Skip to content

Lena release 0.4 (histograms)
Compare
Choose a tag to compare
@ynikitenko ynikitenko released this 07 Nov 18:12
· 128 commits to master since this release
0.4
91875e3

Lena v0.4 was released on 7th November 2021.

What's new

Histograms and related algorithms get great refactoring.

Logic and interface of SplitIntoBins, MapIntoBins and IterateBins have largely improved.
These elements allow analysis to be reused for data subsamples defined by arbitrary values (mapped into bins).

Histogram structure becomes more robust and can be used in other Python code (outside Lena framework).

Vector3 gets a stable initialization interface (not from a list, but from 3 coordinate values).

Adds new elements and a new module input.

  • lena.flow changes:

    • Adds Filter (a standard functional instrument).
    • IterateBins adds a keyword argument select_bins.
    • Adds Progress (estimate processed / remaining data).
    • Adds an iterator Reverse (reverse the flow).
    • Adds RunIf (conditionally run a sequence for selected values from the flow).
      It existed earlier as TransformIf, but was unused and deprecated.
    • Slice supports negative start and stop parameters during run.
    • Selector gets raise_on_error keyword argument
      (previously always returned False).

  • lena.output changes:

    • LaTeXToPDF reprocesses pdf files
      if their tex templates were modified after pdf creation.
    • Adds prefix and suffix keyword arguments to MakeFilename.
      They can be used to create parts of file names
      before they are created (e.g. suffix="_log").
    • RenderLaTeX accepts keyword argument verbose.
      Adds hash symbols to its verbose output.

  • lena.structures changes:

    • Adds HistToGraph.
    • Adds histogram class.
      Histograms are separated into a structure histogram
      and an element Histogram (allowing great conceptual decoupling).
      Should not affect user code in Sequences.

  • math.vector3 supports cylindrical coordinates rho and rho2.

A new module input was created.
Its context name is suggested "input".
At the moment it contains several ROOT bindings:
read_root_file and read_root_tree
(ROOT is a data analysis framework used by physicists, https://root.cern).

lena.output adds a submodule write_root_tree.
Unfortunately, this class is not thoroughly tested
and is not included into the documentation yet.

Bug fixes

  • lena.flow fixes:

    • Fixes Slice.
    • Fixes split_into_bins._iter_bins_with_edges
      (had problems with multidimensional bins; used in IterateBins).
    • Numerous fixes in IterateBins (related to context).
    • Numerous fixes in MapBins (related to context).
    • Numerous fixes in SplitIntoBins (related to context).

  • lena.output fixes:

    • Fixes LaTeXToPDF (didn't print output in case of errors even with verbosity set).
    • Fixes LaTeXToPDF (iteration on a mutated dictionary,
      leading to a runtime error with tens of plots).
    • Fixes RenderLaTeX (didn't work with context.output.template).

Deprecations and backward incompatible changes

  • lena.context changes:

    • Context.formatter is now private.
    • str_to_dict no longer accepts a dictionary.
    • Refactors update_nested.
      other is no longer required to be a dictionary with one key:
      the key is now provided as the first argument.

  • lena.flow changes:

    • Renames flow.ISlice to Slice. ISlice is deprecated.
    • Renames TransformBins to IterateBins.
      Completely rework its context handling.
    • Renames ReduceBinContent to MapBins.
      Changes semantics of a keyword argument drop_bins_context.
      Renames its keyword argument transform to seq.
      Renames keyword argument select to select_bins,
      change order of keyword arguments.
      Completely rework its context handling.
    • SplitIntoBins adds context to histogram and variable
      (not to split_into_bins).
      This allows unification of SplitIntoBins
      with common analysis using histograms and variables
      (useful when creating plots from one template).
      SplitIntoBins is no longer a descendant of FillCompute
      (it is not needed because of structural subtyping).
      Removes initialization keyword argument transform,
      because it can be equally inserted later in the sequence.
      Renames keyword argument arg_func to arg_var
      (since it is a Variable).

  • lena.output changes:

    • Renames Writer to Write. Writer is deprecated.
    • Renames RenderLaTeX keyword argument
      template_path to template_dir (to improve clarity).

  • math.vector3 is initialized not from a vector, but from 3 values x, y and z.
    vector3 no longer transforms its components to floats.
    Thus it behaves like a number in Python
    (if it was integer, it is converted to float only when needed).
    Removes its __cmp__ method (not used).

  • Renames structures.hist_to_graph keyword arguments
    to coincide with those of HistToGraph
    (make_graph_value to make_value, bin_coord to get_coordinate).
    Changes requirements for its make_value argument
    (now accepts one value instead of two).

Technical changes

  • Lena is tested and works with Python 3.10.
    Tox fails for Python 3.5-3.8 (unrelated to Lena).
    Tox uses correct pytest.
  • Moves sphinx requirements to docs/requirements.txt.
    Updates documentation for newer Sphinx.
  • Adds .readthedocs.yaml config (fixes build fails on readthedocs).
  • Changes absolute imports to relative ones in __init__.py in packages.
  • Import of NumpyHistogram becomes more robust
    (less prone to numpy import errors).
  • Improves deprecation messages.
  • ISlice.fill_into is tested with Hypothesis.
  • Adds a private method variable.Variable._update_context.
  • Pytest ignores ROOT tests if ROOT is not installed.
    ROOT tests are marked.
    Add tests/root/conftest.py with rootfile fixture,
    so that ROOT tests will be run in correct order
  • Code improvement and refactoring.
  • Documentation updates and improvements.
  • Several new classes / modules become 100% tested.
  • Adds new tests. Test coverage is 91% (286/3215 missing vs total).
Assets 2