Merge pull request #8 from jngaravitoc/main

Restructure

.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

.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

EXPtools/__init__.py

@@ -0,0 +1,2 @@
+from . import visuals
+from . import basis_builder

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

EXP_tools/basis_utils.py → 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