astro-nifty 0.1.0__tar.gz

astro_nifty-0.1.0/.github/workflows/publish.yml

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+name: Publish Python Package
+
+run-name: Publish ${{ github.ref_name }} to PyPI
+
+on:
+  push:
+    tags:
+      - "v*"
+
+# Prevent two executions for the same tag from publishing simultaneously.
+concurrency:
+  group: pypi-${{ github.ref }}
+
+jobs:
+  build:
+    name: Build and verify distributions
+    runs-on: ubuntu-latest
+
+    # The build job only needs to read the repository.
+    permissions:
+      contents: read
+
+    steps:
+      - name: Check out tagged commit
+        uses: actions/checkout@v6
+
+      - name: Set up Python
+        uses: actions/setup-python@v6
+        with:
+          python-version: "3.x"
+
+      - name: Install build tools
+        run: python3 -m pip install --user build twine
+
+      - name: Build source and wheel distributions
+        run: python3 -m build
+
+      - name: Check distribution integrity
+        run: python3 -m twine check --strict dist/*
+
+      - name: Upload distributions for publishing
+        uses: actions/upload-artifact@v5
+        with:
+          name: python-distributions
+          path: dist/
+
+  publish:
+    name: Publish to PyPI
+    needs:
+      - build
+    runs-on: ubuntu-latest
+
+    environment:
+      name: pypi
+      url: https://pypi.org/p/astro-nifty
+
+    permissions:
+      id-token: write
+
+    steps:
+      - name: Download verified distributions
+        uses: actions/download-artifact@v6
+        with:
+          name: python-distributions
+          path: dist/
+
+      - name: Publish distributions to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1

astro_nifty-0.1.0/.gitignore

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+# Based on the GitHub gitignore template for Python
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+__pycache__/
+*.py[codz]
+*$py.class
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+*.so
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+
+.DS_Store
+src/nifty/_version.py

astro_nifty-0.1.0/BD_NIRCam_MIRI_filters.json

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+{
+  "filter_columns": {
+    "JWST_F090W": {
+      "extension": "CIRC",
+      "flux": "F090W_CIRC3",
+      "error": "F090W_CIRC3_e"
+    },
+    "JWST_F115W": {
+      "extension": "CIRC",
+      "flux": "F115W_CIRC3",
+      "error": "F115W_CIRC3_e"
+    },
+    "JWST_F150W": {
+      "extension": "CIRC",
+      "flux": "F150W_CIRC3",
+      "error": "F150W_CIRC3_e"
+    },
+    "JWST_F162M": {
+      "extension": "CIRC",
+      "flux": "F162M_CIRC3",
+      "error": "F162M_CIRC3_e"
+    },
+    "JWST_F182M": {
+      "extension": "CIRC",
+      "flux": "F182M_CIRC3",
+      "error": "F182M_CIRC3_e"
+    },
+    "JWST_F200W": {
+      "extension": "CIRC",
+      "flux": "F200W_CIRC3",
+      "error": "F200W_CIRC3_e"
+    },
+    "JWST_F210M": {
+      "extension": "CIRC",
+      "flux": "F210M_CIRC3",
+      "error": "F210M_CIRC3_e"
+    },
+    "JWST_F250M": {
+      "extension": "CIRC",
+      "flux": "F250M_CIRC3",
+      "error": "F250M_CIRC3_e"
+    },
+    "JWST_F277W": {
+      "extension": "CIRC",
+      "flux": "F277W_CIRC3",
+      "error": "F277W_CIRC3_e"
+    },
+    "JWST_F300M": {
+      "extension": "CIRC",
+      "flux": "F300M_CIRC3",
+      "error": "F300M_CIRC3_e"
+    },
+    "JWST_F335M": {
+      "extension": "CIRC",
+      "flux": "F335M_CIRC3",
+      "error": "F335M_CIRC3_e"
+    },
+    "JWST_F356W": {
+      "extension": "CIRC",
+      "flux": "F356W_CIRC3",
+      "error": "F356W_CIRC3_e"
+    },
+    "JWST_F410M": {
+      "extension": "CIRC",
+      "flux": "F410M_CIRC3",
+      "error": "F410M_CIRC3_e"
+    },
+    "JWST_F444W": {
+      "extension": "CIRC",
+      "flux": "F444W_CIRC3",
+      "error": "F444W_CIRC3_e"
+    },
+    "JWST_F560W": {
+      "extension": "MIRI",
+      "flux": "F560W_CIRC3",
+      "error": "F560W_CIRC3_e"
+    },
+    "JWST_F770W": {
+      "extension": "MIRI",
+      "flux": "F770W_CIRC3",
+      "error": "F770W_CIRC3_e"
+    },
+    "JWST_F1000W": {
+      "extension": "MIRI",
+      "flux": "F1000W_CIRC3",
+      "error": "F1000W_CIRC3_e"
+    },
+    "JWST_F1280W": {
+      "extension": "MIRI",
+      "flux": "F1280W_CIRC3",
+      "error": "F1280W_CIRC3_e"
+    }
+  }
+}

astro_nifty-0.1.0/LICENSE

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+MIT License
+
+Copyright (c) 2026 NIFTY Authors
+
+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.

astro_nifty-0.1.0/PKG-INFO

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+Metadata-Version: 2.4
+Name: astro-nifty
+Version: 0.1.0
+Summary: Near-Infrared Fitting for T and Y Dwarfs
+Project-URL: Repository, https://github.com/kevinhainline/NIFTY
+License-Expression: MIT
+License-File: LICENSE
+Requires-Python: >=3.13
+Requires-Dist: astro-sedpy>=0.4.1
+Requires-Dist: corner>=2.2.3
+Requires-Dist: emcee>=3.1.6
+Requires-Dist: fitsio>=1.4.0
+Requires-Dist: h5py>=3.16
+Requires-Dist: matplotlib>=3.10
+Requires-Dist: nautilus-sampler>=1.0.6
+Requires-Dist: numpy>=2.4
+Requires-Dist: pandas>=3.0.3
+Requires-Dist: scipy>=1.17
+Requires-Dist: tqdm>=4.67
+Provides-Extra: build-model
+Requires-Dist: h5netcdf>=1.8.1; extra == 'build-model'
+Requires-Dist: xarray>=2026.4; extra == 'build-model'
+Description-Content-Type: text/markdown
+
+<img src="nifty_logo_zoom.png" alt="NIFTY logo" width="300"/>
+
+# NIFTY
+*Near-Infrared Fitting for T and Y Dwarfs*
+
+*Kevin Hainline, Jake Helton, and Evan Chen*
+
+NIFTY is a code designed to fit JWST NIRCam/MIRI photometry or NIRSpec prism 
+spectroscopy of cold brown dwarf candidates with the LOWZ (Meisner et al. 2021), 
+ATMO2020 (Phillips et al. 2020), Sonora Elf Owl v2 (Mukherjee et al. 2024, 
+Wogan et al. 2025), or earlier Sonora Elf Owl (with PH3, Beiler et al. 2024) atmospheric models, using 
+a Bayesian framework with the emcee sampler (https://emcee.readthedocs.io/en/stable/user/sampler/) 
+or the Nautilus sampler (https://nautilus-sampler.readthedocs.io/en/latest/). 
+This code was described in Hainline et al. (2026) (doi.org/10.48550/arXiv.2510.00111).
+
+NIFTY operates in two modes:
+
+- `phot` — fit broadband photometry from a catalog of one or more sources.
+- `spec` — fit a single NIRSpec prism spectrum.
+
+In both modes, NIFTY produces a corner plot, a best-fit SED or spectrum plot, 
+and a text file with the 16th, 50th, and 84th percentiles of all fit parameters.
+Photometry fits typically converge in under 3 minutes per source for ~14 
+bands, though convergence time varies, especially at high SNR. Spectroscopic 
+fits are slightly longer.
+
+## Installation
+
+The installation comes with the NIFTY Python package and the commands `nifty` 
+and `build_model`.
+
+The easiest way to install NIFTY is through pip:
+```
+pip install astro-nifty
+```
+The main pip installation only includes the dependencies required for sampling. 
+If you also want to build your own models, install the optional dependencies:
+```
+pip install astro-nifty[build-model]
+```
+If you are installing with pip, it is recommended that you install within a 
+**virtual environment** to keep dependencies clean. See the
+[Python tutorial](https://docs.python.org/3/tutorial/venv.html) on virtual 
+environments and packages for more information.
+
+Alternatively, you can clone the NIFTY repository and set up an environment 
+using conda or micromamba:
+```
+conda env create -f environment.yml
+conda activate NIFTY
+```
+
+## Running NIFTY
+
+The easiest way to run NIFTY is through the `nifty` command.
+NIFTY runs in two modes: photometry mode and spectroscopy mode, which require 
+slightly different arguments.
+
+To see the available arguments, you can run: `nifty phot -h` or `nifty spec -h` 
+to display the help message for that mode.
+
+### Photometry mode (`nifty phot`)
+
+Fit broadband photometry for one or more sources from a catalog.
+
+**Single source:**
+```
+nifty phot \
+  --model path/to/model_grid.tar.gz \
+  --stub JADES-GS \
+  --config BD_NIRCam_MIRI_filters.json \
+  --id 20541 \
+  path/to/photometry_file.fits
+```
+
+**List of IDs from a file** (one ID per line):
+```
+nifty phot \
+  --model path/to/model_grid.tar.gz \
+  --stub JADES-GS \
+  --config BD_NIRCam_MIRI_filters.json \
+  --idlist all_source_IDs.dat \
+  path/to/photometry_file.fits
+```
+
+**Multiple IDs:**
+```
+nifty phot \
+  --model path/to/model_grid.tar.gz \
+  --stub JADES-GS \
+  --config BD_NIRCam_MIRI_filters.json \
+  --id 20541 --id 452029 --id 430165 \
+  path/to/photometry_file.fits
+```
+
+### Spectroscopy mode (`nifty spec`)
+
+Fit a single NIRSpec prism spectrum. The spectrum file should be a
+whitespace-delimited text file with three columns: wavelength (microns), 
+flux (nJy), and flux error (nJy). The `--id` argument is used only to
+label output files.
+
+```
+nifty spec \
+  --model path/to/model_grid.tar.gz \
+  --stub JADES-GS \
+  --id 20541 \
+  path/to/spectrum.txt
+```
+
+### Optional arguments
+
+| Argument | Description |
+|---|---|
+| `--output` | Output folder (default: `<Model>_output/`) |
+| `--frac_model_floor` | Fractional model flux floor added in quadrature to photometry errors, to account for model systematics (e.g. `0.03` for 3%). Photometry mode only; no floor is applied in spectroscopy mode. |
+| `--sampler` | Sampler used to estimate the posterior. Currently supports `mcmc` and `nautilus` |
+
+## Configuration File (`--config`)
+
+NIFTY uses a single JSON file to describe all filter information needed for 
+photometry fitting. Here is a sample entry:
+
+```json
+{
+  "filter_columns": {
+    "JWST_F115W": {
+      "extension": "CIRC",
+      "flux": "F115W_CIRC3",
+      "error": "F115W_CIRC3_e",
+    },
+    "JWST_F444W": {
+      "extension": "CIRC",
+      "flux": "F444W_CIRC3",
+      "error": "F444W_CIRC3_e",
+    }
+  }
+}
+```
+The filter name must match a [valid sedpy filter](https://github.com/bd-j/sedpy/blob/main/sedpy/data/filters/README.md).
+If no telescope prefix is provided, the prefix is assumed to be "JWST_".
+
+- `extension`: the FITS HDU name where this filter's data lives. Ignored for 
+plain-text catalogs.
+- `flux` / `error`: exact column names in the photometry file.
+
+An example config file for JADES NIRCam + MIRI observations is included as
+`BD_NIRCam_MIRI_filters.json`.
+
+## Photometry File Format
+
+NIFTY can read:
+
+- **FITS** files, with filter fluxes and errors in named HDU extensions and 
+columns as specified in the config JSON.
+- **Plain-text** catalogs, whitespace-delimited, one row per object.
+
+For plain-text catalogs, include an `ID` column (case-sensitive) and flux/error
+columns whose names match the config JSON exactly. Do not prefix the header 
+line with `#`. Example:
+
+```
+ID     F115W_CIRC3     F115W_CIRC3_e     F444W_CIRC3     F444W_CIRC3_e
+101    0.123           0.010             0.456           0.025
+```
+
+All fluxes and errors should be in nJy. A minimum relative flux error of 5% is 
+applied automatically; errors below this floor are inflated to `0.05 * flux`.
+
+## Output Files
+
+For each fitted source, NIFTY writes the following files to the output directory:
+
+Each file name is prefixed with `<stub>_<ID>_<Model>_`.
+| File | Description |
+|---|---|
+| `sampler_backend.h5` | Backend file for sampler (e.g. MCMC chains) |
+| `corner.png` | Corner plot of the posterior |
+| `SED.png` | Best-fit SED or spectrum plot |
+| `SED.txt` | Model spectrum envelope (16th, 50th, 84th percentile flux, in nJy, vs wavelength in microns) |
+| `parameters.txt` | 16th, 50th, and 84th percentile parameter values, plus chi-square. Distance is in parsecs. |
+| `model_photometry.txt` / `model_spectroscopy.txt` | 50th percentile model fit for either spectroscopy or photometry depending on mode.|
+
+## Model Parameters
+
+| Model | Parameters fit |
+|---|---|
+| `SonoraElfOwl` | Teff, log(g), log(Kzz), [M/H], C/O, distance (pc) |
+| `SonoraElfOwlPH3` | Teff, log(g), log(Kzz), [M/H], C/O, distance (pc) |
+| `ATMO2020` | Teff, log(g), [M/H], distance (pc) |
+| `LOWZ` | Teff, log(g), log(Kzz), [M/H], C/O, distance (pc) |
+
+All fits assume a source radius of 1 Jupiter radius. Distances are always
+reported in parsecs.
+
+
+## Creating the ModelGrid Files
+
+Before running NIFTY, download the model grids you want to fit against, then 
+run `build_model` to build the model grid file that NIFTY uses during fitting. 
+
+For a more detailed description of parameters, run `build_model -h`.
+
+```
+build_model \
+    --path path/to/model/files/ \
+    --config BD_NIRCam_MIRI_filters.json \
+    ModelName
+```
+
+The valid model names are `SonoraElfOwl`, `SonoraElfOwlPH3`, `ATMO2020`, `LOWZ`.
+
+Typically, there are two ModelGrid files outputted. The **raw grid** is the 
+grid created by reading in all the points that are part of the model. However, 
+many models do not have values at all grid points, so missing points are filled. 
+with NaN. The **complete grid** has  values for all grid points. If the raw 
+grid is missing values, they are filled by a fitting procedure (see code for 
+details). If the raw grid is already complete, only the complete grid is saved.
+
+By default, the output model grid files are named 
+`<Model>_raw_ModelGrid.tar.gz` and `<Model>_complete_ModelGrid.tar.gz`.
+
+The Sonora Elf Owl model grid spans several tens of GB and can take a few hours
+to process. The other grids are considerably smaller.
+
+### Expected Model File Layouts
+
+**SonoraElfOwl** — directory of temperature-range tarballs containing NetCDF 
+files:
+```
+Sonora_Elf_Owl_v2/
+    teff_275_325.tar.gz
+    teff_350_400.tar.gz
+    ...
+```
+
+**SonoraElfOwlPH3** — a single `.npz` file:
+```
+elf_owl_disequilibrium_PH3.npz
+```
+
+**ATMO2020** — per-metallicity subdirectories containing `.dat` files:
+```
+meisner_2023/
+    grid_m1.0/
+        spec_jwst_t700_g3.5_m1.0_kg_g3.5.dat
+        ...
+    grid_m0.5/
+    grid_p0/
+    grid_p0.3/
+```
+
+**LOWZ** — CSV index and models tarball
+```
+LOWZ/
+    LOWZ_models_index.csv
+    models.tar.gz
+```
+
+## References
+
+- Meisner et al. 2021 (LOWZ): https://doi.org/10.3847/1538-4357/ac013c
+- Phillips et al. 2020 (ATMO2020): https://doi.org/10.1051/0004-6361/201937381 
+- Mukherjee et al. 2024 (Sonora Elf Owl): https://doi.org/10.3847/1538-4357/ad18c2
+- Wogan et al. 2025 (Sonora Elf Owl v2): https://doi.org/10.3847/2515-5172/add407
+- Beiler et al. 2024: https://doi.org/10.5281/zenodo.11370829
+- Foreman-Mackey et al. 2013 (emcee): https://doi.org/10.1086/670067
+- Lange 2023 (nautilus): https://doi.org/10.1093/mnras/stad2441