BLD Update Cython minimum version to `0.29.33` #25342

jjerphan · 2023-01-09T15:45:31Z

Reference Issues/PRs

What does this implement/fix? Explain your changes.

This makes sure we use the latest stable version of Cython which brings support for const fused-typed memoryviews. This supports easing maintenance, improving the transparency of implementations' support for read-only buffers, and allowing using a newer set of interfaces for NumPy C API.

lesteve · 2023-01-09T16:11:29Z

I think you need to update all the lock files by running python build_tools/update_environments_and_lock_files.py

jjerphan · 2023-01-10T11:06:25Z

Hum, some specifications' resolution with pip (e.g. the one of pylatest_pip_openblas_pandas or the one of pylatest_pip_scipy_dev) are not terminating (or are taking a long time to terminate on my machine). Poetry looks stuck resolving PyPi packages' versions. 🤔

ogrisel · 2023-01-10T11:23:06Z

@lesteve I can reproduce the problem with the resolution of pylatest_pip_openblas_pandas which is extremely slow (infinite?). This is weird because this is a build with very few constraints.

It's independent of the Cython min version change in this PR since it also happens on main.

Furthermore it's weird to have a build env named pylatest_* with an explicit "python": "3.9" constraint.

jjerphan · 2023-01-10T13:19:29Z

I've tried removing this constraints on main and regenerating the conda lock files, but it still blocks.

Extracted step with debug mode for logging

conda-lock lock --mamba \
                --log-level=DEBUG \
                --kind explicit \
                --platform linux-64 \
                --file build_tools/azure/pylatest_pip_openblas_pandas_environment.yml \
                --filename-template build_tools/azure/pylatest_pip_openblas_pandas_linux-64_conda.lock

DEBUG:conda_lock.virtual_package:Wrote fake repodata to /tmp/tmpvnsti348
DEBUG:conda_lock.virtual_package:/tmp/tmpvnsti348/
DEBUG:conda_lock.virtual_package:/tmp/tmpvnsti348/win-64
DEBUG:conda_lock.virtual_package:/tmp/tmpvnsti348/win-64/repodata.json
DEBUG:conda_lock.virtual_package:/tmp/tmpvnsti348/osx-arm64
DEBUG:conda_lock.virtual_package:/tmp/tmpvnsti348/osx-arm64/repodata.json
DEBUG:conda_lock.virtual_package:/tmp/tmpvnsti348/osx-64
DEBUG:conda_lock.virtual_package:/tmp/tmpvnsti348/osx-64/repodata.json
DEBUG:conda_lock.virtual_package:/tmp/tmpvnsti348/noarch
DEBUG:conda_lock.virtual_package:/tmp/tmpvnsti348/noarch/repodata.json
DEBUG:conda_lock.virtual_package:/tmp/tmpvnsti348/linux-ppc64le
DEBUG:conda_lock.virtual_package:/tmp/tmpvnsti348/linux-ppc64le/repodata.json
DEBUG:conda_lock.virtual_package:/tmp/tmpvnsti348/linux-aarch64
DEBUG:conda_lock.virtual_package:/tmp/tmpvnsti348/linux-aarch64/repodata.json
DEBUG:conda_lock.virtual_package:/tmp/tmpvnsti348/linux-64
DEBUG:conda_lock.virtual_package:/tmp/tmpvnsti348/linux-64/repodata.json
DEBUG:conda_lock.virtual_package:repo: file:///tmp/tmpvnsti348
DEBUG:urllib3.connectionpool:Starting new HTTPS connection (1): raw.githubusercontent.com:443
DEBUG:urllib3.connectionpool:https://raw.githubusercontent.com:443 "GET /regro/cf-graph-countyfair/master/mappings/pypi/grayskull_pypi_mapping.yaml HTTP/1.1" 200 141700
Locking dependencies for ['linux-64']...
INFO:conda_lock.conda_solver:linux-64 using specs ['python', 'ccache', 'pip *']
DEBUG:root:dry_run_install:
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DEBUG:conda_lock._vendor.poetry.repositories.pypi_repository:<debug>PyPI:</debug> No release information found for scikit-image-0.9.2, skipping
DEBUG:conda_lock._vendor.poetry.repositories.pypi_repository:<debug>PyPI:</debug> 36 packages found for scikit-image *
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DEBUG:conda_lock._vendor.poetry.repositories.pypi_repository:<debug>PyPI:</debug> 67 packages found for coverage *
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DEBUG:conda_lock._vendor.poetry.repositories.pypi_repository:<debug>PyPI:</debug> 93 packages found for numpy *
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DEBUG:conda_lock._vendor.poetry.repositories.pypi_repository:<debug>PyPI:</debug> 3 packages found for imagesize >=1.3
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DEBUG:conda_lock._vendor.poetry.repositories.pypi_repository:<debug>PyPI:</debug> 7 packages found for babel >=2.9
DEBUG:conda_lock._vendor.poetry.repositories.pypi_repository:<debug>PyPI:</debug> 3 packages found for snowballstemmer >=2.0
DEBUG:conda_lock._vendor.poetry.repositories.pypi_repository:<debug>PyPI:</debug> 3 packages found for docutils >=0.18,<0.20
DEBUG:conda_lock._vendor.poetry.repositories.pypi_repository:<debug>PyPI:</debug> 2 packages found for pygments >=2.13
DEBUG:conda_lock._vendor.poetry.repositories.pypi_repository:<debug>PyPI:</debug> 4 packages found for sphinxcontrib-qthelp *
DEBUG:conda_lock._vendor.poetry.repositories.pypi_repository:<debug>PyPI:</debug> 1 packages found for sphinxcontrib-serializinghtml >=1.1.5
DEBUG:conda_lock._vendor.poetry.repositories.pypi_repository:<debug>PyPI:</debug> 1 packages found for sphinxcontrib-htmlhelp >=2.0.0
DEBUG:conda_lock._vendor.poetry.repositories.pypi_repository:<debug>PyPI:</debug> 2 packages found for sphinxcontrib-jsmath *
DEBUG:conda_lock._vendor.poetry.repositories.pypi_repository:<debug>PyPI:</debug> 3 packages found for sphinxcontrib-devhelp *
DEBUG:conda_lock._vendor.poetry.repositories.pypi_repository:<debug>PyPI:</debug> 4 packages found for sphinxcontrib-applehelp *

pylatest_pip_openblas_pandas_environment specification

cat build_tools/azure/pylatest_pip_openblas_pandas_environment.yml

# DO NOT EDIT: this file is generated from the specification found in the
# following script to centralize the configuration for CI builds:
# build_tools/update_environments_and_lock_files.py
channels:
  - defaults
dependencies:
  - python
  - ccache
  - pip
  - pip:
    - numpy
    - scipy
    - cython
    - joblib
    - threadpoolctl
    - matplotlib
    - pandas
    - pyamg
    - pytest
    - pytest-xdist==2.5.0
    - pillow
    - codecov
    - pytest-cov
    - coverage
    - sphinx
    - numpydoc
    - lightgbm
    - scikit-image

lesteve · 2023-01-10T13:24:10Z

Not sure what is happening about conda-lock stalling, for now this is where I am at, I can reproduce with only sphinxcontrib-applehelp in the pip section:

conda-lock lock --log-level DEBUG -f environment.yml -p linux-64

channels:
  - conda-forge
dependencies:
  - python
  - pip
  - pip:
    - sphinxcontrib-applehelp

Not sure what is wrong here and what has changed since last time it worked, I tried pinning sphinxcontrib-applehelp and sphinx to previous versions but that is not enough apparently.

lesteve · 2023-01-11T10:49:30Z

I have opened an issue in conda-lock conda/conda-lock#309

lesteve · 2023-01-11T15:06:19Z

I have opened #25361 to update lock files by installing sphinx with conda to work-around the issue.

…nto dev/use-cython-geq-0.29.33

lesteve · 2023-01-11T16:49:06Z

I merged main to have the work-around from #25361 and pushed an update of the lock files.

jjerphan · 2023-01-12T07:55:54Z

The update has not been applied to all the lock files to take cython>=0.29.33 into account.

Should we enforce this constraint (temporarily) somewhere, e.g. with cython>=0.29.33 or cython==0.29.33 as a default package constraint?

scikit-learn/build_tools/update_environments_and_lock_files.py

Lines 75 to 79 in aca0326

    
           default_package_constraints = { 
        
               # XXX: pin pytest-xdist to workaround: 
        
               # https://github.com/pytest-dev/pytest-xdist/issues/840 
        
               "pytest-xdist": "2.5.0", 
        
           }

lesteve · 2023-01-12T09:21:01Z

It actually seems like cython 0.29.33 does not satisfy some constraints for the environments that don't have it.

E.g. on Linux cython 0.29.33 is not available in the defaults channel:

❯ mamba create -n test -c defaults --override-channels python=3.8 cython=0.29.33

Encountered problems while solving:
  - nothing provides requested cython 0.29.33**

Simplest thing I can think of for this environment is to install it with pip ...

The other problematic environment is the no-openmp one and maybe this is a good excuse to tackle #24694.

jjerphan · 2023-01-12T09:46:05Z

Cython 0.29.33 is available on conda-forge.

Should we use conda-forge rather than the defaults for channels?

lesteve · 2023-01-12T09:58:36Z

Should we use conda-forge rather than the defaults for channels?

Fine with this, IIRC at one point the consensus was to keep at least one build with the defaults channel to check that it still works (a significant portion of users may use the defaults conda channel) but that all the others could move to conda-forge (could not find an issue to link with in our issue tracker in less than 5 minutes)

If we go this direction, we will need to change the name of the environment and lock files (and maybe the build name in the Azure .yml for consistency?)

jjerphan · 2023-01-12T10:06:53Z

Since Cython is a compile dependency, the ideal would be to only resolve Cython using conda-forge and keep the rest unchanged. Do you think this is possible?

lesteve · 2023-01-12T10:22:19Z

Probably not, if we think this is important to minimise changes, using pip to install cython seems the easiest change.

Also maybe in a few days/weeks, the latest cython will be available on the defaults channel who knows ...

Edit: cython 0.29.32 it was uploaded on September 20 on conda-forge and October 25 on the defaults channel so may need to wait a bit.

jjerphan · 2023-01-12T13:45:52Z

I am fine waiting for cython 0.29.33 to be released on the defaults channel.

glemaitre · 2023-01-14T11:22:21Z

We can also try to push asking for an update on this issue tracker: https://github.com/ContinuumIO/anaconda-issues

jjerphan · 2023-01-16T08:15:20Z

Updating conda-lock from 1.2.1 to 1.3.0 allows resolving all the environements.
#25404 has been opened for this update.

…0.29.33

jjerphan · 2023-01-16T13:53:30Z

We can also try to push asking for an update on this issue tracker: ContinuumIO/anaconda-issues

ContinuumIO/anaconda-issues#13120 has been opened accordingly.

Co-authored-by: Loïc Estève <loic.esteve@ymail.com>

lesteve

LGTM

ogrisel

LGTM as well. Thanks!

jjerphan · 2023-01-18T16:12:43Z

Thank you! On the road for cleaner, cleaner and more efficient implementations.

Co-authored-by: Loïc Estève <loic.esteve@ymail.com>

DEV Update Cython minimum version to 0.29.33

60a2959

jjerphan added Build / CI No Changelog Needed cython labels Jan 9, 2023

jjerphan mentioned this pull request Jan 9, 2023

Increase minimum Cython version to 0.29.33 #25322

Closed

jjerphan mentioned this pull request Jan 10, 2023

FIX Better support large or read-only datasets in decomposition.DictionaryLearning #25172

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lesteve mentioned this pull request Jan 11, 2023

sphinx in environment.yml pip section make poetry solver run forever (seems solved with poetry 1.2) conda/conda-lock#309

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lesteve mentioned this pull request Jan 11, 2023

MNT update lock files #25361

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lesteve added 2 commits January 11, 2023 17:39

Merge branch 'main' of https://github.com/scikit-learn/scikit-learn i…

0942508

…nto dev/use-cython-geq-0.29.33

Update lock files

e71a1c6

jjerphan mentioned this pull request Jan 16, 2023

CI Update conda-lock from 1.2.1 to 1.3.0 #25404

Merged

Merge remote-tracking branch 'upstream/main' into dev/use-cython-geq-…

cee7f8c

…0.29.33

jjerphan added the Quick Review For PRs that are quick to review label Jan 16, 2023

jjerphan removed the Quick Review For PRs that are quick to review label Jan 16, 2023

jjerphan mentioned this pull request Jan 16, 2023

Publish cython==0.29.33 on the main channel for linux-64, linux-aarch64, noarch, osx-64, osx-arm64 and win-64 ContinuumIO/anaconda-issues#13120

Closed

4 tasks

jjerphan mentioned this pull request Jan 16, 2023

Python hangs while exploring a GridSearCV with n_jobs=-1 #17543

Closed

CI Get Cython>=0.29.33 via PyPi instead of conda defaults channel

635ec2e

Co-authored-by: Loïc Estève <loic.esteve@ymail.com>

lesteve approved these changes Jan 18, 2023

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ogrisel approved these changes Jan 18, 2023

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ogrisel merged commit 5f70c44 into scikit-learn:main Jan 18, 2023

jjerphan deleted the dev/use-cython-geq-0.29.33 branch January 18, 2023 16:11

Vincent-Maladiere mentioned this pull request Jan 19, 2023

MAINT Remove -Wcpp warnings when compiling arrayfuncs #25415

Merged

jjerphan added a commit to jjerphan/scikit-learn that referenced this pull request Jan 20, 2023

BLD Update Cython minimum version to 0.29.33 (scikit-learn#25342)

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Co-authored-by: Loïc Estève <loic.esteve@ymail.com>

jjerphan added a commit to jjerphan/scikit-learn that referenced this pull request Jan 20, 2023

BLD Update Cython minimum version to 0.29.33 (scikit-learn#25342)

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Co-authored-by: Loïc Estève <loic.esteve@ymail.com>

jakirkham mentioned this pull request Jan 24, 2023

Release 1.2.1 conda-forge/scikit-learn-feedstock#208

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