Merge pull request DarkEnergySurvey#91 from DarkEnergySurvey/lint2

Cleaning up lint

.github/workflows/python-package.yml

@@ -7,9 +7,9 @@ name: build
 
 on:
   push:
-    branches: [ master, actions ]
   pull_request:
-    branches: [ master ]
+  schedule:
+  - cron: '0 0 1 * *'
 
 jobs:
   build:
@@ -38,19 +38,17 @@ jobs:
         source activate env
         export UGALIDIR="$HOME/.ugali"
         python setup.py -q install --isochrones --catalogs
-    - name: Install test data
-      run: |
-        wget https://github.com/DarkEnergySurvey/ugali/releases/download/v1.7.0/ugali-test-data.tar.gz -O ugali-test-data.tar.gz
-        tar -xzf ugali-test-data.tar.gz
     - name: Lint with flake8
-      if: ${{ false }}
+      if: ${{ true }}
       run: |
         source activate env
         conda install -q flake8 -c conda-forge
         # 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
+    - name: Install test data
+      run: |
+        wget https://github.com/DarkEnergySurvey/ugali/releases/download/v1.7.0/ugali-test-data.tar.gz -O ugali-test-data.tar.gz
+        tar -xzf ugali-test-data.tar.gz
     - name: Test with nose
       run: |
         source activate env

ugali/analysis/prior.py

@@ -1,4 +1,9 @@
 #!/usr/bin/env python
+"""
+Incomplete module for dealing with priors...
+"""
+
+import scipy.stats
 
 class Prior(object):
     def __call__(self, value):

ugali/analysis/results.py

@@ -18,7 +18,8 @@
 
 import ugali.utils.stats
 from ugali.utils.stats import Samples
-from ugali.utils.projector import dist2mod,mod2dist,gal2cel,gal2cel_angle
+from ugali.utils.projector import dist2mod,mod2dist
+from ugali.utils.projector import cel2gal,gal2cel,gal2cel_angle
 from ugali.utils.projector import ang2const, ang2iau
 from ugali.utils.config import Config
 from ugali.utils.logger import logger

ugali/analysis/scan.py

@@ -130,10 +130,12 @@ def search(self, coords=None, distance_modulus=None, extension=None, tolerance=1
         self.stellar_mass_array         = np.zeros([nmoduli,npixels],dtype='f4')
         self.fraction_observable_array  = np.zeros([nmoduli,npixels],dtype='f4')
         self.extension_fit_array        = np.zeros([nmoduli,npixels],dtype='f4')
-        # DEPRECATED: ADW 2019-04-27
-        self.richness_lower_array       = np.zeros([nmoduli,npixels],dtype='f4')
-        self.richness_upper_array       = np.zeros([nmoduli,npixels],dtype='f4')
-        self.richness_ulimit_array      = np.zeros([nmoduli,npixels],dtype='f4')
+        if self.config['scan']['full_pdf']:
+            # DEPRECATED: ADW 2019-04-27
+            DeprecationWarning("'full_pdf' is deprecated.")
+            self.richness_lower_array       = np.zeros([nmoduli,npixels],dtype='f4')
+            self.richness_upper_array       = np.zeros([nmoduli,npixels],dtype='f4')
+            self.richness_ulimit_array      = np.zeros([nmoduli,npixels],dtype='f4')
 
         # Specific pixel/distance_modulus
         coord_idx, distance_modulus_idx, extension_idx = None, None, None
@@ -315,6 +317,7 @@ def write(self, outfile):
         data['PIXEL']=self.roi.pixels_target
         # Full data output (too large for survey)
         if self.config['scan']['full_pdf']:
+            DeprecationWarning("'full_pdf' is deprecated.")
             data['LOG_LIKELIHOOD']=self.loglike_array.T
             data['RICHNESS']=self.richness_array.T
             data['RICHNESS_LOWER']=self.richness_lower_array.T

ugali/candidate/associate.py

@@ -54,7 +54,7 @@
 #            glon, glat = ugali.utils.projector.celToGal(lon,lat)
 #        else:
 #            glon,glat = lon, lat
-#        return ugali.utils.projector.match(glon,glat,self.data['glon'],self.data['glat'],tol)
+#        return ugali.utils.projector.match(glon,glat,self['glon'],self['glat'],tol)
 
 
 
@@ -452,7 +452,7 @@ def catalogFactory(name, **kwargs):
     catalogs = odict(inspect.getmembers(sys.modules[__name__], fn))
 
     if name not in list(catalogs.keys()):
-        msg = "%s not found in catalogs:\n %s"%(name,list(kernels.keys()))
+        msg = "%s not found in catalogs:\n %s"%(name,list(catalogs.keys()))
         logger.error(msg)
         msg = "Unrecognized catalog: %s"%name
         raise Exception(msg)

ugali/isochrone/dartmouth.py

@@ -165,7 +165,7 @@ def _parse(self,filename):
         try:
             columns = self.columns[self.survey.lower()]
         except KeyError as e:
-            logger.warning('Unrecognized survey: %s'%(survey))
+            logger.warning('Unrecognized survey: %s'%(self.survey))
             raise(e)
 
         kwargs = dict(comments='#',usecols=list(columns.keys()),dtype=list(columns.values()))

ugali/isochrone/empirical.py

@@ -3,7 +3,10 @@
 Generic python script.
 """
 import os
+from collections import OrderedDict as odict
 
+from ugali.analysis.model import Model, Parameter
+from ugali.utils.shell import mkdir, get_ugali_dir, get_iso_dir
 from ugali.isochrone.parsec import PadovaIsochrone
 
 class EmpiricalPadova(PadovaIsochrone):

ugali/isochrone/mesa.py

@@ -134,7 +134,7 @@ def _parse(self,filename):
         try:
             columns = self.columns[self.survey.lower()]
         except KeyError as e:
-            logger.warning('Unrecognized survey: %s'%(survey))
+            logger.warning('Unrecognized survey: %s'%(self.survey))
             raise(e)
 
         kwargs = dict(comments='#',usecols=list(columns.keys()),dtype=list(columns.values()))

ugali/isochrone/model.py

@@ -322,27 +322,6 @@ def stellar_luminosity(self, steps=10000):
 
         return np.sum(luminosity * d_log_mass * self.imf.pdf(mass, log_mode=True))
 
-    def stellar_luminosity2(self, steps=10000):
-        """
-        DEPRECATED: ADW 2017-09-20
-
-        Compute the stellar luminosity (L_Sol; average per star).
-        Uses "sample" to generate mass sample and pdf.  The range of
-        integration only covers the input isochrone data (no
-        extrapolation used), but this seems like a sub-percent effect
-        if the isochrone goes to 0.15 Msun for the old and metal-poor
-        stellar populations of interest.
-
-        Note that the stellar luminosity is very sensitive to the
-        post-AGB population.
-        """
-        msg = "'%s.stellar_luminosity2': ADW 2017-09-20"%self.__class__.__name__
-        DeprecationWarning(msg)
-        mass_init, mass_pdf, mass_act, mag_1, mag_2 = self.sample(mass_steps=steps)
-        luminosity_interpolation = scipy.interpolate.interp1d(self.mass_init, self.luminosity,fill_value=0,bounds_error=False)
-        luminosity = luminosity_interpolation(mass_init)
-        return np.sum(luminosity * mass_pdf)
-
     # ADW: For temporary backward compatibility
     stellarMass = stellar_mass
     stellarLuminosity = stellar_luminosity
@@ -354,7 +333,6 @@ def absolute_magnitude(self, richness=1, steps=1e4):
         g,r -> V transform equations from Jester 2005
         [astro-ph/0506022].
 
-
         TODO: ADW If richness not specified, should use self.richness
 
         Parameters:

ugali/isochrone/padova.py

@@ -1,7 +1,20 @@
 #!/usr/bin/env python
 """
 Older (pre-PARSEC) Padova isochrones.
+
+Not verified to work...
 """
+import os.path
+from collections import OrderedDict as odict
+
+import numpy as np
+
+from ugali.analysis.model import Model, Parameter
+from ugali.utils.shell import mkdir, get_ugali_dir, get_iso_dir
+from ugali.isochrone.model import Isochrone
+from ugali.isochrone.parsec import Marigo2017 as Padova
+from ugali.isochrone.parsec import defaults_27
+from ugali.utils.logger import logger
 
 class Girardi2002(Padova):
     defaults = dict(defaults_27)
@@ -19,7 +32,7 @@ class Girardi2010b(Padova):
     defaults = dict(defaults_27)
     defaults['isoc_kind'] = 'gi10b'
 
-class Girardi2002(PadovaIsochrone):
+class Girardi2002(Padova):
     #_dirname = '/u/ki/kadrlica/des/isochrones/v5/'
     _dirname =  os.path.join(get_iso_dir(),'{survey}','girardi2002')
     # For use with Marigo et al. (2008) and earlier use Anders & Grevesse 1989
@@ -57,7 +70,7 @@ def _parse(self,filename):
         try:
             columns = self.columns[self.survey.lower()]
         except KeyError as e:
-            logger.warning('did not recognize survey %s'%(survey))
+            logger.warning('did not recognize survey %s'%(self.survey))
             raise(e)
 
         kwargs = dict(delimiter='\t',usecols=list(columns.keys()),dtype=list(columns.values()))

ugali/isochrone/parsec.py

@@ -370,7 +370,7 @@ def _parse(self,filename):
         try:
             columns = self.columns[self.survey.lower()]
         except KeyError as e:
-            logger.warning('Unrecognized survey: %s'%(survey))
+            logger.warning('Unrecognized survey: %s'%(self.survey))
             raise(e)
 
         # delimiter='\t' is used to be compatible with OldPadova...
@@ -455,7 +455,7 @@ class Marigo2017(ParsecIsochrone):
                 (28,('Y',float)),
                 ]),
         )
-    
+
     def _parse(self,filename):
         """Reads an isochrone file in the Padova (Marigo et al. 2017)
         format. Creates arrays with the initial stellar mass and
@@ -464,7 +464,7 @@ def _parse(self,filename):
         try:
             columns = self.columns[self.survey.lower()]
         except KeyError as e:
-            logger.warning('Unrecognized survey: %s'%(survey))
+            logger.warning('Unrecognized survey: %s'%(self.survey))
             raise(e)
 
         kwargs = dict(usecols=list(columns.keys()),dtype=list(columns.values()))