Pachyderm

Added

- Added effective chi squared for simultaneous fit. See: `90a98d916dc6c5fa29a48b98c9ccafec9e5b4769`. Bug fix:
`92ac7b01e77cec033f6bcf41a95b6a6bb53525ab`.
- Write numpy floats to YAML. This helps to avoid a bunch of difficult to debug errors. See:
`474a24203f87dd09595df9144ead0793fc3647e0`.

Changed

- Improve minimization settings. See: `8bb1602b0bd22fa1dd1eb6c49b3b3768522230bc`.

Fixed

- Don't convert the histogram metadata into a numpy array. See: `2fafe779c2be2b254fbc7b957ffbb5f464940db2`.
- Ensure that metadata is copied when copying a histogram. See: `f1d1fbf8a7de0e5a2d81b58b68d44d6447fd0749`.

Added

- Generic fit base class. It can direct fits with minimal work for the user. It's generalized and ported over
from the jet-hadron analysis. See: `83f1a93350c988d3d7267e2f99d3b2c63464d3ec`.
- Histogram statistics calculation for mean, standard deviation, and variance. Can be extracted from ROOT
hists as well as recalculated manually. See: `c5b23a7b079dc0cbf75962b5bfd6e29ee6679bcb`,
`6ee9f7b4fdb5b71016296c18ade0472816777949`, and `aa4cb32252418035adbb6968783f1258da325410`.
- Extended gaussian fit function. See: `af69d29ee931c50b6398a3f536e54bc9341646da`.
- Wrapper for calculating chi squared probability. See: `2277444a4c37e995143459841f1e386a3512462a`.

Changed

- Improved Minuit wrapper fit function argument validation. See: `f09ace01b19e285d1b229a3f0bcde819c59fce34`.
- Refactor Minuit wrapper fit function into the new module with the generic fit class. The interface of the
`pacyhderm.fit` package defined in `__init__.py` did not change. See:
`83f1a93350c988d3d7267e2f99d3b2c63464d3ec`
- Allow for numpy arrays to be written by hand in YAML inputs. See: `235f41f900f40713663fe999718aea35a4201dc8`.

Fixed

- Fix numpy writing to YAML with newer versions of numpy. See: `1fedadc9f3365fd292ba168c47ce4e1d72179a16`.
- Fix typos in docs and comments.

Added

- `isort` to the pre-commit checks. See: `9930ca1ef9dc13b603e21dea40bae832d377d6d9`.
- Scalar multiplication for histograms. See: `522cd73c5d08225edd7f1f4785ba243dc7e4a079`.
- `Histogram1D` validation and sanity checks. The class should be much more robust. See:
`b69ad4ba8481ec89813bef5fc20f671c25ac5552`.
- Support for converting a `TProfile` to `Histogram1D`. A `TProfile` doesn't strictly conceptually convert
quite so nicely, but `Histogram1D` is very useful as a data container, so it's better to support it. See:
`d3395f8ced9d4642d28a18c23daf81e63a51b571`.

Changed

- We're not going to use `numba` for now, so possible code related to it was removed. See:
`a0b65374b20ad08192132e7f7e7c3b61b7a78d32`.
- Split out a `BaseFitResult` class. It's really convenient to have such a class for individual fit
components. See: `6d638b9020e2334feff0bff64357aa94b4caa40f`.
- Imports are now sorted by `isort`. This ensures consistency. See: `0a8c771f8785bc620e6ec5240fba005fdad77254`.
- Improve numpy encoding when writing to YAML files. It will write in the binary format, which won't be as
convenient to edit by hand, but I believe it will avoid a bunch of floating point issues where later digits
fluctuate each time they are calculated, thereby changing the YAML file. See:
`8bf22118d8fb953a5ff1691e12d95edcdf8f8f6a`.

Fixed

- Prevent ROOT from intercepting args when importing type helpers. See:
`9894c3f526712f6eb72df1c0d454444992d58dcb`.
- Improve typing. See: `20d7a06f7879c9d4df869ecb33c5f5e952834824`, `47199d86a1b468cfa2881b4130947872fe92d623`,
and `8bedd17fbc5e5c9481b7bdadfd525e6d96accae4`.

Added

- Fit package utilizing `iminuit`. Includes base fitting functionality (function to direct fitting, fit result
class, etc), cost functions, useful functions (AddPDF, gaussian, etc). All of this functionality is based on
`numpy` and therefore can execute in a vectorized manner (including the error calculation). Some
functionality of the `reaction_plane_fit` package was ported into Pachyderm. Much of the development itself
was done privately in the `reaction_plane_fit` package. These developments include all of the features of
`probfit` that I've used, such that dependence on that package isn't necessary. See:
`b0620e0dc610566565dacc5b2ab899707d275b76`, `2626c20fc0864619d10c10ca3f5bf24a218e76dc`,
`ebb1dd19ab28d0db25723488e847e1bcee59be3a`, and `3e5441f514a104cd1696add779d192c8c2b3a862`.
- Effective chi squared calculation for fit results. See: `4ad189cbc6add79538dce0274f6dda76a0675e7d`.

Fixed

- Typing improvements, fixed tests and import issues, etc. See: `ebac51f782d35cc1ee1b87b66d2409121dc9569e` and
`3994877c8addcc005ddcd610d3b794d7d1d9078e`, amongst others.

Added

- `metadata` field to `Histogram1D` for storing additional information, such as additional error arrays (for
example, systematics). See: `58d35b341f3b4890c59c9cb9ec70b72836793fc2`.

Changed

- Fixed some typing and pinned `ruamel.yaml` to the pre `py.typed` version until the typing information
stabilizes. See: `933a1fb85f3ab7bf1daadeb2d260dacd37732a1a`.

Changed

- Increased default plot font size. This generally makes things much more readable (but of course can be
adjusted for each plot later if necessary). See: `56a6bef789b1329bb810139918cbabdf74336709`.