Transferred latest version from IDL to Python

Author: danehkar

.coveragerc

@@ -2,4 +2,3 @@
 [report]
 omit =
   */__init__.py
-  */orl.py

.coveralls.yml

@@ -1 +1,2 @@
 
+

.travis.yml

@@ -6,14 +6,15 @@ before_install:
 
 python:
   - 2.7
-  - 3.4
-  - 3.5
+  - 3.8
 
 install:
   - pip install --quiet coveralls
   - pip install --quiet nose
   - pip install --quiet coverage
+  - pip install --quiet numpy
   - pip install --quiet scipy
+  - pip install --quiet astropy
   - python setup.py install
 
 script: 

AUTHORS.rst

@@ -0,0 +1,3 @@
+Author:
+
+* Ashkbiz Danehkar (`@danehkar <https://github.com/danehkar>`_)

CONTRIBUTING.md

@@ -0,0 +1,49 @@
+# Contributing to pyEQUIB
+
+The following guidelines are designed for contributors to the pyEQUIB Python package, which is 
+hosted in the [pyEQUIB repository](https://github.com/equib/pyEQUIB) on GitHub. 
+
+## Reporting Issues
+
+The [issue tracker](https://github.com/equib/pyEQUIB/issues) is used to report bugs, request new functionality, and discuss improvements. 
+For reporting a bug or a failed function or requesting a new feature, you can simply open an issue 
+in the [issue tracker](https://github.com/equib/pyEQUIB/issues) of the 
+[pyEQUIB repository](https://github.com/equib/pyEQUIB). If you are reporting a bug, please also include a minimal code
+example that reproduces the problem, and Python version you are using.
+
+## Contributing Code
+
+Fo contributing code to pyEQUIB, you need to set up your [GitHub](https://github.com) 
+account if you do not have and sign in, and request your change(s) or contribution via 
+opening a pull request against the ``master``
+branch in your fork of the [pyEQUIB repository](https://github.com/equib/pyEQUIB). 
+
+To contribute to this package, you need to follow these steps:
+
+- Open a new issue for new feature or failed function in the [Issue tracker](https://github.com/equib/pyEQUIB/issues).
+- Fork the [pyEQUIB repository](https://github.com/equib/pyEQUIB) to your GitHub account.
+- Clone your fork of the [pyEQUIB repository](https://github.com/equib/pyEQUIB):
+
+      $ git clone [email protected]:your-username/pyEQUIB.git
+      
+- Make your change(s) in the `master` branch of your cloned fork.
+- Make sure that it passes all tests and there is no error.
+- Push yout change(s) to your fork in your GitHub account.
+- [Submit a pull request][pr], mentioning what issue has been addressed.
+
+[pr]: https://github.com/equib/pyEQUIB/compare/
+
+Then, you are waiting, until your contribution is checked and merged into the original repository. 
+We will contact you if there is a problem in your code.
+
+While you are opening a pull request for your contribution, be sure that you have included:
+
+* **Code** which you are contributing to this package.
+
+* **Documentation** of this code if it provides new functionality. This should be a
+  description of new functionality added to the API documentation (in ``docs/``). 
+
+- **Tests** of this code to make sure that the previously failed function or the new functionality now works properly.
+
+- **Revision history** if you fixed a bug in the previously failed function or add a code for new functionality, you should
+well document your change(s) or addition in the *Revision History* entry of the changed or added function in your code.

README.rst

@@ -2,7 +2,7 @@ environment:
   matrix:
     - PYTHON_VERSION: 2.7
       MINICONDA: C:\Miniconda
-    - PYTHON_VERSION: 3.6
+    - PYTHON_VERSION: 3.8
       MINICONDA: C:\Miniconda3
 
 matrix:
@@ -19,8 +19,8 @@ install:
   - conda config --set always_yes yes --set changeps1 no
   - conda update -q conda
   - conda info -a
-  - pip install numpy scipy nose
-  - "conda create -q -n test-environment python=%PYTHON_VERSION% numpy scipy nose"
+  - pip install numpy scipy astropy nose
+  - "conda create -q -n test-environment python=%PYTHON_VERSION% numpy scipy astropy nose"
   - activate test-environment
   - pip install coverage
 

appveyor.yml

@@ -0,0 +1,64 @@
+# Example: calc_abundance()
+#     determine ionic abundance from observed
+#     flux intensity for gievn electron density
+#     and temperature using  calc_abundance function
+#     from proEQUIB
+#
+# --- Begin MAIN program. ---------------
+#
+#
+import pyequib
+import atomneb
+import os
+import numpy as np
+
+# Locate datasets
+base_dir = '/home/danehkar/github/AtomNeb-py/'
+data_dir = os.path.join('atomic-data', 'chianti70')
+data_rc_dir = os.path.join('atomic-data-rc')
+atom_elj_file = os.path.join(base_dir,data_dir, 'AtomElj.fits')
+atom_omij_file = os.path.join(base_dir,data_dir, 'AtomOmij.fits')
+atom_aij_file = os.path.join(base_dir,data_dir, 'AtomAij.fits')
+atom_rc_sh95_file = os.path.join(base_dir,data_rc_dir, 'rc_SH95.fits')
+
+atom = 'h'
+ion = 'ii' # H I Rec
+hi_rc_data = atomneb.read_aeff_sh95(atom_rc_sh95_file, atom, ion)
+
+atom = 'o'
+ion = 'iii' # [O III]
+o_iii_elj = atomneb.read_elj(atom_elj_file, atom, ion, level_num=5) # read Energy Levels (Ej)
+o_iii_omij = atomneb.read_omij(atom_omij_file, atom, ion) # read Collision Strengths (Omegaij)
+o_iii_aij = atomneb.read_aij(atom_aij_file, atom, ion) # read Transition Probabilities (Aij)
+
+levels5007 = '3,4/'
+temperature = np.float64(10000.0,)
+density = np.float64(5000.0)
+iobs5007 = np.float64(1200.0)
+abb5007 = np.float64(0.0)
+
+emis = pyequib.calc_emissivity(temperature=temperature, density=density, atomic_levels=levels5007, elj_data=o_iii_elj, omij_data=o_iii_omij, aij_data=o_iii_aij)
+print('Emissivity(O III 5007):', emis)
+
+abb5007 = pyequib.calc_abundance(temperature=temperature, density=density, line_flux=iobs5007, atomic_levels=levels5007,
+                         elj_data=o_iii_elj, omij_data=o_iii_omij, aij_data=o_iii_aij, h_i_aeff_data=hi_rc_data.aeff)
+print('N(O^2+)/N(H+):', abb5007)
+
+nlj = pyequib.calc_populations(temperature=temperature, density=density, elj_data=o_iii_elj, omij_data=o_iii_omij, aij_data=o_iii_aij)
+print('Atomic Level Populations:', nlj)
+
+
+n_crit = pyequib.calc_crit_density(temperature=temperature, elj_data=o_iii_elj, omij_data=o_iii_omij, aij_data=o_iii_aij)
+print('Critical Densities:', n_crit)
+
+temperature = np.float64(10000.0)
+omij_t = pyequib.get_omij_temp(temperature=temperature, omij_data=o_iii_omij, level_num=8)
+print('Effective Collision Strengths: ')
+print(omij_t)
+
+pyequib.print_ionic(temperature=temperature, density=density,
+            elj_data=o_iii_elj, omij_data=o_iii_omij, aij_data=o_iii_aij,
+            h_i_aeff_data=hi_rc_data.aeff)
+#
+# --- End MAIN program. ---------------
+

examples/cel_abundance_example.py

@@ -0,0 +1,67 @@
+# Example: calc_temperature() and calc_density()
+#     determine electron density or temperature from given
+#     flux intensity ratio for a fixed electron density
+#     or temperature using calc_temperature function
+#     calc_density function from proEQUIB
+#
+# --- Begin MAIN program. ---------------
+#
+#
+import pyequib
+import atomneb
+import os
+import numpy as np
+
+# Locate datasets
+base_dir = '/home/danehkar/github/AtomNeb-py/'
+data_dir = os.path.join('atomic-data', 'chianti70')
+data_rc_dir = os.path.join('atomic-data-rc')
+atom_elj_file = os.path.join(base_dir,data_dir, 'AtomElj.fits')
+atom_omij_file = os.path.join(base_dir,data_dir, 'AtomOmij.fits')
+atom_aij_file = os.path.join(base_dir,data_dir, 'AtomAij.fits')
+atom_rc_sh95_file = os.path.join(base_dir,data_rc_dir, 'rc_SH95.fits')
+
+
+atom = 'h'
+ion = 'ii' # H I Rec
+hi_rc_data = atomneb.read_aeff_sh95(atom_rc_sh95_file, atom, ion)
+
+atom = 's'
+ion = 'ii'
+s_ii_elj = atomneb.read_elj(atom_elj_file, atom, ion, level_num=5) # read Energy Levels (Ej)
+s_ii_omij = atomneb.read_omij(atom_omij_file, atom, ion) # read Collision Strengths (Omegaij)
+s_ii_aij = atomneb.read_aij(atom_aij_file, atom, ion) # read Transition Probabilities (Aij)\
+
+upper_levels = '1,2,1,3/'
+lower_levels = '1,5/'
+density = np.float64(2550)
+line_flux_ratio = np.float64(10.753)
+temperature = pyequib.calc_temperature(line_flux_ratio=line_flux_ratio, density=density, upper_levels=upper_levels, lower_levels=lower_levels, elj_data=s_ii_elj, omij_data=s_ii_omij, aij_data=s_ii_aij)
+print("Electron Temperature:", temperature)
+
+upper_levels = '1,2/'
+lower_levels = '1,3/'
+temperature = np.float64(7000.0)
+line_flux_ratio = np.float64(1.506)
+density = pyequib.calc_density(line_flux_ratio=line_flux_ratio, temperature=temperature, upper_levels=upper_levels, lower_levels=lower_levels, elj_data=s_ii_elj, omij_data=s_ii_omij, aij_data=s_ii_aij)
+print("Electron Density:", density)
+
+density = np.float64(1000)
+temperature = np.float64(10000.0)
+nlj = pyequib.calc_populations(temperature=temperature, density=density, elj_data=s_ii_elj, omij_data=s_ii_omij, aij_data=s_ii_aij)
+print('Atomic Level Populations:', nlj)
+
+temperature = np.float64(10000.0)
+n_crit = pyequib.calc_crit_density(temperature=temperature, elj_data=s_ii_elj, omij_data=s_ii_omij, aij_data=s_ii_aij)
+print('Critical Densities:', n_crit)
+
+temperature = np.float64(10000.0)
+omij_t = pyequib.get_omij_temp(temperature=temperature, omij_data=s_ii_omij)
+print('Effective Collision Strengths: ')
+print(omij_t)
+
+pyequib.print_ionic(temperature=temperature, density=density,
+            elj_data=s_ii_elj, omij_data=s_ii_omij, aij_data=s_ii_aij,
+            h_i_aeff_data=hi_rc_data.aeff)
+
+# --- End MAIN program. ---------------