Merge branch 'update-container' into 'master'

Update how container builds (remove conda)

See merge request !56

.gitlab-ci.yml

@@ -18,7 +18,7 @@ variables:
   TRIVY_VERSION: "0.13.0"
   # docker variables
   DOCKER_DRIVER: overlay2
-  FROM_IMAGE: ${CODE_REGISTRY}/devops/images/usgs/centos:7
+  FROM_IMAGE: ${CODE_REGISTRY}/devops/images/usgs/obspy:3.8
   # environment variables
   APP_NAME: geomag-algorithms
   DATA_HOST: "cwbpub.cr.usgs.gov"
@@ -67,15 +67,20 @@ variables:
     - build
 
 .check_code:
-  image: ${DEVOPS_REGISTRY}usgs/conda:latest
-  script:
-    - export PYTHON_VERSION=${PYTHON_VERSION:-3.8}
-    - scripts/ci_check_code.sh
   artifacts:
-    paths:
-      - cov.xml
     reports:
-      junit: cov.xml
+      cobertura: cov.xml
+      junit: junit.xml
+  before_script:
+    # install dependencies
+    - pipenv --site-packages install --dev --pre --skip-lock
+    - pipenv run which python
+  image: ${DEVOPS_REGISTRY}usgs/obspy:latest
+  script:
+    # run checks
+    - pipenv run black --check .
+    - pipenv run pytest --cov=geomagio --cov-report xml:cov.xml --junitxml junit.xml
+    - pipenv run safety check
   stage: test
   tags:
     - development
@@ -148,23 +153,12 @@ variables:
 Check Python 3.6:
   extends:
     - .check_code
-  script:
-    - export PYTHON_VERSION=3.6
-    - scripts/ci_check_code.sh
-
-Check Python 3.7:
-  extends:
-    - .check_code
-  script:
-    - export PYTHON_VERSION=3.7
-    - scripts/ci_check_code.sh
+  image: ${DEVOPS_REGISTRY}usgs/obspy:3
 
 Check Python 3.8:
   extends:
     - .check_code
-  script:
-    - export PYTHON_VERSION=3.8
-    - scripts/ci_check_code.sh
+  image: ${DEVOPS_REGISTRY}usgs/obspy:3.8
 
 ## --------------------------------------------------
 # Integration Stage

Dockerfile

-ARG FROM_IMAGE=usgs/centos:7
+ARG FROM_IMAGE=usgs/obspy:3.8
 
-FROM ${FROM_IMAGE} as conda
+FROM ${FROM_IMAGE}
 LABEL maintainer="Jeremy Fee <jmfee@usgs.gov>"
 
 ARG GIT_BRANCH_NAME=none
 ARG GIT_COMMIT_SHA=none
+ARG WEBSERVICE="false"
 
 # set environment variables
 ENV GIT_BRANCH_NAME=${GIT_BRANCH_NAME} \
     GIT_COMMIT_SHA=${GIT_COMMIT_SHA} \
-    LANG='en_US.UTF-8' \
-    LC_ALL='en_US.UTF-8' \
-    PATH=/conda/bin:$PATH \
-    PIP_CERT=${SSL_CERT_FILE} \
-    PYTHONDONTWRITEBYTECODE=1 \
-    PYTHONUNBUFFERED=1 \
-    REQUESTS_CA_BUNDLE=${SSL_CERT_FILE}
+    WEBSERVICE=${WEBSERVICE}
 
-# install conda
-RUN echo 'export PATH=/conda/bin:$PATH' > /etc/profile.d/conda.sh \
-    && curl \
-    https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh \
-    -o ~/miniconda.sh \
-    && /bin/bash ~/miniconda.sh -b -p /conda \
-    && rm ~/miniconda.sh
-
-# install dependencies via conda
-RUN conda config --set ssl_verify $SSL_CERT_FILE \
-    && conda config --add channels conda-forge \
-    && conda install --yes python=3.7 jupyter obspy pycurl \
-    && conda clean --all -y \
-    && export PIP_CERT=$SSL_CERT_FILE \
-    && pip install pipenv 'virtualenv!=20.0.22' \
-    && yum install -y which \
-    && yum clean all
-
-
-################################################################################
-## Development image
-
-# build by running
-# docker build -t geomag-algorithms-development --target development .
-
-FROM conda as development
-
-# install dependencies via pipenv
-WORKDIR /geomag-algorithms
-COPY Pipfile /geomag-algorithms
-RUN pipenv --site-packages install --dev --skip-lock
-
-# copy library (ignores set in .dockerignore)
-COPY . /geomag-algorithms
-
-
-################################################################################
-## Production image
-
-FROM conda
 
 RUN useradd \
     -c 'Docker image user' \
@@ -72,12 +27,11 @@ USER geomag_user
 # install dependencies via pipenv
 WORKDIR /data
 COPY Pipfile /data/
-RUN pipenv --site-packages install --skip-lock
+RUN pipenv --site-packages install --dev --skip-lock
 
 # copy library (ignores set in .dockerignore)
 COPY . /geomag-algorithms
 
-EXPOSE 8000
-
 # entrypoint needs double quotes
 ENTRYPOINT [ "/geomag-algorithms/docker-entrypoint.sh" ]
+EXPOSE 8000

Pipfile

@@ -6,6 +6,7 @@ verify_ssl = true
 [dev-packages]
 bandit = "*"
 black = "==20.8b1"
+jupyter = "*"
 pre-commit = "*"
 pytest = "*"
 pytest-cov = "*"

docker-entrypoint.sh

@@ -7,9 +7,10 @@ export WEBSERVICE=${WEBSERVICE:-false}
 export PYTHONPATH=/geomag-algorithms
 
 
-if [ $WEBSERVICE = 'false' ]; then
+if [ "${WEBSERVICE}" = "false" ]; then
   # run jupyter notebook server
-  exec jupyter notebook \
+  exec pipenv run jupyter \
+      notebook \
       --ip='*' \
       --notebook-dir=/data \
       --no-browser \

scripts/ci_check_code.sh

-#! /bin/bash -ex
-
-PYTHON_VERSION=${PYTHON_VERSION:-"3.8"}
-
-
-if [ -f "/etc/profile.d/conda.sh" ]; then
-  # Add conda to path
-  source /etc/profile.d/conda.sh
-fi
-
-# Install Project Dependencies
-conda config --add channels conda-forge
-conda install python=${PYTHON_VERSION} obspy pycurl
-pip install pipenv
-pipenv --site-packages install --dev --pre --skip-lock
-pipenv run which python
-# Run Code Checks
-pipenv run black --check .
-pipenv run pytest --cov-report xml:cov.xml --cov=geomagio
-pipenv run safety check