Installation via pip failing due to missing `master` branch in dependency

[henryjburg]

Describe the bug When installing via pip using the example in the README, installation fails when attempting to clone pycisTopic since it attempts to clone the master branch which doesn't exist (I assume it was renamed to main?).

To Reproduce git clone https://github.com/aertslab/scenicplus cd scenicplus pip install -e .

Error output

➜  scenicplus git:(main) pip install -e .
Obtaining file:///Users/henry/scenicplus
  Installing build dependencies ... done
  Checking if build backend supports build_editable ... done
  Getting requirements to build editable ... done
  Installing backend dependencies ... done
  Preparing editable metadata (pyproject.toml) ... done
Collecting pycisTopic@ git+https://github.com/aertslab/pycisTopic@master (from scenicplus==1.0.1.dev8+g1df154c)
  Cloning https://github.com/aertslab/pycisTopic (to revision master) to /private/var/folders/gr/lvdbk_955pb2blnlcsm4kngc0000gp/T/pip-install-wj50ehw7/pycistopic_d1f2594a93b14effbdbb2360b8af878d
  Running command git clone --filter=blob:none --quiet https://github.com/aertslab/pycisTopic /private/var/folders/gr/lvdbk_955pb2blnlcsm4kngc0000gp/T/pip-install-wj50ehw7/pycistopic_d1f2594a93b14effbdbb2360b8af878d
  WARNING: Did not find branch or tag 'master', assuming revision or ref.
  Running command git checkout -q master
  error: pathspec 'master' did not match any file(s) known to git
  error: subprocess-exited-with-error

  × git checkout -q master did not run successfully.
  │ exit code: 1
  ╰─> See above for output.

  note: This error originates from a subprocess, and is likely not a problem with pip.
error: subprocess-exited-with-error

× git checkout -q master did not run successfully.
│ exit code: 1
╰─> See above for output.

note: This error originates from a subprocess, and is likely not a problem with pip.

Expected behavior Installation should proceed without errors, I believe when I was using this about a week ago it was fine.

Version (please complete the following information):

• Python: 3.8
• SCENIC+: latest (commit: 1df154ce6ea93d634a6c2ec88362a473587422eb)
• pycisTopic: latest (commit: e5d5f19c941c7416628a80c846848eb49c3167b9)

Additional context

• I think the default branch was renamed to main in the pycisTopic repo.

[henryjburg]

Changing the line: git+https://github.com/aertslab/pycisTopic@master#egg=pycisTopic to: git+https://github.com/aertslab/pycisTopic@main#egg=pycisTopic in requirements.txt seems to resolve this, but would be good to confirm.

[SeppeDeWinter]

Hi @henryjburg

Yes, that's correct. I forgot to change it. Should be fixed now https://github.com/aertslab/scenicplus/commit/bca365b0a662e10e215e66dfa32f7505e661e25f.

I highly recommend to use the development branch of SCENIC+ though, this will soon become the default code. It's a lot easier to use and a lot more efficient. Tutorials are also online: https://scenicplus.readthedocs.io/en/development/tutorials.html

All the best,

Seppe