DM-14001: Make afw pep8 compliant and enable auto testing

.travis.yml

@@ -0,0 +1,8 @@
+sudo: false
+language: python
+matrix:
+  include:
+    - python: '3.6'
+      install:
+      - pip install flake8
+      script: flake8

bin.src/showCamera.py

@@ -32,8 +32,7 @@
     import argparse
 
     parser = argparse.ArgumentParser(description='Show the layout of CCDs in a camera.',
-                                     epilog=
-                                     'The corresponding obs-package must be setup (e.g. obs_decam ' +
+                                     epilog='The corresponding obs-package must be setup (e.g. obs_decam ' +
                                      'if you want to see DECam)'
                                      )
     parser.add_argument(
@@ -52,7 +51,7 @@
 
     try:
         __import__(obsPackageName)
-    except:
+    except Exception:
         print("Unable to import %s -- is it setup?" %
               (obsPackageName,), file=sys.stderr)
         sys.exit(1)

doc/doxygen.conf.in

@@ -2,15 +2,5 @@ EXAMPLE_PATH = examples
 INPUT += examples/imageDisplay.ipynb
 EXCLUDE += include/lsst/afw/detection/FootprintArray.cc
 EXCLUDE += include/lsst/afw/detection/detail/dgPsf.cc
-EXCLUDE += src/math/Stack.cc
-EXCLUDE += src/image/Utils.cc
-EXCLUDE += src/image/TanWcs.cc
-EXCLUDE += src/math/FunctionLibrary.cc
-EXCLUDE += src/table
-EXCLUDE += src/geom
-EXCLUDE += src/geom/ellipses
-EXCLUDE += src/detection/Psf.cc
-EXCLUDE += src/detection/DoubleGaussianPsf.cc
-EXCLUDE += src/fits.cc
-EXCLUDE += src/fitsCompression.cc
+EXCLUDE_PATTERNS += */src/*/*.cc
 EXCLUDE_SYMBOLS += _swig_property

doc/imageAlgorithm.dox

@@ -1,7 +1,6 @@
 namespace lsst { namespace afw { namespace image {
 /**
 \page afwSecImageAlgorithm  How to use algorithms to manipulate Images
-\section afwSecImageAlgorithm  How to use algorithms to manipulate Images
 
 All of these algorithms require the inclusion of <TT>lsst/afw/image/ImageAlgorithm.h</TT>, and are in namespace @c lsst::afw::image.
 

doc/imageDisplay.dox

@@ -1,7 +1,6 @@
 namespace lsst { namespace afw { namespace image {
 /**
 \page afwSecDisplay  How to display images
-\section afwSecDisplay  How to display images
 
  - \ref afwSecImageDisplay
  - \ref afwSecImageTypes

doc/imagePython.dox

@@ -1,6 +1,6 @@
 namespace lsst { namespace afw { namespace image {
 /**
-\page afwSecPyImage How to manipulate images from python
+\page afwSecPyImagePage How to manipulate images from python
 \section afwSecPyImage How to manipulate images from python
 
 You can use the C++ APIs to manipulate images and bits of images from python, e.g.

doc/mainpage.dox

@@ -19,7 +19,7 @@ by an image processing system.  In particular:
 
 namespace lsst { namespace afw { namespace image {
 /**
-\page afwSecImage Images
+\page afwSecImagePage Images
 
 \section afwSecImage Images
 
@@ -213,7 +213,7 @@ previous APIs)
 
 namespace lsst { namespace afw { namespace image {
 /**
-\page afwSecImageIO Image I/O
+\page afwSecImageIOPage Image/Mask/MaskedImage I/O
 \section afwSecImageIO Image/Mask/MaskedImage I/O
 
 Reading Image%s, Mask%s, and MaskedImage%s from FITS files is achieved via their
@@ -288,7 +288,6 @@ but \b not possible to read it back from a non-default HDU.
 namespace lsst { namespace afw { namespace math {
 /**
 \page afwSecMath Mathematical Operations
-\section afwSecMath Mathematical Operations
 
  - Statistics.
 Annotated examples are available for \link StatisticsExample Statistics\endlink.
@@ -308,7 +307,6 @@ Annotated examples are available for \link BackgroundExample Background Estimati
 namespace lsst { namespace afw { namespace detection {
 /**
 \page afwSecDetection Detection
-\section afwSecDetection Detection
 
 Detected pixels are manipulated using the following classes:
  - Footprint : A set of pixels above (or below) a Threshold

examples/ellipsePixelRegion.py

@@ -29,10 +29,6 @@ def main():
     transX = mgt[0, 0] * allX + mgt[0, 1] * allY + mgt[0, 2]
     transY = mgt[1, 0] * allX + mgt[1, 1] * allY + mgt[1, 2]
     allR = (transX**2 + transY**2)**0.5
-    for span in region:
-        for point in span:
-            transPoint = gt(lsst.afw.geom.Point2D(point))
-            r = (transPoint.getX()**2 + transPoint.getY()**2)**0.5
     pyplot.plot(ellX, ellY, 'ro', markeredgewidth=0, alpha=0.5)
     pyplot.plot(allX[allR < 1], allY[allR < 1], '+')
     pyplot.plot(allX[allR > 1], allY[allR > 1], 'x')

examples/estimateBackground.py

@@ -51,8 +51,6 @@ def simpleBackground(image):
 
     bkgd = afwMath.makeBackground(image, bctrl)
 
-    statsImage = bkgd.getStatsImage()
-
     image -= bkgd.getImageF(afwMath.Interpolate.NATURAL_SPLINE)
 
     return bkgd
@@ -82,9 +80,6 @@ def complexBackground(image):
     statsImage = bkgd.getStatsImage()
     ds9.mtv(statsImage.getVariance())
 
-    bkdgImages = dict(SPLINE = bkgd.getImageF(afwMath.Interpolate.NATURAL_SPLINE),
-                      LINEAR = bkgd.getImageF(afwMath.Interpolate.LINEAR))
-
     return bkgd
 
 

examples/statisticsNaN.py

@@ -43,13 +43,13 @@ def main():
     inImage = afwImage.ImageF(afwGeom.Extent2I(100, 100))
     inImage.set(1)
     if disp:
-        ds9.mtv(inImage, frame = 0)
+        ds9.mtv(inImage, frame=0)
 
     # works
     outImage = afwImage.ImageF(afwGeom.Extent2I(100, 100))
     afwMath.convolve(outImage, inImage, gaussKernel, False, True)
     if disp:
-        ds9.mtv(outImage, frame = 1)
+        ds9.mtv(outImage, frame=1)
     print("Should be a number: ", afwMath.makeStatistics(
         outImage, afwMath.MEAN).getValue())
     print("Should be a number: ", afwMath.makeStatistics(
@@ -59,7 +59,7 @@ def main():
     outImage = afwImage.ImageF(afwGeom.Extent2I(100, 100))
     afwMath.convolve(outImage, inImage, gaussKernel, False, False)
     if disp:
-        ds9.mtv(outImage, frame = 2)
+        ds9.mtv(outImage, frame=2)
     print("Should be a number: ", afwMath.makeStatistics(
         outImage, afwMath.MEAN).getValue())
     print("Should be a number: ", afwMath.makeStatistics(
@@ -68,8 +68,8 @@ def main():
     # This will print nan
     sctrl = afwMath.StatisticsControl()
     sctrl.setNanSafe(False)
-    print ("Should be a nan (nanSafe set to False): " +
-           str(afwMath.makeStatistics(outImage, afwMath.MEAN, sctrl).getValue()))
+    print("Should be a nan (nanSafe set to False): " +
+          str(afwMath.makeStatistics(outImage, afwMath.MEAN, sctrl).getValue()))
 
 
 if __name__ == '__main__':

examples/timeLeastSquares.py

@@ -5,7 +5,7 @@
 import sys
 import numpy
 from matplotlib import pyplot
-from lsst.afw.math import LeastSquares
+from lsst.afw.math import LeastSquares  # noqa F401
 
 nDataList = 2**numpy.arange(4, 14, 2, dtype=int)
 dimensionList = 2**numpy.arange(1, 8, dtype=int)
@@ -37,7 +37,7 @@ def run(number=10):
             for j, dimension in enumerate(dimensionList):
                 if dimension <= nData:
                     results[method][i, j] = timeit.timeit(statement % method, setup % (nData, dimension),
-                                                          number = number) / number
+                                                          number=number) / number
                     progress += 1
                 else:
                     results[method][i, j] = float("NaN")

examples/timeWarpExposure.py

@@ -174,13 +174,13 @@ def run():
                         interpLength,
                     )
                     destWcs = makeWcs(
-                        projName = "TAN",
-                        destCtrInd = destCtrInd,
-                        skyOffset = skyOffset,
-                        rotAng = rotAng,
-                        scaleFac = scaleFac,
-                        srcWcs = srcWcs,
-                        srcCtrInd = srcCtrInd,
+                        projName="TAN",
+                        destCtrInd=destCtrInd,
+                        skyOffset=skyOffset,
+                        rotAng=rotAng,
+                        scaleFac=scaleFac,
+                        srcWcs=srcWcs,
+                        srcCtrInd=srcCtrInd,
                     )
                     destExposure.setWcs(destWcs)
                     dTime, nIter, goodPix = timeWarp(

examples/warpExposure.py

@@ -47,7 +47,7 @@ def main():
                       help="kernel type: bilinear or lancszosN where N = order; default=%s" % (DefKernel,))
     parser.add_option("-v", "--verbosity",
                       type=int, default=DefVerbosity,
-                      help="verbosity of diagnostic trace messages; 1 for just TRACE1, more for more" +
+                      help="verbosity of diagnostic trace messages; 1 for just TRACE1, more for more"
                       " information; default=%s" % (DefVerbosity,))
 
     (opt, args) = parser.parse_args()

include/lsst/afw/image/Filter.h

@@ -162,7 +162,7 @@ class Filter {
      * @param metadata Metadata to process (e.g. a IFITS header)
      * @param force Allow us to construct an unknown Filter
      */
-    explicit Filter(std::shared_ptr<lsst::daf::base::PropertySet const>, bool const force = false);
+    explicit Filter(std::shared_ptr<lsst::daf::base::PropertySet const> metadata, bool const force = false);
 
     Filter(Filter const&) = default;
     Filter(Filter&&) = default;

include/lsst/afw/math/Random.h

@@ -299,7 +299,7 @@ class Random {
      * @throws lsst::pex::exceptions::InvalidParameterError
      *      Thrown if the requested algorithm is not supported.
      */
-    void initialize(std::string const &);
+    void initialize(std::string const & algorithm);
 };
 
 /*

include/lsst/afw/math/detail/Convolve.h

@@ -79,7 +79,7 @@ void basicConvolve(OutImageT& convolvedImage, InImageT const& inImage, lsst::afw
 template <typename OutImageT, typename InImageT>
 void basicConvolve(OutImageT& convolvedImage, InImageT const& inImage,
                    lsst::afw::math::DeltaFunctionKernel const& kernel,
-                   lsst::afw::math::ConvolutionControl const&);
+                   lsst::afw::math::ConvolutionControl const& convolutionControl);
 
 /**
  * A version of basicConvolve that should be used when convolving a LinearCombinationKernel

lib/libafw.so-gdb.py

@@ -1,4 +1,5 @@
-import os, os.path, sys
+import os
+import sys
 import lsst.utils
 import gdb
 #

python/lsst/afw/cameraGeom/assembleImage.py

@@ -68,7 +68,7 @@ def assembleAmplifierImage(destImage, rawImage, amplifier):
     """
     if not amplifier.getHasRawInfo():
         raise RuntimeError("amplifier must contain raw amplifier info")
-    if type(destImage.Factory) != type(rawImage.Factory):
+    if type(destImage.Factory) != type(rawImage.Factory):  # noqa E721
         raise RuntimeError("destImage type = %s != %s = rawImage type" %
                            type(destImage.Factory).__name__, type(rawImage.Factory).__name__)
     inView = rawImage.Factory(rawImage, amplifier.getRawDataBBox())
@@ -95,7 +95,7 @@ def assembleAmplifierRawImage(destImage, rawImage, amplifier):
     """
     if not amplifier.getHasRawInfo():
         raise RuntimeError("amplifier must contain raw amplifier info")
-    if type(destImage.Factory) != type(rawImage.Factory):
+    if type(destImage.Factory) != type(rawImage.Factory):  # noqa E721
         raise RuntimeError("destImage type = %s != %s = rawImage type" %
                            type(destImage.Factory).__name__, type(rawImage.Factory).__name__)
     inBBox = amplifier.getRawBBox()

python/lsst/afw/cameraGeom/camera.py

@@ -29,7 +29,7 @@
 
 class Camera(DetectorCollection):
     """!A collection of Detectors plus additional coordinate system support
-    
+
     Camera.transform transforms points from one camera coordinate system to another.
 
     Camera.getTransform returns a transform between camera coordinate systems.

python/lsst/afw/cameraGeom/cameraConfig.py

@@ -26,13 +26,13 @@ class DetectorConfig(pexConfig.Config):
         "x offset from the origin of the camera in mm in the transposed system.", float)
     offset_y = pexConfig.Field(
         "y offset from the origin of the camera in mm in the transposed system.", float)
-    refpos_x = pexConfig.Field("x position of the reference point in the detector in pixels " +
+    refpos_x = pexConfig.Field("x position of the reference point in the detector in pixels "
                                "in transposed coordinates.", float)
-    refpos_y = pexConfig.Field("y position of the reference point in the detector in pixels " +
+    refpos_y = pexConfig.Field("y position of the reference point in the detector in pixels "
                                "in transposed coordinates.", float)
-    yawDeg = pexConfig.Field("yaw (rotation about z) of the detector in degrees. " +
-                             "This includes any necessary rotation to go from " +
-                             "detector coordinates to camera coordinates " +
+    yawDeg = pexConfig.Field("yaw (rotation about z) of the detector in degrees. "
+                             "This includes any necessary rotation to go from "
+                             "detector coordinates to camera coordinates "
                              "after optional transposition.", float)
     pitchDeg = pexConfig.Field(
         "pitch (rotation about y) of the detector in degrees", float)
@@ -59,8 +59,8 @@ def getCrosstalk(self, numAmps):
             return None
         try:
             return np.array(self.crosstalk, dtype=np.float32).reshape((numAmps, numAmps))
-        except:
-            raise RuntimeError("Cannot reshape 'crosstalk' coefficients to square matrix")
+        except Exception as e:
+            raise RuntimeError("Cannot reshape 'crosstalk' coefficients to square matrix: %s" % (e,))
 
 
 class CameraConfig(pexConfig.Config):

python/lsst/afw/cameraGeom/cameraFactory.py

@@ -36,10 +36,10 @@ def makeDetector(detectorConfig, ampInfoCatalog, focalPlaneToField):
 
     tanPixSys = CameraSys(TAN_PIXELS, detectorConfig.name)
     transforms[tanPixSys] = makePixelToTanPixel(
-        bbox = bbox,
-        orientation = orientation,
-        focalPlaneToField = focalPlaneToField,
-        pixelSizeMm = pixelSizeMm,
+        bbox=bbox,
+        orientation=orientation,
+        focalPlaneToField=focalPlaneToField,
+        pixelSizeMm=pixelSizeMm,
     )
 
     args = [
@@ -154,9 +154,9 @@ def makeCameraFromCatalogs(cameraConfig, ampInfoCatDict,
         ampInfoCatalog = ampInfoCatDict[detectorConfig.name]
 
         detectorList.append(makeDetector(
-            detectorConfig = detectorConfig,
-            ampInfoCatalog = ampInfoCatalog,
-            focalPlaneToField = focalPlaneToField,
+            detectorConfig=detectorConfig,
+            ampInfoCatalog=ampInfoCatalog,
+            focalPlaneToField=focalPlaneToField,
         ))
 
     return Camera(cameraConfig.name, detectorList, transformMap, pupilFactoryClass)

python/lsst/afw/cameraGeom/testUtils.py

@@ -96,10 +96,10 @@ def __init__(self,
                                0.0, self.radialDistortion/pScaleRad]
         focalPlaneToField = afwGeom.makeRadialTransform(radialDistortCoeffs)
         pixelToTanPixel = makePixelToTanPixel(
-            bbox = self.bbox,
-            orientation = self.orientation,
-            focalPlaneToField = focalPlaneToField,
-            pixelSizeMm = self.pixelSize,
+            bbox=self.bbox,
+            orientation=self.orientation,
+            focalPlaneToField=focalPlaneToField,
+            pixelSizeMm=self.pixelSize,
         )
 
         self.transMap = {

python/lsst/afw/cameraGeom/transformConfig.py

@@ -6,12 +6,12 @@
 
 class TransformMapConfig(pexConfig.Config):
     transforms = pexConfig.ConfigDictField(
-        doc = "Dict of coordinate system name: TransformConfig",
-        keytype = str,
-        itemtype = TransformConfig,
+        doc="Dict of coordinate system name: TransformConfig",
+        keytype=str,
+        itemtype=TransformConfig,
     )
     nativeSys = pexConfig.Field(
-        doc = "Name of reference coordinate system",
-        dtype = str,
-        optional = False,
+        doc="Name of reference coordinate system",
+        dtype=str,
+        optional=False,
     )

python/lsst/afw/cameraGeom/utils.py

@@ -155,7 +155,7 @@ def plotFocalPlane(camera, fieldSizeDeg_x=0, fieldSizeDeg_y=None, dx=0.1, dy=0.1
 
 
 def makeImageFromAmp(amp, imValue=None, imageFactory=afwImage.ImageU, markSize=10, markValue=0,
-                     scaleGain = lambda gain: (gain*1000)//10):
+                     scaleGain=lambda gain: (gain*1000)//10):
     """!Make an image from an amp object
 
     Since images are integer images by default, the gain needs to be scaled to give enough dynamic range

python/lsst/afw/detection/footprintMerge.py

@@ -16,12 +16,12 @@ def getMergedSourceCatalog(self, catalogs, filters,
     # if peak is not an array, create an array the size of catalogs
     try:
         len(samePeakDist)
-    except:
+    except TypeError:
         samePeakDist = [samePeakDist] * len(catalogs)
 
     try:
         len(peakDist)
-    except:
+    except TypeError:
         peakDist = [peakDist] * len(catalogs)
 
     if len(peakDist) != len(catalogs):