Pachyderm

Added

- Iteration over analysis objects grouped by selections. See: `0164157982147142561f33d4a790156513cbba34`.
- Recursive `getattr(...)`. Function from [Stack Overflow](https://stackoverflow.com/a/31174427). See:
`381d6ec2be0e7482b92ff3d3afd9847a9aa84375`.
- Recursive `setattr(...)`. Function from [Stack Overflow](https://stackoverflow.com/a/31174427). See:
`22ba4c6df527dc67d10c729ab85192ba8ef173b5`.
- Raise exception if mean or median after outliers removal changes by more than 1%. Such a condition almost
certainly indicates that something went wrong with the outliers removal. See:
`c7d5d0c449a826a4cc7a5c7f83608751da37bd6d`.

Changed

- Quiet down some logging information.
- Naming of `particle_level_axis` -> `outliers_removal_axis` in the `remove_outliers` module. While it is
common to the particle level axis, it isn't always. Further, sometimes we use the axis for projections,
and sometimes it is just for determining which axis to use when removing outliers. So it's better to use a
more general name. See: `12bde27f421eac59e310029c10f2ca750bcd6da6`.
- Specify the outliers removal axis when calling `run(...)` instead of at object creation. This way, we can
use the manager over for different histograms which many have different axes. See:
`12bde27f421eac59e310029c10f2ca750bcd6da6`.
- Ignore the first bin of the outliers removal. Some older embedding trains had some erroneous entries in the
1st bin of the pt hard spectra, regardless of the pt hard bin. In any case, we would never expect to have
outliers in the first bin. See: `354013e1713d2c4d84d48f0a1d21a6bc06afea2e`.

Fixed

- Included new modules in the docs. See: `3c2d30f363e04eca181f7c05d40306bfbb0d0470`.
- Typo: `_determine_outliers_for_moving_avreage` -> `_determine_outliers_for_moving_average`. See:
`11ce7d01905004dfcd3104549548b58ca17e3808`.

Added

- Outliers removal module, `remove_outliers`. It removes outliers from a given histogram. It was developed
based on previous code. See: `dd472b3dff0715f015d27d083258555bd9674028`,
`12268cb696daa9d80ca680fc219e5d5ab01f67d2`, and `6b62e751c773c05be11019980c67d9ef69d1e487`.
- Centralized shared typing. See: `4e00fd66994971b67d40031627cd6b536c0439d0`.

Changed

- Improved YAML dependencies and typing. It is now only handled in the `yaml` module. See:
`ba364f65d152617c5cd1ee88de88a25c69048203`.
- Provide access to wrapper to get a `TAxis` object given a histogram and a selected axis number. See:
`9569bda571fea44142bf3d46bb2d11b4f979562b`.

Fixed

- Fixed 3D projectors axis determination. The axis name was being taken rather than the name of the axis type.
See: `c32ebea1321054eea71bed1c7c6d68c0b3794a9a`.

Removed

- Obsolete YAML read and write code. We can now directly write classes, which is much easier. See:
`f87ede530519761be35b098a66b86f0cb4e26aab`.

Added

- Added very simple context manager for opening ROOT files. Basically a simpler version of
`rootpy.io.root_open`. See: `0d7a923f19d714125ec5f1eaed55ad9203ae718e`.

Changed

- Heavily modified the `projectors` module to simplify projecting single objects. See:
`d578b97fc2b97f0888170ca678014d8807faf876`.
- Modify the `HistProjector` initialization names and objects for improved clarity. See:
`7eb6f18bb72d0c12cbd47e4bf05178a6d934895c`
- Clarify typing information. See: `eac9586a7d7c0bf1e2be1f0ef2235fb75bf0e676` and
`4de3493092b413dbaaeccebc3b3a10d70b3ad0df`.

Fixed

- Improved typing information in the `yaml` module. See: `eac9586a7d7c0bf1e2be1f0ef2235fb75bf0e676`.

Added

- A few more git pre-commit hooks. See: `dcdde76d223b93ec12d1f43cb5f9a94894efa6c8`.

Fixed

- ROOT memory issue that sometimes occurred during testing. Fixed by ensuring that the open ROOT file is
always closed when an exception is raised. Also included ensuring that only python has ownership of the
objects. See: `c21612967376fb15aa1cffa2e2c8c7b663dae90b` (many of the preceding commits are related to
trying to solve this issue).

Changed

- `Histogram1D` now utilizes bin edges to define the axes instead of the bin centers. This allows for variable
sized bins. Further, the bin centers (ie `x`) are easy to calculate from the bin edges, but the edges are
a bit more painful. See: `b053fe8214591da6754e55d5f9dabf79a3cd5f56`.
- `Histogram1D` supports non-uniform binning. See: `32d2ed53f5743e0b8cab353130e045c733677255`.
- `get_array_from_hist2D(...)` can now return an (x, y) mesh using bin edges by enabling the
`return_bin_edges` option. By default, it will use bin centers. See:
`44a760a655eca0ec416042ec0a629cf88eb2ed7b`.

Added

- Improved test coverage to demonstrate why `deepcopy` is necessary when constructing objects. See:
`369da022`.
- `histogram.get_histograms_in_file(filename)` to return all histograms stored in a ROOT file. See:
`5b333884`.

Changed

- Avoided a very expensive `deepcopy` by formatting strings into new objects instead of writing into existing
objects (which had to be copied first). See: `085f8f18`.
- Return the iterables that were actually utilized in `generic_config.create_objects_from_iterables`. It
replaces the iterables names return values with a dict, where the keys are the iterables names and the
values are lists of the utilized iterables. See: `973b85ae`.

Fixed

- `KeyIndex` already could be written to YAML - it didn't need `to_yaml` and `from_yaml` methods.