KrishnaswamyLab / scprep

A collection of scripts and tools for loading, processing, and handling single cell data.
MIT License
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scprep `install_github` tests are failing #127

Open scottgigante-immunai opened 2 years ago

scottgigante-immunai commented 2 years ago

Describe the bug test_install_github fails, preventing all PRs from passing

To Reproduce

cd scprep
pytest -v

Expected behavior Passes.

Actual behavior Fails.

``` ====================================================================== ERROR: test_run.test_install_github_dependencies_None ---------------------------------------------------------------------- Traceback (most recent call last): File "/home/runner/work/scprep/scprep/test/test_run.py", line 58, in test_install_github_dependencies_None scprep.run.install_github("twitter/AnomalyDetection", verbose=False) File "/home/runner/work/scprep/scprep/scprep/run/r_function.py", line 258, in install_github **kwargs, File "/opt/hostedtoolcache/Python/3.7.12/x64/lib/python3.7/site-packages/decorator.py", line 232, in fun return caller(func, *(extras + args), **kw) File "/home/runner/work/scprep/scprep/scprep/utils.py", line 80, in _with_pkg return fun(*args, **kwargs) File "/home/runner/work/scprep/scprep/scprep/run/r_function.py", line 124, in __call__ robject = self.function(*args, **kwargs) File "/opt/hostedtoolcache/Python/3.7.12/x64/lib/python3.7/site-packages/rpy2/robjects/functions.py", line 199, in __call__ .__call__(*args, **kwargs)) File "/opt/hostedtoolcache/Python/3.7.12/x64/lib/python3.7/site-packages/rpy2/robjects/functions.py", line 125, in __call__ res = super(Function, self).__call__(*new_args, **new_kwargs) File "/opt/hostedtoolcache/Python/3.7.12/x64/lib/python3.7/site-packages/rpy2/rinterface_lib/conversion.py", line 45, in _ cdata = function(*args, **kwargs) File "/opt/hostedtoolcache/Python/3.7.12/x64/lib/python3.7/site-packages/rpy2/rinterface.py", line 680, in __call__ raise embedded.RRuntimeError(_rinterface._geterrmessage()) rpy2.rinterface_lib.embedded.RRuntimeError: Error: Failed to install 'unknown package' from GitHub: cannot open URL 'https://api.github.com/repos/twitter/AnomalyDetection/contents/DESCRIPTION?ref=HEAD' ====================================================================== ERROR: test_run.test_install_github_dependencies_True ---------------------------------------------------------------------- Traceback (most recent call last): File "/home/runner/work/scprep/scprep/test/test_run.py", line 76, in test_install_github_dependencies_True "twitter/AnomalyDetection", verbose=False, dependencies=True File "/home/runner/work/scprep/scprep/scprep/run/r_function.py", line 258, in install_github **kwargs, File "/opt/hostedtoolcache/Python/3.7.12/x64/lib/python3.7/site-packages/decorator.py", line 232, in fun return caller(func, *(extras + args), **kw) File "/home/runner/work/scprep/scprep/scprep/utils.py", line 80, in _with_pkg return fun(*args, **kwargs) File "/home/runner/work/scprep/scprep/scprep/run/r_function.py", line 124, in __call__ robject = self.function(*args, **kwargs) File "/opt/hostedtoolcache/Python/3.7.12/x64/lib/python3.7/site-packages/rpy2/robjects/functions.py", line 199, in __call__ .__call__(*args, **kwargs)) File "/opt/hostedtoolcache/Python/3.7.12/x64/lib/python3.7/site-packages/rpy2/robjects/functions.py", line 125, in __call__ res = super(Function, self).__call__(*new_args, **new_kwargs) File "/opt/hostedtoolcache/Python/3.7.12/x64/lib/python3.7/site-packages/rpy2/rinterface_lib/conversion.py", line 45, in _ cdata = function(*args, **kwargs) File "/opt/hostedtoolcache/Python/3.7.12/x64/lib/python3.7/site-packages/rpy2/rinterface.py", line 680, in __call__ raise embedded.RRuntimeError(_rinterface._geterrmessage()) rpy2.rinterface_lib.embedded.RRuntimeError: Error: Failed to install 'unknown package' from GitHub: cannot open URL 'https://api.github.com/repos/twitter/AnomalyDetection/contents/DESCRIPTION?ref=HEAD' ====================================================================== ERROR: test_run.test_install_github_lib ---------------------------------------------------------------------- Traceback (most recent call last): File "/home/runner/work/scprep/scprep/test/test_run.py", line 47, in test_install_github_lib scprep.run.install_github("twitter/AnomalyDetection", verbose=False) File "/home/runner/work/scprep/scprep/scprep/run/r_function.py", line 258, in install_github **kwargs, File "/opt/hostedtoolcache/Python/3.7.12/x64/lib/python3.7/site-packages/decorator.py", line 232, in fun return caller(func, *(extras + args), **kw) File "/home/runner/work/scprep/scprep/scprep/utils.py", line 80, in _with_pkg return fun(*args, **kwargs) File "/home/runner/work/scprep/scprep/scprep/run/r_function.py", line 124, in __call__ robject = self.function(*args, **kwargs) File "/opt/hostedtoolcache/Python/3.7.12/x64/lib/python3.7/site-packages/rpy2/robjects/functions.py", line 199, in __call__ .__call__(*args, **kwargs)) File "/opt/hostedtoolcache/Python/3.7.12/x64/lib/python3.7/site-packages/rpy2/robjects/functions.py", line 125, in __call__ res = super(Function, self).__call__(*new_args, **new_kwargs) File "/opt/hostedtoolcache/Python/3.7.12/x64/lib/python3.7/site-packages/rpy2/rinterface_lib/conversion.py", line 45, in _ cdata = function(*args, **kwargs) File "/opt/hostedtoolcache/Python/3.7.12/x64/lib/python3.7/site-packages/rpy2/rinterface.py", line 680, in __call__ raise embedded.RRuntimeError(_rinterface._geterrmessage()) rpy2.rinterface_lib.embedded.RRuntimeError: Error: Failed to install 'unknown package' from GitHub: cannot open URL 'https://api.github.com/repos/twitter/AnomalyDetection/contents/DESCRIPTION?ref=HEAD' ```

scprep version master