Merge branch 'master' of github.com:nilearn/nilearn into release-060a

* 'master' of github.com:nilearn/nilearn:
  Fix cache mixin tests (nilearn#2161)
  Do not fail if metadata cannot be updated for an image (nilearn#2167)
  [MRG] Nans in view connectome (nilearn#2166)

doc/whats_new.rst

@@ -64,6 +64,9 @@ Changes
   colormap. These arguments were already accepted in `kwargs` but not documented
   before.
 
+- :func:`nilearn.plotting.view_connectome` now converts NaNs in the adjacency
+  matrix to 0.
+
 Fixes
 -----
 

nilearn/datasets/neurovault.py

@@ -1651,19 +1651,25 @@ def _update_image(image_info, download_params):
     """
     if not download_params['write_ok']:
         return image_info
-    collection = _fetch_collection_for_image(
-        image_info, download_params)
-    image_info, collection = _download_image_terms(
-        image_info, collection, download_params)
-    metadata_file_path = os.path.join(
-        os.path.dirname(image_info['absolute_path']),
-        'image_{0}_metadata.json'.format(image_info['id']))
-    _write_metadata(image_info, metadata_file_path)
+    try:
+        collection = _fetch_collection_for_image(
+            image_info, download_params)
+        image_info, collection = _download_image_terms(
+            image_info, collection, download_params)
+        metadata_file_path = os.path.join(
+            os.path.dirname(image_info['absolute_path']),
+            'image_{0}_metadata.json'.format(image_info['id']))
+        _write_metadata(image_info, metadata_file_path)
+    except OSError:
+        warnings.warn(
+            "could not update metadata for image {}, "
+            "most likely because you do not have write "
+            "permissions to its metadata file".format(image_info["id"]))
     return image_info
 
 
 def _update(image_info, collection, download_params):
-    """Update local metadata for an image and its collection."""
+    "Update local metadata for an image and its collection."""
     image_info = _update_image(image_info, download_params)
     return image_info, collection
 

nilearn/plotting/html_connectome.py

@@ -31,7 +31,7 @@ def _get_connectome(adjacency_matrix, coords, threshold=None,
                     marker_size=None, cmap=cm.cold_hot, symmetric_cmap=True):
     connectome = {}
     coords = np.asarray(coords, dtype='<f4')
-    adjacency_matrix = adjacency_matrix.copy()
+    adjacency_matrix = np.nan_to_num(adjacency_matrix, copy=True)
     colors = colorscale(
         cmap, adjacency_matrix.ravel(), threshold=threshold,
         symmetric_cmap=symmetric_cmap)

nilearn/plotting/tests/test_html_connectome.py

@@ -47,6 +47,11 @@ def test_get_connectome():
     assert {'_con_x', '_con_y', '_con_z', '_con_w', 'colorscale'
             }.issubset(connectome.keys())
     assert (connectome['cmin'], connectome['cmax']) == (-2.5, 2.5)
+    adj[adj == 0] = np.nan
+    connectome = html_connectome._get_connectome(adj, coord)
+    con_x = decode(connectome['_con_x'], '<f4')
+    assert (con_x == expected_x).all()
+    assert (connectome['cmin'], connectome['cmax']) == (-2.5, 2.5)
 
 
 def test_view_connectome():
@@ -129,10 +134,11 @@ def test_params_deprecation_view_connectome():
                                         )
     old_params = ['coords', 'threshold', 'cmap', 'marker_size']
 
-    assert len(raised_warnings) == 4
-    for old_param_, raised_warning_ in zip(old_params, raised_warnings):
-        assert warning_msgs[old_param_] == str(raised_warning_.message)
-        assert raised_warning_.category is DeprecationWarning
+    raised_warning_messages = ''.join(
+        str(warning.message) for warning in raised_warnings)
+    print(raised_warning_messages)
+    for old_param_ in old_params:
+        assert warning_msgs[old_param_] in raised_warning_messages
 
 
 def test_get_markers():

nilearn/tests/test_cache_mixin.py

@@ -1,14 +1,12 @@
 """
 Test the _utils.cache_mixin module
 """
-import glob
 import json
 import os
 import shutil
 import tempfile
-from distutils.version import LooseVersion
+from pathlib import Path
 
-import sklearn
 from nose.tools import assert_false, assert_true, assert_equal
 from nilearn._utils.compat import Memory
 
@@ -17,6 +15,11 @@
 from nilearn._utils.testing import assert_raises_regex
 
 
+def _get_subdirs(top_dir):
+    top_dir = Path(top_dir)
+    children = list(top_dir.glob("*"))
+    return [child for child in children if child.is_dir()]
+
 
 def f(x):
     # A simple test function
@@ -26,8 +29,7 @@ def f(x):
 def test_check_memory():
     # Test if _check_memory returns a memory object with the cachedir equal to
     # input path
-    try:
-        temp_dir = tempfile.mkdtemp()
+    with tempfile.TemporaryDirectory() as temp_dir:
 
         mem_none = Memory(cachedir=None)
         mem_temp = Memory(cachedir=temp_dir)
@@ -42,17 +44,11 @@ def test_check_memory():
             assert_equal(memory.cachedir, mem_temp.cachedir)
             assert_true(memory, Memory)
 
-    finally:
-        if os.path.exists(temp_dir):
-            shutil.rmtree(temp_dir)
-
-
 
 def test__safe_cache_dir_creation():
     # Test the _safe_cache function that is supposed to flush the
     # cache if the nibabel version changes
-    try:
-        temp_dir = tempfile.mkdtemp()
+    with tempfile.TemporaryDirectory() as temp_dir:
         mem = Memory(cachedir=temp_dir)
         version_file = os.path.join(temp_dir, 'joblib', 'module_versions.json')
         assert_false(os.path.exists(version_file))
@@ -63,16 +59,12 @@ def test__safe_cache_dir_creation():
         os.unlink(version_file)
         cache_mixin._safe_cache(mem, f)
         assert_false(os.path.exists(version_file))
-    finally:
-        if os.path.exists(temp_dir):
-            shutil.rmtree(temp_dir)
 
 
 def test__safe_cache_flush():
     # Test the _safe_cache function that is supposed to flush the
     # cache if the nibabel version changes
-    try:
-        temp_dir = tempfile.mkdtemp()
+    with tempfile.TemporaryDirectory() as temp_dir:
         mem = Memory(cachedir=temp_dir)
         version_file = os.path.join(temp_dir, 'joblib', 'module_versions.json')
         # Create an mock version_file with old module versions
@@ -96,25 +88,21 @@ def test__safe_cache_flush():
         cache_mixin._safe_cache(mem, f)
         assert_true(os.path.exists(version_file))
         assert_false(os.path.exists(nibabel_dir))
-    finally:
-        pass
-        # if os.path.exists(temp_dir):
-        #    shutil.rmtree(temp_dir)
 
 
 def test_cache_memory_level():
-    temp_dir = tempfile.mkdtemp()
-    job_glob = os.path.join(temp_dir, 'joblib', 'nilearn', 'tests',
-                            'test_cache_mixin', 'f', '*')
-    mem = Memory(cachedir=temp_dir, verbose=0)
-    cache_mixin.cache(f, mem, func_memory_level=2, memory_level=1)(2)
-    assert_equal(len(glob.glob(job_glob)), 0)
-    cache_mixin.cache(f, Memory(cachedir=None))(2)
-    assert_equal(len(glob.glob(job_glob)), 0)
-    cache_mixin.cache(f, mem, func_memory_level=2, memory_level=3)(2)
-    assert_equal(len(glob.glob(job_glob)), 2)
-    cache_mixin.cache(f, mem)(3)
-    assert_equal(len(glob.glob(job_glob)), 3)
+    with tempfile.TemporaryDirectory() as temp_dir:
+        joblib_dir = Path(
+            temp_dir, 'joblib', 'nilearn', 'tests', 'test_cache_mixin', 'f')
+        mem = Memory(cachedir=temp_dir, verbose=0)
+        cache_mixin.cache(f, mem, func_memory_level=2, memory_level=1)(2)
+        assert_equal(len(_get_subdirs(joblib_dir)), 0)
+        cache_mixin.cache(f, Memory(cachedir=None))(2)
+        assert_equal(len(_get_subdirs(joblib_dir)), 0)
+        cache_mixin.cache(f, mem, func_memory_level=2, memory_level=3)(2)
+        assert_equal(len(_get_subdirs(joblib_dir)), 1)
+        cache_mixin.cache(f, mem)(3)
+        assert_equal(len(_get_subdirs(joblib_dir)), 2)
 
 
 class CacheMixinTest(CacheMixin):
@@ -182,17 +170,13 @@ def test_cache_mixin_wrong_dirs():
 
 
 def test_cache_shelving():
-    try:
-        temp_dir = tempfile.mkdtemp()
-        job_glob = os.path.join(temp_dir, 'joblib', 'nilearn', 'tests',
-                                'test_cache_mixin', 'f', '*')
+    with tempfile.TemporaryDirectory() as temp_dir:
+        joblib_dir = Path(
+            temp_dir, 'joblib', 'nilearn', 'tests', 'test_cache_mixin', 'f')
         mem = Memory(cachedir=temp_dir, verbose=0)
         res = cache_mixin.cache(f, mem, shelve=True)(2)
         assert_equal(res.get(), 2)
-        assert_equal(len(glob.glob(job_glob)), 1)
+        assert_equal(len(_get_subdirs(joblib_dir)), 1)
         res = cache_mixin.cache(f, mem, shelve=True)(2)
         assert_equal(res.get(), 2)
-        assert_equal(len(glob.glob(job_glob)), 1)
-    finally:
-        del mem
-        shutil.rmtree(temp_dir, ignore_errors=True)
+        assert_equal(len(_get_subdirs(joblib_dir)), 1)