Manual bisect

.gitignore

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+# Created by https://www.toptal.com/developers/gitignore/api/python,jupyternotebooks
+# Edit at https://www.toptal.com/developers/gitignore?templates=python,jupyternotebooks
+
+### JupyterNotebooks ###
+# gitignore template for Jupyter Notebooks
+# website: http://jupyter.org/
+
+.ipynb_checkpoints
+*/.ipynb_checkpoints/*
+
+# IPython
+profile_default/
+ipython_config.py
+
+# Remove previous ipynb_checkpoints
+#   git rm -r .ipynb_checkpoints/
+
+### Python ###
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+pip-wheel-metadata/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+pytestdebug.log
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+doc/_build/
+
+# PyBuilder
+target/
+
+# Jupyter Notebook
+
+# IPython
+
+# pyenv
+.python-version
+
+# pipenv
+#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+#   However, in case of collaboration, if having platform-specific dependencies or dependencies
+#   having no cross-platform support, pipenv may install dependencies that don't work, or not
+#   install all needed dependencies.
+#Pipfile.lock
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+pythonenv*
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/
+
+# pytype static type analyzer
+.pytype/
+
+# profiling data
+.prof
+
+# Pias add this
+.DS_STORE
+# End of https://www.toptal.com/developers/gitignore/api/python,jupyternotebooks

.travis.yml

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+language: python
+python:
+  - "3.7"
+  - "3.8"
+# command to install dependencies
+install:
+  # install dependencies for testing
+  - pip install pytest pytest-cov
+  # install the package
+  - pip install .
+# command to run tests
+script:
+  - pytest --cov=./

CITATION.md

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+To acknowledge this repository please cite our paper
+
+ ```bibtex
+ @article{Charlene2019,
+   title = {Reproducible {{Brain}}},
+   volume = {12},
+   number = {5},
+   journal = {Brain Technologies \& Signals},
+   doi = {10/v5dar2},
+   author = {{Charlene Bultoc {and} Fulanito Shrug}},
+   month = sep,
+   year = {2019},
+   pages = {8-13},
+   note = {00000}
+ }
+ ```

LICENSE.md

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+BSD 3-Clause License
+
+ Copyright (c) 2019, Charlene Bultoc and others
+ All rights reserved.
+
+ Redistribution and use in source and binary forms, with or without
+ modification, are permitted provided that the following conditions are met:
+
+ 1. Redistributions of source code must retain the above copyright notice, this
+    list of conditions and the following disclaimer.
+
+ 2. Redistributions in binary form must reproduce the above copyright notice,
+    this list of conditions and the following disclaimer in the documentation
+    and/or other materials provided with the distribution.
+
+ 3. Neither the name of the copyright holder nor the names of its
+    contributors may be used to endorse or promote products derived from
+    this software without specific prior written permission.
+
+ THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+ AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+ IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+ DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
+ FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+ DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+ SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+ CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+ OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+ OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

README.md

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+# sagital average
+
+ This is a library that calculate the averages through a sagital plain.
+
+ ## Installation
+
+ Browse to the directory where this file lives, and run:
+ ```bash
+ pip install .
+ ```
+ That command will download any dependencies we have
+
+
+ ## Usage
+
+ Right now we have only one function, you can use it as shown below:
+
+
+ ```python
+ from sagital_averages import sagital_brain
+
+ sagital_brain.run_averages("input_file.csv", "ouput_file.csv")
+ ```
+
+ Or alternativaly you can run it from the terminal as:
+
+ ```bash
+ $ sagverage input_file.csv -o output_file.csv
+ ```
+
+ ## Contributing
+
+ We accept contributions via GitHub!!
+
+ To install the development version, clone this repository and install it on 
+ a virtual environment
+
+ ```bash
+ git clone [email protected]:UCL-RITS/rsd-sagital_average.git
+ python -m venv brain
+ soruce brain/bin/activate
+ cd rsd-sagital_average
+ pip install -e .
+ ... code code code ...
+ deactivate
+ ```
+
+ or using a conda environment as
+
+ ```bash
+ git clone [email protected]:UCL-RITS/rsd-sagital_average.git
+ conda create -n brain python=3.7
+ conda activate brain
+ cd rsd-sagital_average
+ pip install -e .
+ ... code code code ...
+ conda deactivate
+ ```

command.py

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+from argparse import ArgumentParser
+from argparse import ArgumentDefaultsHelpFormatter
+from ..sagital_brain import run_averages
+
+
+def process():
+    parser = ArgumentParser(
+        description="Calculates the average for each sagital-horizontal plane.",
+        formatter_class=ArgumentDefaultsHelpFormatter,
+    )
+    parser.add_argument(
+        "file_input",
+        nargs="?",
+        default="brain_sample.csv",
+        help="Input CSV file with the results from scikit-brain binning algorithm.",
+    )
+    parser.add_argument(
+        "--file_output",
+        "-o",
+        default="brain_average.csv",
+        help="Name of the output CSV file.",
+    )
+    arguments = parser.parse_args()
+
+    run_averages(arguments.file_input, arguments.file_output)

docs/Makefile

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+# 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)