scprep slingshot tests are failing

[scottgigante-immunai]

Describe the bug test_slingshot fails, preventing all PRs from passing

To Reproduce

cd scprep
pytest -v

Expected behavior Passes.

Actual behavior Fails.

``` ====================================================================== ERROR: test_slingshot (test_run.TestSlingshot) ---------------------------------------------------------------------- Traceback (most recent call last): File "/home/runner/work/scprep/scprep/test/test_run.py", line 446, in test_slingshot self.X_pca[:, :2], self.clusters, verbose=False File "/home/runner/work/scprep/scprep/scprep/run/slingshot.py", line 258, in Slingshot rpy_verbose=verbose, 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 in if (is.na(as.numeric(omega))) { : argument is of length zero ====================================================================== ERROR: test_slingshot_errors (test_run.TestSlingshot) ---------------------------------------------------------------------- Traceback (most recent call last): File "/home/runner/work/scprep/scprep/test/test_run.py", line 564, in test_slingshot_errors verbose=False, File "/home/runner/work/scprep/scprep/test/tools/utils.py", line 20, in assert_warns_message return assert_warns_regex(expected_warning, expected_regex, *args, **kwargs) File "/opt/hostedtoolcache/Python/3.7.12/x64/lib/python3.7/unittest/case.py", line 1317, in assertWarnsRegex return context.handle('assertWarnsRegex', args, kwargs) File "/opt/hostedtoolcache/Python/3.7.12/x64/lib/python3.7/unittest/case.py", line 178, in handle callable_obj(*args, **kwargs) File "/home/runner/work/scprep/scprep/scprep/run/slingshot.py", line 258, in Slingshot rpy_verbose=verbose, 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 in if (is.na(as.numeric(omega))) { : argument is of length zero ====================================================================== ERROR: test_slingshot_optional_args (test_run.TestSlingshot) ---------------------------------------------------------------------- Traceback (most recent call last): File "/home/runner/work/scprep/scprep/test/test_run.py", line 513, in test_slingshot_optional_args verbose=False, File "/home/runner/work/scprep/scprep/scprep/run/slingshot.py", line 258, in Slingshot rpy_verbose=verbose, 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 in h(simpleError(msg, call)) : error in evaluating the argument 'X' in selecting a method for function 'lapply': no slot of name "curves" for this object of class "PseudotimeOrdering" ====================================================================== ERROR: test_slingshot_pandas (test_run.TestSlingshot) ---------------------------------------------------------------------- Traceback (most recent call last): File "/home/runner/work/scprep/scprep/test/test_run.py", line 471, in test_slingshot_pandas verbose=False, File "/home/runner/work/scprep/scprep/scprep/run/slingshot.py", line 258, in Slingshot rpy_verbose=verbose, 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 in if (is.na(as.numeric(omega))) { : argument is of length zero ```

scprep version master