Merge pull request #172 from sot/pep8

Fix PEP8 and flake8 issues and add flake8 checking

.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 Ska --count --exclude=Ska/engarchive/file_defs.py --ignore=W503,W504 --max-line-length=100 --show-source --statistics

Ska/engarchive/__init__.py

@@ -1,5 +1,5 @@
 # Licensed under a 3-clause BSD style license - see LICENSE.rst
-from .version import __version__, __git_version__
+from .version import __version__, __git_version__  # noqa
 
 
 def test(*args, **kwargs):

Ska/engarchive/add_derived.py

@@ -167,5 +167,6 @@ def main():
 
         add_colname(msid_files['colnames_all'].rel, 'QUALITY')
 
+
 if __name__ == '__main__':
     main()

Ska/engarchive/cache.py

@@ -1,4 +1,4 @@
-## {{{ http://code.activestate.com/recipes/498245/ (r6)
+# {{{ http://code.activestate.com/recipes/498245/ (r6)
 # Licensed under a 3-clause BSD style license - see LICENSE.rst
 import collections
 import functools
@@ -7,11 +7,16 @@
 from heapq import nsmallest
 from operator import itemgetter
 
+
 class Counter(dict):
     'Mapping where default values are zero'
+
     def __missing__(self, key):
         return 0
 
+
+# TODO: replace with std_library version of this in Py3.6 (issue #173)
+
 def lru_cache(maxsize=30):
     '''Least-recently-used cache decorator.
 
@@ -22,13 +27,13 @@ def lru_cache(maxsize=30):
 
     '''
     maxqueue = maxsize * 10
+
     def decorating_function(user_function,
-            len=len, iter=iter, tuple=tuple, sorted=sorted, KeyError=KeyError):
+                            len=len, iter=iter, tuple=tuple, sorted=sorted, KeyError=KeyError):
         cache = {}                  # mapping of args to results
-        queue = collections.deque() # order that keys have been used
+        queue = collections.deque()  # order that keys have been used
         refcount = Counter()        # times each key is in the queue
         sentinel = object()         # marker for looping around the queue
-        kwd_mark = object()         # separate positional and keyword args
 
         # lookup optimizations (ugly but fast)
         queue_append, queue_popleft = queue.append, queue.popleft
@@ -38,7 +43,7 @@ def decorating_function(user_function,
         def wrapper(*args, **kwds):
             # cache key records both positional args only
             key = args
-            #if kwds:
+            # if kwds:
             #    key += (kwd_mark,) + tuple(sorted(kwds.items()))
 
             # record recent use of this key
@@ -69,11 +74,10 @@ def wrapper(*args, **kwds):
                 refcount.clear()
                 queue_appendleft(sentinel)
                 for key in filterfalse(refcount.__contains__,
-                                        iter(queue_pop, sentinel)):
+                                       iter(queue_pop, sentinel)):
                     queue_appendleft(key)
                     refcount[key] = 1
 
-
             return result
 
         def clear():
@@ -142,7 +146,7 @@ def clear():
 
     @lru_cache(maxsize=20)
     def f(x, y):
-        return 3*x+y
+        return 3 * x + y
 
     domain = list(range(5))
     from random import choice
@@ -153,12 +157,12 @@ def f(x, y):
 
     @lfu_cache(maxsize=20)
     def f(x, y):
-        return 3*x+y
+        return 3 * x + y
 
     domain = list(range(5))
     from random import choice
     for i in range(1000):
         r = f(choice(domain), choice(domain))
 
     print((f.hits, f.misses))
-## end of http://code.activestate.com/recipes/498245/ }}}
+# end of http://code.activestate.com/recipes/498245/ }}}

Ska/engarchive/check_integrity.py

@@ -11,7 +11,6 @@
 import pyyaks.context
 
 import Ska.engarchive.fetch as fetch
-import Ska.engarchive.file_defs as file_defs
 import Ska.DBI
 
 opt = None
@@ -102,7 +101,7 @@ def check_filetype(filetype):
     if archfile['rowstop'] != length:
         logger.info('ERROR: inconsistent archfile {}: '
                     'last rowstop={} MSID length={}'.format(
-            ft['content'], archfile['rowstop'], length))
+                        ft['content'], archfile['rowstop'], length))
         if opt.find_glitch:
             find_glitch()
 
@@ -118,7 +117,7 @@ def find_glitch():
 
     for archfile in archfiles:
         logger.verbose('archfile {} {} {}'.format(
-                archfile['filename'], archfile['year'], archfile['doy']))
+            archfile['filename'], archfile['year'], archfile['doy']))
         tstart = archfile['tstart']
         rowstart = archfile['rowstart']
         if abs(tstart - times[rowstart]) > opt.max_tstart_mismatch:

Ska/engarchive/converters.py

@@ -161,6 +161,7 @@ def _convert(dat):
 
     return _convert
 
+
 orbitephem0 = generic_converter('orbitephem0', add_quality=True)
 lunarephem0 = generic_converter('lunarephem0', add_quality=True)
 solarephem0 = generic_converter('solarephem0', add_quality=True)
@@ -180,6 +181,7 @@ def parse_alias_str(alias_str, invert=False):
             aliases[cxcmsid] = msid
     return aliases
 
+
 ALIASES = {'simdiag': """
     RAMEXEC          3SDSWELF   SEA CSC Exectuting from RAM
     DSTACKPTR        3SDPSTKP   SEA Data Stack Ptr
@@ -526,7 +528,7 @@ def acisdeahk(dat):
         vals = tuple((0.0 if bad else query_vals[id_idxs[query_id]])
                      for bad, query_id in zip(bads, col_query_ids))
         val_tus = tuple((0 if bad else query_val_tus[id_idxs[query_id]])
-                     for bad, query_id in zip(bads, col_query_ids))
+                        for bad, query_id in zip(bads, col_query_ids))
 
         # Now have another pass at finding bad values.  Take these out now so the
         # 5min and daily stats are not frequently corrupted.
@@ -537,11 +539,12 @@ def acisdeahk(dat):
         outs.append((times[i0], quality) + vals)
 
     dtype = [('TIME', numpy.float64),
-              ('QUALITY', numpy.bool, (len(col_names) + 2,))]
+             ('QUALITY', numpy.bool, (len(col_names) + 2,))]
     dtype += [(col_name, numpy.float32) for col_name in col_names]
 
     return numpy.rec.fromrecords(outs, dtype=dtype)
 
+
 def _get_deahk_cols():
     out = [
         {
@@ -746,9 +749,10 @@ def _get_deahk_cols():
             "unit": "V",
             "descr": "Ground"
         }
-        ]
+    ]
     return out
 
+
 def pyfits_to_recarray(dat):
     dtypes = []
     colnames = dat.dtype.names

Ska/engarchive/derived/__init__.py

@@ -9,11 +9,11 @@
 MSIDs.
 """
 
-from .base import *
+from .base import *  # noqa
 
-from .thermal import *
-from .test import *
-from .acispow import *
-from .pcad import *
-from .orbit import *
-from .eps import *
+from .thermal import *  # noqa
+from .test import *  # noqa
+from .acispow import *  # noqa
+from .pcad import *  # noqa
+from .orbit import *  # noqa
+from .eps import *  # noqa

Ska/engarchive/derived/acispow.py

@@ -3,17 +3,17 @@
 Derived parameter MSIDs related to ACIS power.
 """
 
-import numpy as np
 from . import base
 
+
 class DP_DPA_POWER(base.DerivedParameter):
     """ACIS total DPA-A and DPA-B power"""
     rootparams = ['1dp28avo', '1dpicacu', '1dp28bvo', '1dpicbcu']
     time_step = 32.8
     content_root = 'acispow'
 
     def calc(self, data):
-        power = (data['1dp28avo'].vals * data['1dpicacu'].vals + 
+        power = (data['1dp28avo'].vals * data['1dpicacu'].vals +
                  data['1dp28bvo'].vals * data['1dpicbcu'].vals)
         return power
 
@@ -36,8 +36,7 @@ class DP_PSMC_POWER(base.DerivedParameter):
     content_root = 'acispow'
 
     def calc(self, data):
-        power = (data['1dp28avo'].vals * data['1dpicacu'].vals + 
+        power = (data['1dp28avo'].vals * data['1dpicacu'].vals +
                  data['1dp28bvo'].vals * data['1dpicbcu'].vals +
                  data['1de28avo'].vals * data['1deicacu'].vals)
         return power
-

Ska/engarchive/derived/base.py

@@ -1,28 +1,30 @@
 # Licensed under a 3-clause BSD style license - see LICENSE.rst
-from __future__ import print_function, division, absolute_import
 
 from Chandra.Time import DateTime
-from .. import fetch
+from .. import fetch, fetch_eng
 import Ska.Numpy
 import numpy as np
 from .. import cache
- 
+
 __all__ = ['MNF_TIME', 'times_indexes', 'DerivedParameter']
 
 MNF_TIME = 0.25625              # Minor Frame duration (seconds)
 
+
 def times_indexes(start, stop, dt):
     index0 = DateTime(start).secs // dt
     index1 = DateTime(stop).secs // dt + 1
     indexes = np.arange(index0, index1, dtype=np.int64)
     times = indexes * dt
     return times, indexes
 
+
 @cache.lru_cache(20)
 def interpolate_times(keyvals, len_data_times, data_times=None, times=None):
     return Ska.Numpy.interpolate(np.arange(len_data_times),
                                  data_times, times, method='nearest')
 
+
 class DerivedParameter(object):
     max_gap = 66.0              # Max allowed data gap (seconds)
     max_gaps = {}
@@ -41,9 +43,9 @@ def fetch(self, start, stop):
         # Translate state codes "ON" and "OFF" to 1 and 0, respectively.
         for data in dataset.values():
             if (data.vals.dtype.name == 'str96'
-                and set(data.vals).issubset(set(['ON ', 'OFF']))):
+                    and set(data.vals).issubset(set(['ON ', 'OFF']))):
                 data.vals = np.where(data.vals == 'OFF', np.int8(0), np.int8(1))
-                    
+
         times, indexes = times_indexes(start, stop, self.time_step)
         bads = np.zeros(len(times), dtype=np.bool)  # All data OK (false)
 
@@ -59,9 +61,9 @@ def fetch(self, start, stop):
                       .format(msidname, DateTime(start).date, DateTime(stop).date))
             keyvals = (data.content, data.times[0], data.times[-1],
                        len(times), times[0], times[-1])
-            idxs = interpolate_times(keyvals, len(data.times), 
+            idxs = interpolate_times(keyvals, len(data.times),
                                      data_times=data.times, times=times)
-            
+
             # Loop over data attributes like "bads", "times", "vals" etc and
             # perform near-neighbor interpolation by indexing
             for attr in data.colnames:
@@ -92,9 +94,9 @@ def __call__(self, start, stop):
         # Translate state codes "ON" and "OFF" to 1 and 0, respectively.
         for data in dataset.values():
             if (data.vals.dtype.name == 'string24'
-                and set(data.vals) == set(('ON ', 'OFF'))):
+                    and set(data.vals) == set(('ON ', 'OFF'))):
                 data.vals = np.where(data.vals == 'OFF', np.int8(0), np.int8(1))
-                    
+
         dataset.interpolate(dt=self.time_step)
 
         # Return calculated values.  Np.asarray will copy the array only if

Ska/engarchive/derived/eps.py

@@ -16,7 +16,7 @@ class DerivedParameterEps(base.DerivedParameter):
     content_root = 'eps'
 
 
-#--------------------------------------------
+# --------------------------------------------
 class DP_BATT1_TAVE(DerivedParameterEps):
     """Battery 1 Average Temperature. Derived from average of all three battery temperature sensors.
         Telemetry 16x / MF
@@ -30,7 +30,7 @@ def calc(self, data):
         return BATT1_TAVE
 
 
-#--------------------------------------------
+# --------------------------------------------
 class DP_BATT2_TAVE(DerivedParameterEps):
     """Battery 2 Average Temperature. Derived from average of all three battery temperature sensors.
         Telemetry 16x / MF
@@ -44,7 +44,7 @@ def calc(self, data):
         return BATT2_TAVE
 
 
-#--------------------------------------------
+# --------------------------------------------
 class DP_BATT3_TAVE(DerivedParameterEps):
     """Battery 3 Average Temperature. Derived from average of all three battery temperature sensors.
         Telemetry 16x / MF
@@ -58,7 +58,7 @@ def calc(self, data):
         return BATT3_TAVE
 
 
-#--------------------------------------------
+# --------------------------------------------
 class DP_EPOWER1(DerivedParameterEps):
     """Bus Power = ELBI_LOW * ELBV
         Telemetry 8x / MF
@@ -71,7 +71,7 @@ def calc(self, data):
         return EPOWER1
 
 
-#--------------------------------------------
+# --------------------------------------------
 class DP_MYSAPOW(DerivedParameterEps):
     """-Y Solar Array Power = ESAMYI * ELBV
         Telemetry 8x / MF
@@ -84,7 +84,7 @@ def calc(self, data):
         return MYSAPOW
 
 
-#--------------------------------------------
+# --------------------------------------------
 class DP_PYSAPOW(DerivedParameterEps):
     """+Y Solar Array Power = ESAPYI * ELBV
         Telemetry 8x / MF

Ska/engarchive/derived/orbit.py

@@ -70,6 +70,9 @@ def calc_orbital_elements(x, y, z, vx, vy, vz):
     def arccos_2pi(arg, reflect):
         """
         Return arccos(arg) where reflect is False, 2 * pi - arccos(arg) where reflect is True
+
+        :param arg: float, np.ndarray: input arg (radians)
+        :param reflect: bool, np.ndarray of bool: use reflected value
         """
         np_err_handling = np.geterr()
         np.seterr(all='raise')
@@ -81,9 +84,9 @@ def arccos_2pi(arg, reflect):
         np.seterr(**np_err_handling)
 
         try:
-            # Check if arg is a non-scalar numpy array
-            len(arg) and isinstance(arg, np.ndarray)
-        except:
+            # Check if arg has a length
+            len(arg)
+        except TypeError:
             if reflect:
                 out = 2 * pi - out
         else: