Initial Migration to Github Actions #34

seanlaw · 2021-10-31T22:46:21Z

Work-In-Progress. Do not merge!

This is not meant to be comprehensive and takes an initial stab at addressing #31

The Github Actions workflow that is currently being triggered can be viewed here.

TO DO

Generate sdist in addition to wheels (see TravisCI workflow)
Add explicit minimum NumPy build version

seanlaw · 2021-11-08T14:17:51Z

Instead of splitting the frontend/backend, we should just migrate to Github Actions first and have the structure in place to split things post-migration (if necessary).

@louisabraham I'm hoping that you can handle the twine uploading part once this PR gets merged. It'll require changing the last few lines of the github-actions.yml:

pydivsufsort/.github/workflows/github-actions.yml

Lines 71 to 80 in 56264bb

    
                 - name: Upload Builds 
        
                   run: | 
        
                     python -m pip install twine 
        
                     if [ "$RUNNER_OS" == "Linux" ]; then 
        
                       # Replace/remove echo 
        
                       echo "python -m twine upload --skip-existing dist/*" 
        
                     fi 
        
                     # Replace/remove echo 
        
                     echo "python -m twine upload --skip-existing wheelhouse/*.whl" 
        
                   shell: bash

Pierre-Sassoulas · 2021-11-08T15:26:13Z

Regarding the release here's an example of a workflow for it : https://github.com/PyCQA/pylint/blob/main/.github/workflows/release.yml

This will release the package when the release is created in github (tag created then release created by editing the tag description in interface). This can be copy pasted, only the value for:

          TWINE_REPOSITORY: pypi
          TWINE_USERNAME: __token__
          TWINE_PASSWORD: ${{ secrets.PYPI_API_TOKEN }}

needs to be added in the project settings.

seanlaw · 2021-11-08T15:41:43Z

Regarding the release here's an example of a workflow for it : https://github.com/PyCQA/pylint/blob/main/.github/workflows/release.yml

This will release the package when the release is created in github (tag created then release created by editing the tag description in interface). This can be copy pasted, only the value for:
          TWINE_REPOSITORY: pypi
          TWINE_USERNAME: __token__
          TWINE_PASSWORD: ${{ secrets.PYPI_API_TOKEN }}
needs to be added in the project settings.

Thanks @Pierre-Sassoulas.

Frankly, @louisabraham I am not comfortable with handling this step as it will require upping the package version (even for test.pypi). I think this PR should be treated as a proof-of-concept that wheels/sdist and can be built successfully using Github Actions, which I believe is the case (save for correctly choosing the minimum NumPy version support by all platforms). I'll need your help to take it the last mile/meter.

Pierre-Sassoulas · 2021-11-08T15:45:26Z

I am not comfortable with handling this step as it will require upping the package version.

You can test the release by creating an alpha version with a tag: 0.0.5-a0 it won't be recoverable with pip unless users really asks for it with pip install pydivsufsort==0.0.5-a0.

seanlaw · 2021-11-08T15:51:06Z

You can test the release by creating an alpha version with a tag: 0.0.5-a0 it won't be recoverable with pip unless users really asks for it with pip install pydivsufsort==0.0.5-a0.

My comfort level has only ever-so-slightly increased with this knowledge. 😄

@Pierre-Sassoulas Do you think this is something that you can help us with after this PR is merged? I am limited on time and, for this PR, I want to focus on the last major item that will allow us to have stable builds and at least put us in a better position to make progress:

Choose minimum NumPy version available to all platforms/Python versions that we want to support

Pierre-Sassoulas · 2021-11-08T16:00:14Z

I don't have enough time to do it myself but I can help you with it if you have questions. Also I have an example of such a migration: prospector-dev/prospector#427

Pylint also has a coverage job too if you want some inspiration: https://github.com/PyCQA/pylint/blob/main/.github/workflows/ci.yaml#L228

Regarding the minimum numpy version it depends on the deprecation of numpy and of the API you're using I don't know much about numpy nor what you're using. Determining the absolute minimum number might take some time. The lazy bet would be to support what users asks for and do it and test that it works when they do ? (Right now it seems it's numpy 1.19.5 for tensorflow 2.6.0)

seanlaw · 2021-11-08T16:55:59Z

I went through all of the cibuildwheel logs and recorded the minimum NumPy versions that were recognized:

"cp36-manylinux_x86_64 wheel","1.11.3, 1.12.0, 1.12.1, 1.13.0rc1, 1.13.0rc2, 1.13.0, 1.13.1, 1.13.3, 1.14.0rc1, 1.14.0, 1.14.1, 1.14.2, 1.14.3, 1.14.4, 1.14.5, 1.14.6, 1.15.0rc1, 1.15.0rc2, 1.15.0, 1.15.1, 1.15.2, 1.15.3, 1.15.4, 1.16.0rc1, 1.16.0rc2, 1.16.0, 1.16.1, 1.16.2, 1.16.3, 1.16.4, 1.16.5, 1.16.6, 1.17.0rc1, 1.17.0rc2, 1.17.0, 1.17.1, 1.17.2, 1.17.3, 1.17.4, 1.17.5, 1.18.0rc1, 1.18.0, 1.18.1, 1.18.2, 1.18.3, 1.18.4, 1.18.5, 1.19.0rc1, 1.19.0rc2, 1.19.0, 1.19.1, 1.19.2, 1.19.3, 1.19.4, 1.19.5"
"cp37-manylinux_x86_64 wheel","1.14.5, 1.14.6, 1.15.0rc2, 1.15.0, 1.15.1, 1.15.2, 1.15.3, 1.15.4, 1.16.0rc1, 1.16.0rc2, 1.16.0, 1.16.1, 1.16.2, 1.16.3, 1.16.4, 1.16.5, 1.16.6, 1.17.0rc1, 1.17.0rc2, 1.17.0, 1.17.1, 1.17.2, 1.17.3, 1.17.4, 1.17.5, 1.18.0rc1, 1.18.0, 1.18.1, 1.18.2, 1.18.3, 1.18.4, 1.18.5, 1.19.0rc1, 1.19.0rc2, 1.19.0, 1.19.1, 1.19.2, 1.19.3, 1.19.4, 1.19.5, 1.20.0rc1, 1.20.0rc2, 1.20.0, 1.20.1, 1.20.2, 1.20.3, 1.21.0rc1, 1.21.0rc2, 1.21.0, 1.21.1, 1.21.2, 1.21.3, 1.21.4"
"cp38-manylinux_x86_64 wheel","1.17.3, 1.17.4, 1.17.5, 1.18.0rc1, 1.18.0, 1.18.1, 1.18.2, 1.18.3, 1.18.4, 1.18.5, 1.19.0rc1, 1.19.0rc2, 1.19.0, 1.19.1, 1.19.2, 1.19.3, 1.19.4, 1.19.5, 1.20.0rc1, 1.20.0rc2, 1.20.0, 1.20.1, 1.20.2, 1.20.3, 1.21.0rc1, 1.21.0rc2, 1.21.0, 1.21.1, 1.21.2, 1.21.3, 1.21.4"
"cp39-manylinux_x86_64 wheel","1.19.3, 1.19.4, 1.19.5, 1.20.0rc1, 1.20.0rc2, 1.20.0, 1.20.1, 1.20.2, 1.20.3, 1.21.0rc1, 1.21.0rc2, 1.21.0, 1.21.1, 1.21.2, 1.21.3, 1.21.4"
"cp310-manylinux_x86_64 wheel",""
"cp36-manylinux_i686 wheel","1.11.3, 1.12.0, 1.12.1, 1.13.0rc1, 1.13.0rc2, 1.13.0, 1.13.1, 1.13.3, 1.14.0rc1, 1.14.0, 1.14.1, 1.14.2, 1.14.3, 1.14.4, 1.14.5, 1.14.6, 1.15.0rc1, 1.15.0rc2, 1.15.0, 1.15.1, 1.15.2, 1.15.3, 1.15.4, 1.16.0rc1, 1.16.0rc2, 1.16.0, 1.16.1, 1.16.2, 1.16.3, 1.16.4, 1.16.5, 1.16.6, 1.17.0rc1, 1.17.0rc2, 1.17.0, 1.17.1, 1.17.2, 1.17.3, 1.17.4, 1.17.5, 1.18.0rc1, 1.18.0, 1.18.1, 1.18.2, 1.18.3, 1.18.4, 1.18.5, 1.19.0rc1, 1.19.0rc2, 1.19.0, 1.19.1, 1.19.2, 1.19.3, 1.19.4, 1.19.5"
"cp37-manylinux_i686 wheel","1.14.5, 1.14.6, 1.15.0rc2, 1.15.0, 1.15.1, 1.15.2, 1.15.3, 1.15.4, 1.16.0rc1, 1.16.0rc2, 1.16.0, 1.16.1, 1.16.2, 1.16.3, 1.16.4, 1.16.5, 1.16.6, 1.17.0rc1, 1.17.0rc2, 1.17.0, 1.17.1, 1.17.2, 1.17.3, 1.17.4, 1.17.5, 1.18.0rc1, 1.18.0, 1.18.1, 1.18.2, 1.18.3, 1.18.4, 1.18.5, 1.19.0rc1, 1.19.0rc2, 1.19.0, 1.19.1, 1.19.2, 1.19.3, 1.19.4, 1.19.5, 1.20.0rc1, 1.20.0rc2, 1.20.0, 1.20.1, 1.20.2, 1.20.3, 1.21.0rc1, 1.21.0rc2, 1.21.0, 1.21.1, 1.21.2, 1.21.3, 1.21.4"
"cp38-manylinux_i686 wheel","1.17.3, 1.17.4, 1.17.5, 1.18.0rc1, 1.18.0, 1.18.1, 1.18.2, 1.18.3, 1.18.4, 1.18.5, 1.19.0rc1, 1.19.0rc2, 1.19.0, 1.19.1, 1.19.2, 1.19.3, 1.19.4, 1.19.5, 1.20.0rc1, 1.20.0rc2, 1.20.0, 1.20.1, 1.20.2, 1.20.3, 1.21.0rc1, 1.21.0rc2, 1.21.0, 1.21.1, 1.21.2, 1.21.3, 1.21.4"
"cp39-manylinux_i686 wheel","1.19.3, 1.19.4, 1.19.5, 1.20.0rc1, 1.20.0rc2, 1.20.0, 1.20.1, 1.20.2, 1.20.3, 1.21.0rc1, 1.21.0rc2, 1.21.0, 1.21.1, 1.21.2, 1.21.3, 1.21.4"
"cp310-manylinux_i686 wheel",""
"cp36-musllinux_x86_64 wheel",""
"cp37-musllinux_x86_64 wheel",""
"cp38-musllinux_x86_64 wheel",""
"cp39-musllinux_x86_64 wheel",""
"cp310-musllinux_x86_64 wheel",""
"cp36-musllinux_i686 wheel",""
"cp37-musllinux_i686 wheel",""
"cp38-musllinux_i686 wheel",""
"cp39-musllinux_i686 wheel",""
"cp310-musllinux_i686 wheel",""
"cp36-macosx_x86_64 wheel","1.11.3, 1.12.0, 1.12.1, 1.13.0rc1, 1.13.0rc2, 1.13.0, 1.13.1, 1.13.3, 1.14.0rc1, 1.14.0, 1.14.1, 1.14.2, 1.14.3, 1.14.4, 1.14.5, 1.14.6, 1.15.0rc1, 1.15.0rc2, 1.15.0, 1.15.1, 1.15.2, 1.15.3, 1.15.4, 1.16.0rc1, 1.16.0rc2, 1.16.0, 1.16.1, 1.16.2, 1.16.3, 1.16.4, 1.16.5, 1.16.6, 1.17.0rc1, 1.17.0rc2, 1.17.0, 1.17.1, 1.17.2, 1.17.3, 1.17.4, 1.17.5, 1.18.0rc1, 1.18.0, 1.18.1, 1.18.2, 1.18.3, 1.18.4, 1.18.5, 1.19.0rc1, 1.19.0rc2, 1.19.0, 1.19.1, 1.19.2, 1.19.3, 1.19.4, 1.19.5"
"cp37-macosx_x86_64 wheel","1.14.5, 1.14.6, 1.15.0rc2, 1.15.0, 1.15.1, 1.15.2, 1.15.3, 1.15.4, 1.16.0rc1, 1.16.0rc2, 1.16.0, 1.16.1, 1.16.2, 1.16.3, 1.16.4, 1.16.5, 1.16.6, 1.17.0rc1, 1.17.0rc2, 1.17.0, 1.17.1, 1.17.2, 1.17.3, 1.17.4, 1.17.5, 1.18.0rc1, 1.18.0, 1.18.1, 1.18.2, 1.18.3, 1.18.4, 1.18.5, 1.19.0rc1, 1.19.0rc2, 1.19.0, 1.19.1, 1.19.2, 1.19.3, 1.19.4, 1.19.5, 1.20.0rc1, 1.20.0rc2, 1.20.0, 1.20.1, 1.20.2, 1.20.3, 1.21.0rc1, 1.21.0rc2, 1.21.0, 1.21.1, 1.21.2, 1.21.3, 1.21.4"
"cp38-macosx_x86_64 wheel","1.17.3, 1.17.4, 1.17.5, 1.18.0rc1, 1.18.0, 1.18.1, 1.18.2, 1.18.3, 1.18.4, 1.18.5, 1.19.0rc1, 1.19.0rc2, 1.19.0, 1.19.1, 1.19.2, 1.19.3, 1.19.4, 1.19.5, 1.20.0rc1, 1.20.0rc2, 1.20.0, 1.20.1, 1.20.2, 1.20.3, 1.21.0rc1, 1.21.0rc2, 1.21.0, 1.21.1, 1.21.2, 1.21.3, 1.21.4"
"cp39-macosx_x86_64 wheel","1.19.3, 1.19.4, 1.19.5, 1.20.0rc1, 1.20.0rc2, 1.20.0, 1.20.1, 1.20.2, 1.20.3, 1.21.0rc1, 1.21.0rc2, 1.21.0, 1.21.1, 1.21.2, 1.21.3, 1.21.4"
"cp310-macosx_x86_64 wheel","1.21.3, 1.21.4"
"cp36-win32 wheel","1.12.0, 1.12.1, 1.13.0rc1, 1.13.0rc2, 1.13.0, 1.13.1, 1.13.3, 1.14.0rc1, 1.14.0, 1.14.1, 1.14.2, 1.14.3, 1.14.4, 1.14.5, 1.14.6, 1.15.0rc1, 1.15.0rc2, 1.15.0, 1.15.1, 1.15.2, 1.15.3, 1.15.4, 1.16.0rc1, 1.16.0rc2, 1.16.0, 1.16.1, 1.16.2, 1.16.3, 1.16.4, 1.16.5, 1.16.6, 1.17.0rc1, 1.17.0rc2, 1.17.0, 1.17.1, 1.17.2, 1.17.3, 1.17.4, 1.17.5, 1.18.0rc1, 1.18.0, 1.18.1, 1.18.2, 1.18.3, 1.18.4, 1.18.5, 1.19.0rc1, 1.19.0rc2, 1.19.0, 1.19.1, 1.19.2, 1.19.3, 1.19.4, 1.19.5"
"cp36-win_amd64 wheel","1.12.0, 1.12.1, 1.13.0rc1, 1.13.0rc2, 1.13.0, 1.13.1, 1.13.3, 1.14.0rc1, 1.14.0, 1.14.1, 1.14.2, 1.14.3, 1.14.4, 1.14.5, 1.14.6, 1.15.0rc1, 1.15.0rc2, 1.15.0, 1.15.1, 1.15.2, 1.15.3, 1.15.4, 1.16.0rc1, 1.16.0rc2, 1.16.0, 1.16.1, 1.16.2, 1.16.3, 1.16.4, 1.16.5, 1.16.6, 1.17.0rc1, 1.17.0rc2, 1.17.0, 1.17.1, 1.17.2, 1.17.3, 1.17.4, 1.17.5, 1.18.0rc1, 1.18.0, 1.18.1, 1.18.2, 1.18.3, 1.18.4, 1.18.5, 1.19.0rc1, 1.19.0rc2, 1.19.0, 1.19.1, 1.19.2, 1.19.3, 1.19.4, 1.19.5"
"cp37-win32 wheel","1.14.5, 1.14.6, 1.15.0rc2, 1.15.0, 1.15.1, 1.15.2, 1.15.3, 1.15.4, 1.16.0rc1, 1.16.0rc2, 1.16.0, 1.16.1, 1.16.2, 1.16.3, 1.16.4, 1.16.5, 1.16.6, 1.17.0rc1, 1.17.0rc2, 1.17.0, 1.17.1, 1.17.2, 1.17.3, 1.17.4, 1.17.5, 1.18.0rc1, 1.18.0, 1.18.1, 1.18.2, 1.18.3, 1.18.4, 1.18.5, 1.19.0rc1, 1.19.0rc2, 1.19.0, 1.19.1, 1.19.2, 1.19.3, 1.19.4, 1.19.5, 1.20.0rc1, 1.20.0rc2, 1.20.0, 1.20.1, 1.20.2, 1.20.3, 1.21.0rc1, 1.21.0rc2, 1.21.0, 1.21.1, 1.21.2, 1.21.3, 1.21.4"
"cp37-win_amd64 wheel","1.14.5, 1.14.6, 1.15.0rc2, 1.15.0, 1.15.1, 1.15.2, 1.15.3, 1.15.4, 1.16.0rc1, 1.16.0rc2, 1.16.0, 1.16.1, 1.16.2, 1.16.3, 1.16.4, 1.16.5, 1.16.6, 1.17.0rc1, 1.17.0rc2, 1.17.0, 1.17.1, 1.17.2, 1.17.3, 1.17.4, 1.17.5, 1.18.0rc1, 1.18.0, 1.18.1, 1.18.2, 1.18.3, 1.18.4, 1.18.5, 1.19.0rc1, 1.19.0rc2, 1.19.0, 1.19.1, 1.19.2, 1.19.3, 1.19.4, 1.19.5, 1.20.0rc1, 1.20.0rc2, 1.20.0, 1.20.1, 1.20.2, 1.20.3, 1.21.0rc1, 1.21.0rc2, 1.21.0, 1.21.1, 1.21.2, 1.21.3, 1.21.4"
"cp38-win32 wheel","1.17.3, 1.17.4, 1.17.5, 1.18.0rc1, 1.18.0, 1.18.1, 1.18.2, 1.18.3, 1.18.4, 1.18.5, 1.19.0rc1, 1.19.0rc2, 1.19.0, 1.19.1, 1.19.2, 1.19.3, 1.19.4, 1.19.5, 1.20.0rc1, 1.20.0rc2, 1.20.0, 1.20.1, 1.20.2, 1.20.3, 1.21.0rc1, 1.21.0rc2, 1.21.0, 1.21.1, 1.21.2, 1.21.3, 1.21.4"
"cp38-win_amd64 wheel","1.17.3, 1.17.4, 1.17.5, 1.18.0rc1, 1.18.0, 1.18.1, 1.18.2, 1.18.3, 1.18.4, 1.18.5, 1.19.0rc1, 1.19.0rc2, 1.19.0, 1.19.1, 1.19.2, 1.19.3, 1.19.4, 1.19.5, 1.20.0rc1, 1.20.0rc2, 1.20.0, 1.20.1, 1.20.2, 1.20.3, 1.21.0rc1, 1.21.0rc2, 1.21.0, 1.21.1, 1.21.2, 1.21.3, 1.21.4"
"cp39-win32 wheel","1.19.3, 1.19.4, 1.19.5, 1.20.0rc1, 1.20.0rc2, 1.20.0, 1.20.1, 1.20.2, 1.20.3, 1.21.0rc1, 1.21.0rc2, 1.21.0, 1.21.1, 1.21.2, 1.21.3, 1.21.4"
""cp39-win_amd64 wheel,""1.19.3, 1.19.4, 1.19.5, 1.20.0rc1, 1.20.0rc2, 1.20.0, 1.20.1, 1.20.2, 1.20.3, 1.21.0rc1, 1.21.0rc2, 1.21.0, 1.21.1, 1.21.2, 1.21.3, 1.21.4
"cp310-win32 wheel",""
"cp310-win_amd64 wheel","1.21.3, 1.21.4"

seanlaw · 2021-11-09T02:02:59Z

@louisabraham As you can see, there isn't really a "true" minimum version of NumPy that would satisfy all operating systems. Can you please advise on what you'd want me to do?

louisabraham · 2021-11-09T07:52:19Z

Let's do 1.19.5. We can also put instructions for people who get errors so that they can build from source.

…

On Tue, Nov 9, 2021, 03:03 Sean M. Law ***@***.***> wrote: @louisabraham <https://github.com/louisabraham> As you can see, there isn't really a "true" minimum version of NumPy that would satisfy all operating systems. Can you please advise on what you'd want me to do? — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#34 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ADEQQFJM5T6LEK5VL3RSS43ULB6N5ANCNFSM5HCZMXIQ> . Triage notifications on the go with GitHub Mobile for iOS <https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675> or Android <https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub>.

seanlaw · 2021-11-09T12:52:59Z

Let's do 1.19.5

Unfortunately, with numpy==1.19.5, I am still getting the same build error in Github Actions:

E   ValueError: numpy.ndarray size changed, may indicate binary incompatibility. Expected 88 from C header, got 80 from PyObject

I'm trying numpy==1.19 now (without the patch version number) - Update also doesn't work with the same error :(

seanlaw · 2021-11-10T11:50:17Z

@louisabraham I'm encountering the same cibuildwheel issue that you've run into before:

E   OSError: [WinError 193] %1 is not a valid Win32 application

However, in my case (see Github Actions log), after building the cp36-win32 wheel (CPython 3.6 Windows 32bit), I encounter the above error trying to run the unit tests.

I don't know if this is a distraction but, in my Github Actions workflow, I don't have $PLATFORM_OPTION specified, which is referenced in your build.sh file. However, it looked like this environment variable is blank when dealing with win32 (which is wheel referenced above). I have no experience dealing with Windows and I'm hoping that you can provide some guidance here?

louisabraham · 2021-11-10T12:23:48Z

Well I don't have a windows setup anymore so I'm not sure I can efficiently help. Isn't it working now?

I really want to provide binaries for windows as it is one major feature of pydivsufsort compared to other project: provide a one line installation of divsufsort on all platforms.

seanlaw · 2021-11-10T14:21:46Z

Well I don't have a windows setup anymore so I'm not sure I can efficiently help.

Yeah, similarly, I work on a Mac and only have access to Windows via what is available on Github Actions.

Isn't it working now?

The wheels (built with cibuildwheels) seem to work for all of the Linux and MacOS platforms and unit tests all pass. However, for Windows, only amd64 wheels (built with cibuildwheels) are being built correctly with passing tests. I can't seem to build proper wheels for x86 on Github Actions and I'm not sure why it is different from TravisCI.

My hypothesis is that maybe for Github Actions I need to pass the -A win32 flag to cmake when building the wheels for x86 architecture? Whereas, in TravisCI, it was the opposite and we needed to pass in the -A x64 flag to cmake? Any thoughts would be appreciated!

I really want to provide binaries for windows as it is one major feature of pydivsufsort compared to other project: provide a one line installation of divsufsort on all platforms.

In case it matters, I understand and I am not advocating for the removal of Windows support. I just don't have any experience here and am debugging through Github Actions.

Pierre-Sassoulas · 2021-11-10T14:30:38Z

Would it be possible to create an env variable to give to the -A option so it's defined properly for each run?

louisabraham · 2021-11-10T14:43:40Z

Sure but I think the issue is that we are not sure yet about a fix

…

On Wed, Nov 10, 2021, 15:30 Pierre Sassoulas ***@***.***> wrote: Would it be possible to create an env variable to give to the -A option so it's defined properly for each run? — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#34 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ADEQQFJWIFBZC2LXPLKGFS3ULJ6ZRANCNFSM5HCZMXIQ> . Triage notifications on the go with GitHub Mobile for iOS <https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675> or Android <https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub>.

seanlaw · 2021-11-10T14:44:06Z

Would it be possible to create an env variable to give to the -A option so it's defined properly for each run?

@Pierre-Sassoulas That's what I'm thinking as well (and this is what is being done for TravisCI). However, I'm struggling (due to my inexperience) to figure out how I can set the env variable PLATFORM_OPTION="-A win32" for cibuildwheel if and only when it is building the Windows x86 wheels within its container. I couldn't find a cibuildwheel env variable that could tell me what the current architecture is at build time.

seanlaw · 2021-11-10T15:01:23Z

I have posted the question with the cibuildwheel Github Discussions

seanlaw · 2021-11-10T15:44:17Z

I can confirm that setting PLATFORM_OPTION="-A win32" now works for the x86 builds and the unit tests pass! I just need a way to be able to detect when it is x86 or x64 on windows

seanlaw · 2021-11-10T20:16:04Z

Okay, I split the win32 and amd64 windows builds and we now have wheels (passing unit tests) for:

Windows AMD64
  pydivsufsort-0.0.5-cp310-cp310-win_amd64.whl
  pydivsufsort-0.0.5-cp36-cp36m-win_amd64.whl
  pydivsufsort-0.0.5-cp37-cp37m-win_amd64.whl
  pydivsufsort-0.0.5-cp38-cp38-win_amd64.whl
  pydivsufsort-0.0.5-cp39-cp39-win_amd64.whl

Windows x86
  pydivsufsort-0.0.5-cp310-cp310-win32.whl
  pydivsufsort-0.0.5-cp36-cp36m-win32.whl
  pydivsufsort-0.0.5-cp37-cp37m-win32.whl
  pydivsufsort-0.0.5-cp38-cp38-win32.whl
  pydivsufsort-0.0.5-cp39-cp39-win32.whl

MacOSX
  pydivsufsort-0.0.5-cp310-cp310-macosx_10_9_x86_64.whl
  pydivsufsort-0.0.5-cp36-cp36m-macosx_10_9_x86_64.whl
  pydivsufsort-0.0.5-cp37-cp37m-macosx_10_9_x86_64.whl
  pydivsufsort-0.0.5-cp38-cp38-macosx_10_9_x86_64.whl
  pydivsufsort-0.0.5-cp39-cp39-macosx_10_9_x86_64.whl

Linux
  pydivsufsort-0.0.5-cp310-cp310-manylinux_2_12_i686.manylinux2010_i686.whl
  pydivsufsort-0.0.5-cp310-cp310-manylinux_2_12_x86_64.manylinux2010_x86_64.whl
  pydivsufsort-0.0.5-cp310-cp310-musllinux_1_1_i686.whl
  pydivsufsort-0.0.5-cp310-cp310-musllinux_1_1_x86_64.whl
  pydivsufsort-0.0.5-cp36-cp36m-manylinux_2_12_i686.manylinux2010_i686.whl
  pydivsufsort-0.0.5-cp36-cp36m-manylinux_2_12_x86_64.manylinux2010_x86_64.whl
  pydivsufsort-0.0.5-cp36-cp36m-musllinux_1_1_i686.whl
  pydivsufsort-0.0.5-cp36-cp36m-musllinux_1_1_x86_64.whl
  pydivsufsort-0.0.5-cp37-cp37m-manylinux_2_12_i686.manylinux2010_i686.whl
  pydivsufsort-0.0.5-cp37-cp37m-manylinux_2_12_x86_64.manylinux2010_x86_64.whl
  pydivsufsort-0.0.5-cp37-cp37m-musllinux_1_1_i686.whl
  pydivsufsort-0.0.5-cp37-cp37m-musllinux_1_1_x86_64.whl
  pydivsufsort-0.0.5-cp38-cp38-manylinux_2_12_i686.manylinux2010_i686.whl
  pydivsufsort-0.0.5-cp38-cp38-manylinux_2_12_x86_64.manylinux2010_x86_64.whl
  pydivsufsort-0.0.5-cp38-cp38-musllinux_1_1_i686.whl
  pydivsufsort-0.0.5-cp38-cp38-musllinux_1_1_x86_64.whl
  pydivsufsort-0.0.5-cp39-cp39-manylinux_2_12_i686.manylinux2010_i686.whl
  pydivsufsort-0.0.5-cp39-cp39-manylinux_2_12_x86_64.manylinux2010_x86_64.whl
  pydivsufsort-0.0.5-cp39-cp39-musllinux_1_1_i686.whl
  pydivsufsort-0.0.5-cp39-cp39-musllinux_1_1_x86_64.whl

seanlaw · 2021-11-10T20:17:42Z

@louisabraham I think this PR is ready for your review

louisabraham · 2021-11-10T23:00:46Z

That's AWESOME !!!

Thank you so much !!!

There is still the question of M1 binaries but let's wait for a more stable support in CIBW.

I'll have a look at pypi upload

seanlaw · 2021-11-11T01:48:39Z

That's AWESOME !!!
Thank you so much !!!

No, thank you for making this package available! I've enjoyed our collaboration

There is still the question of M1 binaries but let's wait for a more stable support in CIBW.

Agreed

I'll have a look at pypi upload

If you look at this new github-actions.yml file (it's very similar to the .travis.yml file), grep for all of the places where the word twine comes up and those need to be changed accordingly

Also, I didn't get a chance to add the code coverage so I hope that you can take a look. Right now, every PR or commit will trigger this Github Actions workflow so you might want to set up different workflows (i.e., for releases, for checking PRs, etc)

Alexander-Serov · 2021-11-12T12:27:10Z

Thanks, great job guys!

As for numpy version, from what I understood from cython guys answers is that you just need to find the maximal of the minimums for all the platforms of interest. Judging by your log, it is 1.19 if you want to support py39 and up only, or 1.17 for py38+, or 1.14 for py37+ (it is surprising the build with the config I changed to 1.14 failed).

Note also that this is the numpy version you only need for the build. It is not a formal requirement of the package because it just fixes the C interface (according to the answer reposted by @louisabraham )

Alexander-Serov · 2021-11-12T12:28:56Z

Also, I have access to the Windows platform. Let me know what you need to be tested.

seanlaw · 2021-11-12T12:33:06Z

As for numpy version, from what I understood from cython guys answers is that you just need to find the maximal of the minimums for all the platforms of interest. Judging by your log, it is 1.19 if you want to support py39 and up only, or 1.17 for py38+, or 1.14 for py37+ (it is surprising the build with the config I changed to 1.14 failed).

We will allow oldest-supported-numpy to handle this since there are platforms/architectures that have a minimum numpy version of 1.20.x (see #34 (comment)). Using oldest-supported-numpy for building all of our platforms/architectures will lead to the least amount of failures and the maximum compatibility.

Alexander-Serov · 2021-11-12T12:36:01Z

Perfect, thank you! @louisabraham has explained the same thing!
So do I understand it correctly that this is merged and everything is building OK for all platforms? Or do you still need something for x86?

Does this merge close your issue #31 ?

Alexander-Serov · 2021-11-12T12:48:01Z

Are the wheels updated in the repo? Because returning to my original issue #30, the error in my setup is the same with the latest wheels found by pip:

Collecting pydivsufsort>=0.0.5
  Downloading pydivsufsort-0.0.5-cp38-cp38-manylinux_2_12_x86_64.manylinux2010_x86_64.whl (1.4 MB)

ERROR
/usr/local/lib/python3.8/site-packages/pydivsufsort/__init__.py:2: in <module>
    from .stringalg import (
pydivsufsort/stringalg.pyx:1: in init pydivsufsort.stringalg
    ???
E   ValueError: numpy.ndarray size changed, may indicate binary incompatibility. Expected 88 from C header, got 80 from PyObject

seanlaw · 2021-11-12T13:09:44Z

Does this merge close your issue #31 ?

Yes. Manually closed now. Thank you!

Are the wheels updated in the repo? Because returning to my original issue #30, the error in my setup is the same with the latest wheels found by pip:

We have limited this PR for migrating from TravisCI to Github Actions for building our wheels. The final step of uploading the wheels/sdist to PyPI is being tracked in #37.

To answer your question, the new wheels are not available on PyPI yet.

louisabraham · 2021-11-12T14:40:08Z

I have to configure the uploading to PyPI myself. I'll try to find time for this over the WE.

Added back pyproject.toml to branch

0c6f5f8

seanlaw mentioned this pull request Nov 5, 2021

"numpy.ndarray size changed" error when installing pydivsufsort together with tensorflow==2.6.0 #30

Closed

seanlaw added 9 commits November 6, 2021 16:06

Added build of sdist

c3c2131

Removed explicit declaration of python versions for build

43627bf

Only build sdist on Ubuntu

2f03aa6

Added coverage testing

ed1bec3

Minor change

b0b89db

Removed codecov

84823d5

Fixed indenting

fd4f984

Added explicit declaration of bash shell

d3d81ac

Added numpy build version

56264bb

seanlaw changed the title ~~[WIP - Do Not Merge] Separate Build Frontend and Backend~~ [WIP - Do Not Merge] Migrate to Github Actions Nov 8, 2021

seanlaw changed the title ~~[WIP - Do Not Merge] Migrate to Github Actions~~ [WIP - Do Not Merge] Initial Migration to Github Actions Nov 8, 2021

seanlaw mentioned this pull request Nov 8, 2021

Set a lower numpy version for a build #35

Merged

seanlaw added 2 commits November 8, 2021 09:36

Explicitly update pip before build

b619146

Fixed pip syntax

ca46a05

seanlaw added 2 commits November 9, 2021 07:39

Changed min NumPy version to 1.19.5

8ece0de

Removed patch version for NumPy

71f0f01

seanlaw added 2 commits November 9, 2021 09:10

Set NumPy version to 1.18

57f854a

Minor change

e9e6ea9

Skip win32

3a33f58

Skip windows altogether

2ec6f72

Added back win32

091d1ff

seanlaw added 2 commits November 10, 2021 10:06

Check CIBW env variables

6747a5d

Test win32

c709874

seanlaw added 2 commits November 10, 2021 10:49

Check uname

2faa0cc

Split win32 and amd64 builds

cc26e84

seanlaw requested a review from louisabraham November 10, 2021 20:17

louisabraham merged commit 59a2d87 into louisabraham:master Nov 10, 2021

seanlaw changed the title ~~[WIP - Do Not Merge] Initial Migration to Github Actions~~ Initial Migration to Github Actions Nov 12, 2021

seanlaw mentioned this pull request Nov 12, 2021

Initial Migration to Github Actions #31

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