Note: T032 not available under Windows

At the moment, T032 is not available under Windows due to a problem with the ClustalO command line call (CalledProcessError). If fixed, we can add T032 back to the CI (was dropped in https://github.com/volkamerlab/teachopencadd/pull/278/commits/265ae707cf5902d13c7a50ad2a87a50655dcabdc).

_ teachopencadd\talktorials\T032_compound_activity_proteochemometrics\talktorial.ipynb::Cell 13 _
[gw0] win32 -- Python 3.8.15 C:\Miniconda\envs\teachopencadd\python.exe
Notebook cell execution failed
Cell 13: Cell execution caused an exception

Input:
%%bash -s "$MY_EMAIL"
# ClustalO service requires an email address
# If email was set, run ClustalO service, else use pre-calculated alignments
if [ $1 != "None" ]; then
    echo "Email (MY_EMAIL) was set to "$1
    # Query ClustalO webservice from command line
    python scripts/clustalo.py --email $1 --stype protein --sequence data/sequences.fasta --outfmt fa --outdir data --outfile aligned_sequences --order input --pollFreq 20
else
    echo "Email (MY_EMAIL) was not set; use pre-calculated alignments."
fi

Traceback:

---------------------------------------------------------------------------
CalledProcessError                        Traceback (most recent call last)
Cell In[14], line 1
----> 1 get_ipython().run_cell_magic('bash','-s "$MY_EMAIL"','# ClustalO service requires an email address\n# If email was set, run ClustalO service, else use pre-calculated alignments\nif [ $1 != "None" ]; then\n    echo "Email (MY_EMAIL) was set to "$1\n    # Query ClustalO webservice from command line\n    python scripts/clustalo.py --email $1 --stype protein --sequence data/sequences.fasta --outfmt fa --outdir data --outfile aligned_sequences --order input --pollFreq 20\nelse\n    echo "Email (MY_EMAIL) was not set; use pre-calculated alignments."\nfi\n')

File C:\Miniconda\envs\teachopencadd\lib\site-packages\IPython\core\interactiveshell.py:2417, in InteractiveShell.run_cell_magic(self, magic_name, line, cell)
   2415 with self.builtin_trap:
   2416     args = (magic_arg_s, cell)
-> 2417     result = fn(*args,**kwargs)
   2418 return result

File C:\Miniconda\envs\teachopencadd\lib\site-packages\IPython\core\magics\script.py:153, in ScriptMagics._make_script_magic.<locals>.named_script_magic(line, cell)
    151 else:
    152     line = script
--> 153 return self.shebang(line,cell)

File C:\Miniconda\envs\teachopencadd\lib\site-packages\IPython\core\magics\script.py:305, in ScriptMagics.shebang(self, line, cell)
    300 if args.raise_error and p.returncode != 0:
    301     # If we get here and p.returncode is still None, we must have
    302     # killed it but not yet seen its return code. We don't wait for it,
    303     # in case it's stuck in uninterruptible sleep. -9 = SIGKILL
    304     rc = p.returncode or -9
--> 305     raise CalledProcessError(rc, cell)

CalledProcessError: Command 'b'# ClustalO service requires an email address\n# If email was set, run ClustalO service, else use pre-calculated alignments\nif [ $1 != "None" ]; then\n    echo "Email (MY_EMAIL) was set to "$1\n    # Query ClustalO webservice from command line\n    python scripts/clustalo.py --email $1 --stype protein --sequence data/sequences.fasta --outfmt fa --outdir data --outfile aligned_sequences --order input --pollFreq 20\nelse\n    echo "Email (MY_EMAIL) was not set; use pre-calculated alignments."\nfi\n'' returned non-zero exit status 1.

volkamerlab / teachopencadd

Note: T032 not available under Windows #318