Deploy Action fails with ModuleNotFoundError: No module named 'https://github'

[Attol8]

Hi, I have updated my library https://github.com/Attol8/istatapi to use nbdev v2. I keep having a fail in the deploy.yaml github Action. I do not know how to solve this as nbdev_preview works fine locally and also nbdev_prepare.

Specifically I get an error saying ModuleNotFoundError: No module named 'https://github' from nbdev/doclinks.py The error is the following.

Unpacking quarto (1.1.75) ...
Setting up quarto (1.1.75) ...
pandoc -o README.md
  to: gfm+footnotes+tex_math_dollars-yaml_metadata_block
  standalone: true
  default-image-extension: png
  
metadata
  description: Python API wrapper for ISTAT (The Italian National Institute of Statistics)
  title: ISTATAPI
  
Output created: _docs/README.md

Traceback (most recent call last):
  File "/opt/hostedtoolcache/Python/3.10.6/x64/lib/python3.10/site-packages/IPython/core/formatters.py", line 222, in catch_format_error
    r = method(self, *args, **kwargs)
  File "/opt/hostedtoolcache/Python/3.10.6/x64/lib/python3.10/site-packages/IPython/core/formatters.py", line 343, in __call__
    return method()
  File "/opt/hostedtoolcache/Python/3.10.6/x64/lib/python3.10/site-packages/nbdev/showdoc.py", line 166, in _repr_markdown_
    src = NbdevLookup().code(self.fn)
  File "/opt/hostedtoolcache/Python/3.10.6/x64/lib/python3.10/site-packages/nbdev/doclinks.py", line 204, in code
    line = _lineno(sym, py)
  File "/opt/hostedtoolcache/Python/3.10.6/x64/lib/python3.10/site-packages/nbdev/doclinks.py", line 149, in _lineno
    def _lineno(sym, fname): return _get_exps(fname).get(sym.rpartition('.')[2], None) if fname else None
  File "/opt/hostedtoolcache/Python/3.10.6/x64/lib/python3.10/site-packages/nbdev/doclinks.py", line 140, in _get_exps
    mf = _find_mod(mod)
  File "/opt/hostedtoolcache/Python/3.10.6/x64/lib/python3.10/site-packages/nbdev/doclinks.py", line 135, in _find_mod
    loc = Path(importlib.util.find_spec(mp).origin).parent
  File "/opt/hostedtoolcache/Python/3.10.6/x64/lib/python3.10/importlib/util.py", line 94, in find_spec
    parent = __import__(parent_name, fromlist=['__path__'])
ModuleNotFoundError: No module named 'https://github'

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
  File "/opt/hostedtoolcache/Python/3.10.6/x64/bin/nbdev_filter", line 33, in <module>
    sys.exit(load_entry_point('nbdev==2.2.7', 'console_scripts', 'nbdev_filter')())
  File "/opt/hostedtoolcache/Python/3.10.6/x64/lib/python3.10/site-packages/fastcore/script.py", line 117, in _f
    return tfunc(**merge(args, args_from_prog(func, xtra)))
  File "/opt/hostedtoolcache/Python/3.10.6/x64/lib/python3.10/site-packages/nbdev/cli.py", line 64, in nbdev_filter
    with redirect_stdout(dn): filt.nb_proc(nb).process()
  File "/opt/hostedtoolcache/Python/3.10.6/x64/lib/python3.10/site-packages/nbdev/process.py", line 122, in process
    for proc in self.procs: self._proc(proc)
  File "/opt/hostedtoolcache/Python/3.10.6/x64/lib/python3.10/site-packages/nbdev/process.py", line 115, in _proc
    for cell in self.nb.cells: self._process_cell(proc, cell)
  File "/opt/hostedtoolcache/Python/3.10.6/x64/lib/python3.10/site-packages/nbdev/process.py", line 106, in _process_cell
    if callable(proc) and not _is_direc(proc): cell = opt_set(cell, proc(cell))
  File "/opt/hostedtoolcache/Python/3.10.6/x64/lib/python3.10/site-packages/nbdev/processors.py", line 290, in __call__
    if self.k.exc: raise Exception(f"Error{' in notebook: '+title if title else ''} in cell {cell.idx_} :\n{cell.source}") from self.k.exc[1]
Exception: Error in notebook: Base in cell 5 :
#|output: asis
#| echo: false
show_doc(ISTAT)
Error: Process completed with exit code 1.

Can anybody help?

[jph00]

Fixed in master. Will do a release now.

[Attol8]

Thanks Jeremy @jph00 , that was so fast!

I am not sure if you already released it, but I still get another error in the same spot:

AttributeError: 'NoneType' object has no attribute 'origin'

[jph00]

Can you provide a full stack trace and check you've got fastcore and nbdev installed from master?

[jph00]

In the meantime I added a check for this so it shouldn't give an error

[Attol8]

Hi @jph00. I installed nbdev and fastcore from master and I still get the error described above. I believe the error comes from the function show_doc. You can also reproduce it by running this notebook from my library https://github.com/Attol8/istatapi/

Here is the full trace.

---------------------------------------------------------------------------
ModuleNotFoundError                       Traceback (most recent call last)
File ~/anaconda3/lib/python3.9/site-packages/IPython/core/formatters.py:707, in PlainTextFormatter.__call__(self, obj)
    700 stream = StringIO()
    701 printer = pretty.RepresentationPrinter(stream, self.verbose,
    702     self.max_width, self.newline,
    703     max_seq_length=self.max_seq_length,
    704     singleton_pprinters=self.singleton_printers,
    705     type_pprinters=self.type_printers,
    706     deferred_pprinters=self.deferred_printers)
--> 707 printer.pretty(obj)
    708 printer.flush()
    709 return stream.getvalue()

File ~/anaconda3/lib/python3.9/site-packages/IPython/lib/pretty.py:410, in RepresentationPrinter.pretty(self, obj)
    407                         return meth(obj, self, cycle)
    408                 if cls is not object \
    409                         and callable(cls.__dict__.get('__repr__')):
--> 410                     return _repr_pprint(obj, self, cycle)
    412     return _default_pprint(obj, self, cycle)
    413 finally:

File ~/anaconda3/lib/python3.9/site-packages/IPython/lib/pretty.py:778, in _repr_pprint(obj, p, cycle)
    776 """A pprint that just redirects to the normal repr function."""
    777 # Find newlines and replace them with p.break_()
--> 778 output = repr(obj)
    779 lines = output.splitlines()
    780 with p.group():

File ~/anaconda3/lib/python3.9/site-packages/nbdev/showdoc.py:166, in BasicMarkdownRenderer._repr_markdown_(self)
    164 def _repr_markdown_(self):
    165     doc = '---\n\n'
--> 166     src = NbdevLookup().code(self.fn)
    167     if src: doc += _ext_link(src, 'source', 'style="float:right; font-size:smaller"') + '\n\n'
    168     h = '#'*self.title_level

File ~/anaconda3/lib/python3.9/site-packages/nbdev/doclinks.py:204, in NbdevLookup.code(self, sym)
    202 if not isinstance(res, tuple): return None
    203 _,py,gh = res
--> 204 line = _lineno(sym, py)
    205 return f'{gh}#L{line}'

File ~/anaconda3/lib/python3.9/site-packages/nbdev/doclinks.py:149, in _lineno(sym, fname)
--> 149 def _lineno(sym, fname): return _get_exps(fname).get(sym.rpartition('.')[2], None) if fname else None

File ~/anaconda3/lib/python3.9/site-packages/nbdev/doclinks.py:140, in _get_exps(mod)
    138 @lru_cache(None)
    139 def _get_exps(mod):
--> 140     mf = _find_mod(mod)
    141     txt = mf.read_text()
    142     _def_types = ast.FunctionDef,ast.AsyncFunctionDef,ast.ClassDef

File ~/anaconda3/lib/python3.9/site-packages/nbdev/doclinks.py:135, in _find_mod(mod)
    133 def _find_mod(mod):
    134     mp,_,mr = mod.rpartition('/')
--> 135     loc = Path(importlib.util.find_spec(mp).origin).parent
    136     return loc/mr

File ~/anaconda3/lib/python3.9/importlib/util.py:94, in find_spec(name, package)
     92 parent_name = fullname.rpartition('.')[0]
     93 if parent_name:
---> 94     parent = __import__(parent_name, fromlist=['__path__'])
     95     try:
     96         parent_path = parent.__path__

ModuleNotFoundError: No module named 'https://github'

---------------------------------------------------------------------------
ModuleNotFoundError                       Traceback (most recent call last)
File ~/anaconda3/lib/python3.9/site-packages/IPython/core/formatters.py:343, in BaseFormatter.__call__(self, obj)
    341     method = get_real_method(obj, self.print_method)
    342     if method is not None:
--> 343         return method()
    344     return None
    345 else:

File ~/anaconda3/lib/python3.9/site-packages/nbdev/showdoc.py:166, in BasicMarkdownRenderer._repr_markdown_(self)
    164 def _repr_markdown_(self):
    165     doc = '---\n\n'
--> 166     src = NbdevLookup().code(self.fn)
    167     if src: doc += _ext_link(src, 'source', 'style="float:right; font-size:smaller"') + '\n\n'
    168     h = '#'*self.title_level

File ~/anaconda3/lib/python3.9/site-packages/nbdev/doclinks.py:204, in NbdevLookup.code(self, sym)
    202 if not isinstance(res, tuple): return None
    203 _,py,gh = res
--> 204 line = _lineno(sym, py)
    205 return f'{gh}#L{line}'

File ~/anaconda3/lib/python3.9/site-packages/nbdev/doclinks.py:149, in _lineno(sym, fname)
--> 149 def _lineno(sym, fname): return _get_exps(fname).get(sym.rpartition('.')[2], None) if fname else None

File ~/anaconda3/lib/python3.9/site-packages/nbdev/doclinks.py:140, in _get_exps(mod)
    138 @lru_cache(None)
    139 def _get_exps(mod):
--> 140     mf = _find_mod(mod)
    141     txt = mf.read_text()
    142     _def_types = ast.FunctionDef,ast.AsyncFunctionDef,ast.ClassDef

File ~/anaconda3/lib/python3.9/site-packages/nbdev/doclinks.py:135, in _find_mod(mod)
    133 def _find_mod(mod):
    134     mp,_,mr = mod.rpartition('/')
--> 135     loc = Path(importlib.util.find_spec(mp).origin).parent
    136     return loc/mr

File ~/anaconda3/lib/python3.9/importlib/util.py:94, in find_spec(name, package)
     92 parent_name = fullname.rpartition('.')[0]
     93 if parent_name:
---> 94     parent = __import__(parent_name, fromlist=['__path__'])
     95     try:
     96         parent_path = parent.__path__

ModuleNotFoundError: No module named 'https://github'

[jph00]

To fix this, please run nbdev_prepare

[Attol8]

I already tried but with v2.2.9 of nbdev_prepare fails with

Traceback (most recent call last):
  File "/home/jacopo/anaconda3/bin/nbdev_prepare", line 8, in <module>
    sys.exit(prepare())
  File "/home/jacopo/anaconda3/lib/python3.9/site-packages/fastcore/script.py", line 117, in _f
    return tfunc(**merge(args, args_from_prog(func, xtra)))
  File "/home/jacopo/anaconda3/lib/python3.9/site-packages/nbdev/quarto.py", line 161, in prepare
    nbdev_export.__wrapped__()
  File "/home/jacopo/anaconda3/lib/python3.9/site-packages/nbdev/doclinks.py", line 124, in nbdev_export
    for f in files: nb_export(f)
  File "/home/jacopo/anaconda3/lib/python3.9/site-packages/nbdev/export.py", line 49, in nb_export
    nb.process()
  File "/home/jacopo/anaconda3/lib/python3.9/site-packages/nbdev/process.py", line 122, in process
    for proc in self.procs: self._proc(proc)
  File "/home/jacopo/anaconda3/lib/python3.9/site-packages/nbdev/process.py", line 115, in _proc
    for cell in self.nb.cells: self._process_cell(proc, cell)
  File "/home/jacopo/anaconda3/lib/python3.9/site-packages/nbdev/process.py", line 105, in _process_cell
    if f: self._process_comment(f, cell, cmd)
  File "/home/jacopo/anaconda3/lib/python3.9/site-packages/nbdev/process.py", line 111, in _process_comment
    return proc(cell, *args)
TypeError: _default_exp_() takes 3 positional arguments but 6 were given

[jph00]

That's because in your 03_retrieval notebook you have this line:

#| default_exp retrievalfrom istatapi.discovery import DataSet

It appears you accidentally combined two lines there.

[Attol8]

All tests pass now, with wonderful docs from nbdev v2 live! Sorry for missing that line, my bad! And thanks for all the help and the good work you're doing :)