Merge branch 'mnt/v2.0' into 'v2.0'

Mnt/v2.0

See merge request fsl/fslpy!110

COPYRIGHT

-Copyright 2016-2018 University of Oxford, Oxford, UK
+Copyright 2016-2019 University of Oxford, Oxford, UK

LICENSE

 The fslpy library
 
-Copyright 2016-2017 University of Oxford, Oxford, UK.
+Copyright 2016-2019 University of Oxford, Oxford, UK.
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.

MANIFEST.in

+include           AUTHOR
 include           LICENSE
 include           COPYRIGHT
+include           CHANGELOG.rst
+include           README.rst
 include           requirements.txt
 include           requirements-dev.txt
 include           requirements-extra.txt
-include           pytest.ini
+include           setup.cfg
 recursive-include doc      *
 recursive-exclude doc/html *
 recursive-include tests    *

README.rst

@@ -59,13 +59,14 @@ Some extra dependencies are listed in `requirements.txt
 
 
 If you are using Linux, you need to install wxPython first, as binaries are
-not available on PyPI. Change the URL for your specific platform::
+not available on PyPI. Install wxPython like so, changing the URL for your
+specific platform::
 
     pip install -f https://extras.wxpython.org/wxPython4/extras/linux/gtk2/ubuntu-16.04/ wxpython
 
 
-Once wxPython has been installed, you can simply type the following to install
-the rest of the extra dependencies::
+Once wxPython has been installed, you can type the following to install the
+rest of the extra dependencies::
 
     pip install fslpy[extras]
 

fsl/utils/filetree/filetree.py

@@ -185,7 +185,7 @@ class FileTree(object):
         """
         return tuple(self.extract_variables(short_name, fn) for fn in self.get_all(short_name, glob_vars=glob_vars))
 
-    def get_all_trees(self, short_name: str, glob_vars=()) -> Tuple["FileTree"]:
+    def get_all_trees(self, short_name: str, glob_vars=(), set_parent=True) -> Tuple["FileTree"]:
         """
         Gets all the trees that generate the existing files matching the pattern
 
@@ -195,23 +195,31 @@ class FileTree(object):
         :param glob_vars: sequence of undefined variables that can take any possible values when looking for matches on the disk.
             Any defined variables in `glob_vars` will be ignored.
             If glob_vars is set to 'all', all undefined variables will be used to look up matches.
+        :param set_parent: Update the variables of the top-level rather than current tree if True.
+            Ony relevant if `self` is a sub-tree.
         :return: sequence of FileTrees used to generate each file on disk matching the pattern of `short_name`
         """
-        return tuple(self.update(**vars) for vars in self.get_all_vars(short_name, glob_vars=glob_vars))
+        return tuple(self.update(set_parent=set_parent, **vars)
+                     for vars in self.get_all_vars(short_name, glob_vars=glob_vars))
 
-    def update(self, **variables) -> "FileTree":
+    def update(self, set_parent=True, **variables) -> "FileTree":
         """
         Creates a new FileTree with updated variables
 
+        :param set_parent: Update the variables of the top-level rather than current tree if True.
+            Ony relevant if `self` is a sub-tree.
         :param variables: new values for the variables
             Setting a variable to None will cause the variable to be unset
         :return: New FileTree with same templates for directory names and filenames, but updated variables
         """
         new_tree = deepcopy(self)
-        new_tree.variables.update(variables)
+        set_tree = new_tree
+        while set_parent and set_tree.parent is not None:
+            set_tree = set_tree.parent
+        set_tree.variables.update(variables)
         for key, value in variables.items():
             if value is None:
-                del new_tree.variables[key]
+                del set_tree.variables[key]
         return new_tree
 
     def extract_variables(self, short_name: str, filename: str) -> Dict[str, str]:

fsl/version.py

@@ -47,7 +47,7 @@ import            re
 import            string
 
 
-__version__ = '2.0.0.dev0'
+__version__ = '2.0.0'
 """Current version number, as a string. """
 
 

tests/test_filetree/test_read.py

@@ -58,6 +58,17 @@ def test_parent_tree():
     with pytest.raises(KeyError):
         tree.get('sub_var/basename')
 
+    # test updating in parent tree
+    sub0_tree = tree.sub_trees['sub0']
+    same_path(sub0_tree.update(subvar='test').get('../subvar/basename'), 'subvar_test')
+    with pytest.raises(KeyError):
+        sub0_tree.update(subvar='test', set_parent=False).get('../subvar/basename')
+
+    sub0_tree = tree.update(subvar='grot').sub_trees['sub0']
+    same_path(sub0_tree.update(subvar='test').get('../subvar/basename'), 'subvar_test')
+    same_path(sub0_tree.update(subvar='test', set_parent=False).get('../subvar/basename'), 'subvar_grot')
+    same_path(sub0_tree.get('../subvar/basename'), 'subvar_grot')
+
 
 def test_custom_tree():
     directory = op.split(__file__)[0]

tests/test_wrappers.py

@@ -288,3 +288,18 @@ def test_fast():
         expected = [cmd, '-v', '--out=myseg', '--class=3', 'in1', 'in2', 'in3']
 
         assert result.output[0] == ' '.join(expected)
+
+
+
+def test_fsl_anat():
+    with asrt.disabled(), \
+         run.dryrun(), \
+         mockFSLDIR(bin=('fsl_anat',)) as fsldir:
+
+        cmd = op.join(fsldir, 'bin', 'fsl_anat')
+
+        result   = fw.fsl_anat('t1', out='fsl_anat', bias_smoothing=25)
+        expected = [cmd, '-i', 't1', '-o', 'fsl_anat', '-t', 'T1',
+                    '-s', '25']
+
+        assert result.output[0] == ' '.join(expected)