spectraxgk 0.0.1__tar.gz

spectraxgk-0.0.1/.github/ISSUE_TEMPLATE/bug_report.md

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+---
+name: 🐞 Bug report
+about: Something isn’t working as expected
+labels: bug
+---
+
+## Description
+A clear and concise description of the bug.
+
+## Repro Steps
+1. Command(s) you ran (paste exact input):
+```
+
+spectraxgk --input examples/<file>.toml
+
+```
+2. What happened vs what you expected?
+
+## Logs / Traceback
+<details>
+<summary>Expand to show full logs</summary>
+
+```
+
+# paste the full error here
+
+````
+</details>
+
+## Environment
+- OS:
+- Python version: `python --version`
+- spectraxgk version: `python -c "import spectraxgk, importlib.metadata as m; print(m.version('spectraxgk'))"`
+- JAX version: `python -c "import jax; print(jax.__version__)"`
+
+## Config snippet
+If applicable, paste relevant TOML sections:
+
+```toml
+# minimal input that reproduces the bug
+````
+
+## Additional context
+
+Anything else we should know?

spectraxgk-0.0.1/.github/ISSUE_TEMPLATE/config.yml

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+
+blank_issues_enabled: false
+contact_links:
+  - name: Questions / Usage Help
+    url: https://github.com/uwplasma/SPECTRAX-GK/discussions
+    about: Ask general questions or share ideas in Discussions.

spectraxgk-0.0.1/.github/ISSUE_TEMPLATE/feature_request.md

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+---
+name: 💡 Feature request
+about: Suggest an idea or enhancement
+labels: enhancement
+---
+
+## Summary
+What would you like to add or improve?
+
+## Motivation
+Why is this useful (scientific value, UX, performance)?
+
+## Proposal
+- High-level description of the change
+- Interfaces affected (CLI/API/TOML), if any
+- Backward compatibility considerations
+
+## Alternatives
+What alternative solutions have you considered?
+
+## Additional context
+Screenshots, references, or related papers.

spectraxgk-0.0.1/.github/pull_request_template.md

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+
+## Summary
+Explain what this PR changes and why.
+
+## Type of change
+- [ ] Bug fix
+- [ ] New feature
+- [ ] Refactor / cleanup
+- [ ] Docs only
+- [ ] CI / tooling
+
+## How to test
+- Commands / scripts to run:
+```
+
+pytest -q
+ruff check .
+ruff format --check .
+mypy
+
+```
+- If it touches physics, include a quick before/after plot or metric (e.g., growth rate).
+
+## Checklist
+- [ ] Code follows style (Ruff) and types (MyPy)
+- [ ] Tests added or updated
+- [ ] Docs updated (README / examples / docstrings)
+- [ ] Backwards compatible (or migration noted)
+
+## Related issues
+Closes #<issue-number> (if applicable)
+
+## Notes for reviewers
+Anything you want reviewers to pay special attention to.

spectraxgk-0.0.1/.github/workflows/ci.yml

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+name: CI
+
+on:
+  push:
+    branches: [main, master]
+  pull_request:
+
+jobs:
+  lint-type-test:
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.11"
+
+      - name: Install build + runtime deps
+        run: |
+          python -m pip install --upgrade pip
+          pip install -e ".[dev,test]"  # assumes you defined extras in pyproject
+
+      - name: Ruff lint (CI)
+        run: |
+          ruff --version
+          # Fail CI if lint errors remain (no --fix in CI):
+          ruff check .
+
+      - name: Ruff format check (CI)
+        run: |
+          ruff format --check .
+
+      - name: MyPy (types)
+        run: |
+          mypy --version
+          mypy
+
+      - name: Pytest
+        env:
+          MPLBACKEND: Agg         # headless tests for matplotlib
+          JAX_ENABLE_X64: "true"
+        run: |
+          pytest -q --maxfail=1 --disable-warnings

spectraxgk-0.0.1/.github/workflows/docs.yml

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+name: Build and deploy docs
+
+on:
+  push:
+    branches: [ main ]
+    paths:
+      - 'docs/**'
+      - 'mkdocs.yml'
+      - 'spectraxgk/**'
+      - '.github/workflows/docs.yml'
+  workflow_dispatch:
+
+# GitHub Pages needs these permissions
+permissions:
+  contents: read
+  pages: write
+  id-token: write
+
+# Only one Pages deploy at a time
+concurrency:
+  group: "pages"
+  cancel-in-progress: true
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+
+      - name: Setup Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: '3.11'
+
+      - name: Install docs deps
+        run: |
+          python -m pip install --upgrade pip
+          # MkDocs + Material + your plugins
+          pip install \
+            mkdocs \
+            mkdocs-material \
+            mkdocstrings[python] \
+            mkdocs-autorefs \
+            pymdown-extensions
+
+      - name: Build site
+        run: mkdocs build --strict --site-dir site
+
+      - name: Upload artifact
+        uses: actions/upload-pages-artifact@v3
+        with:
+          path: site
+
+  deploy:
+    environment:
+      name: github-pages
+      url: ${{ steps.deployment.outputs.page_url }}
+    runs-on: ubuntu-latest
+    needs: build
+    steps:
+      - name: Deploy to GitHub Pages
+        id: deployment
+        uses: actions/deploy-pages@v4

spectraxgk-0.0.1/.github/workflows/release.yml

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+name: Release
+
+on:
+  push:
+    tags:
+      - "v*.*.*"
+
+permissions:
+  id-token: write
+  contents: read
+
+jobs:
+  build-and-publish:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.11"
+
+      - name: Build artifacts (sdist + wheel)
+        run: |
+          python -m pip install --upgrade pip build
+          python -m build
+
+      - name: Publish to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1

spectraxgk-0.0.1/.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__/
+
+# Manually added
+*.mp4
+.gitignore
+.DS_Store

spectraxgk-0.0.1/.pre-commit-config.yaml

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+repos:
+  # --- Core hygiene ---
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.6.0
+    hooks:
+      - id: trailing-whitespace
+      - id: end-of-file-fixer
+      - id: check-yaml
+      - id: check-toml
+      - id: check-json
+
+  # --- Ruff: lint + import sort + pyupgrade etc. ---
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.6.8
+    hooks:
+      - id: ruff
+        args: [--fix]        # autofix lint issues where safe
+      - id: ruff-format      # use Ruff as the code formatter
+
+  # --- MyPy (type checking) ---
+  - repo: https://github.com/pre-commit/mirrors-mypy
+    rev: v1.11.2
+    hooks:
+      - id: mypy
+        additional_dependencies:
+          - types-setuptools
+          - types-PyYAML
+        # Keep mypy fast: only check project src + CLI, not venvs or notebooks
+        files: ^(spectraxgk/|tests/|examples/|scripts/|cli.py)
+        # You can pass custom mypy config file here if non-standard:
+        args: ["--config-file=pyproject.toml"]
+
+  # --- Spelling (optional but nice) ---
+  - repo: https://github.com/codespell-project/codespell
+    rev: v2.3.0
+    hooks:
+      - id: codespell
+        additional_dependencies: [tomli]
+        args: ["-L", "nd,fo"]   # allowlist false positives

spectraxgk-0.0.1/CONTRIBUTING.md

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+# Contributing to SPECTRAX-GK
+
+We welcome contributions from the community!
+This document explains how to set up your development environment, run tests, and submit changes.
+
+---
+
+## 🛠 Development Setup
+
+1. **Fork and clone** the repository:
+   ```bash
+   git clone https://github.com/<your-username>/SPECTRAX-GK.git
+   cd SPECTRAX-GK
+````
+
+2. **Install in editable mode with dev dependencies**:
+
+   ```bash
+   pip install -e ".[dev]"
+   ```
+
+3. **Enable pre-commit hooks**:
+
+   ```bash
+   pre-commit install
+   ```
+
+---
+
+## 🧪 Running Tests
+
+We use [pytest](https://docs.pytest.org) for unit and regression tests.
+
+Run all tests:
+
+```bash
+pytest -v
+```
+
+Run with coverage:
+
+```bash
+pytest --cov=spectraxgk --cov-report=term-missing
+```
+
+---
+
+## 📏 Code Style & Quality
+
+* **Linting & formatting**: [Ruff](https://github.com/astral-sh/ruff)
+
+  ```bash
+  ruff check .
+  ruff format .
+  ```
+
+* **Type checking**: [MyPy](https://mypy.readthedocs.io)
+
+  ```bash
+  mypy .
+  ```
+
+* **Pre-commit hooks** automatically enforce these checks before commit.
+
+---
+
+## 🔄 Pull Requests
+
+1. Create a feature branch:
+
+   ```bash
+   git checkout -b feature/my-new-feature
+   ```
+
+2. Commit changes with clear messages:
+
+   ```bash
+   git commit -m "feat: add DG solver for bump-on-tail"
+   ```
+
+3. Push and open a Pull Request:
+
+   ```bash
+   git push origin feature/my-new-feature
+   ```
+
+PRs are automatically tested via GitHub Actions.
+
+---
+
+## 🧑‍🔬 What to Contribute
+
+* Bug fixes
+* New physics modules (e.g., collisional operators)
+* Additional diagnostics or visualization tools
+* Documentation improvements
+* Tests for uncovered parts of the code
+
+---
+
+## 📚 Resources
+
+* [JAX docs](https://jax.readthedocs.io)
+* [Diffrax](https://docs.kidger.site/diffrax/)
+* [pytest](https://docs.pytest.org)
+* [Ruff](https://docs.astral.sh/ruff/)
+
+---
+
+Thank you for contributing to **SPECTRAX-GK**!

spectraxgk-0.0.1/LICENSE

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2025 UW Plasma
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

spectraxgk-0.0.1/MANIFEST.in

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+recursive-include examples *.toml
+include README.md LICENSE