[REF,ENH] Makes phys2bids a Python package

.gitattributes

@@ -0,0 +1 @@
+phys2bids/_version.py export-subst

.gitignore

@@ -124,3 +124,4 @@ dmypy.json
 # Pyre type checker
 .pyre/
 
+.vscode/

.travis.yml

@@ -0,0 +1,79 @@
+language: python
+sudo: false
+dist: xenial
+services:
+  - xvfb
+notifications:
+  email: change
+
+python:
+  - 3.6
+  - 3.7
+
+env:
+  matrix:
+    - CHECK_TYPE=linting
+    - CHECK_TYPE=docdoctest
+    - CHECK_TYPE=test
+  global:
+    - INSTALL_TYPE=setup
+
+matrix:
+  include:
+    - python: 3.6
+      env:
+        - INSTALL_TYPE=sdist
+        - CHECK_TYPE=test
+    - python: 3.6
+      env:
+        - INSTALL_TYPE=wheel
+        - CHECK_TYPE=test
+
+before_install:
+  - python -m pip install --upgrade pip
+  - if [ "${CHECK_TYPE}" == "linting" ]; then
+      pip install flake8;
+    fi
+  - if [ "${CHECK_TYPE}" == "test" ]; then
+      pip install "pytest>=3.6" pytest-cov coverage coveralls codecov;
+    fi
+  - if [ "${CHECK_TYPE}" == "docdoctest" ]; then
+      pip install "sphinx>2.0" sphinx_rtd_theme pandas sphinx-argparse;
+    fi
+
+install:
+  - |
+    if [ "${INSTALL_TYPE}" == "setup" ]; then
+      python setup.py install;
+    elif [ "${INSTALL_TYPE}" == "sdist" ]; then
+      python setup.py sdist;
+      pip install dist/*.tar.gz;
+    elif [ "${INSTALL_TYPE}" == "wheel" ]; then
+      python setup.py bdist_wheel;
+      pip install dist/*.whl;
+    else
+      false;
+    fi
+
+script:
+  - |
+    if [ "${CHECK_TYPE}" == "linting" ]; then
+      flake8 phys2bids;
+    elif [ "${CHECK_TYPE}" == "docdoctest" ]; then
+      cd docs;
+      pip install -r ./requirements.txt;
+      make html;
+      make doctest;
+    elif [ "${CHECK_TYPE}" == "test" ]; then
+      mkdir for_testing && cd for_testing;
+      cp ../setup.cfg ./;
+      args="--doctest-modules --cov-report term-missing --cov=phys2bids --pyargs"
+      python -m pytest ${args} phys2bids;
+    else
+      false;
+    fi
+
+after_success:
+  - if [ "${CHECK_TYPE}" == "test" ]; then
+      coveralls; codecov;
+    fi

MANIFEST.in

@@ -0,0 +1,7 @@
+include README.* LICENSE setup* MANIFEST.in requirements.txt
+recursive-include phys2bids/data *
+recursive-include phys2bids/heuristics *
+recursive-include phys2bids/tests/data *
+
+include versioneer.py
+include phys2bids/_version.py

docs/Makefile

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+# Minimal makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line.
+SPHINXOPTS    =
+SPHINXBUILD   = sphinx-build
+SPHINXPROJ    = phys2bids
+SOURCEDIR     = .
+BUILDDIR      = _build
+
+# Put it first so that "make" without argument is like "make help".
+help:
+	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+.PHONY: help Makefile
+
+# For getting rid of generated docs before re-building
+clean:
+	rm -rf $(BUILDDIR)/* auto_examples/ generated/
+
+.PHONY: clean
+
+# Catch-all target: route all unknown targets to Sphinx using the new
+# "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
+%: Makefile
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)

docs/_static/theme_overrides.css

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+/* override table width restrictions */
+@media screen and (min-width: 767px) {
+
+   .wy-table-responsive table td {
+      /* !important prevents the common CSS stylesheets from overriding
+         this as on RTD they are loaded after this stylesheet */
+      white-space: normal !important;
+   }
+
+   .wy-table-responsive {
+      overflow: visible !important;
+   }
+}
+
+.headerlink::after {
+    font-size: 0px;
+}

docs/_templates/class.rst

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+{{ fullname }}
+{{ underline }}
+
+.. currentmodule:: {{ module }}
+
+.. autoclass:: {{ objname }}
+   :no-members:
+   :no-inherited-members:
+
+.. raw:: html
+
+    <div style='clear:both'></div>

docs/_templates/function.rst

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+{{ fullname }}
+{{ underline }}
+
+.. currentmodule:: {{ module }}
+
+.. autofunction:: {{ objname }}
+
+.. .. include:: modules/{{ module }}.{{ objname }}.examples
+
+.. raw:: html
+
+    <div style='clear:both'></div>

docs/cli.rst

@@ -0,0 +1,18 @@
+.. _cli:
+
+------------------
+Command-line usage
+------------------
+
+You can uinvoke the primary workflow of ``phys2bids`` from the command line.
+
+.. _cli_phys2bids:
+
+The ``phys2bids`` command
+=========================
+
+.. argparse::
+   :ref: phys2bids.cli.run._get_parser
+   :prog: phys2bids
+   :nodefault:
+   :nodefaultconst:

docs/conf.py

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+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+#
+# Configuration file for the Sphinx documentation builder.
+
+# -- Path setup --------------------------------------------------------------
+
+# If extensions (or modules to document with autodoc) are in another directory,
+# add these directories to sys.path here. If the directory is relative to the
+# documentation root, use os.path.abspath to make it absolute, like shown here.
+from datetime import datetime
+import os
+import sys
+
+
+# -- Project information -----------------------------------------------------
+
+# Add project name, copyright holder, and author(s)
+project = 'phys2bids'
+author = '{} developers'.format(project)
+copyright = '2019-{}, {}'.format(datetime.now().year, author)
+
+# Import project to get version info
+sys.path.insert(0, os.path.abspath(os.path.pardir))
+import phys2bids  # noqa
+# The short X.Y version
+version = phys2bids.__version__
+# The full version, including alpha/beta/rc tags
+release = phys2bids.__version__
+
+
+# -- General configuration ---------------------------------------------------
+
+# Add any Sphinx extension module names here, as strings. They can be
+# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
+# ones.
+extensions = [
+    'matplotlib.sphinxext.plot_directive',
+    'sphinx.ext.autodoc',
+    'sphinx.ext.autosummary',
+    'sphinx.ext.doctest',
+    'sphinx.ext.intersphinx',
+    'sphinx.ext.napoleon',
+    'sphinx.ext.viewcode',
+    'sphinxarg.ext',
+]
+
+# Generate the API documentation when building
+autosummary_generate = True
+autodoc_default_options = {'members': True, 'inherited-members': True}
+numpydoc_show_class_members = False
+autoclass_content = "class"
+
+# Add any paths that contain templates here, relative to this directory.
+templates_path = ['_templates']
+
+# The suffix(es) of source filenames.
+source_suffix = '.rst'
+
+# The master toctree document.
+master_doc = 'index'
+
+# The language for content autogenerated by Sphinx. Refer to documentation
+# for a list of supported languages.
+#
+# This is also used if you do content translation via gettext catalogs.
+# Usually you set "language" from the command line for these cases.
+language = None
+
+# 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']
+
+# The name of the Pygments (syntax highlighting) style to use.
+pygments_style = 'sphinx'
+
+
+# -- Options for HTML output -------------------------------------------------
+
+# The theme to use for HTML and HTML Help pages.  See the documentation for
+# a list of builtin themes.
+import sphinx_rtd_theme  # noqa
+html_theme = 'sphinx_rtd_theme'
+html_show_sourcelink = False
+
+# Theme options are theme-specific and customize the look and feel of a theme
+# further.  For a list of options available for each theme, see the
+# documentation.
+html_theme_options = {}
+
+# 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']
+
+# https://github.com/rtfd/sphinx_rtd_theme/issues/117
+def setup(app):  # noqa
+    app.add_stylesheet('theme_overrides.css')
+
+
+# -- Options for HTMLHelp output ---------------------------------------------
+
+# Output file base name for HTML help builder.
+htmlhelp_basename = 'phys2bids'
+
+
+# -- Extension configuration -------------------------------------------------
+intersphinx_mapping = {
+    'python': ('https://docs.python.org/3.6', None),
+    'matplotlib': ('https://matplotlib.org', None),
+    'numpy': ('https://docs.scipy.org/doc/numpy', None),
+    'pandas': ('https://pandas-docs.github.io/pandas-docs-travis/', None),
+}

docs/index.rst

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+=========
+phys2bids
+=========
+
+Contents
+--------
+
+.. toctree::
+   :maxdepth: 1
+
+   cli

docs/requirements.txt

@@ -0,0 +1,4 @@
+-r ../requirements.txt
+sphinx>=2.0
+sphinx-argparse
+sphinx_rtd_theme

phys2bids/__init__.py

@@ -0,0 +1,4 @@
+
+from ._version import get_versions
+__version__ = get_versions()['version']
+del get_versions