shine-wl 0.0.2__tar.gz

shine_wl-0.0.2/.all-contributorsrc

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+{
+  "files": [
+    "README.md"
+  ],
+  "imageSize": 100,
+  "commit": false,
+  "commitType": "docs",
+  "commitConvention": "angular",
+  "contributors": [
+    {
+      "login": "CentofantiEze",
+      "name": "Ezequiel Centofanti",
+      "avatar_url": "https://avatars.githubusercontent.com/u/42658822?v=4",
+      "profile": "https://centofantieze.github.io",
+      "contributions": [
+        "ideas",
+        "projectManagement"
+      ]
+    },
+    {
+      "login": "sfarrens",
+      "name": "Samuel Farrens",
+      "avatar_url": "https://avatars.githubusercontent.com/u/6851839?v=4",
+      "profile": "http://sfarrens.github.io",
+      "contributions": [
+        "ideas",
+        "projectManagement"
+      ]
+    },
+    {
+      "login": "Emmaaycoberry",
+      "name": "Emma Ayçoberry",
+      "avatar_url": "https://avatars.githubusercontent.com/u/80262003?v=4",
+      "profile": "https://github.com/Emmaaycoberry",
+      "contributions": [
+        "ideas",
+        "projectManagement"
+      ]
+    },
+    {
+      "login": "EiffL",
+      "name": "Francois Lanusse",
+      "avatar_url": "https://avatars.githubusercontent.com/u/861591?v=4",
+      "profile": "http://flanusse.net/",
+      "contributions": [
+        "ideas",
+        "projectManagement"
+      ]
+    }
+  ],
+  "contributorsPerLine": 4,
+  "skipCi": true,
+  "repoType": "github",
+  "repoHost": "https://github.com",
+  "projectName": "SHINE",
+  "projectOwner": "CosmoStat"
+}

shine_wl-0.0.2/.github/workflows/claude-code-review.yml

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+name: Claude Code Review
+
+on:
+  pull_request:
+    types: [opened, synchronize, ready_for_review, reopened]
+    # Optional: Only run on specific file changes
+    # paths:
+    #   - "src/**/*.ts"
+    #   - "src/**/*.tsx"
+    #   - "src/**/*.js"
+    #   - "src/**/*.jsx"
+
+jobs:
+  claude-review:
+    # Optional: Filter by PR author
+    # if: |
+    #   github.event.pull_request.user.login == 'external-contributor' ||
+    #   github.event.pull_request.user.login == 'new-developer' ||
+    #   github.event.pull_request.author_association == 'FIRST_TIME_CONTRIBUTOR'
+
+    runs-on: ubuntu-latest
+    permissions:
+      contents: read
+      pull-requests: read
+      issues: read
+      id-token: write
+
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v4
+        with:
+          fetch-depth: 1
+
+      - name: Run Claude Code Review
+        id: claude-review
+        uses: anthropics/claude-code-action@v1
+        with:
+          claude_code_oauth_token: ${{ secrets.CLAUDE_CODE_OAUTH_TOKEN }}
+          plugin_marketplaces: 'https://github.com/anthropics/claude-code.git'
+          plugins: 'code-review@claude-code-plugins'
+          prompt: '/code-review:code-review ${{ github.repository }}/pull/${{ github.event.pull_request.number }}'
+          # See https://github.com/anthropics/claude-code-action/blob/main/docs/usage.md
+          # or https://code.claude.com/docs/en/cli-reference for available options
+

shine_wl-0.0.2/.github/workflows/claude.yml

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+name: Claude Code
+
+on:
+  issue_comment:
+    types: [created]
+  pull_request_review_comment:
+    types: [created]
+  issues:
+    types: [opened, assigned]
+  pull_request_review:
+    types: [submitted]
+
+jobs:
+  claude:
+    if: |
+      (github.event_name == 'issue_comment' && contains(github.event.comment.body, '@claude')) ||
+      (github.event_name == 'pull_request_review_comment' && contains(github.event.comment.body, '@claude')) ||
+      (github.event_name == 'pull_request_review' && contains(github.event.review.body, '@claude')) ||
+      (github.event_name == 'issues' && (contains(github.event.issue.body, '@claude') || contains(github.event.issue.title, '@claude')))
+    runs-on: ubuntu-latest
+    permissions:
+      contents: read
+      pull-requests: read
+      issues: read
+      id-token: write
+      actions: read # Required for Claude to read CI results on PRs
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v4
+        with:
+          fetch-depth: 1
+
+      - name: Run Claude Code
+        id: claude
+        uses: anthropics/claude-code-action@v1
+        with:
+          claude_code_oauth_token: ${{ secrets.CLAUDE_CODE_OAUTH_TOKEN }}
+
+          # This is an optional setting that allows Claude to read CI results on PRs
+          additional_permissions: |
+            actions: read
+
+          # Optional: Give a custom prompt to Claude. If this is not specified, Claude will perform the instructions specified in the comment that tagged it.
+          # prompt: 'Update the pull request description to include a summary of changes.'
+
+          # Optional: Add claude_args to customize behavior and configuration
+          # See https://github.com/anthropics/claude-code-action/blob/main/docs/usage.md
+          # or https://code.claude.com/docs/en/cli-reference for available options
+          # claude_args: '--allowed-tools Bash(gh pr:*)'
+

shine_wl-0.0.2/.github/workflows/docs.yml

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+name: Deploy docs
+
+on:
+  push:
+    branches: [main]
+  workflow_dispatch:
+
+permissions:
+  contents: read
+  pages: write
+  id-token: write
+
+concurrency:
+  group: pages
+  cancel-in-progress: false
+
+jobs:
+  deploy:
+    runs-on: ubuntu-latest
+    environment:
+      name: github-pages
+      url: ${{ steps.deployment.outputs.page_url }}
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: actions/setup-python@v5
+        with:
+          python-version: "3.12"
+          cache: pip
+
+      - run: pip install -e ".[docs]"
+
+      - run: mkdocs build --strict
+
+      - uses: actions/upload-pages-artifact@v3
+        with:
+          path: site/
+
+      - id: deployment
+        uses: actions/deploy-pages@v4

shine_wl-0.0.2/.github/workflows/release.yaml

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+# This workflow will upload a Python Package to PyPI 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:
+  release-build:
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: actions/setup-python@v5
+        with:
+          python-version: "3.x"
+
+      - name: Build release distributions
+        run: |
+          # NOTE: put your own distribution build steps here.
+          python -m pip install build
+          python -m build
+
+      - name: Upload distributions
+        uses: actions/upload-artifact@v4
+        with:
+          name: release-dists
+          path: dist/
+
+  pypi-publish:
+    runs-on: ubuntu-latest
+    needs:
+      - release-build
+    permissions:
+      # IMPORTANT: this permission is mandatory for trusted publishing
+      id-token: write
+
+    # Dedicated environments with protections for publishing are strongly recommended.
+    # For more information, see: https://docs.github.com/en/actions/deployment/targeting-different-environments/using-environments-for-deployment#deployment-protection-rules
+    environment:
+      name: pypi
+      # OPTIONAL: uncomment and update to include your PyPI project URL in the deployment status:
+      # url: https://pypi.org/p/YOURPROJECT
+      #
+      # ALTERNATIVE: if your GitHub Release name is the PyPI project version string
+      # ALTERNATIVE: exactly, uncomment the following line instead:
+      # url: https://pypi.org/project/YOURPROJECT/${{ github.event.release.name }}
+
+    steps:
+      - name: Retrieve release distributions
+        uses: actions/download-artifact@v4
+        with:
+          name: release-dists
+          path: dist/
+
+      - name: Publish release distributions to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1
+        with:
+          packages-dir: dist/

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

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+name: Tests
+
+on:
+  push:
+    branches: [ main, prototype ]
+  pull_request:
+    branches: [ main ]
+
+jobs:
+  test:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ['3.11', '3.12', '3.13']
+
+    steps:
+    - uses: actions/checkout@v4
+
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v5
+      with:
+        python-version: ${{ matrix.python-version }}
+
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        # Install JAX-GalSim from GitHub (not yet on PyPI)
+        pip install git+https://github.com/GalSim-developers/JAX-GalSim.git
+        # Install SHINE with test dependencies
+        pip install -e ".[test]"
+
+    - name: Run tests with pytest
+      run: |
+        pytest tests/ -v --cov=shine --cov-report=term-missing
+
+    - name: Upload coverage reports
+      if: matrix.python-version == '3.11'
+      uses: codecov/codecov-action@v4
+      with:
+        fail_ci_if_error: false

shine_wl-0.0.2/.gitignore

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+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[codz]
+*$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
+
+# UV
+#   Similar to Pipfile.lock, it is generally recommended to include uv.lock in version control.
+#   This is especially recommended for binary packages to ensure reproducibility, and is more
+#   commonly ignored for libraries.
+#uv.lock
+
+# poetry
+#   Similar to Pipfile.lock, it is generally recommended to include poetry.lock in version control.
+#   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
+#poetry.toml
+
+# pdm
+#   Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control.
+#   pdm recommends including project-wide configuration in pdm.toml, but excluding .pdm-python.
+#   https://pdm-project.org/en/latest/usage/project/#working-with-version-control
+#pdm.lock
+#pdm.toml
+.pdm-python
+.pdm-build/
+
+# pixi
+#   Similar to Pipfile.lock, it is generally recommended to include pixi.lock in version control.
+#pixi.lock
+#   Pixi creates a virtual environment in the .pixi directory, just like venv module creates one
+#   in the .venv directory. It is recommended not to include this directory in version control.
+.pixi
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow and github.com/pdm-project/pdm
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.envrc
+.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/
+
+# pytype static type analyzer
+.pytype/
+
+# Cython debug symbols
+cython_debug/
+
+# PyCharm
+#  JetBrains specific template is maintained 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/
+
+# Abstra
+# Abstra is an AI-powered process automation framework.
+# Ignore directories containing user credentials, local state, and settings.
+# Learn more at https://abstra.io/docs
+.abstra/
+
+# Visual Studio Code
+#  Visual Studio Code specific template is maintained in a separate VisualStudioCode.gitignore 
+#  that can be found at https://github.com/github/gitignore/blob/main/Global/VisualStudioCode.gitignore
+#  and can be added to the global gitignore or merged into this file. However, if you prefer, 
+#  you could uncomment the following to ignore the entire vscode folder
+# .vscode/
+
+# Ruff stuff:
+.ruff_cache/
+
+# PyPI configuration file
+.pypirc
+
+# Cursor
+#  Cursor is an AI-powered code editor. `.cursorignore` specifies files/directories to
+#  exclude from AI features like autocomplete and code analysis. Recommended for sensitive data
+#  refer to https://docs.cursor.com/context/ignore-files
+.cursorignore
+.cursorindexingignore
+
+# Marimo
+marimo/_static/
+marimo/_lsp/
+__marimo__/
+
+shine/_version.py
+
+results/
+examples/output/
+
+project_plan/

shine_wl-0.0.2/CLAUDE.md

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+# CLAUDE.md - AI Assistant Guide for SHINE
+
+## Project Overview
+
+SHINE (SHear INference Environment) is a JAX-powered framework for probabilistic shear estimation in weak gravitational lensing. It treats shear measurement as a Bayesian inverse problem: generating forward models of the sky, convolving with instrument response, and comparing to observed data to infer posterior distributions of shear parameters.
+
+**Status:** Early development / Alpha. The architectural design is complete (see `DESIGN.md`) but source code implementation has not yet begun — currently only `shine/__init__.py` exists as an empty module.
+
+**Organization:** CosmoStat Lab (CEA / CNRS)
+**License:** MIT
+
+## Repository Structure
+
+```
+SHINE/
+├── .github/workflows/       # CI/CD (Claude PR assistant + code review)
+│   ├── claude.yml           # Claude PR assistant triggered by @claude mentions
+│   └── claude-code-review.yml # Automated code review on PRs
+├── assets/
+│   └── logo.png             # Project logo
+├── external/
+│   └── GalSim/              # External GalSim dependency (placeholder)
+├── shine/                   # Main Python package
+│   └── __init__.py          # Currently empty
+├── CLAUDE.md                # This file
+├── DESIGN.md                # Comprehensive architecture & design document
+├── LICENSE                  # MIT License
+├── README.md                # Project overview and quick start
+└── pyproject.toml           # Build configuration
+```
+
+## Key Technologies
+
+- **JAX** — Core computation: JIT compilation, vmap vectorization, grad for HMC
+- **NumPyro** — Probabilistic programming: hierarchical models, MCMC (NUTS/HMC)
+- **JAX-GalSim** — Differentiable galaxy profile rendering and PSF convolution
+- **BlackJAX** — Optional lower-level inference library for custom samplers
+
+## Planned Module Architecture
+
+These modules are specified in `DESIGN.md` but not yet implemented:
+
+| Module | Purpose |
+|--------|---------|
+| `shine.config` | YAML config parsing and validation (pydantic) |
+| `shine.scene_modelling` | NumPyro generative model definitions |
+| `shine.inference` | Bayesian inference (NUTS, SVI, BlackJAX) |
+| `shine.simulations` | Survey-specific data interfaces (Euclid, LSST, MeerKAT) |
+| `shine.morphology` | Galaxy surface brightness profiles (Sersic, VAE/GAN) |
+| `shine.wms` | Workflow management for HPC/SLURM clusters |
+
+## Build System
+
+- **Build backend:** setuptools (>=61) with setuptools-scm (>=6.2)
+- **Version:** Dynamic, managed by setuptools-scm (writes to `shine/_version.py`)
+- **Python:** >=3.9 (supports 3.9 through 3.13)
+- **Install:** `pip install -e .` for development
+
+## Code Standards (from DESIGN.md Section 4.1)
+
+When implementing code for this project, follow these conventions:
+
+- **Formatter:** Black
+- **Import sorting:** isort
+- **Type hints:** Full PEP 484 compliance required
+- **Docstrings:** Google-style
+- **Testing:** pytest + chex (JAX-specific array shape/type testing)
+- **Documentation:** Sphinx + ReadTheDocs (not yet configured)
+
+## JAX-Specific Guidelines
+
+- JAX-GalSim objects are **immutable** — the pipeline must be purely functional
+- Use `jax.vmap` or `numpyro.plate` for vectorization over galaxies; **never use Python loops** in rendering paths
+- Use `jax.jit` to compile likelihood and gradient functions
+- JAX uses a **functional PRNG** — manage RNG keys carefully, especially within NumPyro models
+- Support reparameterization (e.g., `LocScaleReparam`) for hierarchical models
+
+## Testing Strategy
+
+Not yet implemented. When tests are added, follow this strategy:
+
+- **Unit tests:** Verify individual components (e.g., Sersic profile generation)
+- **Integration tests:** End-to-end runs on small synthetic patches
+- **Validation tests:**
+  - Self-consistency: generate data with known shear, infer it back, verify posterior credible intervals
+  - Comparison: compare with standard (non-JAX) GalSim for numerical accuracy
+- **Run tests with:** `pytest` (when test infrastructure exists)
+
+## Configuration Pattern
+
+SHINE uses GalSim-compatible YAML configuration with a probabilistic extension: any parameter defined as a distribution (e.g., `type: Normal`) becomes a **latent variable** for inference rather than a fixed simulation value. See `DESIGN.md` Section 6.1 for config examples.
+
+## Development Roadmap
+
+1. **Phase 1:** Prototype with simple parametric models (Sersic) and constant PSF
+2. **Phase 2:** Realistic PSF models (Euclid/LSST specific)
+3. **Phase 3:** Non-parametric galaxy morphology (VAE/Diffusion)
+4. **Phase 4:** Large-scale validation on Flagship/CosmoDC2 simulations
+
+## Key Design Reference
+
+The primary design document is `DESIGN.md` (343 lines). Consult it for:
+- Architecture diagrams (Section 2.3)
+- Component API designs (Section 3)
+- Code structure examples (Section 3.2)
+- End-to-end usage examples with config and Python code (Section 6)
+
+## Common Tasks
+
+```bash
+# Install in development mode
+pip install -e .
+
+# Run tests (when available)
+pytest
+
+# Format code (when tooling is configured)
+black shine/
+isort shine/
+```
+
+## Notes for AI Assistants
+
+- Always consult `DESIGN.md` before implementing new modules — it contains detailed API specifications and code structure examples
+- The project has no runtime dependencies listed in `pyproject.toml` yet; add JAX, NumPyro, JAX-GalSim, etc. when implementing modules
+- No linter/formatter configuration files exist yet (no `.flake8`, `pyproject.toml [tool.black]`, etc.) — create them following the standards in DESIGN.md Section 4.1 when needed
+- No test directory or test infrastructure exists yet — create `tests/` following pytest conventions when adding tests
+- The `external/GalSim/` directory is currently an empty placeholder
+- CI/CD currently only includes Claude-based PR workflows; traditional CI (tests, linting) should be added when code exists to test