Joss#322
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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.
…ework#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 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 * Make downstream updates to displacement.py * Revert outdated disp changes * Revert another vestigial change to displacement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 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
* 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 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>
* 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] <support@github.com> * 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] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Scott Staniewicz <scott.j.staniewicz@jpl.nasa.gov>
* 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 <ssangha@trappist.jpl.nasa.gov> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
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 * 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 <smirzaee@aurora.jpl.nasa.gov> Co-authored-by: Scott Staniewicz <scott.j.staniewicz@jpl.nasa.gov> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
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>
* 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 <smirzaee@aurora.jpl.nasa.gov> Co-authored-by: Geoffrey Gunter <12984092+gmgunter@users.noreply.github.com>
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>
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>
* change compressed slc naming in unit tests * change default for tilecostthreshold --------- Co-authored-by: mirzaees <smirzaee@aurora.jpl.nasa.gov> Co-authored-by: Scott Staniewicz <scott.j.staniewicz@jpl.nasa.gov> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
* use `pymdownx.snippets` to cut repeated docs from readme. add `CONTRIBUTING.MD` * remove the extra gpu env file since Jax needs separate installs * Revert isce-framework#252 * update contrib, setup, tutorial map * add JAX GPU setup notes * typos
* 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 <smirzaee@aurora.jpl.nasa.gov> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
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>
* add timeseries step to cli * pre-commit fix --------- Co-authored-by: mirzaees <smirzaee@aurora.jpl.nasa.gov>
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 * correct coherence threshold typing * correct raising error --------- Co-authored-by: mirzaees <smirzaee@aurora.jpl.nasa.gov> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
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 * add comments to clarify --------- Co-authored-by: mirzaees <smirzaee@aurora.jpl.nasa.gov>
* temporary fix for compressed slc metadata Co-authored-by: mirzaees <smirzaee@aurora.jpl.nasa.gov> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
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>
…isce-framework#288) * Do not add COR suffix, in case CONCOMP file * Update constants for conncomp
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 frontmatter yaml
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