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* start paper folder * add skele * fix names * add fig placeholder, new ref * fix makefile * fix paper instructions * add ref * more refs * refs * draft to end * add paper action * missing space * no need to run full test for this branch * typo * fix ref * + * Enforce consistency between jax and jaxlib (#252) Consistency between jax and jaxlib can be enforced by installing the most recent versions via pip, which is currently not possible through conda where the two packages are out of sync. This is necessary as dolphin would crash early on in processing if the two packages are not in sync. * Disable corrections part of pytest, add one for timeseries (#254) * dont exit before unwrapping for full test * make test data have mostly signal, not pure noise * fix the failing test due to len 1 stack losing dimension * raise an error if the reference point selection fails * fix 3d writing, pytest gets farther * `max_bandwidth` can be 1: fix `gt` pydantic restriction * try more * disable corrections pytest This is very annoying to get working with fake data. The current error is: RuntimeError: The -tr option was used, but there's no geotransform or it is rotated. This configuration is not supported. The geometdata for statis layers is wrong * fix jax warning * [skip ci] fix changelog date * Add option to toggle off inversion (#255) * Add option to toggle off inversion Add option to toggle inversion in the config function. By default set to true, like for unwrapping. This allows for more flexibility when running especially large-scale processing. * Make downstream updates to displacement.py * Revert outdated disp changes * Revert another vestigial change to displacement * Add `similarity` module (#256) * add similarity module and `median_similarity` funciton * extract `process_blocks` to an io module * add basic tests * add max sim, add process blocks function * fix argument ordering for `invert` * fix block proc ordering and protocol definitions * fix process check, zip self similarity check * make strictly less * remove `-tap` option from `gdal_merge.py` call (#257) * Goldstein filtering step for unwrapping workflow (#247) * Implement goldstein filtering step for unwrapping workflow * Fix linter checks, reformat * Default goldstein filtering to false * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Fix mypy/ruff issues, add type annotations * Fix numpy typing annotation * Add goldstein pytest --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> * [pre-commit.ci] pre-commit autoupdate (#263) * [pre-commit.ci] pre-commit autoupdate updates: - [github.com/astral-sh/ruff-pre-commit: v0.2.2 → v0.3.2](astral-sh/ruff-pre-commit@v0.2.2...v0.3.2) - [github.com/pre-commit/mirrors-mypy: v1.8.0 → v1.9.0](pre-commit/mirrors-mypy@v1.8.0...v1.9.0) * [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> * Create dependabot.yml (#266) * Bump the actions group with 7 updates (#267) * Bump the actions group with 7 updates Bumps the actions group with 7 updates: | Package | From | To | | --- | --- | --- | | [actions/checkout](https://github.com/actions/checkout) | `3` | `4` | | [actions/cache](https://github.com/actions/cache) | `3` | `4` | | [actions/upload-artifact](https://github.com/actions/upload-artifact) | `3` | `4` | | [actions/setup-python](https://github.com/actions/setup-python) | `4` | `5` | | [docker/login-action](https://github.com/docker/login-action) | `2` | `3` | | [docker/build-push-action](https://github.com/docker/build-push-action) | `4` | `5` | | [akhilerm/tag-push-action](https://github.com/akhilerm/tag-push-action) | `2.1.0` | `2.2.0` | Updates `actions/checkout` from 3 to 4 - [Release notes](https://github.com/actions/checkout/releases) - [Changelog](https://github.com/actions/checkout/blob/main/CHANGELOG.md) - [Commits](actions/checkout@v3...v4) Updates `actions/cache` from 3 to 4 - [Release notes](https://github.com/actions/cache/releases) - [Changelog](https://github.com/actions/cache/blob/main/RELEASES.md) - [Commits](actions/cache@v3...v4) Updates `actions/upload-artifact` from 3 to 4 - [Release notes](https://github.com/actions/upload-artifact/releases) - [Commits](actions/upload-artifact@v3...v4) Updates `actions/setup-python` from 4 to 5 - [Release notes](https://github.com/actions/setup-python/releases) - [Commits](actions/setup-python@v4...v5) Updates `docker/login-action` from 2 to 3 - [Release notes](https://github.com/docker/login-action/releases) - [Commits](docker/login-action@v2...v3) Updates `docker/build-push-action` from 4 to 5 - [Release notes](https://github.com/docker/build-push-action/releases) - [Commits](docker/build-push-action@v4...v5) Updates `akhilerm/tag-push-action` from 2.1.0 to 2.2.0 - [Release notes](https://github.com/akhilerm/tag-push-action/releases) - [Commits](akhilerm/tag-push-action@v2.1.0...v2.2.0) --- updated-dependencies: - dependency-name: actions/checkout dependency-type: direct:production update-type: version-update:semver-major dependency-group: actions - dependency-name: actions/cache dependency-type: direct:production update-type: version-update:semver-major dependency-group: actions - dependency-name: actions/upload-artifact dependency-type: direct:production update-type: version-update:semver-major dependency-group: actions - dependency-name: actions/setup-python dependency-type: direct:production update-type: version-update:semver-major dependency-group: actions - dependency-name: docker/login-action dependency-type: direct:production update-type: version-update:semver-major dependency-group: actions - dependency-name: docker/build-push-action dependency-type: direct:production update-type: version-update:semver-major dependency-group: actions - dependency-name: akhilerm/tag-push-action dependency-type: direct:production update-type: version-update:semver-minor dependency-group: actions ... Signed-off-by: dependabot[bot] <[email protected]> * add write package permission see https://docs.github.com/en/actions/publishing-packages/publishing-docker-images#publishing-images-to-github-packages also https://stackoverflow.com/questions/76607955/error-denied-installation-not-allowed-to-create-organization-package --------- Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Scott Staniewicz <[email protected]> * Toggle zero mask and apply to unw phase field (#262) * Add option to toggle zeromsk for unw * Add unwrapping mask * snaphu ci string fix * tophu ci str fix * remove typo from common * Pass zero unw files if applicable * Fix snaphu cli error --------- Co-authored-by: Simran S Sangha <[email protected]> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> * [pre-commit.ci] pre-commit autoupdate (#270) updates: - [github.com/astral-sh/ruff-pre-commit: v0.3.2 → v0.3.3](astral-sh/ruff-pre-commit@v0.3.2...v0.3.3) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> * Add interpolation option for unwrapping (#264) * add interpolation option for unwrapping * add reference, convert float weights once * remove the extra all check * Remove pymp reference * remove todo * Pass through the correlation threshold for interpolation The last implementation had a default of 0.0 Since every weight was >=0, no pixels were interpolated. * support to have both interpolation and filtering * change the values of all zero sample interferogram * add test for interpolation loop * change docstring to match datatype --------- Co-authored-by: mirzaees <[email protected]> Co-authored-by: Scott Staniewicz <[email protected]> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> * [pre-commit.ci] pre-commit autoupdate (#271) updates: - [github.com/astral-sh/ruff-pre-commit: v0.3.3 → v0.3.4](astral-sh/ruff-pre-commit@v0.3.3...v0.3.4) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> * Grow conncomp (#272) * add grow conncomp * change typing * select reference point with a general condition file * Update src/dolphin/timeseries.py * use a more generic form of Callable * use with to open files --------- Co-authored-by: mirzaees <[email protected]> Co-authored-by: Geoffrey Gunter <[email protected]> * [pre-commit.ci] pre-commit autoupdate (#273) updates: - [github.com/astral-sh/ruff-pre-commit: v0.3.4 → v0.3.5](astral-sh/ruff-pre-commit@v0.3.4...v0.3.5) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> * [pre-commit.ci] pre-commit autoupdate (#275) updates: - [github.com/pre-commit/pre-commit-hooks: v4.5.0 → v4.6.0](pre-commit/pre-commit-hooks@v4.5.0...v4.6.0) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> * Compressed slc naming (#274) * change compressed slc naming in unit tests * change default for tilecostthreshold --------- Co-authored-by: mirzaees <[email protected]> Co-authored-by: Scott Staniewicz <[email protected]> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> * Docs cleanup (#268) * use `pymdownx.snippets` to cut repeated docs from readme. add `CONTRIBUTING.MD` * remove the extra gpu env file since Jax needs separate installs * Revert #252 * update contrib, setup, tutorial map * add JAX GPU setup notes * typos * update the change log (#276) * update the change log * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci --------- Co-authored-by: mirzaees <[email protected]> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> * [pre-commit.ci] pre-commit autoupdate (#278) updates: - [github.com/astral-sh/ruff-pre-commit: v0.3.5 → v0.3.7](astral-sh/ruff-pre-commit@v0.3.5...v0.3.7) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> * Cli timeseries (#279) * add timeseries step to cli * pre-commit fix --------- Co-authored-by: mirzaees <[email protected]> * [pre-commit.ci] pre-commit autoupdate (#280) updates: - [github.com/astral-sh/ruff-pre-commit: v0.3.7 → v0.4.1](astral-sh/ruff-pre-commit@v0.3.7...v0.4.1) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> * correct reference point typing (#281) * correct reference point typing * correct coherence threshold typing * correct raising error --------- Co-authored-by: mirzaees <[email protected]> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> * [pre-commit.ci] pre-commit autoupdate (#283) updates: - [github.com/astral-sh/ruff-pre-commit: v0.4.1 → v0.4.2](astral-sh/ruff-pre-commit@v0.4.1...v0.4.2) - [github.com/pre-commit/mirrors-mypy: v1.9.0 → v1.10.0](pre-commit/mirrors-mypy@v1.9.0...v1.10.0) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> * fix bug for get dates (#284) * fix bug for get dates * add comments to clarify --------- Co-authored-by: mirzaees <[email protected]> * temporary fix for compressed SLC metadata (#287) * temporary fix for compressed slc metadata Co-authored-by: mirzaees <[email protected]> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> * [pre-commit.ci] pre-commit autoupdate (#286) updates: - [github.com/astral-sh/ruff-pre-commit: v0.4.2 → v0.4.3](astral-sh/ruff-pre-commit@v0.4.2...v0.4.3) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> * Enforce convention for conncomp files to be consistent with unw files (#288) * Do not add COR suffix, in case CONCOMP file * Update constants for conncomp * fix names * add fig placeholder, new ref fix makefile fix paper instructions add ref more refs refs draft to end add paper action missing space no need to run full test for this branch typo fix ref + refs, typos * reword example * This is a combination of 2 commits. reword example frontmatter yaml * edits for draft * add image for figure plot * add SNWG ack. --------- Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: Simran S Sangha <[email protected]> Co-authored-by: Ryan Burns <[email protected]> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Simran S Sangha <[email protected]> Co-authored-by: Sara Mirzaee <[email protected]> Co-authored-by: mirzaees <[email protected]> Co-authored-by: Geoffrey Gunter <[email protected]>
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