Merge pull request #33 from astrofrog/fix-bytes

Finish fixing bytes issues

.travis.yml

@@ -7,10 +7,18 @@ python:
     - 3.5
     - 3.6
 
+env:
+  matrix:
+    - PIP_DEPENDENCIES='pytest coveralls pytest-cov pillow numpy astropy'
+    - PIP_DEPENDENCIES='pytest coveralls pytest-cov'
+
 install:
    - export PYTHONIOENCODING=UTF8 # just in case
    - pip install pip --upgrade
-   - pip install pytest pillow numpy astropy
+   - pip install $PIP_DEPENDENCIES
 
 script:
-   - py.test pyavm -p no:warnings
+   - py.test pyavm -p no:warnings --cov pyavm
+
+after_success:
+   - coveralls

pyavm/avm.py

@@ -27,10 +27,7 @@
     basestring = unicode = str
 
 import warnings
-try:
-    from StringIO import StringIO
-except ImportError:
-    from io import BytesIO as StringIO
+from io import BytesIO
 import xml.etree.ElementTree as et
 
 from .specs import SPECS, REVERSE_SPECS
@@ -364,7 +361,7 @@ def __getattr__(self, attribute):
             return object.__getattr__(self, attribute)
 
     @classmethod
-    def from_image(cls, filename, xmp_packet_index=0):
+    def from_image(cls, filename, xmp_packet_index=None):
         """
         Instantiate an AVM object from an existing image.
 
@@ -381,10 +378,12 @@ def from_image(cls, filename, xmp_packet_index=0):
         # Get XMP data from file
         xmp = extract_xmp(filename, xmp_packet_index=xmp_packet_index)
 
+        print(xmp)
+
         # Extract XML
-        start = xmp.index("<?xpacket begin=")
-        start = xmp.index("?>", start) + 2
-        end = xmp.index("</x:xmpmeta>") + 12
+        start = xmp.index(b"<?xpacket begin=")
+        start = xmp.index(b"?>", start) + 2
+        end = xmp.index(b"</x:xmpmeta>") + 12
 
         # Extract XML
         xml = xmp[start:end]
@@ -406,7 +405,7 @@ def from_xml(cls, xml):
         self = cls()
 
         # Parse XML
-        tree = et.parse(StringIO(xml))
+        tree = et.parse(BytesIO(xml))
         root = tree.getroot()
         avm_content = parse_avm_content(root)
 
@@ -461,7 +460,7 @@ def to_wcs(self, use_full_header=False, target_image=None):
 
         if use_full_header and self.Spatial.FITSheader is not None:
             print("Using full FITS header from Spatial.FITSheader")
-            header = fits.Header(txtfile=StringIO(self.Spatial.FITSheader))
+            header = fits.Header(txtfile=BytesIO(self.Spatial.FITSheader))
             return WCS(header)
 
         # Initializing WCS object
@@ -706,8 +705,8 @@ def to_xml(self):
         # Create XML Tree
         tree = et.ElementTree(root)
 
-        # Need to create a StringIO object to write to
-        s = StringIO()
+        # Need to create a BytesIO object to write to
+        s = BytesIO()
         tree.write(s, encoding='utf-8')
 
         # Rewind and read the contents

pyavm/extract.py

@@ -49,7 +49,7 @@ def extract_xmp(image, xmp_packet_index=None):
 
         # Loop through chunks and search for XMP packet
         for chunk in png_file.chunks:
-            if chunk.type == 'iTXt':
+            if chunk.type == b'iTXt':
                 if chunk.data.startswith(b'XML:com.adobe.xmp'):
                     xmp_chunks.append(chunk.data[22:])
 

pyavm/tests/test_avm.py

@@ -0,0 +1,27 @@
+import os
+from ..avm import AVM
+
+ROOT = os.path.join(os.path.dirname(os.path.abspath(__file__)), 'data')
+
+
+def test_from_image_jpg():
+    avm = AVM.from_image(os.path.join(ROOT, 'eso_eso1723a_320.jpg'))
+    assert avm.ID == 'eso1723a'
+
+
+def test_from_image_png():
+    avm = AVM.from_image(os.path.join(ROOT, 'eso_eso1723a_320.png'))
+    assert avm.ID == 'eso1723a'
+
+
+def test_from_image_other(tmpdir):
+    # Here we test the brute-force search
+    with open(os.path.join(ROOT, '3c321.avm.xml'), 'rb') as f:
+        content = f.read()
+    filename = tmpdir.join('testfile').strpath
+    with open(filename, 'wb') as f:
+        f.write(b'<?xpacket begin="<\ufeff>" id="W5M0MpCehiHzreSzNTczkc9d"?>')
+        f.write(content)
+        f.write(b'</x:xmpmeta>')
+    avm = AVM.from_image(filename)
+    assert avm.Publisher == 'Chandra X-ray Observatory'

pyavm/tests/test_header.py

@@ -8,13 +8,17 @@
 import os
 import pytest
 
+pytest.importorskip('astropy')
+
+from astropy.io import fits
+from astropy.wcs import WCS
+
 from ..avm import AVM, NoSpatialInformation
 
 ROOT = os.path.dirname(os.path.abspath(__file__))
 
 
 def test_from_header():
-    from astropy.io import fits
     header = fits.Header.fromtextfile(os.path.join(ROOT, 'data', 'example_header.hdr'))
     a = AVM.from_header(header)
     assert isinstance(a.Spatial.FITSheader, basestring)
@@ -33,7 +37,6 @@ def test_from_header():
 
 
 def test_from_header_cd():
-    from astropy.io import fits
     header = fits.Header.fromtextfile(os.path.join(ROOT, 'data', 'example_header.hdr'))
     header['CD1_1'] = header.pop('CDELT1')
     header['CD2_2'] = header.pop('CDELT2')
@@ -54,7 +57,6 @@ def test_from_header_cd():
 
 
 def test_wcs_1():
-    from astropy.io import fits
     header = fits.Header.fromtextfile(os.path.join(ROOT, 'data', 'example_header.hdr'))
     a = AVM.from_header(header)
     b = AVM.from_wcs(a.to_wcs(), shape=(header['NAXIS2'], header['NAXIS1']))
@@ -72,8 +74,6 @@ def test_wcs_1():
 
 
 def test_wcs_2():
-    from astropy.io import fits
-    from astropy.wcs import WCS
     header = fits.Header.fromtextfile(os.path.join(ROOT, 'data', 'example_header.hdr'))
     a = WCS(header)
     b = AVM.from_wcs(a).to_wcs()

pyavm/tests/test_io.py

@@ -6,24 +6,17 @@
 
 import pytest
 
-try:
-    from PIL import Image
-except ImportError:
-    try:
-        import Image
-    except ImportError:
-        pytest.skip()
+pytest.importorskip('PIL')
+pytest.importorskip('numpy')
 
-try:
-    import numpy as np
-except ImportError:
-    pytest.skip()
+from PIL import Image
+import numpy as np
 
 from .. import AVM
 
-ROOT = os.path.dirname(os.path.abspath(__file__))
+ROOT = os.path.join(os.path.dirname(os.path.abspath(__file__)), 'data')
 
-XML_FILES = glob.glob(os.path.join(ROOT, 'data', '*.xml'))
+XML_FILES = glob.glob(os.path.join(ROOT, '*.xml'))
 
 
 @pytest.mark.parametrize('xml_file', XML_FILES)

pyavm/tests/test_main.py

@@ -39,12 +39,15 @@ def test_to_xmp(filename):
 
 @pytest.mark.parametrize('filename', XML_FILES_WCS)
 def test_to_wcs(filename):
+    pytest.importorskip('astropy')
     a = AVM.from_xml_file(filename)
     a.to_wcs()
 
 
 @pytest.mark.parametrize('filename', XML_FILES_WCS)
 def test_to_wcs_target_image(filename, tmpdir):
+    pytest.importorskip('PIL')
+    pytest.importorskip('astropy')
     from PIL import Image
     image = Image.frombytes(data=b"1111", size=(2, 2), mode="L")
     image_file = tmpdir.join('test.png').strpath
@@ -57,6 +60,7 @@ def test_to_wcs_target_image(filename, tmpdir):
 
 @pytest.mark.parametrize('filename', NO_WCS)
 def test_to_wcs_nowcs(filename):
+    pytest.importorskip('astropy')
     a = AVM.from_xml_file(filename)
     with pytest.raises(NoSpatialInformation):
         a.to_wcs()

setup.py

@@ -1,11 +1,6 @@
 #!/usr/bin/env python
 
-from distutils.core import setup
-
-try:  # Python 3.x
-    from distutils.command.build_py import build_py_2to3 as build_py
-except ImportError:  # Python 2.x
-    from distutils.command.build_py import build_py
+from setuptools import setup
 
 version = '0.9.3.dev'
 
@@ -19,7 +14,6 @@
       packages=['pyavm', 'pyavm.tests'],
       package_data={'pyavm.tests':['data/*.xml', 'data/*.hdr']},
       provides=['pyavm'],
-      cmdclass={'build_py': build_py},
       keywords=['Scientific/Engineering'],
       long_description="PyAVM is a module to represent, read, and write metadata following the `Astronomy Visualization Metadata <http://www.virtualastronomy.org/avm_metadata.php>`_ (AVM) standard.",
       classifiers=[