Added RomanImageReader and new config file for Roman Data

.copier-answers.yml

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+# Changes here will be overwritten by Copier
+_commit: v1.4.3
+_src_path: gh:lincc-frameworks/python-project-template
+author_email: [email protected]
+author_name: Grant Merz
+create_example_module: true
+custom_install: true
+include_benchmarks: false
+include_docs: true
+include_notebooks: true
+mypy_type_checking: none
+package_name: deepdisc
+preferred_linter: pylint
+project_license: MIT
+project_name: deepdisc
+use_gitlfs: none
+use_isort: true

.github/linting.yml

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+# !!! MOVE THIS FILE BACK TO ./workflows WHEN IT'S TIME TO REINTRODUCE PYLINT !!!
+# While this file is outside of the workflows directory, the workflow it defines
+# will not run automatically.
+
+# This workflow will install Python dependencies, then perform static linting analysis.
+# For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions
+
+name: Lint
+
+on:
+  push:
+    branches: [ main ]
+  pull_request:
+    branches: [ main ]
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    defaults:
+      run:
+        shell: bash -l {0}
+    steps:
+    - uses: actions/checkout@v3
+    - uses: mamba-org/setup-micromamba@v1
+      with:
+        create-args: >-
+          python=3.9.15
+        environment-file: ci-environment.yml
+    - name: Install dependencies
+      run: |
+        sudo apt-get update
+        python -m pip install --upgrade pip
+        pip install .
+        pip install 'git+https://github.com/facebookresearch/detectron2.git@80307d2d5e06f06a8a677cc2653f23a4c56402ac'
+        pip install 'git+https://github.com/pmelchior/scarlet.git'
+        pip install .[dev]
+    - name: Analyze code with linter
+
+      run: |
+        pylint -rn -sn --recursive=y ./src --rcfile=./src/.pylintrc

.github/workflows/build-documentation.yml

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+# This workflow will install Python dependencies, build the package and then build the documentation.
+
+name: Build documentation
+
+
+on:
+  push:
+    branches: [ main ]
+  pull_request:
+    branches: [ main ]
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    defaults:
+      run:
+        shell: bash -l {0}
+    steps:
+    - uses: actions/checkout@v3
+    - uses: mamba-org/setup-micromamba@v1
+      with:
+        create-args: >-
+          python=3.9.15
+        environment-file: ci-environment.yml
+    - name: Install dependencies
+      run: |
+        sudo apt-get update
+        python -m pip install --upgrade pip
+        pip install .
+        pip install 'git+https://github.com/facebookresearch/detectron2.git@80307d2d5e06f06a8a677cc2653f23a4c56402ac'
+        pip install 'git+https://github.com/pmelchior/scarlet.git'
+        pip install .[dev]
+        if [ -f docs/requirements.txt ]; then pip install -r docs/requirements.txt; fi
+    - name: Install notebook requirements
+      run: |
+        sudo apt-get install pandoc
+    - name: Build docs
+      run: |
+        sphinx-build -T -E -b html -d docs/build/doctrees ./docs docs/build/html

.github/workflows/pre-commit-ci.yml

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+# This workflow runs pre-commit hooks on pull requests to enforce coding style.
+# To ensure correct configuration, please refer to:
+#   https://lincc-ppt.readthedocs.io/en/latest/practices/ci_precommit.html
+
+name: Run pre-commit hooks
+
+on:
+  # Disabling until we can figure out inconsistencies in bash behavior
+  # between conda setup and pre-commit itself.
+  # pull_request:
+
+jobs:
+  pre-commit-ci:
+    runs-on: ubuntu-latest
+    env: 
+      SKIP: "check-lincc-frameworks-template-version,pytest-check,no-commit-to-branch,validate-pyproject,check-added-large-files,sphinx-build"
+    steps:
+    - uses: actions/checkout@v3
+      with:
+        fetch-depth: 0 
+    - name: Set up Python
+      uses: actions/setup-python@v4
+      with:
+        python-version: '3.10'
+    - name: Install dependencies
+      run: |
+        sudo apt-get update
+        python -m pip install --upgrade pip
+        pip install .
+        pip install .[dev]
+        if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
+    - uses: pre-commit/[email protected]
+      with:
+        extra_args: --from-ref ${{ github.event.pull_request.base.sha }} --to-ref ${{ github.event.pull_request.head.sha }}
+    - uses: pre-commit-ci/[email protected]
+      if: always()

.github/workflows/publish-to-pypi.yml

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+# This workflow will upload a Python Package using Twine when a release is created
+# For more information see: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-python#publishing-to-package-registries
+
+# This workflow uses actions that are not certified by GitHub.
+# They are provided by a third-party and are governed by
+# separate terms of service, privacy policy, and support
+# documentation.
+
+name: Upload Python Package
+
+on:
+  release:
+    types: [published]
+
+permissions:
+  contents: read
+
+jobs:
+  deploy:
+    runs-on: ubuntu-latest
+    defaults:
+      run:
+        shell: bash -l {0}
+    steps:
+    - uses: actions/checkout@v3
+    - uses: mamba-org/setup-micromamba@v1
+      with:
+        create-args: >-
+          python=3.9.15
+        environment-file: ci-environment.yml
+    - name: Install dependencies
+      run: |
+        sudo apt-get update
+        python -m pip install --upgrade pip
+        pip install .
+        pip install 'git+https://github.com/facebookresearch/detectron2.git@80307d2d5e06f06a8a677cc2653f23a4c56402ac'
+        pip install 'git+https://github.com/pmelchior/scarlet.git'
+        pip install .[dev]
+        pip install build
+    - name: Build package
+      run: python -m build
+    - name: Publish package
+      uses: pypa/gh-action-pypi-publish@27b31702a0e7fc50959f5ad993c78deac1bdfc29
+      with:
+        user: __token__
+        password: ${{ secrets.PYPI_API_TOKEN }}

.github/workflows/smoke-test.yml

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+# This workflow will run daily at 06:45.
+# It will install Python dependencies and run tests with a variety of Python versions.
+# See documentation for help debugging smoke test issues:
+#    https://lincc-ppt.readthedocs.io/en/latest/practices/ci_testing.html#version-culprit
+
+name: Unit test smoke test
+
+on:
+
+  # Runs this workflow automatically
+  schedule:
+    - cron: 45 6 * * *
+
+  # Allows you to run this workflow manually from the Actions tab
+  workflow_dispatch:
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    defaults:
+      run:
+        shell: bash -l {0}
+    steps:
+    - uses: actions/checkout@v3
+    - uses: mamba-org/setup-micromamba@v1
+      with:
+        create-args: >-
+          python=3.9.15
+        environment-file: ci-environment.yml
+    - name: Install dependencies
+      run: |
+        sudo apt-get update
+        python -m pip install --upgrade pip
+        pip install .
+        pip install 'git+https://github.com/facebookresearch/detectron2.git@80307d2d5e06f06a8a677cc2653f23a4c56402ac'
+        pip install 'git+https://github.com/pmelchior/scarlet.git'
+        pip install .[dev]
+    - name: List dependencies
+      run: |
+        pip list
+    - name: Run unit tests with pytest
+      run: |
+        python -m pytest tests

.github/workflows/testing-and-coverage.yml

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+# This workflow will install Python dependencies, run tests and report code coverage with a variety of Python versions
+# For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions
+
+name: Unit test and code coverage
+
+on:
+  push:
+    branches: [ main ]
+  pull_request:
+    branches: [ main ]
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    defaults:
+      run:
+        shell: bash -l {0}
+    steps:
+    - uses: actions/checkout@v3
+    - uses: mamba-org/setup-micromamba@v1
+      with:
+        create-args: >-
+          python=3.9.15
+        environment-file: ci-environment.yml
+    - name: Install dependencies
+      run: |
+        sudo apt-get update
+        python -m pip install --upgrade pip
+        pip install .
+        pip install 'git+https://github.com/facebookresearch/detectron2.git@80307d2d5e06f06a8a677cc2653f23a4c56402ac'
+        pip install 'git+https://github.com/pmelchior/scarlet.git'
+        pip install .[dev]
+    - name: Run unit tests with pytest
+      run: |
+        python -m pytest tests --cov=deepdisc --cov-report=xml
+    - name: Upload coverage report to codecov
+      uses: codecov/codecov-action@v3