Merge pull request #235 from satra/ref-etelemetry

fix doc building and updated style

Author: satra

.circleci/config.yml

@@ -49,7 +49,7 @@ jobs:
           command: pip install --no-cache-dir -r docs/requirements.txt
       - run:
           name: Build only this commit
-          command: make -C docs SPHINXOPTS="-W" BUILDDIR="_build/no_version_html" html
+          command: make -C docs SPHINXOPTS="-W" BUILDDIR="_build/no_version_html" SPHINX_APIDOC_OPTIONS="members,undoc-members,show-inheritance,noindex" html
       - store_artifacts:
           path: ./docs/_build/no_version_html
       - run:

.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.

LICENSE

@@ -11,4 +11,3 @@ distributed under the License is distributed on an "AS IS" BASIS,
 WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 See the License for the specific language governing permissions and
 limitations under the License.
-

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
+    )

min-requirements.txt

@@ -2,4 +2,4 @@
 attrs
 cloudpickle == 0.8.0
 filelock == 3.0.0
-etelemetry
+etelemetry == 0.2.0

pydra/__init__.py

@@ -6,6 +6,7 @@
 
 """
 import logging
+
 logger = logging.getLogger("pydra")
 from ._version import get_versions
 
@@ -15,14 +16,18 @@
 from .engine import Submitter, Workflow, AuditFlag, ShellCommandTask, DockerTask, specs
 from . import mark
 
+
 def check_latest_version():
     import etelemetry
-    return etelemetry.check_available_version("nipype/pydra", __version__, lgr=logger)    
+
+    return etelemetry.check_available_version("nipype/pydra", __version__, lgr=logger)
+
 
 # Run telemetry on import for interactive sessions, such as IPython, Jupyter notebooks, Python REPL
 import __main__
 
 if not hasattr(__main__, "__file__"):
     from .engine.core import TaskBase
+
     if TaskBase._etelemetry_version_data is None:
         TaskBase._etelemetry_version_data = check_latest_version()