Example userScript.R fails at generateRawAlignments()

[sumiyaabdi]

The test example code throws an error here. Maybe because in R/main.R this line returns a pandas dataframe which can't be read by nrow in the following lines.

Here is the error:

> output_all <- stringDF %>%
+     generateRawAlignments(
+         regimens = regimens,
+         g = 0.4,
+         Tfac = 0.4,
+         method = "PropDiff",
+         verbose = 0
+     )
Processing patients:   0%|          | 0/4 [00:00<?, ?it/s]/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/ARTEMIS/cython/main.py:26: ChainedAssignmentError: A value is being set on a copy of a DataFrame or Series through chained assignment.
Such chained assignment never works to update the original DataFrame or Series, because the intermediate object on which we are setting values always behaves as a copy (due to Copy-on-Write).

Try using '.loc[row_indexer, col_indexer] = value' instead, to perform the assignment in a single step.

See the documentation for a more detailed explanation: [https://pandas.pydata.org/pandas-docs/stable/user_guide/copy_on_write.html#chained-assignment](vscode-file://vscode-app/Applications/Positron.app/Contents/Resources/app/out/vs/code/electron-browser/workbench/workbench.html#)
  return align_patients_regimens_fast(
Processing patients: 100%|██████████| 4/4 [00:00<00:00, 37.65it/s]
Error in `if (nrow(output) == 0) ...`:
! argument is of length zero
Hide Traceback
    ▆
 1. ├─stringDF %>% ... at [packages/ARTEMIS/userScript.R:59:1](vscode-file://vscode-app/Applications/Positron.app/Contents/Resources/app/out/vs/code/electron-browser/workbench/workbench.html#)
 2. └─ARTEMIS::generateRawAlignments(...)

Some version info:

INSTALLED VERSIONS
------------------
python                : 3.14.3
python-bits           : 64
OS                    : Darwin
OS-release            : 23.6.0
Version               : Darwin Kernel Version 23.6.0: Mon Jul 29 21:14:30 PDT 2024; root:xnu-10063.141.2~1/RELEASE_ARM64_T6000
machine               : arm64
processor             : arm
byteorder             : little
LC_ALL                : None
LANG                  : en_US.UTF-8
LOCALE                : None.UTF-8

pandas                : 3.0.0
numpy                 : 2.4.2
dateutil              : 2.9.0.post0
pip                   : 26.0.1
Cython                : 3.2.4`

[sumiyaabdi]

I added these lines to R/main.R before the line that throws the error. Converts output to a data.frame and that fixed it.

    output = output$to_dict(orient = "list") |> 
      reticulate::py_to_r() |> 
      as.data.frame()