There are a couple issues (possibly due to dependency version changes?) where, after doing a Conda install with environment.yml and then trying to run Tutorial-Command-Line-Interface-Step_2.py (after running through the Step 1 in the notebook), there is a TypeError:
line 575, in <module>
r_plotLigandClusterGrpWindow(refWindow, int(trgtNode),
~~~^^^^^^^^^^
TypeError: only 0-dimensional arrays can be converted to Python scalars
Running with the Python debugger demonstrates that trgtNode is being set to a one-dimensional single-entry array, which throws a TypeError. To fix this, one can update it to read int(trgtNode[0])
A similar error occurs in line 702, where a TypeError is raised because the dataframe "label" column is set to 0, which is numerical, but pandas cannot cast a numerical column to a string (which is what the command in line 702 does). This can be fixed by changing line 690 to read:
This occurs under Python 3.14.3, Pandas 3.0.1 and Numpy 2.4.3
There are a couple issues (possibly due to dependency version changes?) where, after doing a Conda install with
environment.ymland then trying to runTutorial-Command-Line-Interface-Step_2.py(after running through the Step 1 in the notebook), there is a TypeError:Running with the Python debugger demonstrates that
trgtNodeis being set to a one-dimensional single-entry array, which throws aTypeError. To fix this, one can update it to readint(trgtNode[0])A similar error occurs in line 702, where a TypeError is raised because the dataframe "label" column is set to 0, which is numerical, but pandas cannot cast a numerical column to a string (which is what the command in line 702 does). This can be fixed by changing line 690 to read:
This occurs under Python 3.14.3, Pandas 3.0.1 and Numpy 2.4.3