PEP8, flake8 and sphinx RST fixes

.github/workflows/flake8.yml

@@ -0,0 +1,21 @@
+name: Python flake8 check
+
+on: [push]
+
+jobs:
+  build:
+
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v1
+    - name: Set up Python 3.6
+      uses: actions/setup-python@v1
+      with:
+        python-version: 3.6
+    - name: Lint with flake8
+      run: |
+        pip install flake8
+        # Note: only check files in Ska.engarchive package.  Many other files in
+        # the repo are not maintained as PEP8 compliant.
+        flake8 . --count --exclude=docs/conf.py --ignore=W504 --max-line-length=100 --show-source --statistics

proseco/acq.py

@@ -9,7 +9,6 @@
 import numpy as np
 from scipy import ndimage, stats
 from scipy.interpolate import interp1d
-from astropy.table import Table
 
 from chandra_aca.star_probs import acq_success_prob, prob_n_acq
 from chandra_aca.transform import (pixels_to_yagzag, mag_to_count_rate,
@@ -155,7 +154,6 @@ def empty(cls):
         out['halfw'] = np.full(fill_value=0, shape=(0,), dtype=np.int64)
         return out
 
-
     @property
     def fid_set(self):
         if not hasattr(self, '_fid_set'):
@@ -1301,7 +1299,7 @@ def p_fid_id_spoiler(self, box_size, fid_id, acqs):
             fids = acqs.fids
             if fids is None:
                 acqs.add_warning('Requested fid spoiler probability without '
-                                        'setting acqs.fids first')
+                                 'setting acqs.fids first')
                 return 1.0
 
             p_fid_id_spoiler = 1.0
@@ -1311,8 +1309,8 @@ def p_fid_id_spoiler(self, box_size, fid_id, acqs):
                 # This should not happen, but ignore with a warning in any case.  Non-candidate
                 # fid cannot spoil an acq star.
                 acqs.add_warning(f'Requested fid spoiler probability for fid '
-                                        f'{acqs.detector}-{fid_id} but it is '
-                                        f'not a candidate')
+                                 f'{acqs.detector}-{fid_id} but it is '
+                                 f'not a candidate')
             else:
                 if fids.spoils(fid, self.acq, box_size):
                     p_fid_id_spoiler = 0.0

proseco/catalog.py

@@ -223,6 +223,7 @@ def set_attrs_from_kwargs(self, **kwargs):
         compute the effective T_ccd temperatures.
 
         In this ACATable object:
+
         - t_ccd_eff_{acq,guide} are the effective T_ccd values which are adjusted
           if the actual t_ccd{acq,guide} values are above ACA.aca_t_ccd_penalty_limit.
         - t_ccd_{acq,guide} are the actual (or predicted) values from the call
@@ -240,7 +241,6 @@ def set_attrs_from_kwargs(self, **kwargs):
         self.t_ccd_eff_guide = get_effective_t_ccd(self.t_ccd_guide)
         self.version = VERSION
 
-
     def get_review_table(self):
         """Get ACAReviewTable object based on self.
 

proseco/characteristics.py

@@ -43,50 +43,50 @@
               [-374, -374, 347, 347]]  # Fid trap
 
 bad_star_set = set([36178592,
-                   39980640,
-                   185871616,
-                   188751528,
-                   190977856,
-                   260968880,
-                   260972216,
-                   261621080,
-                   296753512,
-                   300948368,
-                   301078152,
-                   301080376,
-                   301465776,
-                   335025128,
-                   335028096,
-                   350392600,
-                   414324824,
-                   444743456,
-                   465456712,
-                   490220520,
-                   502793400,
-                   509225640,
-                   570033768,
-                   614606480,
-                   637144600,
-                   647632648,
-                   650249416,
-                   656409216,
-                   690625776,
-                   692724384,
-                   788418168,
-                   849226688,
-                   914493824,
-                   956175008,
-                   989598624,
-                   1004817824,
-                   1016736608,
-                   1044122248,
-                   1117787424,
-                   1130635848,
-                   1130649544,
-                   1161827976,
-                   1196953168,
-                   1197635184,
-                   1158290496])
+                    39980640,
+                    185871616,
+                    188751528,
+                    190977856,
+                    260968880,
+                    260972216,
+                    261621080,
+                    296753512,
+                    300948368,
+                    301078152,
+                    301080376,
+                    301465776,
+                    335025128,
+                    335028096,
+                    350392600,
+                    414324824,
+                    444743456,
+                    465456712,
+                    490220520,
+                    502793400,
+                    509225640,
+                    570033768,
+                    614606480,
+                    637144600,
+                    647632648,
+                    650249416,
+                    656409216,
+                    690625776,
+                    692724384,
+                    788418168,
+                    849226688,
+                    914493824,
+                    956175008,
+                    989598624,
+                    1004817824,
+                    1016736608,
+                    1044122248,
+                    1117787424,
+                    1130635848,
+                    1130649544,
+                    1161827976,
+                    1196953168,
+                    1197635184,
+                    1158290496])
 
 # Add in entries from the AGASC supplement file, if possible, warn otherwise
 agasc_supplement_file = Path(os.environ['SKA']) / 'data' / 'agasc' / 'agasc_supplement.h5'

proseco/characteristics_acq.py

@@ -84,6 +84,7 @@ def _get_fid_acq_stages():
     out.add_index('spoiler_score')
     return out
 
+
 fid_acq_stages = _get_fid_acq_stages()
 
 # For a given box size, set the mag limit to the magnitude where one expects

proseco/characteristics_guide.py

@@ -35,7 +35,7 @@
     "Intercept": 9,
     "Slope": 0.5,
     "MagDiffLimit": -1 * np.inf,
-    }
+}
 
 # Search Stages
 stages = [{"Stage": 1,
@@ -44,77 +44,76 @@
            "MagLimit": [6.2, 10.2],
            "DoBminusVcheck": 1,
            "Spoiler": {
-            "BgPixThresh": 25,
-            "RegionFrac": .05,
-            },
+               "BgPixThresh": 25,
+               "RegionFrac": .05,
+           },
            "Imposter": {
-            "CentroidOffsetLim": .2,
-            }},
+               "CentroidOffsetLim": .2,
+           }},
           {"Stage": 2,
            "SigErrMultiplier": 2,
            "ASPQ1Lim": 0,
            "MagLimit": [6.2, 10.2],
            "DoBminusVcheck": 1,
            "Spoiler": {
-            "BgPixThresh": 25,
-            "RegionFrac": .05,
-            },
+               "BgPixThresh": 25,
+               "RegionFrac": .05,
+           },
            "Imposter": {
-            "CentroidOffsetLim": .5,
-            }},
+               "CentroidOffsetLim": .5,
+           }},
           {"Stage": 3,
            "SigErrMultiplier": 1,
            "ASPQ1Lim": 10,
            "MagLimit": [6.1, 10.3],
            "DoBminusVcheck": 1,
            "Spoiler": {
-            "BgPixThresh": 25,
-            "RegionFrac": .05,
-            },
+               "BgPixThresh": 25,
+               "RegionFrac": .05,
+           },
            "Imposter": {
-            "CentroidOffsetLim": 1.0,
-            }},
+               "CentroidOffsetLim": 1.0,
+           }},
           {"Stage": 4,
            "SigErrMultiplier": 0,
            "ASPQ1Lim": 20,
            "MagLimit": [6.0, 10.3],
            "DoBminusVcheck": 1,
            "Spoiler": {
-            "BgPixThresh": 25,
-            "RegionFrac": .05,
-            },
+               "BgPixThresh": 25,
+               "RegionFrac": .05,
+           },
            "Imposter": {
-            "CentroidOffsetLim": 2.0,
-            }},
+               "CentroidOffsetLim": 2.0,
+           }},
           {"Stage": 5,
            "SigErrMultiplier": 0,
            "ASPQ1Lim": 20,
            "MagLimit": [5.9, 10.3],
            "DoBminusVcheck": 0,
            "Spoiler": {
-            "BgPixThresh": 25,
-            "RegionFrac": .05,
-            },
+               "BgPixThresh": 25,
+               "RegionFrac": .05,
+           },
            "Imposter": {
-            "CentroidOffsetLim": 3.5,
-            }},
+               "CentroidOffsetLim": 3.5,
+           }},
           {"Stage": 6,
            "SigErrMultiplier": 0,
            "ASPQ1Lim": 20,
            "MagLimit": [5.6, 10.3],
            "DoBminusVcheck": 0,
            "Spoiler": {
-            "BgPixThresh": 25,
-            "RegionFrac": .05,
-            },
+               "BgPixThresh": 25,
+               "RegionFrac": .05,
+           },
            "Imposter": {
-            "CentroidOffsetLim": 4.0,
-            },
+               "CentroidOffsetLim": 4.0,
+           },
            }
           ]
 
 
-
 # Guide cluster checks.
 # Index is the "n_minus" value, so n - 0 stars need minimum 2500 max separation
 # n - 1 stars require 1000 arcsec separation.

proseco/core.py

@@ -333,12 +333,14 @@ def __repr__(self):
         return (f'<{self.__class__.__name__} name={self.name} default={self.default} '
                 f'pickle={self.pickle}>')
 
+
 class QuatMetaAttribute(MetaAttribute):
     def __set__(self, instance, value):
         if not isinstance(value, Quat):
             value = Quat(value)
         instance.meta[self.name] = value
 
+
 class IntMetaAttribute(MetaAttribute):
     def __set__(self, instance, value):
         instance.meta[self.name] = int(value)
@@ -1154,7 +1156,7 @@ def add_agasc_id(self, agasc_id):
         self.add_row(stars[0])
 
     def add_fake_constellation(self, n_stars=8, size=1500, mag=7.0, **attrs):
-        """
+        r"""
         Add a fake constellation of up to 8 stars consisting of a cross and square::
 
                 *
@@ -1206,7 +1208,7 @@ def add_fake_constellation(self, n_stars=8, size=1500, mag=7.0, **attrs):
             self.add_fake_star(**{name: val for name, val in zip(names, vals)})
 
     def add_fake_star(self, **star):
-        """
+        r"""
         Add a star to the current StarsTable.
 
         The input kwargs must have at least:
@@ -1383,48 +1385,48 @@ def get_kwargs_from_starcheck_text(obs_text, include_cat=False, force_catalog=Fa
           'sim_offset': 0,
           'focus_offset': 0}
     try:
-        kw['obsid'] = int(re.search("OBSID:\s(\d+).*", obs_text).group(1))
-    except:
+        kw['obsid'] = int(re.search(r"OBSID:\s(\d+).*", obs_text).group(1))
+    except Exception:
         # Nothing else will work so raise an exception
         raise ValueError('text does not have OBSID: <obsid>, does not look like appropriate text')
 
     try:
         out = get_coords(obs_text)
         kw['att'] = [out['point_ra'], out['point_dec'], out['point_roll']]
-    except:
+    except Exception:
         try:
             out = get_manvrs(obs_text)[-1]
             kw['att'] = [out['target_Q1'], out['target_Q2'], out['target_Q3'], out['target_Q4']]
-        except:
+        except Exception:
             pass
 
     try:
         out = get_manvrs(obs_text)[-1]
         kw['man_angle'] = out['angle_deg']
-    except:
+    except Exception:
         pass
 
     try:
         out = get_dither(obs_text)
         kw['dither'] = (out['dither_y_amp'], out['dither_z_amp'])
-    except:
+    except Exception:
         pass
 
     try:
         ccd_temp = get_pred_temp(obs_text)
         kw['t_ccd'] = ccd_temp
-    except:
+    except Exception:
         pass
 
     try:
         starcat_hdr = get_starcat_header(obs_text)
         kw['date'] = starcat_hdr['mp_starcat_time']
-    except:
+    except Exception:
         pass
 
     try:
         cat = Table(get_catalog(obs_text))
-    except:
+    except Exception:
         pass
     else:
         fid_or_mon = np.in1d(cat['type'], ('FID', 'MON'))
@@ -1444,7 +1446,7 @@ def get_kwargs_from_starcheck_text(obs_text, include_cat=False, force_catalog=Fa
         kw['detector'] = targ['sci_instr']
         kw['sim_offset'] = targ['sim_z_offset_steps']
         kw['focus_offset'] = 0
-    except:
+    except Exception:
         pass
 
     return kw