Data files are now JSON instead of pickles. Fixes #236.

7 files changed, 140 insertions, 135 deletions

diff --git a/CHANGES.txt b/CHANGES.txt
index 5a598d82..3b9b9d26 100644
--- a/CHANGES.txt
+++ b/CHANGES.txt
@@ -6,6 +6,10 @@ Change history for Coverage.py
 Latest
 ------
 
+- The data storage has been completely revamped.  The data file is now JSON
+  instead of a pickle, closing `issue 236`_.  The `CoverageData` class is now
+  a public supported API to the data file.
+
 - All the reporting functions now behave the same if no data had been
   collected, exiting with a status code of 1.  Fixed ``fail_under`` to be
   applied even when the report is empty.  Thanks, Ionel Cristian Mărieș.
@@ -22,10 +26,11 @@ Latest
   ``Coverage.get_data``, and returns the ``CoverageData`` containing the
   collected data.
 
-.. 41 issues closed in 4.0 so far
-
+.. _issue 236: https://bitbucket.org/ned/coveragepy/issues/236/pickles-are-bad-and-you-should-feel-bad
 .. _issue 380: https://bitbucket.org/ned/coveragepy/issues/380/code-executed-by-exec-excluded-from
 
+.. 41 issues closed in 4.0 below here
+
 
 Version 4.0a6 --- 21 June 2015
 ------------------------------
diff --git a/coverage/backunittest.py b/coverage/backunittest.py
index 95b6fcc6..5aff043f 100644
--- a/coverage/backunittest.py
+++ b/coverage/backunittest.py
@@ -22,10 +22,13 @@ class TestCase(unittest.TestCase):
     """
     # pylint: disable=missing-docstring
 
-    if not unittest_has('assertCountEqual'):
-        def assertCountEqual(self, s1, s2):
-            """Assert these have the same elements, regardless of order."""
-            self.assertEqual(set(s1), set(s2))
+    # Many Pythons have this method defined.  But PyPy3 has a bug with it
+    # somehow (https://bitbucket.org/pypy/pypy/issues/2092), so always use our
+    # own implementation that works everywhere, at least for the ways we're
+    # calling it.
+    def assertCountEqual(self, s1, s2):
+        """Assert these have the same elements, regardless of order."""
+        self.assertEqual(sorted(s1), sorted(s2))
 
     if not unittest_has('assertRaisesRegex'):
         def assertRaisesRegex(self, *args, **kwargs):
diff --git a/coverage/backward.py b/coverage/backward.py
index 58d9cfea..46c70fb6 100644
--- a/coverage/backward.py
+++ b/coverage/backward.py
@@ -28,12 +28,6 @@ try:
 except NameError:
     unicode_class = str
 
-# Where do pickles come from?
-try:
-    import cPickle as pickle
-except ImportError:
-    import pickle
-
 # range or xrange?
 try:
     range = xrange
diff --git a/coverage/collector.py b/coverage/collector.py
index eec8703e..8ea0427d 100644
--- a/coverage/collector.py
+++ b/coverage/collector.py
@@ -303,9 +303,9 @@ class Collector(object):
             return dict((abs_file(k), v) for k, v in iitems(d))
 
         if self.branch:
-            covdata.add_arcs(abs_file_dict(self.data))
+            covdata.set_arcs(abs_file_dict(self.data))
         else:
-            covdata.add_lines(abs_file_dict(self.data))
-        covdata.add_plugins(abs_file_dict(self.plugin_data))
+            covdata.set_lines(abs_file_dict(self.data))
+        covdata.set_plugins(abs_file_dict(self.plugin_data))
 
         self.reset()
diff --git a/coverage/data.py b/coverage/data.py
index 6db99ac3..68b02127 100644
--- a/coverage/data.py
+++ b/coverage/data.py
@@ -1,11 +1,12 @@
 """Coverage data for Coverage."""
 
 import glob
+import json
 import os
 import random
 import socket
 
-from coverage.backward import iitems, pickle
+from coverage.backward import iitems
 from coverage.debug import _TEST_NAME_FILE
 from coverage.files import PathAliases
 from coverage.misc import CoverageException, file_be_gone
@@ -47,8 +48,8 @@ class CoverageData(object):
 
 
     Most data files will be created by coverage.py itself, but you can use
-    methods here to create data files if you like.  The :meth:`add_lines`,
-    :meth:`add_arcs`, and :meth:`add_plugins` methods add data, in ways that
+    methods here to create data files if you like.  The :meth:`set_lines`,
+    :meth:`set_arcs`, and :meth:`set_plugins` methods add data, in ways that
     are convenient for coverage.py.  To add a file without any measured data,
     use :meth:`touch_file`.
 
@@ -61,7 +62,7 @@ class CoverageData(object):
 
     """
 
-    # The data file format is a pickled dict, with these keys:
+    # The data file format is JSON, with these keys:
     #
     #     * lines: a dict mapping filenames to lists of line numbers
     #       executed::
@@ -70,7 +71,7 @@ class CoverageData(object):
     #
     #     * arcs: a dict mapping filenames to lists of line number pairs::
     #
-    #         { 'file1': [(17,23), (17,25), (25,26)], ... }
+    #         { 'file1': [[17,23], [17,25], [25,26]], ... }
     #
     #     * plugins: a dict mapping filenames to plugin names::
     #
@@ -93,29 +94,20 @@ class CoverageData(object):
         # which there's an entry for each line number that has been
         # executed:
         #
-        #   {
-        #       'filename1.py': { 12: None, 47: None, ... },
-        #       ...
-        #       }
+        #   { 'filename1.py': [12, 47, 1001], ... }
         #
         self._lines = {}
 
         # A map from canonical Python source file name to a dictionary with an
         # entry for each pair of line numbers forming an arc:
         #
-        #   {
-        #       'filename1.py': { (12,14): None, (47,48): None, ... },
-        #       ...
-        #       }
+        #   { 'filename1.py': [(12,14), (47,48), ... ], ... }
         #
         self._arcs = {}
 
         # A map from canonical source file name to a plugin module name:
         #
-        #   {
-        #       'filename1.py': 'django.coverage',
-        #       ...
-        #       }
+        #   { 'filename1.py': 'django.coverage', ... }
         #
         self._plugins = {}
 
@@ -146,7 +138,7 @@ class CoverageData(object):
                 return [s for s, __ in self._arcs[filename] if s > 0]
         else:
             if filename in self._lines:
-                return list(self._lines[filename])
+                return self._lines[filename]
         return None
 
     def arcs(self, filename):
@@ -157,7 +149,7 @@ class CoverageData(object):
 
         """
         if filename in self._arcs:
-            return list((self._arcs[filename]).keys())
+            return self._arcs[filename]
         return None
 
     def plugin_name(self, filename):
@@ -214,18 +206,13 @@ class CoverageData(object):
         Should only be used on an empty CoverageData object.
 
         """
-        data = pickle.load(file_obj)
-
-        # Unpack the 'lines' item.
-        self._lines = dict([
-            (f, dict.fromkeys(linenos, None))
-            for f, linenos in iitems(data.get('lines', {}))
-        ])
-        # Unpack the 'arcs' item.
-        self._arcs = dict([
-            (f, dict.fromkeys(arcpairs, None))
-            for f, arcpairs in iitems(data.get('arcs', {}))
-        ])
+        data = json.load(file_obj)
+
+        self._lines = data.get('lines', {})
+        self._arcs = dict(
+            (fname, [tuple(pair) for pair in arcs])
+            for fname, arcs in iitems(data.get('arcs', {}))
+        )
         self._plugins = data.get('plugins', {})
 
     def read_file(self, filename):
@@ -233,7 +220,7 @@ class CoverageData(object):
         if self._debug and self._debug.should('dataio'):
             self._debug.write("Reading data from %r" % (filename,))
         try:
-            with open(filename, "rb") as f:
+            with open(filename, "r") as f:
                 self.read(f)
         except Exception as exc:
             raise CoverageException(
@@ -246,31 +233,39 @@ class CoverageData(object):
     ## Writing data
     ##
 
-    def add_lines(self, line_data):
+    def set_lines(self, line_data):
         """Add executed line data.
 
-        `line_data` is { filename: { lineno: None, ... }, ...}
+        `line_data` is a dictionary mapping filenames to dictionaries::
+
+            { filename: { lineno: None, ... }, ...}
+
+        Do not call this more than once, it will not update data, it only sets
+        data.
 
         """
         if self._has_arcs():
             raise CoverageException("Can't add lines to existing arc data")
 
         for filename, linenos in iitems(line_data):
-            self._lines.setdefault(filename, {}).update(linenos)
+            self._lines[filename] = list(linenos)
 
-    def add_arcs(self, arc_data):
+    def set_arcs(self, arc_data):
         """Add measured arc data.
 
         `arc_data` is { filename: { (l1,l2): None, ... }, ...}
 
+        Do not call this more than once, it will not update data, it only sets
+        data.
+
         """
         if self._has_lines():
             raise CoverageException("Can't add arcs to existing line data")
 
         for filename, arcs in iitems(arc_data):
-            self._arcs.setdefault(filename, {}).update(arcs)
+            self._arcs[filename] = list(arcs)
 
-    def add_plugins(self, plugin_data):
+    def set_plugins(self, plugin_data):
         """Add per-file plugin information.
 
         `plugin_data` is { filename: plugin_name, ... }
@@ -293,7 +288,7 @@ class CoverageData(object):
 
     def touch_file(self, filename):
         """Ensure that `filename` appears in the data, empty if needed."""
-        (self._arcs or self._lines).setdefault(filename, {})
+        (self._arcs or self._lines).setdefault(filename, [])
 
     def write(self, file_obj):
         """Write the coverage data to `file_obj`."""
@@ -302,20 +297,20 @@ class CoverageData(object):
         file_data = {}
 
         if self._arcs:
-            file_data['arcs'] = dict((f, list(amap.keys())) for f, amap in iitems(self._arcs))
+            file_data['arcs'] = self._arcs
         else:
-            file_data['lines'] = dict((f, list(lmap.keys())) for f, lmap in iitems(self._lines))
+            file_data['lines'] = self._lines
 
         file_data['plugins'] = self._plugins
 
-        # Write the pickle to the file.
-        pickle.dump(file_data, file_obj, 2)
+        # Write the data to the file.
+        json.dump(file_data, file_obj)
 
     def write_file(self, filename):
         """Write the coverage data to `filename`."""
         if self._debug and self._debug.should('dataio'):
             self._debug.write("Writing data to %r" % (filename,))
-        with open(filename, 'wb') as fdata:
+        with open(filename, 'w') as fdata:
             self.write(fdata)
 
     def erase(self):
@@ -355,14 +350,22 @@ class CoverageData(object):
                 )
 
         # _lines: merge dicts.
-        for filename, file_data in iitems(other_data._lines):
+        for filename, file_lines in iitems(other_data._lines):
             filename = aliases.map(filename)
-            self._lines.setdefault(filename, {}).update(file_data)
+            if filename in self._lines:
+                lines = set(self._lines[filename])
+                lines.update(file_lines)
+                file_lines = list(lines)
+            self._lines[filename] = file_lines
 
         # _arcs: merge dicts.
-        for filename, file_data in iitems(other_data._arcs):
+        for filename, file_arcs in iitems(other_data._arcs):
             filename = aliases.map(filename)
-            self._arcs.setdefault(filename, {}).update(file_data)
+            if filename in self._arcs:
+                arcs = set(self._arcs[filename])
+                arcs.update(file_arcs)
+                file_arcs = list(arcs)
+            self._arcs[filename] = file_arcs
 
     ##
     ## Miscellaneous
diff --git a/tests/test_cmdline.py b/tests/test_cmdline.py
index 36a16fb6..5e4379ea 100644
--- a/tests/test_cmdline.py
+++ b/tests/test_cmdline.py
@@ -522,11 +522,11 @@ class CmdLineWithFilesTest(BaseCmdLineTest):
 
     def test_debug_data(self):
         data = CoverageData()
-        data.add_lines({
+        data.set_lines({
             "file1.py": dict.fromkeys(range(1, 18)),
             "file2.py": dict.fromkeys(range(1, 24)),
         })
-        data.add_plugins({"file1.py": "a_plugin"})
+        data.set_plugins({"file1.py": "a_plugin"})
         data_files = CoverageDataFiles()
         data_files.write(data)
 
diff --git a/tests/test_data.py b/tests/test_data.py
index 4999f25f..ea33a587 100644
--- a/tests/test_data.py
+++ b/tests/test_data.py
@@ -1,12 +1,12 @@
 """Tests for coverage.data"""
 
 import glob
+import json
 import os
 import os.path
 
 import mock
 
-from coverage.backward import pickle
 from coverage.data import CoverageData, CoverageDataFiles
 from coverage.files import PathAliases, canonical_filename
 from coverage.misc import CoverageException
@@ -88,17 +88,17 @@ class CoverageDataTest(DataTestHelpers, CoverageTest):
 
     def test_line_data_is_true(self):
         covdata = CoverageData()
-        covdata.add_lines(LINES_1)
+        covdata.set_lines(LINES_1)
         self.assertTrue(covdata)
 
     def test_arc_data_is_true(self):
         covdata = CoverageData()
-        covdata.add_arcs(ARCS_3)
+        covdata.set_arcs(ARCS_3)
         self.assertTrue(covdata)
 
     def test_adding_lines(self):
         covdata = CoverageData()
-        covdata.add_lines(LINES_1)
+        covdata.set_lines(LINES_1)
         self.assert_line_counts(covdata, SUMMARY_1)
         self.assert_measured_files(covdata, MEASURED_FILES_1)
         self.assertCountEqual(covdata.lines("a.py"), A_PY_LINES_1)
@@ -106,7 +106,7 @@ class CoverageDataTest(DataTestHelpers, CoverageTest):
 
     def test_adding_arcs(self):
         covdata = CoverageData()
-        covdata.add_arcs(ARCS_3)
+        covdata.set_arcs(ARCS_3)
         self.assert_line_counts(covdata, SUMMARY_3)
         self.assert_measured_files(covdata, MEASURED_FILES_3)
         self.assertCountEqual(covdata.lines("x.py"), X_PY_LINES_3)
@@ -115,40 +115,40 @@ class CoverageDataTest(DataTestHelpers, CoverageTest):
         self.assertCountEqual(covdata.arcs("y.py"), Y_PY_ARCS_3)
         self.assertTrue(covdata.has_arcs())
 
-    def test_cant_add_arcs_to_lines(self):
+    def test_cant_set_arcs_with_lines(self):
         covdata = CoverageData()
-        covdata.add_lines(LINES_1)
+        covdata.set_lines(LINES_1)
         with self.assertRaisesRegex(CoverageException, "Can't add arcs to existing line data"):
-            covdata.add_arcs(ARCS_3)
+            covdata.set_arcs(ARCS_3)
 
-    def test_cant_add_lines_to_arcs(self):
+    def test_cant_set_lines_with_arcs(self):
         covdata = CoverageData()
-        covdata.add_arcs(ARCS_3)
+        covdata.set_arcs(ARCS_3)
         with self.assertRaisesRegex(CoverageException, "Can't add lines to existing arc data"):
-            covdata.add_lines(LINES_1)
+            covdata.set_lines(LINES_1)
 
     def test_touch_file_with_lines(self):
         covdata = CoverageData()
-        covdata.add_lines(LINES_1)
+        covdata.set_lines(LINES_1)
         covdata.touch_file('zzz.py')
         self.assert_measured_files(covdata, MEASURED_FILES_1 + ['zzz.py'])
 
     def test_touch_file_with_arcs(self):
         covdata = CoverageData()
-        covdata.add_arcs(ARCS_3)
+        covdata.set_arcs(ARCS_3)
         covdata.touch_file('zzz.py')
         self.assert_measured_files(covdata, MEASURED_FILES_3 + ['zzz.py'])
 
     def test_no_lines_vs_unmeasured_file(self):
         covdata = CoverageData()
-        covdata.add_lines(LINES_1)
+        covdata.set_lines(LINES_1)
         covdata.touch_file('zzz.py')
         self.assertEqual(covdata.lines('zzz.py'), [])
         self.assertIsNone(covdata.lines('no_such_file.py'))
 
     def test_no_arcs_vs_unmeasured_file(self):
         covdata = CoverageData()
-        covdata.add_arcs(ARCS_3)
+        covdata.set_arcs(ARCS_3)
         covdata.touch_file('zzz.py')
         self.assertEqual(covdata.lines('zzz.py'), [])
         self.assertIsNone(covdata.lines('no_such_file.py'))
@@ -157,12 +157,12 @@ class CoverageDataTest(DataTestHelpers, CoverageTest):
 
     def test_plugin_name(self):
         covdata = CoverageData()
-        covdata.add_lines({
+        covdata.set_lines({
             "p1.foo": dict.fromkeys([1, 2, 3]),
             "p2.html": dict.fromkeys([10, 11, 12]),
             "main.py": dict.fromkeys([20]),
         })
-        covdata.add_plugins({"p1.foo": "p1.plugin", "p2.html": "p2.plugin"})
+        covdata.set_plugins({"p1.foo": "p1.plugin", "p2.html": "p2.plugin"})
         self.assertEqual(covdata.plugin_name("p1.foo"), "p1.plugin")
         self.assertEqual(covdata.plugin_name("main.py"), "")
         self.assertIsNone(covdata.plugin_name("p3.not_here"))
@@ -171,27 +171,27 @@ class CoverageDataTest(DataTestHelpers, CoverageTest):
         covdata = CoverageData()
         msg = "Can't add plugin data for unmeasured file 'p1.foo'"
         with self.assertRaisesRegex(CoverageException, msg):
-            covdata.add_plugins({"p1.foo": "p1.plugin"})
+            covdata.set_plugins({"p1.foo": "p1.plugin"})
 
-        covdata.add_lines({"p2.html": dict.fromkeys([10, 11, 12])})
+        covdata.set_lines({"p2.html": dict.fromkeys([10, 11, 12])})
         with self.assertRaisesRegex(CoverageException, msg):
-            covdata.add_plugins({"p1.foo": "p1.plugin"})
+            covdata.set_plugins({"p1.foo": "p1.plugin"})
 
     def test_cant_change_plugin_name(self):
         covdata = CoverageData()
-        covdata.add_lines({"p1.foo": dict.fromkeys([1, 2, 3])})
-        covdata.add_plugins({"p1.foo": "p1.plugin"})
+        covdata.set_lines({"p1.foo": dict.fromkeys([1, 2, 3])})
+        covdata.set_plugins({"p1.foo": "p1.plugin"})
 
         msg = "Conflicting plugin name for 'p1.foo': 'p1.plugin' vs 'p1.plugin.foo'"
         with self.assertRaisesRegex(CoverageException, msg):
-            covdata.add_plugins({"p1.foo": "p1.plugin.foo"})
+            covdata.set_plugins({"p1.foo": "p1.plugin.foo"})
 
     def test_update_lines(self):
         covdata1 = CoverageData()
-        covdata1.add_lines(LINES_1)
+        covdata1.set_lines(LINES_1)
 
         covdata2 = CoverageData()
-        covdata2.add_lines(LINES_2)
+        covdata2.set_lines(LINES_2)
 
         covdata3 = CoverageData()
         covdata3.update(covdata1)
@@ -202,10 +202,10 @@ class CoverageDataTest(DataTestHelpers, CoverageTest):
 
     def test_update_arcs(self):
         covdata1 = CoverageData()
-        covdata1.add_arcs(ARCS_3)
+        covdata1.set_arcs(ARCS_3)
 
         covdata2 = CoverageData()
-        covdata2.add_arcs(ARCS_4)
+        covdata2.set_arcs(ARCS_4)
 
         covdata3 = CoverageData()
         covdata3.update(covdata1)
@@ -216,10 +216,10 @@ class CoverageDataTest(DataTestHelpers, CoverageTest):
 
     def test_update_cant_mix_lines_and_arcs(self):
         covdata1 = CoverageData()
-        covdata1.add_lines(LINES_1)
+        covdata1.set_lines(LINES_1)
 
         covdata2 = CoverageData()
-        covdata2.add_arcs(ARCS_3)
+        covdata2.set_arcs(ARCS_3)
 
         with self.assertRaisesRegex(CoverageException, "Can't combine arc data with line data"):
             covdata1.update(covdata2)
@@ -229,24 +229,24 @@ class CoverageDataTest(DataTestHelpers, CoverageTest):
 
     def test_update_plugins(self):
         covdata1 = CoverageData()
-        covdata1.add_lines({
+        covdata1.set_lines({
             "p1.html": dict.fromkeys([1, 2, 3, 4]),
             "p2.html": dict.fromkeys([5, 6, 7]),
             "main.py": dict.fromkeys([10, 11, 12]),
         })
-        covdata1.add_plugins({
+        covdata1.set_plugins({
             "p1.html": "html.plugin",
             "p2.html": "html.plugin2",
         })
 
         covdata2 = CoverageData()
-        covdata2.add_lines({
+        covdata2.set_lines({
             "p1.html": dict.fromkeys([3, 4, 5, 6]),
             "p2.html": dict.fromkeys([7, 8, 9]),
             "p3.foo": dict.fromkeys([1000, 1001]),
             "main.py": dict.fromkeys([10, 11, 12]),
         })
-        covdata2.add_plugins({
+        covdata2.set_plugins({
             "p1.html": "html.plugin",
             "p2.html": "html.plugin2",
             "p3.foo": "foo_plugin",
@@ -262,12 +262,12 @@ class CoverageDataTest(DataTestHelpers, CoverageTest):
 
     def test_update_conflicting_plugins(self):
         covdata1 = CoverageData()
-        covdata1.add_lines({"p1.html": dict.fromkeys([1, 2, 3])})
-        covdata1.add_plugins({"p1.html": "html.plugin"})
+        covdata1.set_lines({"p1.html": dict.fromkeys([1, 2, 3])})
+        covdata1.set_plugins({"p1.html": "html.plugin"})
 
         covdata2 = CoverageData()
-        covdata2.add_lines({"p1.html": dict.fromkeys([1, 2, 3])})
-        covdata2.add_plugins({"p1.html": "html.other_plugin"})
+        covdata2.set_lines({"p1.html": dict.fromkeys([1, 2, 3])})
+        covdata2.set_plugins({"p1.html": "html.other_plugin"})
 
         msg = "Conflicting plugin name for 'p1.html': 'html.plugin' vs 'html.other_plugin'"
         with self.assertRaisesRegex(CoverageException, msg):
@@ -279,11 +279,11 @@ class CoverageDataTest(DataTestHelpers, CoverageTest):
 
     def test_update_plugin_vs_no_plugin(self):
         covdata1 = CoverageData()
-        covdata1.add_lines({"p1.html": dict.fromkeys([1, 2, 3])})
-        covdata1.add_plugins({"p1.html": "html.plugin"})
+        covdata1.set_lines({"p1.html": dict.fromkeys([1, 2, 3])})
+        covdata1.set_plugins({"p1.html": "html.plugin"})
 
         covdata2 = CoverageData()
-        covdata2.add_lines({"p1.html": dict.fromkeys([1, 2, 3])})
+        covdata2.set_lines({"p1.html": dict.fromkeys([1, 2, 3])})
 
         msg = "Conflicting plugin name for 'p1.html': 'html.plugin' vs ''"
         with self.assertRaisesRegex(CoverageException, msg):
@@ -295,7 +295,7 @@ class CoverageDataTest(DataTestHelpers, CoverageTest):
 
     def test_add_to_hash_with_lines(self):
         covdata = CoverageData()
-        covdata.add_lines(LINES_1)
+        covdata.set_lines(LINES_1)
         hasher = mock.Mock()
         covdata.add_to_hash("a.py", hasher)
         self.assertEqual(hasher.method_calls, [
@@ -305,8 +305,8 @@ class CoverageDataTest(DataTestHelpers, CoverageTest):
 
     def test_add_to_hash_with_arcs(self):
         covdata = CoverageData()
-        covdata.add_arcs(ARCS_3)
-        covdata.add_plugins({"y.py": "hologram_plugin"})
+        covdata.set_arcs(ARCS_3)
+        covdata.set_plugins({"y.py": "hologram_plugin"})
         hasher = mock.Mock()
         covdata.add_to_hash("y.py", hasher)
         self.assertEqual(hasher.method_calls, [
@@ -320,7 +320,7 @@ class CoverageDataTestInTempDir(DataTestHelpers, CoverageTest):
 
     def test_read_write_lines(self):
         covdata1 = CoverageData()
-        covdata1.add_lines(LINES_1)
+        covdata1.set_lines(LINES_1)
         covdata1.write_file("lines.dat")
 
         covdata2 = CoverageData()
@@ -331,7 +331,7 @@ class CoverageDataTestInTempDir(DataTestHelpers, CoverageTest):
 
     def test_read_write_arcs(self):
         covdata1 = CoverageData()
-        covdata1.add_arcs(ARCS_3)
+        covdata1.set_arcs(ARCS_3)
         covdata1.write_file("arcs.dat")
 
         covdata2 = CoverageData()
@@ -379,7 +379,7 @@ class CoverageDataFilesTest(DataTestHelpers, CoverageTest):
 
     def test_writing_and_reading(self):
         covdata1 = CoverageData()
-        covdata1.add_lines(LINES_1)
+        covdata1.set_lines(LINES_1)
         self.data_files.write(covdata1)
 
         covdata2 = CoverageData()
@@ -391,7 +391,7 @@ class CoverageDataFilesTest(DataTestHelpers, CoverageTest):
         # writing files.
         debug = DebugControlString(options=["dataio"])
         covdata1 = CoverageData(debug=debug)
-        covdata1.add_lines(LINES_1)
+        covdata1.set_lines(LINES_1)
         self.data_files.write(covdata1)
 
         covdata2 = CoverageData(debug=debug)
@@ -409,7 +409,7 @@ class CoverageDataFilesTest(DataTestHelpers, CoverageTest):
         # output.
         debug = DebugControlString(options=[])
         covdata1 = CoverageData(debug=debug)
-        covdata1.add_lines(LINES_1)
+        covdata1.set_lines(LINES_1)
         self.data_files.write(covdata1)
 
         covdata2 = CoverageData(debug=debug)
@@ -421,7 +421,7 @@ class CoverageDataFilesTest(DataTestHelpers, CoverageTest):
     def test_explicit_suffix(self):
         self.assert_doesnt_exist(".coverage.SUFFIX")
         covdata = CoverageData()
-        covdata.add_lines(LINES_1)
+        covdata.set_lines(LINES_1)
         self.data_files.write(covdata, suffix='SUFFIX')
         self.assert_exists(".coverage.SUFFIX")
         self.assert_doesnt_exist(".coverage")
@@ -431,7 +431,7 @@ class CoverageDataFilesTest(DataTestHelpers, CoverageTest):
 
         # suffix=True will make a randomly named data file.
         covdata1 = CoverageData()
-        covdata1.add_lines(LINES_1)
+        covdata1.set_lines(LINES_1)
         self.data_files.write(covdata1, suffix=True)
         self.assert_doesnt_exist(".coverage")
         data_files1 = glob.glob(".coverage.*")
@@ -439,7 +439,7 @@ class CoverageDataFilesTest(DataTestHelpers, CoverageTest):
 
         # Another suffix=True will choose a different name.
         covdata2 = CoverageData()
-        covdata2.add_lines(LINES_1)
+        covdata2.set_lines(LINES_1)
         self.data_files.write(covdata2, suffix=True)
         self.assert_doesnt_exist(".coverage")
         data_files2 = glob.glob(".coverage.*")
@@ -453,13 +453,13 @@ class CoverageDataFilesTest(DataTestHelpers, CoverageTest):
         self.assert_doesnt_exist(".coverage.2")
 
         covdata1 = CoverageData()
-        covdata1.add_lines(LINES_1)
+        covdata1.set_lines(LINES_1)
         self.data_files.write(covdata1, suffix='1')
         self.assert_exists(".coverage.1")
         self.assert_doesnt_exist(".coverage.2")
 
         covdata2 = CoverageData()
-        covdata2.add_lines(LINES_2)
+        covdata2.set_lines(LINES_2)
         self.data_files.write(covdata2, suffix='2')
         self.assert_exists(".coverage.2")
 
@@ -472,7 +472,7 @@ class CoverageDataFilesTest(DataTestHelpers, CoverageTest):
 
     def test_erasing(self):
         covdata1 = CoverageData()
-        covdata1.add_lines(LINES_1)
+        covdata1.set_lines(LINES_1)
         self.data_files.write(covdata1)
 
         covdata1.erase()
@@ -484,13 +484,13 @@ class CoverageDataFilesTest(DataTestHelpers, CoverageTest):
         self.assert_line_counts(covdata2, {})
 
     def test_file_format(self):
-        # Write with CoverageData, then read the pickle explicitly.
+        # Write with CoverageData, then read the JSON explicitly.
         covdata = CoverageData()
-        covdata.add_lines(LINES_1)
+        covdata.set_lines(LINES_1)
         self.data_files.write(covdata)
 
-        with open(".coverage", 'rb') as fdata:
-            data = pickle.load(fdata)
+        with open(".coverage", 'r') as fdata:
+            data = json.load(fdata)
 
         lines = data['lines']
         self.assertCountEqual(lines.keys(), MEASURED_FILES_1)
@@ -500,24 +500,24 @@ class CoverageDataFilesTest(DataTestHelpers, CoverageTest):
         self.assertNotIn('arcs', data)
 
     def test_file_format_with_arcs(self):
-        # Write with CoverageData, then read the pickle explicitly.
+        # Write with CoverageData, then read the JSON explicitly.
         covdata = CoverageData()
-        covdata.add_arcs(ARCS_3)
+        covdata.set_arcs(ARCS_3)
         self.data_files.write(covdata)
 
-        with open(".coverage", 'rb') as fdata:
-            data = pickle.load(fdata)
+        with open(".coverage", 'r') as fdata:
+            data = json.load(fdata)
 
         self.assertNotIn('lines', data)
         arcs = data['arcs']
         self.assertCountEqual(arcs.keys(), MEASURED_FILES_3)
-        self.assertCountEqual(arcs['x.py'], X_PY_ARCS_3)
-        self.assertCountEqual(arcs['y.py'], Y_PY_ARCS_3)
+        self.assertCountEqual(arcs['x.py'], map(list, X_PY_ARCS_3))
+        self.assertCountEqual(arcs['y.py'], map(list, Y_PY_ARCS_3))
 
     def test_writing_to_other_file(self):
         data_files = CoverageDataFiles(".otherfile")
         covdata = CoverageData()
-        covdata.add_lines(LINES_1)
+        covdata.set_lines(LINES_1)
         data_files.write(covdata)
         self.assert_doesnt_exist(".coverage")
         self.assert_exists(".otherfile")
@@ -528,18 +528,18 @@ class CoverageDataFilesTest(DataTestHelpers, CoverageTest):
 
     def test_combining_with_aliases(self):
         covdata1 = CoverageData()
-        covdata1.add_lines({
+        covdata1.set_lines({
             '/home/ned/proj/src/a.py': {1: None, 2: None},
             '/home/ned/proj/src/sub/b.py': {3: None},
             '/home/ned/proj/src/template.html': {10: None},
         })
-        covdata1.add_plugins({
+        covdata1.set_plugins({
             '/home/ned/proj/src/template.html': 'html.plugin',
         })
         self.data_files.write(covdata1, suffix='1')
 
         covdata2 = CoverageData()
-        covdata2.add_lines({
+        covdata2.set_lines({
             r'c:\ned\test\a.py': {4: None, 5: None},
             r'c:\ned\test\sub\b.py': {3: None, 6: None},
         })
@@ -561,12 +561,12 @@ class CoverageDataFilesTest(DataTestHelpers, CoverageTest):
 
     def test_combining_from_different_directories(self):
         covdata1 = CoverageData()
-        covdata1.add_lines(LINES_1)
+        covdata1.set_lines(LINES_1)
         os.makedirs('cov1')
         covdata1.write_file('cov1/.coverage.1')
 
         covdata2 = CoverageData()
-        covdata2.add_lines(LINES_2)
+        covdata2.set_lines(LINES_2)
         os.makedirs('cov2')
         covdata2.write_file('cov2/.coverage.2')