Merge pull request #73 from MingjieJian/develop

Merge Develop to master

.github/workflows/release.yml

@@ -1,6 +1,9 @@
 name: pypi-publish
 
-on: push
+on: 
+  push:
+    branches: [master]
+
 
 jobs:
   build:

.gitignore

@@ -1,6 +1,6 @@
 .vscode/
 __pycache__/
 docs/_build/
-build/
+build/**
 *.pyc
 node_modeules/

LICENCE

@@ -1,6 +1,6 @@
 MIT License
 
-Copyright (c) 2023, Mingjie Jian
+Copyright (c) 2024, Mingjie Jian
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal

README.md

@@ -2,6 +2,15 @@
 
 [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.7582434.svg)](https://doi.org/10.5281/zenodo.7582434) [![Documentation Status](https://readthedocs.org/projects/pymoog/badge/?version=latest)](https://pymoog.readthedocs.io/en/latest/?badge=latest)
 
+## News
+
+pymoog is now 1.0.0! The main drivers are all availalbe (binary, doflux, synpop and abpop newly added), with many bugs fixed. 
+Note that there are some breaking changes compared to the previous versions, and the description will be availabe in the [documentation](https://pymoog.readthedocs.io/en/latest/) soon.
+
+Thanks the very useful synpop and abpop example provided by Charli Sakari. 
+
+------------------------------------- 
+
 `pymoog` is a python3 wrapper for running the LTE spectrum synthesis part of the code [MOOG](https://www.as.utexas.edu/~chris/moog.html) written by Chris Sneden.
 It wraps up the (a bit) teidous steps for generating a synthetic spectra into four python commands, while retaining the functions provided by MOOG.
 Besides, it also provides some other functions for analysing the MOOG result, mainly contribution function and fitting stellar parameters.

build/lib/pymoog/__init__.py

@@ -1,5 +1,7 @@
 from . import synth
+from . import doflux
 from . import line_data
+from . import line_analysis
 from . import contri_func
 from . import abfind
 from . import blends
@@ -8,5 +10,7 @@
 from . import binary
 from . import internal
 from . import mpfit
+from . import synpop
+from . import abpop
 
 __version__ = '0.1.3'

build/lib/pymoog/abfind.py

@@ -1,16 +1,13 @@
 #!/usr/bin/python
+from . import moog_structure
 from . import private
-from . import line_data
-from . import model
-from . import rundir_num
-import subprocess
 
 MOOG_path = '{}/.pymoog/moog_nosm/moog_nosm_NOV2019/'.format(private.os.environ['HOME'])
 # self.rundir_path = '{}/.pymoog/rundir/'.format(private.os.environ['HOME'])
 MOOG_file_path = '{}/.pymoog/files/'.format(private.os.environ['HOME'])
 
-class abfind(rundir_num.rundir_num):
-    def __init__(self, teff, logg, m_h, vmicro=2, mass=1, line_list='ges', prefix=''):
+class abfind(moog_structure.moog_structure):
+    def __init__(self, teff, logg, m_h, vmicro=2, mass=1, line_list='ges', prefix='', vmicro_mode='flexible'):
         '''
         Initiate a abfind Instance and read the parameters.
         
@@ -27,109 +24,14 @@ def __init__(self, teff, logg, m_h, vmicro=2, mass=1, line_list='ges', prefix=''
         prefix : str, default ''.
             The prefix to be added to the name of rundir. Convenient when you want to find a specified rundir if there are many.
         '''
-        super(abfind, self).__init__('{}/.pymoog/'.format(private.os.environ['HOME']), 'abfind', prefix=prefix)
+        super(abfind, self).__init__('abfind', prefix=prefix)
         self.teff = teff
         self.logg = logg
         self.m_h = m_h
         self.vmicro = vmicro
         self.mass = mass
-        self.line_list = line_list
-
-    def prepare_file(self, model_file=None, model_format='moog', abun_change=None, atmosphere=1, lines=1, molecules=1, molecules_include=None, model_type='marcs', model_chem='st', model_geo='auto'):
-        '''
-        Prepare the model, linelist and control files for MOOG.
-        Can either provide stellar parameters and wavelengths or provide file names.
-        If fine name(s) provided, the files will be copied to working directory for calculation.  
-        
-        Parameters
-        ----------
-        model_file : str, optional
-            The name of the model file. If not specified, the code will use internal model.
-        model_format : str, optional
-            The type of the INPUT model file. Default is "moog" (then no conversion of format will be done); can be "moog", "kurucz-atlas9", "kurucz-atlas12" or "marcs". Should left as it is when not providing the input model file.
-        abun_change : dict of pairs {int:float, ...}
-            Abundance change, have to be a dict of pairs of atomic number and [X/Fe] values. 
-        atmosphere : int, default 1
-            The atmosphere value described in MOOG documention, section III.
-        lines : int, default 1
-            The lines value described in MOOG documention, section III.
-        molecules : int, default 1
-            The molecules value described in MOOG documention, section III.  
-        molecules_include : list, default None
-            Molecules to be included to molecular calculation. Follows the MOOG notation.          
-        model_type : str, default marcs
-            The type of internal atmosphere model. Must be kurucz or marcs.
-        model_chem : str, default st
-            The chemical composition of marcs model. Only valid when model_type is marcs. 
-        model_geo : str, default auto
-            The geometry of MARCS model, either 's' for spherical, 'p' for plane-parallel or 'auto'.
-        '''
-
-        if model_file == None:
-            # Model file is not specified, will download Kurucz model according to stellar parameters.
-            model.interpolate_model(self.teff, self.logg, self.m_h, vmicro=self.vmicro, mass=self.mass, abun_change=abun_change, molecules_include=molecules_include, save_name=self.rundir_path + 'model.mod', model_type=model_type, chem=model_chem, geo=model_geo)
-            self.model_file = 'model.mod'
-        else:
-            # Model file is specified; record model file name and copy to working directory.
-            if model_format == 'moog':
-                private.subprocess.run(['cp', model_file, self.rundir_path], encoding='UTF-8', stdout=private.subprocess.PIPE)
-                self.model_file = model_file.split('/')[-1]
-            elif model_format[:6] == 'kurucz':
-                model.kurucz2moog(model_path=model_file, abun_change=abun_change, model_format=model_format[7:], molecules_include=molecules_include, converted_model_path=self.rundir_path + 'model.mod')
-                self.model_file = 'model.mod'
-            elif model_format == 'marcs':
-                marcs_model = model.read_marcs_model(model_file)
-                model.marcs2moog(marcs_model, self.rundir_path + 'model.mod', abun_change=abun_change, molecules_include=molecules_include)
-                self.model_file = 'model.mod'
-            else:
-                raise ValueError("The input model_type is not supported. Have to be either 'moog', 'kurucz' or 'marcs.")
-
-
-        # Create line list.
-        if isinstance(self.line_list, str):
-            # Linelist file have to be specified; record linelist file name and copy to working directory.
-            subprocess.run(['cp', self.line_list, self.rundir_path], encoding='UTF-8', stdout=subprocess.PIPE)
-            self.line_list = self.line_list.split('/')[-1]
-        elif isinstance(self.line_list, private.pd.DataFrame):
-            line_data.save_linelist(self.line_list.sort_values('id'), self.rundir_path + 'line.list')
-            self.line_list = 'line.list'
-        else:
-            raise TypeError('Type of input linelist have to be either str or pandas.DataFrame.')
-
-        # Create parameter file.
-        self.create_para_file(atmosphere=atmosphere, lines=lines)    
-
-    def create_para_file(self, atmosphere=1, lines=1, molecules=1):
-        '''
-        Function for creating the parameter file of batch.par for abfind.
-        
-        Parameters
-        ----------
-        atmosphere : int, default 1
-            The atmosphere value described in MOOG documention, section III.
-        lines : int, default 1
-            The lines value described in MOOG documention, section III.
-        molecules : int, default 1
-            The molecules value described in MOOG documention, section III.
-        '''
-        MOOG_para_file = open(self.rundir_path + '/batch.par', 'w')
-        # Parameter list of MOOG: standard output file (1), summary output file (2), smoothed output file (3),
-        #                         begin wavelength, end wavelength, wavelength step;
-        #                         smoothing function, Gaussian FWHM, vsini, limb darkening coefficient,
-        #                         Macrotrubulent FWHM, Lorentzian FWHM
-        #MOOG_para_file = open('batch.par', 'w')
-        MOOG_contant = ["abfind\n",
-                        "standard_out       '{}'\n".format('MOOG.out1'),
-                        "summary_out        '{}'\n".format('MOOG.out2'),
-                        "model_in           '{}'\n".format(self.model_file),
-                        "lines_in           '{}'\n".format(self.line_list),
-                        "atmosphere         {}\n".format(atmosphere),
-                        "lines              {}\n".format(lines),
-                        "molecules          {}\n".format(molecules),
-                        "terminal           'x11'\n",
-                    ]
-        MOOG_para_file.writelines(MOOG_contant)
-        MOOG_para_file.close()
+        self.line_list_in = line_list
+        self.vmicro_mode = vmicro_mode
 
     def run_moog(self, output=False):
         '''
@@ -146,9 +48,6 @@ def run_moog(self, output=False):
         '''
 
         MOOG_run = private.subprocess.run([MOOG_path + '/MOOGSILENT'], stdout=private.subprocess.PIPE, cwd=self.rundir_path)
-
-        # if unlock:
-        #     self.unlock()
 
         MOOG_run = str(MOOG_run.stdout, encoding = "utf-8").split('\n')
         MOOG_output = []
@@ -205,6 +104,6 @@ def read_output(self, remove=True):
             abfind_dict[ele_index] = abfind_s_df
 
         if remove:
-            self.remove()
+            self.remove_rundir()
 
         self.abfind_res = abfind_dict