pip install pulls in obsolete dependency dinopy

[percyfal]

Hi, I'm using phlash in a project where I'm adding it to a virtual environment with pip. Unfortunately, the install fails due to problems with the dependency dinopy. This dependency has been removed (62d71e0) but it is still listed in the PyPI wheels file:

pip download phlash --prefer-binary --no-deps
...
Saved ./phlash-1.0.3-py3-none-any.whl
...

Inspection with less reveals

Metadata-Version: 2.1
Name: phlash
Version: 1.0.3
Summary: Bayesian inference of population size history from recombining sequence data.
Author-Email: Jonathan Terhorst <jonth@umich.edu>
License: MIT
Project-URL: Homepage, https://github.com/jthlab/phlash
Project-URL: Bug reports, https://github.com/jthlab/phlash/issues
Project-URL: Source, https://github.com/jthlab/phlash/
Requires-Python: <4.0,>=3.10
Requires-Dist: blackjax<2.0.0,>=1.1.0
...
Requires-Dist: dinopy>=3.0.0
...
Requires-Dist: nvidia-cuda-nvrtc-cu12>=12.3; extra == "gpu"
Provides-Extra: gpu

Also, this is not the latest phlash version. Could you update the PyPI version to the latest version?

Best,

Per

[percyfal]

Sorry, my bad, dinopy is listed as a dependency for v1.03 - when testing I was installing from source. My problem is then simply that dinopy won't compile and that installing from current main branch does work.

[terhorst]

Thanks for the report! As you noted, we're working on a revised version that removes the dinopy dependency, so this should be a non-issue when we release it in a few weeks. In the meantime, 'pip install git+https://github.com/jthlab/phlash' in a fresh venv works on my machine. What is the error you're getting?

…

On Wed, Jun 4, 2025 at 6:19 AM Per Unneberg ***@***.***> wrote: *percyfal* left a comment (jthlab/phlash#11) <#11 (comment)> Sorry, my bad, dinopy *is* listed as a dependency for v1.03 - when testing I was installing from source. My problem is then simply that dinopy won't compile and that installing from current main branch does work. — Reply to this email directly, view it on GitHub <#11 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAAEOHDCN4R43OUSLEFE7AT3B3BZ5AVCNFSM6AAAAAB6R6XOE6VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDSMZZGQ2TCMZYHA> . You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

[percyfal]

Thanks for the update, and sorry for my confusion. I'm using pixi to manage my dependencies. I can reproduce the error on my laptop by doing

pixi init --format pyproject phlash
cd phlash
pixi add --pypi "phlash[gpu]"

which generates a Cython-related error for dinopy:

Error:   × failed to solve the pypi requirements of 'default' 'linux-64'
  ├─▶ failed to resolve pypi dependencies
  ├─▶ Failed to download and build `dinopy==3.0.0`
  ├─▶ The build backend returned an error
  ╰─▶ Call to `setuptools.build_meta.build_wheel` failed (exit status: 1)

      [stdout]
      Compiling dinopy/processors.pyx because it changed.
      Compiling dinopy/shape.pyx because it changed.
      Compiling dinopy/shaping.pyx because it changed.
      Compiling dinopy/sam_reader.pyx because it changed.
      Compiling dinopy/sam_writer.pyx because it changed.
      Compiling dinopy/sambam.pyx because it changed.
      Compiling dinopy/wrap_sais.pyx because it changed.
      [1/7] Cythonizing dinopy/processors.pyx

      [stderr]

      Error compiling Cython file:
      ------------------------------------------------------------
      ...
              return seq  # Note that we actually modified seq inplace, so strictly
      speaking there's no need to return the reference again
          elif isinstance(seq, str):
              return "".join(random_choice(_iupac_mapping[item]) if item in
      _iupac_mapping else item for item in seq)
          elif isinstance(seq, bytes):
              return bytes([random_choice(_iupac_mapping[item]) if item in
      _iupac_mapping else item for item in seq])
          elif isinstance(seq, (int, long)):
                                     ^
      ------------------------------------------------------------

      dinopy/processors.pyx:649:31: undeclared name not builtin: long
...

So the build error is from a dependency, not phlash itself.

For reference, I can install manually with pip as you suggest (I need the gpu dependencies):

pixi init --format pyproject phlash
cd phlash
pixi add pip
pixi run pip install "phlash[gpu] @ git+https://github.com/jthlab/phlash"
# Alternatively; also works
# pixi add --pypi "phlash[gpu] @ git+https://github.com/jthlab/phlash"

I hadn't figured out the last bit until now but I finally got it 👍

However , activating the venv (pixi shell) and importing plash from python throws this error:

 from numcodecs.blosc import cbuffer_sizes, cbuffer_metainfo
ImportError: cannot import name 'cbuffer_sizes' from 'numcodecs.blosc' (/home/peru/projects/sparrow/phlash/.pixi/envs/default/lib/python3.13/site-packages/numcodecs/blosc.cpython-313-x86_64-linux-gnu.so)

I could open a seperate issue if you want, but I guess this is related to current development efforts.

Thanks!

[percyfal]

FWIW, the last error is related to zarr-developers/zarr-python#2963, solution at zarr-developers/zarr-python#2965.

[terhorst]

@percyfal I believe I've got this fixed. Can you try installing phlash[gpu]==1.0.4 from testpypi and let me know how it goes?

[percyfal]

@terhorst I can confirm it works, thanks!

[terhorst]

Cool, I will push out a new version. Thanks!

PS I haven't forgotten about your other request -- a vacation and some life stuff got in the way. Should have a fix soon!