diff --git a/.travis.yml b/.travis.yml
index 9dc9bc7..17db93e 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -17,5 +17,6 @@ install:
     - python setup.py install
 
 script:
+   - python setup.py check --restructuredtext
    - cd tests
-   - py.test --fits
+   - py.test --arraydiff
diff --git a/README.md b/README.md
index 7647d74..ff90497 100644
--- a/README.md
+++ b/README.md
@@ -46,7 +46,7 @@ Using
 
 To use, you simply need to mark the function where you want to compare images
 using ``@pytest.mark.array_compare``, and make sure that the function
-returns a plain Numpy array::
+returns a plain Numpy array:
 
     python
     import pytest
@@ -91,6 +91,10 @@ def test_image():
     ...
 ```
 
+The default file format can also be specified using the
+``--arraydiff-default-format=<format>`` flag when running ``py.test``, and
+``<format>`` should be either ``fits`` or ``text``.
+
 The supported formats at this time are ``text`` and ``fits``, and contributions
 for other formats are welcome. The default format is ``text``.
 
diff --git a/appveyor.yml b/appveyor.yml
index ab7611c..a689789 100644
--- a/appveyor.yml
+++ b/appveyor.yml
@@ -29,5 +29,4 @@ build: false
 
 test_script:
   - "%CMD_IN_ENV% cd tests"
-  - "%CMD_IN_ENV% py.test --fits"
-
+  - "%CMD_IN_ENV% py.test --arraydiff"
diff --git a/pytest_arraydiff/plugin.py b/pytest_arraydiff/plugin.py
index 300964a..d21dc54 100755
--- a/pytest_arraydiff/plugin.py
+++ b/pytest_arraydiff/plugin.py
@@ -98,6 +98,8 @@ def pytest_addoption(parser):
                     help="directory to generate reference files in, relative to location where py.test is run", action='store')
     group.addoption('--arraydiff-reference-path',
                     help="directory containing reference files, relative to location where py.test is run", action='store')
+    group.addoption('--arraydiff-default-format',
+                    help="Default format for the reference arrays (can be 'fits' or 'text' currently)")
 
 
 def pytest_configure(config):
@@ -115,17 +117,21 @@ def pytest_configure(config):
         if generate_dir is not None:
             reference_dir = os.path.abspath(generate_dir)
 
+        default_format = config.getoption("--arraydiff-default-format") or 'text'
+
         config.pluginmanager.register(ArrayComparison(config,
                                                       reference_dir=reference_dir,
-                                                      generate_dir=generate_dir))
+                                                      generate_dir=generate_dir,
+                                                      default_format=default_format))
 
 
 class ArrayComparison(object):
 
-    def __init__(self, config, reference_dir=None, generate_dir=None):
+    def __init__(self, config, reference_dir=None, generate_dir=None, default_format='text'):
         self.config = config
         self.reference_dir = reference_dir
         self.generate_dir = generate_dir
+        self.default_format = default_format
 
     def pytest_runtest_setup(self, item):
 
@@ -134,7 +140,7 @@ def pytest_runtest_setup(self, item):
         if compare is None:
             return
 
-        file_format = compare.kwargs.get('file_format', 'text')
+        file_format = compare.kwargs.get('file_format', self.default_format)
 
         if file_format not in FORMATS:
             raise ValueError("Unknown format: {0}".format(file_format))
diff --git a/setup.py b/setup.py
index c0c8aa2..6eeb1b9 100755
--- a/setup.py
+++ b/setup.py
@@ -1,3 +1,4 @@
+import sys
 from setuptools import setup
 
 from pytest_arraydiff import __version__
@@ -6,8 +7,11 @@
     import pypandoc
     long_description = pypandoc.convert('README.md', 'rst')
 except (IOError, ImportError):
-    with open('README.md') as infile:
-        long_description = infile.read()
+    if 'register' in sys.argv:
+        raise
+    else:
+        with open('README.md') as infile:
+            long_description = infile.read()
 
 setup(
     version=__version__,
diff --git a/tests/baseline/test_succeeds_class.fits b/tests/baseline/test_succeeds_class.fits
index 2e6c1b1..6b5ccef 100644
Binary files a/tests/baseline/test_succeeds_class.fits and b/tests/baseline/test_succeeds_class.fits differ
diff --git a/tests/baseline/test_succeeds_func.fits b/tests/baseline/test_succeeds_func.fits
deleted file mode 100644
index eee021e..0000000
Binary files a/tests/baseline/test_succeeds_func.fits and /dev/null differ
diff --git a/tests/baseline/test_succeeds_func_default.txt b/tests/baseline/test_succeeds_func_default.txt
new file mode 100644
index 0000000..1e60a17
--- /dev/null
+++ b/tests/baseline/test_succeeds_func_default.txt
@@ -0,0 +1,3 @@
+0 1 2 3 4
+5 6 7 8 9
+10 11 12 13 14
diff --git a/tests/baseline/test_succeeds_func_array.fits b/tests/baseline/test_succeeds_func_fits.fits
similarity index 85%
rename from tests/baseline/test_succeeds_func_array.fits
rename to tests/baseline/test_succeeds_func_fits.fits
index 2950d77..2e452d9 100644
Binary files a/tests/baseline/test_succeeds_func_array.fits and b/tests/baseline/test_succeeds_func_fits.fits differ
diff --git a/tests/baseline/test_succeeds_func_text.txt b/tests/baseline/test_succeeds_func_text.txt
new file mode 100644
index 0000000..1e60a17
--- /dev/null
+++ b/tests/baseline/test_succeeds_func_text.txt
@@ -0,0 +1,3 @@
+0 1 2 3 4
+5 6 7 8 9
+10 11 12 13 14
diff --git a/tests/baseline/test_tolerance.fits b/tests/baseline/test_tolerance.fits
index b6cd48c..9fab1ae 100644
Binary files a/tests/baseline/test_tolerance.fits and b/tests/baseline/test_tolerance.fits differ
diff --git a/tests/test_pytest_arraydiff.py b/tests/test_pytest_arraydiff.py
index 692ba33..afae0bb 100644
--- a/tests/test_pytest_arraydiff.py
+++ b/tests/test_pytest_arraydiff.py
@@ -10,22 +10,22 @@
 
 @pytest.mark.array_compare(reference_dir=reference_dir)
 def test_succeeds_func_default():
-    return np.arange(3 * 5 * 4).reshape((3, 5, 4))
+    return np.arange(3 * 5).reshape((3, 5))
 
 
 @pytest.mark.array_compare(file_format='text', reference_dir=reference_dir)
 def test_succeeds_func_text():
-    return np.arange(3 * 5 * 4).reshape((3, 5, 4))
+    return np.arange(3 * 5).reshape((3, 5))
 
 
 @pytest.mark.array_compare(file_format='fits', reference_dir=reference_dir)
 def test_succeeds_func_fits():
-    return np.arange(3 * 5 * 4).reshape((3, 5, 4))
+    return np.arange(3 * 5).reshape((3, 5))
 
 
 class TestClass(object):
 
-    @pytest.mark.array_compare(reference_dir=reference_dir)
+    @pytest.mark.array_compare(file_format='fits', reference_dir=reference_dir)
     def test_succeeds_class(self):
         return np.arange(2 * 4 * 3).reshape((2, 4, 3))
 
@@ -91,7 +91,34 @@ def test_generate(file_format):
     assert os.path.exists(os.path.join(gen_dir, 'test_gen.' + ('fits' if file_format == 'fits' else 'txt')))
 
 
-@pytest.mark.array_compare(reference_dir=reference_dir, rtol=0.5)
+TEST_DEFAULT = """
+import pytest
+import numpy as np
+from astropy.io import fits
+@pytest.mark.array_compare
+def test_default():
+    return np.arange(6 * 5).reshape((6, 5))
+"""
+
+@pytest.mark.parametrize('file_format', ('fits', 'text'))
+def test_default_format(file_format):
+
+    tmpdir = tempfile.mkdtemp()
+
+    test_file = os.path.join(tmpdir, 'test.py')
+    with open(test_file, 'w') as f:
+        f.write(TEST_DEFAULT)
+
+    gen_dir = os.path.join(tmpdir, 'spam', 'egg')
+
+    # If we do generate, the test should succeed and a new file will appear
+    code = subprocess.call('py.test -s --arraydiff-default-format={0}'
+                           ' --arraydiff-generate-path={1} {2}'.format(file_format, gen_dir, test_file), shell=True)
+    assert code == 0
+    assert os.path.exists(os.path.join(gen_dir, 'test_default.' + ('fits' if file_format == 'fits' else 'txt')))
+
+
+@pytest.mark.array_compare(reference_dir=reference_dir, rtol=0.5, file_format='fits')
 def test_tolerance():
     return np.ones((3,4)) * 1.6