[MRG+1] Read-only input data in common tests #4807

arthurmensch · 2015-06-03T08:02:48Z

Following PR #4775, I added checks in estimator checks in order to verify Estimator behavior on read only mem-mapped data.

A few issues there :

registering _clean_temp_memory with atexit yield failure, as it called at the end of every test, and delete _TEMP_MEMORY whereas the next test has already begun.
I overloaded make_blobs into _make_blobs in order to be able to easily yield a read-only memmap X which is only positive. This looks quite messy though.
cf PR [MRG+1] Read-only data compatibility for Lasso #4775, this does not introduce tests that fails on current master, whereas sklearn/linear_model/cd_fast.pyx still raise errors on some use cases. This is related to the fact that we cannot make Lasso fails using simple read-only memmap as input.

amueller · 2015-06-03T14:07:41Z

sklearn/utils/estimator_checks.py

I know that wasn't you, but why is this commented? that seems... odd.. whoops.

never mind, it is fine. just remove the line please.

arthurmensch · 2015-07-01T09:54:09Z

Thanks to the range of check_array in validation.py, Transformer,Estimator,ClassifierandRegressor` are now tested on read only memmap input (I have checked it).

We observe no failure using files cd_fast.c from master, with which an error is raised in test_dict_learning.test_dict_learning_lassocd_readonly_data (see PR#4775)

amueller · 2015-07-01T20:25:23Z

examples/decomposition/plot_image_denoising.py

Is that on purpose? Why?

Sorry for the noise

GaelVaroquaux · 2015-07-02T09:17:30Z

👍 for merge on my side. I just want you to add the comment on the copy aspect.

Thanks, this is super useful. It may seem to be a detail, but it actually is an important step for scalability.

GaelVaroquaux · 2015-07-02T09:18:12Z

Oops, other TODO: the renaming 'Y' to lowercase :).

arthurmensch · 2015-07-02T09:31:44Z

I rebased this PR so that it does not include changes from PR #4775. Therefore the Y case is now a problem in PR #4775 (sorry i missed your comment on being pragmatic :) )

arthurmensch · 2015-07-03T09:20:28Z

I suspect a glitch in CI... (same problem as nilearn/nilearn#623)

GaelVaroquaux · 2015-07-03T11:39:08Z

Restarted CI => glitch fixed.

ogrisel · 2015-07-03T14:16:56Z

sklearn/utils/validation.py

I wonder if instead we should not do:

1- always use np.asarray here.
2- set array_orig = array at the beginning of the function
3- then at the end of this function, just before returning:

if copy and array is array_orig: array = array.copy()

arthurmensch · 2015-07-06T07:45:51Z

Change in sklearn.utils.validation triggers errors in test_common, mostly due to in place modification of input in fit methods

amueller · 2015-07-11T22:28:10Z

sklearn/utils/estimator_checks.py

blobs are shuffled, right?

arthurmensch · 2015-10-19T13:10:00Z

assert_greater(accuracy_score(y, y_pred), 0.83) fails on AdaBoostClassifier, any idea @ogrisel ?

arthurmensch · 2015-10-20T09:46:43Z

My bad. check_array replaced memory map by array , which is an unwanted behavior that prevent estimator to run out-of-core. This is now fixed with regression test provided. I use np.asarray which transform memory map into arrays but use the provided memory map as the base memory representation. @waterponey is it clearer ?

To sum up these estimators fail on common tests as they have side effects on input X: this should be trivial to fix :

the whole PLS family
Factor analysis
Incremental PCA
NuSVC

Transformers :

KernelCenterer
MaxAbsScaler
MinAbsScaler
RobustScaler
StandardScaler

SkewedChi2Sampler fails on assertion, for a non trivial reason.

I am filling an issue which should be tagged as Easy.

waterponey · 2015-10-20T09:56:33Z

sklearn/utils/validation.py

This is not trivial, I think it might benefits from a bit of explanation.

waterponey · 2015-10-20T16:40:42Z

sklearn/utils/validation.py

I'm not sure but if array is not array_orig but array.base is array_orig and copy = true, shouldn't we create a real copy ?

good remark. I think this should be:

if copy and np.may_share_memory(array, array_orig):

Also I think that might fix the transformer part for the #5481

jnothman · 2017-06-18T15:11:04Z

Should this be labelled "need contributor", @arthurmensch?

raghavrv · 2017-07-16T16:50:36Z

What needs to be done here?

jnothman · 2018-02-04T09:13:14Z

Do we consider this to be blocked by #5481?

jnothman · 2018-02-11T23:50:22Z

Could we wrap this up by bypassing the test on estimators where we expect it to fail, and make it an issue to fix each? @arthurmensch, are you willing to finish it off, or should we find someone else?

lesteve · 2018-02-20T17:15:22Z

FYI I have a (for now) WIP attempt of reviving this PR at #10663.

arthurmensch referenced this pull request in arthurmensch/scikit-learn Jun 3, 2015

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amueller reviewed Jun 3, 2015
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arthurmensch changed the title ~~Read-only input data in common tests~~ [WIP] Read-only input data in common tests Jun 24, 2015

arthurmensch force-pushed the common_test_read_only_improvement branch 2 times, most recently from a6894e4 to b492b44 Compare July 1, 2015 09:36

arthurmensch changed the title ~~[WIP] Read-only input data in common tests~~ [MRG] Read-only input data in common tests Jul 1, 2015

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GaelVaroquaux changed the title ~~[MRG] Read-only input data in common tests~~ [MRG+1] Read-only input data in common tests Jul 2, 2015

arthurmensch force-pushed the common_test_read_only_improvement branch from 2e4776c to 31269f8 Compare July 2, 2015 09:27

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blobs are shuffled, right?

arthurmensch force-pushed the common_test_read_only_improvement branch from e057735 to a664269 Compare October 19, 2015 13:45

Read only input checks in common tests

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arthurmensch force-pushed the common_test_read_only_improvement branch from 610c6a0 to 80ec85a Compare October 20, 2015 09:01

waterponey reviewed Oct 20, 2015
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This is not trivial, I think it might benefits from a bit of explanation.

arthurmensch added 2 commits October 20, 2015 13:25

Cleaning

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arthurmensch mentioned this pull request Oct 20, 2015

Estimators should not try to modify X and y inplace in order to handle readonly memory maps #5481

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waterponey reviewed Oct 20, 2015
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amueller mentioned this pull request Oct 21, 2015

[WIP] Fix read only mmap tests #5507

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arthurmensch added 3 commits October 21, 2015 16:11

FIX may share memory

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FIX may share memory

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arthurmensch mentioned this pull request Dec 11, 2015

ValueError: assignment destination is read-only, when paralleling with n_jobs > 1 #5956

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lesteve added help wanted and removed Need Contributor labels Oct 18, 2017

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lesteve mentioned this pull request Feb 20, 2018

[MRG+1] Read-only memmap input data in common tests #10663

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glemaitre closed this in #10663 Apr 23, 2018

lesteve mentioned this pull request Jun 29, 2018

RFC On the relative harm of cosmetic changes #11336

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glemaitre mentioned this pull request Sep 12, 2024

TST add a few more tests to API checks #29832

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[MRG+1] Read-only input data in common tests #4807

[MRG+1] Read-only input data in common tests #4807

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