markovmodel / PyEMMA

🚂 Python API for Emma's Markov Model Algorithms 🚂
http://pyemma.org
GNU Lesser General Public License v3.0
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setup.py needs --remote option in git submodule update? #1446

Closed fabian-paul closed 4 years ago

fabian-paul commented 4 years ago

When trying to run python setup.py develop, I get the following errors:

fatal: reference is not a tree: e43e1cc01ae6d4e4e5ba10557a057d7f3d5ece0d
Unable to checkout 'e43e1cc01ae6d4e4e5ba10557a057d7f3d5ece0d' in submodule path 'ext/pybind11'
Traceback (most recent call last):
  File "setup.py", line 331, in <module>
    subprocess.check_call(cmd.format(mod=m).split(' '))
  File "/home/fab/opt/anaconda3/lib/python3.7/subprocess.py", line 347, in check_call
    raise CalledProcessError(retcode, cmd)
subprocess.CalledProcessError: Command '['git', 'submodule', 'update', '--init', 'ext/pybind11']' returned non-zero exit status 1.

Looking into ext/pybind11, I realized that the directory was empty. I fixed this by replacing in the command "git submodule update --init {mod}" in setup.py by "git submodule update --remote --init {mod}"

Can you confirm that this is the correct fix?

clonker commented 4 years ago

On which platform are you? Did you try this from a clean clone? For me everything works as-is.

fabian-paul commented 4 years ago

Yeah, something messed up with my branches. Downloaded a fresh copy of the project,, then the error goes away...