Code

The final carsus merge#786

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wkerzendorf merged 92 commits intotardis-sn:mastertardis-sn/tardis:masterfrom yeganer:carsus_mergeyeganer/tardis:carsus_mergeCopy head branch name to clipboardAug 31, 2017

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Commits

Commits on Aug 31, 2017

• move atomic.py and test_atomic.py to io

  

  mishinma

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  d182924

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• fix imports

  

  mishinma

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  4be5f1e

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• fix data_path in atomic.py

  

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• fix the imports in conftest

  

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• fix links in atomic_data_description

  

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  53a27b4

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• fix paths in test_atomic

  

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• fix import in test_w7

  

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• implement tests_data_path in atomic

  

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• fix import in tardis/base.py

  

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  493289f

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• refactor from_hdf and __init__

  

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• ditch all read functions

  

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• ditch symbol2atomic_number

  

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• write better docstrings

  

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• set lines attr in __init__

  

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• fix a typo with _v_attrs

  

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• add attributes and methods to AtomData's docstring

  

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• add attributes in the else clauses

  

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• change _df to _data

  

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• change the description of the dataframes to comply with the old ones

  

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• return symbol2atomic_number and atomic_number2symbol

  

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  64e9087

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• uncomment zeta_data, synpp_refs and ion_cx_data

  

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• remove conversion to cgs units

  

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• remove set multiindex for synpp_refs

  

  mishinma

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• change from_hdfstore and md5 in the kurucz_atomic_data fixture

  

  mishinma

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• download kurucz_cd23_chianti_H_He.h5 from carsus-db

  

  mishinma

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• change the dataframes names in the hdfstore

  

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• Rewrite AtomData.prepare_atom_data

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• Change from_hdfstore to from_hdf

  

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• Restructure AtomData.__init__

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• Ditch the "has_some_data" attributes

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• Get collision temps in another try..except block

  

  mishinma

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  a1892c2

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• Fix a typo

  

  mishinma

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• Remove a comment

  

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  4588586

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• Fix a typo

  

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  c3ebde6

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• Rename macro_atom attributes in init

  

  mishinma

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  c2c6f86

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• Update AtomData docstring

  

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  2b3a3af

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• Clear imports

  

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  494260b

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• Fix a typo in name

  

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  e3535c0

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• Replace has_some_data with is not None

  

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• Use a dict to instantiate AtomData

  

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• Use logger instead of print stmts

  

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• Correct a typo in hdf names

  

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  b48d485

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• Use try..except to read md5 and uuid1

  

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• Check either all or none of the related dfs are given

  

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• Convert values to CGS in init

  

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• Add a comment

  

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• Use loc to create and set columns

  

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• Remove extra blank lines

  

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• Move helper functions from atomic to util

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• Make fname a positional argument

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• Remove girname

  

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• Remove unused fixtures from conftest

  

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• Clean imports in conftest

  

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• Use --atomic-dataset instead of chianti_he_db

  

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• Change method name to from_hdf

  

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• Reimplement tests for atomic

  

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• Use global variable for defauld UUID

  

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• Change the default UUID

  

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• Change method name

  

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• Print a 'non provided' AtomData logging info message only if there are non provided atomic data.

  

  ftsamis

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• Rename leftover calls of AtomData.from_hdf5 to AtomData.from_hdf.

  

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  26ecf38

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• Finish rebase onto upstream/master

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• Update the test database to the new format

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• Change ionization_data from DataFrame to Series

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  9c6f6c7

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• [PEP8] Fixes in tardis/io/atomic.py

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• [PEP8] Fixes in tardis/io/atomic.py

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• The AtomData now comes with indexes set

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• Fix several issues with indices

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• [PEP8] In file tardis/io/atomic.py

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• Remove some pd.DataFrame.copy()

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• Remove unused parameter 'max_ion_number'

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• Change default AtomData UUID

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• Fix a bug in _main_nlte_calculation

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• Small changes to the plasma tests

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• fixup! Change default AtomData UUID

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• Fix tests for io/atomic.py

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• Add 'tardis_ref_data' and 'generate_reference' fixtures

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• Rewrite tests_plasmas_full to use 'tardis-refdata'

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• [IO] Open HDFStore only once during to_hdf

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• Update tardis-refdata version to pull

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• Rewrite test_tardis_full

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• Rewrite test_simulation

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• Rewrite test_plasmas_full

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• Add warning to test_complete_plasmas

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• Remove old reference files

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• Fix a bug when calculating the 'block_references'

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• Remove all occurences of 'plasma_array' in code

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• Use np.zeros_like to initialize collision_matrix

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• Add docstring to idfn in test_complete_plasmas.py

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• Delete old test

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• Always overwrite Reference data when regenerating

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• Download chianti_He.h5 during travis

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