firepype 0.0.1__tar.gz

firepype-0.0.1/LICENSE

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+MIT License
+
+Copyright (c) 2026 Gemma Cheng
+
+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.

firepype-0.0.1/PKG-INFO

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+Metadata-Version: 2.4
+Name: firepype
+Version: 0.0.1
+Summary: FIRE AB-pair NIR reduction pipeline
+Author: Gemma Cheng
+License: MIT
+Project-URL: Homepage, https://github.com/gemma-cheng/firepype
+Project-URL: Repository, https://github.com/gemma-cheng/firepype.git
+Project-URL: Issues, https://github.com/gemma-cheng/firepype/issues
+Keywords: astronomy,spectroscopy,FIRE,infrared,data-reduction
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3 :: Only
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Operating System :: OS Independent
+Classifier: Topic :: Scientific/Engineering :: Astronomy
+Requires-Python: >=3.10
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: numpy>=1.22
+Requires-Dist: scipy>=1.9
+Requires-Dist: astropy>=5.2
+Requires-Dist: matplotlib>=3.6
+Provides-Extra: dev
+Requires-Dist: pytest; extra == "dev"
+Requires-Dist: pytest-cov; extra == "dev"
+Requires-Dist: ruff; extra == "dev"
+Requires-Dist: black; extra == "dev"
+Requires-Dist: isort; extra == "dev"
+Requires-Dist: mypy; extra == "dev"
+Requires-Dist: build; extra == "dev"
+Requires-Dist: twine; extra == "dev"
+Dynamic: license-file
+
+# firepype
+
+Python pipeline for Magellan/FIRE Prism-mode data. Experimental; validated on a limited dataset. Verify outputs against established pipelines (e.g. [FireHose_v2](https://github.com/jgagneastro/FireHose_v2/)).
+
+## Features
+
+- Slit edge and object detection with robust heuristics
+- Arc 1D extraction and line matching
+- Robust Chebyshev dispersion solution with optional anchors
+- Parity-aware A–B/B–A differencing and robust negative-beam scaling
+- Footprint median extraction with error estimates
+- Interpolation-edge masking and inverse-variance coaddition
+- Telluric correction:
+  - POS-only standard extraction
+  - Band-wise scaling with deep-gap masking
+  - Vega model broadened to the instrument resolution
+  - Transmission (T) smoothing only inside dense contiguous regions
+- Optional QA plots: arc overlays, labeled arc 1D, final coadd, telluric T(λ), corrected spectra
+
+## Installation
+
+Installation (PyPi):
+
+```python -m venv .venv
+. .venv/bin/activate  # Windows: .venv\Scripts\activate
+python -m pip install -U pip
+pip install firepype
+```
+
+Alternatively, install from source:
+
+```python -m venv .venv
+. .venv/bin/activate
+python -m pip install -U pip
+git clone https://github.com/gemma-cheng/firepype
+cd firepype
+pip install -e .[dev]
+```
+
+Requirements:
+- Python 3.10–3.12
+- numpy ≥ 1.22, scipy ≥ 1.9, astropy ≥ 5.2, matplotlib ≥ 3.6
+
+
+## Quickstart
+
+Minimal end-to-end reduction:
+
+```
+firepype \
+  --raw-dir /path/to/raw \
+  --out-dir ./out \
+  --arc /path/to/raw/fire_0123.fits \
+  --ref-list /path/to/ref/line_list.lst \
+  --spec "1-4, 10-7"
+```
+
+Telluric/response only:
+```
+firepype-telluric \
+  --standard ./out/standard_extracted.fits \
+  --out-dir ./out/telluric \
+  --stype A0V --plot
+```
+
+Outputs
+- ./output/qa/ … if QA enabled
+- Coadded spectrum FITS: wavelength_um, flux
+- Telluric and response FITS in out/telluric/
+
+
+## Basic Tutorials
+
+Basic usage tutorials can be found in the [`tutorials`](./tutorials/) directory
+
+
+## Notes on telluric method
+
+- Standard extraction: POS-only column, tuned aperture/background; alternative beam used if POS median is non-positive
+- Wavecal: average across a small footprint around the chosen standard column, using ARC + line list
+- Vega model: broadened to instrument resolution (R ~ 6000 by default) in log-λ space
+- Continuum: robust Chebyshev fit to the standard/model ratio within each band (J/H/K), excluding deep telluric gaps and known A0V intrinsic lines; fit is used to normalize before deriving T
+- Transmission T(λ): computed and lightly smoothed only within dense contiguous support (prevents spreading across gaps)
+- Application: science flux and errors are divided by T within overlap where T_min ≤ T ≤ T_max; elsewhere, values are left as NaN to avoid artifacts
+
+
+## Limitations and validation
+
+- Tested on a limited set of FIRE Prism-mode observations; results are not guaranteed.
+- Validate outputs against established pipelines (e.g. [FireHose_v2](https://github.com/jgagneastro/FireHose_v2/)):
+  - Wavelength RMS per region
+  - Sky residuals around OH lines
+  - Merged-order continuity
+  - S/N consistency
+
+
+## License
+
+MIT (see [`LICENSE`](./LICENSE)).
+
+
+## File Structure
+
+- `firepype/`
+  - `__init__.py` — package API (exposes `run_ab_pairs`, `apply_telluric_correction`)
+  - `config.py` — dataclasses for configuration
+  - `io.py` — FITS I/O, path builders, ID pairing
+  - `utils.py` — math helpers, masks, line-list loader
+  - `calibration.py` — peak detection, line matching, dispersion solver
+  - `detection.py` — slit/object detection, parity, negative scaling
+  - `extraction.py` — 1D extraction routines
+  - `coadd.py` — coaddition accumulator
+  - `plotting.py` — optional QA plotting
+  - `pipeline.py` — high-level AB-pair orchestration
+  - `telluric.py` — telluric correction API
+  - `cli.py` — command-line interface (pipeline + telluric subcommand if enabled)
+- `tests/` — minimal tests for core functionality
+- `pyproject.toml` — packaging configuration
+- `README.md` — this file
+- `LICENSE`

firepype-0.0.1/README.md

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+# firepype
+
+Python pipeline for Magellan/FIRE Prism-mode data. Experimental; validated on a limited dataset. Verify outputs against established pipelines (e.g. [FireHose_v2](https://github.com/jgagneastro/FireHose_v2/)).
+
+## Features
+
+- Slit edge and object detection with robust heuristics
+- Arc 1D extraction and line matching
+- Robust Chebyshev dispersion solution with optional anchors
+- Parity-aware A–B/B–A differencing and robust negative-beam scaling
+- Footprint median extraction with error estimates
+- Interpolation-edge masking and inverse-variance coaddition
+- Telluric correction:
+  - POS-only standard extraction
+  - Band-wise scaling with deep-gap masking
+  - Vega model broadened to the instrument resolution
+  - Transmission (T) smoothing only inside dense contiguous regions
+- Optional QA plots: arc overlays, labeled arc 1D, final coadd, telluric T(λ), corrected spectra
+
+## Installation
+
+Installation (PyPi):
+
+```python -m venv .venv
+. .venv/bin/activate  # Windows: .venv\Scripts\activate
+python -m pip install -U pip
+pip install firepype
+```
+
+Alternatively, install from source:
+
+```python -m venv .venv
+. .venv/bin/activate
+python -m pip install -U pip
+git clone https://github.com/gemma-cheng/firepype
+cd firepype
+pip install -e .[dev]
+```
+
+Requirements:
+- Python 3.10–3.12
+- numpy ≥ 1.22, scipy ≥ 1.9, astropy ≥ 5.2, matplotlib ≥ 3.6
+
+
+## Quickstart
+
+Minimal end-to-end reduction:
+
+```
+firepype \
+  --raw-dir /path/to/raw \
+  --out-dir ./out \
+  --arc /path/to/raw/fire_0123.fits \
+  --ref-list /path/to/ref/line_list.lst \
+  --spec "1-4, 10-7"
+```
+
+Telluric/response only:
+```
+firepype-telluric \
+  --standard ./out/standard_extracted.fits \
+  --out-dir ./out/telluric \
+  --stype A0V --plot
+```
+
+Outputs
+- ./output/qa/ … if QA enabled
+- Coadded spectrum FITS: wavelength_um, flux
+- Telluric and response FITS in out/telluric/
+
+
+## Basic Tutorials
+
+Basic usage tutorials can be found in the [`tutorials`](./tutorials/) directory
+
+
+## Notes on telluric method
+
+- Standard extraction: POS-only column, tuned aperture/background; alternative beam used if POS median is non-positive
+- Wavecal: average across a small footprint around the chosen standard column, using ARC + line list
+- Vega model: broadened to instrument resolution (R ~ 6000 by default) in log-λ space
+- Continuum: robust Chebyshev fit to the standard/model ratio within each band (J/H/K), excluding deep telluric gaps and known A0V intrinsic lines; fit is used to normalize before deriving T
+- Transmission T(λ): computed and lightly smoothed only within dense contiguous support (prevents spreading across gaps)
+- Application: science flux and errors are divided by T within overlap where T_min ≤ T ≤ T_max; elsewhere, values are left as NaN to avoid artifacts
+
+
+## Limitations and validation
+
+- Tested on a limited set of FIRE Prism-mode observations; results are not guaranteed.
+- Validate outputs against established pipelines (e.g. [FireHose_v2](https://github.com/jgagneastro/FireHose_v2/)):
+  - Wavelength RMS per region
+  - Sky residuals around OH lines
+  - Merged-order continuity
+  - S/N consistency
+
+
+## License
+
+MIT (see [`LICENSE`](./LICENSE)).
+
+
+## File Structure
+
+- `firepype/`
+  - `__init__.py` — package API (exposes `run_ab_pairs`, `apply_telluric_correction`)
+  - `config.py` — dataclasses for configuration
+  - `io.py` — FITS I/O, path builders, ID pairing
+  - `utils.py` — math helpers, masks, line-list loader
+  - `calibration.py` — peak detection, line matching, dispersion solver
+  - `detection.py` — slit/object detection, parity, negative scaling
+  - `extraction.py` — 1D extraction routines
+  - `coadd.py` — coaddition accumulator
+  - `plotting.py` — optional QA plotting
+  - `pipeline.py` — high-level AB-pair orchestration
+  - `telluric.py` — telluric correction API
+  - `cli.py` — command-line interface (pipeline + telluric subcommand if enabled)
+- `tests/` — minimal tests for core functionality
+- `pyproject.toml` — packaging configuration
+- `README.md` — this file
+- `LICENSE`

firepype-0.0.1/firepype/__init__.py

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+# firepype/__init__.py
+from __future__ import annotations
+
+__version__ = "0.0.1"
+
+from .config import (
+    PipelineConfig,
+    RunSpec,
+    QASettings,
+    WavecalSettings,
+    ExtractionSettings,
+    SlitDetectionSettings,
+)
+from .pipeline import run_ab_pairs
+from .telluric import apply_telluric_correction
+
+__all__ = [
+    "__version__",
+    "PipelineConfig",
+    "RunSpec",
+    "QASettings",
+    "WavecalSettings",
+    "ExtractionSettings",
+    "SlitDetectionSettings",
+    "run_ab_pairs",
+    "apply_telluric_correction",
+]