Create package

.github/workflows/python-tests.yml

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+name: Python package
+
+on: [push]
+
+jobs:
+  build:
+
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ["3.8", "3.10"]
+
+    steps:
+      - uses: actions/checkout@v3
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v4
+        with:
+          python-version: ${{ matrix.python-version }}
+      - name: Install dependencies
+        # This case we are only updating pip, but you could add other dependencies needed.
+        run: |
+          python -m pip install --upgrade pip
+          python -m pip install pytest
+          python -m pip install pytest-cov
+          python -m pip install pyyaml
+          python -m pip install numpy
+      - name: Test with pytest
+        run: |
+          pytest
+          pytest --cov="."

.gitignore

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+# Created by https://www.toptal.com/developers/gitignore/api/python,visualstudiocode
+# Edit at https://www.toptal.com/developers/gitignore?templates=python,visualstudiocode
+
+### 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/
+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/
+cover/
+
+# 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/
+
+# PyBuilder
+.pybuilder/
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+#   For a library or package, you might want to ignore these files since the code is
+#   intended to run in multiple environments; otherwise, check them in:
+# .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
+
+# poetry
+#   Similar to Pipfile.lock, it is generally recommended to include poetry.lock in version control.
+#   This is especially recommended for binary packages to ensure reproducibility, and is more
+#   commonly ignored for libraries.
+#   https://python-poetry.org/docs/basic-usage/#commit-your-poetrylock-file-to-version-control
+#poetry.lock
+
+# pdm
+#   Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control.
+#pdm.lock
+#   pdm stores project-wide configurations in .pdm.toml, but it is recommended to not include it
+#   in version control.
+#   https://pdm.fming.dev/#use-with-ide
+.pdm.toml
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow and github.com/pdm-project/pdm
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# 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/
+
+# Cython debug symbols
+cython_debug/
+
+# PyCharm
+#  JetBrains specific template is maintained in a separate JetBrains.gitignore that can
+#  be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore
+#  and can be added to the global gitignore or merged into this file.  For a more nuclear
+#  option (not recommended) you can uncomment the following to ignore the entire idea folder.
+#.idea/
+
+### Python Patch ###
+# Poetry local configuration file - https://python-poetry.org/docs/configuration/#local-configuration
+poetry.toml
+
+
+### VisualStudioCode ###
+.vscode/*
+!.vscode/settings.json
+!.vscode/tasks.json
+!.vscode/launch.json
+!.vscode/extensions.json
+!.vscode/*.code-snippets
+
+# Local History for Visual Studio Code
+.history/
+
+# Built Visual Studio Code Extensions
+*.vsix
+
+### VisualStudioCode Patch ###
+# Ignore all local history of files
+.history
+.ionide
+
+# End of https://www.toptal.com/developers/gitignore/api/python,visualstudiocode

CITATION.md

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+If you wish to refer to this course, please cite the URL
+http://github-pages.ucl.ac.uk/rsd-engineeringcourse/
+
+Portions of the material are taken from [Software Carpentry](http://software-carpentry.org/)

LICENSE.md

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+(C) University College London 2022
+
+This "sagittal_average" package is granted into the public domain.

README.md

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+# Sagittal Average
+
+This is a package used to calculate and produce a file of the sagittal average in a brain sample. 
+
+## Installation
+
+```bash
+pip install git+https://github.com/UCL-COMP0233-22-23/sagittal_average/
+```
+
+## Usage
+
+Invoke the tool with `sagittal_average_run <path/to/csv/with/brain/sample>` or use it on your own library:
+
+```python
+from sagittal_average_module import sagittal_brain
+
+sagittal_brain.run_averages(file_input, file_output)
+```

sagittal_average_module/brain_average.csv

@@ -0,0 +1 @@
+0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,1.0

sagittal_average_module/brain_sample.csv

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+0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
+0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
+0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
+0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
+0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
+0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
+0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
+0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
+0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
+0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
+0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
+0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
+0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
+0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
+0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
+0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
+0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
+0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
+0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
+1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1

sagittal_average_module/command.py

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+import sys
+from sagittal_average_module.sagittal_brain import *
+
+def process():
+    argumens = sys.argv
+    file_input = None
+    file_output = None
+    if len(argumens) > 1:
+        file_input = sys.argv[1]
+    if len(argumens) > 2:
+        file_output = sys.argv[2]
+    return run_averages(file_input, file_output)
+
+
+if __name__ == "__main__":
+    process()

sagittal_average_module/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)

sagittal_average_module/docs/_build/html/.buildinfo

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+# Sphinx build info version 1
+# This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
+config: df3ba79d8324703f972a4b5d3df955cf
+tags: 645f666f9bcd5a90fca523b33c5a78b7

sagittal_average_module/docs/_build/html/_sources/content/sagittal-brain-docs.rst.txt

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+Sagittal Average - Run Average Documentation
+=============================================
+
+.. automodule:: sagittal_average_module.sagittal_brain.run_averages

sagittal_average_module/docs/_build/html/_sources/index.rst.txt

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+.. Sagittal Average documentation master file, created by
+   sphinx-quickstart on Mon Nov 28 17:54:43 2022.
+   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!
+============================================
+Calculates and outputs the sagittal average of a brain sample.
+
+.. toctree::
+   :maxdepth: 2
+   :caption: Contents:
+
+   /content/sagittal-brain-docs
+
+
+
+Indices and tables
+==================
+
+* :ref:`genindex`
+* :ref:`modindex`
+* :ref:`search`