delete unused functions and fix style

Author: nicolocin

.azure-pipelines/windows.yml

@@ -35,4 +35,4 @@ jobs:
     - script: |
         pytest -vs -n auto --cov pydra --cov-config .coveragerc --cov-report xml:cov.xml --doctest-modules pydra
       displayName: 'Pytest tests'
-       
+

.github/ISSUE_TEMPLATE/bug_report.md

@@ -24,4 +24,4 @@ Like this:
 ```
 <code>
 ```
--->
+-->

.github/ISSUE_TEMPLATE/question.md

@@ -12,4 +12,4 @@ Include the following:
 ------------------------
 What are you trying to accomplish?
 What have you tried?
--->
+-->

.github/PULL_REQUEST_TEMPLATE.md

@@ -12,10 +12,10 @@
 - [ ] All tests passing
 - [ ] I have added tests to cover my changes
 - [ ] I have updated documentation (if necessary)
-- [ ] My code follows the code style of this project 
-(we are using `black`: you can `pip install pre-commit`, 
-run `pre-commit install` in the `pydra` directory 
+- [ ] My code follows the code style of this project
+(we are using `black`: you can `pip install pre-commit`,
+run `pre-commit install` in the `pydra` directory
 and `black` will be run automatically with each commit)
 
 ## Acknowledgment
-- [ ] I acknowledge that this contribution will be available under the Apache 2 license.
+- [ ] I acknowledge that this contribution will be available under the Apache 2 license.

.travis.yml

@@ -57,7 +57,6 @@ matrix:
   allow_failures:
   - python: 3.7
     env: INSTALL_DEPENDS="pip==10.0.1 setuptools==30.3.0"
-  - os: windows
 
 
 before_install:

MANIFEST.in

@@ -1,3 +1,3 @@
 include versioneer.py
 include pydra/_version.py
-include pydra/schema/context.jsonld
+include pydra/schema/context.jsonld

docs/conf.py

@@ -13,17 +13,18 @@
 import sys
 from pathlib import Path
 from packaging.version import Version
+
 sys.path.insert(0, str(Path(__file__).parent.parent.absolute()))
-sys.path.insert(1, str(Path(__file__).parent / 'sphinxext'))
+sys.path.insert(1, str(Path(__file__).parent / "sphinxext"))
 from pydra import __version__
 from github_link import make_linkcode_resolve
 
 
 # -- Project information -----------------------------------------------------
 
-project = 'Pydra: A simple dataflow engine with scalable semantics'
-copyright = '2019 - 2020, The Nipype Developers team'
-author = 'The Nipype Developers team'
+project = "Pydra: A simple dataflow engine with scalable semantics"
+copyright = "2019 - 2020, The Nipype Developers team"
+author = "The Nipype Developers team"
 
 # The full version, including alpha/beta/rc tags
 release = __version__
@@ -36,75 +37,66 @@
 # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
 # ones.
 extensions = [
-    'sphinx.ext.autodoc',
-    'sphinx.ext.doctest',
-    'sphinx.ext.intersphinx',
-    'sphinx.ext.coverage',
-    'sphinx.ext.mathjax',
-    'sphinx.ext.ifconfig',
-    'sphinx.ext.linkcode',
-    'sphinx.ext.githubpages',
-    'sphinxcontrib.apidoc',
-    'sphinxcontrib.napoleon'
+    "sphinx.ext.autodoc",
+    "sphinx.ext.doctest",
+    "sphinx.ext.intersphinx",
+    "sphinx.ext.coverage",
+    "sphinx.ext.mathjax",
+    "sphinx.ext.ifconfig",
+    "sphinx.ext.linkcode",
+    "sphinx.ext.githubpages",
+    "sphinxcontrib.apidoc",
+    "sphinxcontrib.napoleon",
 ]
 
 # Add any paths that contain templates here, relative to this directory.
-templates_path = ['_templates']
+templates_path = ["_templates"]
 
 # List of patterns, relative to source directory, that match files and
 # directories to ignore when looking for source files.
 # This pattern also affects html_static_path and html_extra_path.
-exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store', 'api/pydra.rst']
+exclude_patterns = ["_build", "Thumbs.db", ".DS_Store", "api/pydra.rst"]
 
 
 # -- Options for HTML output -------------------------------------------------
 
 # The theme to use for HTML and HTML Help pages.  See the documentation for
 # a list of builtin themes.
 #
-html_theme = 'sphinx_rtd_theme'
+html_theme = "sphinx_rtd_theme"
 
 # Add any paths that contain custom static files (such as style sheets) here,
 # relative to this directory. They are copied after the builtin static files,
 # so a file named "default.css" will overwrite the builtin "default.css".
-html_static_path = ['_static']
+html_static_path = ["_static"]
 
 # -- Options for extensions ---------------------------------------------------
 
 # Autodoc
-autodoc_mock_imports = [
-    'cloudpickle',
-    'matplotlib',
-    'numpy',
-    'psutil',
-]
-apidoc_module_dir = '../pydra'
-apidoc_output_dir = 'api'
-apidoc_excluded_paths = ['conftest.py', '*/tests/*', 'tests/*', 'data/*']
+autodoc_mock_imports = ["cloudpickle", "matplotlib", "numpy", "psutil"]
+apidoc_module_dir = "../pydra"
+apidoc_output_dir = "api"
+apidoc_excluded_paths = ["conftest.py", "*/tests/*", "tests/*", "data/*"]
 apidoc_separate_modules = True
-apidoc_extra_args = ['--module-first', '-d 1', '-T']
+apidoc_extra_args = ["--module-first", "-d 1", "-T"]
 
 # Napoleon
 # Accept custom section names to be parsed for numpy-style docstrings
 # of parameters.
 # Requires pinning sphinxcontrib-napoleon to a specific commit while
 # https://github.com/sphinx-contrib/napoleon/pull/10 is merged.
 napoleon_use_param = False
-napoleon_custom_sections = [
-    ('Inputs', 'Parameters'),
-    ('Outputs', 'Parameters'),
-]
+napoleon_custom_sections = [("Inputs", "Parameters"), ("Outputs", "Parameters")]
 
 # Intersphinx
-intersphinx_mapping = {
-    'https://docs.python.org/': None,
-}
+intersphinx_mapping = {"https://docs.python.org/": None}
 
 # Linkcode
 # The following is used by sphinx.ext.linkcode to provide links to github
 linkcode_resolve = make_linkcode_resolve(
-    'pydra', 'https://github.com/nipype/pydra/blob/{revision}/'
-    '{package}/{path}#L{lineno}')
+    "pydra",
+    "https://github.com/nipype/pydra/blob/{revision}/" "{package}/{path}#L{lineno}",
+)
 
 # Sphinx-versioning
 scv_show_banner = True

docs/sphinxext/github_link.py

@@ -9,16 +9,16 @@
 import sys
 from functools import partial
 
-REVISION_CMD = 'git rev-parse --short HEAD'
+REVISION_CMD = "git rev-parse --short HEAD"
 
 
 def _get_git_revision():
     try:
         revision = subprocess.check_output(REVISION_CMD.split()).strip()
     except (subprocess.CalledProcessError, OSError):
-        print('Failed to execute git to get revision')
+        print("Failed to execute git to get revision")
         return None
-    return revision.decode('utf-8')
+    return revision.decode("utf-8")
 
 
 def _linkcode_resolve(domain, info, package, url_fmt, revision):
@@ -38,18 +38,18 @@ def _linkcode_resolve(domain, info, package, url_fmt, revision):
 
     if revision is None:
         return
-    if domain not in ('py', 'pyx'):
+    if domain not in ("py", "pyx"):
         return
-    if not info.get('module') or not info.get('fullname'):
+    if not info.get("module") or not info.get("fullname"):
         return
 
-    class_name = info['fullname'].split('.')[0]
+    class_name = info["fullname"].split(".")[0]
     if type(class_name) != str:
         # Python 2 only
-        class_name = class_name.encode('utf-8')
-    module = __import__(info['module'], fromlist=[class_name])
+        class_name = class_name.encode("utf-8")
+    module = __import__(info["module"], fromlist=[class_name])
     try:
-        obj = attrgetter(info['fullname'])(module)
+        obj = attrgetter(info["fullname"])(module)
     except AttributeError:
         return
 
@@ -65,14 +65,12 @@ def _linkcode_resolve(domain, info, package, url_fmt, revision):
     if not fn:
         return
 
-    fn = os.path.relpath(fn,
-                         start=os.path.dirname(__import__(package).__file__))
+    fn = os.path.relpath(fn, start=os.path.dirname(__import__(package).__file__))
     try:
         lineno = inspect.getsourcelines(obj)[1]
     except Exception:
-        lineno = ''
-    return url_fmt.format(revision=revision, package=package,
-                          path=fn, lineno=lineno)
+        lineno = ""
+    return url_fmt.format(revision=revision, package=package, path=fn, lineno=lineno)
 
 
 def make_linkcode_resolve(package, url_fmt):
@@ -87,5 +85,6 @@ def make_linkcode_resolve(package, url_fmt):
                                    '{path}#L{lineno}')
     """
     revision = _get_git_revision()
-    return partial(_linkcode_resolve, revision=revision, package=package,
-                   url_fmt=url_fmt)
+    return partial(
+        _linkcode_resolve, revision=revision, package=package, url_fmt=url_fmt
+    )

pydra/engine/helpers_file.py

@@ -66,49 +66,6 @@ def split_filename(fname):
     return pth, fname, ext
 
 
-def fname_presuffix(fname, prefix="", suffix="", newpath=None, use_ext=True):
-    """
-    Manipulate path and name of input filename.
-
-    Parameters
-    ----------
-    fname : :obj:`str`
-        A filename (may or may not include path)
-    prefix : :obj:`str`
-        Characters to prepend to the filename
-    suffix : :obj:`str`
-        Characters to append to the filename
-    newpath : :obj:`str`
-        Path to replace the path of the input fname
-    use_ext : :obj:`bool`
-        If True (default), appends the extension of the original file
-        to the output name.
-
-    Return
-    ------
-    path : :obj:`str`
-        Absolute path of the modified filename
-
-    Examples
-    --------
-    >>> import pytest, sys
-    >>> if sys.platform.startswith('win'): pytest.skip()
-    >>> from pydra.engine.helpers_file import fname_presuffix
-    >>> fname = 'foo.nii.gz'
-    >>> fname_presuffix(fname,'pre','post','/tmp')
-    '/tmp/prefoopost.nii.gz'
-
-    """
-    pth, fname, ext = split_filename(fname)
-    if not use_ext:
-        ext = ""
-
-    # No need for isdefined: bool(Undefined) evaluates to False
-    if newpath:
-        pth = op.abspath(newpath)
-    return str(Path(pth) / (prefix + fname + suffix + ext))
-
-
 def hash_file(afile, chunk_len=8192, crypto=sha256, raise_notfound=True):
     """Compute hash of a file using 'crypto' module."""
     from .specs import LazyField

pydra/engine/tests/test_helpers_file.py

@@ -1,12 +1,11 @@
-import os, sys
+import os
 import time
 import warnings
 import pytest
 from pathlib import Path
 
 from ..helpers_file import (
     split_filename,
-    fname_presuffix,
     copyfile,
     copyfiles,
     on_cifs,
@@ -38,18 +37,6 @@ def test_split_filename(filename, split):
     assert res == split
 
 
-@pytest.mark.skipif(sys.platform.startswith("win"), reason="windows drive not known in advance",)
-def test_fname_presuffix():
-    fname = "foo.nii"
-    pth = fname_presuffix(fname, "pre_", "_post", "/tmp")
-    assert pth == str(Path("/tmp/pre_foo_post.nii"))
-    fname += ".gz"
-    pth = fname_presuffix(fname, "pre_", "_post", "/tmp")
-    assert pth == str(Path("/tmp/pre_foo_post.nii.gz"))
-    pth = fname_presuffix(fname, "pre_", "_post", "/tmp", use_ext=False)
-    assert pth == str(Path("/tmp/pre_foo_post"))
-
-
 @pytest.fixture()
 def _temp_analyze_files(tmpdir):
     """Generate temporary analyze file pair."""