Implementation of transport utils and ELM model

.github/workflows/tests.yml

@@ -32,10 +32,6 @@ jobs:
     - name: Run test_basic.py
       run: |
         python examples/test_basic.py
-
-    - name: Run facit_basic.py
-      run: |
-        python examples/facit_basic.py
     - name: Run FSA_ioniz.py
       run: |
         python examples/FSA_ioniz.py

.gitignore

@@ -7,6 +7,13 @@ __pycache__
 */#*
 */.#*
 
+# Ignore all folders which are not the default ones
+/*/
+!aurora/
+!aurora.jl/
+!docs/
+!examples/
+
 # Aurora animations
 *.mp4
 
@@ -51,3 +58,7 @@ junit
 # folder-related macbook files
 *.DS_Store
 docs/.idea/*
+aurora/config.py
+
+# Compilation outputs
+builds/*

README.rst

@@ -53,21 +53,11 @@ Both the PyPI and conda installation are automatically updated at every package
 
 To look at the code and contribute to the Aurora repository, it is recommended to install from source, by git-cloning the  `Aurora repo <https://github.com/fsciortino/aurora>`_ from Github. This will ensure that you can access the latest version of the tools. 
 
-For compilation after git-cloning, users can make use of the `setup.py` file, e.g. using 
+For compilation after git-cloning, users must compile the Fortran code manually, using
 
-    python setup.py -e .
+    mkdir builds; cd builds; cmake ..; make; cp *.so ../aurora
 
-or use the makefile in the package directory to build the Fortran code using 
-
-    make clean; make
-
-Note that the makefile will not install any of the dependencies, listed in the `requirements.txt` file in the main directory. You can use this file to quickly install dependencies within a Python virtual environment, or install each dependency one at a time.
-
-The Julia version of the code is not built by default. If you have Julia installed on your system, you can do  
-
-    make julia
-
-from the main package directory. This will build a Julia `sysimage` to speed up access of Julia source code from Python, but it is not strictly necessary. See the documentation to read about interfacing Python and Julia. 
+Note that the compilation process will not install any of the dependencies, listed in the `requirements.txt` file in the main directory. You can use this file to quickly install dependencies within a Python virtual environment, or install each dependency one at a time.
 
 
 Atomic data

aurora/__init__.py

@@ -1,5 +1,5 @@
 name = "aurora"
-__version__ = "3.0.0"
+__version__ = "3.1.1"
 
 import numpy as np, os
 
@@ -11,6 +11,7 @@
 from .trim_files import *
 
 from .source_utils import *
+from .transport_utils import *
 from .default_nml import *
 from .grids_utils import *
 from .coords import *

aurora/atomic.py

@@ -32,7 +32,6 @@
 import scipy.ndimage
 from scipy.linalg import svd
 from scipy import constants
-from scipy.integrate import simps
 from . import adas_files