Merge pull request #2 from jennyfothergill/update/github

Update/GitHub

.github/workflows/build.yml

@@ -0,0 +1,43 @@
+name: build
+
+on:
+  push:
+    branches: [ master ]
+    # Run when container or environment is changed
+    paths:
+        - 'containers/dockerfile'
+        - 'environment.yml'
+  # Allows workflow to be manually triggered
+  workflow_dispatch:
+
+jobs:
+  build_cpu:
+    runs-on: ubuntu-latest
+
+    steps:
+      -
+        name: Checkout
+        uses: actions/checkout@v2
+      -
+        name: Set up QEMU
+        uses: docker/setup-qemu-action@v1
+      -
+        name: Set up Docker Buildx
+        uses: docker/setup-buildx-action@v1
+      -
+        name: Login to DockerHub
+        uses: docker/login-action@v1 
+        with:
+          username: ${{ secrets.DOCKERHUB_USERNAME }}
+          password: ${{ secrets.DOCKERHUB_TOKEN }}
+      -
+        name: Build and push
+        uses: docker/build-push-action@v2
+        with:
+          context: .
+          file: ./containers/dockerfile
+          push: true
+          tags: cmelab/cmeutils:latest
+      -
+        name: Image digest
+        run: echo ${{ steps.docker_build.outputs.digest }}

.github/workflows/pytest.yml

@@ -0,0 +1,29 @@
+name: pytest
+
+on:
+  push:
+    branches: [ master ]
+    paths:
+      - 'cmeutils/*'
+  pull_request:
+    branches: [ master ]
+    paths:
+      - 'cmeutils/*'
+
+jobs:
+  pytest:
+    runs-on: ubuntu-latest
+    container: 
+        image: cmelab/cmeutils:latest
+
+    steps:
+    - uses: actions/checkout@v2
+
+    - name: Run pytest with coverage report
+      run: python -m pytest --cov=./ --cov-report=xml -v
+
+    - name: Upload coverage to Codecov
+      uses: codecov/codecov-action@v1
+      with:
+        token: ${{ secrets.CODECOV_TOKEN }}
+        file: ./coverage.xml

README.md

@@ -1,17 +1,18 @@
 # CME Lab Utilies
 
-Helpful functions used by the [CME Lab](https://www.boisestate.edu/coen-cmsl).
+Helpful functions used by the [CME Lab](https://www.boisestate.edu/coen-cmelab/).
 
 ### Installation
 Installation of CME Lab Utilities requires the conda package manager. We recommend [Miniconda](https://docs.conda.io/en/latest/miniconda.html).
 1. Clone this repository:
 ```
-git clone git@gitlab.com:bsu/cme-lab/cme_lab_utils.git
-cd cme_lab_utils
+git git@github.com:cmelab/cmeutils.git
+cd cmeutils
 ```
 2. Set up and activate environment:
 ```
 conda env create -f environment.yml
+conda activate cmeutils
 ```
 3. Install this package with pip:
 ```

cmeutils/__version__.py

@@ -0,0 +1 @@
+__version__ = "0.0.0"

containers/dockerfile

@@ -0,0 +1,21 @@
+FROM continuumio/miniconda3:4.9.2
+
+WORKDIR /opt/app
+
+# Make RUN commands use `bash --login`: -- fixes conda init
+# https://pythonspeed.com/articles/activate-conda-dockerfile/
+SHELL ["/bin/bash", "--login", "-c"]
+
+# Create the environment
+COPY environment.yml ./
+
+# Install in base environment
+RUN conda env update -n base -f environment.yml && \
+    conda clean --all --yes -f 
+
+# Install curl for Codecov
+RUN apt-get update && apt-get upgrade -y && apt-get install -y curl
+
+# Prevent python from loading packages from outside the container
+# default empty pythonpath
+ENV PYTHONPATH /ignore/pythonpath

environment.yml

@@ -1,7 +1,9 @@
-name: cmelab
+name: cmeutils
 channels:
   - conda-forge
 dependencies:
-  - python=3.7
-  - pip
   - numpy
+  - pip
+  - python=3.7
+  - pytest
+  - pytest-cov

setup.py

@@ -1,12 +1,20 @@
+import os
 from setuptools import setup
 
-setup(name='cme_lab_utils',
-      version='0.0',
-      description='Helpful functions used in the CME lab'
-      url='https://gitlab.com/bsu/cme-lab/cme_lab_utils',
+
+NAME = "cmeutils"
+here = os.path.abspath(os.path.dirname(__file__))
+about = {}
+with open(os.path.join(here, NAME, "__version__.py")) as f:
+    exec(f.read(), about)
+
+setup(name=NAME,
+      version=about["__version__"],
+      description='Helpful functions used in the CME lab',
+      url='https://github.com/cmelab/cmeutils',
       author='CME Lab',
       author_email='ericjankowski@boisestate.edu',
       license='GPLv3',
-      packages=['cme_lab_utils'],
+      packages=['cmeutils'],
       zip_safe=False,
       )