Error when running PC alg (some CSV file)

Hi, As you know, I have installed most of the packages and attempted to run PC alg on sachs as well as fsgnn. I thought I was out of trouble as the R setup looked fine, but when calling the following python3.6 snippet

from cdt.causality.graph.PC import PC

pc = PC(CItest="hsic",method_indep="rcit")
pcgraph = pc.predict(data)

The interpreter spat out the following error message:

pandas/_libs/parsers.pyx in pandas._libs.parsers.TextReader._setup_parser_source()

FileNotFoundError: [Errno 2] File b'/tmp/cdt_pc_0f4d2452-ff3c-4a84-81dd-73ab5b4d474b//result.csv' does not exist: b'/tmp/cdt_pc_0f4d2452-ff3c-4a84-81dd-73ab5b4d474b//result.csv'

Any idea of what this is about?

Regards, A.V

NB: here is the full error printout

--------------------------------------------------------------------
FileNotFoundError                  Traceback (most recent call last)
<ipython-input-50-db1fca6dbddc> in <module>
----> 1 pcgraph = pc.predict(data)

~/progtools/python/virtualenvs/tfcuda/lib/python3.6/site-packages/cdt/causality/graph/model.py in predict(self, df_data, graph, **kwargs)
     61         """
     62         if graph is None:
---> 63             return self.create_graph_from_data(df_data, **kwargs)
     64         elif isinstance(graph, nx.DiGraph):
     65             return self.orient_directed_graph(df_data, graph, **kwargs)

~/progtools/python/virtualenvs/tfcuda/lib/python3.6/site-packages/cdt/causality/graph/PC.py in create_graph_from_data(self, data, **kwargs)
    257         self.arguments['{VERBOSE}'] = str(self.verbose).upper()
    258 
--> 259         results = self._run_pc(data, verbose=self.verbose)
    260 
    261         return nx.relabel_nodes(nx.DiGraph(results),

~/progtools/python/virtualenvs/tfcuda/lib/python3.6/site-packages/cdt/causality/graph/PC.py in _run_pc(self, data, fixedEdges, fixedGaps, verbose)
    300         except Exception as e:
    301             rmtree(run_dir)
--> 302             raise e
    303         except KeyboardInterrupt:
    304             rmtree(run_dir)

~/progtools/python/virtualenvs/tfcuda/lib/python3.6/site-packages/cdt/causality/graph/PC.py in _run_pc(self, data, fixedEdges, fixedGaps, verbose)
    296 
    297             pc_result = launch_R_script("{}/R_templates/pc.R".format(os.path.dirname(os.path.realpath(__file__))),
--> 298                                         self.arguments, output_function=retrieve_result, verbose=verbose)
    299         # Cleanup
    300         except Exception as e:

~/progtools/python/virtualenvs/tfcuda/lib/python3.6/site-packages/cdt/utils/R.py in launch_R_script(template, arguments, output_function, verbose, debug)
    198         if not debug:
    199             rmtree(base_dir)
--> 200         raise e
    201     except KeyboardInterrupt:
    202         if not debug:

~/progtools/python/virtualenvs/tfcuda/lib/python3.6/site-packages/cdt/utils/R.py in launch_R_script(template, arguments, output_function, verbose, debug)
    192                                            stdout=subprocess.DEVNULL, stderr=subprocess.DEVNULL)
    193             process.wait()
--> 194             output = output_function()
    195 
    196     # Cleaning up

~/progtools/python/virtualenvs/tfcuda/lib/python3.6/site-packages/cdt/causality/graph/PC.py in retrieve_result()
    284 
    285         def retrieve_result():
--> 286             return read_csv('{}/result.csv'.format(run_dir), delimiter=',').values
    287 
    288         try:

~/progtools/python/virtualenvs/tfcuda/lib/python3.6/site-packages/pandas/io/parsers.py in parser_f(filepath_or_buffer, sep, delimiter, header, names, index_col, usecols, squeeze, prefix, mangle_dupe_cols, dtype, engine, converters, true_values, false_values, skipinitialspace, skiprows, skipfooter, nrows, na_values, keep_default_na, na_filter, verbose, skip_blank_lines, parse_dates, infer_datetime_format, keep_date_col, date_parser, dayfirst, cache_dates, iterator, chunksize, compression, thousands, decimal, lineterminator, quotechar, quoting, doublequote, escapechar, comment, encoding, dialect, error_bad_lines, warn_bad_lines, delim_whitespace, low_memory, memory_map, float_precision)
    683         )
    684 
--> 685         return _read(filepath_or_buffer, kwds)
    686 
    687     parser_f.__name__ = name

~/progtools/python/virtualenvs/tfcuda/lib/python3.6/site-packages/pandas/io/parsers.py in _read(filepath_or_buffer, kwds)
    455 
    456     # Create the parser.
--> 457     parser = TextFileReader(fp_or_buf, **kwds)
    458 
    459     if chunksize or iterator:

~/progtools/python/virtualenvs/tfcuda/lib/python3.6/site-packages/pandas/io/parsers.py in __init__(self, f, engine, **kwds)
    893             self.options["has_index_names"] = kwds["has_index_names"]
    894 
--> 895         self._make_engine(self.engine)
    896 
    897     def close(self):

~/progtools/python/virtualenvs/tfcuda/lib/python3.6/site-packages/pandas/io/parsers.py in _make_engine(self, engine)
   1133     def _make_engine(self, engine="c"):
   1134         if engine == "c":
-> 1135             self._engine = CParserWrapper(self.f, **self.options)
   1136         else:
   1137             if engine == "python":

~/progtools/python/virtualenvs/tfcuda/lib/python3.6/site-packages/pandas/io/parsers.py in __init__(self, src, **kwds)
   1915         kwds["usecols"] = self.usecols
   1916 
-> 1917         self._reader = parsers.TextReader(src, **kwds)
   1918         self.unnamed_cols = self._reader.unnamed_cols
   1919 

pandas/_libs/parsers.pyx in pandas._libs.parsers.TextReader.__cinit__()

pandas/_libs/parsers.pyx in pandas._libs.parsers.TextReader._setup_parser_source()

FileNotFoundError: [Errno 2] File b'/tmp/cdt_pc_0f4d2452-ff3c-4a84-81dd-73ab5b4d474b//result.csv' does not exist: b'/tmp/cdt_pc_0f4d2452-ff3c-4a84-81dd-73ab5b4d474b//result.csv'

[Diviyan-Kalainathan]

Sorry for the delay. To solve @ArnoVel 's issue, it originates from :

pc = PC(CItest="hsic",method_indep="rcit")

These two options are incompatible. to use RCIT, you should use CItest=‘randomized’. I should change the API to make it simpler to avoid these issues.

[Diviyan-Kalainathan]

It should be much easier to understand, and errors might be avoided in the future 😃