dist-s1 0.0.2__tar.gz

dist_s1-0.0.2/.github/dependabot.yml

@@ -0,0 +1,7 @@
+version: 2
+updates:
+  # Maintain dependencies for GitHub Actions
+  - package-ecosystem: "github-actions"
+    directory: "/"
+    schedule:
+      interval: "weekly"

dist_s1-0.0.2/.github/workflows/bump-tag-for-release.yml

@@ -0,0 +1,15 @@
+name: Annotated Git Tag on Main (bump version)
+
+on:
+  push:
+    branches:
+      - main
+
+jobs:
+  call-bump-version-workflow:
+    uses: ASFHyP3/actions/.github/workflows/reusable-bump-version.yml@v0.11.2
+    with:
+      user: opera-pst-dev 
+      email: opera-pst-dev@jpl.nasa.gov
+    secrets:
+      USER_TOKEN: ${{ secrets.OPERA_PST_DIST_TOKEN }}

dist_s1-0.0.2/.github/workflows/changelog-update.yml

@@ -0,0 +1,16 @@
+name: Changelog updated?
+
+on:
+  pull_request:
+    types:
+      - opened
+      - labeled
+      - unlabeled
+      - synchronize
+    branches:
+      - main
+      - dev
+
+jobs:
+  call-changelog-check-workflow:
+    uses: ASFHyP3/actions/.github/workflows/reusable-changelog-check.yml@v0.11.2

dist_s1-0.0.2/.github/workflows/docker-build.yml

@@ -0,0 +1,29 @@
+name: Build
+
+on:
+  push:
+    branches:
+      - main
+      - dev
+  pull_request:
+    branches:
+      - main
+      - dev
+
+jobs:
+  call-version-info-workflow:
+    uses: ASFHyP3/actions/.github/workflows/reusable-version-info.yml@v0.12.0
+    with:
+        python_version: '3.12'
+
+  call-docker-ghcr-workflow:
+    needs: call-version-info-workflow
+    uses: ASFHyP3/actions/.github/workflows/reusable-docker-ghcr.yml@v0.12.0
+    with:
+      version_tag: ${{ needs.call-version-info-workflow.outputs.version_tag }}
+      user: ${{ github.actor }}
+      release_branch: main     
+      develop_branch: dev  
+      file: Dockerfile 
+    secrets:
+      USER_TOKEN: ${{ secrets.GITHUB_TOKEN }}

dist_s1-0.0.2/.github/workflows/github-release.yml

@@ -0,0 +1,16 @@
+name: Create Release on Github
+
+on:
+  push:
+    tags:
+      - 'v*'
+
+jobs:
+  call-release-workflow:
+    uses: ASFHyP3/actions/.github/workflows/reusable-release.yml@v0.11.2
+    with:
+      release_prefix: dist-s1
+      develop_branch: dev
+      sync_pr_label: team-bot
+    secrets:
+      USER_TOKEN: ${{ secrets.OPERA_PST_DIST_TOKEN }}

dist_s1-0.0.2/.github/workflows/labeled-pr.yml

@@ -0,0 +1,15 @@
+name: Is PR labeled?
+
+on:
+  pull_request:
+    types:
+      - opened
+      - labeled
+      - unlabeled
+      - synchronize
+    branches:
+      - main
+
+jobs:
+  call-labeled-pr-check-workflow:
+    uses: ASFHyP3/actions/.github/workflows/reusable-labeled-pr-check.yml@v0.11.2

dist_s1-0.0.2/.github/workflows/pypi-delivery.yml

@@ -0,0 +1,37 @@
+name: Distribute to PyPI
+
+on:
+  push:
+    tags:
+      - v*
+
+jobs:
+  distribute:
+    runs-on: ubuntu-latest
+    outputs:
+      SDIST_VERSION: ${{ steps.build.outputs.version }}
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: actions/setup-python@v5
+        with:
+          python-version: 3.12
+
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          python -m pip install --upgrade setuptools build "setuptools-scm[toml]"
+
+      - name: Build distribuion
+        id: build
+        run: |
+          git fetch origin +refs/tags/*:refs/tags/*
+          export SDIST_VERSION=$(python -m setuptools_scm)
+          echo "::set-output name=version::${SDIST_VERSION}"
+          python -m build
+
+      - name: upload to PyPI.org
+        uses: pypa/gh-action-pypi-publish@release/v1
+        with:
+          user: __token__
+          password: ${{ secrets.OPERA_PST_PYPI_TOKEN }}

dist_s1-0.0.2/.github/workflows/static_analysis.yml

@@ -0,0 +1,16 @@
+name: Static Analysis (Flake8/Ruff)
+
+on: push
+
+jobs:
+  # Docs: https://github.com/ASFHyP3/actions
+  call-flake8-workflow:
+    uses: ASFHyP3/actions/.github/workflows/reusable-flake8.yml@v0.11.2
+    with:
+      local_package_names: dist_s1
+
+  call-secrets-analysis-workflow:
+    uses: ASFHyP3/actions/.github/workflows/reusable-secrets-analysis.yml@v0.11.2
+  
+  call-ruff-workflow:
+    uses: ASFHyP3/actions/.github/workflows/reusable-ruff.yml@v0.11.2

dist_s1-0.0.2/.github/workflows/test.yml

@@ -0,0 +1,21 @@
+name: Test
+
+on:
+  workflow_dispatch:
+  push:
+    branches:
+      - main
+      - dev
+  pull_request:
+    branches:
+      - main
+      - dev
+
+jobs:
+  call-pytest-workflow:
+    # Docs: https://github.com/ASFHyP3/actions
+    uses: ASFHyP3/actions/.github/workflows/reusable-pytest.yml@v0.11.2
+    with:
+      local_package_name: dist_s1
+      python_versions: >-
+        ["3.12", "3.13"]

dist_s1-0.0.2/.gitignore

@@ -0,0 +1,85 @@
+# OS Files
+**/.DS_Store
+**/.DS_Store?
+
+# vscode
+.vscode
+
+# env file
+.env
+
+# Vim files
+*.sw[mnop]
+
+# Notebooks used for presentations
+notebooks_plots/
+
+# Test output
+tests/out/
+
+# .pyenv files
+.python-version
+
+# pytest files
+.pytest_cache/
+
+# Jupyter files
+*.ipynb_checkpoints
+
+# Python build files
+build/
+
+# Rope Files
+.ropeproject/
+
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# Setuptools distribution folder.
+/dist/
+
+# Python egg metadata, regenerated from source files by setuptools.
+**/*.egg-info
+
+# Environments
+.env
+.envrc
+
+# Gdal and other image formats
+*.shp
+*.sbx
+*.sbn
+*.shx
+*.prj
+*.qpj
+*.dbf
+*.cpg
+*.msk
+*.kmz
+*.jpg
+*.wld
+*.geojson
+*.xml
+
+# VRT
+*.vrt
+
+# Log files
+*.log
+
+# Pickle Data
+*.pkl
+
+# Ignore pdf Files
+*.pdf
+
+# Ignore json
+*.json
+
+# Coverage
+*.coverage
+
+# pre-commit
+.pre-commit-config.yaml

dist_s1-0.0.2/CHANGELOG.md

@@ -0,0 +1,29 @@
+# Changelog
+
+All notable changes to this project will be documented in this file.
+
+The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
+and this project adheres to [PEP 440](https://www.python.org/dev/peps/pep-0440/)
+and uses [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
+
+## [0.0.2]
+
+### Added
+
+- Pypi delivery workflow
+- Entrypoint for CLI to localize data via internet (the SAS workflow is assumed not to have internet access)
+- Data models for output data and product naming conventions
+- Ensures output products follow the product and the tif layers follow the expected naming conventions
+  - Provides testing/validation of the structure (via tmp directories)
+
+### Changed
+
+- CLI entrypoints now utilize `dist-s1 run_sas` and `dist-s1 run` rathern than just `dist-s1`. 
+  - The `dist-s1 run_sas` is the primary entrypoint for Science Application Software (SAS) for SDS operations. 
+  - The `dist-s1 run` is the simplified entrypoint for external users, allowing for the localization of data from publicly available data sources.
+
+## [0.0.1]
+
+### Added
+
+- Initial internal release of the DIST-S1 project. Test github release workflow

dist_s1-0.0.2/Dockerfile

@@ -0,0 +1,41 @@
+FROM condaforge/mambaforge:latest
+
+LABEL description="DIST-S1 Container"
+
+ARG DEBIAN_FRONTEND=noninteractive
+ENV PYTHONDONTWRITEBYTECODE=true
+
+# Install libgl1-mesa-glx unzip vim
+RUN apt-get update && apt-get install -y --no-install-recommends libgl1-mesa-glx unzip vim && \
+    apt-get clean && rm -rf /var/lib/apt/lists/*
+
+# run commands in a bash login shell
+SHELL ["/bin/bash", "-l", "-c"]
+
+# Create non-root user/group with default inputs
+ARG UID=1000
+ARG GID=1000
+
+RUN groupadd -g "${GID}" --system dist_user && \
+    useradd -l -u "${UID}" -g "${GID}" --system -d /home/ops -m  -s /bin/bash dist_user && \
+    chown -R dist_user:dist_user /opt
+
+# Switch to non-root user
+USER dist_user
+WORKDIR /home/ops
+
+# Ensures we cached mamba install per
+# https://docs.docker.com/develop/develop-images/dockerfile_best-practices/#leverage-build-cache
+COPY --chown=dist_user:dist_user environment.yml /home/ops/dist-s1/environment.yml
+COPY --chown=dist_user:dist_user . /home/ops/dist-s1
+
+# Create the environment with mamba
+RUN mamba env create -f /home/ops/dist-s1/environment.yml && \
+    conda clean -afy
+
+# Ensure that environment is activated on startup
+RUN echo ". /opt/conda/etc/profile.d/conda.sh" >> ~/.profile && \
+    echo "conda activate dist-s1-env" >> ~/.profile
+
+# Install repository with pip
+RUN python -m pip install --no-cache-dir /home/ops/dist-s1

dist_s1-0.0.2/LICENSE

@@ -0,0 +1,202 @@
+
+                                 Apache License
+                           Version 2.0, January 2004
+                        http://www.apache.org/licenses/
+
+   TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION
+
+   1. Definitions.
+
+      "License" shall mean the terms and conditions for use, reproduction,
+      and distribution as defined by Sections 1 through 9 of this document.
+
+      "Licensor" shall mean the copyright owner or entity authorized by
+      the copyright owner that is granting the License.
+
+      "Legal Entity" shall mean the union of the acting entity and all
+      other entities that control, are controlled by, or are under common
+      control with that entity. For the purposes of this definition,
+      "control" means (i) the power, direct or indirect, to cause the
+      direction or management of such entity, whether by contract or
+      otherwise, or (ii) ownership of fifty percent (50%) or more of the
+      outstanding shares, or (iii) beneficial ownership of such entity.
+
+      "You" (or "Your") shall mean an individual or Legal Entity
+      exercising permissions granted by this License.
+
+      "Source" form shall mean the preferred form for making modifications,
+      including but not limited to software source code, documentation
+      source, and configuration files.
+
+      "Object" form shall mean any form resulting from mechanical
+      transformation or translation of a Source form, including but
+      not limited to compiled object code, generated documentation,
+      and conversions to other media types.
+
+      "Work" shall mean the work of authorship, whether in Source or
+      Object form, made available under the License, as indicated by a
+      copyright notice that is included in or attached to the work
+      (an example is provided in the Appendix below).
+
+      "Derivative Works" shall mean any work, whether in Source or Object
+      form, that is based on (or derived from) the Work and for which the
+      editorial revisions, annotations, elaborations, or other modifications
+      represent, as a whole, an original work of authorship. For the purposes
+      of this License, Derivative Works shall not include works that remain
+      separable from, or merely link (or bind by name) to the interfaces of,
+      the Work and Derivative Works thereof.
+
+      "Contribution" shall mean any work of authorship, including
+      the original version of the Work and any modifications or additions
+      to that Work or Derivative Works thereof, that is intentionally
+      submitted to Licensor for inclusion in the Work by the copyright owner
+      or by an individual or Legal Entity authorized to submit on behalf of
+      the copyright owner. For the purposes of this definition, "submitted"
+      means any form of electronic, verbal, or written communication sent
+      to the Licensor or its representatives, including but not limited to
+      communication on electronic mailing lists, source code control systems,
+      and issue tracking systems that are managed by, or on behalf of, the
+      Licensor for the purpose of discussing and improving the Work, but
+      excluding communication that is conspicuously marked or otherwise
+      designated in writing by the copyright owner as "Not a Contribution."
+
+      "Contributor" shall mean Licensor and any individual or Legal Entity
+      on behalf of whom a Contribution has been received by Licensor and
+      subsequently incorporated within the Work.
+
+   2. Grant of Copyright License. Subject to the terms and conditions of
+      this License, each Contributor hereby grants to You a perpetual,
+      worldwide, non-exclusive, no-charge, royalty-free, irrevocable
+      copyright license to reproduce, prepare Derivative Works of,
+      publicly display, publicly perform, sublicense, and distribute the
+      Work and such Derivative Works in Source or Object form.
+
+   3. Grant of Patent License. Subject to the terms and conditions of
+      this License, each Contributor hereby grants to You a perpetual,
+      worldwide, non-exclusive, no-charge, royalty-free, irrevocable
+      (except as stated in this section) patent license to make, have made,
+      use, offer to sell, sell, import, and otherwise transfer the Work,
+      where such license applies only to those patent claims licensable
+      by such Contributor that are necessarily infringed by their
+      Contribution(s) alone or by combination of their Contribution(s)
+      with the Work to which such Contribution(s) was submitted. If You
+      institute patent litigation against any entity (including a
+      cross-claim or counterclaim in a lawsuit) alleging that the Work
+      or a Contribution incorporated within the Work constitutes direct
+      or contributory patent infringement, then any patent licenses
+      granted to You under this License for that Work shall terminate
+      as of the date such litigation is filed.
+
+   4. Redistribution. You may reproduce and distribute copies of the
+      Work or Derivative Works thereof in any medium, with or without
+      modifications, and in Source or Object form, provided that You
+      meet the following conditions:
+
+      (a) You must give any other recipients of the Work or
+          Derivative Works a copy of this License; and
+
+      (b) You must cause any modified files to carry prominent notices
+          stating that You changed the files; and
+
+      (c) You must retain, in the Source form of any Derivative Works
+          that You distribute, all copyright, patent, trademark, and
+          attribution notices from the Source form of the Work,
+          excluding those notices that do not pertain to any part of
+          the Derivative Works; and
+
+      (d) If the Work includes a "NOTICE" text file as part of its
+          distribution, then any Derivative Works that You distribute must
+          include a readable copy of the attribution notices contained
+          within such NOTICE file, excluding those notices that do not
+          pertain to any part of the Derivative Works, in at least one
+          of the following places: within a NOTICE text file distributed
+          as part of the Derivative Works; within the Source form or
+          documentation, if provided along with the Derivative Works; or,
+          within a display generated by the Derivative Works, if and
+          wherever such third-party notices normally appear. The contents
+          of the NOTICE file are for informational purposes only and
+          do not modify the License. You may add Your own attribution
+          notices within Derivative Works that You distribute, alongside
+          or as an addendum to the NOTICE text from the Work, provided
+          that such additional attribution notices cannot be construed
+          as modifying the License.
+
+      You may add Your own copyright statement to Your modifications and
+      may provide additional or different license terms and conditions
+      for use, reproduction, or distribution of Your modifications, or
+      for any such Derivative Works as a whole, provided Your use,
+      reproduction, and distribution of the Work otherwise complies with
+      the conditions stated in this License.
+
+   5. Submission of Contributions. Unless You explicitly state otherwise,
+      any Contribution intentionally submitted for inclusion in the Work
+      by You to the Licensor shall be under the terms and conditions of
+      this License, without any additional terms or conditions.
+      Notwithstanding the above, nothing herein shall supersede or modify
+      the terms of any separate license agreement you may have executed
+      with Licensor regarding such Contributions.
+
+   6. Trademarks. This License does not grant permission to use the trade
+      names, trademarks, service marks, or product names of the Licensor,
+      except as required for reasonable and customary use in describing the
+      origin of the Work and reproducing the content of the NOTICE file.
+
+   7. Disclaimer of Warranty. Unless required by applicable law or
+      agreed to in writing, Licensor provides the Work (and each
+      Contributor provides its Contributions) on an "AS IS" BASIS,
+      WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or
+      implied, including, without limitation, any warranties or conditions
+      of TITLE, NON-INFRINGEMENT, MERCHANTABILITY, or FITNESS FOR A
+      PARTICULAR PURPOSE. You are solely responsible for determining the
+      appropriateness of using or redistributing the Work and assume any
+      risks associated with Your exercise of permissions under this License.
+
+   8. Limitation of Liability. In no event and under no legal theory,
+      whether in tort (including negligence), contract, or otherwise,
+      unless required by applicable law (such as deliberate and grossly
+      negligent acts) or agreed to in writing, shall any Contributor be
+      liable to You for damages, including any direct, indirect, special,
+      incidental, or consequential damages of any character arising as a
+      result of this License or out of the use or inability to use the
+      Work (including but not limited to damages for loss of goodwill,
+      work stoppage, computer failure or malfunction, or any and all
+      other commercial damages or losses), even if such Contributor
+      has been advised of the possibility of such damages.
+
+   9. Accepting Warranty or Additional Liability. While redistributing
+      the Work or Derivative Works thereof, You may choose to offer,
+      and charge a fee for, acceptance of support, warranty, indemnity,
+      or other liability obligations and/or rights consistent with this
+      License. However, in accepting such obligations, You may act only
+      on Your own behalf and on Your sole responsibility, not on behalf
+      of any other Contributor, and only if You agree to indemnify,
+      defend, and hold each Contributor harmless for any liability
+      incurred by, or claims asserted against, such Contributor by reason
+      of your accepting any such warranty or additional liability.
+
+   END OF TERMS AND CONDITIONS
+
+   APPENDIX: How to apply the Apache License to your work.
+
+      To apply the Apache License to your work, attach the following
+      boilerplate notice, with the fields enclosed by brackets "[]"
+      replaced with your own identifying information. (Don't include
+      the brackets!)  The text should be enclosed in the appropriate
+      comment syntax for the file format. We also recommend that a
+      file or class name and description of purpose be included on the
+      same "printed page" as the copyright notice for easier
+      identification within third-party archives.
+
+   Copyright 2024 Charlie Marshak
+
+   Licensed under the Apache License, Version 2.0 (the "License");
+   you may not use this file except in compliance with the License.
+   You may obtain a copy of the License at
+
+       http://www.apache.org/licenses/LICENSE-2.0
+
+   Unless required by applicable law or agreed to in writing, software
+   distributed under the License is distributed on an "AS IS" BASIS,
+   WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+   See the License for the specific language governing permissions and
+   limitations under the License.

dist_s1-0.0.2/PKG-INFO

@@ -0,0 +1,76 @@
+Metadata-Version: 2.1
+Name: dist-s1
+Version: 0.0.2
+Summary: The workflow to generate the DIST-S1 product
+Author-email: "Richard West, Charlie Marshak, Talib Oliver-Cabrera, and Jungkyo Jung" <charlie.z.marshak@jpl.nasa.gov>
+License: Apache-2.0
+Project-URL: Homepage, https://github.com/opera-adt/dist-s1
+Project-URL: Bug Tracker, https://github.com/opera-adt/dist-s1/issues
+Project-URL: Discussions, https://github.com/opera-adt/dist-s1/discussions
+Project-URL: Changelog, https://github.com/opera-adt/dist-s1/releases
+Classifier: Intended Audience :: Developers
+Classifier: Intended Audience :: Science/Research
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python
+Classifier: Topic :: Scientific/Engineering
+Requires-Python: >=3.12
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: numpy
+Requires-Dist: asf_search
+Requires-Dist: geopandas
+Requires-Dist: rasterio
+
+# dist-s1
+
+[![PyPI license](https://img.shields.io/pypi/l/dist-s1.svg)](https://pypi.python.org/pypi/dist-s1/)
+[![PyPI pyversions](https://img.shields.io/pypi/pyversions/dist-s1.svg)](https://pypi.python.org/pypi/dist-s1/)
+[![PyPI version](https://img.shields.io/pypi/v/dist-s1.svg)](https://pypi.python.org/pypi/dist-s1/)
+[![Conda version](https://img.shields.io/conda/vn/conda-forge/dist_s1)](https://anaconda.org/conda-forge/dist_s1)
+[![Conda platforms](https://img.shields.io/conda/pn/conda-forge/dist_s1)](https://anaconda.org/conda-forge/dist_s1)
+
+This is the workflow that generates OPERA's DIST-S1 product. This workflow is designed to delineate *generic* disturbance from a time-series of OPERA Radiometric and Terrain Corrected Sentinel-1 (RTC-S1) products.
+
+## Install
+
+```
+mamba update -f environment.yml
+pip install -e .
+conda activate dist-s1-env
+python -m ipykernel install --user --name dist-s1-env
+```
+
+## Usage
+
+```
+dist-s1 --runconfig_yml_path <path/to/runconfig.yml>
+```
+
+See `tests/test_main.py` for an example of how to use the CLI with sample data.
+
+
+## Docker
+
+### Downloading a Docker Image
+
+```
+docker pull ghcr.io/asf-hyp3/dist-s1:<tag>
+```
+Where `<tag>` is the semantic version of the release you want to download.
+
+### Building the Docker Image Locally
+
+Make sure you have Docker installed (e.g. for MacOS: https://docs.docker.com/desktop/setup/install/mac-install/)
+
+```
+docker build -f Dockerfile -t dist_s1_img .
+```
+
+### Running the Container Interactively
+
+To run the container interactively:
+```
+docker run -ti dist_s1_img
+```
+Within the container, you can run the CLI commands and the test suite.

dist_s1-0.0.2/README.md

@@ -0,0 +1,52 @@
+# dist-s1
+
+[![PyPI license](https://img.shields.io/pypi/l/dist-s1.svg)](https://pypi.python.org/pypi/dist-s1/)
+[![PyPI pyversions](https://img.shields.io/pypi/pyversions/dist-s1.svg)](https://pypi.python.org/pypi/dist-s1/)
+[![PyPI version](https://img.shields.io/pypi/v/dist-s1.svg)](https://pypi.python.org/pypi/dist-s1/)
+[![Conda version](https://img.shields.io/conda/vn/conda-forge/dist_s1)](https://anaconda.org/conda-forge/dist_s1)
+[![Conda platforms](https://img.shields.io/conda/pn/conda-forge/dist_s1)](https://anaconda.org/conda-forge/dist_s1)
+
+This is the workflow that generates OPERA's DIST-S1 product. This workflow is designed to delineate *generic* disturbance from a time-series of OPERA Radiometric and Terrain Corrected Sentinel-1 (RTC-S1) products.
+
+## Install
+
+```
+mamba update -f environment.yml
+pip install -e .
+conda activate dist-s1-env
+python -m ipykernel install --user --name dist-s1-env
+```
+
+## Usage
+
+```
+dist-s1 --runconfig_yml_path <path/to/runconfig.yml>
+```
+
+See `tests/test_main.py` for an example of how to use the CLI with sample data.
+
+
+## Docker
+
+### Downloading a Docker Image
+
+```
+docker pull ghcr.io/asf-hyp3/dist-s1:<tag>
+```
+Where `<tag>` is the semantic version of the release you want to download.
+
+### Building the Docker Image Locally
+
+Make sure you have Docker installed (e.g. for MacOS: https://docs.docker.com/desktop/setup/install/mac-install/)
+
+```
+docker build -f Dockerfile -t dist_s1_img .
+```
+
+### Running the Container Interactively
+
+To run the container interactively:
+```
+docker run -ti dist_s1_img
+```
+Within the container, you can run the CLI commands and the test suite.