PyPI and Anaconda about cellrank HOT 9 CLOSED

Now that #178 is merged, I will focus on this.

from cellrank.

Hi, @flying-sheep,
I'm struggling to put CellRank on testpypi, the main culprit being here: https://github.com/theislab/cellrank/blob/master/setup.py#L42
The problem is this: HTTPError: 400 Client Error: Invalid value for requires_dist. Error: Can't have direct dependency: 'msmtools @ git+git://github.com/msmdev/msmtools@krylov_schur#egg=msmtools' for url: https://test.pypi.org/legacy/
This problem occures when I build bdist_wheel. If I only build sdist, it gets uploaded.
However, after running pip install -i https://test.pypi.org/simple/ cellrank==1.2.3.dev2,
I get the following error and I don't know how to fix it:

Installing build dependencies ... error
  ERROR: Command errored out with exit status 1:
   command: /home/michal/.miniconda3/envs/cellrank/bin/python /home/michal/.miniconda3/envs/cellrank/lib/python3.8/site-packages/pip install --ignore-installed --no-user --prefix /tmp/pip-build-env-ant09w4q/overlay --no-warn-script-location --no-binary :none: --only-binary :none: -i https://test.pypi.org/simple/ -- setuptools setuptools_scm wheel
       cwd: None
  Complete output (3 lines):
  Looking in indexes: https://test.pypi.org/simple/
  ERROR: Could not find a version that satisfies the requirement setuptools (from versions: none)
  ERROR: No matching distribution found for setuptools
  ----------------------------------------
ERROR: Command errored out with exit status 1: /home/michal/.miniconda3/envs/cellrank/bin/python /home/michal/.miniconda3/envs/cellrank/lib/python3.8/site-packages/pip install --ignore-installed --no-user --prefix /tmp/pip-build-env-ant09w4q/overlay --no-warn-script-location --no-binary :none: --only-binary :none: -i https://test.pypi.org/simple/ -- setuptools setuptools_scm wheel Check the logs for full command output.

Here's the full log.

Based on this, I'm not sure if it's even possible to specify dependency that way.
As far as I know, dependency_links could've worked (haven't tried them, they were deprecated).
Other thing I tried is using cmdclass in setup.py, calling pip install <the package>, similar to this, but it always fails with not being able to find pip:

Traceback (most recent call last):
      File "/home/michal/.miniconda3/envs/cellrank/bin/pip", line 7, in <module>
        from pip._internal.cli.main import main
    ModuleNotFoundError: No module named 'pip'

Any help on this would be greatly appreciated!

from cellrank.

In the meantime, I would vote for putting it on pypi without the msmtools dependency, include msmtools it in the installation instructions and initiate a merge of the krylov-schur branch into upstream msmtools.

from cellrank.

We could even let functions/methods default to CFLARE if no msmtools is found and print a message, urging the user to install msmtools...

from cellrank.

@flying-sheep, can you help us with this?

from cellrank.

The reason one can’t have URLs as dependencies is explained in pypa/pip#6301.

One option to solve this is to vendorize it, i.e. bundle the dependency with your package. One advantage is that other packages can depend on the regular version of msmtools while only you see and import from the version you need. This tool could help, I think it’s able to resolve and install from an URL since it uses pip.

The way it works is that you use the CLI command python-vendorize to install the package to a local (git-ignored) directory, and include that directory when building a package for PyPI.

I suggest you use an URL with a commit hash instead of the branch name in the URL. This way when building a package, you always get the same version and not whatever is the newest one at build time.

from cellrank.

@flying-sheep Thanks a lot!
That's what I was afraid of - bundling stuff together, but if it's the only solution, then so be it. There were some issues with docs + tests, but #225 should make it work.

from cellrank.

Done via #225 and later commit. Will create separate issue for Anaconda.

from cellrank.

Amazing, thanks so much.

from cellrank.