📦 Packaging solution 📦

.github/workflows/pytest.yml

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+name: Installation, test and coverage
+on: [push]
+
+jobs:
+  test:
+    # Multiple platforms have been disabled because Windows and OSx needs more credits than what we have.
+    # Don't use them during class or the assignment
+    name: py${{ matrix.python-version }} # ${{ matrix.platform }}
+    runs-on: ubuntu-latest # ${{ matrix.platform }}
+    strategy:
+      matrix:
+        # platform: [ubuntu-latest, windows-latest, macos-latest]
+        python-version: [3.9, 3.11]
+
+    steps:
+      # Checkout the repository and setups the machine to use python
+      - uses: actions/checkout@v3
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v4
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: Install testing dependencies
+        run: |
+          pip install pytest pytest-cov
+
+      - name: Install package
+        run: |
+          pip install .
+
+      - name: Run tests
+        run: pytest --cov=./

.gitignore

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+# Created by https://www.gitignore.io/api/python
+# Edit at https://www.gitignore.io/?templates=python
+
+### 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
+.hypothesis/
+.pytest_cache/
+
+# Translations
+*.mo
+*.pot
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+target/
+
+# 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
+
+# celery beat schedule file
+celerybeat-schedule
+
+# SageMath parsed files
+*.sage.py
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# Mr Developer
+.mr.developer.cfg
+.project
+.pydevproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/
+
+# End of https://www.gitignore.io/api/python

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

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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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+# sagittal average
+
+This is a library that calculate the averages through a sagittal plane.
+
+## 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 sagittal_averages import sagittal_brain
+
+sagittal_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-MPHY0021-21-22/sagittal_average.git
+python -m venv brain
+soruce brain/bin/activate
+cd sagittal_average
+pip install -e .
+... code code code ...
+deactivate
+```
+
+or using a conda environment as
+
+```bash
+git clone [email protected]:UCL-MPHY0021-21-22/sagittal_average.git
+conda create -n brain python=3.8
+conda activate brain
+cd sagittal_average
+pip install -e .
+... code code code ...
+conda deactivate
+```
+
+

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)

docs/conf.py

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+# Configuration file for the Sphinx documentation builder.
+#
+# This file only contains a selection of the most common options. For a full
+# list see the documentation:
+# https://www.sphinx-doc.org/en/master/usage/configuration.html
+
+# -- 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.
+#
+# import os
+# import sys
+# sys.path.insert(0, os.path.abspath('.'))
+
+
+# -- Project information -----------------------------------------------------
+
+project = 'sagittal-average'
+copyright = '2019, Charlene Bultoc'
+author = 'Charlene Bultoc'
+
+# The full version, including alpha/beta/rc tags
+release = '0.1'
+
+
+# -- 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 = [
+    'sphinx.ext.autodoc',  # Support automatic documentation
+    'sphinx.ext.coverage', # Automatically check if functions are documented
+    'sphinx.ext.mathjax',  # Allow support for algebra
+    'sphinx.ext.viewcode', # Include the source code in documentation
+]
+
+# Add any paths that contain templates here, relative to this directory.
+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']
+
+
+# -- 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 = 'alabaster'
+
+# 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']

docs/index.rst

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+.. sagittal-average documentation master file, created by
+   sphinx-quickstart on Thu Nov 21 19:42:38 2019.
+   You can adapt this file completely to your liking, but it should at least
+   contain the root `toctree` directive.
+
+Welcome to sagittal-average's documentation!
+===========================================
+
+.. toctree::
+   :maxdepth: 2
+   :caption: Contents:
+
+
+
+Indices and tables
+==================
+
+* :ref:`genindex`
+* :ref:`modindex`
+* :ref:`search`