From 28796b00db3b6c476ce3470ea87dac9a922ae5bb Mon Sep 17 00:00:00 2001 From: Anubhav Jain Date: Sun, 3 May 2020 19:52:14 -0700 Subject: [PATCH] Update to v0.6.3 --- docs/_sources/changelog.rst.txt | 10 + docs/_sources/dataset_summary.rst.txt | 2 +- docs/_sources/featurizer_summary.rst.txt | 4 + docs/_static/documentation_options.js | 2 +- docs/changelog.html | 15 +- docs/contributors.html | 6 +- docs/dataset_addition_guide.html | 10 +- docs/dataset_summary.html | 8 +- docs/example_bulkmod.html | 52 ++--- docs/featurizer_summary.html | 42 ++-- docs/genindex.html | 42 +++- docs/index.html | 6 +- docs/installation.html | 6 +- docs/matminer.data_retrieval.html | 12 +- docs/matminer.data_retrieval.tests.html | 6 +- docs/matminer.datasets.html | 6 +- docs/matminer.datasets.tests.html | 6 +- docs/matminer.featurizers.html | 238 ++++++++++++++++++++- docs/matminer.featurizers.tests.html | 21 +- docs/matminer.featurizers.utils.html | 16 +- docs/matminer.featurizers.utils.tests.html | 6 +- docs/matminer.figrecipes.html | 8 +- docs/matminer.figrecipes.tests.html | 6 +- docs/matminer.html | 6 +- docs/matminer.utils.data_files.html | 6 +- docs/matminer.utils.html | 14 +- docs/matminer.utils.tests.html | 6 +- docs/modules.html | 6 +- docs/objects.inv | Bin 7985 -> 8101 bytes docs/py-modindex.html | 6 +- docs/search.html | 6 +- docs/searchindex.js | 2 +- docs_rst/changelog.rst | 10 + docs_rst/dataset_summary.rst | 2 +- docs_rst/featurizer_summary.rst | 4 + matminer/__init__.py | 2 +- setup.py | 2 +- 37 files changed, 460 insertions(+), 142 deletions(-) diff --git a/docs/_sources/changelog.rst.txt b/docs/_sources/changelog.rst.txt index 13b20689f..bdb8a1c2b 100644 --- a/docs/_sources/changelog.rst.txt +++ b/docs/_sources/changelog.rst.txt @@ -5,6 +5,16 @@ matminer Changelog ================== +**v0.6.3** + +* add IntersticeDistribution featurizer (Q. Wang) +* change Dimensionality featurizer to be more accurate (A. Ganose) +* add CohesiveEnergyMP featurizer that gets MP cohesive energy from MP Rester (A. Jain) +* default mp dataretrieval to decode mp entities by default (A. Dunn) +* update dependencies and tests (A. Ganose) +* misc fixes / documentation updates (Q. Wang, A. Dunn, A. Jain, L. Ward, S.P. Ong, A. Ganose) + + **v0.6.2** * Update forum to Discourse link (A. Ganose) diff --git a/docs/_sources/dataset_summary.rst.txt b/docs/_sources/dataset_summary.rst.txt index 2edff88d2..c432d3dc6 100644 --- a/docs/_sources/dataset_summary.rst.txt +++ b/docs/_sources/dataset_summary.rst.txt @@ -2040,7 +2040,7 @@ url={http://dx.doi.org/10.1038/sdata.2018.65} --------------- matbench_steels --------------- -Matbench v0.1 dataset for predicting steel yeild strengths from chemical composition alone. Retrieved from Citrine informatics. Deduplicated. +Matbench v0.1 dataset for predicting steel yield strengths from chemical composition alone. Retrieved from Citrine informatics. Deduplicated. **Number of entries:** 312 diff --git a/docs/_sources/featurizer_summary.rst.txt b/docs/_sources/featurizer_summary.rst.txt index a1456c28e..7a1d2c456 100644 --- a/docs/_sources/featurizer_summary.rst.txt +++ b/docs/_sources/featurizer_summary.rst.txt @@ -91,6 +91,8 @@ Features based on a material's composition. - Class to calculate fraction of magnetic transition metals in a composition. * - :code:`CohesiveEnergy` - Cohesive energy per atom using elemental cohesive energies and + * - :code:`CohesiveEnergyMP` + - Cohesive energy per atom lookup using Materials Project * - :code:`Miedema` - Formation enthalpies of intermetallic compounds, from Miedema et al. * - :code:`YangSolidSolution` @@ -207,6 +209,8 @@ Features from individual sites in a material's crystal structure. - A local order parameter fingerprint for periodic crystals. * - :code:`VoronoiFingerprint` - Voronoi tessellation-based features around target site. + * - :code:`IntersticeDistribution` + - Interstice distribution in the neighboring cluster around an atom site. * - :code:`ChemicalSRO` - Chemical short range ordering, deviation of local site and nominal structure compositions * - :code:`GaussianSymmFunc` diff --git a/docs/_static/documentation_options.js b/docs/_static/documentation_options.js index c20ae8132..0e96c14cc 100644 --- a/docs/_static/documentation_options.js +++ b/docs/_static/documentation_options.js @@ -1,6 +1,6 @@ var DOCUMENTATION_OPTIONS = { URL_ROOT: document.getElementById("documentation_options").getAttribute('data-url_root'), - VERSION: '0.6.2', + VERSION: '0.6.3', LANGUAGE: 'None', COLLAPSE_INDEX: false, FILE_SUFFIX: '.html', diff --git a/docs/changelog.html b/docs/changelog.html index efd69ef15..1d44d07f0 100644 --- a/docs/changelog.html +++ b/docs/changelog.html @@ -4,7 +4,7 @@ - MatMiner Changelog — matminer 0.6.2 documentation + MatMiner Changelog — matminer 0.6.3 documentation @@ -27,7 +27,7 @@

Navigation

  • modules |
    • -
  • matminer 0.6.2 documentation »
    • +
  • matminer 0.6.3 documentation »
    • @@ -38,6 +38,15 @@

    Navigation

    matminer Changelog

    +

    v0.6.3

    +

    v0.6.2

    diff --git a/docs/contributors.html b/docs/contributors.html index 150930c7f..e2126f02f 100644 --- a/docs/contributors.html +++ b/docs/contributors.html @@ -4,7 +4,7 @@ - MatMiner Contributors — matminer 0.6.2 documentation + MatMiner Contributors — matminer 0.6.3 documentation @@ -27,7 +27,7 @@

    Navigation

  • modules |
    • -
  • matminer 0.6.2 documentation »
    • +
  • matminer 0.6.3 documentation »
    • @@ -142,7 +142,7 @@

    Navigation

  • modules |
    • -
  • matminer 0.6.2 documentation »
    • +
  • matminer 0.6.3 documentation »
    • diff --git a/docs/dataset_addition_guide.html b/docs/dataset_addition_guide.html index 3a0087e6c..149e886fd 100644 --- a/docs/dataset_addition_guide.html +++ b/docs/dataset_addition_guide.html @@ -4,7 +4,7 @@ - Guide to adding datasets to matminer — matminer 0.6.2 documentation + Guide to adding datasets to matminer — matminer 0.6.3 documentation @@ -27,7 +27,7 @@

    Navigation

  • modules |
    • -
  • matminer 0.6.2 documentation »
    • +
  • matminer 0.6.3 documentation »
    • @@ -232,8 +232,8 @@

    5. Update the dataset tests and loading code
    def load_elastic_tensor(version="2015", include_metadata=False, data_home=None,
-                        download_if_missing=True):
+
    def load_elastic_tensor(version="2015", include_metadata=False, data_home=None,
+                        download_if_missing=True):
     """
     Convenience function for loading the elastic_tensor dataset.
 
@@ -328,7 +328,7 @@ 
    Navigation
    
         
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diff --git a/docs/dataset_summary.html b/docs/dataset_summary.html
index d4b6d3a66..0f48c5b5f 100644
--- a/docs/dataset_summary.html
+++ b/docs/dataset_summary.html
@@ -4,7 +4,7 @@
 
   
     
-    Datasets Available in Matminer — matminer 0.6.2 documentation
+    Datasets Available in Matminer — matminer 0.6.3 documentation
     
     
     
@@ -27,7 +27,7 @@ 
    Navigation
    
         
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@@ -2011,7 +2011,7 @@ 
    matbench_phonons
 
    matbench_steels
    
-
    Matbench v0.1 dataset for predicting steel yeild strengths from chemical composition alone. Retrieved from Citrine informatics. Deduplicated.
    
+
    Matbench v0.1 dataset for predicting steel yield strengths from chemical composition alone. Retrieved from Citrine informatics. Deduplicated.
    
 
    Number of entries: 312
    
 @@ -2557,7 +2557,7 @@ 
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diff --git a/docs/example_bulkmod.html b/docs/example_bulkmod.html
index d922ac84a..ccfdcea99 100644
--- a/docs/example_bulkmod.html
+++ b/docs/example_bulkmod.html
@@ -4,7 +4,7 @@
 
-    Predicting bulk moduli with matminer — matminer 0.6.2 documentation
+    Predicting bulk moduli with matminer — matminer 0.6.3 documentation
@@ -27,7 +27,7 @@ 
    Navigation
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@@ -52,13 +52,13 @@ 
    Preambleimport warnings
 warnings.filterwarnings('ignore')
 
-import numpy as np
-import pandas as pd
+import numpy as np
+import pandas as pd
 
 # Set pandas view options
 pd.set_option('display.width', 1000)
-pd.set_option('display.max_columns', None)
-pd.set_option('display.max_rows', None)
+pd.set_option('display.max_columns', None)
+pd.set_option('display.max_rows', None)
 
 
 
@@ -67,11 +67,11 @@ 
    Step 1: Use matminer to obtain data from MP (automatically) in a “pandas
 
    Step 1a: Import matminer’s MP data retrieval tool and get calculated bulk moduli and possible descriptors.
    
 
    from matminer.data_retrieval.retrieve_MP import MPDataRetrieval
 
-api_key = None   # Set your MP API key here. If set as an environment variable 'MAPI_KEY', set it to 'None'
+api_key = None   # Set your MP API key here. If set as an environment variable 'MAPI_KEY', set it to 'None'
 mpr = MPDataRetrieval(api_key)     # Create an adapter to the MP Database.
 
 # criteria is to get all entries with elasticity (K_VRH is bulk modulus) data
-criteria = {'elasticity.K_VRH': {'$ne': None}}
+criteria = {'elasticity.K_VRH': {'$ne': None}}
 
 # properties are the materials attributes we want
 # See https://github.com/materialsproject/mapidoc for available properties you can specify
@@ -80,7 +80,7 @@ 
    Step 1: Use matminer to obtain data from MP (automatically) in a “pandas
 
 # get the data!
 df_mp = mpr.get_dataframe(criteria=criteria, properties=properties)
-print 'Number of bulk moduli extracted = {}'.format(len(df_mp))
+print 'Number of bulk moduli extracted = {}'.format(len(df_mp))
 
    
 
    
 
    Number of bulk moduli extracted = 6023
    
@@ -140,7 +140,7 @@ 
    Step 3: Fit a Linear Regression model, get R2 and RMSE'volume', 'nsites', 'spacegroup.symbol', 'e_above_hull', 'composition']]
 X = df_mp.as_matrix(X_cols)
 
-print("Possible descriptors are: {}".format(X_cols))
+print("Possible descriptors are: {}".format(X_cols))
 
 
 
    Possible descriptors are: ['formation_energy_per_atom', 'band_gap', 'density', 'vpa', 'mean X', 'mean atomic_mass',
@@ -158,8 +158,8 @@ 
    Step 3: Fit a Linear Regression model, get R2 and RMSElr.fit(X, y)
 
 # get fit statistics
-print 'R2 = ' + str(round(lr.score(X, y), 3))
-print 'RMSE = %.3f' % np.sqrt(mean_squared_error(y_true=y, y_pred=lr.predict(X)))
+print 'R2 = ' + str(round(lr.score(X, y), 3))
+print 'RMSE = %.3f' % np.sqrt(mean_squared_error(y_true=y, y_pred=lr.predict(X)))
 
    
 
    
 
    R2 = 0.804
@@ -170,15 +170,15 @@ 
    Step 3: Fit a Linear Regression model, get R2 and RMSE
    from sklearn.model_selection import KFold, cross_val_score
 
 # Use 10-fold cross validation (90% training, 10% test)
-crossvalidation = KFold(n_splits=10, shuffle=True, random_state=1)
+crossvalidation = KFold(n_splits=10, shuffle=True, random_state=1)
 
 # compute cross validation scores for random forest model
 scores = cross_val_score(lr, X, y, scoring='mean_squared_error',
                          cv=crossvalidation, n_jobs=1)
 rmse_scores = [np.sqrt(abs(s)) for s in scores]
 
-print 'Cross-validation results:'
-print 'Folds: %i, mean RMSE: %.3f' % (len(scores), np.mean(np.abs(rmse_scores)))
+print 'Cross-validation results:'
+print 'Folds: %i, mean RMSE: %.3f' % (len(scores), np.mean(np.abs(rmse_scores)))
 
    
 
    
 
    Cross-validation results:
@@ -204,9 +204,9 @@ 
    Step 4: Plot the results with FigRecipes'y_col': [0, 400],
              'color': 'black',
              'mode': 'lines',
-             'legend': None,
-             'text': None,
-             'size': None}
+             'legend': None,
+             'text': None,
+             'size': None}
 
 pf.xy_plot(x_col=y,
            y_col=lr.predict(X),
@@ -228,8 +228,8 @@ 
    Step 5: Follow similar steps for a Random Forest modelrf = RandomForestRegressor(n_estimators=50, random_state=1)
 
 rf.fit(X, y)
-print 'R2 = ' + str(round(rf.score(X, y), 3))
-print 'RMSE = %.3f' % np.sqrt(mean_squared_error(y_true=y, y_pred=rf.predict(X)))
+print 'R2 = ' + str(round(rf.score(X, y), 3))
+print 'RMSE = %.3f' % np.sqrt(mean_squared_error(y_true=y, y_pred=rf.predict(X)))
 
    
 
    
 
    R2 = 0.988
@@ -241,8 +241,8 @@ 
    Step 5: Follow similar steps for a Random Forest modelscores = cross_val_score(rf, X, y, scoring='mean_squared_error', cv=crossvalidation, n_jobs=1)
 
 rmse_scores = [np.sqrt(abs(s)) for s in scores]
-print 'Cross-validation results:'
-print 'Folds: %i, mean RMSE: %.3f' % (len(scores), np.mean(np.abs(rmse_scores)))
+print 'Cross-validation results:'
+print 'Folds: %i, mean RMSE: %.3f' % (len(scores), np.mean(np.abs(rmse_scores)))
 
    
 
    
 
    Cross-validation results:
@@ -269,9 +269,9 @@ 
    Step 6: Plot our results and determine what features are the most important<
            'y_col': [0, 450],
            'color': 'black',
            'mode': 'lines',
-           'legend': None,
-           'text': None,
-           'size': None}
+           'legend': None,
+           'text': None,
+           'size': None}
 
 
 pf_rf.xy_plot(x_col=y,
@@ -358,7 +358,7 @@ 
    Navigation
    
         
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           modules |
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  • matminer 0.6.2 documentation »
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diff --git a/docs/featurizer_summary.html b/docs/featurizer_summary.html
index 1f6acc06e..17b46241d 100644
--- a/docs/featurizer_summary.html
+++ b/docs/featurizer_summary.html
@@ -4,7 +4,7 @@
 
   
     
-    Table of Featurizers — matminer 0.6.2 documentation
+    Table of Featurizers — matminer 0.6.3 documentation
     
     
     
@@ -27,7 +27,7 @@ 
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@@ -149,13 +149,16 @@ 
    Features based on a material’s composition.
    
-
+
+
+
+
-
+
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+
@@ -295,40 +298,43 @@ 
    Features from individual sites in a material’s crystal structure.
    
-
+
+
+
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diff --git a/docs/genindex.html b/docs/genindex.html
index 1b6ec6f33..0d2f10e85 100644
--- a/docs/genindex.html
+++ b/docs/genindex.html
@@ -5,7 +5,7 @@
 
-    Index — matminer 0.6.2 documentation
+    Index — matminer 0.6.3 documentation
@@ -28,7 +28,7 @@ 
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@@ -95,6 +95,8 @@ 
    _
  • (matminer.featurizers.composition.AtomicPackingEfficiency method)
 
  • (matminer.featurizers.composition.CohesiveEnergy method)
+
    • 
+        
  • (matminer.featurizers.composition.CohesiveEnergyMP method)
 
  • (matminer.featurizers.composition.ElectronAffinity method)
 
    • 
@@ -175,6 +177,8 @@ 
    _
  • (matminer.featurizers.site.GaussianSymmFunc method)
 
  • (matminer.featurizers.site.GeneralizedRadialDistributionFunction method)
+
    • 
+        
  • (matminer.featurizers.site.IntersticeDistribution method)
 
  • (matminer.featurizers.site.LocalPropertyDifference method)
 
    • 
@@ -282,6 +286,12 @@ 
    A
  • AbstractPairwise (class in matminer.featurizers.utils.grdf)
 
  • AGNIFingerprints (class in matminer.featurizers.site)
+
    • 
+      
  • analyze_area_interstice() (matminer.featurizers.site.IntersticeDistribution static method)
+
    • 
+      
  • analyze_dist_interstices() (matminer.featurizers.site.IntersticeDistribution static method)
+
    • 
+      
  • analyze_vol_interstice() (matminer.featurizers.site.IntersticeDistribution static method)
 
  • AngularFourierSeries (class in matminer.featurizers.site)
 
    • 
@@ -399,6 +409,8 @@ 
    C
  • (matminer.featurizers.composition.CationProperty method)
 
  • (matminer.featurizers.composition.CohesiveEnergy method)
+
    • 
+        
  • (matminer.featurizers.composition.CohesiveEnergyMP method)
 
  • (matminer.featurizers.composition.ElectronAffinity method)
 
    • 
@@ -471,6 +483,8 @@ 
    C
  • (matminer.featurizers.site.GaussianSymmFunc method)
 
  • (matminer.featurizers.site.GeneralizedRadialDistributionFunction method)
+
    • 
+        
  • (matminer.featurizers.site.IntersticeDistribution method)
 
  • (matminer.featurizers.site.LocalPropertyDifference method)
 
    • 
@@ -548,6 +562,8 @@ 
    C
  • CohesiveEnergy (class in matminer.featurizers.composition)
 
  • CohesiveEnergyData (class in matminer.utils.data)
+
    • 
+      
  • CohesiveEnergyMP (class in matminer.featurizers.composition)
 
  • compile_crystal() (matminer.data_retrieval.retrieve_MPDS.MPDSDataRetrieval static method)
 
    • 
@@ -693,6 +709,8 @@ 
    F
  • (matminer.featurizers.composition.CationProperty method)
 
  • (matminer.featurizers.composition.CohesiveEnergy method)
+
    • 
+        
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  • (matminer.featurizers.composition.ElectronAffinity method)
 
    • 
@@ -757,6 +775,8 @@ 
    F
  • (matminer.featurizers.site.GaussianSymmFunc method)
 
  • (matminer.featurizers.site.GeneralizedRadialDistributionFunction method)
+
    • 
+        
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  • (matminer.featurizers.site.LocalPropertyDifference method)
 
    • 
@@ -847,6 +867,8 @@ 
    F
  • (matminer.featurizers.composition.CationProperty method)
 
  • (matminer.featurizers.composition.CohesiveEnergy method)
+
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+        
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  • (matminer.featurizers.composition.ElectronAffinity method)
 
    • 
@@ -927,6 +949,8 @@ 
    F
  • (matminer.featurizers.site.GaussianSymmFunc method)
 
  • (matminer.featurizers.site.GeneralizedRadialDistributionFunction method)
+
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+        
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  • (matminer.featurizers.site.LocalPropertyDifference method)
 
    • 
@@ -1303,6 +1327,8 @@ 
    I
  • (matminer.featurizers.composition.BandCenter method)
 
  • (matminer.featurizers.composition.CohesiveEnergy method)
+
    • 
+        
  • (matminer.featurizers.composition.CohesiveEnergyMP method)
 
  • (matminer.featurizers.composition.ElectronAffinity method)
 
    • 
@@ -1381,6 +1407,8 @@ 
    I
  • (matminer.featurizers.site.GaussianSymmFunc method)
 
  • (matminer.featurizers.site.GeneralizedRadialDistributionFunction method)
+
    • 
+        
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  • (matminer.featurizers.site.LocalPropertyDifference method)
 
    • 
@@ -1452,6 +1480,8 @@ 
    I
  • initialize_pairwise_function() (in module matminer.featurizers.utils.grdf)
 
  • interpolate_soft_anions() (matminer.utils.data.IUCrBondValenceData method)
+
    • 
+      
  • IntersticeDistribution (class in matminer.featurizers.site)
 
  • inverse_mean() (matminer.featurizers.utils.stats.PropertyStats static method)
 
    • 
@@ -2044,6 +2074,8 @@ 
    T
  • test_cns() (matminer.featurizers.tests.test_site.FingerprintTests method)
 
  • test_cohesive_energy() (matminer.featurizers.tests.test_composition.CompositionFeaturesTest method)
+
    • 
+      
  • test_cohesive_energy_mp() (matminer.featurizers.tests.test_composition.CompositionFeaturesTest method)
 
  • test_composition_features() (matminer.featurizers.tests.test_structure.StructureFeaturesTest method)
 
    • 
@@ -2218,6 +2250,10 @@ 
    T
  • test_indices() (matminer.featurizers.tests.test_base.TestBaseClass method)
 
  • test_inplace() (matminer.featurizers.tests.test_base.TestBaseClass method)
+
    • 
+      
  • test_interstice_distribution_of_crystal() (matminer.featurizers.tests.test_site.FingerprintTests method)
+
    • 
+      
  • test_interstice_distribution_of_glass() (matminer.featurizers.tests.test_site.FingerprintTests method)
 
  • test_ionic() (matminer.featurizers.tests.test_composition.CompositionFeaturesTest method)
 
    • 
@@ -2530,7 +2566,7 @@ 
    Navigation
  • 
           modules |
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  • matminer 0.6.2 documentation »
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+        
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diff --git a/docs/index.html b/docs/index.html
index 09788612d..bf4695585 100644
--- a/docs/index.html
+++ b/docs/index.html
@@ -4,7 +4,7 @@
 
-    matminer (Materials Data Mining) — matminer 0.6.2 documentation
+    matminer (Materials Data Mining) — matminer 0.6.3 documentation
@@ -27,7 +27,7 @@ 
    Navigation
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           modules |
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+        
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@@ -254,7 +254,7 @@ 
    Navigation
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diff --git a/docs/installation.html b/docs/installation.html
index 7ea68f58a..4332f6aec 100644
--- a/docs/installation.html
+++ b/docs/installation.html
@@ -4,7 +4,7 @@
 
-    Installing matminer — matminer 0.6.2 documentation
+    Installing matminer — matminer 0.6.3 documentation
@@ -27,7 +27,7 @@ 
    Navigation
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diff --git a/docs/matminer.data_retrieval.html b/docs/matminer.data_retrieval.html
index 444fee151..6f61722e8 100644
--- a/docs/matminer.data_retrieval.html
+++ b/docs/matminer.data_retrieval.html
@@ -4,7 +4,7 @@
 
-    matminer.data_retrieval package — matminer 0.6.2 documentation
+    matminer.data_retrieval package — matminer 0.6.3 documentation
@@ -27,7 +27,7 @@ 
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           modules |
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-        
  • matminer 0.6.2 documentation »
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@@ -325,7 +325,7 @@ 
    matminer.data_retrieval.retrieve_AFLOW module
 
    
-get_data(criteria, properties, mp_decode=False, index_mpid=True)
    
+get_data(criteria, properties, mp_decode=True, index_mpid=True)
 
    
 
    Args:
    
 
    criteria: (str/dict) see MPRester.query() for a description of this
    parameter. String examples: “mp-1234”, “Fe2O3”, “Li-Fe-O’,
@@ -399,7 +399,7 @@ 
    matminer.data_retrieval.retrieve_AFLOW module
 
    
 exception matminer.data_retrieval.retrieve_MPDS.APIError(msg, code=0)
    
-
    Bases: Exception
    
+
    Bases: Exception
    
 
    Simple error handling
    
 
    
 
    
@@ -648,7 +648,7 @@ 
    matminer.data_retrieval.retrieve_AFLOW module
 
    
 class matminer.data_retrieval.retrieve_base.BaseDataRetrieval
    
-
    Bases: object
    
+
    Bases: object
    
 
    Abstract class to retrieve data from various material APIs while adhering to
 a quasi-standard format for querying.
    
 
    ## Implementing a new DataRetrieval class
    
@@ -790,7 +790,7 @@ 
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diff --git a/docs/matminer.data_retrieval.tests.html b/docs/matminer.data_retrieval.tests.html
index 2263a4767..bb63b31de 100644
--- a/docs/matminer.data_retrieval.tests.html
+++ b/docs/matminer.data_retrieval.tests.html
@@ -4,7 +4,7 @@
 
   
     
-    matminer.data_retrieval.tests package — matminer 0.6.2 documentation
+    matminer.data_retrieval.tests package — matminer 0.6.3 documentation
     
     
     
@@ -27,7 +27,7 @@ 
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@@ -214,7 +214,7 @@ 
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diff --git a/docs/matminer.datasets.html b/docs/matminer.datasets.html
index aad324eab..5a088831c 100644
--- a/docs/matminer.datasets.html
+++ b/docs/matminer.datasets.html
@@ -4,7 +4,7 @@
 
   
     
-    matminer.datasets package — matminer 0.6.2 documentation
+    matminer.datasets package — matminer 0.6.3 documentation
     
     
     
@@ -27,7 +27,7 @@ 
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@@ -683,7 +683,7 @@ 
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diff --git a/docs/matminer.datasets.tests.html b/docs/matminer.datasets.tests.html
index eec9cd98b..4a280628b 100644
--- a/docs/matminer.datasets.tests.html
+++ b/docs/matminer.datasets.tests.html
@@ -4,7 +4,7 @@
 
   
     
-    matminer.datasets.tests package — matminer 0.6.2 documentation
+    matminer.datasets.tests package — matminer 0.6.3 documentation
     
     
     
@@ -27,7 +27,7 @@ 
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@@ -238,7 +238,7 @@ 
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diff --git a/docs/matminer.featurizers.html b/docs/matminer.featurizers.html
index 0abb61d2f..d2e8e58bd 100644
--- a/docs/matminer.featurizers.html
+++ b/docs/matminer.featurizers.html
@@ -4,7 +4,7 @@
 
   
     
-    matminer.featurizers package — matminer 0.6.2 documentation
+    matminer.featurizers package — matminer 0.6.3 documentation
     
     
     
@@ -27,7 +27,7 @@ 
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  • matminer 0.6.2 documentation »
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@@ -1402,6 +1402,73 @@ 
    Submodules
+
    
+class matminer.featurizers.composition.CohesiveEnergyMP(mapi_key=None)
    
+
    Bases: matminer.featurizers.base.BaseFeaturizer
    
+
    Cohesive energy per atom lookup using Materials Project
    
+
    
+
    Parameters:
    
+
    mapi_key (str): Materials API key for looking up cohesive energy
    by composition alone.
    
+
    
+
    
+
    
+
    
+
    
+
    
+__init__(mapi_key=None)
    
+
    Initialize self.  See help(type(self)) for accurate signature.
    
+
    
+
+
    
+
    
+citations()
    
+
    Citation(s) and reference(s) for this feature.
    
+
    
+
    Returns:
    
+
    (list) each element should be a string citation,
    ideally in BibTeX format.
    
+
    
+
    
+
    
+
    
+
    
+
+
    
+
    
+feature_labels()
    
+
    Generate attribute names.
    
+
    
+
    Returns:
    ([str]) attribute labels.
    
+
    
+
    
+
    
+
+
    
+
    
+featurize(comp)
    
+
    
+
    Args:
    comp: (str) compound composition, eg: “NaCl”
    
+
    
+
    
+
    
+
+
    
+
    
+implementors()
    
+
    List of implementors of the feature.
    
+
    
+
    Returns:
    
+
    (list) each element should either be a string with author name (e.g.,
    “Anubhav Jain”) or a dictionary  with required key “name” and other
+keys like “email” or “institution” (e.g., {“name”: “Anubhav
+Jain”, “email”: “ajain@lbl.gov”, “institution”: “LBNL”}).
    
+
    
+
    
+
    
+
    
+
    
+
+
    
+
 
    
 
    
 class matminer.featurizers.composition.ElectronAffinity
    
@@ -5257,6 +5324,163 @@ 
    Submodules
+
    
+class matminer.featurizers.site.IntersticeDistribution(cutoff=6.5, interstice_types=None, stats=None, radius_type='MiracleRadius')
    
+
    Bases: matminer.featurizers.base.BaseFeaturizer
    
+
    Interstice distribution in the neighboring cluster around an atom site.
    
+
    The interstices are categorized to distance, area and volume interstices.
+Each of these metrics is a measures of the relative amount of empty space
+around each atom as determined using atomic sphere models. The distance
+interstice is the fraction of a bonding line unoccupied by the atom spheres;
+The area interstice is the unoccupied area within the triangulated surface
+formed by atom triplets in convex hull formed by neighbors, and the volume
+interstice is the unoccupied portion of a tetrahedron formed between the
+central atom and neighbor atom triplets. Please refer to the original paper
+for more details (Wang et al. Nat Commun 10, 5537 (2019))
    
+
    For amorphous alloys (metallic glasses), the coordination environments are
+anisotropic, which can be reflected in the inequality of the interstices
+present around an atom. To describe the anisotropy, here we derive statistics
+of the interstices to featurize the interstice distribution around the atom.
+Other methods can be grouping the interstices into histogram grids of fixed
+bins and the features are then a vector of the values of the histograms.
    
+
    User note:
+This class is particularly designed for featuring the site-specific packing
+heterogeneity in metallic glasses, especially the all-metallic-element ones.
+If non-metallic-elements are present in the structures, the interstice
+estimates may have larger deviation from actual values (despite this
+deviation is systematic and thus the interstice estimates can still be
+used to represent the packing heterogeneity).
    
+
    
+
    Args:
    
+
    cutoff (float): cutoff distance in determining the potential
    neighbors for Voronoi tessellation analysis. (default: 6.5)
    
+
    
+
    interstice_types (str or [str]): interstice distribution types,
    support sub-list of [‘dist’, ‘area’, ‘vol’].
    
+
    
+
    
+
    stats ([str]): statistics of distance/area/volume interstices.
+radius_type (str): source of radius estimate. (default: “MiracleRadius”)
    
+
    
+
    
+
    
+
    
+__init__(cutoff=6.5, interstice_types=None, stats=None, radius_type='MiracleRadius')
    
+
    Initialize self.  See help(type(self)) for accurate signature.
    
+
    
+
+
    
+
    
+static analyze_area_interstice(nn_coords, nn_rs, convex_hull_simplices)
    
+
    Analyze the area interstices in the neighbor convex hull facets.
+Args:
    
+
    
+
    nn_coords (array-like, shape (N, 3)): Nearest Neighbors’ coordinates
+nn_rs ([float]): Nearest Neighbors’ radii.
+convex_hull_simplices (array-like, shape (M, 3)): Indices of points
    
+
    
+
    forming the simplicial facets of convex hull.
    
+
    
+
    
+
    
+
    Returns:
    area_interstice_list ([float]): Area interstice list.
    
+
    
+
    
+
    
+
+
    
+
    
+static analyze_dist_interstices(center_r, nn_rs, nn_dists)
    
+
    Analyze the distance interstices between center atom and neighbors.
+Args:
    
+
    
+
    center_r (float): central atom’s radius.
+nn_rs ([float]): Nearest Neighbors’ radii.
+nn_dists ([float]): Nearest Neighbors’ distances.
    
+
    
+
    
+
    Returns:
    dist_interstice_list ([float]): Distance interstice list.
    
+
    
+
    
+
    
+
+
    
+
    
+static analyze_vol_interstice(center_coords, nn_coords, center_r, nn_rs, convex_hull_simplices)
    
+
    Analyze the volume interstices in the tetrahedra formed by center
+atom and neighbor convex hull triplets.
+Args:
    
+
    
+
    center_coords ([float]): Central atomic coordinates.
+nn_coords (array-like, shape (N, 3)): Nearest Neighbors’ coordinates
+center_r (float): central atom’s radius.
+nn_rs ([float]): Nearest Neighbors’ radii.
+convex_hull_simplices (array-like, shape (M, 3)): Indices of points
    
+
    
+
    forming the simplicial facets of convex hull.
    
+
    
+
    
+
    
+
    Returns:
    volume_interstice_list ([float]): Volume interstice list.
    
+
    
+
    
+
    
+
+
    
+
    
+citations()
    
+
    Citation(s) and reference(s) for this feature.
    
+
    
+
    Returns:
    
+
    (list) each element should be a string citation,
    ideally in BibTeX format.
    
+
    
+
    
+
    
+
    
+
    
+
+
    
+
    
+feature_labels()
    
+
    Generate attribute names.
    
+
    
+
    Returns:
    ([str]) attribute labels.
    
+
    
+
    
+
    
+
+
    
+
    
+featurize(struct, idx)
    
+
    Get interstice distribution fingerprints of site with given index in
+input structure.
+Args:
    
+
    
+
    struct (Structure): Pymatgen Structure object.
+idx (int): index of target site in structure.
    
+
    
+
    
+
    Returns:
    interstice_fps ([float]): Interstice distribution fingerprints.
    
+
    
+
    
+
    
+
+
    
+
    
+implementors()
    
+
    List of implementors of the feature.
    
+
    
+
    Returns:
    
+
    (list) each element should either be a string with author name (e.g.,
    “Anubhav Jain”) or a dictionary  with required key “name” and other
+keys like “email” or “institution” (e.g., {“name”: “Anubhav
+Jain”, “email”: “ajain@lbl.gov”, “institution”: “LBNL”}).
    
+
    
+
    
+
    
+
    
+
    
+
+
    
+
 
    
 
    
 class matminer.featurizers.site.LocalPropertyDifference(data_source=<matminer.utils.data.MagpieData object>, weight='area', properties=('Electronegativity', ), signed=False)
    
@@ -6541,17 +6765,17 @@ 
    Submodules
 
    
-class matminer.featurizers.structure.Dimensionality(**kwargs)
    
+class matminer.featurizers.structure.Dimensionality(nn_method=<pymatgen.analysis.local_env.CrystalNN object>)
 
    Bases: matminer.featurizers.base.BaseFeaturizer
    
 
    Returns dimensionality of structure: 1 means linear chains of atoms OR
 isolated atoms/no bonds, 2 means layered, 3 means 3D connected
 structure. This feature is sensitive to bond length tables that you use.
    
 
    
 
    
-__init__(**kwargs)
    
+__init__(nn_method=<pymatgen.analysis.local_env.CrystalNN object>)
 
    
 
    Args:
    
-
    **kwargs: keyword args to pass to get_dimensionality() method of
    pymatgen.
    
+
    **nn_method: The nearest neighbor method used to determine atomic
    connectivity.
    
 
    
 
    
 
    
@@ -7936,7 +8160,7 @@ 
    Submodules*Note for nth mode, stat must be ‘n*_mode’; e.g. stat=‘2nd_mode’
    
+*Note for nth mode, stat must be ‘n*_mode’; e.g. stat=’2nd_mode’
    
 
 
    
 
    min_oxi (int): minimum site oxidation state for inclusion (e.g.,
    zero means metals/cations only)
    
@@ -8424,7 +8648,7 @@ 
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diff --git a/docs/matminer.featurizers.tests.html b/docs/matminer.featurizers.tests.html
index 3e2e96f4d..0aa4edd21 100644
--- a/docs/matminer.featurizers.tests.html
+++ b/docs/matminer.featurizers.tests.html
@@ -4,7 +4,7 @@
 
   
     
-    matminer.featurizers.tests package — matminer 0.6.2 documentation
+    matminer.featurizers.tests package — matminer 0.6.3 documentation
     
     
     
@@ -27,7 +27,7 @@ 
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@@ -626,6 +626,11 @@ 
    Submodulestest_cohesive_energy()
 
    
 
+
    
+
    
+test_cohesive_energy_mp()
    
+
    
+
 
    
 
    
 test_elec_affin()
    
@@ -947,6 +952,16 @@ 
    Submodulestest_grdf()
 
    
 
+
    
+
    
+test_interstice_distribution_of_crystal()
    
+
    
+
+
    
+
    
+test_interstice_distribution_of_glass()
    
+
    
+
 
    
 
    
 test_local_prop_diff()
    
@@ -1186,7 +1201,7 @@ 
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diff --git a/docs/matminer.featurizers.utils.html b/docs/matminer.featurizers.utils.html
index 214cc6890..818a1e0d6 100644
--- a/docs/matminer.featurizers.utils.html
+++ b/docs/matminer.featurizers.utils.html
@@ -4,7 +4,7 @@
 
   
     
-    matminer.featurizers.utils package — matminer 0.6.2 documentation
+    matminer.featurizers.utils package — matminer 0.6.3 documentation
     
     
     
@@ -27,7 +27,7 @@ 
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@@ -61,7 +61,7 @@ 
    Submodules
 
    
 class matminer.featurizers.utils.cgcnn.AtomCustomArrayInitializer(elem_embedding)
    
-
    Bases: object
    
+
    Bases: object
    
 
    Initialize atom feature vectors using a JSON file, which is a python
 dictionary mapping from element number to a list representing the
 feature vector of the element.
    
@@ -80,7 +80,7 @@ 
    Submodules
 
    
 class matminer.featurizers.utils.cgcnn.CIFDataWrapper(X, y, atom_init_fea, max_num_nbr=12, radius=8, dmin=0, step=0.2, random_seed=123)
    
-
    Bases: object
    
+
    Bases: object
    
 
    Wrapper for a dataset containing pymatgen Structure objects.
 This is modified from CGCNN repo’s CIFData for wrapping dataset where the
 structures are stored in CIF files.
@@ -107,7 +107,7 @@ 
    Submodules
 
    
 class matminer.featurizers.utils.cgcnn.CrystalGraphConvNetWrapper(orig_atom_fea_len, nbr_fea_len, atom_fea_len=64, n_conv=3, h_fea_len=128, n_h=1, classification=False)
    
-
    Bases: object
    
+
    Bases: object
    
 
    Wrapper for CrystalGraphConvNet in the CGCNN repo and add extract_feature
 function to extract the feature vector after pooling layer of CGCNN model
 as features for the structures.
@@ -176,7 +176,7 @@ 
    Submodules
 
    
 class matminer.featurizers.utils.grdf.AbstractPairwise
    
-
    Bases: object
    
+
    Bases: object
    
 
    Abstract class for pairwise functions used in Generalized Radial Distribution Function
    
 
    
 
    
@@ -355,7 +355,7 @@ 
    Submodules
 
    
 class matminer.featurizers.utils.stats.PropertyStats
    
-
    Bases: object
    
+
    Bases: object
    
 
    This class contains statistical operations that are commonly employed
 when computing features.
    
 
    The primary way for interacting with this class is to call the
@@ -656,7 +656,7 @@ 
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  • matminer 0.6.2 documentation »
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+        
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diff --git a/docs/matminer.featurizers.utils.tests.html b/docs/matminer.featurizers.utils.tests.html
index f799b5a9b..1db3d85fc 100644
--- a/docs/matminer.featurizers.utils.tests.html
+++ b/docs/matminer.featurizers.utils.tests.html
@@ -4,7 +4,7 @@
 
   
     
-    matminer.featurizers.utils.tests package — matminer 0.6.2 documentation
+    matminer.featurizers.utils.tests package — matminer 0.6.3 documentation
     
     
     
@@ -27,7 +27,7 @@ 
    Navigation
    
         
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  • matminer 0.6.2 documentation »
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+        
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@@ -248,7 +248,7 @@ 
    Navigation
    
         
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  • matminer 0.6.2 documentation »
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+        
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diff --git a/docs/matminer.figrecipes.html b/docs/matminer.figrecipes.html
index 8304e14f3..ba3816606 100644
--- a/docs/matminer.figrecipes.html
+++ b/docs/matminer.figrecipes.html
@@ -4,7 +4,7 @@
 
   
     
-    matminer.figrecipes package — matminer 0.6.2 documentation
+    matminer.figrecipes package — matminer 0.6.3 documentation
     
     
     
@@ -27,7 +27,7 @@ 
    Navigation
    
         
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  • matminer 0.6.2 documentation »
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+        
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@@ -59,7 +59,7 @@ 
    Submodules
 
    
 class matminer.figrecipes.plot.PlotlyFig(df=None, mode='offline', title=None, x_title=None, y_title=None, colorbar_title='auto', x_scale='linear', y_scale='linear', ticksize=25, fontscale=1, fontsize=25, fontfamily='Courier', bgcolor='white', fontcolor=None, colorscale='Viridis', height=None, width=None, resolution_scale=None, margins=100, pad=0, username=None, api_key=None, filename='temp-plot', show_offline_plot=True, hovermode='closest', hoverinfo='x+y+text', hovercolor=None)
    
-
    Bases: object
    
+
    Bases: object
    
 
    
 
    
 __init__(df=None, mode='offline', title=None, x_title=None, y_title=None, colorbar_title='auto', x_scale='linear', y_scale='linear', ticksize=25, fontscale=1, fontsize=25, fontfamily='Courier', bgcolor='white', fontcolor=None, colorscale='Viridis', height=None, width=None, resolution_scale=None, margins=100, pad=0, username=None, api_key=None, filename='temp-plot', show_offline_plot=True, hovermode='closest', hoverinfo='x+y+text', hovercolor=None)
    
@@ -701,7 +701,7 @@ 
    Navigation
    
         
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  • matminer 0.6.2 documentation »
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+        
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diff --git a/docs/matminer.figrecipes.tests.html b/docs/matminer.figrecipes.tests.html
index a855fd010..b8b77646f 100644
--- a/docs/matminer.figrecipes.tests.html
+++ b/docs/matminer.figrecipes.tests.html
@@ -4,7 +4,7 @@
 
   
     
-    matminer.figrecipes.tests package — matminer 0.6.2 documentation
+    matminer.figrecipes.tests package — matminer 0.6.3 documentation
     
     
     
@@ -27,7 +27,7 @@ 
    Navigation
    
         
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@@ -176,7 +176,7 @@ 
    Navigation
    
         
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diff --git a/docs/matminer.html b/docs/matminer.html
index b1f4d0d23..b56c862c9 100644
--- a/docs/matminer.html
+++ b/docs/matminer.html
@@ -4,7 +4,7 @@
 
   
     
-    matminer package — matminer 0.6.2 documentation
+    matminer package — matminer 0.6.3 documentation
     
     
     
@@ -27,7 +27,7 @@ 
    Navigation
    
         
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+        
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@@ -238,7 +238,7 @@ 
    Navigation
    
         
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+        
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diff --git a/docs/matminer.utils.data_files.html b/docs/matminer.utils.data_files.html
index 387f1eb39..a928d9a56 100644
--- a/docs/matminer.utils.data_files.html
+++ b/docs/matminer.utils.data_files.html
@@ -4,7 +4,7 @@
 
   
     
-    matminer.utils.data_files package — matminer 0.6.2 documentation
+    matminer.utils.data_files package — matminer 0.6.3 documentation
     
     
     
@@ -27,7 +27,7 @@ 
    Navigation
    
         
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@@ -95,7 +95,7 @@ 
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diff --git a/docs/matminer.utils.html b/docs/matminer.utils.html
index f35626142..75e83feef 100644
--- a/docs/matminer.utils.html
+++ b/docs/matminer.utils.html
@@ -4,7 +4,7 @@
 
   
     
-    matminer.utils package — matminer 0.6.2 documentation
+    matminer.utils package — matminer 0.6.3 documentation
     
     
     
@@ -27,7 +27,7 @@ 
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           modules |
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@@ -104,7 +104,7 @@ 
    Submodules
 
    
 class matminer.utils.data.AbstractData
    
-
    Bases: object
    
+
    Bases: object
    
 
    Abstract class for retrieving elemental properties
    
 
    All classes must implement the get_elemental_property operation. These operations
 should return scalar values (ideally floats) and nan if a property does not exist
    
@@ -224,7 +224,7 @@ 
    Submodules
 
    
 class matminer.utils.data.IUCrBondValenceData(interpolate_soft=True)
    
-
    Bases: object
    
+
    Bases: object
    
 
    Get empirical bond valence parameters.
    
 
    Data come from International Union of Crystallography 2016 tables.
 (https://www.iucr.org/resources/data/datasets/bond-valence-parameters)
@@ -403,7 +403,7 @@ 
    Submodules
 
    
 class matminer.utils.data.MixingEnthalpy
    
-
    Bases: object
    
+
    Bases: object
    
 
    Values of \Delta H^{max}_{AB} for different pairs of elements.
    
 
    
 
    Based on the Miedema model. Tabulated by:
    A. Takeuchi, A. Inoue, Classification of Bulk Metallic Glasses by Atomic
@@ -476,7 +476,7 @@ 
    Submodules
 
    
 class matminer.utils.data.OxidationStatesMixin
    
-
    Bases: object
    
+
    Bases: object
    
 
    Abstract class interface for retrieving the oxidation states
 of each element
    
 
    
@@ -824,7 +824,7 @@ 
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diff --git a/docs/matminer.utils.tests.html b/docs/matminer.utils.tests.html
index 64fc279b2..9ae837e8e 100644
--- a/docs/matminer.utils.tests.html
+++ b/docs/matminer.utils.tests.html
@@ -4,7 +4,7 @@
 
   
     
-    matminer.utils.tests package — matminer 0.6.2 documentation
+    matminer.utils.tests package — matminer 0.6.3 documentation
     
     
     
@@ -27,7 +27,7 @@ 
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@@ -342,7 +342,7 @@ 
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diff --git a/docs/modules.html b/docs/modules.html
index cb5939afc..46c578031 100644
--- a/docs/modules.html
+++ b/docs/modules.html
@@ -4,7 +4,7 @@
 
   
     
-    matminer — matminer 0.6.2 documentation
+    matminer — matminer 0.6.3 documentation
     
     
     
@@ -27,7 +27,7 @@ 
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@@ -145,7 +145,7 @@ 
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package","matminer"],titleterms:{"class":5,"function":[5,13],"import":4,"long":2,Use:4,access:6,add:4,adding:2,analysi:6,arrai:6,automat:4,avail:3,band:6,bandstructur:[5,13],base:[5,12,13],benchmark:6,biggest:6,boltztrap_mp:3,brgoch_superhard_train:3,bulk:4,cach:19,calcul:[4,5],castelli_perovskit:3,cgcnn:15,changelog:[0,6],chicago:1,cite:6,citrin:6,citrine_thermal_conduct:3,code:[2,6],composit:[5,6,13],content:[8,9,10,11,12,13,14,15,16,17,18,19,20,21],contribut:6,contributor:1,convenience_load:11,convers:[5,13,19],crystal:5,data:[4,6,19],data_fil:20,data_retriev:[9,10],databas:6,datafram:[4,6],dataset:[2,3,6,11,12],dataset_retriev:11,decor:6,deml_elementdata:20,densiti:5,deprec:13,deriv:5,descriptor:[4,6],determin:4,develop:7,dielectric_const:3,document:6,dos:[5,13],double_perovskites_gap:3,double_perovskites_gap_lumo:3,either:6,elastic_tensor_2015:3,electron:5,ever:6,exampl:6,expand:5,exploratori:6,expt_formation_enthalpi:3,expt_gap:3,featur:[4,5,6,13,14,15,16],figrecip:[4,6,17,18],file:2,fit:4,flatten_dict:19,flla:3,follow:4,forest:4,fork:2,format:6,from:[4,5,6],gener:5,get:4,github:2,glass_binari:3,glass_binary_v2:3,glass_ternary_hipt:3,glass_ternary_landolt:3,grdf:15,group:1,guid:2,hack:1,heusler_magnet:3,host:2,individu:5,instal:[6,7],interpret:6,jarvis_dft_2d:3,jarvis_dft_3d:3,jarvis_ml_dft_train:3,kernel:19,lbnl:1,leav:6,linear:4,load:2,m2ax:3,made:6,make:2,matbench_dielectr:3,matbench_expt_gap:3,matbench_expt_is_met:3,matbench_glass:3,matbench_jdft2d:3,matbench_log_gvrh:3,matbench_log_kvrh:3,matbench_mp_e_form:3,matbench_mp_gap:3,matbench_mp_is_met:3,matbench_perovskit:3,matbench_phonon:3,matbench_steel:3,materi:[1,4,5,6],matmin:[0,1,2,3,4,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22],meta:5,metadata:2,mine:4,mode:7,model:4,modul:[8,9,10,11,12,13,14,15,16,17,18,19,20,21],moduli:4,most:4,mp_all:3,mp_nostruct:3,obtain:4,other:[1,5],our:4,overview:6,packag:[8,9,10,11,12,13,14,15,16,17,18,19,20,21],panda:[4,6],parent:5,persson:1,phonon_dielectric_mp:3,piezoelectric_tensor:3,pip:7,pipelin:19,plot:[4,6,17],plotli:6,preambl:4,predict:4,prepar:2,preprocess:2,project:[4,6],pull:2,python:6,random:4,readi:6,regress:4,repositori:2,request:2,result:4,retriev:6,retrieve_aflow:9,retrieve_bas:9,retrieve_citrin:9,retrieve_mdf:9,retrieve_mongodb:9,retrieve_mp:9,retrieve_mpd:9,rmse:4,script:2,set:5,similar:4,site:[5,13],stat:15,state:5,steel_strength:3,step:4,structur:[5,6,13],submodul:[9,10,11,12,13,14,15,16,17,18,19,20,21],subpackag:[8,9,11,13,15,17,19],support:6,tabl:5,term:2,test:[2,6,10,12,14,16,18,21],test_bandstructur:14,test_bas:14,test_cach:21,test_cgcnn:16,test_composit:14,test_convenience_load:12,test_convers:[14,21],test_data:21,test_dataset:12,test_dataset_retriev:12,test_do:14,test_flatten_dict:21,test_funct:14,test_grdf:16,test_io:21,test_plot:18,test_retrieve_aflow:10,test_retrieve_citrin:10,test_retrieve_mdf:10,test_retrieve_mongodb:10,test_retrieve_mp:10,test_retrieve_mpd:10,test_sit:14,test_stat:16,test_structur:14,test_util:12,tip:7,tool:6,univers:1,updat:[2,7],upload:2,using:6,util:[5,11,15,16,19,20,21],via:7,what:4,without:6,wolverton_oxid:3,your:2}})
\ No newline at end of file
diff --git a/docs_rst/changelog.rst b/docs_rst/changelog.rst
index 13b20689f..bdb8a1c2b 100644
--- a/docs_rst/changelog.rst
+++ b/docs_rst/changelog.rst
@@ -5,6 +5,16 @@
 matminer Changelog
 ==================
 
+**v0.6.3**
+
+* add IntersticeDistribution featurizer (Q. Wang)
+* change Dimensionality featurizer to be more accurate (A. Ganose)
+* add CohesiveEnergyMP featurizer that gets MP cohesive energy from MP Rester (A. Jain)
+* default mp dataretrieval to decode mp entities by default (A. Dunn)
+* update dependencies and tests (A. Ganose)
+* misc fixes / documentation updates (Q. Wang, A. Dunn, A. Jain, L. Ward, S.P. Ong, A. Ganose)
+
+
 **v0.6.2**
 
 * Update forum to Discourse link (A. Ganose)
diff --git a/docs_rst/dataset_summary.rst b/docs_rst/dataset_summary.rst
index 2edff88d2..c432d3dc6 100644
--- a/docs_rst/dataset_summary.rst
+++ b/docs_rst/dataset_summary.rst
@@ -2040,7 +2040,7 @@ url={http://dx.doi.org/10.1038/sdata.2018.65}
 ---------------
 matbench_steels
 ---------------
-Matbench v0.1 dataset for predicting steel yeild strengths from chemical composition alone. Retrieved from Citrine informatics. Deduplicated.
+Matbench v0.1 dataset for predicting steel yield strengths from chemical composition alone. Retrieved from Citrine informatics. Deduplicated.
 
 **Number of entries:** 312
 
diff --git a/docs_rst/featurizer_summary.rst b/docs_rst/featurizer_summary.rst
index a1456c28e..7a1d2c456 100644
--- a/docs_rst/featurizer_summary.rst
+++ b/docs_rst/featurizer_summary.rst
@@ -91,6 +91,8 @@ Features based on a material's composition.
      - Class to calculate fraction of magnetic transition metals in a composition.     
    * - :code:`CohesiveEnergy`
      - Cohesive energy per atom using elemental cohesive energies and     
+   * - :code:`CohesiveEnergyMP`
+     - Cohesive energy per atom lookup using Materials Project     
    * - :code:`Miedema`
      - Formation enthalpies of intermetallic compounds, from Miedema et al.     
    * - :code:`YangSolidSolution`
@@ -207,6 +209,8 @@ Features from individual sites in a material's crystal structure.
      - A local order parameter fingerprint for periodic crystals.     
    * - :code:`VoronoiFingerprint`
      - Voronoi tessellation-based features around target site.     
+   * - :code:`IntersticeDistribution`
+     - Interstice distribution in the neighboring cluster around an atom site.     
    * - :code:`ChemicalSRO`
      - Chemical short range ordering, deviation of local site and nominal structure compositions     
    * - :code:`GaussianSymmFunc`
diff --git a/matminer/__init__.py b/matminer/__init__.py
index fdf32954c..7e621b18e 100644
--- a/matminer/__init__.py
+++ b/matminer/__init__.py
@@ -1,3 +1,3 @@
-__version__ = '0.6.2'
+__version__ = '0.6.3'
 
 from matminer.figrecipes.plot import PlotlyFig
diff --git a/setup.py b/setup.py
index 1eaef887d..4ad4f8e34 100644
--- a/setup.py
+++ b/setup.py
@@ -31,7 +31,7 @@
 if __name__ == "__main__":
     setup(
         name='matminer',
-        version='0.6.2',
+        version='0.6.3',
         description='matminer is a library that contains tools for data '
                     'mining in Materials Science',
         long_description=open(os.path.join(module_dir, 'README.md')).read(),

    
 

          
       
     
   
     
     
     
     
          
       
     
    CohesiveEnergy
    		
 
    Cohesive energy per atom using elemental cohesive energies and
    		
 
    Miedema
    CohesiveEnergyMP
    Cohesive energy per atom lookup using Materials Project
    Miedema
    		
 
    Formation enthalpies of intermetallic compounds, from Miedema et al.
    		
 
    YangSolidSolution
    YangSolidSolution
    		
 
    Mixing thermochemistry and size mismatch terms of Yang and Zhang (2012)
    		
 
    AtomicPackingEfficiency
    AtomicPackingEfficiency
    		
 
    Packing efficiency based on a geometric theory of the amorphous packing
    		
 
    
 
    VoronoiFingerprint
    		
 
    Voronoi tessellation-based features around target site.
    		
 
    ChemicalSRO
    IntersticeDistribution
    Interstice distribution in the neighboring cluster around an atom site.
    ChemicalSRO
    		
 
    Chemical short range ordering, deviation of local site and nominal structure compositions
    		
 
    GaussianSymmFunc
    GaussianSymmFunc
    		
 
    Gaussian symmetry function features suggested by Behler et al.
    		
 
    EwaldSiteEnergy
    EwaldSiteEnergy
    		
 
    Compute site energy from Coulombic interactions
    		
 
    ChemEnvSiteFingerprint
    ChemEnvSiteFingerprint
    		
 
    Resemblance of given sites to ideal environments
    		
 
    CoordinationNumber
    CoordinationNumber
    		
 
    Number of first nearest neighbors of a site.
    		
 
    GeneralizedRadialDistributionFunction
    GeneralizedRadialDistributionFunction
    		
 
    Compute the general radial distribution function (GRDF) for a site.
    		
 
    AngularFourierSeries
    AngularFourierSeries
    		
 
    Compute the angular Fourier series (AFS), including both angular and radial info
    		
 
    LocalPropertyDifference
    LocalPropertyDifference
    		
 
    Differences in elemental properties between site and its neighboring sites.
    		
 
    BondOrientationalParameter
    BondOrientationalParameter
    		
 
    Averages of spherical harmonics of local neighbors
    		
 
    SiteElementalProperty
    SiteElementalProperty
    		
 
    Elemental properties of atom on a certain site
    		
 
    AverageBondLength
    AverageBondLength
    		
 
    Determines the average bond length between one specific site
    		
 
    AverageBondAngle
    AverageBondAngle
    		
 
    Determines the average bond angles of a specific site with