Merge branch 'release/v0.5.1'

database_builder/filters/SCUBA450.dat

 # SCUBA450
 #photon
 # SCUBA 450um
-  375000.00   1.0E-4
-  380035.47   2.0E-4
-  390015.60   4.0E-4
-  400000.00   0.0012
-  410004.10   0.0046
-  420050.41   0.0178
-  430045.87   0.1134
-  435034.80   0.2508
-  440011.73   0.3843
-  445037.83   0.4042
-  450045.00   0.3963
-  455028.06   0.3803
-  460052.14   0.2996
-  465044.18   0.1942
-  470072.08   0.1072
-  475059.38   0.0482
-  480000.00   0.0212
-  485044.46   0.0117
-  490035.94   0.0105
-  500000.00   0.0074
-  510030.60   0.0047
-  520020.80   0.0029
-  540054.00   9.0E-4
-  560014.93   3.0E-4
-  580046.40   2.0E-4
-  600000.00   1.0E-4
+  3750000.0   1.0E-4
+  3800354.7   2.0E-4
+  3900156.0   4.0E-4
+  4000000.0   0.0012
+  4100041.0   0.0046
+  4200504.1   0.0178
+  4300458.7   0.1134
+  4350348.0   0.2508
+  4400117.3   0.3843
+  4450378.3   0.4042
+  4500450.0   0.3963
+  4550280.6   0.3803
+  4600521.4   0.2996
+  4650441.8   0.1942
+  4700720.8   0.1072
+  4750593.8   0.0482
+  4800000.0   0.0212
+  4850444.6   0.0117
+  4900359.4   0.0105
+  5000000.0   0.0074
+  5100306.0   0.0047
+  5200208.0   0.0029
+  5400540.0   9.0E-4
+  5600149.3   3.0E-4
+  5800464.0   2.0E-4
+  6000000.0   1.0E-4

pcigale/analysis_modules/pdf_analysis/__init__.py

@@ -60,7 +60,7 @@ class PdfAnalysis(AnalysisModule):
             "array of strings",
             "List of the variables (in the SEDs info dictionaries) for which "
             "the statistical analysis will be done.",
-            ["sfr", "average_sfr"]
+            ["sfr", "sfr10Myrs", "sfr100Myrs"]
         )),
         ("save_best_sed", (
             "boolean",

pcigale/analysis_modules/pdf_analysis/workers.py

@@ -338,7 +338,7 @@ def analysis(idx, obs):
         # We check how many unique parameter values are analysed and if less
         # than Npdf (= 100), the PDF is initally built assuming a number of
         # bins equal to the number of unique values for a given parameter
-        # (e.g., average_sfr, age, attenuation.uv_bump_amplitude,
+        # (e.g., sfr, age, attenuation.uv_bump_amplitude,
         # dust.luminosity, attenuation.FUV, etc.).
         Npdf = 100
         var = np.empty((Npdf, len(analysed_averages)))

pcigale/analysis_modules/savefluxes/__init__.py

@@ -48,12 +48,13 @@ class SaveFluxes(AnalysisModule):
     parameter_list = OrderedDict([
         ("output_file", (
             "string",
-            "Name of the output file.",
+            "Name of the output file that contains the parameters of the model(s) "
+            "and the flux densities in the bands",
             "computed_fluxes.txt"
         )),
         ("save_sed", (
             "boolean",
-            "If True, save the generated SED.",
+            "If True, save the generated spectrum for each model.",
             "False"
         )),
         ("output_format", (

pcigale/creation_modules/bc03.py

@@ -50,8 +50,10 @@ class BC03(CreationModule):
     out_parameter_list = OrderedDict([
         ("sfr", "Instantaneous Star Formation Rate in solar mass per year, "
                 "at the age of the galaxy."),
-        ("average_sfr", "Average SFR in the last 100 Myr (default) of the "
-                        "galaxy history."),
+        ('sfr10Myrs', 'Average SFR in the last 10 Myr (default) of the '
+                        'galaxy history.'),
+        ('sfr100Myrs', 'Average SFR in the last 100 Myr (default) of the '
+                        'galaxy history.'),
         ("ssp_m_star", "Total mass in stars in Solar mass."),
         ("ssp_m_gas", "Mass returned to the ISM by evolved stars in Solar "
                       "mass."),

pcigale/creation_modules/dale2014.py

@@ -31,8 +31,9 @@ class Dale2014(CreationModule):
     parameter_list = OrderedDict([
         ('fracAGN', (
             'float',
-            "AGN fraction.",
-            0.1
+            "AGN fraction "
+            "[it is not recommended to combine this AGN emission with that of Fritz et al. (2006)]",
+            0.0
         )),
         ('alpha', (
             'float',

pcigale/creation_modules/m2005.py

@@ -62,7 +62,9 @@ class M2005(CreationModule):
     out_parameter_list = OrderedDict([
         ('sfr', 'Instantaneous Star Formation Rate in solar mass per year, '
                 'at the age of the galaxy.'),
-        ('average_sfr', 'Average SFR in the last 100 Myr (default) of the '
+        ('sfr10Myrs', 'Average SFR in the last 10 Myr (default) of the '
+                        'galaxy history.'),
+        ('sfr100Myrs', 'Average SFR in the last 100 Myr (default) of the '
                         'galaxy history.'),
         ('mass_total', 'Total stellar mass of the galaxy in solar mass.'),
         ('mass_alive', 'Mass of alive stars in solar mass.'),

pcigale/sed/__init__.py

@@ -85,7 +85,9 @@ class SED(object):
             sfh_age = sfh_time[-1] - sfh_time
             self._sfh = value
             self.add_info("sfr", sfh_sfr[-1], True, True)
-            self.add_info("average_sfr", np.mean(sfh_sfr[-AV_LAPSE:]),
+            self.add_info("sfr10Myrs", np.mean(sfh_sfr[-10:]),
+                          True, True)
+            self.add_info("sfr100Myrs", np.mean(sfh_sfr[-100:]),
                           True, True)
             self.add_info("age", sfh_time[-1], False, True)
 

pcigale_plots/__init__.py

@@ -188,11 +188,11 @@ def _sed_worker(obs, mod, filters, sed_type, nologo):
                            label="Dust emission", color='r', marker=None,
                            nonposy='clip', linestyle='-', linewidth=0.5)
             # AGN emission Fritz
-            if 'agn_fritz2006_therm' in sed.columns:
+            if 'agn.fritz2006_therm' in sed.columns:
                 ax1.loglog(wavelength_spec[wsed],
-                           (sed['agn_fritz2006_therm'][wsed] +
-                            sed['agn_fritz2006_scatt'][wsed] +
-                            sed['agn_fritz2006_agn'][wsed]),
+                           (sed['agn.fritz2006_therm'][wsed] +
+                            sed['agn.fritz2006_scatt'][wsed] +
+                            sed['agn.fritz2006_agn'][wsed]),
                            label="AGN emission", color='g', marker=None,
                            nonposy='clip', linestyle='-', linewidth=0.5)
             # Radio emission

setup.py

@@ -3,9 +3,10 @@
 # Licensed under the CeCILL-v2 licence - see Licence_CeCILL_V2-en.txt
 # Author: Yannick Roehlly
 
-from setuptools import setup, find_packages
 from distutils.command.build import build
 
+from setuptools import find_packages, setup
+
 
 class custom_build(build):
     def run(self):
@@ -17,12 +18,13 @@ class custom_build(build):
         build.run(self)
 
 entry_points = {
-    'console_scripts': ['pcigale = pcigale:main', 'pcigale-plots = pcigale_plots:main']
+    'console_scripts': ['pcigale = pcigale:main',
+                        'pcigale-plots = pcigale_plots:main']
 }
 
 setup(
     name="pcigale",
-    version="0.1a",
+    version="0.5.1",
     packages=find_packages(exclude=["database_builder"]),
 
     install_requires=['numpy', 'scipy', 'sqlalchemy', 'matplotlib',
@@ -30,14 +32,13 @@ setup(
 
     entry_points=entry_points,
 
-    include_package_data=True,
     cmdclass={"build": custom_build},
-    package_data={'pcigale': ['data/data.db'], 'pcigale-plots':['data/CIGALE.png']},
+    package_data={'pcigale': ['data/data.db'],
+                  'pcigale_plots': ['data/CIGALE.png']},
 
-    author="Yannick Roehlly",
-    author_email="yannick.roehlly@oamp.fr",
+    author="The CIGALE team",
+    author_email="cigale@lam.fr",
     description="Python Code Investigating Galaxy Emission",
     license="CeCILL-V2",
     keywords="astrophysics, galaxy, SED fitting"
-
 )