https://github.com/zstone19/pypetal
A pipeline for estimating AGN time lags
Science Score: 13.0%
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○Scientific vocabulary similarity
Low similarity (15.6%) to scientific vocabulary
Keywords
Repository
A pipeline for estimating AGN time lags
Basic Info
- Host: GitHub
- Owner: Zstone19
- License: mit
- Language: Python
- Default Branch: main
- Homepage: https://pypetal.readthedocs.io
- Size: 331 MB
Statistics
- Stars: 11
- Watchers: 2
- Forks: 0
- Open Issues: 2
- Releases: 6
Topics
Metadata Files
README.md
pyPETaL: A Pipeline for Estimating AGN Time Lags
pyPETaL is a time-series data analysis pipeline for AGN reverberation mapping (RM) data. It combines multiple different popular softwares using for AGN RM analysis, including PyCCF, PyZDCF, JAVELIN, and PyROA. This pipeline also implements outlier rejection using Damped Random Walk Gaussian process fitting, and detrending through the LinMix algorithm. pyPetal implements a weighting scheme (for all modules) in order to mitigate aliasing in peaks of time lag distributions between light curves.
pyPetal is very flexible, with almost every argument for each module allowing user input. pyPetal is designed to work with any combination of modules being run, allowing it to scale from the simplest to the most complex of projects.
Installation
pyPetal
pyPetal is available on PyPI and can be installed with pip:
pip install pypetal
Or, if you want to install the latest development version:
git clone https://github.com/Zstone19/pypetal.git
cd pypetal
pip install .
PLIKE is an optional algorithm that is used in pyPetal. There is a script available in the main directory to install and compile PLIKE (assuming that gfortran is installed). To install PLIKE, run the following command:
sh build_plike.sh
Detrending
pyPetal offers the option to detrend the input light curves via the LinMix algorithm. This package is not offered in the base version of pyPetal, but can be installed with pip:
pip install "linmix @ git+https://github.com/jmeyers314/linmix.git"
Or with poetry:
poetry install --with extra
MICA2
pyPetal also offers MICA2 as an optional module. This package is more complex to install than the others - to find out more, read the MICA2 installation guide.
poetry can help to install some easily-installable python dependencies for MICA2:
poetry install --with extra
The functionality and inputs of the MICA2 module are identical to the original software, so the best way to learn how this module functions is to read the MICA2 documentation.
NOTE: Seeing as this is an optional module, pyPetal will still compile and run if MICA2's dependencies are not installed. Each pyPetal run will assume run_mica2=False.
pyPetal and JAVELIN
The JAVELIN software used in pyPetal runs on Python 2, though the bulk of pyPetal software relies on Python >=3.8. To circumvent this issue, pyPetal has a JAVELIN "module" (pypetal-jav) that can be installed as a separate package and used in conjunction with pyPetal, in a Python 2 environment.
External requirements (not installed by pip or setup.py):
A Fortran compiler (>F90)
pyPetal-jav is available on PyPI and can be installed with pip:
pip install --no-deps pypetal-jav
pip install pypetal-jav
Or, if you want to install the latest development version:
git clone https://github.com/Zstone19/pypetal-jav.git
cd pypetal-jav
pip install .
NOTE: The user may need to install NumPy before installing pyPetal-jav through pip or setup.py. This is because JAVELIN requires NumPy in order to be installed. This can be done with:
pip install numpy
Citing pyPetal
To cite the pyPetal code itself, use the ASCL reference:
Stone Z., 2024, version xxxx, Astrophysics Source Code Library, record ascl:2401.004
Cite the paper pyPetal was used in: Shen et al. (2023)
Owner
- Name: Zachary Stone
- Login: Zstone19
- Kind: user
- Repositories: 9
- Profile: https://github.com/Zstone19
Astronomy Grad Student at UIUC working on AGN Variability
GitHub Events
Total
- Watch event: 4
- Delete event: 1
- Push event: 12
- Pull request event: 4
- Create event: 2
Last Year
- Watch event: 4
- Delete event: 1
- Push event: 12
- Pull request event: 4
- Create event: 2
Issues and Pull Requests
Last synced: 6 months ago
All Time
- Total issues: 2
- Total pull requests: 33
- Average time to close issues: 2 days
- Average time to close pull requests: 9 days
- Total issue authors: 2
- Total pull request authors: 2
- Average comments per issue: 0.5
- Average comments per pull request: 0.18
- Merged pull requests: 28
- Bot issues: 0
- Bot pull requests: 5
Past Year
- Issues: 0
- Pull requests: 4
- Average time to close issues: N/A
- Average time to close pull requests: less than a minute
- Issue authors: 0
- Pull request authors: 1
- Average comments per issue: 0
- Average comments per pull request: 0.25
- Merged pull requests: 4
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- Zstone19 (1)
- YuanzheJiang (1)
Pull Request Authors
- Zstone19 (28)
- pre-commit-ci[bot] (5)
Top Labels
Issue Labels
Pull Request Labels
Packages
- Total packages: 1
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Total downloads:
- pypi 28 last-month
- Total dependent packages: 0
- Total dependent repositories: 0
- Total versions: 6
- Total maintainers: 1
pypi.org: pypetal
A pipeline for estimating AGN time lags
- Homepage: https://github.com/Zstone19/pypetal
- Documentation: https://pypetal.readthedocs.io
- License: MIT
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Latest release: 1.0.1
published almost 2 years ago
Rankings
Maintainers (1)
Dependencies
- actions/checkout v3 composite
- actions/setup-python v4 composite
- codecov/codecov-action v3 composite
- ipykernel >=6.17.l
- nbsphinx >=0.8.10
- sphinx >=5.3.0
- sphinx-copybutton >=0.5.1
- sphinx_rtd_theme >=1.1.1
- nbsphinx *
- sphinx-copybutton *
- sphinx_rtd_theme *
- sphinxcontrib-bibtex *