Add `output_options.epsg` as a configurable option (#646)

* Add `output_options.epsg` as a configurable option

Closes #147

* Pass through the config to `stitching_bursts`

* Add test for dest epsg in workflow

* Fix missing `bounds_wkt` pass along for `stitching_bursts`

closes #638

* debug print test

* fix 0 count sim and test

[pre-commit.ci] pre-commit autoupdate (#644)

updates:
- [github.com/astral-sh/ruff-pre-commit: v0.12.11 → v0.12.12](astral-sh/ruff-pre-commit@v0.12.11...v0.12.12)

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

Refactor to check for nans in JAX crlb calculation (#637)

* update changelog thru 0.42.0

* Refactor to check for nans in JAX crlb calculation

* fix test for new args

* delete tile, use broadcast_to

* Add script to write out accumulative closure phase

Stitch and output all per-ministack `temporal_coherence_` and `simila…

…rity_` files (#615)

* Return all temporal coherence/phase similarity files during sequential runs

* Fix stitching and outputs after merging by date

* fix test

* If renaming, replace the list

* Keep backwards compat, and dont duplicate for 1 ministack

* Make a named tuple for the long wrapped_phase output

* Clean up docker, add missing tyro

Closes #629

* Fix the _average stitching naming problem

Add changelog entries for 0.40

Add `CHANGELOG` entries missing since 0.36.0

Use `is_symlink` when checking for existing scratch files in spurt (#568

)

`filtering.py`: Change default `sigma` calculation, add docstring exp…

…lanation (#560)

* filtering.py`: Change default `sigma` calculation, add docstring explanation

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

---------

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

Nisar datasets (#559)

* add dataset to input arguments for nisar

* set subdataset argument default value to None

---------

Co-authored-by: mirzaees <smirzaee@aurora.jpl.nasa.gov>

Move `WriteArray` calls after `SetNoDataValue` calls (#555)

As a precaution against striping found here: nasa/PROTEUS#54