Merge pull request #14 from Toth-Technology/matlab

Merging milestone 1 from Matlab to master.

.env-scripts/dev_requirements.txt

@@ -0,0 +1,8 @@
+autopep8
+mypy
+jupyterlab
+pylint
+sphinx
+sphinx-rtd-theme
+recommonmark
+twine

.env-scripts/setup.bat

@@ -0,0 +1,5 @@
+python -m venv .env
+python -m pip install --upgrade pip
+pip install --upgrade setuptools wheel
+pip install -r .env-scripts/dev_requirements.txt
+pip install -r requirements.txt

.env-scripts/setup.sh

@@ -0,0 +1,7 @@
+rm -r .env
+python3 -m venv .env
+source .env/bin/activate
+python -m pip install --upgrade pip
+pip install --upgrade setuptools wheel
+pip install -r .env-scripts/dev_requirements.txt
+pip install -r requirements.txt

.github/workflows/pypi-publish.yml

@@ -0,0 +1,41 @@
+name: Python package for pypi
+
+on:
+  push:
+    tags:
+    - 'v*'
+
+jobs:
+  build:
+
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: [3.8]
+
+    steps:
+    - uses: actions/checkout@v2
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v2
+      with:
+        python-version: ${{ matrix.python-version }}
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip setuptools wheel
+        pip install -r .env-scripts/dev_requirements.txt
+        pip install -r requirements.txt
+    - name: Package Dependencies
+      run: |
+        cd src
+        python setup.py sdist bdist_wheel
+    - name: List Environment variables
+      run: |
+        printenv
+    - name: Deploy package to test Pypi
+      env:
+        USERNAME: ${{ secrets.TWINE_PROD_USERNAME }}
+        PASSWORD: ${{ secrets.TWINE_PROD_PASSWORD }}
+      run: |
+        cd src
+        twine upload -r pypi -u $USERNAME -p $PASSWORD dist/*
+    

.github/workflows/testpypi-publish.yml

@@ -0,0 +1,38 @@
+name: Python package for testpypi
+
+on: [push]
+
+jobs:
+  build:
+
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: [3.8]
+
+    steps:
+    - uses: actions/checkout@v2
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v2
+      with:
+        python-version: ${{ matrix.python-version }}
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip setuptools wheel
+        pip install -r .env-scripts/dev_requirements.txt
+        pip install -r requirements.txt
+    - name: Package Dependencies
+      run: |
+        cd src
+        python setup.py sdist bdist_wheel
+    - name: List Environment variables
+      run: |
+        printenv
+    - name: Deploy package to test Pypi
+      env:
+        USERNAME: ${{ secrets.TWINE_TEST_USERNAME }}
+        PASSWORD: ${{ secrets.TWINE_TEST_PASSWORD }}
+      run: |
+        cd src
+        twine upload -r testpypi -u $USERNAME -p $PASSWORD dist/*
+    

.gitignore

@@ -127,3 +127,5 @@ dmypy.json
 
 # Pyre type checker
 .pyre/
+
+*DS_Store

.vscode/launch.json

@@ -0,0 +1,16 @@
+{
+    // Use IntelliSense to learn about possible attributes.
+    // Hover to view descriptions of existing attributes.
+    // For more information, visit: https://go.microsoft.com/fwlink/?linkid=830387
+    "version": "0.2.0",
+    "configurations": [
+        {
+            "name": "Python: Current File",
+            "type": "python",
+            "request": "launch",
+            "program": "${file}",
+            "console": "integratedTerminal",
+            "args": []
+        }
+    ]
+}

.vscode/settings.json

@@ -0,0 +1,3 @@
+{
+    "python.pythonPath": ".env/bin/python",
+}

README.md

@@ -1 +1,71 @@
-# bric-morphology
+# Getting started with topology radiomics
+
+## Installing using pip
+
+You can find our package on pypi
+
+Run the below command to install the package:
+
+```
+pip install topology_radiomics
+```
+
+## Running with docker
+
+First clone this repository
+
+```
+git clone https://github.com/radxtools/topology-radiomics.git
+```
+
+There are multiple ways to get started.
+
+1. docker-compose
+2. docker run
+
+### docker-compose
+
+Run the following commands to start the docker container
+
+```
+cd docker
+docker-compose up
+```
+
+### docker run
+
+With this step, you don't need to clone the url.
+Run the following commands to start the docker container
+
+```
+docker rm radxtools/topology-radiomics-examples
+docker pull radxtools/topology-radiomics-examples
+docker run -d -p 3000:3000 --name topology-radiomics-examples radxtools/topology-radiomics-examples
+```
+
+## Tutorials
+
+Once the docker image is up and running. You can view our notebooks. You can get started with the notebook to learn how to use the package. You should start with `Tutorial - Getting started with topology_radiomics.ipynb`
+
+Tutorial Notebooks:
+
+1. Tutorial - Getting started with topoplogy_radiomics.ipynb
+2. Tutorial - Using topology_radiomics to visualize features.ipynb
+3. Tutorial - Working with medpy and topology_radiomics.ipynb
+
+The notebooks can be viewed by opening the browser and visting the url http://localhost:3000
+
+
+# Contribution Guide:
+
+Please follow google style formatting for [docstrings](https://google.github.io/styleguide/pyguide.html#38-comments-and-docstrings)
+
+## Bugs and Feature Request
+
+Please submit bugs and features to our github page.
+
+
+## Pull Requests
+Create a issue on our board.
+Create a pull request with your changes. Tag your changes with the issue number (commit message should have issue number).
+Someone from the team will review your request and merge your changes for the next release.

docker/docker-compose.yml

@@ -0,0 +1,6 @@
+version: '2'
+services:
+  app:
+    image: radxtools/topology-radiomics-examples:latest
+    ports:
+        - "3000:3000"

docker/notebook.dockerfile

@@ -0,0 +1,29 @@
+# set base image (host OS)
+FROM python:3.8
+
+# install graphics libs
+RUN apt-get update && apt-get install -y libglu1-mesa-dev freeglut3-dev mesa-common-dev
+
+# set the working directory in the container
+WORKDIR /notebooks
+
+# copy the dependencies file to the working directory
+COPY requirements.txt .
+COPY .env-scripts/dev_requirements.txt .
+COPY notebooks ./notebooks
+
+
+# install dpendencies
+RUN PIP_INSTALL="python -m pip install --upgrade --no-cache-dir --retries 10 --timeout 60" && \
+    $PIP_INSTALL -r dev_requirements.txt && \
+    $PIP_INSTALL install -r requirements.txt
+
+COPY src ./src
+
+# copy the content of the local src directory to the working directory
+RUN cd src && python setup.py develop
+
+# # command to run on container start
+CMD [ "jupyter", "notebook", "--port=3000", "--no-browser", "--ip=0.0.0.0", "--allow-root", "--NotebookApp.token=" ]
+
+EXPOSE 3000

docs/docker.md

@@ -0,0 +1,52 @@
+The below documentation explains how to create and run docker containers.
+
+# Prerequisites:
+Software Installation
+1. Docker
+
+# Build
+
+This command will create the image using the file `docker/notebook.dockerfile` and will name the name image `notebook`
+
+```sh
+docker build -f docker/notebook.dockerfile -t notebook .
+docker tag notebook radxtools/topology-radiomics-examples
+```
+
+# Run
+
+This command will create a container called `topology-radiomics-examples` that will start the image `notebook`
+
+```sh
+docker rm topology-radiomics-examples
+docker run -d -p 3000:3000 --name topology-radiomics-examples notebook
+```
+
+# Compose
+
+```sh
+cd docker
+docker-compose up
+```
+
+# Pushing to Docker Repo
+
+The docker repo can be found [here](https://hub.docker.com/repository/docker/radxtools/topology-radiomics-examples)
+
+```sh
+docker login
+>>username
+>>password
+docker tag notebook radxtools/topology-radiomics-examples
+docker push radxtools/topology-radiomics-examples:latest
+```
+
+# Debugging the docker build
+
+If the app is already running, we can open a shell using the following command.
+
+```
+docker exec -it topology-radiomics-examples /bin/bash
+```
+
+This will create a shell. You can use this shell to troubleshoot other things like installed packages, file system paths and etc...

docs/sphinx.md

@@ -0,0 +1,42 @@
+This article discusses how to build documentation for this project using sphinx.
+
+
+# Generating Source Files
+
+The following command will create the source documentation files
+
+```
+cd src
+sphinx-apidoc -o docs/source topology_radiomics
+```
+
+# Building the docs
+
+## Method 1
+
+We can build using the setup utils.
+
+```
+python setup.py build_sphinx
+```
+
+## Method 2
+
+We can build using the sphinx cli
+
+```
+cd docs
+make html
+```
+
+# Notes
+
+More information can be found here:
+
+* [Python Docstring guide](https://google.github.io/styleguide/pyguide)
+
+* [Napolean Guide](https://sphinxcontrib-napoleon.readthedocs.io/en/latest/index.html)
+
+* [sphinx-apidoc guide](https://www.sphinx-doc.org/en/master/man/sphinx-apidoc.html#sphinx-apidoc-manual-page)
+
+* [Blog post on getting started with sphnix](https://samnicholls.net/2016/06/15/how-to-sphinx-readthedocs)