Week07 group5

.gitignore

@@ -0,0 +1,199 @@
+# File created using '.gitignore Generator' for Visual Studio Code: https://bit.ly/vscode-gig
+
+# Created by https://www.toptal.com/developers/gitignore/api/visualstudiocode,macos,jupyternotebooks,python
+# Edit at https://www.toptal.com/developers/gitignore?templates=visualstudiocode,macos,jupyternotebooks,python
+
+### 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/
+
+### macOS ###
+# General
+.DS_Store
+.AppleDouble
+.LSOverride
+
+# Icon must end with two \r
+Icon
+
+# Thumbnails
+._*
+
+# Files that might appear in the root of a volume
+.DocumentRevisions-V100
+.fseventsd
+.Spotlight-V100
+.TemporaryItems
+.Trashes
+.VolumeIcon.icns
+.com.apple.timemachine.donotpresent
+
+# Directories potentially created on remote AFP share
+.AppleDB
+.AppleDesktop
+Network Trash Folder
+Temporary Items
+.apdisk
+
+### 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
+
+### VisualStudioCode ###
+.vscode/*
+!.vscode/tasks.json
+!.vscode/launch.json
+*.code-workspace
+
+### VisualStudioCode Patch ###
+# Ignore all local history of files
+.history
+.ionide
+
+# End of https://www.toptal.com/developers/gitignore/api/visualstudiocode,macos,jupyternotebooks,python
+
+# Custom rules (everything added below won't be overriden by 'Generate .gitignore File' if you use 'Update' option)
+

sagital/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

sagital/brain_sample.csv

@@ -0,0 +1,20 @@
+0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
+0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
+0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
+0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
+0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
+0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
+0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
+0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
+0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
+0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
+0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
+0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
+0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
+0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
+0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
+0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
+0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
+0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
+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

sagital/command.py

@@ -0,0 +1,24 @@
+from argparse import ArgumentParser
+from .sagital_brain import run_averages
+import sys
+
+
+def process():
+
+    parser = ArgumentParser(description="Weighted mean of squared numbers")
+    # parser.add_argument("numbers", nargs='+', help="the list of numbers")
+    parser.add_argument("numbers", type=int, nargs='+', help="the list of numbers")
+    parser.add_argument("--weights", "-w", type=int, nargs='+', help="the list of weights")
+    arguments = parser.parse_args()
+
+    # numbers = convert_numbers(arguments.numbers)
+    numbers = arguments.numbers
+    if arguments.weights:
+        weights = arguments.weights
+    else:
+        weights = [1] * len(numbers)
+
+    run_averages(numbers, weights)
+
+if __name__ == "__main__":
+    process()

sagital_brain.py → sagital/sagital_brain.py

@@ -31,13 +31,4 @@ def run_averages(file_input, file_output):
     with open(file_output, 'w') as myoutput:
              myoutput.write(','.join(sagital_averages) +  '\n')
 
-if __name__ == "__main__":
-    import sys
-    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]
-    run_averages(file_input, file_output)
+

sagital/tests/test_sagital_history.py

@@ -0,0 +1,53 @@
+
+import numpy as np
+
+def test_basic():
+    # Make new output file
+    data_input = np.zeros((20, 20))
+    data_input[-1, :] = 1
+    np.savetxt("brain_sample.csv", data_input, fmt='%d', delimiter=',')
+
+    # Run sagital brain file to generate output
+    exec(open("sagital_brain.py").read())
+
+    # Load output
+    loaded = np.loadtxt('brain_average.csv', delimiter=',')
+
+    # Expected output
+    expected = np.array([0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,1.0])
+
+    # Check the values are identical
+    np.testing.assert_array_equal(loaded, expected)
+
+
+def test_better():
+    data_input = np.zeros((20, 20))
+    data_input[-1, :] = 1
+    np.savetxt("brain_sample.csv", data_input, fmt='%d', delimiter=',')
+
+
+
+'''
+
+import subprocess 
+import numpy as np
+
+# generated data
+data_input = np.zeros((20, 20))
+data_input[-1, :] = 1
+np.savetxt("brain_sample.csv", data_input, fmt='%d', delimiter=',')
+
+# run 
+subprocess.run(["python", "sagital_brain.py"]) 
+
+# read output to then compare
+result = np.loadtxt('brain_average.csv', delimiter=',')
+
+# Generate an expected result
+
+expected = np.zeros(20)
+expected[-1] = 1
+
+np.testing.assert_array_equal(result, expected) # error if it fails
+
+'''

setup.py

@@ -0,0 +1,9 @@
+from setuptools import setup, find_packages
+
+setup(
+    name="sagital",
+    version="0.1.0",
+    packages=find_packages(),
+    entry_points={'console_scripts': [
+        'run_averages= sagital.command:process']}
+)