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Merge pull request #80 from rseng/update/analysis-2023-07-19
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Update from update/analysis-2023-07-19
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vsoch committed Jul 19, 2023
2 parents 0797656 + 2dcc65b commit 5a111c2
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10 changes: 5 additions & 5 deletions _data/language_counts.json
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@@ -1,21 +1,21 @@
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"unknown": 163,
"Python": 1965,
"Jupyter Notebook": 389,
"Python": 1970,
"Jupyter Notebook": 392,
"Modelica": 1,
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"HTML": 81,
"Perl": 45,
"R": 624,
"C++": 524,
"C++": 527,
"Java": 100,
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"C": 310,
"Rust": 28,
"JavaScript": 78,
"AMPL": 1,
"MATLAB": 38,
"Haskell": 2,
"Fortran": 138,
"Fortran": 139,
"Clojure": 4,
"Groovy": 6,
"E": 1,
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83 changes: 79 additions & 4 deletions _data/repos.json
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Expand Up @@ -17952,7 +17952,43 @@
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"github/EdanRein/pyPplusS": [],
"github/cconroy20/alf": [],
"github/mtceballos/SIRENAdoc": []
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"github/fgbuster/fgbuster": [],
"github/Extraweich/homopy": [],
"github/eXtremeGravityInstitute/LISA-Massive-Black-Hole": [],
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"github/taxprofiler/taxpasta": [
"metagenomics",
"python",
"standardisation",
"bioinformatics",
"profiling",
"classification",
"metagenomic-classification",
"taxonomic-classifications",
"taxonomic-profiling"
],
"github/lgbouma/gyro-interp": [],
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"science-research",
"tides",
"exoplanets",
"planetary-science",
"orbital-mechanics",
"orbital-dynamics"
],
"github/marbl/MashMap": [],
"github/geodynamics/burnman": [],
"github/QuaCaTeam/quaca": [
"physics",
"fluctuations",
"integration",
"casimir",
"quantum"
]
},
"language": {
"gitlab/chiemotono/mdcontactcom": "unknown",
Expand Down Expand Up @@ -22882,7 +22918,20 @@
"github/JulianBMunoz/RelicFast": "C",
"github/EdanRein/pyPplusS": "Python",
"github/cconroy20/alf": "Fortran",
"github/mtceballos/SIRENAdoc": "HTML"
"github/mtceballos/SIRENAdoc": "HTML",
"github/ulebreui/shark": "Fortran",
"github/oliverphilcox/PolyBin": "Jupyter Notebook",
"github/fgbuster/fgbuster": "Python",
"github/Extraweich/homopy": "Python",
"github/eXtremeGravityInstitute/LISA-Massive-Black-Hole": "C",
"github/DMGW-Goethe/imripy": "Jupyter Notebook",
"github/hpc4cmb/toast": "C++",
"github/taxprofiler/taxpasta": "Python",
"github/lgbouma/gyro-interp": "Python",
"github/jrenaud90/TidalPy": "Jupyter Notebook",
"github/marbl/MashMap": "C++",
"github/geodynamics/burnman": "Python",
"github/QuaCaTeam/quaca": "C++"
},
"url": {
"gitlab/chiemotono/mdcontactcom": "https://gitlab.com/chiemotono/mdcontactcom",
Expand Down Expand Up @@ -27812,7 +27861,20 @@
"github/JulianBMunoz/RelicFast": "https://github.com/JulianBMunoz/RelicFast",
"github/EdanRein/pyPplusS": "https://github.com/EdanRein/pyPplusS",
"github/cconroy20/alf": "https://github.com/cconroy20/alf",
"github/mtceballos/SIRENAdoc": "https://github.com/mtceballos/SIRENAdoc"
"github/mtceballos/SIRENAdoc": "https://github.com/mtceballos/SIRENAdoc",
"github/ulebreui/shark": "https://github.com/ulebreui/shark",
"github/oliverphilcox/PolyBin": "https://github.com/oliverphilcox/PolyBin",
"github/fgbuster/fgbuster": "https://github.com/fgbuster/fgbuster",
"github/Extraweich/homopy": "https://github.com/Extraweich/homopy",
"github/eXtremeGravityInstitute/LISA-Massive-Black-Hole": "https://github.com/eXtremeGravityInstitute/LISA-Massive-Black-Hole",
"github/DMGW-Goethe/imripy": "https://github.com/DMGW-Goethe/imripy",
"github/hpc4cmb/toast": "https://github.com/hpc4cmb/toast",
"github/taxprofiler/taxpasta": "https://github.com/taxprofiler/taxpasta",
"github/lgbouma/gyro-interp": "https://github.com/lgbouma/gyro-interp",
"github/jrenaud90/TidalPy": "https://github.com/jrenaud90/TidalPy",
"github/marbl/MashMap": "https://github.com/marbl/MashMap",
"github/geodynamics/burnman": "https://github.com/geodynamics/burnman",
"github/QuaCaTeam/quaca": "https://github.com/QuaCaTeam/quaca"
},
"description": {
"gitlab/chiemotono/mdcontactcom": "",
Expand Down Expand Up @@ -32742,6 +32804,19 @@
"github/JulianBMunoz/RelicFast": "Code to find scale-dependent halo bias quickly and accurately",
"github/EdanRein/pyPplusS": "pyPplusS code package for modeling exoplanets with rings",
"github/cconroy20/alf": "Absorption Line Fitter",
"github/mtceballos/SIRENAdoc": "SIRENA documentation"
"github/mtceballos/SIRENAdoc": "SIRENA documentation",
"github/ulebreui/shark": "This is the public repository of the shark code (Lebreuilly et al., 2023)",
"github/oliverphilcox/PolyBin": "Binned polyspectrum estimation on the full sky, optionally polarized and mask-deconvolved",
"github/fgbuster/fgbuster": "Parametric component separation for Cosmic Microwave Background observations",
"github/Extraweich/homopy": "Your solution for stiffness problems",
"github/eXtremeGravityInstitute/LISA-Massive-Black-Hole": null,
"github/DMGW-Goethe/imripy": "A python code able to simulate Intermediate Mass Ratio Inspirals (IMRI)",
"github/hpc4cmb/toast": "Time Ordered Astrophysics Scalable Tools",
"github/taxprofiler/taxpasta": "TAXnomic Profile Aggregation and STAndardisation",
"github/lgbouma/gyro-interp": "Gyrochronology via interpolation of open cluster rotation sequences.",
"github/jrenaud90/TidalPy": "Software suite to perform solid-body tidal dissipation calculations for rocky and icy worlds",
"github/marbl/MashMap": "A fast approximate aligner for long DNA sequences",
"github/geodynamics/burnman": "BurnMan is a library for modeling mantle thermodynamics and thermoelasticity constrained by mineral physics experiments.",
"github/QuaCaTeam/quaca": "QuaCa is an open-source library which provides fast calculations of nonequilibrium atom-surface interactions."
}
}
2 changes: 1 addition & 1 deletion _data/repos_counts_languages.json
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@@ -1,5 +1,5 @@
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"Python": 5345,
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"Js": 1537,
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6 changes: 3 additions & 3 deletions _data/stats.json
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@@ -1,9 +1,9 @@
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}
20 changes: 20 additions & 0 deletions _repos/github/DMGW-Goethe/imripy/README.md
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---
title: github/DMGW-Goethe/imripy
layout: repo
tipue_search_active: true
exclude_from_search: true
---
# Software Credit

|Manager|Name|Credit|
|-------|----|------|
|setup.py|github/DMGW-Goethe/imripy|0.01|
|pypi|[numpy](https://www.numpy.org)|0.007|
|pypi|[scipy](https://www.scipy.org)|0.003|
|pypi|[matplotlib](https://matplotlib.org)|0.003|


> Note that credit values are rounded and expanded (so shared dependencies are represented as one record) and may not add to 1.0. Rounded values that hit zero are removed.

- Generated by [CiteLang](https://github.com/vsoch/citelang)
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22 changes: 22 additions & 0 deletions _repos/github/DMGW-Goethe/imripy/data.json
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@@ -0,0 +1,22 @@
{
"setup.py": {
"github/DMGW-Goethe/imripy": {
"credit": 0.01,
"url": null
}
},
"pypi": {
"numpy": {
"credit": 0.006567,
"url": "https://www.numpy.org"
},
"scipy": {
"credit": 0.0033000000000000004,
"url": "https://www.scipy.org"
},
"matplotlib": {
"credit": 0.0033000000000000004,
"url": "https://matplotlib.org"
}
}
}
63 changes: 63 additions & 0 deletions _repos/github/DMGW-Goethe/imripy/setup.py
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"""A setuptools based setup module.
See:
https://packaging.python.org/guides/distributing-packages-using-setuptools/
https://github.com/pypa/sampleproject
"""

from setuptools import setup, find_packages
import pathlib

here = pathlib.Path(__file__).parent.resolve()

long_description = (here / 'README.md').read_text(encoding='utf-8')


setup(
name='imripy', # Required
version='0.5.0', # Required

description='A python project to calulcate the physics of an Intermediate Mass Ratio Inspiral', # Optional

long_description=long_description, # Optional
long_description_content_type='text/markdown', # Optional (see note above)

# url='https://github.com/LauraSagunski/DM-density-spikes-GWs-BH-shadows', # Optional

author='Niklas Becker', # Optional

author_email='nbecker@itp.uni-frankfurt.de', # Optional

classifiers=[
'Development Status :: 3 - Alpha',

# Indicate who your project is intended for
'Intended Audience :: Researchers',
'Topic :: Physics Sim',

# Pick your license as you wish
'License :: MIT License',

'Programming Language :: Python :: 3',
'Programming Language :: Python :: 3.6',
'Programming Language :: Python :: 3.7',
'Programming Language :: Python :: 3.8',
'Programming Language :: Python :: 3.9',
'Programming Language :: Python :: 3 :: Only',
],


keywords='simulation, physics, gravitational waves', # Optional

# When your source code is in a subdirectory under the project root, e.g.
# `src/`, it is necessary to specify the `package_dir` argument.
package_dir={'': 'src'}, # Optional


packages=find_packages(where='src'), # Required

python_requires='>=3.6, <4',

install_requires=['numpy', 'scipy', 'matplotlib'], # Optional

)

20 changes: 20 additions & 0 deletions _repos/github/Extraweich/homopy/README.md
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---
title: github/Extraweich/homopy
layout: repo
tipue_search_active: true
exclude_from_search: true
---
# Software Credit

|Manager|Name|Credit|
|-------|----|------|
|setup.py|github/Extraweich/homopy|0.01|
|pypi|[numpy](https://www.numpy.org)|0.007|
|pypi|[matplotlib](https://matplotlib.org)|0.003|
|pypi|[scipy](https://www.scipy.org)|0.003|


> Note that credit values are rounded and expanded (so shared dependencies are represented as one record) and may not add to 1.0. Rounded values that hit zero are removed.

- Generated by [CiteLang](https://github.com/vsoch/citelang)
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22 changes: 22 additions & 0 deletions _repos/github/Extraweich/homopy/data.json
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{
"setup.py": {
"github/Extraweich/homopy": {
"credit": 0.01,
"url": null
}
},
"pypi": {
"numpy": {
"credit": 0.006567,
"url": "https://www.numpy.org"
},
"matplotlib": {
"credit": 0.0033000000000000004,
"url": "https://matplotlib.org"
},
"scipy": {
"credit": 0.0033000000000000004,
"url": "https://www.scipy.org"
}
}
}
23 changes: 23 additions & 0 deletions _repos/github/Extraweich/homopy/setup.py
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import setuptools

with open("README.md", "r") as fh:
long_description = fh.read()


setuptools.setup(
name="homopy",
version="1.1.0",
author="Nicolas Christ",
author_email="nicolas.christ@kit.edu",
description="Your solution for stiffness problems",
long_description=long_description,
long_description_content_type="text/markdown",
url="https://github.com/Extraweich/homopy",
packages=["homopy"],
install_requires=["numpy", "matplotlib", "scipy"],
classifiers=[
"Programming Language :: Python :: 3",
"License :: OSI Approved :: MIT License",
"Operating System :: OS Independent",
],
)
2 changes: 1 addition & 1 deletion _repos/github/PDB-REDO/libcifpp/CMakeLists.txt
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Expand Up @@ -458,7 +458,7 @@ endif()

# Optionally install the update scripts for CCD and dictionary files
if(CIFPP_INSTALL_UPDATE_SCRIPT)
if(${CMAKE_SYSTEM_NAME} STREQUAL "Linux")
if(${CMAKE_SYSTEM_NAME} STREQUAL "Linux" OR ${CMAKE_SYSTEM_NAME} STREQUAL "GNU")
set(CIFPP_CRON_DIR "${CIFPP_ETC_DIR}/cron.weekly")
elseif(UNIX) # assume all others are like FreeBSD...
set(CIFPP_CRON_DIR "${CIFPP_ETC_DIR}/periodic/weekly")
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48 changes: 48 additions & 0 deletions _repos/github/QuaCaTeam/quaca/CMakeLists.txt
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cmake_minimum_required(VERSION 3.7.2)
project(QuaCa VERSION 1.0.0 LANGUAGES CXX)

# set c++ standard
set(CMAKE_CXX_STANDARD 14)

# set general compiler flags
set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -O3")
set(CMAKE_CXX_FLAGS_DEBUG "${CMAKE_CXX_FLAGS_DEBUG} -Wall -Werror -Wpedantic")

# define output directories for library files and binaries
set(CMAKE_LIBRARY_OUTPUT_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}/lib)
set(CMAKE_ARCHIVE_OUTPUT_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}/lib)
set(CMAKE_RUNTIME_OUTPUT_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}/bin)

# find boost libraries
set(Boost_NO_BOOST_CMAKE ON)
find_package(Boost COMPONENTS program_options filesystem system REQUIRED)
include_directories(${Boost_INCLUDE_DIRS})

# find gsl
find_package(GSL REQUIRED)
include_directories(${GSL_INCLUDE_DIRS})

# find lapack and use armadillo without runtimelibrary, so that it wraps blas and lapack
find_package(LAPACK REQUIRED)
find_package(BLAS REQUIRED)
set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -DARMA_DONT_USE_WRAPPER")

#find OpenMP library
find_package(OpenMP REQUIRED)
#add -fopenmp to the cxx_flags
set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${OpenMP_CXX_FLAGS}")

# set include directories
include_directories(
${PROJECT_SOURCE_DIR}/include
${PROJECT_SOURCE_DIR}/include/armadillo-9.870.2/include
)

# catch2
add_library(catch2 INTERFACE)
target_include_directories(catch2 INTERFACE ${PROJECT_SOURCE_DIR}/include)

# Subdirectories
add_subdirectory(src)
add_subdirectory(app)
add_subdirectory(test)
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