lh3 / minimap2

A versatile pairwise aligner for genomic and spliced nucleotide sequences
https://lh3.github.io/minimap2
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Updating the mappy build system [Help wanted!] #1053

Closed lh3 closed 1 year ago

lh3 commented 1 year ago

Minimap2 currently uses setup.py for build and distributing the mappy Python module. However, with the old system being deprecated, I am unable to update the module at PyPI now. Could someone help? Thanks.

In the past, I was running

python setup.py sdist upload -r pypi

Now on my M1 Mac, I got the following errors (only showing the end of the log):

copying python/mappy.pyx -> mappy-2.25/python
copying python/minimap2.py -> mappy-2.25/python
copying sse2neon/emmintrin.h -> mappy-2.25/sse2neon
Writing mappy-2.25/setup.cfg
creating dist
Creating tar archive
removing 'mappy-2.25' (and everything under it)
running upload
Traceback (most recent call last):
  File "/Users/hli/Dropbox/dev/github/minimap2/setup.py", line 35, in <module>
    setup(
  File "/Users/hli/conda/lib/python3.10/site-packages/setuptools/__init__.py", line 87, in setup
    return distutils.core.setup(**attrs)
  File "/Users/hli/conda/lib/python3.10/site-packages/setuptools/_distutils/core.py", line 185, in setup
    return run_commands(dist)
  File "/Users/hli/conda/lib/python3.10/site-packages/setuptools/_distutils/core.py", line 201, in run_commands
    dist.run_commands()
  File "/Users/hli/conda/lib/python3.10/site-packages/setuptools/_distutils/dist.py", line 969, in run_commands
    self.run_command(cmd)
  File "/Users/hli/conda/lib/python3.10/site-packages/setuptools/dist.py", line 1208, in run_command
    super().run_command(command)
  File "/Users/hli/conda/lib/python3.10/site-packages/setuptools/_distutils/dist.py", line 988, in run_command
    cmd_obj.run()
  File "/Users/hli/conda/lib/python3.10/site-packages/setuptools/_distutils/command/upload.py", line 72, in run
    self.upload_file(command, pyversion, filename)
  File "/Users/hli/conda/lib/python3.10/site-packages/setuptools/_distutils/command/upload.py", line 81, in upload_file
    raise AssertionError("unsupported schema " + schema)
AssertionError: unsupported schema

PS: I can build and use the mappy module but I am unable to upload the package to PyPI.

lh3 commented 1 year ago

It seems that I can use twine to upload. Close it for now.