Install¶
Below we assume you have the default Python environment already configured on
your computer and you intend to install mgcpy
inside of it. If you want
to create and work with Python virtual environments, please follow instructions
on venv and virtual
environments.
First, make sure you have the latest version of pip
(the Python package manager)
installed. If you do not, refer to the Pip documentation and install pip
first.
Install the released version¶
Install the current release of mgcpy
with pip
:
$ pip install mgcpy
To upgrade to a newer release use the --upgrade
flag:
$ pip install --upgrade mgcpy
If you do not have permission to install software systemwide, you can
install into your user directory using the --user
flag:
$ pip install --user mgcpy
Alternatively, you can manually download mgcpy
from
GitHub or
PyPI.
To install one of these versions, unpack it and run the following from the
top-level source directory using the Terminal:
$ pip install .
Install from Github¶
To install from Github, run the following from the top-level source directory using the Terminal:
$ git clone https://github.com/neurodata/mgcpy
$ cd mgcpy
$ python3 setup.py install
sudo
, if requiredpython3 setup.py build_ext --inplace # for cython
, if you want to test in-place, first execute this
Setting up the development environment¶
- To build image and run from scratch:
- Install [docker](https://docs.docker.com/install/)
- Build the docker image,
docker build -t mgcpy:latest .
- This takes 10-15 mins to build
- Launch the container to go into mgcpy’s dev env,
docker run -it --rm --name mgcpy-env mgcpy:latest
- Pull image from Dockerhub and run:
docker pull tpsatish95/mgcpy:latest
ordocker pull tpsatish95/mgcpy:development
docker run -it --rm -p 8888:8888 --name mgcpy-env tpsatish95/mgcpy:latest
- To run demo notebooks (from within Docker):
cd demos
jupyter notebook --ip 0.0.0.0 --no-browser --allow-root
- Then copy the url it generates, it looks something like this:
http://(0de284ecf0cd or 127.0.0.1):8888/?token=e5a2541812d85e20026b1d04983dc8380055f2d16c28a6ad
- Edit this:
(0de284ecf0cd or 127.0.0.1)
to:127.0.0.1
, in the above link and open it in your browser - Then open
mgc.ipynb
- To mount/load local files into docker container:
- Do
docker run -it --rm -v <local_dir_path>:/root/workspace/ -p 8888:8888 --name mgcpy-env tpsatish95/mgcpy:latest
, replace<local_dir_path>
with your local dir path. - Do
cd ../workspace
when you are inside the container to view the mounted files. The mgcpy package code will be in/root/code
directory.
- Do
Python package dependencies¶
mgcpy requires the following packages:
- numpy
- scikit-learn
- scipy
- Cython
- pandas
- h5py
- seaborn
Hardware requirements¶
mgcpy package requires only a standard computer with enough RAM to support the in-memory operations.
OS Requirements¶
This package is supported for macOS and partly on Linux.
Testing¶
mgcpy uses the Python pytest
testing package. If you don’t already have
that package installed, follow the directions on the pytest homepage.