[MAINT] Optional imports (#42)

* [MAINT] Optional imports * try optional deps * try again * try again * Update setup.cfg * try again * try again * try again * Update README.md

Author: nbara

.github/workflows/pythonpackage.yml

@@ -14,22 +14,19 @@ jobs:
  strategy:
  max-parallel: 4
  matrix:
- python-version: [3.6, 3.7, 3.8]
+ python-version: [3.6, 3.7, 3.8, 3.9]
 
  steps:
  - uses: actions/checkout@v1
  - name: Set up Python ${{ matrix.python-version }}
  uses: actions/setup-python@v1
  with:
  python-version: ${{ matrix.python-version }}
- - name: Install dependencies
+ - name: Install meegkit and dependencies
  run: |
  python -m pip install --upgrade pip
  pip install -r requirements.txt
- pip install git+https://github.com/pymanopt/pymanopt
- - name: Install meegkit
- run: |
- pip install -e .
+ pip install -e ".[extra]"
  - name: Lint with flake8
  run: |
  make pep

.travis.yml

@@ -12,8 +12,7 @@ python:
 install:
  - sudo apt-get update
  - pip install -r requirements.txt
- - pip install -e .
- - pip install git+https://github.com/pymanopt/pymanopt
+ - pip install -e ".[extra]"
 script:
  - mkdir docs
  - cd doc

README.md

@@ -24,14 +24,29 @@ This package can be installed easily using `pip+git`:
 pip install git+https://github.com/nbara/python-meegkit.git
 ```
 
-Or you can clone this repository and run the following command inside the `python-meegkit` directory:
+Or you can clone this repository and run the following commands inside the `python-meegkit` directory:
 
 ```bash
+pip install -r requirements.txt
 pip install .
 ```
 
 *Note* : Use developer mode with the `-e` flag (`pip install -e .`) to be able to modify the sources even after install.
 
+### Advanced installation instructions
+
+Some ASR variants require additional dependencies such as `pymanopt`. To install meegkit with these optional packages, use:
+
+```bash
+pip install -e '.[extra]'
+```
+
+or:
+
+```bash
+pip install git+https://github.com/nbara/python-meegkit.git#egg=meegkit[extra]
+```
+
 ## References
 
 ### 1. CCA, STAR, SNS, DSS, ZapLine, and robust detrending

meegkit/utils/covariances.py

@@ -1,9 +1,5 @@
 """Covariance calculation."""
 import numpy as np
-import pymanopt
-from pymanopt import Problem
-from pymanopt.manifolds import Grassmann
-from pymanopt.solvers import TrustRegions
 from scipy import linalg
 
 from .base import mldivide
@@ -445,6 +441,11 @@ def nonlinear_eigenspace(L, k, alpha=1):
  Analysis and Applications, 36(2), 752-774, 2015.
 
  """
+ import pymanopt
+ from pymanopt import Problem
+ from pymanopt.manifolds import Grassmann
+ from pymanopt.solvers import TrustRegions
+
  n = L.shape[0]
  assert L.shape[1] == n, 'L must be square.'
 

requirements.txt

@@ -12,4 +12,4 @@ codespell
 pydocstyle
 tqdm
 statsmodels
-git+git://github.com/alexandrebarachant/pyRiemann
+pyriemann @ git+https://github.com/alexandrebarachant/pyRiemann

setup.cfg

@@ -17,3 +17,7 @@ all_files = 1
 
 [upload_sphinx]
 upload-dir = doc/_build/html
+
+[options.extras_require]
+extra = pymanopt @ git+https://github.com/pymanopt/pymanopt@master
+

setup.py

@@ -7,7 +7,7 @@
  description='M/EEG denoising in Python',
  url='http://github.com/nbara/python-meegkit/',
  author='N Barascud',
- author_email='nicolas.barascud@ens.fr',
+ author_email='nicolas.barascud@gmail.com',
  license='UNLICENSED',
  version='0.1.1',
  packages=find_packages(exclude=['doc', 'tests']),