halo-analysis 1.0.0__tar.gz

halo_analysis-1.0.0/LICENSE.md

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+Copiright 2014-2024 by Andrew Wetzel <arwetzel@gmail.com>, Shea Garrison-Kimmel, Zach Hafen, Nico Garavito-Camargo
+
+If you use this package, please cite it, along the lines of: 'This work used HaloAnalysis (http://ascl.net/2002.014), which first was used in Wetzel et al 2016 (https://ui.adsabs.harvard.edu/abs/2016ApJ...827L..23W).'
+
+You are free to use, edit, share, and do whatever you want. But please cite it and report bugs!
+
+Less succinctly, this software is governed by the MIT License:
+
+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 aAUTHORS 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.\href{https://github.com/jngaravitoc/nba}{NBA}, Cranes. 

halo_analysis-1.0.0/PKG-INFO

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+Metadata-Version: 2.1
+Name: halo_analysis
+Version: 1.0.0
+Summary: read and analyze halo/galaxy catalogs
+Author: Shea Garrison-Kimmel, Zach Hafen, Nico Garavito-Camargo
+Author-email: Andrew Wetzel <arwezel@gmail.com>
+Maintainer-email: Andrew Wetzel <arwetzel@gmail.com>
+License: Copiright 2014-2024 by Andrew Wetzel <arwetzel@gmail.com>, Shea Garrison-Kimmel, Zach Hafen, Nico Garavito-Camargo
+        
+        If you use this package, please cite it, along the lines of: 'This work used HaloAnalysis (http://ascl.net/2002.014), which first was used in Wetzel et al 2016 (https://ui.adsabs.harvard.edu/abs/2016ApJ...827L..23W).'
+        
+        You are free to use, edit, share, and do whatever you want. But please cite it and report bugs!
+        
+        Less succinctly, this software is governed by the MIT License:
+        
+        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 aAUTHORS 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.\href{https://github.com/jngaravitoc/nba}{NBA}, Cranes. 
+        
+Project-URL: Repository, https://bitbucket.org/awetzel/halo_analysis/src/master/
+Project-URL: Issues, https://bitbucket.org/awetzel/halo_analysis/issues?status=new&status=open&status=submitted
+Keywords: gizmo,astronomy,astrophysics,cosmology,galaxies,stars,dark matter
+Classifier: Programming Language :: Python :: 3
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Topic :: Scientific/Engineering :: Astronomy
+Classifier: Development Status :: 4 - Beta
+Classifier: Operating System :: OS Independent
+Requires-Python: >=3.8
+Description-Content-Type: text/markdown
+License-File: LICENSE.md
+Requires-Dist: numpy>=1.22.2
+Requires-Dist: scipy>=1.13.1
+Requires-Dist: h5py>=3.9.0
+Requires-Dist: matplotlib>=3.8
+Requires-Dist: utilities-awetzel>=1.0
+
+# Description
+
+Python package to read and analyze halo/galaxy catalogs (generated from Rockstar or AHF) and merger trees (generated from ConsistentTrees).
+
+
+---
+# Requirements
+
+python 3, numpy, scipy, h5py, matplotlib
+
+This package also requires the [utilities/](https://bitbucket.org/awetzel/utilities) python package for low-level utility functions.
+
+
+---
+# Contents
+
+## halo_analysis
+
+### halo_io.py
+* read halo files, convert from text to hdf5 format, assign particle species to dark-matter halos
+
+### halo_plot.py
+* analyze and plot halos/galaxies
+
+### halo_select.py
+* select halos from large simulations for generating initial conditions for zoom-in
+
+## tutorials
+
+### halo_tutorial.ipynb
+* Jupyter notebook tutorial for using this package
+
+## data
+
+### snapshot_times.txt
+* example file for storing information about snapshots: scale-factors, redshifts, times, etc
+
+
+---
+# Units
+
+Unless otherwise noted, this package stores all quantities in (combinations of) these base units
+* mass [M_sun]
+* position [kpc comoving]
+* distance, radius [kpc physical]
+* time [Gyr]
+* temperature [K]
+* magnetic field [Gauss]
+* elemental abundance [linear mass fraction]
+
+These are the common exceptions to those standards
+* velocity [km/s]
+* acceleration [km/s / Gyr]
+* gravitational potential [km^2 / s^2]
+* rates (star formation, cooling, accretion) [M_sun / yr]
+* metallicity (if converted from stored massfraction) [log10(mass_fraction / mass_fraction_solar)], using Asplund et al 2009 for Solar
+
+
+---
+# Installing
+
+The easiest way to install the analysis code and all dependencies is by using `pip` or conda.
+
+```
+python -m pip install halo_analysis
+
+```
+
+To install from source, clone the latest version of `gizmo_analysis` from `bitbucket` using `git`:
+
+```
+git clone git://bitbucket.org/awetzel/halo_analysis.git
+``` 
+
+To build and install the project, inside the cloned `halo_analysis` directory:
+
+```
+python -m pip install .
+```
+
+
+---
+# Using
+
+Once installed, you can use individual modules like this:
+
+```
+import halo_analysis
+halo_analysis.halo_io
+```
+
+or more succinctly like this
+
+```
+import halo_analysis as halo
+halo.io
+```
+
+
+---
+# Citing
+
+If you use this package, please cite it, along the lines of: 'This work used HaloAnalysis (http://ascl.net/2002.014), which first was used in Wetzel et al 2016 (https://ui.adsabs.harvard.edu/abs/2016ApJ...827L..23W).'

halo_analysis-1.0.0/README.md

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+# Description
+
+Python package to read and analyze halo/galaxy catalogs (generated from Rockstar or AHF) and merger trees (generated from ConsistentTrees).
+
+
+---
+# Requirements
+
+python 3, numpy, scipy, h5py, matplotlib
+
+This package also requires the [utilities/](https://bitbucket.org/awetzel/utilities) python package for low-level utility functions.
+
+
+---
+# Contents
+
+## halo_analysis
+
+### halo_io.py
+* read halo files, convert from text to hdf5 format, assign particle species to dark-matter halos
+
+### halo_plot.py
+* analyze and plot halos/galaxies
+
+### halo_select.py
+* select halos from large simulations for generating initial conditions for zoom-in
+
+## tutorials
+
+### halo_tutorial.ipynb
+* Jupyter notebook tutorial for using this package
+
+## data
+
+### snapshot_times.txt
+* example file for storing information about snapshots: scale-factors, redshifts, times, etc
+
+
+---
+# Units
+
+Unless otherwise noted, this package stores all quantities in (combinations of) these base units
+* mass [M_sun]
+* position [kpc comoving]
+* distance, radius [kpc physical]
+* time [Gyr]
+* temperature [K]
+* magnetic field [Gauss]
+* elemental abundance [linear mass fraction]
+
+These are the common exceptions to those standards
+* velocity [km/s]
+* acceleration [km/s / Gyr]
+* gravitational potential [km^2 / s^2]
+* rates (star formation, cooling, accretion) [M_sun / yr]
+* metallicity (if converted from stored massfraction) [log10(mass_fraction / mass_fraction_solar)], using Asplund et al 2009 for Solar
+
+
+---
+# Installing
+
+The easiest way to install the analysis code and all dependencies is by using `pip` or conda.
+
+```
+python -m pip install halo_analysis
+
+```
+
+To install from source, clone the latest version of `gizmo_analysis` from `bitbucket` using `git`:
+
+```
+git clone git://bitbucket.org/awetzel/halo_analysis.git
+``` 
+
+To build and install the project, inside the cloned `halo_analysis` directory:
+
+```
+python -m pip install .
+```
+
+
+---
+# Using
+
+Once installed, you can use individual modules like this:
+
+```
+import halo_analysis
+halo_analysis.halo_io
+```
+
+or more succinctly like this
+
+```
+import halo_analysis as halo
+halo.io
+```
+
+
+---
+# Citing
+
+If you use this package, please cite it, along the lines of: 'This work used HaloAnalysis (http://ascl.net/2002.014), which first was used in Wetzel et al 2016 (https://ui.adsabs.harvard.edu/abs/2016ApJ...827L..23W).'

halo_analysis-1.0.0/halo_analysis/__init__.py

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+from . import halo_default as default
+from . import halo_io as io
+from . import halo_plot as plot
+from . import halo_select as select

halo_analysis-1.0.0/halo_analysis/halo_default.py

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+'''
+Default names and values for files and directories used throughout this package.
+If you prefer a different default, change it here, and it should propagate througout the package.
+Some names have wildcards, such as '*', or '!', these represent name bases, generally for finding
+any/all such files in a directory via glob.
+
+@author: Andrew Wetzel <arwetzel@gmail.com>
+'''
+
+# base directory of a simulation
+# setting to '.' assumes that you are running analysis from within a simulation directory
+simulation_directory = '.'
+
+# directory of all halo files, typically the first directory within simulation_directory
+halo_directory = 'halo/'
+
+# directory of all rockstar files (needs to include root halo_directory if within it)
+rockstar_directory = halo_directory + 'rockstar_dm/'
+
+# directory of rockstar raw text files, within rockstar_directory
+rockstar_catalog_directory = 'catalog/'
+
+# directory of rockstar processed hdf5 files, within rockstar_directory
+rockstar_catalog_hdf5_directory = 'catalog_hdf5/'
+
+# directory of rockstar processed hdf5 files
+rockstar_job_directory = 'rockstar_jobs/'