Use Github Actions to Build and Test DeepBedMap #91

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Merged

weiji14 merged 11 commits into master from github-actions/init

Aug 4, 2019

.github/codefresh.yml

This file was deleted.

.github/main.workflow

-Original file line number
+Diff line change
@@ -0,0 +1,15 @@
+    workflow "Build and Test DeepBedMap" {
+      resolves = ["Run Tests"]
+      on = "push"
+    }
+    action "Build DeepBedMap App" {
+      uses = "actions/docker/cli@86ff551d26008267bb89ac11198ba7f1d807b699"
+      args = "build --file Dockerfile --tag weiji14/deepbedmap --target app ."
+    }
+    action "Run Tests" {
+      uses = "actions/docker/cli@86ff551d26008267bb89ac11198ba7f1d807b699"
+      args = "run weiji14/deepbedmap python -m pytest --verbose --disable-warnings --nbval test_ipynb.ipynb"
+      needs = ["Build DeepBedMap App"]
+    }

Dockerfile

            
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    @@ -1,11 +1,13 @@
  
    FROM buildpack-deps:bionic@sha256:59661846ab0c581272f4b4688702617e6cc83ef1a9ae1cf918978126babbc858

    FROM buildpack-deps:bionic@sha256:59661846ab0c581272f4b4688702617e6cc83ef1a9ae1cf918978126babbc858 AS base

    LABEL maintainer "https://github.com/weiji14"

    ENV LANG C.UTF-8

    ENV LC_ALL C.UTF-8

    # Initiate docker container with user 'jovyan'

    ENV NB_USER jovyan

    ENV NB_UID 1000

    ARG NB_USER=jovyan

    ARG NB_UID=1000

    ENV NB_USER ${NB_USER}

    ENV NB_UID ${NB_UID}

    ENV HOME /home/${NB_USER}

    RUN adduser --disabled-password \

    @@ -14,21 +16,19 @@ RUN adduser --disabled-password \
  
        ${NB_USER}

    # Setup conda

    ENV CONDA_DIR /opt/conda

    ENV CONDA_DIR ${HOME}/.conda

    ENV NB_PYTHON_PREFIX ${CONDA_DIR}

    ENV MINICONDA_VERSION 4.6.14

    ENV PATH ${CONDA_DIR}/bin:$HOME/.local/bin:${PATH}

    ENV MINICONDA_VERSION 4.7.10

    RUN cd /tmp && \

        wget --quiet https://repo.continuum.io/miniconda/Miniconda3-${MINICONDA_VERSION}-Linux-x86_64.sh && \

        echo "718259965f234088d785cad1fbd7de03 *Miniconda3-${MINICONDA_VERSION}-Linux-x86_64.sh" | md5sum -c - && \

        echo "1c945f2b3335c7b2b15130b1b2dc5cf4 *Miniconda3-${MINICONDA_VERSION}-Linux-x86_64.sh" | md5sum -c - && \

        /bin/bash Miniconda3-${MINICONDA_VERSION}-Linux-x86_64.sh -f -b -p $CONDA_DIR && \

        rm Miniconda3-${MINICONDA_VERSION}-Linux-x86_64.sh && \

        $CONDA_DIR/bin/conda config --system --prepend channels conda-forge && \

        $CONDA_DIR/bin/conda config --system --set auto_update_conda false && \

        $CONDA_DIR/bin/conda config --system --set show_channel_urls true && \

        conda clean --all --yes && \

        rm -rf /home/${NB_USER}/.cache/yarn && \

        $CONDA_DIR/bin/conda clean --all --quiet --yes && \

        $CONDA_DIR/bin/conda init --verbose

    # Setup $HOME directory with correct permissions

    @@ -37,26 +37,37 @@ RUN chown -R ${NB_UID} ${HOME}
  
    USER ${NB_USER}

    WORKDIR ${HOME}

    # Change to bash shell

    SHELL ["/bin/bash", "-c"]

    # Change to interactive bash shell, so that `conda activate base` works

    SHELL ["/bin/bash", "-ic"]

    # Install dependencies in environment.yml file using conda

    COPY environment.yml ${HOME}

    RUN conda env create -n deepbedmap -f environment.yml && \

    RUN conda env update -n base -f environment.yml && \

        conda clean --all --yes && \

        conda list -n deepbedmap

        conda list -n base

    # Install dependencies in Pipfile.lock using pipenv

    COPY Pipfile* ${HOME}/

    RUN source activate deepbedmap && \

        export LD_LIBRARY_PATH=$CONDA_PREFIX/lib && \

        pipenv install --python $CONDA_PREFIX/bin/python --dev --deploy && \

        rm --recursive ~/.cache/pipenv && \

    RUN conda activate base && \

        export LD_LIBRARY_PATH=${CONDA_PREFIX}/lib && \

        pipenv install --python ${CONDA_PREFIX}/bin/python --dev --deploy && \

        rm --recursive ${HOME}/.cache/pip* && \

        pipenv graph

    # Setup DeepBedMap virtual environment properly

    RUN conda activate base && \

        pipenv run python -m ipykernel install --user --name deepbedmap && \

        pipenv run jupyter kernelspec list --json

    # Copy remaining files to $HOME

    COPY --chown=1000:1000 . ${HOME}

    FROM base AS app

    # Run Jupyter Lab via pipenv in conda environment

    EXPOSE 8888

    CMD source activate deepbedmap && pipenv run jupyter lab --ip 0.0.0.0

    RUN echo -e '#!/bin/bash -i\nset -e\nconda activate\npipenv run "$@"' > .entrypoint.sh && \

        chmod +x .entrypoint.sh

    ENTRYPOINT ["./.entrypoint.sh"]

    CMD ["jupyter", "lab", "--ip", "0.0.0.0"]

README.md

            
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    @@ -6,7 +6,7 @@ Also a convenient [flat file](https://en.wikipedia.org/wiki/Flat-file_database)
  
    ![GitHub top language](https://img.shields.io/github/languages/top/weiji14/deepbedmap.svg)

    [![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/ambv/black)

    [![Comet.ML: experiments](https://img.shields.io/badge/Comet.ml-experiments-orange.svg?logo=data:image/png;base64,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)](https://www.comet.ml/weiji14/deepbedmap/)

    [![Codefresh build status](https://g.codefresh.io/api/badges/pipeline/weiji14_marketplace/weiji14%2Fdeepbedmap%2Fdeepbedmap?type=cf-1)](https://g.codefresh.io/public/accounts/weiji14_marketplace/pipelines/weiji14/deepbedmap/deepbedmap)

    [![Github Actions Build Status](https://img.shields.io/endpoint.svg?url=https%3A%2F%2Factions-badge.atrox.dev%2Fweiji14%2Fdeepbedmap%2Fbadge&style=flat)](https://github.com/weiji14/deepbedmap/actions)

    [![Dependabot Status](https://api.dependabot.com/badges/status?host=github&repo=weiji14/deepbedmap)](https://dependabot.com)

    ![DeepBedMap DEM over entire Antarctic continent, EPSG:3031 projection](https://user-images.githubusercontent.com/23487320/60510321-6e0cb280-9ccf-11e9-8096-d2a32eb28e6c.png)

    @@ -54,9 +54,9 @@ Also a convenient [flat file](https://en.wikipedia.org/wiki/Flat-file_database)
  
    ## Quickstart

    Launch Binder (Interactive jupyter notebook/lab environment in the cloud).

    Launch in [Pangeo Binder](https://pangeo-binder.readthedocs.io) (Interactive jupyter notebook/lab environment in the cloud).

    [![Binder](https://mybinder.org/badge.svg)](https://mybinder.org/v2/gh/weiji14/deepbedmap/master?urlpath=lab)

    [![Binder](https://binder.pangeo.io/badge_logo.svg)](https://binder.pangeo.io/v2/gh/weiji14/deepbedmap/master)

    ## Installation

    @@ -66,7 +66,7 @@ Start by cloning this [repo-url](/../../)
  
        git clone <repo-url>

    Then I recommend [using conda](https://pdal.io/download.html#conda) to install the non-python binaries (e.g. GMT, CUDA, etc).

    Then I recommend [using conda](https://conda.io/projects/conda/en/latest/user-guide/install/index.html) to install the non-python binaries (e.g. GMT, CUDA, etc).

    The conda virtual environment will also be created with Python and [pipenv](https://pipenv.readthedocs.io) installed.

        cd deepbedmap

environment.yml

            
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    @@ -4,9 +4,9 @@ channels:
  
      - nodefaults

    dependencies:

      - hcc::cuda_driver=410.73[md5=941787b750b372f4a240287634589d24]

      - defaults::cudatoolkit=10.0[md5=4388ad6015992501b042eea5197eb447]

      - conda-forge/label/dev::gmt=6.0.0rc1[md5=983ab0490b3ea8789136267cd7e7ed02]

      - pip=18.1[md5=d68c7e5109ba0bf4b1cfe60f0f47870a]

      - anaconda::cudatoolkit=10.0[md5=4388ad6015992501b042eea5197eb447]

      - conda-forge/label/dev::gmt=6.0.0rc3[md5=5dd95d211fff2434e792dac514063721]

      - conda-forge::pip=19.2.1[md5=95e1564d40edda4b98171de82ceba8ab]

      - conda-forge::python=3.6.7[md5=787937284685efaaa233453b49a9e719]

      - conda-forge::libspatialindex=1.9.0[md5=ef8f25a228de3a0dc716566b8d3de593]

      - pip:

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