Fractopo

This release drops support for `pygeos` and Python 3.8 🐍 following
upstream packages. This has resulting in code refactoring and fixes. No
new features.

Bug Fixes

- **analysis:** Topological plotting fixes
- **cli:**
- Fix allow_fix option for `network tracevalidate`
- **tval:**
- Improve stacked (`STACKED TRACES`) detection
- Handle empty trace geodataframe
- Handle split overlap error
- Handle flaky `shapely` overlap detection
- Force return types for some flaky functions (convert to `float`)
- Remove all `pygeos` references, i.e., stop using it as it is merged
into `shapely`

New Features

- **analysis:** Allow creating contour grids without determination of
branches and nodes i.e. topology
([854d1e03](https://github.com/nialov/fractopo/commit/854d1e034d932afba648bde25c41039cae6f7ccc))

Fixes

- **analysis:** Disable parallel processing on Windows due to
instability
([614070fd](https://github.com/nialov/fractopo/commit/614070fd679e170126d40a0e66722ed92ae5853e))

New Features

- A basic input geometry check is done before starting `tracevalidate` and
`network` command-line invocations as suggested in
<https://github.com/nialov/fractopo/issues/36>.

- `joblib` cache settings can be set from environment
variables.

Fixes

- (branches_and_nodes): Fixed `angle_to_point` by setting distance
and similarity checks to more reasonable accuracy.

- (general): Now crs is added before merging geodataframes in
`dissolve_multi_part_traces`

- (length_distribution): Handle empty arrays in in `powerlaw.Fit`
invocations by returning `None` instead of a `Fit` instance.

- (analysis): Length plot ticks are set explicitly in `setup_ax_for_ld` to
avoid differences between Python package versions
(<https://github.com/nialov/fractopo/issues/25>).

- Z-coordinates are now *handled* across `fractopo` i.e. they do not raise
errors. However, they are not guaranteed to be kept in results such as
validated traces. Reported in
<https://github.com/nialov/fractopo/issues/21>.

- (analysis): Removed function signatures with mutable default arguments.

Full set of changes:
[`v0.5.2...v0.5.3`](https://github.com/nialov/fractopo/compare/v0.5.2...v0.5.3)

New Features

- Add `plain` keyword argument to output less visualized rose and
length plots.

Fixes

- Deprecated `CachedNetwork`.

- Fixed typos in code.

Build

- Restructured continous integration and build structure.

- E.g. optimized *auxiliary* task runs on GitHub Actions and added
a binary cache for runs.

Docs

- Added `./paper` directory with a manuscript describing `fractopo`.

Full set of changes:
[`v0.5.1...v0.5.2`](https://github.com/nialov/fractopo/compare/v0.5.1...v0.5.2)

Fixes

- (analysis): Fixed XYI and branch ternary plot sample count to only report the
valid node and branch counts.

- (analysis): Fixed the cut-off vertical line to correspond to the
actual cut-off rather than the lowest remaining length.

- (general): Allow MultiLineStrings in `determine_valid_intersection_points`.

- (analysis): Made sure the order of lengths used in plotting the fitted y values
is correct in multi-scale length plots.

Full set of changes:
[`v0.5.0...v0.5.1`](https://github.com/nialov/fractopo/compare/v0.5.0...v0.5.1)

New Features

- Implemented caching and parallel execution of expensive functions
in `Network` analysis. This should speed up (repeated) runs on the
same datasets. This implementation is based on `joblib` which provided
the functionality without issue.

- (analysis): Implemented plotting length data with the Probability Density
Function (PDF) on the y-axis instead of Complementary Cumulative Number (CCM)

Fixes

- (analysis): Reported `CachedNetwork` deprecation

Full set of changes:
[`v0.4.1...v0.5.0`](https://github.com/nialov/fractopo/compare/v0.4.1...v0.5.0)