Notebooks no longer compatible with PyPi release.

[CompRhys]

Was attempting to run the BaTiO3 notebook on colab and have had some errors installing from pip as that notebooks do not match the release.

---------------------------------------------------------------------------
TypeError                                 Traceback (most recent call last)
<ipython-input-17-d8c3c8f46d03> in <module>()
      7     allow_gas_release=True,
      8     confine_competing_to_icsd=False,
----> 9     add_elements=['C']
     10 )

TypeError: __init__() got an unexpected keyword argument 'confine_competing_to_icsd'

[CompRhys]

installing the git package directly, i.e. pip install git+https://github.com/TRI-AMDD/piro.git, yeilds more errors due to pymatgen version not being specified and a change in the pymatgen API for MPRester where they removed top level imports.

---------------------------------------------------------------------------
ImportError                               Traceback (most recent call last)
<ipython-input-3-8a4e35725ecd> in <module>()
      1 import pandas as pd
----> 2 from piro.route import SynthesisRoutes
      3 pd.set_option('display.width', 700)
      4 pd.set_option('display.max_colwidth', 300)

/usr/local/lib/python3.7/dist-packages/piro/route.py in <module>()
      9 import json
     10 from copy import deepcopy
---> 11 from pymatgen import MPRester
     12 from pymatgen.analysis.phase_diagram import PhaseDiagram
     13 from pymatgen.util.string import latexify

ImportError: cannot import name 'MPRester' from 'pymatgen' (unknown location)

---------------------------------------------------------------------------
NOTE: If your import is failing due to a missing package, you can
manually install dependencies using either !pip or !apt.

To view examples of installing some common dependencies, click the
"Open Examples" button below.
---------------------------------------------------------------------------

[CompRhys]

Additionally the pip installation doesn't appear to package the resource directory RXN_FILES = os.path.join(RXN_ROOT, 'files') which can be seen by the lack of the files directory when we call tree on the install location.

!apt-get install tree
!tree /usr/local/lib/python3.7/dist-packages/piro/

Reading package lists... Done
Building dependency tree       
Reading state information... Done
The following NEW packages will be installed:
  tree
0 upgraded, 1 newly installed, 0 to remove and 37 not upgraded.
Need to get 40.7 kB of archives.
After this operation, 105 kB of additional disk space will be used.
Get:1 http://archive.ubuntu.com/ubuntu bionic/universe amd64 tree amd64 1.7.0-5 [40.7 kB]
Fetched 40.7 kB in 0s (123 kB/s)
Selecting previously unselected package tree.
(Reading database ... 155047 files and directories currently installed.)
Preparing to unpack .../tree_1.7.0-5_amd64.deb ...
Unpacking tree (1.7.0-5) ...
Setting up tree (1.7.0-5) ...
Processing triggers for man-db (2.8.3-2ubuntu0.1) ...
/usr/local/lib/python3.7/dist-packages/piro/
├── data.py
├── __init__.py
├── mongodb.py
├── __pycache__
│   ├── data.cpython-37.pyc
│   ├── __init__.cpython-37.pyc
│   ├── mongodb.cpython-37.pyc
│   ├── route.cpython-37.pyc
│   └── utils.cpython-37.pyc
├── route.py
└── utils.py

[JosephMontoya-TRI]

Thanks for the tip! Will debug today.

[JosephMontoya-TRI]

Updated the release to include the files directory, it's working for me on colab now, will you test and let me know?

[CompRhys]

yep, now works! could be cool to have a example.

#@title Input Materials Project API KEY

!pip install git+https://github.com/TRI-AMDD/piro.git

MP_API_KEY = '<your api key here>' #@param {type:"string"}

!pmg config --add PMG_MAPI_KEY {MP_API_KEY}

all I needed to add was this cell at the top to do the config and then no other changes

[sgbaird]

Ditto on the colab example