diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml new file mode 100644 index 0000000..92dd368 --- /dev/null +++ b/.github/workflows/build.yml @@ -0,0 +1,94 @@ +name: "Test Ubuntu Build" + +on: + push: + branches: + - main + pull_request: + +jobs: + pyexp: + strategy: + matrix: + os: [ubuntu-latest] + cc: [gcc, mpicc] + + name: "Test pyEXP Build" + runs-on: ${{ matrix.os }} + steps: + - name: Checkout + uses: actions/checkout@v3 + + - name: Install core dependencies - ubuntu + if: runner.os == 'Linux' + run: | + sudo apt-get update + sudo apt-get install -y build-essential libeigen3-dev libfftw3-dev libhdf5-dev libopenmpi-dev + + - name: Setup submodule and build + run: | + git submodule update --init --recursive + mkdir -p build/install + + - name: Compile pyEXP - Linux + if: runner.os == 'Linux' + env: + CC: ${{ matrix.cc }} + working-directory: ./build + run: >- + cmake + -DENABLE_NBODY=NO + -DENABLE_PYEXP=YES + -DCMAKE_BUILD_TYPE=Release + -DEigen3_DIR=/usr/include/eigen3/share/eigen3/cmake + -DCMAKE_INSTALL_PREFIX=./install + -Wno-dev + .. + + - name: Make + working-directory: ./build + run: make -j 2 + + # ----------------------------------------------------------------------------------- + + exp: + strategy: + matrix: + os: [ubuntu-latest] + cc: [gcc, mpicc] + + name: "Test Full EXP Build" + runs-on: ${{ matrix.os }} + steps: + - name: Checkout + uses: actions/checkout@v3 + + - name: Install core dependencies - ubuntu + if: runner.os == 'Linux' + run: | + sudo apt-get update + sudo apt-get install -y build-essential libeigen3-dev libfftw3-dev libhdf5-dev libopenmpi-dev + + - name: Setup submodule and build + run: | + git submodule update --init --recursive + mkdir -p build/install + + - name: Compile Full EXP - Linux + if: runner.os == 'Linux' + env: + CC: ${{ matrix.cc }} + working-directory: ./build + run: >- + cmake + -DENABLE_NBODY=YES + -DENABLE_PYEXP=NO + -DCMAKE_BUILD_TYPE=Release + -DEigen3_DIR=/usr/include/eigen3/share/eigen3/cmake + -DCMAKE_INSTALL_PREFIX=./install + -Wno-dev + .. + + - name: Make + working-directory: ./build + run: make -j 2 diff --git a/.github/workflows/python-package.yml b/.github/workflows/python-package.yml new file mode 100644 index 0000000..841659e --- /dev/null +++ b/.github/workflows/python-package.yml @@ -0,0 +1,41 @@ +# This workflow will install Python dependencies, run tests and lint with a variety of Python versions +# For more information see: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-python + +name: Python package + +on: + push: + branches: [ "main" ] + pull_request: + branches: [ "main" ] + +jobs: + build: + + runs-on: ubuntu-latest + strategy: + fail-fast: false + matrix: + python-version: ["3.9", "3.10", "3.11"] + + steps: + - uses: actions/checkout@v3 + - name: Set up Python ${{ matrix.python-version }} + uses: actions/setup-python@v3 + with: + python-version: ${{ matrix.python-version }} + - name: Install dependencies + run: | + python -m pip install --upgrade pip + python -m pip install flake8 pytest + if [ -f requirements.txt ]; then pip install -r requirements.txt; fi + - name: Lint with flake8 + run: | + # stop the build if there are Python syntax errors or undefined names + flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics + # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide + flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics + # Tests not working at the moment -- pyEXP requirement! + #- name: Test with pytest + # run: | + # pytest diff --git a/EXP_tools/__init__.py b/EXP_tools/__init__.py deleted file mode 100755 index 11c9ca6..0000000 --- a/EXP_tools/__init__.py +++ /dev/null @@ -1,3 +0,0 @@ -from . import visualize -from . import makemodel -from . import basis_utils diff --git a/EXP_tools/makemodel.py b/EXP_tools/makemodel.py deleted file mode 100644 index 31a1ba8..0000000 --- a/EXP_tools/makemodel.py +++ /dev/null @@ -1,172 +0,0 @@ -import numpy as np - -def makemodel(func,M,funcargs,rvals = 10.**np.linspace(-2.,4.,2000),pfile='',plabel = '',verbose=True): - """make an EXP-compatible spherical basis function table - - inputs - ------------- - func : (function) the callable functional form of the density - M : (float) the total mass of the model, sets normalisations - funcargs : (list) a list of arguments for the density function. - rvals : (array of floats) radius values to evaluate the density function - pfile : (string) the name of the output file. If '', will not print file - plabel : (string) comment string - verbose : (boolean) - - outputs - ------------- - R : (array of floats) the radius values - D : (array of floats) the density - M : (array of floats) the mass enclosed - P : (array of floats) the potential - - """ - - R = np.nanmax(rvals) - - # query out the density values - dvals = func(rvals,*funcargs) - - # make the mass and potential arrays - mvals = np.zeros(dvals.size) - pvals = np.zeros(dvals.size) - pwvals = np.zeros(dvals.size) - - # initialise the mass enclosed an potential energy - mvals[0] = 1.e-15 - pwvals[0] = 0. - - # evaluate mass enclosed and potential energy by recursion - for indx in range(1,dvals.size): - mvals[indx] = mvals[indx-1] +\ - 2.0*np.pi*(rvals[indx-1]*rvals[indx-1]*dvals[indx-1] +\ - rvals[indx]*rvals[indx]*dvals[indx])*(rvals[indx] - rvals[indx-1]); - pwvals[indx] = pwvals[indx-1] + \ - 2.0*np.pi*(rvals[indx-1]*dvals[indx-1] + rvals[indx]*dvals[indx])*(rvals[indx] - rvals[indx-1]); - - # evaluate potential (see theory document) - pvals = -mvals/(rvals+1.e-10) - (pwvals[dvals.size-1] - pwvals) - - # get the maximum mass and maximum radius - M0 = mvals[dvals.size-1] - R0 = rvals[dvals.size-1] - - # compute scaling factors - Beta = (M/M0) * (R0/R); - Gamma = np.sqrt((M0*R0)/(M*R)) * (R0/R); - if verbose: - print("! Scaling: R=",R," M=",M) - - rfac = np.power(Beta,-0.25) * np.power(Gamma,-0.5); - dfac = np.power(Beta,1.5) * Gamma; - mfac = np.power(Beta,0.75) * np.power(Gamma,-0.5); - pfac = Beta; - - if verbose: - print(rfac,dfac,mfac,pfac) - - # save file if desired - if pfile != '': - f = open(pfile,'w') - print('! ',plabel,file=f) - print('! R D M P',file=f) - - print(rvals.size,file=f) - - for indx in range(0,rvals.size): - print('{0} {1} {2} {3}'.format( rfac*rvals[indx],\ - dfac*dvals[indx],\ - mfac*mvals[indx],\ - pfac*pvals[indx]),file=f) - - f.close() - - return rvals*rfac,dfac*dvals,mfac*mvals,pfac*pvals - - - -def powerhalo(r,rs=1.,rc=0.,alpha=1.,beta=1.e-7): - """return generic twopower law distribution - - inputs - ---------- - r : (float) radius values - rs : (float, default=1.) scale radius - rc : (float, default=0. i.e. no core) core radius - alpha : (float, default=1.) inner halo slope - beta : (float, default=1.e-7) outer halo slope - - returns - ---------- - densities evaluated at r - - notes - ---------- - different combinations are known distributions. - alpha=1,beta=2 is NFW - alpha=1,beta=3 is Hernquist - alpha=2.5,beta=0 is a typical single power law halo - - - """ - ra = r/rs - return 1./(((ra+rc/rs)**alpha)*((1+ra)**beta)) - - -def powerhalorolloff(r,rs=1.,rc=0.,alpha=1.,beta=1.e-7): - """return generic twopower law distribution with an erf rolloff - - inputs - ---------- - r : (float) radius values - rs : (float, default=1.) scale radius - rc : (float, default=0. i.e. no core) core radius - alpha : (float, default=1.) inner halo slope - beta : (float, default=1.e-7) outer halo slope - - returns - ---------- - densities evaluated at r - - notes - ---------- - different combinations are known distributions. - alpha=1,beta=2 is NFW - alpha=1,beta=3 is Hernquist - alpha=2.5,beta=0 is a typical single power law halo - - - """ - ra = r/rs - dens = 1./(((ra+rc/rs)**alpha)*((1+ra)**beta)) - rtrunc = 25*rs - wtrunc = rtrunc*0.2 - rolloff = 0.5 - 0.5*special.erf((r-rtrunc)/wtrunc) - return dens*rolloff - - -def plummer_density(radius,scale_radius=1.0,mass=1.0,astronomicalG=1.0): - """basic plummer density profile""" - return ((3.0*mass)/(4*np.pi))*(scale_radius**2.)*((scale_radius**2 + radius**2)**(-2.5)) - -def twopower_density_withrolloff(r,a,alpha,beta,rcen,wcen): - """a twopower density profile""" - ra = r/a - prefac = 0.5*(1.-scipy.special.erf((ra-rcen)/wcen)) - return prefac*(ra**-alpha)*(1+ra)**(-beta+alpha) - -def hernquist_halo(r, a): - return 1 / ( 2*np.pi * (r/a) * (1 + r/a)**3) - - -""" -plummer_b = 1.0 -R,D,M,P = makemodel(plummer_density,1.,[plummer_b],rvals = 10.**np.linspace(-3.,1.,2000)) - -alpha=1 -beta=2 -concentration = 15. -rs = 1/concentration -rc = 0.0001 -R,D,M,P = makemodel(powerhalo,1.,[rs,rc,alpha,beta],rvals = 10.**np.linspace(-5.,0.3,2000)pfile='NFWModelc{}.txt'.format(concentration),plabel = 'NFWModelc{}.txt'.format(concentration)) -""" \ No newline at end of file diff --git a/EXPtools/__init__.py b/EXPtools/__init__.py new file mode 100755 index 0000000..372e92d --- /dev/null +++ b/EXPtools/__init__.py @@ -0,0 +1,2 @@ +from . import visuals +from . import basis_builder diff --git a/EXPtools/basis_builder/__init__.py b/EXPtools/basis_builder/__init__.py new file mode 100644 index 0000000..d07fca5 --- /dev/null +++ b/EXPtools/basis_builder/__init__.py @@ -0,0 +1,5 @@ +from . import makemodel +from . import profiles +from .makemodel import makemodel +from .profiles import Profiles +from .basis_utils import makebasis diff --git a/EXP_tools/basis_utils.py b/EXPtools/basis_builder/basis_utils.py similarity index 95% rename from EXP_tools/basis_utils.py rename to EXPtools/basis_builder/basis_utils.py index f1d70d5..0afd0d0 100644 --- a/EXP_tools/basis_utils.py +++ b/EXPtools/basis_builder/basis_utils.py @@ -1,7 +1,6 @@ import os, sys, pickle, pyEXP import numpy as np -import makemodel -from makemodel import hernquist_halo +from . import makemodel def make_config(basis_id, numr, rmin, rmax, lmax, nmax, scale, modelname='', cachename='.slgrid_sph_cache'): @@ -206,9 +205,9 @@ def make_exp_basis_table(radius, density, outfile='', plabel='', return rvals*rfac, dfac*dvals, mfac*mvals, pfac*pvals -def make_a_BFE(pos, mass, config=None, basis_id='sphereSL', time=0, +def makebasis(pos, mass, basis_model, config=None, basis_id='sphereSL', time=0, numr=500, rmin=0.61, rmax=599, lmax=4, nmax=20, scale=22.5, - modelname='dens_table.txt', cachename='.slgrid_sph_cache', add_coef = False, coef_file='', empirical=False): + modelname='dens_table.txt', cachename='.slgrid_sph_cache', add_coef = False, coef_file=''): """ Create a BFE expansion for a given set of particle positions and masses. @@ -217,6 +216,7 @@ def make_a_BFE(pos, mass, config=None, basis_id='sphereSL', time=0, and each column represents the coordinate of that particle. mass (numpy.ndarray): The masses of particles. The length of this array should be the same as the number of particles. + basismodel (): config (pyEXP.config.Config, optional): A configuration object that specifies the basis set. If not provided, an empirical density profile will be computed and a configuration object will be created automatically. @@ -239,16 +239,20 @@ def make_a_BFE(pos, mass, config=None, basis_id='sphereSL', time=0, The basis is an instance of pyEXP.basis.Basis, and the coefficients are an instance of pyEXP.coefs.Coefs. """ - + """ if os.path.isfile(modelname) == False: print("-> File model not found so we are computing one \n") if empirical == True: print('-> Computing empirical model') rad, rho = empirical_density_profile(pos, mass, nbins=numr) - R, D, M, P = makemodel_empirical(r_exact, rho, outfile=modelname, return_values=True) elif empirical == False: + makemodel.hernquist_halo() + + makemodel.Profiles(density_profile) + + R, D, M, P = makemodel.makemodel(rvals=np.logspace(np.log10(rmin), np.log10(rmax), numr), rho, outfile=modelname, return_values=True) print('-> Computing analytical Hernquist model') - R, D, M, P = makemodel.makemodel(hernquist_halo, 1, [scale], rvals=np.logspace(np.log10(rmin), np.log10(rmax), numr), pfile=modelname) + R, D, M, P = makemodel.makemodel(hernquist_halo, 1, [scale], rvals=, pfile=modelname) print('-> Model computed: rmin={}, rmax={}, numr={}'.format(R[0], R[-1], len(R))) else: R, D, M, P = np.loadtxt(modelname, skiprows=3, unpack=True) @@ -278,4 +282,5 @@ def make_a_BFE(pos, mass, config=None, basis_id='sphereSL', time=0, coefs.ExtendH5Coefs(coef_file) return basis, coefs - + """ + return None diff --git a/EXPtools/basis_builder/makemodel.py b/EXPtools/basis_builder/makemodel.py new file mode 100644 index 0000000..6489ce4 --- /dev/null +++ b/EXPtools/basis_builder/makemodel.py @@ -0,0 +1,104 @@ +""" +TODO: +""" + +import numpy as np + + +def makemodel(dvals, rvals, M, unit_physical=False, return_val=False, + pfile='', plabel = '', verbose=True): + """ + Make an EXP-compatible spherical basis function table + + inputs + ------------- + basis_type : (str) + func : (function) the callable functional form of the density + M : (float) the total mass of the model, sets normalisations + funcargs : (list) a list of arguments for the density function. + rvals : (array of floats) radius values to evaluate the density function + = 10.**np.linspace(-2.,4.,2000) + pfile : (string) the name of the output file. If '', will not print file + plabel : (string) comment string + verbose : (boolean) + + outputs + ------------- + R : (array of floats) the radius values + D : (array of floats) the density + M : (array of floats) the mass enclosed + P : (array of floats) the potential + + """ + + R = np.nanmax(rvals) + + # query out the density values + + # make the mass and potential arrays + mvals = np.zeros(dvals.size) + pvals = np.zeros(dvals.size) + pwvals = np.zeros(dvals.size) + + # initialise the mass enclosed an potential energy + mvals[0] = 1.e-15 + pwvals[0] = 0. + + # evaluate mass enclosed and potential energy by recursion + for indx in range(1,dvals.size): + mvals[indx] = mvals[indx-1] +\ + 2.0*np.pi*(rvals[indx-1]*rvals[indx-1]*dvals[indx-1] +\ + rvals[indx]*rvals[indx]*dvals[indx])*(rvals[indx] - rvals[indx-1]); + pwvals[indx] = pwvals[indx-1] + \ + 2.0*np.pi*(rvals[indx-1]*dvals[indx-1] + rvals[indx]*dvals[indx])*(rvals[indx] - rvals[indx-1]); + + # evaluate potential (see theory document) + pvals = -mvals/(rvals+1.e-10) - (pwvals[dvals.size-1] - pwvals) + + # get the maximum mass and maximum radius + M0 = mvals[dvals.size-1] + R0 = rvals[dvals.size-1] + + # compute scaling factors + Beta = (M/M0) * (R0/R); + Gamma = np.sqrt((M0*R0)/(M*R)) * (R0/R); + if verbose: + print("! Scaling: R=",R," M=",M) + + rfac = np.power(Beta,-0.25) * np.power(Gamma,-0.5); + dfac = np.power(Beta,1.5) * Gamma; + mfac = np.power(Beta,0.75) * np.power(Gamma,-0.5); + pfac = Beta; + + if verbose: + print(rfac,dfac,mfac,pfac) + + # save file if desired + if pfile != '': + f = open(pfile,'w') + print('! ',plabel,file=f) + print('! R D M P',file=f) + + print(rvals.size,file=f) + + if unit_physical == True: + for indx in range(0,rvals.size): + print('{0} {1} {2} {3}'.format(rvals[indx], + dvals[indx], + mvals[indx], + pvals[indx]),file=f) + else: + for indx in range(0,rvals.size): + print('{0} {1} {2} {3}'.format(rvals[indx], + dvals[indx]*dfac, + mvals[indx]*mfac, + pvals[indx]*pfac),file=f) + + f.close() + + if return_val==True: + if unit_physical==True: + return rvals, dvals, mvals, pvals + else: + return rvals*rfac, dfac*dvals, mfac*mvals, pfac*pvals + diff --git a/EXPtools/basis_builder/profiles.py b/EXPtools/basis_builder/profiles.py new file mode 100644 index 0000000..cc7a6d2 --- /dev/null +++ b/EXPtools/basis_builder/profiles.py @@ -0,0 +1,127 @@ +import numpy as np +from scipy import special + +class Profiles: + def __init__(self, radius, scale_radius, alpha=1., beta=2.0): + """ + Class with density profiles of Dark Matter halos + + inputs + ---------- + r : (float) radius values + rs : (float, default=1.) scale radius + alpha : (float, default=1.) inner halo slope + beta : (float, default=1.e-7) outer halo slope + + notes + ---------- + different combinations are known distributions. + alpha=1,beta=2 is NFW (default) + alpha=1,beta=3 is Hernquist + alpha=2.5, beta=0 is a typical single power law halo + + """ + + self.radius = radius + self.scale_radius = scale_radius + self.alpha = alpha + self.beta = beta + self.ra = self.radius/self.scale_radius + + + def powerhalo(self, rc=0.0): + """ + Generic two power law distribution + + inputs + ---------- + rc : (float, default=0. i.e. no core) core radius + + returns + ---------- + densities evaluated at r + + notes + ---------- + different combinations are known distributions. + alpha=1,beta=2 is NFW + alpha=1,beta=3 is Hernquist + alpha=2.5,beta=0 is a typical single power law halo + + + + """ + return 1./(((self.ra+rc/self.scale_radius)**self.alpha)*((1+self.ra)**self.beta)) + + + def powerhalorolloff(self, rc=0.0): + """ + Generic twopower law distribution with an erf rolloff + + + inputs + ---------- + rc : (float, default=0. i.e. no core) core radius + + returns + ---------- + densities evaluated at r + + notes + ---------- + different combinations are known distributions. + alpha=1,beta=2 is NFW + alpha=1,beta=3 is Hernquist + alpha=2.5,beta=0 is a typical single power law halo + + + """ + dens = 1./(((self.ra+rc/self.scale_radius)**self.alpha)*((1+self.ra)**self.beta)) + rtrunc = 25*self.scale_radius + wtrunc = rtrunc*0.2 + rolloff = 0.5 - 0.5*special.erf((self.radius-rtrunc)/wtrunc) + return dens*rolloff + + + def plummer_density(self): + """ + Plummer density profile + + inputs + --------- + + + returns + ---------- + densities evaluated at r + """ + return ((3.0)/(4*np.pi))*(self.scale_radius**2.)*((self.scale_radius**2 + self.radius**2)**(-2.5)) + + def twopower_density_withrolloff(self, rcen, wcen): + """ + inputs + --------- + + + returns + ---------- + densities evaluated at r + """ + + + prefac = 0.5*(1.-special.erf((self.ra-rcen)/wcen)) + return prefac*(self.ra**-self.alpha)*(1+self.ra)**(-self.beta+self.alpha) + + def hernquist_halo(self): + """ + TODO: Do we need these profile + Hernquist halo + + inputs + --------- + + returns + ---------- + densities evaluated at r + """ + return 1 / ( 2*np.pi * (self.radius/self.scale_radius) * (1 + self.radius/self.scale_radius)**3) diff --git a/EXP_tools/visualize.py b/EXPtools/visuals/visualize.py similarity index 99% rename from EXP_tools/visualize.py rename to EXPtools/visuals/visualize.py index 8db665d..f0aae3f 100644 --- a/EXP_tools/visualize.py +++ b/EXPtools/visuals/visualize.py @@ -179,7 +179,7 @@ def return_fields_in_grid(basis, coefficients, times=[0], field_gen = pyEXP.field.FieldGenerator(times, pmin, pmax, grid) - return field_gen.volumes(basis, coefs), xgrid + return field_gen.volumes(basis, coefficients), xgrid def slice_fields(basis, coefficients, time=0, projection='XY', proj_plane=0, npoints=300, diff --git a/LICENSE b/LICENSE new file mode 100644 index 0000000..d159169 --- /dev/null +++ b/LICENSE @@ -0,0 +1,339 @@ + GNU GENERAL PUBLIC LICENSE + Version 2, June 1991 + + Copyright (C) 1989, 1991 Free Software Foundation, Inc., + 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA + Everyone is permitted to copy and distribute verbatim copies + of this license document, but changing it is not allowed. + + Preamble + + The licenses for most software are designed to take away your +freedom to share and change it. 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Of course, the commands you use may +be called something other than `show w' and `show c'; they could even be +mouse-clicks or menu items--whatever suits your program. + +You should also get your employer (if you work as a programmer) or your +school, if any, to sign a "copyright disclaimer" for the program, if +necessary. Here is a sample; alter the names: + + Yoyodyne, Inc., hereby disclaims all copyright interest in the program + `Gnomovision' (which makes passes at compilers) written by James Hacker. + + , 1 April 1989 + Ty Coon, President of Vice + +This General Public License does not permit incorporating your program into +proprietary programs. If your program is a subroutine library, you may +consider it more useful to permit linking proprietary applications with the +library. If this is what you want to do, use the GNU Lesser General +Public License instead of this License. diff --git a/README.md b/README.md index 7930a4f..a1e84df 100644 --- a/README.md +++ b/README.md @@ -1,2 +1,9 @@ -# EXP_tools -This is a shared repo with all the tools developed for cosmological+external simulations +# EXPtools +EXPtools is a Python library that contains analysis routines for [pyEXP](https://github.com/EXP-code/EXP). EXPtools was designed with the aim of analyze cosmological and idealized N-body simulations + +### Installation: + +```bash +python -m pip install . +``` +[![Python package](https://github.com/jngaravitoc/EXP_tools/actions/workflows/python-package.yml/badge.svg)](https://github.com/jngaravitoc/EXP_tools/actions/workflows/python-package.yml) diff --git a/docs/Makefile b/docs/Makefile new file mode 100644 index 0000000..d0c3cbf --- /dev/null +++ b/docs/Makefile @@ -0,0 +1,20 @@ +# Minimal makefile for Sphinx documentation +# + +# You can set these variables from the command line, and also +# from the environment for the first two. +SPHINXOPTS ?= +SPHINXBUILD ?= sphinx-build +SOURCEDIR = source +BUILDDIR = build + +# Put it first so that "make" without argument is like "make help". +help: + @$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O) + +.PHONY: help Makefile + +# Catch-all target: route all unknown targets to Sphinx using the new +# "make mode" option. $(O) is meant as a shortcut for $(SPHINXOPTS). +%: Makefile + @$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O) diff --git a/docs/make.bat b/docs/make.bat new file mode 100644 index 0000000..747ffb7 --- /dev/null +++ b/docs/make.bat @@ -0,0 +1,35 @@ +@ECHO OFF + +pushd %~dp0 + +REM Command file for Sphinx documentation + +if "%SPHINXBUILD%" == "" ( + set SPHINXBUILD=sphinx-build +) +set SOURCEDIR=source +set BUILDDIR=build + +%SPHINXBUILD% >NUL 2>NUL +if errorlevel 9009 ( + echo. + echo.The 'sphinx-build' command was not found. Make sure you have Sphinx + echo.installed, then set the SPHINXBUILD environment variable to point + echo.to the full path of the 'sphinx-build' executable. Alternatively you + echo.may add the Sphinx directory to PATH. + echo. + echo.If you don't have Sphinx installed, grab it from + echo.https://www.sphinx-doc.org/ + exit /b 1 +) + +if "%1" == "" goto help + +%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O% +goto end + +:help +%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O% + +:end +popd diff --git a/docs/source/conf.py b/docs/source/conf.py new file mode 100644 index 0000000..a9c81a6 --- /dev/null +++ b/docs/source/conf.py @@ -0,0 +1,28 @@ +# Configuration file for the Sphinx documentation builder. +# +# For the full list of built-in configuration values, see the documentation: +# https://www.sphinx-doc.org/en/master/usage/configuration.html + +# -- Project information ----------------------------------------------------- +# https://www.sphinx-doc.org/en/master/usage/configuration.html#project-information + +project = 'EXPtools' +copyright = '2023, Nicolas Garavito-Camargo' +author = 'Nicolas Garavito-Camargo' +release = '0.1' + +# -- General configuration --------------------------------------------------- +# https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration + +extensions = [] + +templates_path = ['_templates'] +exclude_patterns = [] + + + +# -- Options for HTML output ------------------------------------------------- +# https://www.sphinx-doc.org/en/master/usage/configuration.html#options-for-html-output + +html_theme = 'alabaster' +html_static_path = ['_static'] diff --git a/docs/source/index.rst b/docs/source/index.rst new file mode 100644 index 0000000..e3e81bf --- /dev/null +++ b/docs/source/index.rst @@ -0,0 +1,20 @@ +.. EXPtools documentation master file, created by + sphinx-quickstart on Sun Nov 12 12:37:16 2023. + You can adapt this file completely to your liking, but it should at least + contain the root `toctree` directive. + +Welcome to EXPtools's documentation! +==================================== + +.. toctree:: + :maxdepth: 2 + :caption: Contents: + + + +Indices and tables +================== + +* :ref:`genindex` +* :ref:`modindex` +* :ref:`search` diff --git a/setup.py b/setup.py index c81664a..64d6e2b 100755 --- a/setup.py +++ b/setup.py @@ -6,5 +6,5 @@ author="B-BFE collaboration", author_email="ngaravito@flatironinstitute.org", description="Analysis tools for EXP and other BFE packages", - packages=["EXP_tools"], + packages=["EXPtools", "EXPtools/basis_builder/", "EXPtools/visuals"], ) diff --git a/tests/test_basis_utils.py b/tests/test_basis_utils.py new file mode 100644 index 0000000..0c1c514 --- /dev/null +++ b/tests/test_basis_utils.py @@ -0,0 +1,4 @@ +import numpy as np +from EXPtools import basis_builder + +# test integration between functions! diff --git a/tests/test_profiles.py b/tests/test_profiles.py new file mode 100644 index 0000000..2fc671f --- /dev/null +++ b/tests/test_profiles.py @@ -0,0 +1,32 @@ +import numpy as np +from EXPtools.basis_builder import profiles + +# Test output of functions +# Test document test functions + +def test_profile_class(): + """ + Density profiles tests + """ + r = np.logspace(0, 3, 100) + scale_length = 1 + + alpha1 = 1 + beta2 = 2 + alpha2 = 2.5 + beta3 = 3 + beta0 = 0 + + # NFW + NFW = profiles.Profiles(r, scale_length, alpha1, beta2) + rho_NFW = NFW.powerhalo() + + # Hernquist + Hernquist = profiles.Profiles(r, scale_length, alpha1, beta3) + rho_Hern = Hernquist.powerhalo() + + # Single power law + SPL = profiles.Profiles(r, scale_length, alpha2, beta0) + rho_SPL = SPL.powerhalo() + + return None