ExoGibbs 0.2.1__tar.gz

exogibbs-0.2.1/.github/workflows/main.yml

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+name: Run pytest
+
+on:
+  push:
+    branches: [ "develop", "main" ]
+  pull_request:
+    branches: [ "develop", "main" ]
+
+permissions:
+  checks: write
+  contents: write
+  pull-requests: write
+
+jobs:
+  pytest:
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout (with full history & tags for setuptools-scm)
+        uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+
+      - name: Set up Python 3.11
+        uses: actions/setup-python@v5
+        with:
+          python-version: '3.11'
+
+      - name: Install package and test deps
+        run: |
+          python -m pip install --upgrade pip wheel
+          pip install -e .
+          pip install pytest
+          # if using extras: pip install -e .[test]
+
+      - name: Run tests and generate XML report
+        run: |
+          mkdir -p results
+          pytest tests/unittests --junit-xml results/pytest.xml
+        continue-on-error: true
+
+      - name: Upload Unit Test Results
+        if: ${{ always() }}
+        uses: actions/upload-artifact@v4
+        with:
+          name: Unit Test Results (Python 3.11)
+          path: results/*.xml
+
+      - name: Download Artifacts
+        if: success() || failure()
+        uses: actions/download-artifact@v4
+        with:
+          path: artifacts
+
+      - name: Publish Unit Test Results
+        uses: EnricoMi/publish-unit-test-result-action@v2
+        with:
+          files: artifacts/**/*.xml

exogibbs-0.2.1/.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
+
+# 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
+
+# pdm
+#   Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control.
+#pdm.lock
+#   pdm stores project-wide configurations in .pdm.toml, but it is recommended to not include it
+#   in version control.
+#   https://pdm.fming.dev/latest/usage/project/#working-with-version-control
+.pdm.toml
+.pdm-python
+.pdm-build/
+
+# 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
+.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/
+
+# Ruff stuff:
+.ruff_cache/
+
+# PyPI configuration file
+.pypirc

exogibbs-0.2.1/CLAUDE.md

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+# CLAUDE.md
+
+This file provides guidance to Claude Code (claude.ai/code) when working with code in this repository.
+
+## Project Overview
+
+ExoGibbs is an auto-differentiable thermochemical equilibrium solver implemented in JAX. It computes chemical equilibrium states by minimizing Gibbs free energy, with applications in planetary atmosphere modeling and chemical process simulation.
+
+## Key Architecture
+
+- **Core equilibrium calculations**: `src/exogibbs/equilibrium/gibbs.py` - Contains Gibbs energy computation and chemical potential interpolation
+- **Optimization algorithms**: `src/exogibbs/optimize/` - Core optimization functions (`minimize.py`), KL mirror descent, projected gradient descent, and Lagrange multiplier methods for constrained optimization
+- **Data handling**: `src/exogibbs/io/load_data.py` - Loads JANAF thermochemical data from `src/exogibbs/data/`
+- **Stoichiometry**: `src/exogibbs/stoichiometry/analyze_formula_matrix.py` - Chemical formula matrix analysis for mass balance constraints
+- **Test data generation**: `src/exogibbs/test/generate_gibbs.py` - Creates test cases for equilibrium calculations
+- **Testing**: Uses pytest framework with tests in `tests/unittests/` organized by module structure
+
+## Development Commands
+
+**Installation**: 
+```bash
+pip install -e .
+```
+
+**Testing**:
+```bash
+# Run all tests
+python -m pytest tests/unittests/
+
+# Run specific test file
+python -m pytest tests/unittests/equilibrium/gibbs_test.py
+
+# Run individual test function
+python -m pytest tests/unittests/equilibrium/gibbs_test.py::test_total_gibbs_energy
+```
+
+**Key Dependencies**: JAX/JAXlib for auto-differentiation, pandas for data handling, pytest for testing
+
+## Important Notes
+
+- **JAX Compatibility**: The project uses JAX for auto-differentiation and JIT compilation - ensure JAX operations are used consistently. Be careful with JAX compatibility when adding new functions
+- **Keep It Simple**: Stay simple, do not add complex tests and functions
+- Chemical potential data is interpolated from JANAF tables stored in `src/exogibbs/data/`
+- Optimization operates in log-space to handle numerical stability with exponential functions
+- Formula matrices encode stoichiometric constraints for mass balance during equilibrium calculation

exogibbs-0.2.1/LICENSE

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+MIT License
+
+Copyright (c) 2025 Hajime Kawahara
+
+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.

exogibbs-0.2.1/MANIFEST.in

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+include src/exogibbs/data/janaf_raw_sample.txt
+include src/exogibbs/data/testdata.dat
+include src/exogibbs/data/matrix_v3.dat
+include src/exogibbs/data/molname_v3.dat
+include src/exogibbs/data/gibbs_matrices.npz
+include src/exogibbs/data/number_of_species.sample.list

exogibbs-0.2.1/PKG-INFO

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+Metadata-Version: 2.4
+Name: ExoGibbs
+Version: 0.2.1
+Summary: Differentiable Thermochemical Equilibrium Solver for Exoplanet Atmospheres
+Author-email: Hajime Kawahara <divrot@gmail.com>
+Maintainer-email: Hajime Kawahara <divrot@gmail.com>
+License: MIT
+Project-URL: Homepage, https://github.com/HajimeKawahara/exogibbs
+Project-URL: Repository, https://github.com/HajimeKawahara/exogibbs
+Project-URL: Issues, https://github.com/HajimeKawahara/exogibbs/issues
+Classifier: Programming Language :: Python
+Classifier: Programming Language :: Python :: 3.9
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Operating System :: OS Independent
+Requires-Python: >=3.9
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: interpax
+Requires-Dist: jax<0.7,>=0.4.30
+Requires-Dist: tqdm
+Requires-Dist: pandas
+Requires-Dist: thermochem
+Dynamic: license-file
+
+# ExoGibbs
+
+Differentiable Thermochemical Equilibrium, powered by JAX. 
+
+The optimization scheme is based on the Lagrange multiplier, similar to NASA/CEA algorithm. 
+The terminology follows Smith and Missen. 
+
+ExoGibbs is designed to plug into [ExoJAX](https://github.com/HajimeKawahara/exojax) and enable gradient-based equilibrium retrievals. 
+It is still in a very beta stage, so please use it at your own risk.

exogibbs-0.2.1/README.md

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+# ExoGibbs
+
+Differentiable Thermochemical Equilibrium, powered by JAX. 
+
+The optimization scheme is based on the Lagrange multiplier, similar to NASA/CEA algorithm. 
+The terminology follows Smith and Missen. 
+
+ExoGibbs is designed to plug into [ExoJAX](https://github.com/HajimeKawahara/exojax) and enable gradient-based equilibrium retrievals. 
+It is still in a very beta stage, so please use it at your own risk.

exogibbs-0.2.1/documents/Makefile

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+# Minimal makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line, and also
+# from the environment for the first two.
+SPHINXOPTS    ?=
+SPHINXBUILD   ?= sphinx-build
+SOURCEDIR     = .
+BUILDDIR      = _build
+
+# Put it first so that "make" without argument is like "make help".
+help:
+	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+.PHONY: help Makefile
+
+# Catch-all target: route all unknown targets to Sphinx using the new
+# "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
+%: Makefile
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)

exogibbs-0.2.1/documents/conf.py

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+# Configuration file for the Sphinx documentation builder.
+#
+# This file only contains a selection of the most common options. For a full
+# list see the documentation:
+# http://www.sphinx-doc.org/en/master/config
+
+# -- Path setup --------------------------------------------------------------
+
+# If extensions (or modules to document with autodoc) are in another directory,
+# add these directories to sys.path here. If the directory is relative to the
+# documentation root, use os.path.abspath to make it absolute, like shown here.
+#
+import sphinx_rtd_theme
+import os
+import sys
+
+sys.path.insert(0, os.path.abspath("~/exogibbs"))
+
+
+# -- Project information -----------------------------------------------------
+
+project = "Exogibbs"
+copyright = "2025, ExoGibbs contributors"
+author = "Exogibbs contributors"
+
+# The full version, including alpha/beta/rc tags
+release = "2.0.0"
+
+
+# -- General configuration ---------------------------------------------------
+
+# Add any Sphinx extension module names here, as strings. They can be
+# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
+# ones.
+extensions = [
+    "sphinx.ext.autodoc",
+    "sphinx.ext.napoleon",
+    "sphinxemoji.sphinxemoji",
+    "sphinx_gallery.gen_gallery",
+]
+
+# Add any paths that contain templates here, relative to this directory.
+templates_path = ["_templates"]
+
+# List of patterns, relative to source directory, that match files and
+# directories to ignore when looking for source files.
+# This pattern also affects html_static_path and html_extra_path.
+exclude_patterns = ["_build", "Thumbs.db", ".DS_Store"]
+
+
+# -- Options for HTML output -------------------------------------------------
+
+# The theme to use for HTML and HTML Help pages.  See the documentation for
+# a list of builtin themes.
+#
+html_theme = "sphinx_rtd_theme"
+# Add any paths that contain custom static files (such as style sheets) here,
+# relative to this directory. They are copied after the builtin static files,
+# so a file named "default.css" will overwrite the builtin "default.css".
+html_static_path = ["_static"]
+html_logo = "_static/logo.png"
+
+# html_theme_options = {
+#    'style_nav_header_background': '#333',
+# }
+html_css_files = ["header.css"]
+
+# Sphinx-Gallery
+from sphinx_gallery.sorting import FileNameSortKey
+sphinx_gallery_conf = {
+    "examples_dirs": ["../examples"],
+    "gallery_dirs": ["examples"],
+    "within_subsection_order": FileNameSortKey,
+    "filename_pattern": "/plot_",
+    "ignore_pattern": "/_",
+    "backreferences_dir": "backreferences",
+    "doc_module": ("exogibbs",),
+    "reference_url": {"exogibbs": None},
+}