Develop Reference

Problem getting python to "find" the pyglet module

I am learning python via a Great Course lecture series, and in the second half of the course need to install the pyglet module. Although I have (apparently) downloaded the module successfully, my PyCharm IDE is not able to locate it, so my .py program with the instruction "import pyglet" generates the following error:
"C:\Users\the_m\PycharmProjects\Program 1\venv\Scripts\python.exe" "C:\Users\the_m\PycharmProjects\Program 1\basketball.py"
Traceback (most recent call last):
File "C:\Users\the_m\PycharmProjects\Program 1\basketball.py", line 1, in <module>
import pyglet
ModuleNotFoundError: No module named 'pyglet'
I am really enjoying the course, and enjoying getting back to coding after a multi-decade hiatus. I am working on a PC. Can anyone suggest a solution?
file locations for python and what I think are the pyglet module are as follows:
C:\Users\the_m>py -m pip --version
pip 23.0 from C:\Users\the_m\AppData\Local\Programs\Python\Python311\Lib\site-packages\pip (python 3.11)
C:\Users\the_m>py -m pip install --upgrade pip setuptools wheel
Requirement already satisfied: pip in c:\users\the_m\appdata\local\programs\python\python311\lib\site-packages (23.0)
Requirement already satisfied: setuptools in c:\users\the_m\appdata\local\programs\python\python311\lib\site-packages (65.5.0)
Collecting setuptools
Downloading setuptools-67.2.0-py3-none-any.whl (1.1 MB)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.1/1.1 MB 607.4 kB/s eta 0:00:00
Collecting wheel
Downloading wheel-0.38.4-py3-none-any.whl (36 kB)
Installing collected packages: wheel, setuptools
WARNING: The script wheel.exe is installed in 'C:\Users\the_m\AppData\Local\Programs\Python\Python311\Scripts' which is not on PATH.
Consider adding this directory to PATH or, if you prefer to suppress this warning, use --no-warn-script-location.
Attempting uninstall: setuptools
Found existing installation: setuptools 65.5.0
Uninstalling setuptools-65.5.0:
Successfully uninstalled setuptools-65.5.0
Successfully installed setuptools-67.2.0 wheel-0.38.4

Deploying an Rmarkdown file containing Python code (enabled by reticulate) to shinyapp.io

I have a problem that I have been trying to fix for a really long time now and I would really appreciate any help with it. So, I wrote an rmarkdown with both R and Python code. Everything runs fine locally. The document knits nicely (it also displays a shiny app I created inside it). The problem comes when I try to deploy it to shinyapp.io. I get a warning and an error when I do that.
Warning:
using reticulate but python was not specified; will use python at /usr/bin/python. Did you forget to set the RETICULATE_PYTHON environment variable in your .Rprofile before publishing?
Error:
Error in py_call_impl: ImportError: No module named spacy. When I start installing numPy first, it gives the same error saying it can't find numPy.
(I got these from the log in shinyapp.io. I have put the entire log at the bottom)
Here is the relevant part of my code:
reticulate::virtualenv_create(envname = 'test', python = "python")
reticulate::virtualenv_install(envname = 'test', packages =
c('spacy','numpy'))
reticulate::use_virtualenv(virtualenv = 'test', required = FALSE)
And I also have a .Rprofile file that contains the line Sys.setenv(RETICULATE_PYTHON = ".venv/bin/python"). This file is in the same directory as the Rmd file I am deploying.
I have searched for a solution everywhere and everything I have found hasn't been useful. Some similar Github issues are still open and some similar questions on Stack Overflow don't have answers. The most useful thing I have found is this and I have tried everything they suggest there. Here is what I have tried so far:
I have downgraded rsconnect. Initially, I couldn't even deploy the Rmd. I was able to do that after downgrading rsconnect, but this didn't solve the two problems that came next.
I read that I could change the file name .Rprofile to .rsconnect_profile but this hasn't helped at all.
I have tried using Python 3.6 by specifying it when creating the virtual environment (virtualenv_create(envname = 'test', python = "python3.6"). This made things worse. Moreover, shinyappy.io keeps overriding my choice of Python. It always defaults to Python2.7.
What is that I am missing here? Did I specify the virtual environments wrong? What is the difference between the virtual environment in .Rprofile and test, the one that I create in my code and install Python packages in? How are they related? At some point, test was actually RETICULATE_PYTHON and that didn't make a difference. Having read about all of this, I am actually even more confused.
This is the rest of the log:
Server version: 1.7.6-6
LANG: en_US.UTF-8
R version: 3.6.1
shiny version: 1.3.2
httpuv version: 1.5.1
rmarkdown version: 1.14
knitr version: 1.23
jsonlite version: 1.6
RJSONIO version: (none)
htmltools version: 0.3.6
warning: using reticulate but python was not specified; will use python at /usr/bin/python
Did you forget to set the RETICULATE_PYTHON environment variable in your .Rprofile before publishing?
Using pandoc at /opt/connect/ext/pandoc2
Using jsonlite for JSON processing
Starting R with process ID: '23'
Listening on http://127.0.0.1:46584
processing file: index.Rmd
|
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|... | 5%
ordinary text without R code
|
|...... | 10%
label: setup (with options)
List of 1
$ include: logi FALSE
New python executable in /home/shiny/.virtualenvs/test/bin/python2
Also creating executable in /home/shiny/.virtualenvs/test/bin/python
Installing setuptools, pkg_resources, pip, wheel...done.
Running virtualenv with interpreter /usr/bin/python2
DEPRECATION: Python 2.7 will reach the end of its life on January 1st, 2020. Please upgrade your Python as Python 2.7 won't be maintained after that date. A future version of pip will drop support for Python 2.7.
Collecting spacy
Downloading https://files.pythonhosted.org/packages/0f/bf/f76eed483f5bcb9772869a002b0029eb2888dd662f75538b3bcc197bb655/spacy-2.1.6-cp27-cp27mu-manylinux1_x86_64.whl (30.8MB)
Collecting numpy
Downloading https://files.pythonhosted.org/packages/1f/c7/198496417c9c2f6226616cff7dedf2115a4f4d0276613bab842ec8ac1e23/numpy-1.16.4-cp27-cp27mu-manylinux1_x86_64.whl (17.0MB)
Collecting blis<0.3.0,>=0.2.2 (from spacy)
Downloading https://files.pythonhosted.org/packages/61/b7/6f32b1e2506937525802d94136eb73dec2cacd4a21c9bec9c90549e2b413/blis-0.2.4-cp27-cp27mu-manylinux1_x86_64.whl (3.2MB)
Collecting thinc<7.1.0,>=7.0.8 (from spacy)
Downloading https://files.pythonhosted.org/packages/c4/d9/944e0d409e8af994d8d09268a3b7fb9eacbdd08f9bc72b9b0b66c405c05a/thinc-7.0.8-cp27-cp27mu-manylinux1_x86_64.whl (2.1MB)
Downloading https://files.pythonhosted.org/packages/ac/aa/9b065a76b9af472437a0059f77e8f962fe350438b927cb80184c32f075eb/pathlib-1.0.1.tar.gz (49kB)
Collecting pathlib==1.0.1; python_version < "3.4" (from spacy)
Downloading https://files.pythonhosted.org/packages/51/bd/23c926cd341ea6b7dd0b2a00aba99ae0f828be89d72b2190f27c11d4b7fb/requests-2.22.0-py2.py3-none-any.whl (57kB)
Collecting requests<3.0.0,>=2.13.0 (from spacy)
Collecting preshed<2.1.0,>=2.0.1 (from spacy)
Downloading https://files.pythonhosted.org/packages/df/b1/4ff2cbd423184bd68e85f1daa6692753cd7710b0ba68552eb64542906a57/cymem-2.0.2-cp27-cp27mu-manylinux1_x86_64.whl
Collecting cymem<2.1.0,>=2.0.2 (from spacy)
Collecting plac<1.0.0,>=0.9.6 (from spacy)
Collecting murmurhash<1.1.0,>=0.28.0 (from spacy)
Downloading https://files.pythonhosted.org/packages/ed/31/247b34db5ab06afaf5512481e77860fb4cd7a0c0ddff9d2566651c8c2f07/murmurhash-1.0.2-cp27-cp27mu-manylinux1_x86_64.whl
Downloading https://files.pythonhosted.org/packages/9e/9b/62c60d2f5bc135d2aa1d8c8a86aaf84edb719a59c7f11a4316259e61a298/plac-0.9.6-py2.py3-none-any.whl
Collecting srsly<1.1.0,>=0.0.6 (from spacy)
Downloading https://files.pythonhosted.org/packages/3d/17/e003b2e9122500762a9ba6f3dfe4db912604e6be840c7d3041ae72787ae3/srsly-0.0.7-cp27-cp27mu-manylinux1_x86_64.whl (175kB)
Collecting wasabi<1.1.0,>=0.2.0 (from spacy)
Downloading https://files.pythonhosted.org/packages/25/b1/9098d07e70b960001a8a9b99435c6987006d0d7bcbf20523adce9272f66e/preshed-2.0.1-cp27-cp27mu-manylinux1_x86_64.whl (80kB)
Collecting tqdm<5.0.0,>=4.10.0 (from thinc<7.1.0,>=7.0.8->spacy)
Downloading https://files.pythonhosted.org/packages/be/ba/08c53c55cc97f62310ed83e1a4d91e424f221645c88c2dddd41f179fd1f7/wasabi-0.2.2.tar.gz
Downloading https://files.pythonhosted.org/packages/9f/3d/7a6b68b631d2ab54975f3a4863f3c4e9b26445353264ef01f465dc9b0208/tqdm-4.32.2-py2.py3-none-any.whl (50kB)
Collecting urllib3!=1.25.0,!=1.25.1,<1.26,>=1.21.1 (from requests<3.0.0,>=2.13.0->spacy)
Downloading https://files.pythonhosted.org/packages/e6/60/247f23a7121ae632d62811ba7f273d0e58972d75e58a94d329d51550a47d/urllib3-1.25.3-py2.py3-none-any.whl (150kB)
Collecting certifi>=2017.4.17 (from requests<3.0.0,>=2.13.0->spacy)
Downloading https://files.pythonhosted.org/packages/69/1b/b853c7a9d4f6a6d00749e94eb6f3a041e342a885b87340b79c1ef73e3a78/certifi-2019.6.16-py2.py3-none-any.whl (157kB)
Collecting chardet<3.1.0,>=3.0.2 (from requests<3.0.0,>=2.13.0->spacy)
Downloading https://files.pythonhosted.org/packages/bc/a9/01ffebfb562e4274b6487b4bb1ddec7ca55ec7510b22e4c51f14098443b8/chardet-3.0.4-py2.py3-none-any.whl (133kB)
Collecting idna<2.9,>=2.5 (from requests<3.0.0,>=2.13.0->spacy)
Downloading https://files.pythonhosted.org/packages/14/2c/cd551d81dbe15200be1cf41cd03869a46fe7226e7450af7a6545bfc474c9/idna-2.8-py2.py3-none-any.whl (58kB)
Building wheels for collected packages: pathlib, wasabi
Building wheel for pathlib (setup.py): started
Building wheel for pathlib (setup.py): finished with status 'done'
Stored in directory: /home/shiny/.cache/pip/wheels/f9/b2/4a/68efdfe5093638a9918bd1bb734af625526e849487200aa171
Building wheel for wasabi (setup.py): started
Building wheel for wasabi (setup.py): finished with status 'done'
Stored in directory: /home/shiny/.cache/pip/wheels/b3/2c/d1/78fd1255da73ff77b372ecc56bcdb15115ab0882bb6f67af17
Successfully built pathlib wasabi
Installing collected packages: numpy, blis, tqdm, wasabi, pathlib, plac, cymem, preshed, murmurhash, srsly, thinc, urllib3, certifi, chardet, idna, requests, spacy
Successfully installed blis-0.2.4 certifi-2019.6.16 chardet-3.0.4 cymem-2.0.2 idna-2.8 murmurhash-1.0.2 numpy-1.16.4 pathlib-1.0.1 plac-0.9.6 preshed-2.0.1 requests-2.22.0 spacy-2.1.6 srsly-0.0.7 thinc-7.0.8 tqdm-4.32.2 urllib3-1.25.3 wasabi-0.2.2
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ordinary text without R code
label: load_packages (with options)
List of 2
$ include: logi FALSE
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$ engine : chr "python"
Quitting from lines 22-29 (index.Rmd)
Warning: Error in py_call_impl: ImportError: No module named spacy
File "<string>", line 1, in <module>
Detailed traceback:
149: <Anonymous>

Have you tried:
reticulate::use_virtualenv(virtualenv = 'test', required = TRUE)
So far it seems logical to enforce.
I also came across this one:
https://github.com/ranikay/shiny-reticulate-app

Where is symfit?

I pip'ed symfit, (https://pythonhosted.org/symfit/) and it appears to have been installed, to wit:
C:\>pip install symfit
Collecting symfit
Using cached https://files.pythonhosted.org/packages/6e/58/0a58f7a7e39c052afe790ae0989c070e1a2d1c7d472ae3cfd4ee785f1c55/symfit-0.4.5-py2.py3-none-any.whl
Collecting numpy>=1.12 (from symfit)
Downloading https://files.pythonhosted.org/packages/d2/9a/e377ff2dabf66493ac607f6b45b4efeda898ad3fbc43b418bd7dba4a1d67/numpy-1.15.3-cp34-none-win_amd64.whl (13.5MB)
100% |████████████████████████████████| 13.5MB 975kB/s
Collecting sympy<=1.1.1 (from symfit)
Collecting scipy>=1.0 (from symfit)
Using cached https://files.pythonhosted.org/packages/6f/ee/cfce56ea456a809b983ac4089876dbffd15233c17df7bca1e35e84c3ce95/scipy-1.1.0-cp34-none-win_amd64.whl
Collecting mpmath>=0.19 (from sympy<=1.1.1->symfit)
Installing collected packages: numpy, mpmath, sympy, scipy, symfit
Found existing installation: numpy 1.8.1
Cannot uninstall 'numpy'. It is a distutils installed project and thus we cannot
accurately determine which files belong to it which would lead to only a partial uninstall.
But it is not found when I try to import it into a python program, and a
dir /s symfit
from the root directory of the drive fails to find symfit.
Where did pip put it, and how can I access it?

Jnius installation bug, "Unable to determine JDK_HOME"

I tried to install jnius Python module by typing 'pip install jnius' in CMD.
This is the message I got:
Complete output from command python setup.py egg_info:
Traceback (most recent call last):
File "<string>", line 1, in <module>
File "c:\users\sm\appdata\local\temp\pip-install-vu2sb5\jnius\setup.py", line 111, in <module>
raise Exception('Unable to determine JDK_HOME')
Exception: Unable to determine JDK_HOME
----------------------------------------
Command "python setup.py egg_info" failed with error code 1 in
c:\users\sm\appdata\local\temp\pip-install-vu2sb5\jnius\
I restarted CMD, but it didn't help.

I have finally resolved it. I have installed Cython before this happened and I installed both Java JDK and JRE after #Chris comment. And I have also added JAVA_HOME and JDK_HOME to system variables.Thank you #Chris, but it didn't resolve problem completely.
Then I got another error message. There was written that I have to install Microsoft Visual C++ Compiler for Python 2.7 from this page:
https://www.microsoft.com/en-us/download/confirmation.aspx?id=44266
After that I tried to install jnius again but the error message said that permission is denied so I ran CMD as administrator and finally installed jnius by typing pip install jnius.
I spent a lot of time to resolve it and hope that it will help everyone with same or similar problem.

I have resolved the problem in windows os.
1st step:
I have installed cython by using pip install cython
C:\Users>pip install cython
Collecting cython
Downloading Cython-0.29.22-cp38-cp38-win_amd64.whl (1.7 MB)
|████████████████████████████████| 1.7 MB 1.3 MB/s
Installing collected packages: cython
Successfully installed cython-0.29.22
2nd step:
I have installed jnius by using pip install pyjnius command
C:\Users>pip install pyjnius
Collecting pyjnius
Downloading pyjnius-1.3.0-cp38-cp38-win_amd64.whl (226 kB)
|████████████████████████████████| 226 kB 3.2 MB/s
Requirement already satisfied: cython in c:\users\sss\appdata\local\programs\python\python38\lib\site-packages (from pyjnius) (0.29.22)
Requirement already satisfied: six>=1.7.0 in c:\users\sss\appdata\local\programs\python\python38\lib\site-packages (from pyjnius) (1.15.0)
Installing collected packages: pyjnius
Successfully installed pyjnius-1.3.0
I hope this solves your problem.

The thing that worked for me was simply adding JAVA_HOME and JDK_HOME variables.

Pip wheel is building a new wheel when one is already present

I'm trying to build a wheel for pandas at 0.17.1. I want it to use numpy version 1.9.2. I have a wheel for that version of numpy already built in $PWD/wheelhouse, and a few other pandas dependencies as well:
ls wheelhouse/
numpy-1.9.2-cp34-cp34m-linux_x86_64.whl python_dateutil-2.4.2-py2.py3-none-any.whl pytz-2015.7-py2.py3-none-any.whl six-1.10.0-py2.py3-none-any.whl
However, when I tell pandas to build, even though I inform it of the wheelhouse folder with --find-links, it still builds a new wheel of numpy:
$ pip --version
pip 6.0.8 from /home/me/.pyenv/versions/3.4.3/lib/python3.4/site-packages (python 3.4)
$ pip wheel pandas==0.17.1 --find-links=$PWD/wheelhouse
Collecting pandas==0.17.1
Using cached pandas-0.17.1.tar.gz
[... snipped, building stuff ...]
Collecting python-dateutil>=2 (from pandas==0.17.1)
File was already downloaded /home/me/rebuild_numpy_py3/wheelhouse/python_dateutil-2.4.2-py2.py3-none-any.whl
Collecting pytz>=2011k (from pandas==0.17.1)
File was already downloaded /home/me/rebuild_numpy_py3/wheelhouse/pytz-2015.7-py2.py3-none-any.whl
Collecting numpy>=1.7.0 (from pandas==0.17.1)
Using cached numpy-1.10.2.tar.gz
Running from numpy source directory.
Collecting six>=1.5 (from python-dateutil>=2->pandas==0.17.1)
File was already downloaded /home/me/rebuild_numpy_py3/wheelhouse/six-1.10.0-py2.py3-none-any.whl
Skipping python-dateutil, due to already being wheel.
Skipping pytz, due to already being wheel.
Skipping six, due to already being wheel.
Building wheels for collected packages: pandas, numpy
Running setup.py bdist_wheel for pandas
Destination directory: /home/me/rebuild_numpy_py3/wheelhouse
Running setup.py bdist_wheel for numpy
Destination directory: /home/me/rebuild_numpy_py3/wheelhouse
Successfully built pandas numpy
$ ls wheelhouse/
numpy-1.10.2-cp34-cp34m-linux_x86_64.whl numpy-1.9.2-cp34-cp34m-linux_x86_64.whl pandas-0.17.1-cp34-cp34m-linux_x86_64.whl python_dateutil-2.4.2-py2.py3-none-any.whl pytz-2015.7-py2.py3-none-any.whl six-1.10.0-py2.py3-none-any.whl
The version bound on pandas is >=1.7.0, so certainly the wheel that's there should work. So why is it building a new wheel? How can I force it to use the existing one?

That's not how wheel works. pandas requires a >= 1.7.0 version of numpy. You're trying to force it to look for 1.9.2 even though there's already a newer version of numpy. Even if you already have it in your wheelhouse dir, it will check PyPI for the latest version of numpy as this is what is stated in pandas' setup.py file.