First commit

.copier-answers.yml

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+# Changes here will be overwritten by Copier
+_commit: v0.3.2
+_src_path: gh://lsstdesc/RAIL-project-template
+author_email: lsst-desc-rail-admin@slac.stanford.edu
+author_name: LSST Dark Energy Science Collaboration (DESC)
+create_example_module: false
+package_name: deepdisc
+project_name: pz-rail-deepdisc

.github/ISSUE_TEMPLATE/0-general_issue.md

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+---
+name: General issue
+about: Quickly create a general issue
+title: ''
+labels: ''
+assignees: ''
+
+---

.github/ISSUE_TEMPLATE/1-bug_report.md

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+---
+name: Bug report
+about: Tell us about a problem to fix
+title: 'Short description'
+labels: 'bug'
+assignees: ''
+
+---
+**Bug report**
+
+
+**Before submitting**
+Please check the following:
+
+- [ ] I have described the situation in which the bug arose, including what code was executed, information about my environment, and any applicable data others will need to reproduce the problem.
+- [ ] I have included available evidence of the unexpected behavior (including error messages, screenshots, and/or plots) as well as a descriprion of what I expected instead.
+- [ ] If I have a solution in mind, I have provided an explanation and/or pseudocode and/or task list.

.github/ISSUE_TEMPLATE/2-feature_request.md

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+---
+name: Feature request
+about: Suggest an idea for this project
+title: 'Short description'
+labels: 'enhancement'
+assignees: ''
+
+---
+
+** Feature request**
+
+
+**Before submitting**
+Please check the following:
+
+- [ ] I have described the purpose of the suggested change, specifying what I need the enhancement to accomplish, i.e. what problem it solves.
+- [ ] I have included any relevant links, screenshots, environment information, and data relevant to implementing the requested feature, as well as pseudocode for how I want to access the new functionality.
+- [ ] If I have ideas for how the new feature could be implemented, I have provided explanations and/or pseudocode and/or task lists for the steps.

.github/pull_request_template.md

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+## Problem & Solution Description (including issue #)
+
+
+## Code Quality
+- [ ] My code follows [the code style of this project](https://rail-hub.readthedocs.io/en/latest/source/contributing.html#naming-conventions)
+- [ ] I have written unit tests or justified all instances of `#pragma: no cover`; in the case of a bugfix, a new test that breaks as a result of the bug has been added
+- [ ] My code contains relevant comments and necessary documentation for future maintainers; the change is reflected in applicable demos/tutorials (with output cleared!) and added/updated docstrings use the [NumPy docstring format](https://numpydoc.readthedocs.io/en/latest/format.html)
+- [ ] Any breaking changes, described above, are accompanied by backwards compatibility and deprecation warnings

.github/workflows/add-issue-to-project-tracker.yml

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+name: Add bugs to bugs project
+
+on:
+  issues:
+    types:
+      - opened
+  pull_request:
+    types: [opened, reopened]
+
+jobs:
+  add-to-project:
+    name: Add issue to project
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/add-to-project@v0.4.0
+        with:
+          # You can target a repository in a different organization
+          # to the issue
+          project-url: https://github.com/orgs/LSSTDESC/projects/6
+          github-token: ${{ secrets.ADD_TO_PROJECT_PAT }}

.github/workflows/linting.yml

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+# 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 ]
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v3
+    - name: Set up Python
+      uses: actions/setup-python@v4
+      with:
+        python-version: '3.11'
+    - 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
+    - name: Analyze code with linter
+      run: |
+        pylint -rn -sn --recursive=y ./src
+        pylint -rn -sn --recursive=y ./tests
+      # the following line allows the CI test to pass, even if pylint fails
+      continue-on-error: true

.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://github.com/pypa/gh-action-pypi-publish#trusted-publishing
+
+# 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
+    permissions:
+      id-token: write
+    steps:
+    - uses: actions/checkout@v3
+    - name: Set up Python
+      uses: actions/setup-python@v4
+      with:
+        python-version: '3.10'
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install build
+    - name: Build package
+      run: python -m build
+    - name: Publish package
+      uses: pypa/gh-action-pypi-publish@release/v1

.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.
+
+name: Unit test smoke test
+
+on:
+  schedule:
+    - cron: 45 6 * * *
+
+  # Allows you to run this workflow manually from the Actions tab
+  workflow_dispatch:
+
+jobs:
+  build:
+
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ['3.9', '3.10', '3.11']
+
+    steps:
+    - uses: actions/checkout@v3
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v4
+      with:
+        python-version: ${{ matrix.python-version }}
+    - 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
+    - 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
+    strategy:
+      matrix:
+        python-version: ['3.9', '3.10', '3.11']
+
+    steps:
+    - uses: actions/checkout@v3
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v4
+      with:
+        python-version: ${{ matrix.python-version }}
+    - 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
+    - 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

.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/
+pip-wheel-metadata/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+_version.py
+
+# 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/
+
+# 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/
+_readthedocs/
+
+# PyBuilder
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+.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
+
+# 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
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/
+
+# vscode
+.vscode/
+
+# dask
+dask-worker-space/
+
+# tmp directory
+tmp/