MNT: Drop Python 2 support

nipype/info.py

@@ -2,7 +2,6 @@
 settings in setup.py, the nipy top-level docstring, and for building the
 docs. In setup.py in particular, we exec this file, so it cannot import nipy
 """
-import sys
 
 # nipype version information. An empty version_extra corresponds to a
 # full release. '.dev' as a version_extra string means this is a development
@@ -152,9 +151,6 @@ def get_nipype_gitversion():
  'futures; python_version == "2.7"',
 ]
 
-if sys.version_info <= (3, 4):
- REQUIRES.append('configparser')
-
 TESTS_REQUIRES = ['pytest-cov', 'codecov', 'pytest-env', 'coverage<5']
 
 EXTRA_REQUIRES = {

nipype/interfaces/base/specs.py

@@ -15,7 +15,7 @@
 from warnings import warn
 from packaging.version import Version
 
-from ...utils.filemanip import md5, hash_infile, hash_timestamp, to_str
+from ...utils.filemanip import md5, hash_infile, hash_timestamp
 from .traits_extension import (
  traits,
  Undefined,
@@ -251,7 +251,7 @@ def get_hashval(self, hash_method=None):
  True,
  hash_method=hash_method,
  hash_files=hash_files)))
- return list_withhash, md5(to_str(list_nofilename).encode()).hexdigest()
+ return list_withhash, md5(str(list_nofilename).encode()).hexdigest()
 
  def _get_sorteddict(self,
  objekt,

nipype/interfaces/base/support.py

@@ -14,7 +14,7 @@
 
 from ... import logging
 from ...utils.misc import is_container
-from ...utils.filemanip import md5, to_str, hash_infile
+from ...utils.filemanip import md5, hash_infile
 iflogger = logging.getLogger('nipype.interface')
 
 HELP_LINEWIDTH = 70
@@ -161,7 +161,7 @@ def _get_bunch_hash(self):
  # Sort the items of the dictionary, before hashing the string
  # representation so we get a predictable order of the
  # dictionary.
- sorted_dict = to_str(sorted(dict_nofilename.items()))
+ sorted_dict = str(sorted(dict_nofilename.items()))
  return dict_withhash, md5(sorted_dict.encode()).hexdigest()
 
  def _repr_pretty_(self, p, cycle):

nipype/interfaces/tests/test_io.py

@@ -5,9 +5,7 @@
 import copy
 import simplejson
 import glob
-import shutil
 import os.path as op
-import sys
 from subprocess import Popen
 import hashlib
 from collections import namedtuple
@@ -577,8 +575,6 @@ def test_jsonsink(tmpdir, inputs_attributes):
 # There are three reasons these tests will be skipped:
 @pytest.mark.skipif(not have_pybids,
  reason="Pybids is not installed")
-@pytest.mark.skipif(sys.version_info < (3, 0),
- reason="Pybids no longer supports Python 2")
 @pytest.mark.skipif(not dist_is_editable('pybids'),
  reason="Pybids is not installed in editable mode")
 def test_bids_grabber(tmpdir):
@@ -594,8 +590,6 @@ def test_bids_grabber(tmpdir):
 
 @pytest.mark.skipif(not have_pybids,
  reason="Pybids is not installed")
-@pytest.mark.skipif(sys.version_info < (3, 0),
- reason="Pybids no longer supports Python 2")
 @pytest.mark.skipif(not dist_is_editable('pybids'),
  reason="Pybids is not installed in editable mode")
 def test_bids_fields(tmpdir):
@@ -610,8 +604,6 @@ def test_bids_fields(tmpdir):
 
 @pytest.mark.skipif(not have_pybids,
  reason="Pybids is not installed")
-@pytest.mark.skipif(sys.version_info < (3, 0),
- reason="Pybids no longer supports Python 2")
 @pytest.mark.skipif(not dist_is_editable('pybids'),
  reason="Pybids is not installed in editable mode")
 def test_bids_infields_outfields(tmpdir):

nipype/pipeline/engine/nodes.py

@@ -21,8 +21,8 @@
 from ...utils.misc import flatten, unflatten, str2bool, dict_diff
 from ...utils.filemanip import (md5, FileNotFoundError, ensure_list,
  simplify_list, copyfiles, fnames_presuffix,
- loadpkl, split_filename, load_json, makedirs,
- emptydirs, savepkl, to_str, indirectory)
+ loadpkl, split_filename, load_json,
+ emptydirs, savepkl, indirectory)
 
 from ...interfaces.base import (traits, InputMultiPath, CommandLine, Undefined,
  DynamicTraitedSpec, Bunch, InterfaceResult,
@@ -267,7 +267,7 @@ def output_dir(self):
  def set_input(self, parameter, val):
  """Set interface input value"""
  logger.debug('[Node] %s - setting input %s = %s', self.name, parameter,
- to_str(val))
+ str(val))
  setattr(self.inputs, parameter, deepcopy(val))
 
  def get_output(self, parameter):
@@ -453,7 +453,7 @@ def run(self, updatehash=False):
  os.remove(filename)
 
  # Make sure outdir is created
- makedirs(outdir, exist_ok=True)
+ os.makedirs(outdir, exist_ok=True)
 
  # Store runtime-hashfile, pre-execution report, the node and the inputs set.
  _save_hashfile(hashfile_unfinished, self._hashed_inputs)
@@ -663,7 +663,7 @@ def _copyfiles_to_wd(self, execute=True, linksonly=False):
  if execute and linksonly:
  olddir = outdir
  outdir = op.join(outdir, '_tempinput')
- makedirs(outdir, exist_ok=True)
+ os.makedirs(outdir, exist_ok=True)
 
  for info in filecopy_info:
  files = self.inputs.trait_get().get(info['key'])
@@ -1019,13 +1019,13 @@ def set_input(self, parameter, val):
  Set interface input value or nodewrapper attribute
  Priority goes to interface.
  """
- logger.debug('setting nodelevel(%s) input %s = %s', to_str(self),
- parameter, to_str(val))
+ logger.debug('setting nodelevel(%s) input %s = %s', str(self),
+ parameter, str(val))
  self._set_mapnode_input(parameter, deepcopy(val))
 
  def _set_mapnode_input(self, name, newvalue):
- logger.debug('setting mapnode(%s) input: %s -> %s', to_str(self), name,
- to_str(newvalue))
+ logger.debug('setting mapnode(%s) input: %s -> %s', str(self), name,
+ str(newvalue))
  if name in self.iterfield:
  setattr(self._inputs, name, newvalue)
  else:

nipype/pipeline/engine/tests/test_utils.py

@@ -4,7 +4,6 @@
 """Tests for the engine utils module
 """
 import os
-import sys
 from copy import deepcopy
 import pytest
 
@@ -159,8 +158,6 @@ def dummy_func(value):
  return value + 1
 
 
-@pytest.mark.skipif(
- sys.version_info < (3, 0), reason="the famous segfault #1788")
 def test_mapnode_crash(tmpdir):
  """Test mapnode crash when stop_on_first_crash is True"""
  cwd = os.getcwd()
@@ -180,8 +177,6 @@ def test_mapnode_crash(tmpdir):
  os.chdir(cwd)
 
 
-@pytest.mark.skipif(
- sys.version_info < (3, 0), reason="the famous segfault #1788")
 def test_mapnode_crash2(tmpdir):
  """Test mapnode crash when stop_on_first_crash is False"""
  cwd = os.getcwd()
@@ -200,8 +195,6 @@ def test_mapnode_crash2(tmpdir):
  os.chdir(cwd)
 
 
-@pytest.mark.skipif(
- sys.version_info < (3, 0), reason="the famous segfault #1788")
 def test_mapnode_crash3(tmpdir):
  """Test mapnode crash when mapnode is embedded in a workflow"""
  tmpdir.chdir()

nipype/pipeline/engine/utils.py

@@ -21,9 +21,7 @@
 from ... import logging, config, LooseVersion
 from ...utils.filemanip import (
  relpath,
- makedirs,
  fname_presuffix,
- to_str,
  ensure_list,
  get_related_files,
  FileNotFoundError,
@@ -117,7 +115,7 @@ def write_report(node, report_type=None, is_mapnode=False):
  cwd = node.output_dir()
  report_dir = os.path.join(cwd, '_report')
  report_file = os.path.join(report_dir, 'report.rst')
- makedirs(report_dir, exist_ok=True)
+ os.makedirs(report_dir, exist_ok=True)
 
  logger.debug('[Node] Writing %s-exec report to "%s"', report_type[:-4],
  report_file)
@@ -627,7 +625,7 @@ def _get_valid_pathstr(pathstr):
  Replaces: ',' -> '.'
  """
  if not isinstance(pathstr, (str, bytes)):
- pathstr = to_str(pathstr)
+ pathstr = str(pathstr)
  pathstr = pathstr.replace(os.sep, '..')
  pathstr = re.sub(r'''[][ (){}?:<>#!|"';]''', '', pathstr)
  pathstr = pathstr.replace(',', '.')
@@ -1355,7 +1353,7 @@ def export_graph(graph_in,
  if base_dir is None:
  base_dir = os.getcwd()
 
- makedirs(base_dir, exist_ok=True)
+ os.makedirs(base_dir, exist_ok=True)
  out_dot = fname_presuffix(
  dotfilename, suffix='_detailed.dot', use_ext=False, newpath=base_dir)
  _write_detailed_dot(graph, out_dot)

nipype/pipeline/engine/workflows.py

@@ -22,7 +22,7 @@
 
 from ...interfaces.base import (traits, TraitedSpec, TraitDictObject,
  TraitListObject)
-from ...utils.filemanip import save_json, makedirs, to_str
+from ...utils.filemanip import save_json
 from .utils import (generate_expanded_graph, export_graph, write_workflow_prov,
  write_workflow_resources, format_dot, topological_sort,
  get_print_name, merge_dict, format_node)
@@ -218,12 +218,12 @@ def connect(self, *args, **kwargs):
  edge_data = self._graph.get_edge_data(srcnode, destnode, None)
  if edge_data:
  logger.debug('(%s, %s): Edge data exists: %s', srcnode,
- destnode, to_str(edge_data))
+ destnode, str(edge_data))
  for data in connects:
  if data not in edge_data['connect']:
  edge_data['connect'].append(data)
  if disconnect:
- logger.debug('Removing connection: %s', to_str(data))
+ logger.debug('Removing connection: %s', str(data))
  edge_data['connect'].remove(data)
  if edge_data['connect']:
  self._graph.add_edges_from([(srcnode, destnode,
@@ -240,7 +240,7 @@ def connect(self, *args, **kwargs):
  })])
  edge_data = self._graph.get_edge_data(srcnode, destnode)
  logger.debug('(%s, %s): new edge data: %s', srcnode, destnode,
- to_str(edge_data))
+ str(edge_data))
 
  def disconnect(self, *args):
  """Disconnect nodes
@@ -256,7 +256,7 @@ def disconnect(self, *args):
 
  for srcnode, dstnode, conn in connection_list:
  logger.debug('disconnect(): %s->%s %s', srcnode, dstnode,
- to_str(conn))
+ str(conn))
  if self in [srcnode, dstnode]:
  raise IOError(
  'Workflow connect cannot contain itself as node: src[%s] '
@@ -277,10 +277,10 @@ def disconnect(self, *args):
  # idx = ed_conns.index(edge)
  remove.append((edge[0], edge[1]))
 
- logger.debug('disconnect(): remove list %s', to_str(remove))
+ logger.debug('disconnect(): remove list %s', str(remove))
  for el in remove:
  edge_data['connect'].remove(el)
- logger.debug('disconnect(): removed connection %s', to_str(el))
+ logger.debug('disconnect(): removed connection %s', str(el))
 
  if not edge_data['connect']:
  self._graph.remove_edge(srcnode, dstnode)
@@ -410,7 +410,7 @@ def write_graph(self,
  base_dir = op.join(base_dir, self.name)
  else:
  base_dir = os.getcwd()
- base_dir = makedirs(base_dir, exist_ok=True)
+ os.makedirs(base_dir, exist_ok=True)
  if graph2use in ['hierarchical', 'colored']:
  if self.name[:1].isdigit(): # these graphs break if int
  raise ValueError('{} graph failed, workflow name cannot begin '
@@ -576,7 +576,7 @@ def run(self, plugin=None, plugin_args=None, updatehash=False):
  flatgraph = self._create_flat_graph()
  self.config = merge_dict(deepcopy(config._sections), self.config)
  logger.info('Workflow %s settings: %s', self.name,
- to_str(sorted(self.config)))
+ str(sorted(self.config)))
  self._set_needed_outputs(flatgraph)
  execgraph = generate_expanded_graph(deepcopy(flatgraph))
  for index, node in enumerate(execgraph.nodes()):
@@ -609,7 +609,7 @@ def _write_report_info(self, workingdir, name, graph):
  if workingdir is None:
  workingdir = os.getcwd()
  report_dir = op.join(workingdir, name)
- makedirs(report_dir, exist_ok=True)
+ os.makedirs(report_dir, exist_ok=True)
  shutil.copyfile(
  op.join(op.dirname(__file__), 'report_template.html'),
  op.join(report_dir, 'index.html'))
@@ -821,7 +821,7 @@ def _set_node_input(self, node, param, source, sourceinfo):
  newval = dict(val)
  if isinstance(val, TraitListObject):
  newval = val[:]
- logger.debug('setting node input: %s->%s', param, to_str(newval))
+ logger.debug('setting node input: %s->%s', param, str(newval))
  node.set_input(param, deepcopy(newval))
 
  def _get_all_nodes(self):
@@ -881,9 +881,9 @@ def _generate_flatgraph(self):
  # dj: added list() for networkx ver.2
  for u, _, d in list(
  self._graph.in_edges(nbunch=node, data=True)):
- logger.debug('in: connections-> %s', to_str(d['connect']))
+ logger.debug('in: connections-> %s', str(d['connect']))
  for cd in deepcopy(d['connect']):
- logger.debug("in: %s", to_str(cd))
+ logger.debug("in: %s", str(cd))
  dstnode = node._get_parameter_node(cd[1], subtype='in')
  srcnode = u
  srcout = cd[0]
@@ -896,9 +896,9 @@ def _generate_flatgraph(self):
  # dj: for ver 2 use list(out_edges)
  for _, v, d in list(
  self._graph.out_edges(nbunch=node, data=True)):
- logger.debug('out: connections-> %s', to_str(d['connect']))
+ logger.debug('out: connections-> %s', str(d['connect']))
  for cd in deepcopy(d['connect']):
- logger.debug("out: %s", to_str(cd))
+ logger.debug("out: %s", str(cd))
  dstnode = v
  if isinstance(cd[0], tuple):
  parameter = cd[0][0]

nipype/pipeline/plugins/tools.py

@@ -12,7 +12,7 @@
 from traceback import format_exception
 
 from ... import logging
-from ...utils.filemanip import savepkl, crash2txt, makedirs
+from ...utils.filemanip import savepkl, crash2txt
 
 logger = logging.getLogger('nipype.workflow')
 
@@ -42,7 +42,7 @@ def report_crash(node, traceback=None, hostname=None):
  str(uuid.uuid4()))
  crashdir = node.config['execution'].get('crashdump_dir', os.getcwd())
 
- makedirs(crashdir, exist_ok=True)
+ os.makedirs(crashdir, exist_ok=True)
  crashfile = os.path.join(crashdir, crashfile)
 
  if node.config['execution']['crashfile_format'].lower() in ['text', 'txt']:
@@ -115,8 +115,7 @@ def create_pyscript(node, updatehash=False, store_exception=True):
 batchdir = '%s'
 from nipype.utils.filemanip import loadpkl, savepkl
 try:
- if not sys.version_info < (2, 7):
- from collections import OrderedDict
+ from collections import OrderedDict
  config_dict=%s
  config.update_config(config_dict)
  ## Only configure matplotlib if it was successfully imported,

nipype/sphinxext/plot_workflow.py

@@ -144,23 +144,6 @@ def format_template(template, **kw):
 
 
 
-def _mkdirp(folder):
- """
- Equivalent to bash's mkdir -p
- """
- if sys.version_info > (3, 4, 1):
- os.makedirs(folder, exist_ok=True)
- return folder
-
- try:
- os.makedirs(folder)
- except OSError as exc:
- if exc.errno != EEXIST or not os.path.isdir(folder):
- raise
-
- return folder
-
-
 def wf_directive(name, arguments, options, content, lineno, content_offset,
  block_text, state, state_machine):
  if len(missing_imports) == 0:
@@ -737,7 +720,7 @@ def run(arguments, content, options, state_machine, state, lineno):
  state_machine.insert_input(total_lines, source=source_file_name)
 
  # copy image files to builder's output directory, if necessary
- _mkdirp(dest_dir)
+ os.makedirs(dest_dir, exist_ok=True)
  for code_piece, images in results:
  for img in images:
  for fn in img.filenames():