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[WIP] pandas migration#1347

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sstanovnik wants to merge 140 commits intobiolab:masterbiolab/orange3:masterfrom sstanovnik:koalasCopy head branch name to clipboard

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Commits on Aug 26, 2016

• Extend str in Variable.

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• pandas migration: first huge, breaking, table update.

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• Enable strict read-only access on Table X/Y/meta views.

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• Further changes to Table, as per recent comments.

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• Add Table.attributes to the pandas persistence scheme.

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• Insert pandas into requirements-core.

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• Table constructors and other fixes.

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• OWSelectRows: transform usage of Filter into pandas syntax.

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• Completely remove Filter.

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• Table Domain changes, Variable inference and miscellaneous fixes.

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• Make indexing and weights work from empty Tables.

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• Remove RowInstance completely.

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• Remove and transform infrequently-used old syntax.

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• Completely remove Instance.

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• Remove Storage.

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• Some minor fixes and cleanup in Table.

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• A multitude of small fixes of bugs shown by tests.

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• Use pandas' reader for csv and tab.

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• Tab reader fixes for less common behaviour.

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• Port ExcelReader to use pandas' Excel reader.

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• Improve DiscreteVariable discreteness determination and parsing.

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• Transform values we interpret as null with actual null values when

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• Handle NA weights when setting them.

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• Use pandas' categorical coltype for DiscreteVariable.

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• Convert TimeVariable functionality to pandas.

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• Small fixes: sniffer size, NA weights handling.

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• Variable equality fix and TimeVariable test modification.

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• A lot of small fixes for issues found by tests.

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• Fix handling null values in TimeVariable columns.

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• Improve reading tab and csv files.

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• Remove an unneeded test.

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• Compatibility shims for SQL table.

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• Make Data Table work, transfer basic stats to pandas.

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• Multiple fixes: TableSeries retain attributes, constructor works

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• Remove Value.

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• Fix recent TimeVariable changes.

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• Some basic fixes for subscripting pandas.

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• Migrate distributions to pandas.

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• Ported contingency to pandas.

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• Remove statistics/util.py.

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• Adapt distances and tests to work with the new Table.

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• Adapt preprocessors (discretize, impute) to work with the new Table.

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• Loads of test and compatibility fixes.

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• k-Means compatibility fixes.

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• Transform Continuize for usage with pandas.

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• Fix parsing files with discrete variables which specify values.

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• Discretization pandas compatibility, also test fixes.

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• Evaluation - scoring test compatibility fix.

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• Intepret missing value markers when reading from file.

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• Impute pandas adaptation, with tests.

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• Fix transforming discrete ordinal values into descriptor values.

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• Distributions should use weights instead of counts.

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• Miscellaneous test adaptations.

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• Convert normalization, use groupby instead of value_count in distributions.

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• Add copying to table constructors, very important!

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• Migrate randomization to pandas.

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• A small fix for caching table transformations.

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• Miscellaneous test compatibility fixes.

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• Migrate remover and its tests.

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• Simple tree and softmax adaptation.

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• Only allow one of specified delimiters when reading file.

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• Remove Value tests.

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• Miscellaneous table test compatibility fixes.

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• Use 0 instead of NA when values don't exist in distributions.

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• Feature scoring test compatibility.

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• A bucketload of fixes for widgets.

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• Fix owcontinuize to use proper continuization behaviour.

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• Don't intepret None as a missing value when reading a table.

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• Use proper top-level imports. D'oh!

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• Use a more robust way of computing basic stats.

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• A small fix for the new single-class test.

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• Fixes for some elusive tests.

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• Port SQLTable to a pandas backend. Some breaking changes.

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• Completely overhaul the Table class inheritance structure.

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• Fix some broken Table imports.

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• Basic SparseTable functionality.

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• Distributions for sparse tables.

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• A snail-paced implementationof contingency computation for sparse

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• Improved the reading capabilities.

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• Fix elusive tests.

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• Use add numexpr to requirements-core.

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• Use actual values instead of indices when constructing discretes.

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• Merge domain when not rowstacking concatenated tables.

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• Widget test adaptation and widget fixes.

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• REVIEWME: 'fixed' displaying SQL tables.

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• Test fixes, remove sql.compat.Value

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• Hopefully fix some strange failing tests.

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• Remove val_from_str_add.

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• Add to_var_col, a slightly optimized version of to_val.

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• Remove TableBase.DENSE and related indicators.

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• Remove PanelBase and SparseTablePanel.

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• Docstring bonanza!

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• Remove some old, unused, deprecated things from TableBase.

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• Remove variable.to_val_col.

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• Documentation slightly updated.

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• Increase test coverage, some bugfixes.

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• Improve distributions, also coverage.

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• Increase contingency coverage.

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• Fix OWHeatmap and its recent tests.

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• Bump minimum version of pandas above 0.18.0.

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• Sparse fixes and improvements.

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• Excel sheet naming.

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• A multitude of fixes.

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• A truckload of changes.

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• Remove Table.append.

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• From list with missing class fixes, indent, lesser __setitem__ breakage.

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• Remove the many missing-value replaces.

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• Prevent multiple calls to __init__.

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• Proper finalization and domain filtering.

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• Custom __str__ and __repr__, needs some work.

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• REVIEWME: custom __iter__, iterates over rows, breaks pandas contract.

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• Merge Data fix, new fun TableBase.merge method!

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• Fix venn diagram.

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• Fix Data Table.

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• Switch inputs from Table to TableBase.

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• Much better __str__, uses pandas magic.

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• Except Orange instead of pandas behaviour in constructors.

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• Use pure nnumpy ops for transforming discretes into categoricals.

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• Change usages of checksum to hash.

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• Add a notificatoin comment and test for the iterrows wrapper.

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• Remove shuffle in favour of .sample(frac=1).

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• Consolidate usages of the _transferer hack.

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• Comments and tests to setUpClass, other test fixes.

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• Add time component awareness to TimeVariable.

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• Fix a failing doctest.

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• Improve time column display with month and day.

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• Add a pandas git build to travis.

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• Some general fixes, report test fixes.

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• Requirements.txt requires a different requirement format.

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• Further improvements to the documentation.

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• Revert 68b18c5: overriding __iter__.

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• Simplify weight assignment.

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• Cherry-pick: sstanovnik/orange3:benches.

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• Weight setting robustness.

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• Properer sparse handling.

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• Always convert weights to floats on assignment.

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• Fix visualizing continuous variables in Data Table.

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• Significantly improve feature constructor performance.

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• Domain editor fix and file reader hardening.

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• Fix a failing owkmeans test.

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