Merge pull request #10 from opera-adt/dev

v0.0.3

.Dockerignore

@@ -0,0 +1,24 @@
+# Mypy
+.mypy_cache
+.pytest_cache
+
+# MacOS
+.DS_Store
+.DS_Store?
+
+# vscode
+.vscode
+
+# Git
+.git
+.github
+
+# Environment
+.env
+
+# Ignore build artifacts
+build/
+*.egg-info/
+
+# Ignore Jupyter checkpoints
+.ipynb_checkpoints/

CHANGELOG.md

@@ -6,6 +6,16 @@ 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).
 
+## [0.0.3]
+
+### Added
+
+- Python 3.13 support
+- Updated dockerimage to ensure on login the conda environment is activated
+- Instructions in the README for OPERA delivery.
+- A `.Dockerignore` file to remove extraneous files from the docker image
+- Allow `/home/ops` directory in Docker image to be open to all users
+
 ## [0.0.2]
 
 ### Added

Dockerfile

@@ -29,6 +29,9 @@ WORKDIR /home/ops
 COPY --chown=dist_user:dist_user environment.yml /home/ops/dist-s1/environment.yml
 COPY --chown=dist_user:dist_user . /home/ops/dist-s1
 
+# Ensure all files are read/write by the user
+RUN chmod -R 777 /home/ops
+
 # Create the environment with mamba
 RUN mamba env create -f /home/ops/dist-s1/environment.yml && \
     conda clean -afy
@@ -37,5 +40,7 @@ RUN mamba env create -f /home/ops/dist-s1/environment.yml && \
 RUN echo ". /opt/conda/etc/profile.d/conda.sh" >> ~/.profile && \
     echo "conda activate dist-s1-env" >> ~/.profile
 
+RUN echo "conda activate dist-s1-env" >> ~/.bashrc
+
 # Install repository with pip
 RUN python -m pip install --no-cache-dir /home/ops/dist-s1

README.md

@@ -6,9 +6,29 @@
 [![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.
+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 (OPERA RTC-S1) products. The output DIST-S1 product is resampled to a 30 meter Military Grid Reference System (MGRS) tile.
 
-## Install
+Currently, this workflow is just *scaffolding*. It is not ready for use!
+
+## Installation
+
+### Using `pip`
+
+We recommend using the mamba/conda package manager to install the DIST-S1 workflow, manage the environment, and install the dependencies.
+
+```
+mamba update -f environment.yml
+pip install dist-s1  # update to conda when it is ready on conda-forge
+conda activate dist-s1-env
+python -m ipykernel install --user --name dist-s1-env
+```
+
+The last command is optional, but will allow this project to be imported into a Jupyter notebook.
+
+
+### Development Installation
+
+As above, we recommend using the mamba/conda package manager to install the DIST-S1 workflow, manage the environment, and install the dependencies.
 
 ```
 mamba update -f environment.yml
@@ -19,12 +39,24 @@ python -m ipykernel install --user --name dist-s1-env
 
 ## Usage
 
+There are two entrypoints for the DIST-S1 workflow:
+
+1. `dist-s1 run_sas` - This is the primary entrypoint for Science Data System (SDS) operations in which this library is viewed as the Science Application Software (SAS) for DIST-S1 within JPL's Hybrid Science Data System (HySDS).
+2. `dist-s1 run` (not implemented yet) - This is the simplified entrypoint for scientific and research users (non-SDS), allowing for the localization of data from publicly available data sources with more human readable inputs.
+
+It is worth noting that the SDS workflow (`dist-s1 run_sas`) is *not* user friendly requiring the explicit specification of the numerous input RTC-S1 datasets (nominally there are 100s of these files required for the generation of a single DIST-S1 product over an MGRS tile). The `dist-s1 run` entrypoint has far fewer inputs and is designed to be human-operable. Specifically, the `dist-s1 run` takes care of the localization and accounting of the all the necessary input RTC-S1 datasets.
+
+### The `dist-s1 run_sas` Entrypoint
+
 ```
-dist-s1 --runconfig_yml_path <path/to/runconfig.yml>
+dist-s1 run_sas --runconfig_yml_path <path/to/runconfig.yml>
 ```
 
 See `tests/test_main.py` for an example of how to use the CLI with sample data.
 
+### The `dist-s1 run` Entrypoint
+
+This is not yet implemented.
 
 ## Docker
 
@@ -35,18 +67,43 @@ docker pull ghcr.io/asf-hyp3/dist-s1:<tag>
 ```
 Where `<tag>` is the semantic version of the release you want to download.
 
+Notes: 
+- our image does not currently support the `arm64` (i.e. Mac M1) architecture. Therefore, you will need to build the image from the Dockerfile yourself.
+- Currently, the image is still under development and we will likely update it to ensure compatibility with GPU processing.
+
 ### Building the Docker Image Locally
 
-Make sure you have Docker installed (e.g. for MacOS: https://docs.docker.com/desktop/setup/install/mac-install/)
+Make sure you have Docker installed for [Mac](https://docs.docker.com/desktop/setup/install/mac-install/) or [Windows](https://docs.docker.com/desktop/setup/install/windows-install/). We call the docker image `dist_s1_img` for the remainder of this README.
 
 ```
-docker build -f Dockerfile -t dist_s1_img .
+docker build -f Dockerfile -t dist-s1 .
 ```
 
 ### Running the Container Interactively
 
 To run the container interactively:
 ```
-docker run -ti dist_s1_img
+docker run -ti dist-s1
 ```
 Within the container, you can run the CLI commands and the test suite.
+
+
+# Delivery Instructions
+
+There are certain releases associated with OPERA project deliveries. Here we provide instructions for how to run and verify the DIST-S1 workflow.
+
+We have included sample input data, associated a Docker image via the Github registry, and run tests via github actions all within this repository.
+
+```
+docker pull ghcr.io/opera-adt/dist-s1
+```
+If a specific version is required (or assumed for a delivery), then you use `docker pull ghcr.io/opera-adt/dist-s1:<version>` e.g.
+```
+docker pull ghcr.io/opera-adt/dist-s1:0.0.4
+```
+The command will pull the latest released version of the Docker image. To run the test suite, run:
+```
+docker run ghcr.io/opera-adt/dist-s1 bash -l -c 'cd dist-s1 && pytest tests'
+``` 
+
+

pyproject.toml

@@ -16,6 +16,7 @@ classifiers = [
   "Intended Audience :: Science/Research",
   "Programming Language :: Python :: 3",
   "Programming Language :: Python :: 3.12",
+  "Programming Language :: Python :: 3.13",
   "Programming Language :: Python",
   "Topic :: Scientific/Engineering",
 ]