Merge pull request #1 from gshiroma/main

Add first implementation of the OPERA RTC workflow for IF delivery

.circleci/config.yml

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+version: 2.1
+
+jobs:
+  build:
+    machine:
+      image: ubuntu-2004:current
+    resource_class: medium
+    steps:
+      - checkout
+      - run:
+          name: "Build RTC docker image"
+          command: |
+            docker build . -f docker/Dockerfile
+
+workflows:
+  build-workflow:
+    jobs:
+      - build

.github/ISSUE_TEMPLATE/bug_report.yml

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+name: Bug Report
+description: Create a report to help us improve
+title: "[Bug]: "
+labels: ["bug", "needs triage"]
+body:
+  - type: markdown
+    attributes:
+      value: |
+        > _Thanks for filing a bug ticket. We appreciate your time and effort. Please answer a few questions._
+  - type: dropdown
+    id: checked-for-duplicates
+    attributes:
+      label: Checked for duplicates
+      description: Have you checked for duplicate issue tickets?
+      multiple: false
+      options:
+        - "Yes - I've already checked"
+        - "No - I haven't checked"
+    validations:
+      required: yes
+  - type: textarea
+    id: description
+    attributes:
+      label: Describe the bug
+      description: A clear and concise description of what the bug is. Plain-text snippets preferred but screenshots welcome.
+      placeholder: Tell us what you saw
+      value: "When I did [...] action, I noticed [...]"
+    validations:
+      required: true
+  - type: textarea
+    id: expected-behavior
+    attributes:
+      label: What did you expect?
+      description: A clear and concise description of what you expect to happen
+      placeholder: Tell us what you expected
+      value: "I expected [...]"
+    validations:
+      required: true
+  - type: textarea
+    id: reproduction
+    attributes:
+      label: Reproducible steps
+      description: "How would we reproduce this bug? Please walk us through it step by step. Plain-text snippets preferred but screenshots welcome."
+      value: |
+        1.
+        2.
+        3.
+        ...
+      render: bash
+  - type: textarea
+    id: environment
+    attributes:
+      label: Environment
+      description: "What is your environment?"
+      value: |
+        - Version of this software [e.g. vX.Y.Z]
+        - Operating System: [e.g. MacOSX with Docker Desktop vX.Y]
+        ...
+      render: bash

.github/ISSUE_TEMPLATE/feature_request.yml

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+name: New Feature
+description: Submit a new feature request
+title: "[New Feature]: "
+labels: ["enhancement", "needs triage"]
+body:
+  - type: markdown
+    attributes:
+      value: |
+        > _Thanks for filing a new feature request. We appreciate your time and effort. Please answer a few questions._
+  - type: dropdown
+    id: checked-for-duplicates
+    attributes:
+      label: Checked for duplicates
+      description: Have you checked for duplicate issue tickets?
+      multiple: false
+      options:
+        - "Yes - I've already checked"
+        - "No - I haven't checked"
+    validations:
+      required: yes
+  - type: dropdown
+    id: checked-alternatives
+    attributes:
+      label: Alternatives considered
+      description: Have you considered alternative solutions to your feature request?
+      options:
+        - "Yes - and alternatives don't suffice"
+        - "No - I haven't considered"
+    validations:
+      required: yes
+  - type: textarea
+    id: related-problems
+    attributes:
+      label: Related problems
+      description: Is your feature request related to any problems? Please help us understand if so, including linking to any other issue tickets.
+      placeholder: Tell us the problems
+      value: "I'm frustrated when [...] happens as documented in issue-XYZ"
+    validations:
+      required: false
+  - type: textarea
+    id: description
+    attributes:
+      label: Describe the feature request
+      description: A clear and concise description of your request. 
+      placeholder: Tell us what you want
+      value: "I need or want [...]"
+    validations:
+      required: true

.gitignore

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+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+cover/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+.pybuilder/
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+#   For a library or package, you might want to ignore these files since the code is
+#   intended to run in multiple environments; otherwise, check them in:
+# .python-version
+
+# pipenv
+#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+#   However, in case of collaboration, if having platform-specific dependencies or dependencies
+#   having no cross-platform support, pipenv may install dependencies that don't work, or not
+#   install all needed dependencies.
+#Pipfile.lock
+
+# poetry
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+#   This is especially recommended for binary packages to ensure reproducibility, and is more
+#   commonly ignored for libraries.
+#   https://python-poetry.org/docs/basic-usage/#commit-your-poetrylock-file-to-version-control
+#poetry.lock
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
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+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/
+
+# pytype static type analyzer
+.pytype/
+
+# Cython debug symbols
+cython_debug/
+
+# PyCharm
+#  JetBrains specific template is maintainted in a separate JetBrains.gitignore that can
+#  be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore
+#  and can be added to the global gitignore or merged into this file.  For a more nuclear
+#  option (not recommended) you can uncomment the following to ignore the entire idea folder.
+#.idea/
+
+

Docker/Dockerfile

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+FROM ubuntu:22.04
+
+LABEL author="OPERA ADT" \
+      description="RTC interface release" \
+      version="interface_0.1"
+
+RUN apt-get -y update &&\
+    apt-get -y install curl zip make &&\
+    adduser --disabled-password rtc_user
+
+RUN mkdir -p /home/rtc_user/OPERA/RTC
+COPY . /home/rtc_user/OPERA/RTC
+RUN chmod -R 755 /home/rtc_user &&\
+    chown -R rtc_user:rtc_user /home/rtc_user/OPERA
+USER rtc_user 
+
+ENV CONDA_PREFIX=/home/rtc_user/miniconda3
+
+
+#Install conda and 
+WORKDIR /home/rtc_user
+RUN curl -sSL https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -o miniconda.sh &&\
+    bash miniconda.sh -b -p ${CONDA_PREFIX} &&\
+    chmod -R 755 ${HOME}/miniconda3 &&\
+    rm ${HOME}/miniconda.sh
+
+ENV PATH=${CONDA_PREFIX}/bin:${PATH}
+ENV POSTFIX_ISCE3="rtc"
+ENV ISCEHOME=/home/rtc_user
+
+RUN ${CONDA_PREFIX}/bin/conda init bash
+
+#Install ISCE3 from source code
+RUN echo "Installing Conda environment for ISCE3" &&\
+    mkdir -p ${ISCEHOME}/tools/isce_${POSTFIX_ISCE3}/src &&\
+    mkdir -p ${ISCEHOME}/tools/isce_${POSTFIX_ISCE3}/build &&\
+    mkdir -p ${ISCEHOME}/tools/isce_${POSTFIX_ISCE3}/install &&\
+    cd ${ISCEHOME} &&\
+    curl -sSL https://github.com/gshiroma/isce3/archive/refs/heads/opera_rtc.zip -o isce3_opera_rtc.zip &&\
+    unzip -d ${ISCEHOME}/tools/isce_${POSTFIX_ISCE3} isce3_opera_rtc.zip &&\
+    cd ${ISCEHOME}/tools/isce_${POSTFIX_ISCE3}/src &&\
+    ln -s ../isce3-opera_rtc isce3 &&\
+    rm ${ISCEHOME}/isce3_opera_rtc.zip &&\
+    cd ${HOME} &&\
+    conda create --name isce3_rtc --file ./OPERA/RTC/Docker/specfile.txt &&\
+    chmod -R 755 ${CONDA_PREFIX}/envs/isce3_rtc &&\
+    cd ${ISCEHOME}/tools/isce_$POSTFIX_ISCE3/src
+
+SHELL ["conda", "run", "-n", "isce3_rtc", "/bin/bash", "-c"]
+
+ENV CC=${CONDA_PREFIX}/envs/isce3_rtc/bin/x86_64-conda-linux-gnu-gcc
+ENV CXX=${CONDA_PREFIX}/envs/isce3_rtc/bin/x86_64-conda-linux-gnu-g++
+ENV PATH=$PATH:${ISCEHOME}/tools/isce_$POSTFIX_ISCE3/install/bin
+ENV PYTHONPATH=$PYTHONPATH:${ISCEHOME}/tools/isce_$POSTFIX_ISCE3/install/packages
+ENV LD_LIBRARY_PATH=$LD_LIBRARY_PATH:${ISCEHOME}/tools/isce_${POSTFIX_ISCE3}/install/lib
+
+RUN cd ${ISCEHOME}/tools/isce_$POSTFIX_ISCE3/build &&\
+    cmake -DCMAKE_INSTALL_PREFIX=${ISCEHOME}/tools/isce_${POSTFIX_ISCE3}/install -DWITH_CUDA=OFF ${ISCEHOME}/tools/isce_${POSTFIX_ISCE3}/src/isce3 &&\
+    make -j32 VERBOSE=ON &&\
+    make install &&\
+    rm -r ${ISCEHOME}/tools/isce_${POSTFIX_ISCE3}/build &&\
+    rm -r ${ISCEHOME}/tools/isce_${POSTFIX_ISCE3}/isce3-opera_rtc &&\
+    chmod -R 755 ${ISCEHOME}/tools/isce_${POSTFIX_ISCE3}/install &&\
+    cd /home/rtc_user/miniconda3/envs/isce3_rtc/lib &&\
+    ln -s ${ISCEHOME}/tools/isce_${POSTFIX_ISCE3}/install/lib/libisce3.so &&\
+    echo 'ISCE3 installation successful!'
+
+RUN echo "Installing OPERA s1-reader and RTC" &&\
+    mkdir -p $HOME/OPERA &&\
+    cd $HOME/OPERA &&\
+    curl -sSL https://github.com/seongsujeong/s1-reader/archive/refs/heads/correction_and_calibration.zip -o s1_reader.zip &&\
+    unzip s1_reader.zip &&\
+    chmod -R 755 s1-reader-correction_and_calibration &&\
+    ln -s s1-reader-correction_and_calibration s1-reader &&\
+    rm s1_reader.zip &&\
+    python -m pip install ./s1-reader &&\
+    cd $HOME/OPERA &&\
+    pip install ./RTC &&\
+    mkdir /home/rtc_user/scratch &&\
+    echo 'conda activate isce3_rtc' >>/home/rtc_user/.bashrc
+
+WORKDIR /home/rtc_user/scratch
+
+ENTRYPOINT ["conda", "run", "-n", "isce3_rtc","rtc_s1.py"]

Docker/environment.yml

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+name: isce3_rtc
+channels:
+  - conda-forge
+dependencies:
+  - python>=3.9,<3.10
+  - cmake
+  - eigen
+  - fftw
+  - gdal
+  - gmock
+  - gtest
+  - gcc_linux-64 < 10
+  - gxx_linux-64 < 10
+  - gfortran_linux-64
+  - h5py
+  - hdf5
+  - libgcc-ng
+  - libstdcxx-ng
+  - numpy
+  - pybind11
+  - pyre
+  - pytest
+  - cython
+  - ruamel.yaml
+  - scipy
+  - shapely
+  - yamale
+  - backoff