Merge remote-tracking branch 'upstream/main' into asl

docs/about.rst

@@ -1,5 +1,5 @@
 ===================
-Background 
+Background
 ===================
 
 Motivation
@@ -19,7 +19,7 @@ their computational time and resources** effectively.
 
 ``CuBIDS`` is designed to facilitate the curation of large, neuroimaging data so
 that users can infer useful information from descriptive and accurate BIDS labels
-before running pipelines *en masse*. ``CuBIDS`` accomplishes this by summarizing 
+before running pipelines *en masse*. ``CuBIDS`` accomplishes this by summarizing
 BIDS data using :ref:`keygroup`, :ref:`paramgroup`, and :ref:`acquisitiongroup` categorizations in your data (we'll explain what these
 are in more detail in the next section).
 
@@ -40,7 +40,7 @@ Definitions
 
     * A set of scans whose filenames share all `BIDS filename key-value pairs <https://bids-specification.readthedocs.io/en/stable/02-common-principles.html#file-name-structure>`_, excluding subject and session
     * Derived from the BIDS Filename
-    * Example structure: ``acquisition-*_datatype-*_run-*_task-*_suffix`` 
+    * Example structure: ``acquisition-*_datatype-*_run-*_task-*_suffix``
 
 .. topic:: Parameter (Param) Group
 
@@ -53,15 +53,15 @@ Definitions
     * The Param Group that contains the most scans in its Key Group
 
 .. topic:: Variant Group
-    
+
     * Any Param Group that is non-dominant
 
 .. topic:: Rename Key Group
 
-    * Auto-generated, recommended new Key Group name for Variant Groups 
-    * Based on the metadata parameters that cause scans in Variant Groups to vary from those in their respective Dominant Groups 
+    * Auto-generated, recommended new Key Group name for Variant Groups
+    * Based on the metadata parameters that cause scans in Variant Groups to vary from those in their respective Dominant Groups
 
-.. topic:: Acquisition Group 
+.. topic:: Acquisition Group
 
     * A collection of sessions across participants that contains the exact same set of Key and Param Groups
 
@@ -85,4 +85,4 @@ In the next section, we'll discuss these definitions in more detail and demonstr
 
 .. [#f1] See the `BIDS Specification <https://bids-specification.readthedocs.io>`_.
 .. [#f2] See this list of amazing `BIDS apps <https://bids-apps.neuroimaging.io/>`_.
-.. [#f3] See `DataLad <https://www.datalad.org/>`_.
+.. [#f3] See `DataLad <https://www.datalad.org/>`_.

docs/conf.py

@@ -16,60 +16,61 @@
 # 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.
-#
 import os
 import sys
-sys.path.insert(0, os.path.abspath('..'))
-from sphinx import __version__ as sphinxversion
+
+sys.path.insert(0, os.path.abspath(".."))
+
 import cubids
-from packaging import version as pver  # Avoid distutils.LooseVersion which is deprecated
 
 # 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.
-sys.path.append(os.path.abspath('sphinxext'))
-sys.path.insert(0, os.path.abspath('../wrapper'))
+sys.path.append(os.path.abspath("sphinxext"))
+sys.path.insert(0, os.path.abspath("../wrapper"))
 
 # -- General configuration ---------------------------------------------
 
 # If your documentation needs a minimal Sphinx version, state it here.
 #
-needs_sphinx = '1.5.3'
+needs_sphinx = "1.5.3"
 
 # Add any Sphinx extension module names here, as strings. They can be
 # 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',
-    'sphinxarg.ext',  # argparse extension
-    'sphinx.ext.viewcode'
+    "nbsphinx",
+    "sphinx.ext.autodoc",
+    "sphinx.ext.doctest",
+    "sphinx.ext.intersphinx",
+    "sphinx.ext.coverage",
+    "sphinx.ext.mathjax",
+    "sphinxarg.ext",  # argparse extension
+    "sphinx.ext.viewcode",
+    "sphinx_gallery.load_style",
 ]
 
 # Mock modules in autodoc:
 autodoc_mock_imports = [
-    'numpy',
-    'nitime',
-    'matplotlib',
+    "numpy",
+    "nitime",
+    "matplotlib",
 ]
 
 # Add any paths that contain templates here, relative to this directory.
-templates_path = ['_templates']
+templates_path = ["_templates"]
 
 # The suffix(es) of source filenames.
 # You can specify multiple suffix as a list of string:
 #
 # source_suffix = ['.rst', '.md']
-source_suffix = '.rst'
+source_suffix = ".rst"
 
 # The master toctree document.
-master_doc = 'index'
+master_doc = "index"
 
 # General information about the project.
-project = 'CuBIDS'
+project = "CuBIDS"
 copyright = "2020, PennLINC"
 author = "PennLINC"
 
@@ -87,15 +88,15 @@
 #
 # This is also used if you do content translation via gettext catalogs.
 # Usually you set "language" from the command line for these cases.
-language = 'en'
+language = "en"
 
 # List of patterns, relative to source directory, that match files and
 # directories to ignore when looking for source files.
 # This patterns also effect to html_static_path and html_extra_path
-exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store']
+exclude_patterns = ["_build", "Thumbs.db", ".DS_Store"]
 
 # The name of the Pygments (syntax highlighting) style to use.
-pygments_style = 'sphinx'
+pygments_style = "sphinx"
 
 # If true, `todo` and `todoList` produce output, else they produce nothing.
 todo_include_todos = False
@@ -106,8 +107,10 @@
 # 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_path = ["_themes", ]
+html_theme = "sphinx_rtd_theme"
+html_theme_path = [
+    "_themes",
+]
 
 # 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
@@ -118,13 +121,13 @@
 # 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 HTMLHelp output ---------------------------------------
 
 # Output file base name for HTML help builder.
-htmlhelp_basename = 'cubidsdoc'
+htmlhelp_basename = "cubidsdoc"
 
 
 # -- Options for LaTeX output ------------------------------------------
@@ -133,15 +136,12 @@
     # The paper size ('letterpaper' or 'a4paper').
     #
     # 'papersize': 'letterpaper',
-
     # The font size ('10pt', '11pt' or '12pt').
     #
     # 'pointsize': '10pt',
-
     # Additional stuff for the LaTeX preamble.
     #
     # 'preamble': '',
-
     # Latex figure (float) alignment
     #
     # 'figure_align': 'htbp',
@@ -151,21 +151,15 @@
 # (source start file, target name, title, author, documentclass
 # [howto, manual, or own class]).
 latex_documents = [
-    (master_doc, 'cubids.tex',
-     'CuBIDS Documentation',
-     'PennLINC', 'manual'),
+    (master_doc, "cubids.tex", "CuBIDS Documentation", "PennLINC", "manual"),
 ]
 
 
 # -- Options for manual page output ------------------------------------
 
 # One entry per manual page. List of tuples
 # (source start file, name, description, authors, manual section).
-man_pages = [
-    (master_doc, 'cubids',
-     'CuBIDS Documentation',
-     [author], 1)
-]
+man_pages = [(master_doc, "cubids", "CuBIDS Documentation", [author], 1)]
 
 
 # -- Options for Texinfo output ----------------------------------------
@@ -174,14 +168,16 @@
 # (source start file, target name, title, author,
 #  dir menu entry, description, category)
 texinfo_documents = [
-    (master_doc, 'cubids',
-     'CuBIDS Documentation',
-     author,
-     'cubids',
-     'One line description of project.',
-     'Miscellaneous'),
+    (
+        master_doc,
+        "cubids",
+        "CuBIDS Documentation",
+        author,
+        "cubids",
+        "One line description of project.",
+        "Miscellaneous",
+    ),
 ]
 
 # -- Fix automodule config
 add_module_names = False
-

docs/examples.rst

@@ -0,0 +1,14 @@
+Thumbnails gallery
+==================
+
+.. nbgallery::
+   notebooks/Fieldmaps
+   notebooks/FirstProofofConcept
+   notebooks/HTML_param_groups
+   notebooks/JSON_PoC_read_write
+   notebooks/Key_and_Param_Groups
+   notebooks/keyparamgrouptest
+   notebooks/metadata_image_param
+   notebooks/PofC_Key_Values2
+   notebooks/rename_files_work
+   notebooks/workwithtestdata

docs/index.rst

@@ -12,6 +12,7 @@ Contents
    usage
    installation
    example
-   contributing
-   authors
-   history
+   examples
+   ../CONTRIBUTING
+   ../AUTHORS
+   ../HISTORY

notebooks/Fieldmaps.ipynb → docs/notebooks/Fieldmaps.ipynb

@@ -4,7 +4,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "# Fieldmaps OK?\n",
+    "# Check If Field Maps Are Defined For a Dataset\n",
     "\n",
     "This notebook shows how we check if fieldmaps are defined for the data set. There are two approaches:\n",
     "\n",
@@ -29,19 +29,19 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "# USE THIS BEFORE TESTING! \n",
-    "import sys \n",
+    "# USE THIS BEFORE TESTING!\n",
+    "import sys\n",
     "sys.path.append(\"..\")\n",
-    "from pathlib import Path \n",
+    "from pathlib import Path\n",
     "import shutil\n",
     "import os\n",
     "\n",
-    "from pkg_resources import resource_filename as pkgrf \n",
+    "from pkg_resources import resource_filename as pkgrf\n",
     "\n",
     "# returns string path to testdata\n",
     "TEST_DATA = pkgrf(\"cubids\", \"testdata\")\n",
     "\n",
-    "# should give you the full path \n",
+    "# should give you the full path\n",
     "tmp_path = Path().resolve()\n",
     "#print(tmp_path)\n",
     "\n",
@@ -100,10 +100,10 @@
     "import json\n",
     "\n",
     "def read_intendedfor(path):\n",
-    "    \n",
+    "\n",
     "    with open(str(path), 'r') as infile:\n",
     "        data = json.load(infile)\n",
-    "        \n",
+    "\n",
     "    return data.get('IntendedFor')"
    ]
   },
@@ -143,9 +143,9 @@
     "mapping = {}\n",
     "\n",
     "for fm in fmaps:\n",
-    "    \n",
+    "\n",
     "    intfor = read_intendedfor(fm)\n",
-    "    \n",
+    "\n",
     "    mapping[str(fm)] = intfor"
    ]
   },
@@ -184,21 +184,21 @@
     "all_files = [str(x) for x in pathlib.Path(data_root).rglob(\"*.nii*\")]\n",
     "\n",
     "for k, v in mapping.items():\n",
-    "    \n",
+    "\n",
     "    if not v:\n",
-    "        \n",
+    "\n",
     "        print(\"{}: This fieldmap is not intended for any files!\".format(k))\n",
-    "        \n",
+    "\n",
     "        continue\n",
-    "        \n",
+    "\n",
     "    for fi in v:\n",
-    "        \n",
+    "\n",
     "        if any([fi in x for x in all_files]):\n",
-    "            \n",
+    "\n",
     "            print(\"{}: This fieldmap has a file\".format(k))\n",
-    "            \n",
+    "\n",
     "        else:\n",
-    "            \n",
+    "\n",
     "            print(\"{}: The file this fieldmap is intended for doesn't exist\".format(k))"
    ]
   },