junifer 0.0.7.dev332__py3-none-any.whl → 0.0.8__py3-none-any.whl

junifer/external/BrainPrint/brainprint/cli/parser.py

@@ -0,0 +1,150 @@
+import argparse
+import pathlib
+import sys
+
+from . import help_text
+
+
+def parse_options():
+    """
+    Initiates the option parser and return the parsed object.
+    """
+    parser = argparse.ArgumentParser(
+        description=help_text.CLI_DESCRIPTION, add_help=False
+    )
+
+    # Required arguments
+    required = parser.add_argument_group(title="Required arguments")
+    required.add_argument(
+        "--sdir",
+        dest="subjects_dir",
+        help=help_text.SUBJECTS_DIR,
+        default=None,
+        metavar="<directory>",
+        required=True,
+        type=pathlib.Path,
+    )
+    required.add_argument(
+        "--sid",
+        dest="subject_id",
+        help=help_text.SUBJECT_ID,
+        default=None,
+        metavar="<string>",
+        required=True,
+    )
+
+    # Optional arguments
+    optional = parser.add_argument_group(title="Processing directives")
+    optional.add_argument(
+        "--num",
+        dest="num",
+        help=help_text.NUM,
+        default=50,
+        metavar="<num>",
+        type=int,
+        required=False,
+    )
+    optional.add_argument(
+        "--evec",
+        dest="keep_eigenvectors",
+        help=help_text.EVEC,
+        default=False,
+        action="store_true",
+        required=False,
+    )
+    optional.add_argument(
+        "--skipcortex",
+        dest="skip_cortex",
+        help=help_text.SKIP_CORTEX,
+        default=False,
+        action="store_true",
+        required=False,
+    )
+    optional.add_argument(
+        "--norm",
+        dest="norm",
+        help=help_text.NORM,
+        default="none",
+        metavar="<surface|volume|geometry|none>",
+        choices=["surface", "volume", "geometry", "none"],
+        required=False,
+    )
+    optional.add_argument(
+        "--reweight",
+        dest="reweight",
+        help=help_text.REWEIGHT,
+        default=False,
+        action="store_true",
+        required=False,
+    )
+    optional.add_argument(
+        "--asymmetry",
+        dest="asymmetry",
+        help=help_text.ASYM,
+        default=False,
+        action="store_true",
+        required=False,
+    )
+    optional.add_argument(
+        "--asym-distance",
+        dest="asymmetry_distance",
+        help=help_text.ASYM_DISTANCE,
+        default="euc",
+        metavar="<euc>",
+        choices=["euc"],
+        required=False,
+    )
+    optional.add_argument(
+        "--cholmod",
+        dest="use_cholmod",
+        help=help_text.CHOLMOD,
+        default=False,
+        action="store_true",
+        required=False,
+    )
+
+    # Output options
+    output = parser.add_argument_group(title="Output parameters")
+    output.add_argument(
+        "--outdir",
+        dest="destination",
+        help=help_text.OUTPUT_DIRECTORY,
+        default=None,
+        metavar="<directory>",
+        required=False,
+        type=pathlib.Path,
+    )
+    output.add_argument(
+        "--keep-temp",
+        dest="keep_temp",
+        help=help_text.KEEP_TEMP,
+        default=False,
+        action="store_true",
+        required=False,
+    )
+
+    # Help
+    help = parser.add_argument_group(title="Getting help")
+    help.add_argument("--help", help=help_text.HELP, action="help")
+    help.add_argument(
+        "--more-help",
+        dest="more_help",
+        help=help_text.MORE_HELP,
+        default=False,
+        action="store_true",
+        required=False,
+    )
+
+    no_input = len(sys.argv) == 1
+    more_help = "--more-help" in sys.argv
+    if no_input:
+        args = parser.parse_args(["--help"])
+        return
+    elif more_help:
+        print(help_text.HELPTEXT)
+        return
+    else:
+        args = vars(parser.parse_args())
+        del args["more_help"]
+
+    return args

junifer/external/BrainPrint/brainprint/cli/utils.py

@@ -0,0 +1,14 @@
+"""
+Utility functions for the :mod:`brainprint.cli` module.
+"""
+from . import help_text
+
+
+def get_help(print_help: bool = True):
+    """
+    Returns a detailed help message.
+    """
+    if print_help:
+        print(help_text.HELPTEXT)
+    else:
+        return help_text.HELPTEXT

junifer/external/BrainPrint/brainprint/commands/sys_info.py

@@ -0,0 +1,18 @@
+import argparse
+
+from .. import sys_info
+
+
+def run():
+    """Run sys_info() command."""
+    parser = argparse.ArgumentParser(
+        prog=f"{__package__.split('.')[0]}-sys_info", description="sys_info"
+    )
+    parser.add_argument(
+        "--developer",
+        help="display information for optional dependencies",
+        action="store_true",
+    )
+    args = parser.parse_args()
+
+    sys_info(developer=args.developer)

junifer/external/BrainPrint/brainprint/utils/tests/test_config.py

@@ -0,0 +1,33 @@
+from io import StringIO
+
+from .._config import sys_info
+
+
+def test_sys_info():
+    """Test info-showing utility."""
+    out = StringIO()
+    sys_info(fid=out)
+    value = out.getvalue()
+    out.close()
+    assert "Platform:" in value
+    assert "Executable:" in value
+    assert "CPU:" in value
+    assert "Physical cores:" in value
+    assert "Logical cores" in value
+    assert "RAM:" in value
+    assert "SWAP:" in value
+
+    assert "numpy" in value
+    assert "psutil" in value
+
+    assert "style" not in value
+    assert "test" not in value
+
+    out = StringIO()
+    sys_info(fid=out, developer=True)
+    value = out.getvalue()
+    out.close()
+
+    assert "build" in value
+    assert "style" in value
+    assert "test" in value

junifer/external/BrainPrint/doc/Makefile

@@ -0,0 +1,20 @@
+# Minimal makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line, and also
+# from the environment for the first two.
+SPHINXOPTS    ?=
+SPHINXBUILD   ?= sphinx-build
+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
+
+# 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)

junifer/external/BrainPrint/doc/_templates/autosummary/class.rst

@@ -0,0 +1,10 @@
+{{ fullname | escape | underline }}
+
+.. currentmodule:: {{ module }}
+
+.. autoclass:: {{ objname }}
+   :members:
+   :inherited-members:
+
+.. minigallery:: {{ fullname }}
+    :add-heading:

junifer/external/BrainPrint/doc/_templates/autosummary/function.rst

@@ -0,0 +1,8 @@
+{{ fullname | escape | underline }}
+
+.. currentmodule:: {{ module }}
+
+.. autofunction:: {{ objname }}
+
+.. minigallery:: {{ fullname }}
+    :add-heading:

junifer/external/BrainPrint/doc/_templates/autosummary/module.rst

@@ -0,0 +1,6 @@
+{{ fullname }}
+{{ underline }}
+
+.. automodule:: {{ fullname }}
+    :members:
+

junifer/external/BrainPrint/doc/api/index.rst

@@ -0,0 +1,11 @@
+API References
+==============
+
+.. currentmodule:: brainprint
+
+.. autosummary::
+    :toctree: generated/
+
+    brainprint
+    asymmetry
+    surfaces

junifer/external/BrainPrint/doc/conf.py

@@ -0,0 +1,272 @@
+# Configuration file for the Sphinx documentation builder.
+#
+# For the full list of built-in configuration values, see the documentation:
+# https://www.sphinx-doc.org/en/master/usage/configuration.html
+
+# -- Project information -----------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#project-information
+
+
+import inspect
+from datetime import date
+from importlib import import_module
+from typing import Dict, Optional
+
+# from sphinx_gallery.sorting import FileNameSortKey
+
+import brainprint
+
+project = "BrainPrint"
+author = "Martin Reuter"
+copyright = f"{date.today().year}, {author}"
+release = brainprint.__version__
+package = brainprint.__name__
+gh_url = "https://github.com/Deep-MI/BrainPrint"
+
+# -- General configuration ---------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration
+
+# If your documentation needs a minimal Sphinx version, state it here.
+needs_sphinx = "5.0"
+
+# The document name of the “root” document, that is, the document that contains
+# the root toctree directive.
+root_doc = "index"
+
+# 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.autosectionlabel",
+    "sphinx.ext.autosummary",
+    "sphinx.ext.intersphinx",
+    "sphinx.ext.linkcode",
+    "numpydoc",
+    "sphinxcontrib.bibtex",
+    "sphinx_copybutton",
+    "sphinx_design",
+]
+
+templates_path = ["_templates"]
+exclude_patterns = [
+    "_build",
+    "Thumbs.db",
+    ".DS_Store",
+    "**.ipynb_checkpoints",
+]
+
+# Sphinx will warn about all references where the target cannot be found.
+nitpicky = False
+nitpick_ignore = []
+
+# A list of ignored prefixes for module index sorting.
+modindex_common_prefix = [f"{package}."]
+
+# The name of a reST role (builtin or Sphinx extension) to use as the default
+# role, that is, for text marked up `like this`. This can be set to 'py:obj' to
+# make `filter` a cross-reference to the Python function “filter”.
+default_role = "py:obj"
+
+# -- Options for HTML output -------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#options-for-html-output
+html_theme = "furo"
+html_static_path = ["_static"]
+html_title = project
+html_show_sphinx = False
+
+# Documentation to change footer icons:
+# https://pradyunsg.me/furo/customisation/footer/#changing-footer-icons
+html_theme_options = {
+    "footer_icons": [
+        {
+            "name": "GitHub",
+            "url": gh_url,
+            "html": """
+                <svg stroke="currentColor" fill="currentColor" stroke-width="0" viewBox="0 0 16 16">
+                    <path fill-rule="evenodd" d="M8 0C3.58 0 0 3.58 0 8c0 3.54 2.29 6.53 5.47 7.59.4.07.55-.17.55-.38 0-.19-.01-.82-.01-1.49-2.01.37-2.53-.49-2.69-.94-.09-.23-.48-.94-.82-1.13-.28-.15-.68-.52-.01-.53.63-.01 1.08.58 1.23.82.72 1.21 1.87.87 2.33.66.07-.52.28-.87.51-1.07-1.78-.2-3.64-.89-3.64-3.95 0-.87.31-1.59.82-2.15-.08-.2-.36-1.02.08-2.12 0 0 .67-.21 2.2.82.64-.18 1.32-.27 2-.27.68 0 1.36.09 2 .27 1.53-1.04 2.2-.82 2.2-.82.44 1.1.16 1.92.08 2.12.51.56.82 1.27.82 2.15 0 3.07-1.87 3.75-3.65 3.95.29.25.54.73.54 1.48 0 1.07-.01 1.93-.01 2.2 0 .21.15.46.55.38A8.013 8.013 0 0 0 16 8c0-4.42-3.58-8-8-8z"></path>
+                </svg>
+            """,
+            "class": "",
+        },
+    ],
+}
+
+# -- autosummary -------------------------------------------------------------
+autosummary_generate = True
+
+# -- autodoc -----------------------------------------------------------------
+autodoc_typehints = "none"
+autodoc_member_order = "groupwise"
+autodoc_warningiserror = True
+autoclass_content = "class"
+
+# -- intersphinx -------------------------------------------------------------
+intersphinx_mapping = {
+    "matplotlib": ("https://matplotlib.org/stable", None),
+    "mne": ("https://mne.tools/stable/", None),
+    "numpy": ("https://numpy.org/doc/stable", None),
+    "pandas": ("https://pandas.pydata.org/pandas-docs/stable/", None),
+    "python": ("https://docs.python.org/3", None),
+    "scipy": ("https://docs.scipy.org/doc/scipy", None),
+    "sklearn": ("https://scikit-learn.org/stable/", None),
+}
+intersphinx_timeout = 5
+
+# -- sphinx-issues -----------------------------------------------------------
+issues_github_path = gh_url.split("https://github.com/")[-1]
+
+# -- autosectionlabels -------------------------------------------------------
+autosectionlabel_prefix_document = True
+
+# -- numpydoc ----------------------------------------------------------------
+#numpydoc_class_members_toctree = False
+#numpydoc_attributes_as_param_list = False
+
+# x-ref
+numpydoc_xref_param_type = True
+numpydoc_xref_aliases = {
+    # Matplotlib
+    "Axes": "matplotlib.axes.Axes",
+    "Figure": "matplotlib.figure.Figure",
+    # Python
+    "bool": ":class:`python:bool`",
+    "Path": "pathlib.Path",
+    "TextIO": "io.TextIOBase",
+    # Scipy
+    "csc_matrix": "scipy.sparse.csc_matrix",
+}
+#numpydoc_xref_ignore = {}
+
+# validation
+# https://numpydoc.readthedocs.io/en/latest/validation.html#validation-checks
+error_ignores = {
+    "GL01",  # docstring should start in the line immediately after the quotes
+    "EX01",  # section 'Examples' not found
+    "ES01",  # no extended summary found
+    "SA01",  # section 'See Also' not found
+    "RT02",  # The first line of the Returns section should contain only the type, unless multiple values are being returned  # noqa
+}
+numpydoc_validate = True
+numpydoc_validation_checks = {"all"} | set(error_ignores)
+numpydoc_validation_exclude = {  # regex to ignore during docstring check
+    r"\.__getitem__",
+    r"\.__contains__",
+    r"\.__hash__",
+    r"\.__mul__",
+    r"\.__sub__",
+    r"\.__add__",
+    r"\.__iter__",
+    r"\.__div__",
+    r"\.__neg__",
+}
+
+# -- sphinxcontrib-bibtex ----------------------------------------------------
+bibtex_bibfiles = ["./references.bib"]
+
+# -- sphinx.ext.linkcode -----------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/extensions/linkcode.html
+
+#  Alternative method for linking to code by Osama, not sure which one is better
+from urllib.parse import quote
+def linkcode_resolve(domain, info):
+    if domain != "py":
+        return None
+    if not info["module"]:
+        return None
+    filename = quote(info["module"].replace(".", "/"))
+    if not filename.startswith("tests"):
+        filename = "/" + filename
+    if "fullname" in info:
+        anchor = info["fullname"]
+        anchor = "#:~:text=" + quote(anchor.split(".")[-1])
+    else:
+        anchor = ""
+    result = f"{gh_url}/blob/main/{filename}.py{anchor}"
+    return result
+
+# def linkcode_resolve(domain: str, info: Dict[str, str]) -> Optional[str]:
+#     """Determine the URL corresponding to a Python object.
+
+#     Parameters
+#     ----------
+#     domain : str
+#         One of 'py', 'c', 'cpp', 'javascript'.
+#     info : dict
+#         With keys "module" and "fullname".
+
+#     Returns
+#     -------
+#     url : str | None
+#         The code URL. If None, no link is added.
+#     """
+#     if domain != "py":
+#         return None  # only document python objects
+
+#     # retrieve pyobject and file
+#     try:
+#         module = import_module(info["module"])
+#         pyobject = module
+#         for elt in info["fullname"].split("."):
+#             pyobject = getattr(pyobject, elt)
+#         fname = inspect.getsourcefile(pyobject).replace("\\", "/")
+#     except Exception:
+#         # Either the object could not be loaded or the file was not found.
+#         # For instance, properties will raise.
+#         return None
+
+#     # retrieve start/stop lines
+#     source, start_line = inspect.getsourcelines(pyobject)
+#     lines = "L%d-L%d" % (start_line, start_line + len(source) - 1)
+
+#     # create URL
+#     if "dev" in release:
+#         branch = "main"
+#     else:
+#         return None  # alternatively, link to a maint/version branch
+#     fname = fname.rsplit(f"/{package}/")[1]
+#     url = f"{gh_url}/blob/{branch}/{package}/{fname}#{lines}"
+#     return url
+
+
+# # -- sphinx-gallery ----------------------------------------------------------
+# sphinx_gallery_conf = {
+#     "backreferences_dir": "generated/backreferences",
+#     "doc_module": (f"{package}",),
+#     "examples_dirs": ["generated/examples"],
+#     "exclude_implicit_doc": {},  # set
+#     "filename_pattern": r"\d{2}_",
+#     "gallery_dirs": ["generated/examples"],
+#     "line_numbers": False,
+#     "plot_gallery": True,
+#     "reference_url": {f"{package}": None},
+#     "remove_config_comments": True,
+#     "show_memory": True,
+#     "within_subsection_order": FileNameSortKey,
+# }
+
+
+# -- make sure pandoc gets installed -----------------------------------------
+from inspect import getsourcefile
+import os
+
+# Get path to directory containing this file, conf.py.
+DOCS_DIRECTORY = os.path.dirname(os.path.abspath(getsourcefile(lambda: 0)))
+
+def ensure_pandoc_installed(_):
+    import pypandoc
+
+    # Download pandoc if necessary. If pandoc is already installed and on
+    # the PATH, the installed version will be used. Otherwise, we will
+    # download a copy of pandoc into docs/bin/ and add that to our PATH.
+    pandoc_dir = os.path.join(DOCS_DIRECTORY, "bin")
+    # Add dir containing pandoc binary to the PATH environment variable
+    if pandoc_dir not in os.environ["PATH"].split(os.pathsep):
+        os.environ["PATH"] += os.pathsep + pandoc_dir
+    pypandoc.ensure_pandoc_installed(
+        targetfolder=pandoc_dir,
+        delete_installer=True,
+    )
+
+def setup(app):
+    app.connect("builder-inited", ensure_pandoc_installed)