jwspecfit 1.1.0__tar.gz

jwspecfit-1.1.0/.github/workflows/publish.yml

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+name: Publish to PyPI
+
+# Fires on every published GitHub Release.  Uses OIDC trusted publishing —
+# no API tokens stored anywhere.  Setup:
+#   1. Register pending publisher on PyPI:
+#      https://pypi.org/manage/account/publishing/
+#      project name: jwspecfit | owner: raunaq-rai | repo: jwspecfit
+#      workflow: publish.yml | environment: pypi
+#   2. Create GitHub Environment named "pypi" under repo Settings.
+on:
+  release:
+    types: [published, released]
+  workflow_dispatch:  # allows manual runs from the Actions tab
+
+jobs:
+  build:
+    name: Build sdist and wheel
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: actions/setup-python@v5
+        with:
+          python-version: "3.11"
+
+      - run: python -m pip install --upgrade pip build
+
+      - run: python -m build
+
+      - uses: actions/upload-artifact@v4
+        with:
+          name: dist
+          path: dist/
+
+  publish:
+    name: Publish to PyPI
+    needs: build
+    runs-on: ubuntu-latest
+    environment:
+      name: pypi
+      url: https://pypi.org/p/jwspecfit
+    permissions:
+      id-token: write  # required for OIDC trusted publishing
+    steps:
+      - uses: actions/download-artifact@v4
+        with:
+          name: dist
+          path: dist/
+
+      - uses: pypa/gh-action-pypi-publish@release/v1

jwspecfit-1.1.0/.gitignore

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+# Python
+__pycache__/
+*.py[cod]
+*.egg-info/
+*.eggs/
+dist/
+build/
+.eggs/
+
+# Virtual environments
+.venv/
+venv/
+
+# IDE
+.idea/
+.vscode/
+*.swp
+*.swo
+
+# OS
+.DS_Store
+Thumbs.db
+
+# Jupyter
+.ipynb_checkpoints/
+
+# Sphinx / ReadTheDocs build artefacts
+docs/_build/
+docs/api_reference/generated/
+
+# Keep FITS data in repo (small test files)
+# !data/*.fits
+# !data/*.npz
+# !data/*.txt

jwspecfit-1.1.0/.readthedocs.yaml

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+version: 2
+
+build:
+  os: ubuntu-22.04
+  tools:
+    python: "3.11"
+
+sphinx:
+  configuration: docs/conf.py
+  fail_on_warning: false
+
+python:
+  install:
+    - requirements: docs/requirements.txt
+    - method: pip
+      path: .
+      extra_requirements:
+        - abund
+
+formats:
+  - pdf
+  - htmlzip

jwspecfit-1.1.0/CITATION.cff

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+cff-version: 1.2.0
+message: >
+  If you use this software in a publication, please cite it using the
+  metadata below.  To mint a permanent DOI, enable the repository on
+  Zenodo and create a GitHub release — see the README for the full
+  procedure.
+title: "jwspecfit: resolution-aware emission-line fitting, MCMC sampling, and chemical abundances for JWST NIRSpec"
+abstract: >
+  jwspecfit is a coordinated suite of three Python packages for the
+  analysis of JWST NIRSpec spectra: least-squares Gaussian line fitting
+  with resolution-aware bin-averaged profiles (jwspecfit), Bayesian MCMC
+  fitting via NUTS, emcee, or nautilus (jwspecmcmc), and chemical
+  abundance derivation via direct-Te (PyNEB), Bayesian forward model
+  (Cullen+25), or strong-line calibrations (Sanders+25) with
+  Balmer-decrement dust correction anchored on Halpha or Hbeta
+  (jwspecabund).
+type: software
+authors:
+  - family-names: "Rai"
+    given-names: "Raunaq"
+    affiliation: "UCL Department of Physics & Astronomy"
+    email: "raunaq.rai.22@ucl.ac.uk"
+version: "1.1.0"
+date-released: "2026-05-20"
+license: MIT
+repository-code: "https://github.com/raunaq-rai/jwspecfit"
+url: "https://jwspecfit.readthedocs.io/"
+keywords:
+  - astronomy
+  - astrophysics
+  - JWST
+  - NIRSpec
+  - spectroscopy
+  - emission-line fitting
+  - chemical abundances
+  - high-redshift galaxies
+  - Python
+doi: "10.5281/zenodo.19679794"
+# Once a companion paper is published, add it here:
+# preferred-citation:
+#   type: article
+#   authors:
+#     - family-names: "Rai"
+#       given-names: "Raunaq"
+#   title: "..."
+#   journal: "MNRAS"
+#   year: 2026
+#   doi: "10.1093/mnras/XXXXXXX"

jwspecfit-1.1.0/LICENCE

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+MIT License
+
+Copyright (c) 2025 Raunaq Rai
+
+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.

jwspecfit-1.1.0/PKG-INFO

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+Metadata-Version: 2.4
+Name: jwspecfit
+Version: 1.1.0
+Summary: JWST NIRSpec emission-line fitting with resolution-aware Gaussian models
+Author-email: Raunaq Rai <raunaq.rai.22@ucl.ac.uk>
+License-Expression: MIT
+Project-URL: Homepage, https://github.com/raunaq-rai/jwspecfit
+Project-URL: Documentation, https://jwspecfit.readthedocs.io/
+Project-URL: Source, https://github.com/raunaq-rai/jwspecfit
+Project-URL: Issues, https://github.com/raunaq-rai/jwspecfit/issues
+Project-URL: Changelog, https://github.com/raunaq-rai/jwspecfit/blob/main/docs/changelog.md
+Keywords: astronomy,astrophysics,JWST,NIRSpec,spectroscopy,emission-line fitting,chemical abundances,MCMC,high-redshift galaxies
+Classifier: Development Status :: 4 - Beta
+Classifier: Intended Audience :: Science/Research
+Classifier: Operating System :: OS Independent
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Topic :: Scientific/Engineering :: Astronomy
+Classifier: Topic :: Scientific/Engineering :: Physics
+Requires-Python: >=3.10
+Description-Content-Type: text/markdown
+License-File: LICENCE
+Requires-Dist: numpy>=1.24
+Requires-Dist: scipy>=1.10
+Requires-Dist: astropy>=5.3
+Requires-Dist: matplotlib>=3.7
+Requires-Dist: tqdm>=4.60
+Requires-Dist: joblib>=1.3
+Requires-Dist: plotly>=5.0
+Provides-Extra: dev
+Requires-Dist: pytest>=7.0; extra == "dev"
+Requires-Dist: ruff>=0.1; extra == "dev"
+Provides-Extra: mcmc
+Requires-Dist: emcee>=3.1; extra == "mcmc"
+Requires-Dist: nautilus-sampler>=0.7; extra == "mcmc"
+Requires-Dist: corner>=2.2; extra == "mcmc"
+Requires-Dist: h5py>=3.8; extra == "mcmc"
+Provides-Extra: nuts
+Requires-Dist: jax>=0.4; extra == "nuts"
+Requires-Dist: jaxlib>=0.4; extra == "nuts"
+Requires-Dist: numpyro>=0.13; extra == "nuts"
+Provides-Extra: abund
+Requires-Dist: pyneb>=1.1.25; extra == "abund"
+Provides-Extra: dla
+Requires-Dist: dynesty>=2.1; extra == "dla"
+Dynamic: license-file
+
+<p align="center">
+  <img src="docs/_static/logos/logo.svg" alt="jwspecfit logo" width="128"/>
+</p>
+
+# jwspecfit
+
+**Emission-line fitting, MCMC, and chemical abundances for JWST NIRSpec spectra.**
+
+[![Python](https://img.shields.io/badge/python-3.10+-blue.svg)](https://www.python.org/downloads/)
+[![License: MIT](https://img.shields.io/badge/license-MIT-green.svg)](LICENCE)
+[![Tests](https://img.shields.io/badge/tests-pytest-lightgrey.svg)](tests/)
+[![Docs](https://readthedocs.org/projects/jwspecfit/badge/?version=latest)](https://jwspecfit.readthedocs.io/en/latest/)
+[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.19679794.svg)](https://doi.org/10.5281/zenodo.19679794)
+
+Three packages, one pipeline — from 1-D NIRSpec spectra to element abundances.
+
+| Package             | What it does                                                       |
+| ------------------- | ------------------------------------------------------------------ |
+| **`jwspecfit`**     | Resolution-aware Gaussian line fitting with bootstrap errors       |
+| **`jwspecmcmc`**    | Bayesian MCMC fitting (NUTS · emcee · nautilus)                    |
+| **`jwspecabund`**   | Chemical abundances — direct T_e · forward model · strong-line     |
+
+## Key features
+
+- **Resolution-aware line profiles**: bin-averaged Gaussians via erf — correct for prism, gratings, and stacks.
+- **Broad-Balmer detection**: BIC-based selection across four nested models.
+- **UV doublets**: flux-ratio and kinematic tying for C IV, N V, N III], O III], C III], N IV].
+- **Lyα + DLA**: skewed Gaussian + IGM transmission + dynesty N_HI retrieval.
+- **Dust correction**: multi-Balmer A_V anchored on Hβ **or** Hα, Salim+18 or Cardelli+89 curves.
+- **Abundances**: direct T_e ([O III] 4363 or UV 1666), Cullen+25 forward model, Sanders+25 strong-line.
+- **ICFs**: Martinez+25 (N/O) · Izotov+06 (S, Ne, Ar) · Garnett+97 (C/O).
+- **Lyα escape fraction** with Monte Carlo propagation of A_V uncertainty.
+
+## Install
+
+```bash
+git clone https://github.com/raunaq-rai/jwspecfit.git
+cd jwspecfit
+pip install -e ".[dev,nuts,mcmc,abund]"
+```
+
+Requires Python ≥ 3.10. See the [installation guide](https://jwspecfit.readthedocs.io/en/latest/installation.html) for individual extras.
+
+## Example
+
+```python
+import jwspecfit, jwspecabund
+
+spec   = jwspecfit.read_fits("spectrum.fits", z=6.0)
+result = jwspecfit.fit_lines(spec, z=6.0)
+abund  = jwspecabund.compute_abundances(result, z=6.0)
+
+print(abund.summary())
+```
+
+## Documentation
+
+Usage guides, API reference, and methodology:
+**https://jwspecfit.readthedocs.io/**
+
+Worked examples: [`docs/notebooks/`](docs/notebooks/).
+
+## Tests
+
+```bash
+pytest tests/
+```
+
+## Citation
+
+If you use `jwspecfit` in your research, **please cite it**. Choose
+whichever format your reference manager or journal prefers.
+
+> ### 📖 DOI: [10.5281/zenodo.19679794](https://doi.org/10.5281/zenodo.19679794)
+>
+> Concept DOI — always resolves to the latest Zenodo-archived release.
+
+### Plain text
+
+> Rai, R. (2026). *jwspecfit: Resolution-aware emission-line fitting,
+> MCMC sampling, and chemical abundances for JWST NIRSpec* (v1.0.1).
+> Zenodo. <https://doi.org/10.5281/zenodo.19679794>
+
+### BibTeX
+
+```bibtex
+@software{rai_jwspecfit,
+  author       = {Rai, Raunaq},
+  title        = {{jwspecfit}: Resolution-aware emission-line fitting,
+                  MCMC sampling, and chemical abundances for JWST NIRSpec},
+  year         = {2026},
+  version      = {1.0.1},
+  publisher    = {Zenodo},
+  doi          = {10.5281/zenodo.19679794},
+  url          = {https://doi.org/10.5281/zenodo.19679794},
+}
+```
+
+### Other formats
+
+APA · Chicago · IEEE · Harvard · MLA · CSL-JSON · DataCite XML are all
+available from the [Zenodo record page](https://zenodo.org/records/19679794)
+(Export panel on the right).
+
+GitHub's **"Cite this repository"** button (top-right of the repo page)
+reads [`CITATION.cff`](CITATION.cff) and produces APA/BibTeX on the fly.
+
+### Pinning a specific version
+
+The concept DOI above always points to the latest release. If a paper
+needs to cite the *exact* code version used for reproducibility, pick
+the per-version DOI from the "Versions" list on the Zenodo page.
+
+## Licence
+
+MIT — see [LICENCE](LICENCE).

jwspecfit-1.1.0/README.md

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+<p align="center">
+  <img src="docs/_static/logos/logo.svg" alt="jwspecfit logo" width="128"/>
+</p>
+
+# jwspecfit
+
+**Emission-line fitting, MCMC, and chemical abundances for JWST NIRSpec spectra.**
+
+[![Python](https://img.shields.io/badge/python-3.10+-blue.svg)](https://www.python.org/downloads/)
+[![License: MIT](https://img.shields.io/badge/license-MIT-green.svg)](LICENCE)
+[![Tests](https://img.shields.io/badge/tests-pytest-lightgrey.svg)](tests/)
+[![Docs](https://readthedocs.org/projects/jwspecfit/badge/?version=latest)](https://jwspecfit.readthedocs.io/en/latest/)
+[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.19679794.svg)](https://doi.org/10.5281/zenodo.19679794)
+
+Three packages, one pipeline — from 1-D NIRSpec spectra to element abundances.
+
+| Package             | What it does                                                       |
+| ------------------- | ------------------------------------------------------------------ |
+| **`jwspecfit`**     | Resolution-aware Gaussian line fitting with bootstrap errors       |
+| **`jwspecmcmc`**    | Bayesian MCMC fitting (NUTS · emcee · nautilus)                    |
+| **`jwspecabund`**   | Chemical abundances — direct T_e · forward model · strong-line     |
+
+## Key features
+
+- **Resolution-aware line profiles**: bin-averaged Gaussians via erf — correct for prism, gratings, and stacks.
+- **Broad-Balmer detection**: BIC-based selection across four nested models.
+- **UV doublets**: flux-ratio and kinematic tying for C IV, N V, N III], O III], C III], N IV].
+- **Lyα + DLA**: skewed Gaussian + IGM transmission + dynesty N_HI retrieval.
+- **Dust correction**: multi-Balmer A_V anchored on Hβ **or** Hα, Salim+18 or Cardelli+89 curves.
+- **Abundances**: direct T_e ([O III] 4363 or UV 1666), Cullen+25 forward model, Sanders+25 strong-line.
+- **ICFs**: Martinez+25 (N/O) · Izotov+06 (S, Ne, Ar) · Garnett+97 (C/O).
+- **Lyα escape fraction** with Monte Carlo propagation of A_V uncertainty.
+
+## Install
+
+```bash
+git clone https://github.com/raunaq-rai/jwspecfit.git
+cd jwspecfit
+pip install -e ".[dev,nuts,mcmc,abund]"
+```
+
+Requires Python ≥ 3.10. See the [installation guide](https://jwspecfit.readthedocs.io/en/latest/installation.html) for individual extras.
+
+## Example
+
+```python
+import jwspecfit, jwspecabund
+
+spec   = jwspecfit.read_fits("spectrum.fits", z=6.0)
+result = jwspecfit.fit_lines(spec, z=6.0)
+abund  = jwspecabund.compute_abundances(result, z=6.0)
+
+print(abund.summary())
+```
+
+## Documentation
+
+Usage guides, API reference, and methodology:
+**https://jwspecfit.readthedocs.io/**
+
+Worked examples: [`docs/notebooks/`](docs/notebooks/).
+
+## Tests
+
+```bash
+pytest tests/
+```
+
+## Citation
+
+If you use `jwspecfit` in your research, **please cite it**. Choose
+whichever format your reference manager or journal prefers.
+
+> ### 📖 DOI: [10.5281/zenodo.19679794](https://doi.org/10.5281/zenodo.19679794)
+>
+> Concept DOI — always resolves to the latest Zenodo-archived release.
+
+### Plain text
+
+> Rai, R. (2026). *jwspecfit: Resolution-aware emission-line fitting,
+> MCMC sampling, and chemical abundances for JWST NIRSpec* (v1.0.1).
+> Zenodo. <https://doi.org/10.5281/zenodo.19679794>
+
+### BibTeX
+
+```bibtex
+@software{rai_jwspecfit,
+  author       = {Rai, Raunaq},
+  title        = {{jwspecfit}: Resolution-aware emission-line fitting,
+                  MCMC sampling, and chemical abundances for JWST NIRSpec},
+  year         = {2026},
+  version      = {1.0.1},
+  publisher    = {Zenodo},
+  doi          = {10.5281/zenodo.19679794},
+  url          = {https://doi.org/10.5281/zenodo.19679794},
+}
+```
+
+### Other formats
+
+APA · Chicago · IEEE · Harvard · MLA · CSL-JSON · DataCite XML are all
+available from the [Zenodo record page](https://zenodo.org/records/19679794)
+(Export panel on the right).
+
+GitHub's **"Cite this repository"** button (top-right of the repo page)
+reads [`CITATION.cff`](CITATION.cff) and produces APA/BibTeX on the fly.
+
+### Pinning a specific version
+
+The concept DOI above always points to the latest release. If a paper
+needs to cite the *exact* code version used for reproducibility, pick
+the per-version DOI from the "Versions" list on the Zenodo page.
+
+## Licence
+
+MIT — see [LICENCE](LICENCE).