From e0a05c8e53983b4a57ecfbd2f838de784903433b Mon Sep 17 00:00:00 2001 From: Anubhav Jain Date: Fri, 6 Jul 2018 10:56:13 -0700 Subject: [PATCH] Update to v0.3.6 --- docs/_sources/changelog.rst.txt | 8 +++ docs/_sources/contributors.rst.txt | 1 + docs/_sources/matminer.utils.rst.txt | 8 +++ docs/_static/documentation_options.js | 2 +- docs/changelog.html | 13 +++- docs/contributors.html | 7 ++- docs/example_bulkmod.html | 6 +- docs/featurizer_summary.html | 6 +- docs/genindex.html | 20 +++--- docs/index.html | 6 +- docs/installation.html | 6 +- docs/matminer.data_retrieval.html | 46 ++++++++++++-- docs/matminer.datasets.html | 6 +- docs/matminer.datasets.test_datasets.html | 6 +- docs/matminer.descriptors.html | 6 +- docs/matminer.distance_metrics.html | 6 +- docs/matminer.featurizers.data_files.html | 6 +- docs/matminer.featurizers.html | 14 ++--- docs/matminer.figrecipes.html | 8 +-- ...tminer.figrecipes.matplotlib.examples.html | 6 +- docs/matminer.figrecipes.matplotlib.html | 6 +- docs/matminer.figrecipes.plotly.html | 6 +- docs/matminer.html | 7 ++- docs/matminer.learners.html | 6 +- docs/matminer.learners.tests.html | 6 +- docs/matminer.models.html | 6 +- docs/matminer.utils.data_files.html | 6 +- docs/matminer.utils.html | 58 ++++++++++-------- docs/matminer.utils.tests.html | 6 +- docs/modules.html | 7 ++- docs/objects.inv | Bin 4336 -> 4362 bytes docs/py-modindex.html | 11 +++- docs/search.html | 6 +- docs/searchindex.js | 2 +- docs_rst/changelog.rst | 8 +++ docs_rst/contributors.rst | 1 + docs_rst/matminer.utils.rst | 8 +++ matminer/__init__.py | 2 +- setup.py | 2 +- 39 files changed, 216 insertions(+), 125 deletions(-) diff --git a/docs/_sources/changelog.rst.txt b/docs/_sources/changelog.rst.txt index 54ed2728e..b0f64d627 100644 --- a/docs/_sources/changelog.rst.txt +++ b/docs/_sources/changelog.rst.txt @@ -5,6 +5,14 @@ matminer Changelog ================== + +**v0.3.6** + +* Improve MPDataRetrieval to serialize objects (A. Faghaninia) +* Some fixes to GDRF and AFS (L. Williams, M. Dylla) +* Some fixes for Ewald (A. Faghaninia) +* improve error messages (A. Jain) + **v0.3.5** * some tools for sklearn Pipeline integration (J. Brenneck) diff --git a/docs/_sources/contributors.rst.txt b/docs/_sources/contributors.rst.txt index b3a1e8649..533cf0470 100644 --- a/docs/_sources/contributors.rst.txt +++ b/docs/_sources/contributors.rst.txt @@ -48,3 +48,4 @@ Other * Evgeny Blokhin (Tilde Lab) * Max Dylla (Snyder Research Group, Northwestern University) * David Waroquiers (UC Louvain, Belgium) +* Logan Williams (U Michigan Ann Arbor) \ No newline at end of file diff --git a/docs/_sources/matminer.utils.rst.txt b/docs/_sources/matminer.utils.rst.txt index b1af52f2e..a35101be5 100644 --- a/docs/_sources/matminer.utils.rst.txt +++ b/docs/_sources/matminer.utils.rst.txt @@ -60,6 +60,14 @@ matminer.utils.pipeline module :undoc-members: :show-inheritance: +matminer.utils.utils module +--------------------------- + +.. automodule:: matminer.utils.utils + :members: + :undoc-members: + :show-inheritance: + Module contents --------------- diff --git a/docs/_static/documentation_options.js b/docs/_static/documentation_options.js index 49a94c75b..876142acf 100644 --- a/docs/_static/documentation_options.js +++ b/docs/_static/documentation_options.js @@ -1,6 +1,6 @@ var DOCUMENTATION_OPTIONS = { URL_ROOT: '', - VERSION: '0.3.5', + VERSION: '0.3.6', LANGUAGE: 'None', COLLAPSE_INDEX: false, FILE_SUFFIX: '.html', diff --git a/docs/changelog.html b/docs/changelog.html index fa180e058..6fa21894e 100644 --- a/docs/changelog.html +++ b/docs/changelog.html @@ -6,7 +6,7 @@ - MatMiner Changlog — matminer 0.3.5 documentation + MatMiner Changlog — matminer 0.3.6 documentation @@ -28,7 +28,7 @@

Navigation

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  • matminer 0.3.5 documentation »
    • +
  • matminer 0.3.6 documentation »
    • @@ -39,6 +39,13 @@

    Navigation

    matminer Changelog

    +

    v0.3.6

    +

    v0.3.5

    diff --git a/docs/contributors.html b/docs/contributors.html index 9bb4db4eb..3ac415a3b 100644 --- a/docs/contributors.html +++ b/docs/contributors.html @@ -6,7 +6,7 @@ - MatMiner Contributors — matminer 0.3.5 documentation + MatMiner Contributors — matminer 0.3.6 documentation @@ -28,7 +28,7 @@

    Navigation

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    • @@ -79,6 +79,7 @@

    Other
  • Evgeny Blokhin (Tilde Lab)
  • Max Dylla (Snyder Research Group, Northwestern University)
  • David Waroquiers (UC Louvain, Belgium)
    • +
  • Logan Williams (U Michigan Ann Arbor)
    • @@ -132,7 +133,7 @@

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    • diff --git a/docs/example_bulkmod.html b/docs/example_bulkmod.html index 2e2b3c316..a24cd0029 100644 --- a/docs/example_bulkmod.html +++ b/docs/example_bulkmod.html @@ -6,7 +6,7 @@ - Predicting bulk moduli with matminer — matminer 0.3.5 documentation + Predicting bulk moduli with matminer — matminer 0.3.6 documentation @@ -28,7 +28,7 @@

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    • @@ -927,7 +927,7 @@

    H

  • holder_mean() (matminer.featurizers.stats.PropertyStats static method)
    • -
  • homogenize_multiindex() (in module matminer.utils.conversions) +
  • homogenize_multiindex() (in module matminer.utils.utils)
    • @@ -1143,10 +1143,10 @@

    M

  • matminer.figrecipes.plot (module)
    • - - +
  • test_json_to_object() (matminer.utils.tests.test_conversions.TestConversions method)
    • - - +
  • triangle() (matminer.figrecipes.plot.PlotlyFig method) +
    • +
  • try_get_prop_by_material_id() (matminer.data_retrieval.retrieve_MP.MPDataRetrieval method)
    • @@ -1456,7 +1460,7 @@

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    • @@ -326,12 +326,46 @@

    Submodules
    Args:
    -
    all arguments including criteria, properties and index_mpid are the -same as in get_data
    +

    criteria (dict): the same as in get_data +properties ([str]): the same properties supported as in get_data

    +
    +
    plus: “structure”, “initial_structure”, “final_structure”, +“bandstructure” (line mode), “bandstructure_uniform”, +“phonon_bandstructure”, “phonon_ddb”, “phonon_bandstructure”, +“phonon_dos”. Note that for a long list of compounds, it may +take a long time to retrieve some of these objects.
    +

    index_mpid (bool): the same as in get_data +kwargs (dict): the same keyword arguments as in get_data

    +

    Returns (pandas.Dataframe):

    +
    +
    +try_get_prop_by_material_id(prop, material_id_list, **kwargs)
    +

    Call the relevant get_prop_by_material_id. “prop” is a property such +as bandstructure that is not readily available in supported properties +of the get_data function but via the get_bandstructure_by_material_id +method for example.

    +
    +
    Args:
    +
    +
    prop (str): the name of the property. Options are:
    +
    “bandstructure”, “dos”, “phonon_dos”, “phonon_bandstructure”, +“phonon_ddb”
    +
    +

    material_id_list ([str]): list of material_id of compounds +kwargs (dict): other keyword arguments that get_*_by_material_id

    +
    +
    may have; e.g. line_mode in get_bandstructure_by_material_id
    +
    +
    Returns ([target prop object or NaN]):
    +
    If the target property is not available for a certain material_id, +NaN is returned.
    +
    +
    + @@ -420,7 +454,7 @@

    matminer.data_retrieval.retrieve_MPDS 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

    @@ -564,7 +598,7 @@

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    • @@ -3957,7 +3957,7 @@

    Submodules
    -static from_preset(width=0.5, spacing=0.5, cutoff=10, mode='GRDF')
    +static from_preset(width=1.0, spacing=1.0, cutoff=10, mode='GRDF')
    Preset bin functionals for this featurizer. Example use:
    >>> GRDF = GeneralizedRadialDistributionFunction.from_preset('gaussian')
@@ -4353,7 +4353,7 @@ 
    Submodules
 
    
 class matminer.featurizers.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
@@ -5304,7 +5304,7 @@ 
    Submodules
 
    
-class matminer.featurizers.structure.EwaldEnergy(accuracy=None)
    
+class matminer.featurizers.structure.EwaldEnergy(accuracy=4)
 
    Bases: matminer.featurizers.base.BaseFeaturizer
    
 
    Compute the energy from Coulombic interactions.
    
 
    Note: The energy is computed using _charges already defined for the structure_.
    
@@ -5314,7 +5314,7 @@ 
    Submodules
 
    
-__init__(accuracy=None)
    
+__init__(accuracy=4)
 
    
 
    Args:
    
 
    accuracy (int): Accuracy of Ewald summation, number of decimal places
    
@@ -6519,7 +6519,7 @@ 
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    diff --git a/docs/matminer.figrecipes.html b/docs/matminer.figrecipes.html index 29908c602..f12095e4a 100644 --- a/docs/matminer.figrecipes.html +++ b/docs/matminer.figrecipes.html @@ -6,7 +6,7 @@ - matminer.figrecipes package — matminer 0.3.5 documentation + matminer.figrecipes package — matminer 0.3.6 documentation @@ -28,7 +28,7 @@

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    • @@ -47,7 +47,7 @@

    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)
    @@ -686,7 +686,7 @@

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    Subpackagesmatminer.utils.flatten_dict module
  • matminer.utils.kernels module
  • matminer.utils.pipeline module
    • +
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  • Module contents
    • @@ -173,7 +174,7 @@

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    • diff --git a/docs/matminer.models.html b/docs/matminer.models.html index 590dd4eba..88233febb 100644 --- a/docs/matminer.models.html +++ b/docs/matminer.models.html @@ -6,7 +6,7 @@ - matminer.models package — matminer 0.3.5 documentation + matminer.models package — matminer 0.3.6 documentation @@ -28,7 +28,7 @@

    Navigation

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    • diff --git a/docs/matminer.utils.html b/docs/matminer.utils.html index 0cfee1746..3c0e8f9ca 100644 --- a/docs/matminer.utils.html +++ b/docs/matminer.utils.html @@ -6,7 +6,7 @@ - matminer.utils package — matminer 0.3.5 documentation + matminer.utils package — matminer 0.3.6 documentation @@ -28,7 +28,7 @@

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    • @@ -124,27 +124,6 @@

    Submodules -
    -matminer.utils.conversions.homogenize_multiindex(df, default_key, coerce=False)
    -

    Homogenizes a dataframe column index to a 2-level multiindex.

    -
    -
    Args:
    -

    df (pandas DataFrame): A dataframe -default_key (str): The key to use when a single Index must be converted

    -
    -
    to a 2-level index. This key is then used as a parent of all -keys present in the original 1-level index.
    -
    -
    coerce (bool): If True, try to force a 2+ level multiindex to a 2-level
    -
    multiindex.
    -
    -
    -
    Returns:
    -
    df (pandas DataFrame): A dataframe with a 2-layer multiindex.
    -
    -

    -
    matminer.utils.conversions.json_to_object(series)
    @@ -216,7 +195,7 @@

    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

    @@ -377,7 +356,7 @@

    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:
    @@ -444,7 +423,7 @@

    Submodules
    class matminer.utils.data.OxidationStatesMixin
    -

    Bases: object

    +

    Bases: object

    Abstract class interface for retrieving the oxidation states of each element

    @@ -657,6 +636,30 @@

    Submodules +

    matminer.utils.utils module

    +
    +
    +matminer.utils.utils.homogenize_multiindex(df, default_key, coerce=False)
    +

    Homogenizes a dataframe column index to a 2-level multiindex.

    +
    +
    Args:
    +

    df (pandas DataFrame): A dataframe +default_key (str): The key to use when a single Index must be converted

    +
    +
    to a 2-level index. This key is then used as a parent of all +keys present in the original 1-level index.
    +
    +
    coerce (bool): If True, try to force a 2+ level multiindex to a 2-level
    +
    multiindex.
    +
    +
    +
    Returns:
    +
    df (pandas DataFrame): A dataframe with a 2-layer multiindex.
    +
    +
    + diff --git a/docs/matminer.utils.tests.html b/docs/matminer.utils.tests.html index ea78661de..f69cf4c5f 100644 --- a/docs/matminer.utils.tests.html +++ b/docs/matminer.utils.tests.html @@ -6,7 +6,7 @@ - matminer.utils.tests package — matminer 0.3.5 documentation + matminer.utils.tests package — matminer 0.3.6 documentation @@ -28,7 +28,7 @@

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    • @@ -90,6 +90,7 @@

    matminermatminer.utils.flatten_dict module
  • matminer.utils.kernels module
  • matminer.utils.pipeline module
    • +
  • matminer.utils.utils module
  • Module contents
    • @@ -140,7 +141,7 @@

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\ No newline at end of file diff --git a/docs_rst/changelog.rst b/docs_rst/changelog.rst index 54ed2728e..b0f64d627 100644 --- a/docs_rst/changelog.rst +++ b/docs_rst/changelog.rst @@ -5,6 +5,14 @@ matminer Changelog ================== + +**v0.3.6** + +* Improve MPDataRetrieval to serialize objects (A. Faghaninia) +* Some fixes to GDRF and AFS (L. Williams, M. Dylla) +* Some fixes for Ewald (A. Faghaninia) +* improve error messages (A. Jain) + **v0.3.5** * some tools for sklearn Pipeline integration (J. Brenneck) diff --git a/docs_rst/contributors.rst b/docs_rst/contributors.rst index b3a1e8649..533cf0470 100644 --- a/docs_rst/contributors.rst +++ b/docs_rst/contributors.rst @@ -48,3 +48,4 @@ Other * Evgeny Blokhin (Tilde Lab) * Max Dylla (Snyder Research Group, Northwestern University) * David Waroquiers (UC Louvain, Belgium) +* Logan Williams (U Michigan Ann Arbor) \ No newline at end of file diff --git a/docs_rst/matminer.utils.rst b/docs_rst/matminer.utils.rst index b1af52f2e..a35101be5 100644 --- a/docs_rst/matminer.utils.rst +++ b/docs_rst/matminer.utils.rst @@ -60,6 +60,14 @@ matminer.utils.pipeline module :undoc-members: :show-inheritance: +matminer.utils.utils module +--------------------------- + +.. automodule:: matminer.utils.utils + :members: + :undoc-members: + :show-inheritance: + Module contents --------------- diff --git a/matminer/__init__.py b/matminer/__init__.py index 4292c48ab..809cb8316 100644 --- a/matminer/__init__.py +++ b/matminer/__init__.py @@ -1,3 +1,3 @@ -__version__ = '0.3.5' +__version__ = '0.3.6' from matminer.figrecipes.plot import PlotlyFig diff --git a/setup.py b/setup.py index db83a9641..c19944467 100644 --- a/setup.py +++ b/setup.py @@ -9,7 +9,7 @@ if __name__ == "__main__": setup( name='matminer', - version='0.3.5', + version='0.3.6', 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(), url='https://github.com/hackingmaterials/matminer',