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Bump the actions group with 7 updates #267

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merged 2 commits into from
Mar 14, 2024

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@dependabot dependabot bot commented on behalf of github Mar 14, 2024

Bumps the actions group with 7 updates:

Package From To
actions/checkout 3 4
actions/cache 3 4
actions/upload-artifact 3 4
actions/setup-python 4 5
docker/login-action 2 3
docker/build-push-action 4 5
akhilerm/tag-push-action 2.1.0 2.2.0

Updates actions/checkout from 3 to 4

Release notes

Sourced from actions/checkout's releases.

v4.0.0

What's Changed

New Contributors

Full Changelog: actions/checkout@v3...v4.0.0

v3.6.0

What's Changed

New Contributors

Full Changelog: actions/checkout@v3.5.3...v3.6.0

v3.5.3

What's Changed

New Contributors

Full Changelog: actions/checkout@v3...v3.5.3

v3.5.2

What's Changed

Full Changelog: actions/checkout@v3.5.1...v3.5.2

v3.5.1

What's Changed

New Contributors

... (truncated)

Changelog

Sourced from actions/checkout's changelog.

Changelog

v4.1.2

v4.1.1

v4.1.0

v4.0.0

v3.6.0

v3.5.3

v3.5.2

v3.5.1

v3.5.0

v3.4.0

v3.3.0

v3.2.0

... (truncated)

Commits

Updates actions/cache from 3 to 4

Release notes

Sourced from actions/cache's releases.

v4.0.0

What's Changed

New Contributors

Full Changelog: actions/cache@v3...v4.0.0

v3.3.3

What's Changed

New Contributors

Full Changelog: actions/cache@v3...v3.3.3

v3.3.2

What's Changed

New Contributors

Full Changelog: actions/cache@v3...v3.3.2

v3.3.1

What's Changed

Full Changelog: actions/cache@v3...v3.3.1

v3.3.0

What's Changed

... (truncated)

Changelog

Sourced from actions/cache's changelog.

Releases

4.0.1

  • Updated isGhes check

4.0.0

  • Updated minimum runner version support from node 12 -> node 20

3.3.3

  • Updates @​actions/cache to v3.2.3 to fix accidental mutated path arguments to getCacheVersion actions/toolkit#1378
  • Additional audit fixes of npm package(s)

3.3.2

  • Fixes bug with Azure SDK causing blob downloads to get stuck.

3.3.1

  • Reduced segment size to 128MB and segment timeout to 10 minutes to fail fast in case the cache download is stuck.

3.3.0

  • Added option to lookup cache without downloading it.

3.2.6

  • Fix zstd not being used after zstd version upgrade to 1.5.4 on hosted runners.

3.2.5

  • Added fix to prevent from setting MYSYS environment variable globally.

3.2.4

  • Added option to fail job on cache miss.

3.2.3

  • Support cross os caching on Windows as an opt-in feature.
  • Fix issue with symlink restoration on Windows for cross-os caches.

3.2.2

  • Reverted the changes made in 3.2.1 to use gnu tar and zstd by default on windows.

3.2.1

... (truncated)

Commits

Updates actions/upload-artifact from 3 to 4

Release notes

Sourced from actions/upload-artifact's releases.

v4.0.0

What's Changed

The release of upload-artifact@v4 and download-artifact@v4 are major changes to the backend architecture of Artifacts. They have numerous performance and behavioral improvements.

ℹ️ However, this is a major update that includes breaking changes. Artifacts created with versions v3 and below are not compatible with the v4 actions. Uploads and downloads must use the same major actions versions. There are also key differences from previous versions that may require updates to your workflows.

For more information, please see:

  1. The changelog post.
  2. The README.
  3. The migration documentation.
  4. As well as the underlying npm package, @​actions/artifact documentation.

New Contributors

Full Changelog: actions/upload-artifact@v3...v4.0.0

v3.1.3

What's Changed

Full Changelog: actions/upload-artifact@v3...v3.1.3

v3.1.2

  • Update all @actions/* NPM packages to their latest versions- #374
  • Update all dev dependencies to their most recent versions - #375

v3.1.1

  • Update actions/core package to latest version to remove set-output deprecation warning #351

v3.1.0

What's Changed

Commits
  • 5d5d22a Merge pull request #515 from actions/eggyhead/update-artifact-v2.1.1
  • f1e993d update artifact license
  • 4881bfd updating dist:
  • a30777e @​eggyhead
  • 3a80482 Merge pull request #511 from actions/robherley/migration-docs-typo
  • 9d63e3f Merge branch 'main' into robherley/migration-docs-typo
  • dfa1ab2 fix typo with v3 artifact downloads in migration guide
  • d00351b Merge pull request #509 from markmssd/patch-1
  • 707f5a7 Update limitation of 10 artifacts upload to 500
  • 26f96df Merge pull request #505 from actions/robherley/merge-artifacts
  • Additional commits viewable in compare view

Updates actions/setup-python from 4 to 5

Release notes

Sourced from actions/setup-python's releases.

v5.0.0

What's Changed

In scope of this release, we update node version runtime from node16 to node20 (actions/setup-python#772). Besides, we update dependencies to the latest versions.

Full Changelog: actions/setup-python@v4.8.0...v5.0.0

v4.8.0

What's Changed

In scope of this release we added support for GraalPy (actions/setup-python#694). You can use this snippet to set up GraalPy:

steps:
- uses: actions/checkout@v4
- uses: actions/setup-python@v4 
  with:
    python-version: 'graalpy-22.3' 
- run: python my_script.py

Besides, the release contains such changes as:

New Contributors

Full Changelog: actions/setup-python@v4...v4.8.0

v4.7.1

What's Changed

Full Changelog: actions/setup-python@v4...v4.7.1

v4.7.0

In scope of this release, the support for reading python version from pyproject.toml was added (actions/setup-python#669).

      - name: Setup Python
        uses: actions/setup-python@v4
</tr></table> 

... (truncated)

Commits

Updates docker/login-action from 2 to 3

Release notes

Sourced from docker/login-action's releases.

v3.0.0

Full Changelog: docker/login-action@v2.2.0...v3.0.0

v2.2.0

Full Changelog: docker/login-action@v2.1.0...v2.2.0

v2.1.0

  • Ensure AWS temp credentials are redacted in workflow logs by @​crazy-max (#275)
  • Bump @​actions/core from 1.6.0 to 1.10.0 (#252 #292)
  • Bump @​aws-sdk/client-ecr from 3.53.0 to 3.186.0 (#298)
  • Bump @​aws-sdk/client-ecr-public from 3.53.0 to 3.186.0 (#299)

Full Changelog: docker/login-action@v2.0.0...v2.1.0

Commits
  • e92390c Merge pull request #685 from docker/dependabot/npm_and_yarn/aws-sdk-dependenc...
  • 1e752e2 chore: update generated content
  • 51c6097 build(deps): bump the aws-sdk-dependencies group with 2 updates
  • 8f079fb Merge pull request #676 from docker/dependabot/npm_and_yarn/proxy-agent-depen...
  • 16fa768 chore: update generated content
  • 46d1619 build(deps): bump the proxy-agent-dependencies group with 2 updates
  • 8c291c5 Merge pull request #682 from docker/dependabot/npm_and_yarn/docker/actions-to...
  • ec726f4 build(deps): bump @​docker/actions-toolkit from 0.14.0 to 0.18.0
  • 5139682 Merge pull request #677 from docker/dependabot/npm_and_yarn/undici-5.28.3
  • 6d4e2ba chore: update generated content
  • Additional commits viewable in compare view

Updates docker/build-push-action from 4 to 5

Release notes

Sourced from docker/build-push-action's releases.

v5.0.0

Full Changelog: docker/build-push-action@v4.2.1...v5.0.0

v4.2.1

Note

Buildx v0.10 enables support for a minimal SLSA Provenance attestation, which requires support for OCI-compliant multi-platform images. This may introduce issues with registry and runtime support (e.g. Google Cloud Run and AWS Lambda). You can optionally disable the default provenance attestation functionality using provenance: false.

Full Changelog: docker/build-push-action@v4.2.0...v4.2.1

v4.2.0

Note

Buildx v0.10 enables support for a minimal SLSA Provenance attestation, which requires support for OCI-compliant multi-platform images. This may introduce issues with registry and runtime support (e.g. Google Cloud Run and AWS Lambda). You can optionally disable the default provenance attestation functionality using provenance: false.

Full Changelog: docker/build-push-action@v4.1.1...v4.2.0

v4.1.1

Note

Buildx v0.10 enables support for a minimal SLSA Provenance attestation, which requires support for OCI-compliant multi-platform images. This may introduce issues with registry and runtime support (e.g. Google Cloud Run and AWS Lambda). You can optionally disable the default provenance attestation functionality using provenance: false.

Full Changelog: docker/build-push-action@v4.1.0...v4.1.1

v4.1.0

Note

Buildx v0.10 enables support for a minimal SLSA Provenance attestation, which requires support for OCI-compliant multi-platform images. This may introduce issues with registry and runtime support (e.g. Google Cloud Run and AWS Lambda). You can optionally disable the default provenance attestation functionality using provenance: false.

Full Changelog: docker/build-push-action@v4.0.0...v4.1.0

Commits
  • af5a7ed Merge pull request #1074 from crazy-max/build-cmd-debug
  • 2a85189 chore: update generated content
  • 6c20794 disable quotes detection for "outputs" input
  • afdf0c0 chore: debug build cmd and args
  • 00ae31a Merge pull request #1070 from docker/dependabot/npm_and_yarn/docker/actions-t...
  • 701942b chore: update generated content
  • 90e54d0 chore(deps): Bump @​docker/actions-toolkit from 0.14.0 to 0.18.0
  • 831ca17 Merge pull request #1066 from crazy-max/ci-local-cache
  • 6bd0e54 ci: local-cache job to test local cache feature
  • b3eddbb Merge pull request #1057 from docker/dependabot/npm_and_yarn/undici-5.28.3
  • Additional commits viewable in compare view

Updates akhilerm/tag-push-action from 2.1.0 to 2.2.0

Release notes

Sourced from akhilerm/tag-push-action's releases.

v2.2.0

Highlights

  • update to nodejs 20

What's Changed

Full Changelog: akhilerm/tag-push-action@v2.1.0...v2.2.0

Commits
  • f35ff2c Use compatible versions of jest and jest-circus
  • af4f7e0 Update to node20
  • fc28234 Merge pull request #355 from akhilerm/dependabot/npm_and_yarn/types/node-20.10.5
  • a0d8fec Bump @​types/node from 16.18.3 to 20.10.5
  • 84ce71e Merge pull request #358 from akhilerm/dependabot/npm_and_yarn/eslint-plugin-p...
  • 51189cb Merge pull request #347 from akhilerm/dependabot/npm_and_yarn/typescript-esli...
  • cbee172 Merge pull request #345 from akhilerm/dependabot/npm_and_yarn/actions/core-1....
  • 8beac5b Merge pull request #296 from akhilerm/dependabot/npm_and_yarn/json5-1.0.2
  • 0d92471 Bump eslint-plugin-prettier from 4.2.1 to 5.1.2
  • f769510 Bump @​typescript-eslint/parser from 5.42.1 to 5.62.0
  • Additional commits viewable in compare view

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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]>
@dependabot dependabot bot added the dependencies Pull requests that update a dependency file label Mar 14, 2024
@scottstanie scottstanie merged commit 83c1f06 into main Mar 14, 2024
8 checks passed
@scottstanie scottstanie deleted the dependabot/github_actions/actions-f999b3eeec branch March 14, 2024 00:42
scottstanie added a commit to scottstanie/dolphin that referenced this pull request May 17, 2024
* 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]>
scottstanie added a commit that referenced this pull request Jun 21, 2024
* 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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