Joss updates

[karink520]

A bunch of small updates to paper.md and README.md

fixes #76
fixes #75
fixes #74
fixes #73
fixes #72
fixes #71
fixes #70
fixes #68
fixes #66
fixes #65
fixes #64
fixes #61

[gabeschoenbach]

This all looks good! My only thoughts/suggestions have to do with the installation instructions in the README:

• I tried running pip install pyei on my base conda environment and got an error (traceback at the bottom of this review). I tried running pip uninstall pyei and then reinstalling, and it worked fine...
• I like the cleaner one-line conda install to get the development environment up and running. But after we do that and activate the environment, we should run pip install pyei to get pyei in that environment as well, no? Can we just add it to the requirements.txt?

Below is the error from running pip install pyei. I think it was just happening because I had already had an older version of pyei installed, but wanted to document the error here just in case you're interested...

ERROR: Error while checking for conflicts. Please file an issue on pip's issue tracker: https://github.com/pypa/pip/issues/new
Traceback (most recent call last):
  File "/Users/gabe/miniconda3/lib/python3.8/site-packages/pip/_vendor/pkg_resources/__init__.py", line 3021, in _dep_map
    return self.__dep_map
  File "/Users/gabe/miniconda3/lib/python3.8/site-packages/pip/_vendor/pkg_resources/__init__.py", line 2815, in __getattr__
    raise AttributeError(attr)
AttributeError: _DistInfoDistribution__dep_map

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/Users/gabe/miniconda3/lib/python3.8/site-packages/pip/_vendor/pkg_resources/__init__.py", line 3012, in _parsed_pkg_info
    return self._pkg_info
  File "/Users/gabe/miniconda3/lib/python3.8/site-packages/pip/_vendor/pkg_resources/__init__.py", line 2815, in __getattr__
    raise AttributeError(attr)
AttributeError: _pkg_info

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/Users/gabe/miniconda3/lib/python3.8/site-packages/pip/_internal/commands/install.py", line 520, in _determine_conflicts
    return check_install_conflicts(to_install)
  File "/Users/gabe/miniconda3/lib/python3.8/site-packages/pip/_internal/operations/check.py", line 108, in check_install_conflicts
    package_set, _ = create_package_set_from_installed()
  File "/Users/gabe/miniconda3/lib/python3.8/site-packages/pip/_internal/operations/check.py", line 50, in create_package_set_from_installed
    package_set[name] = PackageDetails(dist.version, dist.requires())
  File "/Users/gabe/miniconda3/lib/python3.8/site-packages/pip/_vendor/pkg_resources/__init__.py", line 2736, in requires
    dm = self._dep_map
  File "/Users/gabe/miniconda3/lib/python3.8/site-packages/pip/_vendor/pkg_resources/__init__.py", line 3023, in _dep_map
    self.__dep_map = self._compute_dependencies()
  File "/Users/gabe/miniconda3/lib/python3.8/site-packages/pip/_vendor/pkg_resources/__init__.py", line 3032, in _compute_dependencies
    for req in self._parsed_pkg_info.get_all('Requires-Dist') or []:
  File "/Users/gabe/miniconda3/lib/python3.8/site-packages/pip/_vendor/pkg_resources/__init__.py", line 3014, in _parsed_pkg_info
    metadata = self.get_metadata(self.PKG_INFO)
  File "/Users/gabe/miniconda3/lib/python3.8/site-packages/pip/_vendor/pkg_resources/__init__.py", line 1420, in get_metadata
    value = self._get(path)
  File "/Users/gabe/miniconda3/lib/python3.8/site-packages/pip/_vendor/pkg_resources/__init__.py", line 1616, in _get
    with open(path, 'rb') as stream:
FileNotFoundError: [Errno 2] No such file or directory: '/Users/gabe/miniconda3/lib/python3.8/site-packages/maup-0.7.dist-info/METADATA'

[karink520]

Thanks!
Re: point 1. Right, I'm not concerned either, but thanks for documenting it here, in case this issue comes up for someone else.

Re: point 2. Thanks for bringing this up. I'm going to add back in the in pip install -e ., which will install pyei into the current environment (when run from the directory where someone has cloned pyei. Without it, at least in my setup, I can't run the notebooks right away, and we need it to make pytest work too.

[karink520]

Also fixes #62, fixes #67, fixes #69

Added pip install -e . back into dev installation instructions

[karink520]

Also fixes #63, fixes #77

[gabeschoenbach]

Looks good!