Conform spectral_embedding_.py to pep8.
Update label_propagation.py
Conform to pep8.
Refactor imports.
Add n_jobs parameter to LabelSpreading.__init__ method.
Update dbscan function call.
Remove n_jobs argument from dbscan call, as it is already being given by self.get_params().
Add n_jobs parameter to KernelPCA.__init__ method.
Update KernelPCA construction in Isomap.
Remove unnecessary parentesis in isomap.py:211,29.
Update docs: pipeline.rst
Revert "Fix n_jobs usage"
This reverts commit 9480630a69bbb68b01d1176d476222fc665cdd1e.
Fix usage of n_jobs property in Isomap
Passing 1D arrays to check_array, without setting `ensure_2d` to false now
raises a deprecation warning before reshaping it. This will later throw an
error.
All Scaler classes also throw warnings when 1D arrays are passed.
All unit tests/doctests are modified to ensure that no 1D arrays are passed,
except in explicit 1D array tests where the warnings have been silenced.
Additional tests are also included which check for different 1D array cases.
2D array tests with one samples and one features are also added and where
they failed, `check_array` call has been modified to give a more useful error
message
DOC max_iterations -> max_iter. Make it consistent with kmeans
MAINT Replace the deprecated dx parameter with d in the docstrings
MAINT Deprecation warning for max_iterations parameter.
Albert Villanova del Moral
Hanmin Qin