Merge branch 'master' of https://github.com/SUNCAT-Center/CatLearn

Fixing bugs in catlearn/optimize/mlmin.py in line 300 or the failed mlmin will repeat infinety

.gitattributes

@@ -0,0 +1 @@
+*.ipynb linguist-vendored

.travis.yml

@@ -1,9 +1,10 @@
 sudo: required
 language: python
 python:
- - "2.7"
- - "3.5"
+
  - "3.6"
+ - "3.7"
+ - "3.8"
 
 notifications:
  email:

CHANGELOG.md

@@ -1,5 +1,16 @@
 # dev
 
+# Version 0.6.2 (March 2020)
+
+- Added module for site featurization and GA feature selection.
+- Fixed ML-NEB compatibility issue with FHI-AIMS ase calculator.
+- Compatibility updated for ASE 3.19.0
+- Compatibility updated for Pandas 0.24.0
+- Compatibility updated for Scikit-learn 0.22.0
+- Dropped support for python 2.
+- Dropped support for python 3.5
+- Added testing for python 3.7 and 3.8
+
 # Version 0.6.1 (April 2019)
 
 - Fixed compatibility issue with MLNEB and [GPAW](https://wiki.fysik.dtu.dk/gpaw/index.html)

catlearn/__init__.py

@@ -1 +1 @@
-__version__ = "0.6.1"
+__version__ = "0.6.2"

catlearn/featurize/setup.py

@@ -136,7 +136,7 @@ def featurize_atomic_pairs(self, candidates):
  for atoms in tqdm(candidates):
  # One hot encode elements.
  dummies = pd.get_dummies(atoms.numbers)
- d = dummies.T.reindex(self.atom_types).fillna(0).T.as_matrix()
+ d = dummies.T.reindex(self.atom_types).fillna(0).T.to_numpy()
 
  # Number of pairs by 1 + number of element types data matrix.
  n_pairs = len(atoms) ** 2
@@ -272,9 +272,9 @@ def _concatenate_vec(self, atoms, vec_names):
  fingerprint_vector.dtype.type is not np.str_) or
  (arr.dtype.type is not np.str_ and
  fingerprint_vector.dtype.type is np.str_)):
-  raise AssertionError("Fingerprints should be float" +
-  " type, and returned separately" +
-  " from str types.")
+ raise AssertionError("Fingerprints should be float" +
+ " type, and returned separately" +
+ " from str types.")
  fingerprint_vector = np.concatenate((fingerprint_vector,
  arr))