Import Error

[Marius1311]

even after installing nodejs, I get

---------------------------------------------------------------------------
RuntimeError                              Traceback (most recent call last)
<ipython-input-3-63a36eb98d45> in <module>
      6 
      7 from bokeh.io import output_notebook
----> 8 output_notebook()

~/miniconda3/envs/cellrank/lib/python3.6/site-packages/bokeh/io/output.py in output_notebook(resources, verbose, hide_banner, load_timeout, notebook_type)
    115     # verify notebook_type first in curstate().output_notebook
    116     curstate().output_notebook(notebook_type)
--> 117     run_notebook_hook(notebook_type, 'load', resources, verbose, hide_banner, load_timeout)
    118 
    119 def reset_output(state=None):

~/miniconda3/envs/cellrank/lib/python3.6/site-packages/bokeh/io/notebook.py in run_notebook_hook(notebook_type, action, *args, **kw)
    300     if _HOOKS[notebook_type][action] is None:
    301         raise RuntimeError("notebook hook for %r did not install %r action" % notebook_type, action)
--> 302     return _HOOKS[notebook_type][action](*args, **kw)
    303 
    304 #-----------------------------------------------------------------------------

~/miniconda3/envs/cellrank/lib/python3.6/site-packages/bokeh/io/notebook.py in load_notebook(resources, verbose, hide_banner, load_timeout)
    411     _NOTEBOOK_LOADED = resources
    412 
--> 413     custom_models_js = bundle_all_models() or ""
    414 
    415     nb_js = _loading_js(resources, element_id, custom_models_js, load_timeout, register_mime=True)

~/miniconda3/envs/cellrank/lib/python3.6/site-packages/bokeh/util/compiler.py in bundle_all_models()
    345 def bundle_all_models():
    346     """Create a bundle of all models. """
--> 347     return bundle_models(None)
    348 
    349 #-----------------------------------------------------------------------------

~/miniconda3/envs/cellrank/lib/python3.6/site-packages/bokeh/util/compiler.py in bundle_models(models)
    336     if bundle is None:
    337         try:
--> 338             _bundle_cache[key] = bundle = _bundle_models(custom_models)
    339         except CompilationError as error:
    340             print("Compilation failed:", file=sys.stderr)

~/miniconda3/envs/cellrank/lib/python3.6/site-packages/bokeh/util/compiler.py in _bundle_models(custom_models)
    553     bundles = ["bokeh", "bokeh-api", "bokeh-widgets", "bokeh-tables", "bokeh-gl"]
    554     known_modules = set(sum([ read_json(name) for name in bundles ], []))
--> 555     custom_impls = _compile_models(custom_models)
    556 
    557     extra_modules = {}

~/miniconda3/envs/cellrank/lib/python3.6/site-packages/bokeh/util/compiler.py in _compile_models(custom_models)
    533         compiled = _CACHING_IMPLEMENTATION(model, impl)
    534         if compiled is None:
--> 535             compiled = nodejs_compile(impl.code, lang=impl.lang, file=impl.file)
    536 
    537         if "error" in compiled:

~/miniconda3/envs/cellrank/lib/python3.6/site-packages/bokeh/util/compiler.py in nodejs_compile(code, lang, file)
    109                    "Use JavaScript or TypeScript directly instead.")
    110     compilejs_script = join(bokehjs_dir, "js", "compiler.js")
--> 111     output = _run_nodejs([compilejs_script], dict(code=code, lang=lang, file=file, bokehjs_dir=bokehjs_dir))
    112     lines = output.split("\n")
    113     for i, line in enumerate(lines):

~/miniconda3/envs/cellrank/lib/python3.6/site-packages/bokeh/util/compiler.py in _run_nodejs(argv, input)
    480 
    481 def _run_nodejs(argv, input=None):
--> 482     return _run(_nodejs_path(), argv, input)
    483 
    484 def _run_npmjs(argv, input=None):

~/miniconda3/envs/cellrank/lib/python3.6/site-packages/bokeh/util/compiler.py in _nodejs_path()
    456     global _nodejs
    457     if _nodejs is None:
--> 458         _nodejs = _detect_nodejs()
    459     return _nodejs
    460 

~/miniconda3/envs/cellrank/lib/python3.6/site-packages/bokeh/util/compiler.py in _detect_nodejs()
    448     version = ".".join(map(str, nodejs_min_version))
    449     raise RuntimeError('node.js v%s or higher is needed to allow compilation of custom models ' % version +
--> 450                        '("conda install nodejs" or follow https://nodejs.org/en/download/)')
    451 
    452 _nodejs = None

RuntimeError: node.js v6.10.0 or higher is needed to allow compilation of custom models ("conda install nodejs" or follow https://nodejs.org/en/download/)

> /Users/marius/miniconda3/envs/cellrank/lib/python3.6/site-packages/bokeh/util/compiler.py(450)_detect_nodejs()
    448     version = ".".join(map(str, nodejs_min_version))
    449     raise RuntimeError('node.js v%s or higher is needed to allow compilation of custom models ' % version +
--> 450                        '("conda install nodejs" or follow https://nodejs.org/en/download/)')
    451 
    452 _nodejs = None

[michalk8]

Do you have the correct version? It states it requires node.js v6.10.0 or higher.

[michalk8]

@Marius1311 Any news on this?

[Marius1311]

I just had another look at this. I have nodejs 10.13.0 h0a44026_0 installed but I still get the error.

[Marius1311]

Here is what I call:

from bokeh.io import output_notebook
from collections import OrderedDict as odict
output_notebook()

import holoviews as hv

hv.extension('bokeh')

and here is the exact traceback:

---------------------------------------------------------------------------
RuntimeError                              Traceback (most recent call last)
<ipython-input-5-c375ba5017bd> in <module>
      1 from bokeh.io import output_notebook
      2 from collections import OrderedDict as odict
----> 3 output_notebook()
      4 
      5 import holoviews as hv

~/miniconda3/envs/cellrank/lib/python3.6/site-packages/bokeh/io/output.py in output_notebook(resources, verbose, hide_banner, load_timeout, notebook_type)
    115     # verify notebook_type first in curstate().output_notebook
    116     curstate().output_notebook(notebook_type)
--> 117     run_notebook_hook(notebook_type, 'load', resources, verbose, hide_banner, load_timeout)
    118 
    119 def reset_output(state=None):

~/miniconda3/envs/cellrank/lib/python3.6/site-packages/bokeh/io/notebook.py in run_notebook_hook(notebook_type, action, *args, **kw)
    300     if _HOOKS[notebook_type][action] is None:
    301         raise RuntimeError("notebook hook for %r did not install %r action" % notebook_type, action)
--> 302     return _HOOKS[notebook_type][action](*args, **kw)
    303 
    304 #-----------------------------------------------------------------------------

~/miniconda3/envs/cellrank/lib/python3.6/site-packages/bokeh/io/notebook.py in load_notebook(resources, verbose, hide_banner, load_timeout)
    411     _NOTEBOOK_LOADED = resources
    412 
--> 413     custom_models_js = bundle_all_models() or ""
    414 
    415     nb_js = _loading_js(resources, element_id, custom_models_js, load_timeout, register_mime=True)

~/miniconda3/envs/cellrank/lib/python3.6/site-packages/bokeh/util/compiler.py in bundle_all_models()
    345 def bundle_all_models():
    346     """Create a bundle of all models. """
--> 347     return bundle_models(None)
    348 
    349 #-----------------------------------------------------------------------------

~/miniconda3/envs/cellrank/lib/python3.6/site-packages/bokeh/util/compiler.py in bundle_models(models)
    336     if bundle is None:
    337         try:
--> 338             _bundle_cache[key] = bundle = _bundle_models(custom_models)
    339         except CompilationError as error:
    340             print("Compilation failed:", file=sys.stderr)

~/miniconda3/envs/cellrank/lib/python3.6/site-packages/bokeh/util/compiler.py in _bundle_models(custom_models)
    553     bundles = ["bokeh", "bokeh-api", "bokeh-widgets", "bokeh-tables", "bokeh-gl"]
    554     known_modules = set(sum([ read_json(name) for name in bundles ], []))
--> 555     custom_impls = _compile_models(custom_models)
    556 
    557     extra_modules = {}

~/miniconda3/envs/cellrank/lib/python3.6/site-packages/bokeh/util/compiler.py in _compile_models(custom_models)
    533         compiled = _CACHING_IMPLEMENTATION(model, impl)
    534         if compiled is None:
--> 535             compiled = nodejs_compile(impl.code, lang=impl.lang, file=impl.file)
    536 
    537         if "error" in compiled:

~/miniconda3/envs/cellrank/lib/python3.6/site-packages/bokeh/util/compiler.py in nodejs_compile(code, lang, file)
    109                    "Use JavaScript or TypeScript directly instead.")
    110     compilejs_script = join(bokehjs_dir, "js", "compiler.js")
--> 111     output = _run_nodejs([compilejs_script], dict(code=code, lang=lang, file=file, bokehjs_dir=bokehjs_dir))
    112     lines = output.split("\n")
    113     for i, line in enumerate(lines):

~/miniconda3/envs/cellrank/lib/python3.6/site-packages/bokeh/util/compiler.py in _run_nodejs(argv, input)
    480 
    481 def _run_nodejs(argv, input=None):
--> 482     return _run(_nodejs_path(), argv, input)
    483 
    484 def _run_npmjs(argv, input=None):

~/miniconda3/envs/cellrank/lib/python3.6/site-packages/bokeh/util/compiler.py in _nodejs_path()
    456     global _nodejs
    457     if _nodejs is None:
--> 458         _nodejs = _detect_nodejs()
    459     return _nodejs
    460 

~/miniconda3/envs/cellrank/lib/python3.6/site-packages/bokeh/util/compiler.py in _detect_nodejs()
    448     version = ".".join(map(str, nodejs_min_version))
    449     raise RuntimeError('node.js v%s or higher is needed to allow compilation of custom models ' % version +
--> 450                        '("conda install nodejs" or follow https://nodejs.org/en/download/)')
    451 
    452 _nodejs = None

RuntimeError: node.js v6.10.0 or higher is needed to allow compilation of custom models ("conda install nodejs" or follow https://nodejs.org/en/download/)

[Marius1311]

This used to work for me, but now I run into the same error again. My nodejs version is

nodejs                    12.4.0               h6de7cb9_0    conda-forge

[Marius1311]

Imorting works if I don't call output_notebook()

[michalk8]

That sounds very strange, maybe it's using your system nodejs (if you have one - can you try which nodejs in the terminal, then nodejs --version and post the output?). Can you try running it with a fresh new environment? If that doesn't work, let's talk about this on Wednesday.