I am working on an existing Python 3 code-base that provides a setup.py so the code is installed as a Python library. I am trying to get this internal library installed with its own dependencies (the usual data science ones e.g. pandas, pyodbc, sqlalchemy etc).
I would like to have this internal library to deal with these dependencies and assume that if that library is installed, then all the transitive dependencies are assumed to be installed. I also would like to have the Anaconda (conda) version of the package rather than the pip version.
I started with a requirements.txt, but moved quickly to this field in setup.py:
install_requires=[
"pyodbc>=4.0.27",
"sqlalchemy>=1.3.8",
"pandas>=0.25.1",
"requests>=2.22.0",
"assertpy>=0.14",
"cycler>=0.10.0",
]
However when I run the installation process:
either with python setup.py install --record installed_files.txt
or with pip install .
I see that there is some gcc / C++ compilation going on that shows logs about Python wheels (I don't completely understand the implications of Python eggs and Python wheels, but AFAIK if conda is available then I should go with the conda version rather than eggs/wheels because then I don't have to take care of the C++ code underneath the Python code).
I really would prefer having conda to install these C++ blobs wrapped in some Python code as a libraries e.g. pandas.
is it possible at all to have conda driving the installation process described in setup.py so I am not dealing with gcc?
how can I make sure that other Python code depending on this internal library (installed via setup.py) is using the same (transitive) dependencies defined in that setup.py?
Regardless the installation method, how can I make sure that the dependencies for e.g. pandas are installed as well? Sometimes I see that numpy as a dependency of pandas is not installed when running setup.py, but I would like to avoid doing this manually (e.g. with some requirements.txt file).
pip doesn't know about conda, so you cannot build a pip-installable package that pulls in its dependencies from conda channels.
conda doesn't care about setup.py, it uses a different format for recording dependencies.
To install your code with conda, you should create a conda package, and specify your dependencies in a meta.yaml file. Refer to the documentation of "conda build" for details.
https://docs.conda.io/projects/conda-build/en/latest/resources/define-metadata.html
Related
all. I am trying to install shapely via the .whl using pip. I have python 3.6.13 running on anaconda prompt. I have downloaded the shapely .whl using this site. However, when I run the commands shown in the image below, I get the error "shapely... is not a supported wheel on this platform."
From what I understand, I have a 64 bit architecture and python 3.6 (although it is python 3.6.13). I have tried to just request python 3.6 flat from the virtual environment setup by using the following command:
conda create -n stormEnv python=3.6
However, this command always returns a python version that is higher than a flat 3.6.
I am wondering if there is a way to get a python version that is a flat 3.6, or if I am just using the wrong .whl file from https://www.lfd.uci.edu/~gohlke/pythonlibs/
I have also tried the 3.6 32bit architecture as shown in the next image without any success:
Thanks for any help you can provide.
Since you're working with conda, the first thing you should try is:
conda install shapely
There is likely to be an existing build for your platform available in conda forge.
Wheel files are tagged with compatibility markers, and you should not attempt to install an incompatible wheel directly, because the the compiled artifacts inside the wheel will not work on your platform. You'll have to find a wheel which is supported on your platform - to see the list of supported tags run:
python -m pip debug -v
If there are no compatible wheels available, you'll have to install the necessary build dependencies and then install directly from source code.
Just as a background, I am an R user but learning python:
I have installed python libraries I want to get familiar with (pandas, numpy, Pytorch, tensorflow...), but when I start a new project, it does not detect the packages when I try to import and requests that I install them, even though I definitely did at one point. I am obviously making mistakes when installing them, but don't know what.
I use pip as a package manager if that is relevant
Have you attempted installing pip3 and using that in place of pip? I know I had some issues a while back where pip would install my packages for python 2.X and not 3.X.
When installing Theano anaconda automatically tries to install pygpu despite this being an optional dependency. I have deleted the .theanorc file from my windows user directory.
Also when running my application Theano tries to load from the GPU. It's like it remembers somehow?
conda install theano
Fetching package metadata .............
Solving package specifications: .
Package plan for installation in environment
C:\Users\zebco\Miniconda3\envs\py35:
The following NEW packages will be INSTALLED:
libgpuarray: 0.6.9-vc14_0
pygpu: 0.6.9-py36_0
theano: 0.9.0-py36_0
Proceed ([y]/n)?
As you can see I've only specified to install theano yet conda wants to install everything including optional dependancies.
Your assumption that pygpu is optional is dependent on the package manager you are using.
Regular Python (pip)
If you are using a direct Python install (obtained using brew or Python site) then you would be using pip to install theano. This basically comes from
https://pypi.python.org/pypi/Theano/1.0.0
If you download the file and unzip it. Open setup.py, you will see below lines
install_requires=['numpy>=1.9.1', 'scipy>=0.14', 'six>=1.9.0'],
So they are set as the dependencies for this package. Which means when you install theano you will also get numpy, scipy and six.
Anaconda Python (conda)
Now coming to Anaconda python. Anaconda doesn't use a package format that PyPI or pip uses. It uses its own format. In case of Anaconda you should be using conda to install the packages you need and not pip.
Conda has channels which is nothing but a repository which has some packages available. You can install a package from any channel using below
conda install -c <channel-name> <package-name>
The default channel is conda-forge. If you look at the theano package over there
https://anaconda.org/conda-forge/theano/files
And download and extract it. There will be a info/recipe/meta.yml file. You will notice below content in the same
requirements:
build:
- ca-certificates 2017.7.27.1 0
- certifi 2017.7.27.1 py36_0
- ncurses 5.9 10
- openssl 1.0.2l 0
- python 3.6.2 0
- readline 6.2 0
- setuptools 36.3.0 py36_0
- sqlite 3.13.0 1
- tk 8.5.19 2
- xz 5.2.3 0
- zlib 1.2.11 0
run:
- python
- setuptools
- six >=1.9.0
- numpy >=1.9.1
- scipy >=0.14
- pygpu >=0.6.5,<0.7
Which specifies that if you want to run this package then pygpu is also on of its dependencies. So conda downloads pygpu as a dependency which you though was optional (which is probably true if you were using regular python and pip)
Update:
Usually, 'Optional Dependency' is an oxymoron. Something optional is not a dependency, a dependency is a software package another piece of software depends on to function for features.
One may get by without a dependency if the dependency does not interact with the package except for one atomized feature which is not being used. As a beginner I would suggest you not take this path.
I am not super familiar with Theano, but Theano can use the system's GPU to speed up its computations, and it seems to me pygpu and gpulibarray are what enable this functionality. Which means it is not optional.
I believe pygpu is 'optional' if you do not wish to use the GPU for speeding up computation (only done if the GPU is powerful enough to be useful for this).
The --no-deps command above allows you to install a package without its dependencies but that is rarely wise, unless one really knows what they are doing. As a beginner I would not recommend you go down this path yet. Conda was designed specifically to ensure scientific packages are easily managed with all necessary stuff installed without any fuss or muss. pip is a general python package manager, but is not built specifically for scientific packages.
If you wish to install theano without installing its dependencies, then you have one of three options:
use conda install theano --no-deps.
Install it using pip instead of conda, using pip install theano. This will install theano, numpy, scipy and six but not pygpu and libgpuarray.
Create a custom conda build file for Theano. Documentation is at:
https://conda.io/docs/user-guide/tasks/build-packages/index.html
Original Answer:
You probably know this already but, use this command instead:
conda install theano --no-deps
This does not install dependencies of the package. If you already have the essential dependencies installed, as it would seem, this should work out for you.
libgpuarray is a dependency of pygpu. With this command switch neither will be installed.
Can you share the .yaml file that you edited?
I'm new in python and anaconda . I have some cods and I need a lots of requirements for run , how can I install that packages? The requirements includes Python 3.3 or later numexpr numpy 1.9 or later pandas 0.15.2 or later scikit-learn 0.16 scipy 0.15 or later six C/C++ compiler ipython (optional) seaborn (optional) Tnx
It's a good practice to first create a virtual environment using the virtualenv command, and then activate it with source <environment_path>/bin/activate.
After loading the virtual environment, you should be able to use pip install -r requirements.txt to install the requirements listed in the file.
Anaconda comes with its own package manager conda. You should probably use that to install extra packages.
With the possible exception of a C/C++ compiler (although it includes cython, which needs a compiler IIRC), all packages that you need come with anaconda. You'l find a list of included packages here.
i'm trying to install pydot in python3 and i came up with some questions:
The packages referenced by pip3.3 are the same referenced by pip2.7 or there is a different repository for the packages ?
How does all the packaging/distribution work in python ?
What should i do for installing pydot through pip ?
Actually the creator say that python3 is not supported, but pydot is listed in pip3.3
A fork of pydot (https://bitbucket.org/prologic/pydot) working on Python3 exists, why it is not listed in pip?
Can I install pydot through pip?
Almost all package/program distribution in python is done with distutils. This is very good documented in the python documentation.
To your specific problem: pip usually searches the PyPI for the package and then downloads a distribution of that package. Most often this is a source-package and needs to be byte-compiled. If that succeeds the package is most probably compatible to the python version you're using, if it's not you will most probably get SyntaxErrors or something like that.
As i know PyPI has no other, ultimate-sure version classifiers.
So the most sure way to tell if the package is compatible, is to try to install it and then try if it works.