merge

.github/workflows/test_ci.yml

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+# This is a basic workflow to help you get started with Actions
+
+name: CI
+
+# Controls when the action will run. 
+on:
+  # Triggers the workflow on push or pull request events but only for the reorganize branch
+  push:
+    branches: [ reorganize ]
+  pull_request:
+    branches: [ reorganize, develop ]
+
+  # Allows you to run this workflow manually from the Actions tab
+  workflow_dispatch:
+
+# A workflow run is made up of one or more jobs that can run sequentially or in parallel
+jobs:
+  # This workflow contains a single job called "build"
+  build:
+    # The type of runner that the job will run on
+    runs-on: ubuntu-latest
+
+    # Initialize docker:
+    services:
+      localstack:
+        image: localstack/localstack
+        ports:  
+          - 4566:4566
+
+    # Steps represent a sequence of tasks that will be executed as part of the job
+    steps:
+      # Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it
+      - uses: actions/checkout@v2
+
+      - name: Setup
+        uses: actions/setup-python@v2
+        with:
+          python-version: 3.6
+
+      # Log in to docker hub. 
+      - name: Login to Docker Hub
+        uses: docker/login-action@v1
+        with:  
+          username: ${{ secrets.DOCKER_HUB_USERNAME }}
+          password: ${{ secrets.DOCKER_HUB_ACCESS_TOKEN }} 
+
+
+      # Runs a single command using the runners shell
+      - name: Installation
+        run: |
+          cd $GITHUB_WORKSPACE
+          wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh;
+          bash miniconda.sh -b -p $HOME/miniconda
+          source "$HOME/miniconda/etc/profile.d/conda.sh"
+          hash -r
+          conda config --set always_yes yes --set changeps1 no
+          conda update -q conda
+          conda config --append envs_dirs $HOME/miniconda/envs 
+          conda create -n neurocaas
+          conda activate neurocaas
+          python -m pip install --upgrade pip
+          pip install -r requirements.txt
+          pip install ./src
+
+      - name: Pull hello-world image
+        run: docker pull hello-world
+
+      - name: Run tests
+        run: |
+          echo $HOME $GITHUB_WORKSPACE "locations."
+          ls $HOME/miniconda/bin
+          ls $HOME/miniconda/envs
+          conda config --describe envs_dirs
+          conda env list
+          
+          pytest tests/
+        env:
+          AWS_DEFAULT_REGION: "us-east-1"
+
+      # Runs a set of commands using the runners shell
+      - name: Run a multi-line script
+        run: |
+          echo Add other actions to build,
+          echo test, and deploy your project.

.gitignore

@@ -0,0 +1,149 @@
+# Mac OS
+*.DS_Store
+
+# Backups
+*.swp
+*.swo
+
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*/__pycache__/
+*/*/__pycache__/
+*/*/*/__pycache__/
+*/*/*/*/__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/
+src/*.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/
+
+# 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
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# 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/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/
+
+
+# Build files: 
+
+# Log files
+src/neurocaas_contrib/template_mats/DATASET_NAME-dataset_update.ext_STATUS.txt.json
+logs/*
+

.gitignore.orig

@@ -0,0 +1,150 @@
+# Mac OS
+*.DS_Store
+
+# Backups
+*.swp
+*.swo
+
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*/__pycache__/
+*/*/__pycache__/
+*/*/*/__pycache__/
+<<<<<<< HEAD
+=======
+*/*/*/*/__pycache__/
+>>>>>>> 1ff29ae2391cf4d1c6c2b98550a826c328e4ea34
+*.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/
+
+# 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
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# 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/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/
+
+
+# Build files: 
+
+# Log files
+src/neurocaas_contrib/template_mats/DATASET_NAME-dataset_update.ext_STATUS.txt.json
+