Gnatss

<!-- Release notes generated using configuration in .github/release.yml at main -->

What's Changed
* docs: Update README.md to add Zenodo DOI badge by lsetiawan in https://github.com/seafloor-geodesy/gnatss/pull/292
* docs: Create CITATION.cff by lsetiawan in https://github.com/seafloor-geodesy/gnatss/pull/293
* Update docs by johnbdesanto in https://github.com/seafloor-geodesy/gnatss/pull/290
* docs: Fix latex formatting, and ignore file by lsetiawan in https://github.com/seafloor-geodesy/gnatss/pull/297
* test(): Add test for 'ecef2ae' by Jinay01 in https://github.com/seafloor-geodesy/gnatss/pull/298
* fix: Ignore pings without replies from every transponder by johnbdesanto in https://github.com/seafloor-geodesy/gnatss/pull/301
* fix: Set posfilter files to no longer load when --from-cache set by johnbdesanto in https://github.com/seafloor-geodesy/gnatss/pull/302
* chore: pin pydantic to v2.8.2 by johnbdesanto in https://github.com/seafloor-geodesy/gnatss/pull/305
* ci: Fix failing ci tests due to deprecated disutils by lsetiawan in https://github.com/seafloor-geodesy/gnatss/pull/309
* Feat: Residual range limit by johnbdesanto in https://github.com/seafloor-geodesy/gnatss/pull/316

New Contributors
* Jinay01 made their first contribution in https://github.com/seafloor-geodesy/gnatss/pull/298

**Full Changelog**: https://github.com/seafloor-geodesy/gnatss/compare/v0.2.0...v0.2.1

We are excited to announce the major release of GNATSS, featuring significant enhancements and new functionalities, including Data Standard usage and posfilter functionality.

What's Changed

New Features
* **Posfilter:**
* Added ops function to compute transducer offset from the antenna [217](https://github.com/seafloor-geodesy/gnatss/pull/217)
* Loader function for roll-pitch-heading now accepts optional covariance rows [225](https://github.com/seafloor-geodesy/gnatss/pull/225)
* Created loaders for wave glider L1 data for roll-pitch-heading and their std-devs [231](https://github.com/seafloor-geodesy/gnatss/pull/231)
* Added Kalman Filtering functionality [238](https://github.com/seafloor-geodesy/gnatss/pull/238)
* Simplified the posfilter module to get at kf, si, rot [255](https://github.com/seafloor-geodesy/gnatss/pull/255)

* **General:**
* Added 'gpsws_to_time' function to convert GPS Week, Seconds to Astropy Time [230](https://github.com/seafloor-geodesy/gnatss/pull/230)
* Added spline interpolation and updated ops for tt [237](https://github.com/seafloor-geodesy/gnatss/pull/237)
* Configuration updates, adding data spec, and initial end-to-end function [239](https://github.com/seafloor-geodesy/gnatss/pull/239)
* Added flag '--version' to get software version [248](https://github.com/seafloor-geodesy/gnatss/pull/248)
* Extended `calc_twtt_model` to allow other methods [250](https://github.com/seafloor-geodesy/gnatss/pull/250)
* Added flags to skip steps [245](https://github.com/seafloor-geodesy/gnatss/pull/245)

Enhancements and Fixes
* Fixed deprecated `delim_whitespace` with `sep` for pandas [236](https://github.com/seafloor-geodesy/gnatss/pull/236)
* Updated outliers message to use `--remove-outliers` flag [251](https://github.com/seafloor-geodesy/gnatss/pull/251)
* Fixed bug when running NDP1 example [252](https://github.com/seafloor-geodesy/gnatss/pull/252)
* Performed style updates and fixes [284](https://github.com/seafloor-geodesy/gnatss/pull/284)

Refactorings
* Major refactor of the codebase to ensure more modularity and clarity [242](https://github.com/seafloor-geodesy/gnatss/pull/242)
* Cleaned up old code, moved old main to `legacy_main.py`, and removed `garpos.py` [253](https://github.com/seafloor-geodesy/gnatss/pull/253)

Testing
* Added tests for `read_novatel_L1_data_files` and fixed broken unittests [254](https://github.com/seafloor-geodesy/gnatss/pull/254)
* Configuration model changes breaking unittests [260](https://github.com/seafloor-geodesy/gnatss/pull/260)
* Updated test data to be in a zip file stored in git lfs [263](https://github.com/seafloor-geodesy/gnatss/pull/263)
* Removed the use of git lfs and added a testing module [268](https://github.com/seafloor-geodesy/gnatss/pull/268)
* Fixed failing tests caused by recent updates to the code [262](https://github.com/seafloor-geodesy/gnatss/pull/262)
* Added unittests for posfilter rotation and Kalman filtering functionalities [273](https://github.com/seafloor-geodesy/gnatss/pull/273)
* Increased project unittest coverage from 50% to 75.9% [279](https://github.com/seafloor-geodesy/gnatss/pull/279)

Documentation
* Fixed documentation for some modules [266](https://github.com/seafloor-geodesy/gnatss/pull/266)
* Updated documentation to reflect current functions [287](https://github.com/seafloor-geodesy/gnatss/pull/287)
* Added Code of Conduct [272](https://github.com/seafloor-geodesy/gnatss/pull/272)
* Updated badges and added nox badge [271](https://github.com/seafloor-geodesy/gnatss/pull/271) [#288](https://github.com/seafloor-geodesy/gnatss/pull/288)
* Updated main docstring for `run_gnatss` [289](https://github.com/seafloor-geodesy/gnatss/pull/289)

Continuous Integration
* Updated nox to pull test data and updated CI to use nox [265](https://github.com/seafloor-geodesy/gnatss/pull/265)
* Fixed codecov action step [285](https://github.com/seafloor-geodesy/gnatss/pull/285)
* Created `release.yml` [291](https://github.com/seafloor-geodesy/gnatss/pull/291)

Chores
* Bumped setup python from 5.0 to 5.1 [243](https://github.com/seafloor-geodesy/gnatss/pull/243)
* Bumped pypi publish from 1.8.11 to 1.8.14 [244](https://github.com/seafloor-geodesy/gnatss/pull/244)
* Prepared for release, merging dev to main [269](https://github.com/seafloor-geodesy/gnatss/pull/269)
* Updated pre-commit and ran it [270](https://github.com/seafloor-geodesy/gnatss/pull/270)

Contributors
* lsetiawan
* madhavmk

**Full Changelog**: https://github.com/seafloor-geodesy/gnatss/compare/v0.1.1...v0.2.0

What's Changed
* docs: Add a small section about the benchmarking by lsetiawan in https://github.com/seafloor-geodesy/gnatss/pull/204
* chore(deps): bump actions/setup-python from 4.8.0 to 5.0.0 by dependabot in https://github.com/seafloor-geodesy/gnatss/pull/203
* chore(deps): bump actions/upload-artifact from 3 to 4 by dependabot in https://github.com/seafloor-geodesy/gnatss/pull/205
* chore(deps): bump actions/download-artifact from 3 to 4 by dependabot in https://github.com/seafloor-geodesy/gnatss/pull/206
* refactor: Update run flags for distance center, process dataset, and qc by madhavmk in https://github.com/seafloor-geodesy/gnatss/pull/210
* test: Added RPH_TWTT test dataset by lsetiawan in https://github.com/seafloor-geodesy/gnatss/pull/212
* (feat): Add atd_offset to posfilter config model by madhavmk in https://github.com/seafloor-geodesy/gnatss/pull/213
* fix: Fixed the ignoring of 'parsed' files by lsetiawan in https://github.com/seafloor-geodesy/gnatss/pull/215
* test: Update test to remove failures by lsetiawan in https://github.com/seafloor-geodesy/gnatss/pull/216


**Full Changelog**: https://github.com/seafloor-geodesy/gnatss/compare/v0.1.0...v0.1.1

Overview

This is the initial release of GNATSS. It is a major release that includes the changes below.

Setup and Configuration

- Setup `seagap` Python package by lsetiawan [PR 56](https://github.com/seafloor-geodesy/gnatss/pull/56)
- Update badge to docs by lsetiawan [PR 58](https://github.com/seafloor-geodesy/gnatss/pull/58)
- Setup initial configuration file spec for solver by lsetiawan [PR 57](https://github.com/seafloor-geodesy/gnatss/pull/57)
- Update package manager to `hatch` by lsetiawan [PR 62](https://github.com/seafloor-geodesy/gnatss/pull/62)
- Add coverage report and upload to codecov by lsetiawan [PR 68](https://github.com/seafloor-geodesy/gnatss/pull/68)
- Add codespaces configuration by lsetiawan [PR 89](https://github.com/seafloor-geodesy/gnatss/pull/89)
- Update codespace to install package and ipykernel by lsetiawan [PR 91](https://github.com/seafloor-geodesy/gnatss/pull/91)

Code Structure and Modules

- Add io utilities and io configurations to YAML spec by lsetiawan [PR 59](https://github.com/seafloor-geodesy/gnatss/pull/59)
- Add geo.py module for geospatial operations by lsetiawan [PR 69](https://github.com/seafloor-geodesy/gnatss/pull/69)
- Initialize CLI by lsetiawan [PR 67](https://github.com/seafloor-geodesy/gnatss/pull/67)
- Initialize ops module with necessary functions by lsetiawan [PR 80](https://github.com/seafloor-geodesy/gnatss/pull/80)
- Update and add tests for ops/data module by lsetiawan [PR 96](https://github.com/seafloor-geodesy/gnatss/pull/96)

Documentation

- Add docstring to jupyter book by lsetiawan [PR 81](https://github.com/seafloor-geodesy/gnatss/pull/81)
- Add docstring and initial test for main.py by lsetiawan [PR 92](https://github.com/seafloor-geodesy/gnatss/pull/92)
- docs: Add contributing section in README by lsetiawan [PR 110](https://github.com/seafloor-geodesy/gnatss/pull/110)
- docs: add CONTRIBUTING docs for setting up dev by lsetiawan [PR 114](https://github.com/seafloor-geodesy/gnatss/pull/114)
- docs: update repo readme by lsetiawan [PR 115](https://github.com/seafloor-geodesy/gnatss/pull/115)
- docs: clean up docs and pre-commit by lsetiawan [PR 112](https://github.com/seafloor-geodesy/gnatss/pull/112)
- docs: add doc about CLI and clean terminal doc for CLI by lsetiawan [PR 132](https://github.com/seafloor-geodesy/gnatss/pull/132)
- docs(readme): Add codefactor badge by lsetiawan [PR 136](https://github.com/seafloor-geodesy/gnatss/pull/136)
- docs: update codefactor and ci badge by lsetiawan [PR 199](https://github.com/seafloor-geodesy/gnatss/pull/199)
- docs: Update codecov and links by lsetiawan [PR 200](https://github.com/seafloor-geodesy/gnatss/pull/200)

Features and Functionalities

- Add method for computing harmonic mean by lsetiawan [PR 66](https://github.com/seafloor-geodesy/gnatss/pull/66)
- Add distance from center computation by lsetiawan [PR 138](https://github.com/seafloor-geodesy/gnatss/pull/138)
- feat(posfilter): Adds config model for Position Filtering by lsetiawan [PR 134](https://github.com/seafloor-geodesy/gnatss/pull/134)
- feat: Add a feature to extract and save process results to netcdf file by lsetiawan [PR 143](https://github.com/seafloor-geodesy/gnatss/pull/143)
- feat: Add flags to override 'residual' and 'distance' by lsetiawan [PR 146](https://github.com/seafloor-geodesy/gnatss/pull/146)
- feat(loaders): Add loader function for RPH and flexible file gathering by lsetiawan [PR 147](https://github.com/seafloor-geodesy/gnatss/pull/147)
- feat: Add feature to export and use outliers by lsetiawan [PR 144](https://github.com/seafloor-geodesy/gnatss/pull/144)
- feat: Add numba harmonic mean implementation by lsetiawan [PR 194](https://github.com/seafloor-geodesy/gnatss/pull/194)
- feat: Add option for gnatss for user flag file to remove bad data by madhavmk [PR 195](https://github.com/seafloor-geodesy/gnatss/pull/195)
- feat: Add session_time attribute to process dataset by lsetiawan [PR 201](https://github.com/seafloor-geodesy/gnatss/pull/201)

Testing

- test(utilities): add test case to return False when checking files by lizimu0709 [PR 101](https://github.com/seafloor-geodesy/gnatss/pull/101)
- test(seagap): add test case to raise ValueError by lizimu0709 [PR 103](https://github.com/seafloor-geodesy/gnatss/pull/103)
- test(geo): add test for geo module by lsetiawan [PR 98](https://github.com/seafloor-geodesy/gnatss/pull/98)
- test(solve): add docstrings and tests for solve module by lsetiawan [PR 99](https://github.com/seafloor-geodesy/gnatss/pull/99)
- test(loaders): Add test for load_configuration by madhavmk [PR 164](https://github.com/seafloor-geodesy/gnatss/pull/164)
- test(loaders): Add test for load_sound_speed by madhavmk [PR 166](https://github.com/seafloor-geodesy/gnatss/pull/166)
- test(loaders): Add test for load_gps_solutions 126 by madhavmk [PR 168](https://github.com/seafloor-geodesy/gnatss/pull/168)
- test(loaders): Add test for load_travel_times 125 by madhavmk [PR 169](https://github.com/seafloor-geodesy/gnatss/pull/169)
- test(loaders): Add test for load_deletions 127 by madhavmk [PR 179](https://github.com/seafloor-geodesy/gnatss/pull/179)

Bug Fixes

- Fix definition of Unix J2000 format and add unittesting by madhavmk [PR 109](https://github.com/seafloor-geodesy/gnatss/pull/109)
- fix: update time scale to 'tt' as default assumption by lsetiawan [PR 117](https://github.com/seafloor-geodesy/gnatss/pull/117)
- fix(io): Add a catch for directory only path by lsetiawan [PR 154](https://github.com/seafloor-geodesy/gnatss/pull/154)
- fix: Fix runtime message that shows wrong info by lsetiawan [PR 180](https://github.com/seafloor-geodesy/gnatss/pull/180)
- feat: Ticks for plots need to be hourly by madhavmk [PR 189](https://github.com/seafloor-geodesy/gnatss/pull/189)
- feat: File inputs not able to be a single file by madhavmk [PR 190](https://github.com/seafloor-geodesy/gnatss/pull/190)
- fix: Add geoid undulation for final height by lsetiawan [PR 192](https://github.com/seafloor-geodesy/gnatss/pull/192)

Dependency Updates

- Bump min py >= 3.9 and pin dependencies max by lsetiawan [PR 93](https://github.com/seafloor-geodesy/gnatss/pull/93)

New Contributors

* lsetiawan made their first contribution in https://github.com/seafloor-geodesy/gnatss/pull/56
* lizimu0709 made their first contribution in https://github.com/seafloor-geodesy/gnatss/pull/101
* madhavmk made their first contribution in https://github.com/seafloor-geodesy/gnatss/pull/109
* johnbdesanto made their first contribution in https://github.com/seafloor-geodesy/gnatss/pull/186

**Full Changelog**: https://github.com/seafloor-geodesy/gnatss/commits/v0.1.0