smart-astro 1.0.0__tar.gz

smart_astro-1.0.0/LICENSE

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+MIT License
+
+Copyright (c) 2020 Dino Chih-Chun Hsu
+
+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.

smart_astro-1.0.0/PKG-INFO

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+Metadata-Version: 2.4
+Name: smart-astro
+Version: 1.0.0
+Summary: The Spectral Modeling Analysis and RV Tool
+Home-page: https://github.com/chihchunhsu/smart
+Author: Chih-Chun Hsu
+Author-email: chsu@northwestern.edu
+License: MIT
+Classifier: Programming Language :: Python :: 3
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Operating System :: OS Independent
+Requires-Python: >=3.6
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: numpy
+Requires-Dist: scipy
+Requires-Dist: pandas
+Requires-Dist: matplotlib
+Requires-Dist: astropy
+Requires-Dist: emcee
+Requires-Dist: corner
+Dynamic: author
+Dynamic: author-email
+Dynamic: classifier
+Dynamic: description
+Dynamic: description-content-type
+Dynamic: home-page
+Dynamic: license
+Dynamic: license-file
+Dynamic: requires-dist
+Dynamic: requires-python
+Dynamic: summary
+
+# SMART (Spectral Modeling Analysis and RV Tool)
+The `SMART` is a Markov Chain Monte Carlo (MCMC) forward-modeling framework for spectroscopic data, currently working for the Keck/NIRSPEC, SDSS/APOGEE, and IGRINS high-resolution near-infrared spectrometers. A slightly modified version that can model the Keck/OSIRIS medium-resolution near-infrared spectrometer is available [here](https://github.com/ctheissen/osiris_fmp).
+
+For NIRSPEC users, required adjustments need to be made before reducing private data using [NIRSPEC-Data-Reduction-Pipeline(NSDRP)](https://github.com/Keck-DataReductionPipelines/NIRSPEC-Data-Reduction-Pipeline), to perform telluric wavelength calibrations, and to forward model spectral data. The code is currently being developed.
+
+Authors:
+* Dino Chih-Chun Hsu (Northwestern, UCSD)
+* Adam Burgasser, PI (UCSD)
+* Chris Theissen (UCSD, BU)
+* Jessica Birky (UW, UCSD)
+* Lingfeng Wei (UCSD)
+
+## Code Setup:
+Dependencies. The `SMART` has been tested under the following environments:
+* Python 3.6.10/3.7.3
+* astropy 3.0.4/3.0.5
+* numpy 1.12.1/1.13.3/1.18.1
+* scipy 0.19.0/1.4.1
+* matplotlib 2.2.3/3.1.3
+* pandas 0.20.1/0.23.4/1.0.1
+* emcee 3.0.2/3.0.3.dev4+gc14b212
+* corner 2.0.1
+* openpyxl 3.0.10
+* wavelets (for defringeflat)
+
+Download the `SMART` and the forked and modified version of the NSDRP to your computer.
+
+There are two ways of setting up the code:
+
+<br/>(i) In the terminal under the `SMART` folder, 
+
+```
+pip install -e .
+```
+
+<br/>(ii) Set up the environment variables in the `.bashrc` or `.bash_profile`
+
+```
+export PYTHONPATH="/path/to/smart:${PYTHONPATH}"
+```
+
+To model the SDSS/APOGEE spectra, you will also need to put the associated APOGEE LSF and wavelength fits files under `forward_model/apogee/`:
+
+[apLSF-a-05440020.fits](https://dr13.sdss.org/sas/dr13/apogee/spectro/redux/r6/cal/lsf/apLSF-a-05440020.fits)<br/>
+[apLSF-b-05440020.fits](https://dr13.sdss.org/sas/dr13/apogee/spectro/redux/r6/cal/lsf/apLSF-b-05440020.fits)<br/>
+[apLSF-c-05440020.fits](https://dr13.sdss.org/sas/dr13/apogee/spectro/redux/r6/cal/lsf/apLSF-c-05440020.fits)<br/>
+[apWave-a-02420038.fits](https://dr13.sdss.org/sas/dr13/apogee/spectro/redux/r6/cal/wave/apWave-a-02420038.fits)<br/>
+[apWave-b-02420038.fits](https://dr13.sdss.org/sas/dr13/apogee/spectro/redux/r6/cal/wave/apWave-b-02420038.fits)<br/>
+[apWave-c-02420038.fits](https://dr13.sdss.org/sas/dr13/apogee/spectro/redux/r6/cal/wave/apWave-c-02420038.fits)<br/>
+
+The codes under the apogee folder are from Jo Bovy's [apogee](https://github.com/jobovy/apogee) package.
+
+## Defringe Flats:
+The algorithm follows Rojo & Harrington (2006) to remove fringe patterns from flat files. The example and sample outputs are under the example folder.
+
+```
+>>> import smart
+>>> smart.defringeflatAll(data_folder_path, diagnostic=False)
+```
+
+## Reducing the data using NSDRP:
+To reduce the data for the whole folder, use the forked [NSDRP](https://github.com/ctheissen/NIRSPEC-Data-Reduction-Pipeline) on the terminal:
+
+```
+$ python ~/path/to/NIRSPEC-Data-Reduction-Pipeline/nsdrp.py rawData/ reducedData/ -oh_filename ~/path/to/NIRSPEC-Data-Reduction-Pipeline/ir_ohlines.dat -spatial_jump_override -verbose -debug
+```
+
+, where the directory rawData/ is the path to the raw data is, and reducedData/ is the path where you want to store the reduced data.
+
+To reduce the data of two nodding positions with a single flat file, you can run the following command:
+
+```
+$ python ~/path/to/NIRSPEC-Data-Reduction-Pipeline/nsdrp.py flat_file.fits nod_A_file.fits -b nod_B_file.fits -oh_filename ~/path/to/NIRSPEC-Data-Reduction-Pipeline/ir_ohlines.dat -spatial_jump_override -verbose -debug
+```
+
+## Wavelength Calibration using Telluric Standard Spectra:
+To calibrate the most precise wavelength solutions with a given data, we rely on the telluric spectrum using the algorithm that follows [Blake at el. (2010)](https://ui.adsabs.harvard.edu/abs/2010ApJ...723..684B/abstract) and [Burgasser et al. (2016)](https://ui.adsabs.harvard.edu/abs/2016ApJ...827...25B/abstract) to cross-correlate the [ESO atmospheric model](https://ui.adsabs.harvard.edu/abs/2014A%26A...568A...9M/abstract) and an observed telluric spectrum, fit the residual, and iterate the process until the standard deviation of the residual reaches a mininum.
+
+```
+>>> import smart
+>>> smart.run_wave_cal(data_name, data_path, order_list, save_to_path, test=False, save=True, applymask=True, pwv='0.5')
+```
+
+The parameters `data_name`, `data_path`, `save_to_path` have the type str, while `order_list` has the type list. The optional parameter `applymask` provides a simple sigma-clipping mask to remove cosmic rays in the telluric spectrum. The optional parameter `pwv` is the precipitable water vapor parameter for users to adjust. Typically, 0.5 mm to 3.0 mm can fit most cases under different weather conditions. 
+
+## Forward Modeling Science and Telluric Spectra:
+To fit the science data, `SMART` provides various self-consistent synthetic modeling grids to forward-model the data that are available to download [here](https://drive.google.com/drive/folders/1_23bl-BXqlFlrO7EIJX3FeFI4Rix-6kP?usp=sharing). Users will need to place the downloaded files in `smart/libraries`.
+
+We perform the MCMC forward-modeling fitting to the high-resolution near-infrared spectroscopic data for both the telluric and science files.
+
+The telluric spectrum after being calibrated with its wavelength solution is modeled with the equation:
+
+```math
+D[p] = C[p] \times \Bigg[ \bigg(M \Big[p^* \big(\lambda \big[ 1 + \frac{RV^*}{c}\big] \big) , T_{\text{eff}}, \log{g} \Big] \otimes \kappa_R (v\sin{i}) \bigg) \times T \big[ p^*(\lambda) \big] \Bigg] \otimes \kappa_G (\Delta \nu_{inst}) + C_{flux}
+```
+
+, where $D[p]$ is the forward-model telluric spectrum, $C[p(\lambda)]$ is the continuum, $T \big[ p^*(\lambda) \big]$ is the earth atmosphere absorption model as a function of airmass and precipitable water vapor (pwv), $\Delta \nu_{inst}(p)$ is the instrumental line-spread function, and $C_{flux}$ is the nuisance parameter accounting for small flux offsets.
+
+You can run the following command on the terminal:
+
+```
+>>> python /SMART_BASE/smart/smart/forward_model/run_mcmc_telluric_airmass_pwv.py order date_obs tell_data_name tell_path save_to_path -nwalkers 50 -step 600 -burn 300 -pixel_start 50 -pixel_end -80
+```
+
+The required parameters are nirspec order sorting filter `order` (e.g. 33), data of observation (e.g. 20100101) `date_obs`, telluric data name (e.g. nspec200101_1001) `tell_data_name`, telluric file path `tell_path` (e.g. BASE/data_obs), saving path `save_to_path`, and optional paramters MCMC number of chains/walkers `-nwalkers`, number of steps `-step`, burn-in `-burn`, starting/ending pixels `-pixel_start` and `-pixel_end`.
+
+The most important parameter used as the input in the science modeling is the NIRSPEC instrumental line-spread function `lsf`.
+
+The science spectrum is modeled with the equation:
+
+```math
+D[p] = C[p] \times \Bigg[ \bigg(M \Big[p^* \big(\lambda \big[ 1 + \frac{RV^*}{c}\big] \big) , T_{\text{eff}}, \log{g} \Big] \otimes \kappa_R (v\sin{i}) \bigg) \times T \big[ p^*(\lambda) \big] \Bigg] \otimes \kappa_G (\Delta \nu_{inst}) + C_{flux}
+```
+
+, where $D[p]$ is the forward-model science spectrum, $C[p(\lambda)]$ is the continuum, $`M \big[ p^*(\lambda) \big]`$ is the self-consistent synthetic stellar/substellar modeling grids as a function of effective temperature $T_{\text{eff}}$ and surface gravity $\log{g}$, corrected with radial velocity $RV$ and projected rotational velocity $v\sin{i}$, $[ T \big[ p^*(\lambda) \big]$ is the earth atmosphere absorption model, $\Delta \nu_{inst}(p)$ is the instrumental line-spread function, $C_{flux}$ is the nuisance parameter accounting for small flux offsets. There are also two nudge factors for small wavelength offsets and noise scaling factors in the routine.
+
+You can run the following command on the terminal:
+
+```
+>>> python /SMART_BASE/smart/smart/forward_model/run_mcmc_science.py order date_obs sci_data_name tell_data_name data_path tell_path save_to_path lsf -outlier_rejection 3.0 -nwalkers 50 -step 1000 -burn 800 -moves 2.0 -pixel_start 10 -pixel_end -80 -applymask False -modelset btsettl08
+```
+
+The required parameters order sorting filter `order`, data of observation `date_obs`, science data name `sci_data_name`, telluric data name `tell_data_name`, science file path `data_path`, telluric file path `tell_path`, saving path `save_to_path`, optional paramters MCMC number of chains/walkers `-nwalkers`, number of steps `-step`, burn-in `-burn`, starting/ending pixels `-pixel_start` and `-pixel_end` are defined the same as the telluric data modeling routine. The NIRSPEC line-spread function `lsf` is obtained from the telluric data modeling (typically 4.8 km/s). The outlier rejection `-outlier_rejection` is to perform a sigma-clipping outlier rejection (in this case sigma=3.0) to remove bad pixels by comparing the residual of the best-fit model and observed data. Finally, the model set to use `-modelset` in this case is the [BT-Settl](https://ui.adsabs.harvard.edu/abs/2012RSPTA.370.2765A/abstract) models. Other model sets are available and described in detail [here](https://github.com/chihchunhsu/smart/tree/master/smart/libraries).
+
+## Citation:
+
+If you use this code in your research, please cite [Hsu et al. 2021; ApJS, 257, 45](https://ui.adsabs.harvard.edu/abs/2021ApJS..257...45H/abstract) and the frozen version is on [Hsu et al. 2021 Zenodo](https://ui.adsabs.harvard.edu/abs/2021zndo...4765258H/abstract)
+
+Depending on which model sets you choose, please also cite the corresponding references listed under [here](https://github.com/chihchunhsu/smart/tree/main/smart/libraries).
+
+Please also cite [Carvalho & Johns-Krull (2023)](https://github.com/Adolfo1519/RotBroadInt) if you enable slow (but accurate) rotational broadening in the forward-modeling routine.
+
+
+

smart_astro-1.0.0/README.md

@@ -0,0 +1,134 @@
+# SMART (Spectral Modeling Analysis and RV Tool)
+The `SMART` is a Markov Chain Monte Carlo (MCMC) forward-modeling framework for spectroscopic data, currently working for the Keck/NIRSPEC, SDSS/APOGEE, and IGRINS high-resolution near-infrared spectrometers. A slightly modified version that can model the Keck/OSIRIS medium-resolution near-infrared spectrometer is available [here](https://github.com/ctheissen/osiris_fmp).
+
+For NIRSPEC users, required adjustments need to be made before reducing private data using [NIRSPEC-Data-Reduction-Pipeline(NSDRP)](https://github.com/Keck-DataReductionPipelines/NIRSPEC-Data-Reduction-Pipeline), to perform telluric wavelength calibrations, and to forward model spectral data. The code is currently being developed.
+
+Authors:
+* Dino Chih-Chun Hsu (Northwestern, UCSD)
+* Adam Burgasser, PI (UCSD)
+* Chris Theissen (UCSD, BU)
+* Jessica Birky (UW, UCSD)
+* Lingfeng Wei (UCSD)
+
+## Code Setup:
+Dependencies. The `SMART` has been tested under the following environments:
+* Python 3.6.10/3.7.3
+* astropy 3.0.4/3.0.5
+* numpy 1.12.1/1.13.3/1.18.1
+* scipy 0.19.0/1.4.1
+* matplotlib 2.2.3/3.1.3
+* pandas 0.20.1/0.23.4/1.0.1
+* emcee 3.0.2/3.0.3.dev4+gc14b212
+* corner 2.0.1
+* openpyxl 3.0.10
+* wavelets (for defringeflat)
+
+Download the `SMART` and the forked and modified version of the NSDRP to your computer.
+
+There are two ways of setting up the code:
+
+<br/>(i) In the terminal under the `SMART` folder, 
+
+```
+pip install -e .
+```
+
+<br/>(ii) Set up the environment variables in the `.bashrc` or `.bash_profile`
+
+```
+export PYTHONPATH="/path/to/smart:${PYTHONPATH}"
+```
+
+To model the SDSS/APOGEE spectra, you will also need to put the associated APOGEE LSF and wavelength fits files under `forward_model/apogee/`:
+
+[apLSF-a-05440020.fits](https://dr13.sdss.org/sas/dr13/apogee/spectro/redux/r6/cal/lsf/apLSF-a-05440020.fits)<br/>
+[apLSF-b-05440020.fits](https://dr13.sdss.org/sas/dr13/apogee/spectro/redux/r6/cal/lsf/apLSF-b-05440020.fits)<br/>
+[apLSF-c-05440020.fits](https://dr13.sdss.org/sas/dr13/apogee/spectro/redux/r6/cal/lsf/apLSF-c-05440020.fits)<br/>
+[apWave-a-02420038.fits](https://dr13.sdss.org/sas/dr13/apogee/spectro/redux/r6/cal/wave/apWave-a-02420038.fits)<br/>
+[apWave-b-02420038.fits](https://dr13.sdss.org/sas/dr13/apogee/spectro/redux/r6/cal/wave/apWave-b-02420038.fits)<br/>
+[apWave-c-02420038.fits](https://dr13.sdss.org/sas/dr13/apogee/spectro/redux/r6/cal/wave/apWave-c-02420038.fits)<br/>
+
+The codes under the apogee folder are from Jo Bovy's [apogee](https://github.com/jobovy/apogee) package.
+
+## Defringe Flats:
+The algorithm follows Rojo & Harrington (2006) to remove fringe patterns from flat files. The example and sample outputs are under the example folder.
+
+```
+>>> import smart
+>>> smart.defringeflatAll(data_folder_path, diagnostic=False)
+```
+
+## Reducing the data using NSDRP:
+To reduce the data for the whole folder, use the forked [NSDRP](https://github.com/ctheissen/NIRSPEC-Data-Reduction-Pipeline) on the terminal:
+
+```
+$ python ~/path/to/NIRSPEC-Data-Reduction-Pipeline/nsdrp.py rawData/ reducedData/ -oh_filename ~/path/to/NIRSPEC-Data-Reduction-Pipeline/ir_ohlines.dat -spatial_jump_override -verbose -debug
+```
+
+, where the directory rawData/ is the path to the raw data is, and reducedData/ is the path where you want to store the reduced data.
+
+To reduce the data of two nodding positions with a single flat file, you can run the following command:
+
+```
+$ python ~/path/to/NIRSPEC-Data-Reduction-Pipeline/nsdrp.py flat_file.fits nod_A_file.fits -b nod_B_file.fits -oh_filename ~/path/to/NIRSPEC-Data-Reduction-Pipeline/ir_ohlines.dat -spatial_jump_override -verbose -debug
+```
+
+## Wavelength Calibration using Telluric Standard Spectra:
+To calibrate the most precise wavelength solutions with a given data, we rely on the telluric spectrum using the algorithm that follows [Blake at el. (2010)](https://ui.adsabs.harvard.edu/abs/2010ApJ...723..684B/abstract) and [Burgasser et al. (2016)](https://ui.adsabs.harvard.edu/abs/2016ApJ...827...25B/abstract) to cross-correlate the [ESO atmospheric model](https://ui.adsabs.harvard.edu/abs/2014A%26A...568A...9M/abstract) and an observed telluric spectrum, fit the residual, and iterate the process until the standard deviation of the residual reaches a mininum.
+
+```
+>>> import smart
+>>> smart.run_wave_cal(data_name, data_path, order_list, save_to_path, test=False, save=True, applymask=True, pwv='0.5')
+```
+
+The parameters `data_name`, `data_path`, `save_to_path` have the type str, while `order_list` has the type list. The optional parameter `applymask` provides a simple sigma-clipping mask to remove cosmic rays in the telluric spectrum. The optional parameter `pwv` is the precipitable water vapor parameter for users to adjust. Typically, 0.5 mm to 3.0 mm can fit most cases under different weather conditions. 
+
+## Forward Modeling Science and Telluric Spectra:
+To fit the science data, `SMART` provides various self-consistent synthetic modeling grids to forward-model the data that are available to download [here](https://drive.google.com/drive/folders/1_23bl-BXqlFlrO7EIJX3FeFI4Rix-6kP?usp=sharing). Users will need to place the downloaded files in `smart/libraries`.
+
+We perform the MCMC forward-modeling fitting to the high-resolution near-infrared spectroscopic data for both the telluric and science files.
+
+The telluric spectrum after being calibrated with its wavelength solution is modeled with the equation:
+
+```math
+D[p] = C[p] \times \Bigg[ \bigg(M \Big[p^* \big(\lambda \big[ 1 + \frac{RV^*}{c}\big] \big) , T_{\text{eff}}, \log{g} \Big] \otimes \kappa_R (v\sin{i}) \bigg) \times T \big[ p^*(\lambda) \big] \Bigg] \otimes \kappa_G (\Delta \nu_{inst}) + C_{flux}
+```
+
+, where $D[p]$ is the forward-model telluric spectrum, $C[p(\lambda)]$ is the continuum, $T \big[ p^*(\lambda) \big]$ is the earth atmosphere absorption model as a function of airmass and precipitable water vapor (pwv), $\Delta \nu_{inst}(p)$ is the instrumental line-spread function, and $C_{flux}$ is the nuisance parameter accounting for small flux offsets.
+
+You can run the following command on the terminal:
+
+```
+>>> python /SMART_BASE/smart/smart/forward_model/run_mcmc_telluric_airmass_pwv.py order date_obs tell_data_name tell_path save_to_path -nwalkers 50 -step 600 -burn 300 -pixel_start 50 -pixel_end -80
+```
+
+The required parameters are nirspec order sorting filter `order` (e.g. 33), data of observation (e.g. 20100101) `date_obs`, telluric data name (e.g. nspec200101_1001) `tell_data_name`, telluric file path `tell_path` (e.g. BASE/data_obs), saving path `save_to_path`, and optional paramters MCMC number of chains/walkers `-nwalkers`, number of steps `-step`, burn-in `-burn`, starting/ending pixels `-pixel_start` and `-pixel_end`.
+
+The most important parameter used as the input in the science modeling is the NIRSPEC instrumental line-spread function `lsf`.
+
+The science spectrum is modeled with the equation:
+
+```math
+D[p] = C[p] \times \Bigg[ \bigg(M \Big[p^* \big(\lambda \big[ 1 + \frac{RV^*}{c}\big] \big) , T_{\text{eff}}, \log{g} \Big] \otimes \kappa_R (v\sin{i}) \bigg) \times T \big[ p^*(\lambda) \big] \Bigg] \otimes \kappa_G (\Delta \nu_{inst}) + C_{flux}
+```
+
+, where $D[p]$ is the forward-model science spectrum, $C[p(\lambda)]$ is the continuum, $`M \big[ p^*(\lambda) \big]`$ is the self-consistent synthetic stellar/substellar modeling grids as a function of effective temperature $T_{\text{eff}}$ and surface gravity $\log{g}$, corrected with radial velocity $RV$ and projected rotational velocity $v\sin{i}$, $[ T \big[ p^*(\lambda) \big]$ is the earth atmosphere absorption model, $\Delta \nu_{inst}(p)$ is the instrumental line-spread function, $C_{flux}$ is the nuisance parameter accounting for small flux offsets. There are also two nudge factors for small wavelength offsets and noise scaling factors in the routine.
+
+You can run the following command on the terminal:
+
+```
+>>> python /SMART_BASE/smart/smart/forward_model/run_mcmc_science.py order date_obs sci_data_name tell_data_name data_path tell_path save_to_path lsf -outlier_rejection 3.0 -nwalkers 50 -step 1000 -burn 800 -moves 2.0 -pixel_start 10 -pixel_end -80 -applymask False -modelset btsettl08
+```
+
+The required parameters order sorting filter `order`, data of observation `date_obs`, science data name `sci_data_name`, telluric data name `tell_data_name`, science file path `data_path`, telluric file path `tell_path`, saving path `save_to_path`, optional paramters MCMC number of chains/walkers `-nwalkers`, number of steps `-step`, burn-in `-burn`, starting/ending pixels `-pixel_start` and `-pixel_end` are defined the same as the telluric data modeling routine. The NIRSPEC line-spread function `lsf` is obtained from the telluric data modeling (typically 4.8 km/s). The outlier rejection `-outlier_rejection` is to perform a sigma-clipping outlier rejection (in this case sigma=3.0) to remove bad pixels by comparing the residual of the best-fit model and observed data. Finally, the model set to use `-modelset` in this case is the [BT-Settl](https://ui.adsabs.harvard.edu/abs/2012RSPTA.370.2765A/abstract) models. Other model sets are available and described in detail [here](https://github.com/chihchunhsu/smart/tree/master/smart/libraries).
+
+## Citation:
+
+If you use this code in your research, please cite [Hsu et al. 2021; ApJS, 257, 45](https://ui.adsabs.harvard.edu/abs/2021ApJS..257...45H/abstract) and the frozen version is on [Hsu et al. 2021 Zenodo](https://ui.adsabs.harvard.edu/abs/2021zndo...4765258H/abstract)
+
+Depending on which model sets you choose, please also cite the corresponding references listed under [here](https://github.com/chihchunhsu/smart/tree/main/smart/libraries).
+
+Please also cite [Carvalho & Johns-Krull (2023)](https://github.com/Adolfo1519/RotBroadInt) if you enable slow (but accurate) rotational broadening in the forward-modeling routine.
+
+
+

smart_astro-1.0.0/setup.cfg

@@ -0,0 +1,4 @@
+[egg_info]
+tag_build = 
+tag_date = 0
+

smart_astro-1.0.0/setup.py

@@ -0,0 +1,38 @@
+#! /usr/bin/env python
+# -*- coding: utf-8 -*-
+
+import re
+import setuptools
+
+#import smart
+#from smart.__init__ import __version__
+
+# PyPI
+with open("smart/__init__.py") as f:
+    __version__ = re.search(r'__version__\s*=\s*["\']([^"\']+)["\']', f.read()).group(1)
+
+with open("README.md", "r") as fh:
+    long_description = fh.read()
+
+setuptools.setup(
+    name="smart-astro",
+    version=__version__,
+    author="Chih-Chun Hsu",
+    author_email="chsu@northwestern.edu",
+    packages=setuptools.find_packages(),
+    url="https://github.com/chihchunhsu/smart",
+    license="MIT",
+    description=("The Spectral Modeling Analysis and RV Tool"),
+    long_description=open("README.md").read(),
+    long_description_content_type="text/markdown", # for PyPI
+    package_data={"": ["LICENSE", "AUTHORS.rst"]},
+    include_package_data=False,
+    install_requires=["numpy", "scipy", "pandas", "matplotlib", "astropy", "emcee", "corner"],
+    classifiers=[
+        "Programming Language :: Python :: 3",
+        "License :: OSI Approved :: MIT License",
+        "Operating System :: OS Independent",
+    ],
+    python_requires='>=3.6',
+    zip_safe=False,
+)

smart_astro-1.0.0/smart/__init__.py

@@ -0,0 +1,36 @@
+__version__ = "1.0.0"
+
+from .initialize import *
+from .utils.barycorr import barycorr
+from .forward_model.classModel import Model
+from .forward_model.classSpectrum import Spectrum
+from .forward_model.classForwardModelInit import ForwardModelInit
+from .forward_model.integralResample import integralResample
+from .forward_model.InterpolateModel import InterpModel
+from .forward_model.rotation_broaden import lsf_rotate, broaden
+from .forward_model.continuum import *
+from .forward_model.tellurics import InterpTelluricModel, convolveTelluric
+from .forward_model.model_fit import *
+from .forward_model.fringe_model import double_sine, doub_sine_wave_dependent, double_sine_fringe, double_sine_fringe_telluric
+from .forward_model.mcmc import run_mcmc, telluric_mcmc, run_mcmc2, run_mcmc3
+from .forward_model.apogee.lsf_function import computeAPLSF, convolveAPLSF
+try:
+	from .forward_model.apogee.lsf import eval
+except FileNotFoundError:
+	print("You need to put the APOGEE LSF and wavelength fits files under forward_model/apogee. See README.md for more details.")
+	pass
+from .forward_model.apogee.bitmask import bits_set
+from .wavelength_calibration.telluric_wavelength_fit import *
+from .wavelength_calibration.residual import residual
+from .utils.stats import chisquare
+from .utils.addKeyword import add_nsdrp_keyword, add_wfits_keyword
+from .utils.listTarget import makeTargetList
+from .utils.compute_uvw_velocity import compute_uvw_velocity
+from .utils.compute_galactic_thin_thick_disk import compute_galactic_pop_prob
+from .utils.interpolations import bilinear_interpolation, trilinear_interpolation, quadlinear_interpolation
+try:
+	from .utils.defringeflat import defringeflat, defringeflatAll
+except ImportError:
+	print("You need to install the wavelets package (https://github.com/aaren/wavelets) to use defringeflat functions.")
+	pass
+#from .utils.subtractDark import subtractDark