[MRG] MNT Include all pxd files in the package #15626

jeremiedbb · 2019-11-14T16:32:14Z

Alternative to #14896

We can specify, in the top level setup, the files that need to be included in the package. (in combination to manifest.in but .pxd are already included in it).

I just tested it and it works:

conda create -n tmp python=3.7 pip numpy scipy cython
git clean -xdf
python setup.py sdist
pip install dist/scikit-learn-0.22.dev0.tar.gz

then
find /path/to/conda/envs/tmp/lib/python3.7/site-packages/sklearn/ -name '*.pxd'
shows all 17 .pxd files as in the sklearn repo.

@rth @ogrisel @jnothman @adrinjalali @realead

ogrisel

I like the simplicity of this solution better. Let's assume that package_data is properly tested.

rth

I'm happy with this solution as well (I have not double-checked that it works as expected).

Can we just recognize the contribution of the author in #14896 in some way? Either by merging part of their validation script under maint_tools in that PR, or by adding them a co-author to this PR (I think adding Signed-off-by: to the final commit message would do it). They did significant work on this, and didn't receive much timely feedback..

jeremiedbb · 2019-11-14T17:17:50Z

or by adding them a co-author to this PR (I think adding Signed-off-by: to the final commit message would do it

Of course. I opened this PR because I was reviewing his PR and found a simpler method by chance.

I don't think the validation script is necessary. It's the role of setuptools to test that package_data works.

ogrisel · 2019-11-14T17:31:53Z

We could have a bit of bash script that checks the content of a generated sdist tarball as a CI job. I also think we should change at least one of our CI jobs to build and install from the sdist tarball and run the tests on the installed scikit-learn in a new empty env using the pytest --pyargs sklearn pattern.

But this can be done in a later PR.

realead · 2019-11-14T18:52:23Z

There is my reasoning why I didn't opt for this solution:

Having a pxd doesn't mean you can use it/cimport it, for example because of https://github.com/scikit-learn/scikit-learn/blob/master/sklearn/svm/_libsvm.pxd#L42 _libsvm.pxd cannot be cimported/used: libsvm_helper.c is missing in the installation (but this is not the only problem).

It is not enough to tests that a pxd-file is present in the installation - one must really tests that an extension using it gets compiled/linked/loaded (see _libsvm.pxd as a problematic example) - the script in maint_tool checks exactly this.

Thus, I opted to include only pxd-files which really can be used when installed, and skipped others.

However, IMO using package_data is a good idea, if one checks that all pxd-files can be cimported/used (and not only whether they are present) and fixes the cases for which pxd-files don't work (which was a too large change for me).

jeremiedbb · 2019-11-15T09:58:14Z

Can someone remind me why we want the .pxd files in the installed package ? @rth ?
They are all part of the private api, so my understanding is we include them but provide no support and no guaranty for their use. Am I wrong ?
Under that perspective, I don't think we need to test that they all can be used by third party libraries.

jeremiedbb · 2019-11-15T09:59:59Z

We could have a bit of bash script that checks the content of a generated sdist tarball as a CI job.

@ogrisel they are already in the sdist (otherwise pip install could not build sklearn), what this pr does and what could be tested is that they are in the installed package.

jeremiedbb · 2019-11-15T10:04:21Z

_libsvm.pxd cannot be cimported/used: libsvm_helper.c is missing in the installation (but this is not the only problem).

We could include the .c and .h files as well ?

NicolasHug · 2019-11-15T17:13:12Z

Can someone remind me why we want the .pxd files in the installed package ? @rth ?

I assume it's for people to be able to use scikit-learn's private API in their own scripts without having to download the source? Sort of like a -dev linux package.
But if we do that, I agree it would make sense to also include any .c or .h that isn't generated by Cython, else only some parts of scikit-learn can be built.

I think I like this solution too. Worst case scenario, the installed package contains .pxd that cannot actually be used... which is OK right?

Can we just recognize the contribution of the author in #14896 in some way?

+1. We can add a what's new entry crediting both this PR and the former one.

realead · 2019-11-19T20:52:45Z

@jeremiedbb

We could include the .c and .h files as well ?

That is true, but usually one just would like to write "cimport xxxx" without hunting all dependencies down.

numpy.pxd is a little bit different, but at least there is np.get_includes().

After thinking about it, probably _libsvm.pxd and _liblinear.pxd should be actually pxi-files and not pxd-files.

jeremiedbb · 2019-11-20T16:49:55Z

After thinking about it, probably _libsvm.pxd and _liblinear.pxd should be actually pxi-files and not pxd-files.

Indeed (although not mandatory). I renamed those files. Should be ok since it's private now. Thus they won't be included in the install

@realead I added a test to check that all pxd files included in the installation directory can be cimported. It's inspired from your test but a bit simpler because I don't check that all pxd files from the repo are actually in the install. Let me know what you think about it.

realead · 2019-11-21T10:34:37Z

@jeremiedbb looks good to me! I think we can assume setuptools will collect all *.pxd correctly.

ogrisel

I like the idea of a centralized Cython check. Here are a few cosmetic suggestions but feel free to ignore them ;)

ogrisel · 2019-11-21T15:22:21Z

maint_tools/check_pxd_in_installation.py

+        with open('tst.pyx', 'w') as f:
+            for file in pxd_files:
+                to_import = file.replace(os.path.sep, '.')


nipick: file -> pxd_file to avoid shadowing the file built-in type in the globals namespace.

ogrisel · 2019-11-21T15:23:52Z

maint_tools/check_pxd_in_installation.py

+                       check=True)
+
+    except subprocess.CalledProcessError:
+        raise


Why do you need this except clause? Just a try / finally construct would work fine, no?

But actually we can get rid of the try / finally if you remove the os.chdir calls.

ogrisel · 2019-11-21T16:18:47Z

maint_tools/check_pxd_in_installation.py

+
+with tempfile.TemporaryDirectory() as tmpdir:
+    try:
+        os.chdir(tmpdir)


I would avoid os.chdir and instead:

with open(tmpdir.name +os.path.sep + 'tst.pyx', 'w') as f: ... setup_path = tmpdir.name + os.path.sep + "setup_tst.py"

and then:

subprocess.run(["python", setup_path, "build_ext", "-i"], check=True, cwd=tmpdir.name)

ogrisel · 2019-11-21T16:20:01Z

sklearn/utils/_weight_vector.pxd

-cdef extern from "math.h":
-    cdef extern double sqrt(double x)
-
-


nice catch!

ogrisel · 2019-11-21T16:22:16Z

maint_tools/check_pxd_in_installation.py

+
+
+skl_dir = sys.argv[1]
+skl_dir = os.path.abspath(skl_dir)


Nitpick, let's use a oneliner with with a more explicit variable name:

Suggested change

skl_dir = os.path.abspath(skl_dir)

sklearn_dir = os.path.abspath(sys.argv[1])

ogrisel · 2019-11-21T16:30:51Z

maint_tools/check_pxd_in_installation.py

+skl_dir = os.path.abspath(skl_dir)
+
+# find all .pxd files
+pxd_files = glob.glob(os.path.join(skl_dir, '**', '*.pxd'), recursive=True)


By the way for this kind of helper maintenance script we could use recent feature of Python 3.6+ such as pathlib:

import pathlib tmpdir = pathlib.Path(tmpdir.name) setup_path = tmpdir / "setup.py" sklearn_dir = pathlib.Path(sys.argv[1]) pxd_files = sklearn_dir.glob("**/*.pxd") print("> Found pxd files:") for pxd_file in pxd_files: print(' -', str(pxd_file)) ...

adrinjalali · 2019-11-25T11:18:15Z

Is this ready to be merged now? I can't give a review, but it'd be nice to have in the RC3 (working on it now).

jeremiedbb · 2019-11-25T12:48:15Z

I addressed all comments from @ogrisel so I guess it should be good to go

jnothman

Should this be run by CI? If it's costly, it can go into the wheel build

jeremiedbb · 2019-11-26T11:35:56Z

If it's costly, it can go into the wheel build

It's not costly at all (takes a few seconds) but its goal is to be run on scikit-learn installed from source distribution. it could be interesting to generate the sdist and install from that in one of the ci jobs however.

adrinjalali · 2019-11-26T12:37:13Z

Can we merge this, have in the RC, and do the CI later?

jeremiedbb · 2019-11-26T12:48:28Z

Ok for me

* include all pxd files in package * _libsvm _liblinear to pxi + add a test * simplify stuff + use pathlib * cln * more cln

include all pxd files in package

6772684

jeremiedbb added this to the 0.22 milestone Nov 14, 2019

ogrisel approved these changes Nov 14, 2019

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rth approved these changes Nov 14, 2019

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jeremiedbb added 2 commits November 20, 2019 13:58

Merge branch 'master' into include-pxd-files

8b7272c

_libsvm _liblinear to pxi + add a test

4c86cd8

ogrisel approved these changes Nov 21, 2019

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jeremiedbb added 3 commits November 22, 2019 17:21

simplify stuff + use pathlib

6d713da

cln

7eb0355

more cln

a0d2046

This was referenced Nov 25, 2019

Release 0.22rc3 #15714

Closed

Release 0.22rc3 #15715

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jnothman approved these changes Nov 25, 2019

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adrinjalali merged commit 9e5819a into scikit-learn:master Nov 26, 2019

jnothman pushed a commit that referenced this pull request Nov 28, 2019

MNT Include all pxd files in the package (#15626)

5fab501

* include all pxd files in package * _libsvm _liblinear to pxi + add a test * simplify stuff + use pathlib * cln * more cln

panpiort8 pushed a commit to panpiort8/scikit-learn that referenced this pull request Mar 3, 2020

MNT Include all pxd files in the package (scikit-learn#15626)

b31cab4

* include all pxd files in package * _libsvm _liblinear to pxi + add a test * simplify stuff + use pathlib * cln * more cln

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[MRG] MNT Include all pxd files in the package #15626

[MRG] MNT Include all pxd files in the package #15626

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	skl_dir = os.path.abspath(skl_dir)
	sklearn_dir = os.path.abspath(sys.argv[1])

[MRG] MNT Include all pxd files in the package #15626

[MRG] MNT Include all pxd files in the package #15626

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