From afe0a5e3650cccc19803f4e766848d2362cdff4f Mon Sep 17 00:00:00 2001 From: James Turner Date: Wed, 21 Dec 2016 21:49:16 -0300 Subject: Rename iraf.kepler, since it depends on pyraf, and patch it to use io.fits instead of pyfits (etc.). There are still a couple of broken imports left -- one that was also missing in Ureka and another that currently prevents the pkg loading. --- iraf.kepler/bld.bat | 2 - iraf.kepler/build.sh | 8 - iraf.kepler/meta.yaml | 37 --- iraf.kepler/post-link.sh | 3 - iraf.kepler/pre-unlink.sh | 1 - iraf.kepler/ur_extern.pkg | 2 - iraf.kepler/ur_manifest | 0 iraf.kepler/ur_mkhelp_cmd | 1 - iraf.kepler/ur_mkpkg_cmd | 0 iraf.kepler/ur_mkpkg_patterns | 0 pyraf.kepler/ac.iraf.kepler.patch | 551 ++++++++++++++++++++++++++++++++++++++ pyraf.kepler/bld.bat | 2 + pyraf.kepler/build.sh | 8 + pyraf.kepler/meta.yaml | 40 +++ pyraf.kepler/post-link.sh | 3 + pyraf.kepler/pre-unlink.sh | 1 + pyraf.kepler/ur_extern.pkg | 2 + pyraf.kepler/ur_manifest | 0 pyraf.kepler/ur_mkhelp_cmd | 1 + pyraf.kepler/ur_mkpkg_cmd | 0 pyraf.kepler/ur_mkpkg_patterns | 0 21 files changed, 608 insertions(+), 54 deletions(-) delete mode 100644 iraf.kepler/bld.bat delete mode 100644 iraf.kepler/build.sh delete mode 100644 iraf.kepler/meta.yaml delete mode 100644 iraf.kepler/post-link.sh delete mode 100644 iraf.kepler/pre-unlink.sh delete mode 100644 iraf.kepler/ur_extern.pkg delete mode 100644 iraf.kepler/ur_manifest delete mode 100644 iraf.kepler/ur_mkhelp_cmd delete mode 100644 iraf.kepler/ur_mkpkg_cmd delete mode 100644 iraf.kepler/ur_mkpkg_patterns create mode 100644 pyraf.kepler/ac.iraf.kepler.patch create mode 100644 pyraf.kepler/bld.bat create mode 100644 pyraf.kepler/build.sh create mode 100644 pyraf.kepler/meta.yaml create mode 100644 pyraf.kepler/post-link.sh create mode 100644 pyraf.kepler/pre-unlink.sh create mode 100644 pyraf.kepler/ur_extern.pkg create mode 100644 pyraf.kepler/ur_manifest create mode 100644 pyraf.kepler/ur_mkhelp_cmd create mode 100644 pyraf.kepler/ur_mkpkg_cmd create mode 100644 pyraf.kepler/ur_mkpkg_patterns diff --git a/iraf.kepler/bld.bat b/iraf.kepler/bld.bat deleted file mode 100644 index e1aca7a..0000000 --- a/iraf.kepler/bld.bat +++ /dev/null @@ -1,2 +0,0 @@ -echo Not supported on Windows -exit 1 diff --git a/iraf.kepler/build.sh b/iraf.kepler/build.sh deleted file mode 100644 index 2353907..0000000 --- a/iraf.kepler/build.sh +++ /dev/null @@ -1,8 +0,0 @@ -# Configure the environment for IRAF, since conda build appears not to do -# "source activate" after installing dependencies (this would instead need to -# eval $PREFIX/iraf/unix/hlib/setup directly if "--level" needs specifying): -. setup_iraf.sh - -# Build from source in envs/_build (using build script from astroconda-utils): -ac_build_iraf_pkg - diff --git a/iraf.kepler/meta.yaml b/iraf.kepler/meta.yaml deleted file mode 100644 index 19a2ab5..0000000 --- a/iraf.kepler/meta.yaml +++ /dev/null @@ -1,37 +0,0 @@ -# This package is still missing dependencies in AstroConda and is not fully -# functional yet: -# - The package source needs patching to convert pyfits references to io.fits. -# - The "analysis" (& "transit"?) module used by ma02.py and, in turn, -# lightcurve.py & keptransit.py are missing from both AstroConda and Ureka. - -about: - home: http://iraf.noao.edu/ - license: US government notice, BSD, attribution requirement - summary: KEPLER package for IRAF -build: - binary_relocation: False - number: '0' - # These must be copied from astroconda-iraf-helpers, since conda disallows - # the post-install step from depending on other packages: - always_include_files: - - bin/ac_config_iraf_pkg - - bin/ac_update_extern_pkg -package: - name: iraf.kepler - version: "2.6.2" -source: - fn: PyKE_2.6.2.tar - url: http://astroconda-source:4440/PyKE_2.6.2.tar -requirements: - build: - - astroconda-iraf-helpers - - iraf !=2.16.1,>=2.16.UR - run: - - iraf !=2.16.1,>=2.16.UR - - pyraf - - astropy - - matplotlib - - numpy - - scipy - - mdp - diff --git a/iraf.kepler/post-link.sh b/iraf.kepler/post-link.sh deleted file mode 100644 index f0e5a63..0000000 --- a/iraf.kepler/post-link.sh +++ /dev/null @@ -1,3 +0,0 @@ -# Call a common script that updates extern.pkg for the new IRAF package: - -"$PREFIX/bin/ac_config_iraf_pkg" kepler diff --git a/iraf.kepler/pre-unlink.sh b/iraf.kepler/pre-unlink.sh deleted file mode 100644 index e8b9801..0000000 --- a/iraf.kepler/pre-unlink.sh +++ /dev/null @@ -1 +0,0 @@ -"$PREFIX/bin/ac_config_iraf_pkg" --remove kepler diff --git a/iraf.kepler/ur_extern.pkg b/iraf.kepler/ur_extern.pkg deleted file mode 100644 index 9b23cce..0000000 --- a/iraf.kepler/ur_extern.pkg +++ /dev/null @@ -1,2 +0,0 @@ -reset kepler = UR_VDIR -task kepler.pkg = kepler$kepler.cl diff --git a/iraf.kepler/ur_manifest b/iraf.kepler/ur_manifest deleted file mode 100644 index e69de29..0000000 diff --git a/iraf.kepler/ur_mkhelp_cmd b/iraf.kepler/ur_mkhelp_cmd deleted file mode 100644 index b193179..0000000 --- a/iraf.kepler/ur_mkhelp_cmd +++ /dev/null @@ -1 +0,0 @@ -echo "No help to build for kepler/PyKe" diff --git a/iraf.kepler/ur_mkpkg_cmd b/iraf.kepler/ur_mkpkg_cmd deleted file mode 100644 index e69de29..0000000 diff --git a/iraf.kepler/ur_mkpkg_patterns b/iraf.kepler/ur_mkpkg_patterns deleted file mode 100644 index e69de29..0000000 diff --git a/pyraf.kepler/ac.iraf.kepler.patch b/pyraf.kepler/ac.iraf.kepler.patch new file mode 100644 index 0000000..b83b1c8 --- /dev/null +++ b/pyraf.kepler/ac.iraf.kepler.patch @@ -0,0 +1,551 @@ +diff -Nur ../original/keparith.py ./keparith.py +--- ../original/keparith.py 2012-07-03 01:41:39.000000000 -0400 ++++ ./keparith.py 2016-12-21 20:27:17.646485000 -0300 +@@ -12,7 +12,7 @@ + + + import sys +-import pyfits ++import astropy.io.fits as pyfits + import matplotlib.pyplot as plt + import kepio, kepmsg, kepkey, kepfit, kepstat + from numpy import median,subtract,maximum,ones,multiply,float32,shape,absolute,mean,std,isfinite,where,nan +diff -Nur ../original/kepbin.py ./kepbin.py +--- ../original/kepbin.py 2012-05-18 18:34:31.000000000 -0400 ++++ ./kepbin.py 2016-12-21 20:27:17.703543000 -0300 +@@ -4,7 +4,7 @@ + sys.path.append('/usr/stsci/kepler/' ) + import kepio, kepmsg, kepkey + +-import pyfits ++import astropy.io.fits as pyfits + import pylab as plt + from scipy.interpolate import interp1d + from scipy import integrate +diff -Nur ../original/kepbls.py ./kepbls.py +--- ../original/kepbls.py 2014-06-26 19:42:44.000000000 -0400 ++++ ./kepbls.py 2016-12-21 20:27:17.723564000 -0300 +@@ -1,6 +1,6 @@ +-import numpy, scipy, sys, time, pyfits, pylab, math, re ++import numpy, scipy, sys, time, astropy.io.fits as pyfits, pylab, math, re + from scipy import stats +-from pyfits import * ++from astropy.io.fits import * + from pylab import * + from matplotlib import * + from math import * +diff -Nur ../original/kepclip.py ./kepclip.py +--- ../original/kepclip.py 2013-11-23 03:27:41.000000000 -0300 ++++ ./kepclip.py 2016-12-21 20:27:17.733572000 -0300 +@@ -1,6 +1,6 @@ + +-import numpy, sys, time, pyfits, pylab, math, re +-from pyfits import * ++import numpy, sys, time, astropy.io.fits as pyfits, pylab, math, re ++from astropy.io.fits import * + from pylab import * + from matplotlib import * + from math import * +diff -Nur ../original/kepconvert.py ./kepconvert.py +--- ../original/kepconvert.py 2014-03-26 18:16:28.000000000 -0300 ++++ ./kepconvert.py 2016-12-21 20:27:17.791629000 -0300 +@@ -1,6 +1,6 @@ + +-import numpy, sys, time, pyfits, re +-from pyfits import * ++import numpy, sys, time, astropy.io.fits as pyfits, re ++from astropy.io.fits import * + from numpy import * + import kepio, kepmsg, kepkey + +diff -Nur ../original/kepcotrend_cl.py ./kepcotrend_cl.py +--- ../original/kepcotrend_cl.py 2012-05-18 18:34:31.000000000 -0400 ++++ ./kepcotrend_cl.py 2016-12-21 20:27:17.812648000 -0300 +@@ -25,7 +25,7 @@ + from scipy.optimize import leastsq + from scipy.optimize import fmin as effmin + from scipy.interpolate import interp1d +-import pyfits ++import astropy.io.fits as pyfits + import sys + from numpy.linalg import lstsq, inv + from numpy import interp as interpolat +diff -Nur ../original/kepcotrend.py ./kepcotrend.py +--- ../original/kepcotrend.py 2014-03-26 18:16:28.000000000 -0300 ++++ ./kepcotrend.py 2016-12-21 20:27:17.801638000 -0300 +@@ -25,7 +25,7 @@ + from scipy.optimize import leastsq + from scipy.optimize import fmin as effmin + from scipy.interpolate import interp1d +-import pyfits ++import astropy.io.fits as pyfits + from numpy.linalg import lstsq, inv + from numpy import interp as interpolat + from numpy import * +diff -Nur ../original/kepdeltapix.py ./kepdeltapix.py +--- ../original/kepdeltapix.py 2013-04-25 20:45:18.000000000 -0300 ++++ ./kepdeltapix.py 2016-12-21 20:27:17.834670000 -0300 +@@ -1,8 +1,8 @@ +-import pylab, numpy, pyfits ++import pylab, numpy, astropy.io.fits as pyfits + from pylab import * + from matplotlib import * + from numpy import * +-from pyfits import * ++from astropy.io.fits import * + import kepio, kepmsg, kepkey, kepplot, kepfit, keparray + import sys, time, re, math, glob, random + +diff -Nur ../original/kepdetrend.py ./kepdetrend.py +--- ../original/kepdetrend.py 2013-02-25 23:05:36.000000000 -0300 ++++ ./kepdetrend.py 2016-12-21 20:27:17.844680000 -0300 +@@ -1,6 +1,6 @@ + +-import numpy, sys, time, pyfits, pylab, math, re +-from pyfits import * ++import numpy, sys, time, astropy.io.fits as pyfits, pylab, math, re ++from astropy.io.fits import * + from pylab import * + from matplotlib import * + from math import * +diff -Nur ../original/kepdiffim.py ./kepdiffim.py +--- ../original/kepdiffim.py 2012-06-08 12:16:03.000000000 -0400 ++++ ./kepdiffim.py 2016-12-21 20:27:17.858694000 -0300 +@@ -1,9 +1,9 @@ + +-import pylab, numpy, pyfits ++import pylab, numpy, astropy.io.fits as pyfits + from pylab import * + from matplotlib import * + from numpy import * +-from pyfits import * ++from astropy.io.fits import * + import kepio, kepmsg, kepkey, kepplot, kepstat + import sys, time, re, math + +diff -Nur ../original/kepdip.py ./kepdip.py +--- ../original/kepdip.py 2012-05-18 18:34:31.000000000 -0400 ++++ ./kepdip.py 2016-12-21 20:27:17.870706000 -0300 +@@ -5,8 +5,8 @@ + """ + + from pyraf import iraf +-import numpy, sys, time, pyfits, pylab +-from pyfits import * ++import numpy, sys, time, astropy.io.fits as pyfits, pylab ++from astropy.io.fits import * + from pylab import * + from matplotlib import * + from math import * +diff -Nur ../original/kepdynamic.py ./kepdynamic.py +--- ../original/kepdynamic.py 2012-06-08 12:25:45.000000000 -0400 ++++ ./kepdynamic.py 2016-12-21 20:27:17.890726000 -0300 +@@ -1,6 +1,6 @@ + +-import numpy, sys, time, pyfits, pylab, math, re +-from pyfits import * ++import numpy, sys, time, astropy.io.fits as pyfits, pylab, math, re ++from astropy.io.fits import * + from numpy import * + from pylab import * + from matplotlib import * +diff -Nur ../original/kepextract.py ./kepextract.py +--- ../original/kepextract.py 2014-09-13 21:03:07.000000000 -0300 ++++ ./kepextract.py 2016-12-21 20:27:17.900736000 -0300 +@@ -1,7 +1,7 @@ + +-import numpy, sys, time, pyfits, pylab, math ++import numpy, sys, time, astropy.io.fits as pyfits, pylab, math + from numpy import * +-from pyfits import * ++from astropy.io.fits import * + from pylab import * + from matplotlib import * + from scipy.optimize import leastsq +diff -Nur ../original/kepfake.py ./kepfake.py +--- ../original/kepfake.py 2013-09-05 11:31:51.000000000 -0400 ++++ ./kepfake.py 2016-12-21 20:27:17.911747000 -0300 +@@ -1,8 +1,8 @@ +-import pylab, numpy, pyfits, scipy ++import pylab, numpy, astropy.io.fits as pyfits, scipy + from pylab import * + from matplotlib import * + from numpy import * +-from pyfits import * ++from astropy.io.fits import * + import kepmsg, kepio, kepfunc + import sys, glob + #import kepio, kepmsg, kepkey, kepplot, kepfit, keparray, kepfunc +diff -Nur ../original/kepffi.py ./kepffi.py +--- ../original/kepffi.py 2013-09-16 19:37:31.000000000 -0300 ++++ ./kepffi.py 2016-12-21 20:27:17.922762000 -0300 +@@ -1,5 +1,5 @@ + +-import pylab, numpy, pyfits ++import pylab, numpy, astropy.io.fits as pyfits + from pylab import * + from matplotlib import * + from numpy import * +diff -Nur ../original/kepfield.py ./kepfield.py +--- ../original/kepfield.py 2014-03-25 22:04:36.000000000 -0300 ++++ ./kepfield.py 2016-12-21 20:27:17.933769000 -0300 +@@ -1,9 +1,9 @@ +-import pylab, numpy, pyfits, scipy ++import pylab, numpy, astropy.io.fits as pyfits, scipy + from pylab import * + from matplotlib import * + from numpy import * + from scipy import * +-from pyfits import * ++from astropy.io.fits import * + import kepio, kepmsg, kepkey, kepplot, kepfit, keparray, kepstat + import sys, time, re, math, glob, urllib + +diff -Nur ../original/kepfilter.py ./kepfilter.py +--- ../original/kepfilter.py 2012-06-08 12:27:31.000000000 -0400 ++++ ./kepfilter.py 2016-12-21 20:27:17.947783000 -0300 +@@ -1,6 +1,6 @@ + +-import numpy, sys, time, pyfits, pylab +-from pyfits import * ++import numpy, sys, time, astropy.io.fits as pyfits, pylab ++from astropy.io.fits import * + from pylab import * + from matplotlib import * + from math import * +diff -Nur ../original/kepflatten.py ./kepflatten.py +--- ../original/kepflatten.py 2013-10-27 14:10:42.000000000 -0300 ++++ ./kepflatten.py 2016-12-21 20:27:18.033867000 -0300 +@@ -1,6 +1,6 @@ +-import numpy, scipy, sys, time, pyfits, pylab, math, re ++import numpy, scipy, sys, time, astropy.io.fits as pyfits, pylab, math, re + from scipy import stats +-from pyfits import * ++from astropy.io.fits import * + from pylab import * + from matplotlib import * + from math import * +diff -Nur ../original/kepfoldimg.py ./kepfoldimg.py +--- ../original/kepfoldimg.py 2014-06-26 19:36:48.000000000 -0400 ++++ ./kepfoldimg.py 2016-12-21 20:27:18.054887000 -0300 +@@ -1,7 +1,7 @@ + from pyraf import iraf +-import numpy, sys, time, pyfits, pylab ++import numpy, sys, time, astropy.io.fits as pyfits, pylab + from numpy import * +-from pyfits import * ++from astropy.io.fits import * + from pylab import * + from matplotlib import * + import kepio, kepmsg, kepkey, kepstat, kepfit +diff -Nur ../original/kepfold.py ./kepfold.py +--- ../original/kepfold.py 2014-06-26 19:08:29.000000000 -0400 ++++ ./kepfold.py 2016-12-21 20:27:18.045878000 -0300 +@@ -1,8 +1,8 @@ + +-import numpy, scipy, sys, time, pyfits, pylab ++import numpy, scipy, sys, time, astropy.io.fits as pyfits, pylab + from numpy import * + from scipy import stats +-from pyfits import * ++from astropy.io.fits import * + from pylab import * + from matplotlib import * + import kepio, kepmsg, kepkey, kepstat, kepfit +diff -Nur ../original/kepft.py ./kepft.py +--- ../original/kepft.py 2012-06-08 12:28:10.000000000 -0400 ++++ ./kepft.py 2016-12-21 20:27:18.073907000 -0300 +@@ -1,6 +1,6 @@ + +-import numpy, sys, time, pyfits, pylab, math, re +-from pyfits import * ++import numpy, sys, time, astropy.io.fits as pyfits, pylab, math, re ++from astropy.io.fits import * + from pylab import * + from matplotlib import * + from math import * +diff -Nur ../original/kephead.py ./kephead.py +--- ../original/kephead.py 2014-06-26 19:34:27.000000000 -0400 ++++ ./kephead.py 2016-12-21 20:27:18.096929000 -0300 +@@ -1,9 +1,9 @@ + +-import pylab, numpy, pyfits ++import pylab, numpy, astropy.io.fits as pyfits + from pylab import * + from matplotlib import * + from numpy import * +-from pyfits import * ++from astropy.io.fits import * + import kepio, kepmsg, kepkey + import sys, time, re + +diff -Nur ../original/kepimages.py ./kepimages.py +--- ../original/kepimages.py 2014-08-19 20:19:26.000000000 -0400 ++++ ./kepimages.py 2016-12-21 20:27:18.106938000 -0300 +@@ -1,6 +1,6 @@ +-import time, numpy, sys, pyfits ++import time, numpy, sys, astropy.io.fits as pyfits + from numpy import array +-from pyfits import * ++from astropy.io.fits import * + import kepio, kepmsg, kepkey, kepstat + + def kepimages(infile,outfix,imtype,ranges,clobber,verbose,logfile,status): +diff -Nur ../original/kepio.py ./kepio.py +--- ../original/kepio.py 2014-09-04 12:17:40.000000000 -0400 ++++ ./kepio.py 2016-12-21 20:27:18.120952000 -0300 +@@ -1,7 +1,7 @@ + #!/usr/bin/env python + + import kepmsg, kepkey +-import sys, pyfits, tempfile, os, shutil, glob, numpy, warnings ++import sys, astropy.io.fits as pyfits, tempfile, os, shutil, glob, numpy, warnings + + # ----------------------------------------------------------- + # delete a file +diff -Nur ../original/kepitermask.py ./kepitermask.py +--- ../original/kepitermask.py 2013-08-29 18:56:50.000000000 -0400 ++++ ./kepitermask.py 2016-12-21 20:27:18.131966000 -0300 +@@ -1,8 +1,8 @@ +-import pylab, numpy, pyfits ++import pylab, numpy, astropy.io.fits as pyfits + from pylab import * + from matplotlib import * + from numpy import * +-from pyfits import * ++from astropy.io.fits import * + from scipy.stats import * + import kepio, kepmsg, kepkey, kepplot, kepstat, kepfunc, kepfit + import sys, time, re, math +diff -Nur ../original/kepkey.py ./kepkey.py +--- ../original/kepkey.py 2014-06-26 19:15:24.000000000 -0400 ++++ ./kepkey.py 2016-12-21 20:27:18.141973000 -0300 +@@ -1,7 +1,7 @@ + #!/usr/bin/env python + + import kepmsg, kepio +-import pyfits, numpy ++import astropy.io.fits as pyfits, numpy + + # ----------------------------------------------------------- + # get keyword value +diff -Nur ../original/kepmask.py ./kepmask.py +--- ../original/kepmask.py 2013-11-05 21:48:39.000000000 -0300 ++++ ./kepmask.py 2016-12-21 20:27:18.161993000 -0300 +@@ -1,5 +1,5 @@ + +-import pylab, numpy, pyfits ++import pylab, numpy, astropy.io.fits as pyfits + from pylab import * + from matplotlib import * + from numpy import * +diff -Nur ../original/kepoutlier.py ./kepoutlier.py +--- ../original/kepoutlier.py 2014-08-23 18:02:05.000000000 -0400 ++++ ./kepoutlier.py 2016-12-21 20:27:18.183014000 -0300 +@@ -1,6 +1,6 @@ + +-import numpy, sys, time, pyfits, pylab, math, re +-from pyfits import * ++import numpy, sys, time, astropy.io.fits as pyfits, pylab, math, re ++from astropy.io.fits import * + from pylab import * + from matplotlib import * + from math import * +diff -Nur ../original/keppca.py ./keppca.py +--- ../original/keppca.py 2014-09-08 04:33:38.000000000 -0300 ++++ ./keppca.py 2016-12-21 20:27:18.197027000 -0300 +@@ -1,6 +1,6 @@ + import sys, re +-import numpy, pyfits, scipy, pylab +-from pyfits import * ++import numpy, astropy.io.fits as pyfits, scipy, pylab ++from astropy.io.fits import * + from numpy import * + from pylab import * + from matplotlib import * +diff -Nur ../original/keppixseries.py ./keppixseries.py +--- ../original/keppixseries.py 2014-05-15 16:12:03.000000000 -0400 ++++ ./keppixseries.py 2016-12-21 20:27:18.213049000 -0300 +@@ -1,9 +1,9 @@ + +-import pylab, numpy, pyfits ++import pylab, numpy, astropy.io.fits as pyfits + from pylab import * + from matplotlib import * + from numpy import * +-from pyfits import * ++from astropy.io.fits import * + import kepio, kepmsg, kepkey, kepplot, kepstat, kepfunc + import sys, time, re, math + +diff -Nur ../original/kepprfphot.py ./kepprfphot.py +--- ../original/kepprfphot.py 2014-06-26 19:24:15.000000000 -0400 ++++ ./kepprfphot.py 2016-12-21 21:22:32.482847000 -0300 +@@ -1,14 +1,14 @@ +-import pylab, numpy, pyfits, scipy, multiprocessing, itertools ++import pylab, numpy, astropy.io.fits as pyfits, scipy, multiprocessing, itertools + from pylab import * + from matplotlib import * + from numpy import * +-from pyfits import * ++from astropy.io.fits import * + import kepio, kepmsg, kepkey, kepplot, kepfit, keparray, kepfunc + import sys, time, re, math, glob + from scipy import stats, interpolate, optimize, ndimage + from scipy.optimize import fmin_powell + from scipy.interpolate import RectBivariateSpline +-from scipy.stats import nanmean ++from numpy import nanmean + + # ----------------------------------------------------------- + # core code +diff -Nur ../original/kepprf.py ./kepprf.py +--- ../original/kepprf.py 2014-09-13 23:49:53.000000000 -0300 ++++ ./kepprf.py 2016-12-21 21:22:09.321038000 -0300 +@@ -1,9 +1,9 @@ +-import pylab, numpy, pyfits, scipy ++import pylab, numpy, astropy.io.fits as pyfits, scipy + from pylab import * + from matplotlib import * + from matplotlib import pyplot + from numpy import * +-from pyfits import * ++from astropy.io.fits import * + import kepio, kepmsg, kepkey, kepplot, kepfit, keparray, kepfunc, kepstat + import sys, time, re, math, glob + from scipy import interpolate, optimize, ndimage, stats +@@ -11,7 +11,7 @@ + from scipy.interpolate import RectBivariateSpline, interp2d + from scipy.ndimage import interpolation + from scipy.ndimage.interpolation import shift, rotate +-from scipy.stats import nanmean ++from numpy import nanmean + + # ----------------------------------------------------------- + # core code +diff -Nur ../original/keprange.py ./keprange.py +--- ../original/keprange.py 2013-11-03 20:26:09.000000000 -0300 ++++ ./keprange.py 2016-12-21 20:27:18.257086000 -0300 +@@ -1,5 +1,5 @@ + +-import numpy, sys, time, pyfits, pylab ++import numpy, sys, time, astropy.io.fits as pyfits, pylab + from numpy import * + from pylab import * + from matplotlib import * +diff -Nur ../original/kepregr.py ./kepregr.py +--- ../original/kepregr.py 2012-05-18 18:34:32.000000000 -0400 ++++ ./kepregr.py 2016-12-21 20:27:18.277107000 -0300 +@@ -3,8 +3,8 @@ + """ + + from pyraf import iraf +-import numpy, sys, time, pyfits, pylab +-from pyfits import * ++import numpy, sys, time, astropy.io.fits as pyfits, pylab ++from astropy.io.fits import * + from pylab import * + from matplotlib import * + from math import * +diff -Nur ../original/kepsmooth.py ./kepsmooth.py +--- ../original/kepsmooth.py 2012-10-23 04:20:41.000000000 -0300 ++++ ./kepsmooth.py 2016-12-21 20:27:18.339167000 -0300 +@@ -1,6 +1,6 @@ + +-import numpy, sys, time, pyfits, pylab +-from pyfits import * ++import numpy, sys, time, astropy.io.fits as pyfits, pylab ++from astropy.io.fits import * + from pylab import * + from matplotlib import * + from math import * +diff -Nur ../original/kepstddev.py ./kepstddev.py +--- ../original/kepstddev.py 2014-01-18 20:14:38.000000000 -0300 ++++ ./kepstddev.py 2016-12-21 20:27:18.359187000 -0300 +@@ -1,4 +1,4 @@ +-import numpy, scipy, sys, time, pyfits, pylab, copy, math ++import numpy, scipy, sys, time, astropy.io.fits as pyfits, pylab, copy, math + from pylab import * + from matplotlib import * + import kepio, kepmsg, kepstat, kepkey +diff -Nur ../original/kepstitch.py ./kepstitch.py +--- ../original/kepstitch.py 2012-09-19 05:20:26.000000000 -0300 ++++ ./kepstitch.py 2016-12-21 20:27:18.368197000 -0300 +@@ -1,5 +1,5 @@ + +-import numpy, sys, time, pyfits ++import numpy, sys, time, astropy.io.fits as pyfits + import kepio, kepmsg, kepkey, kepstat + + def kepstitch(infiles,outfile,clobber,verbose,logfile,status): +diff -Nur ../original/keptimefix.py ./keptimefix.py +--- ../original/keptimefix.py 2014-06-26 19:21:51.000000000 -0400 ++++ ./keptimefix.py 2016-12-21 20:27:18.377206000 -0300 +@@ -1,6 +1,6 @@ + import numpy as np + import matplotlib.pyplot as plt +-import pyfits ++import astropy.io.fits as pyfits + import kepio + import kepmsg + import sys +diff -Nur ../original/keptransitmodel.py ./keptransitmodel.py +--- ../original/keptransitmodel.py 2012-11-14 12:48:58.000000000 -0300 ++++ ./keptransitmodel.py 2016-12-21 20:27:18.399225000 -0300 +@@ -1,7 +1,7 @@ + import lightcurve as tmod + import matplotlib.pyplot as plt + import numpy as np +-import pyfits ++import astropy.io.fits as pyfits + from scipy.optimize import leastsq, fmin + #remove this line + import sys +diff -Nur ../original/keptransit.py ./keptransit.py +--- ../original/keptransit.py 2012-12-11 23:18:44.000000000 -0300 ++++ ./keptransit.py 2016-12-21 20:27:18.389217000 -0300 +@@ -29,7 +29,7 @@ + import matplotlib.pyplot as plt + import numpy as np + from numpy import logical_and, isfinite, nan +-import pyfits ++import astropy.io.fits as pyfits + from scipy.optimize import leastsq, fmin, anneal + #remove this line + import sys +diff -Nur ../original/keptrial.py ./keptrial.py +--- ../original/keptrial.py 2012-06-08 12:41:58.000000000 -0400 ++++ ./keptrial.py 2016-12-21 20:27:18.409236000 -0300 +@@ -1,6 +1,6 @@ + +-import numpy, sys, time, pyfits, pylab, math, re +-from pyfits import * ++import numpy, sys, time, astropy.io.fits as pyfits, pylab, math, re ++from astropy.io.fits import * + from pylab import * + from matplotlib import * + import matplotlib.mlab as mlab +diff -Nur ../original/keptrim.py ./keptrim.py +--- ../original/keptrim.py 2014-09-04 12:11:05.000000000 -0400 ++++ ./keptrim.py 2016-12-21 20:27:18.419246000 -0300 +@@ -1,6 +1,6 @@ +-import numpy, sys, time, pyfits, pylab, urllib ++import numpy, sys, time, astropy.io.fits as pyfits, pylab, urllib + from numpy import * +-from pyfits import * ++from astropy.io.fits import * + from pylab import * + from matplotlib import * + import kepio, kepmsg, kepkey, kepstat +diff -Nur ../original/kepwindow.py ./kepwindow.py +--- ../original/kepwindow.py 2012-06-08 12:42:53.000000000 -0400 ++++ ./kepwindow.py 2016-12-21 20:27:18.429257000 -0300 +@@ -1,6 +1,6 @@ + +-import numpy, sys, time, pyfits, pylab, math, re +-from pyfits import * ++import numpy, sys, time, astropy.io.fits as pyfits, pylab, math, re ++from astropy.io.fits import * + from pylab import * + from matplotlib import * + from math import * diff --git a/pyraf.kepler/bld.bat b/pyraf.kepler/bld.bat new file mode 100644 index 0000000..e1aca7a --- /dev/null +++ b/pyraf.kepler/bld.bat @@ -0,0 +1,2 @@ +echo Not supported on Windows +exit 1 diff --git a/pyraf.kepler/build.sh b/pyraf.kepler/build.sh new file mode 100644 index 0000000..2353907 --- /dev/null +++ b/pyraf.kepler/build.sh @@ -0,0 +1,8 @@ +# Configure the environment for IRAF, since conda build appears not to do +# "source activate" after installing dependencies (this would instead need to +# eval $PREFIX/iraf/unix/hlib/setup directly if "--level" needs specifying): +. setup_iraf.sh + +# Build from source in envs/_build (using build script from astroconda-utils): +ac_build_iraf_pkg + diff --git a/pyraf.kepler/meta.yaml b/pyraf.kepler/meta.yaml new file mode 100644 index 0000000..002f11b --- /dev/null +++ b/pyraf.kepler/meta.yaml @@ -0,0 +1,40 @@ +# Note that this package is NOT fully working in AstroConda. It has been +# patched to use astropy.io.fits (etc.) but the functionality has not been +# tested properly. The "analysis" & "transit" modules used by lightcurve.py & +# keptransit.py (via ma02.py) are missing from both AstroConda and Ureka. +# The deprecated scipy.optimize.anneal in keptransit.py needs replacing with +# optimize.basinhopping (possibly amongst other API changes). + +about: + home: http://iraf.noao.edu/ + license: US government notice, BSD, attribution requirement + summary: KEPLER package for PyRAF +build: + binary_relocation: False + number: '0' + # These must be copied from astroconda-iraf-helpers, since conda disallows + # the post-install step from depending on other packages: + always_include_files: + - bin/ac_config_iraf_pkg + - bin/ac_update_extern_pkg +package: + name: pyraf.kepler + version: "2.6.2" +source: + fn: PyKE_2.6.2.tar + url: http://astroconda-source:4440/PyKE_2.6.2.tar + patches: + - ac.iraf.kepler.patch # converts pyfits imports to io.fits for AstroConda +requirements: + build: + - astroconda-iraf-helpers + - iraf !=2.16.1,>=2.16.UR + run: + - iraf !=2.16.1,>=2.16.UR + - pyraf + - astropy + - matplotlib + - numpy + - scipy + - mdp + diff --git a/pyraf.kepler/post-link.sh b/pyraf.kepler/post-link.sh new file mode 100644 index 0000000..f0e5a63 --- /dev/null +++ b/pyraf.kepler/post-link.sh @@ -0,0 +1,3 @@ +# Call a common script that updates extern.pkg for the new IRAF package: + +"$PREFIX/bin/ac_config_iraf_pkg" kepler diff --git a/pyraf.kepler/pre-unlink.sh b/pyraf.kepler/pre-unlink.sh new file mode 100644 index 0000000..e8b9801 --- /dev/null +++ b/pyraf.kepler/pre-unlink.sh @@ -0,0 +1 @@ +"$PREFIX/bin/ac_config_iraf_pkg" --remove kepler diff --git a/pyraf.kepler/ur_extern.pkg b/pyraf.kepler/ur_extern.pkg new file mode 100644 index 0000000..9b23cce --- /dev/null +++ b/pyraf.kepler/ur_extern.pkg @@ -0,0 +1,2 @@ +reset kepler = UR_VDIR +task kepler.pkg = kepler$kepler.cl diff --git a/pyraf.kepler/ur_manifest b/pyraf.kepler/ur_manifest new file mode 100644 index 0000000..e69de29 diff --git a/pyraf.kepler/ur_mkhelp_cmd b/pyraf.kepler/ur_mkhelp_cmd new file mode 100644 index 0000000..b193179 --- /dev/null +++ b/pyraf.kepler/ur_mkhelp_cmd @@ -0,0 +1 @@ +echo "No help to build for kepler/PyKe" diff --git a/pyraf.kepler/ur_mkpkg_cmd b/pyraf.kepler/ur_mkpkg_cmd new file mode 100644 index 0000000..e69de29 diff --git a/pyraf.kepler/ur_mkpkg_patterns b/pyraf.kepler/ur_mkpkg_patterns new file mode 100644 index 0000000..e69de29 -- cgit