Pip install error ModuleNotFoundError: No module named 'pystan'

[msoedov]

pip --version
pip 9.0.1 from /Users/miasool/pyenvs/xor_ai/lib/python3.6/site-packages (python 3.6)

pip install fbprophet
Collecting fbprophet
  Downloading fbprophet-0.2.1.tar.gz
Requirement already satisfied: matplotlib in /Users/miasool/pyenvs/xor_ai/lib/python3.6/site-packages (from fbprophet)
Requirement already satisfied: pandas>=0.18.1 in /Users/miasool/pyenvs/xor_ai/lib/python3.6/site-packages (from fbprophet)
Collecting pystan>=2.14 (from fbprophet)
  Downloading pystan-2.17.0.0-cp36-cp36m-macosx_10_6_intel.macosx_10_9_intel.macosx_10_9_x86_64.macosx_10_10_intel.macosx_10_10_x86_64.whl (35.2MB)
    100% |████████████████████████████████| 35.2MB 43kB/s
Requirement already satisfied: python-dateutil>=2.0 in /Users/miasool/pyenvs/xor_ai/lib/python3.6/site-packages (from matplotlib->fbprophet)
Requirement already satisfied: pyparsing!=2.0.4,!=2.1.2,!=2.1.6,>=2.0.1 in /Users/miasool/pyenvs/xor_ai/lib/python3.6/site-packages (from matplotlib->fbprophet)
Requirement already satisfied: cycler>=0.10 in /Users/miasool/pyenvs/xor_ai/lib/python3.6/site-packages (from matplotlib->fbprophet)
Requirement already satisfied: numpy>=1.7.1 in /Users/miasool/pyenvs/xor_ai/lib/python3.6/site-packages (from matplotlib->fbprophet)
Requirement already satisfied: six>=1.10 in /Users/miasool/pyenvs/xor_ai/lib/python3.6/site-packages (from matplotlib->fbprophet)
Requirement already satisfied: pytz in /Users/miasool/pyenvs/xor_ai/lib/python3.6/site-packages (from matplotlib->fbprophet)
Collecting Cython!=0.25.1,>=0.22 (from pystan>=2.14->fbprophet)
  Downloading Cython-0.27.3-cp36-cp36m-macosx_10_6_intel.macosx_10_9_intel.macosx_10_9_x86_64.macosx_10_10_intel.macosx_10_10_x86_64.whl (4.7MB)
    100% |████████████████████████████████| 4.7MB 290kB/s
Building wheels for collected packages: fbprophet
  Running setup.py bdist_wheel for fbprophet ... error
  Complete output from command /Users/miasool/pyenvs/xor_ai/bin/python3.6 -u -c "import setuptools, tokenize;__file__='/private/var/folders/c0/mz0pnjn131d5rsl43kr5my6xh2lw2t/T/pip-build-19fj5puw/fbprophet/setup.py';f=getattr(tokenize, 'open', open)(__file__);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, __file__, 'exec'))" bdist_wheel -d /var/folders/c0/mz0pnjn131d5rsl43kr5my6xh2lw2t/T/tmpe7pukz0npip-wheel- --python-tag cp36:
  running bdist_wheel
  running build
  running build_py
  creating build
  creating build/lib
  creating build/lib/fbprophet
  creating build/lib/fbprophet/stan_models
  Traceback (most recent call last):
    File "<string>", line 1, in <module>
    File "/private/var/folders/c0/mz0pnjn131d5rsl43kr5my6xh2lw2t/T/pip-build-19fj5puw/fbprophet/setup.py", line 126, in <module>
      """
    File "/Users/miasool/pyenvs/xor_ai/lib/python3.6/site-packages/setuptools/__init__.py", line 129, in setup
      return distutils.core.setup(**attrs)
    File "/usr/local/Cellar/python3/3.6.2/Frameworks/Python.framework/Versions/3.6/lib/python3.6/distutils/core.py", line 148, in setup
      dist.run_commands()
    File "/usr/local/Cellar/python3/3.6.2/Frameworks/Python.framework/Versions/3.6/lib/python3.6/distutils/dist.py", line 955, in run_commands
      self.run_command(cmd)
    File "/usr/local/Cellar/python3/3.6.2/Frameworks/Python.framework/Versions/3.6/lib/python3.6/distutils/dist.py", line 974, in run_command
      cmd_obj.run()
    File "/Users/miasool/pyenvs/xor_ai/lib/python3.6/site-packages/wheel/bdist_wheel.py", line 204, in run
      self.run_command('build')
    File "/usr/local/Cellar/python3/3.6.2/Frameworks/Python.framework/Versions/3.6/lib/python3.6/distutils/cmd.py", line 313, in run_command
      self.distribution.run_command(command)
    File "/usr/local/Cellar/python3/3.6.2/Frameworks/Python.framework/Versions/3.6/lib/python3.6/distutils/dist.py", line 974, in run_command
      cmd_obj.run()
    File "/usr/local/Cellar/python3/3.6.2/Frameworks/Python.framework/Versions/3.6/lib/python3.6/distutils/command/build.py", line 135, in run
      self.run_command(cmd_name)
    File "/usr/local/Cellar/python3/3.6.2/Frameworks/Python.framework/Versions/3.6/lib/python3.6/distutils/cmd.py", line 313, in run_command
      self.distribution.run_command(command)
    File "/usr/local/Cellar/python3/3.6.2/Frameworks/Python.framework/Versions/3.6/lib/python3.6/distutils/dist.py", line 974, in run_command
      cmd_obj.run()
    File "/private/var/folders/c0/mz0pnjn131d5rsl43kr5my6xh2lw2t/T/pip-build-19fj5puw/fbprophet/setup.py", line 46, in run
      build_stan_models(target_dir)
    File "/private/var/folders/c0/mz0pnjn131d5rsl43kr5my6xh2lw2t/T/pip-build-19fj5puw/fbprophet/setup.py", line 28, in build_stan_models
      from pystan import StanModel
  ModuleNotFoundError: No module named 'pystan'

  ----------------------------------------
  Failed building wheel for fbprophet
  Running setup.py clean for fbprophet
Failed to build fbprophet
Installing collected packages: Cython, pystan, fbprophet
  Running setup.py install for fbprophet ... done
Successfully installed Cython-0.27.3 fbprophet-0.2.1 pystan-2.17.0.0

However with the second run it showed no error

pip install fbprophet
Requirement already satisfied: fbprophet in /Users/miasool/pyenvs/xor_ai/lib/python3.6/site-packages
Requirement already satisfied: matplotlib in /Users/miasool/pyenvs/xor_ai/lib/python3.6/site-packages (from fbprophet)
Requirement already satisfied: pandas>=0.18.1 in /Users/miasool/pyenvs/xor_ai/lib/python3.6/site-packages (from fbprophet)
Requirement already satisfied: pystan>=2.14 in /Users/miasool/pyenvs/xor_ai/lib/python3.6/site-packages (from fbprophet)
Requirement already satisfied: pyparsing!=2.0.4,!=2.1.2,!=2.1.6,>=2.0.1 in /Users/miasool/pyenvs/xor_ai/lib/python3.6/site-packages (from matplotlib->fbprophet)
Requirement already satisfied: numpy>=1.7.1 in /Users/miasool/pyenvs/xor_ai/lib/python3.6/site-packages (from matplotlib->fbprophet)
Requirement already satisfied: six>=1.10 in /Users/miasool/pyenvs/xor_ai/lib/python3.6/site-packages (from matplotlib->fbprophet)
Requirement already satisfied: cycler>=0.10 in /Users/miasool/pyenvs/xor_ai/lib/python3.6/site-packages (from matplotlib->fbprophet)
Requirement already satisfied: pytz in /Users/miasool/pyenvs/xor_ai/lib/python3.6/site-packages (from matplotlib->fbprophet)
Requirement already satisfied: python-dateutil>=2.0 in /Users/miasool/pyenvs/xor_ai/lib/python3.6/site-packages (from matplotlib->fbprophet)
Requirement already satisfied: Cython!=0.25.1,>=0.22 in /Users/miasool/pyenvs/xor_ai/lib/python3.6/site-packages (from pystan>=2.14->fbprophet)

[bletham]

That's odd. Did pystan actually install?

import pystan
pystan.__version__

If not could you try

pip install --upgrade pystan

and see if it works? and then same for fbprophet?

[maartenmennes]

I encountered the same issue upon install

[bletham]

@maartenmennes Can you check the pystan info from my previous post? and is there Anaconda or something like that involved?

[maartenmennes]

everything seemed to have installed fine, despite the error message regarding pystan.

It was a clean environment created on centos7.2 with: conda create --name py36 python=3.6 anaconda

[bletham]

Including fbprophet is working?

[maartenmennes]

Yep, from fbprophet import Prophet is working as advertised... It then only took me a while to realize that your X and Y variables HAVE to be called 'ds' and 'y'...

[bletham]

Interesting, I'm not sure what is going on with that error, I haven't seen this myself with pip installs.

As for ds and y, yes that definitely should give better error messages, #433.

[rogeriomgatto]

It seems this error only occurs when package wheel is already installed. If wheel is not installed, setup.py bdist_wheel will not be invoked. If wheel is installed, wheel building fails because it happens before pystan has been installed. Perhaps pystan should be listed in both install_requires and setup_requires?

[robertmuil]

I have seen this issue too: +1 for including pystan explicitly in package requirements.

[k6ef]

Just recently came across this and found that removing pystan and re-installing it, I was able to build/install fbprophet.

[robertmuil]

@k6ef Yes, simply retrying the installation will usually work because PyStan is installed after fbprophet fails the first time. Be nice if it worked first time though.
BTW, installing with conda instead of pip works first time.

[bletham]

So, adding pystan to setup_requires does indeed make sure that it is in place before trying to build fbprophet, and thus avoids this confusing error message.

However, it seems (TIL) that pip does not directly interact with setup_requires. Rather, during the build it uses easy_install to install everything from setup_requires. easy_install does not support wheels, and so it means that pystan has to be built from source. This takes forever and uses a ton of RAM. It is thus not a good option here.

I think the best fix we can get for this is just to update the install instructions to say to install pystan with pip before installing fbprophet with pip.

[rogeriomgatto]

This is on the release notes for pip 10:

Support for packages specifying build dependencies in pyproject.toml (see PEP 518). Packages which specify one or more build dependencies this way will be built into wheels in an isolated environment with those dependencies installed. (#3691)

I did a quick check and adding python/pyproject.toml (and a corresponding entry in MANIFEST.in) seems to solve the issue with pip >= 10, although I would prefer that more people tested this before committing.

Should I send a merge request? It's a very simple change:

diff --git a/python/MANIFEST.in b/python/MANIFEST.in
index 10c5fe3..a80a5ec 100644
--- a/python/MANIFEST.in
+++ b/python/MANIFEST.in
@@ -6,4 +6,7 @@ include LICENSE
 prune fbprophet/stan_models
 
 # Necessary for tests to run
-include fbprophet/tests/*.csv
\ No newline at end of file
+include fbprophet/tests/*.csv
+
+# build dependencies
+include pyproject.toml

$ cat python/pyproject.toml 
[build-system]
# Minimum requirements for the build system to execute.
requires = ["setuptools", "wheel", "pystan>=2.14"]