Merge branch 'master' into 'england1'

Move CI changes from master to england1

See merge request !5

.gitlab-ci.yml

 stages:
-  - pull
-  - build
-  - push
+  - triggerpdf
 
-
-s3pull:
-  stage: pull
+buildpdf:
+  stage: triggerpdf
   
   rules:
     - if: '$CI_PIPELINE_SOURCE == "trigger"'
     
-  image:
-    name: amazon/aws-cli:2.2.4
-    entrypoint: ["/bin/sh", "-c"]
+  image: fhm-chicas-code.lancs.ac.uk:5050/jewell/pyriskreport:latest
     
   script:
     - mkdir -p staged_data
@@ -21,49 +16,13 @@ s3pull:
     - for obj in reproduction_number.nc prediction.gpkg config.yaml; do
         /usr/local/bin/aws --endpoint-url $MINIO_URL s3 cp $S3TARGET/${obj} staged_data/${obj};
       done
-
-  artifacts:
-    paths:
-      - staged_data/
-    expire_in: 20 mins
-
-
-build:
-  stage: build
-  
-  rules:
-    - if: '$CI_PIPELINE_SOURCE == "trigger"'
-    
-  image: dockershelf/latex:basic
-  
-  before_script:
-    - apt-get update
-    - apt-get install -y python3-pip
-    - pip3 install -r requirements.txt
-    
-  script:
     - pweave -i noweb -f tex -o spim_report.tex spim_report.pnw staged_data
     - pdflatex spim_report.tex
     - pdflatex spim_report.tex
     - pdflatex spim_report.tex
+    - /usr/local/bin/aws --endpoint-url $MINIO_URL s3 cp spim_report.pdf $S3TARGET/spim_report.pdf
   
   artifacts:
     paths:
       - spim_report.tex
       - spim_report.pdf
-
-
-s3push:
-  stage: push
-
-  rules:
-    - if: '$CI_PIPELINE_SOURCE == "trigger"'
-
-  image:
-    name: amazon/aws-cli:2.2.4
-    entrypoint: ["/bin/sh", "-c"]
-    
-  script:
-    - export AWS_ACCESS_KEY_ID=$MINIO_ACCESS_KEY_ID
-    - export AWS_SECRET_ACCESS_KEY=$MINIO_ACCESS_KEY_SECRET
-    - /usr/local/bin/aws --endpoint-url $MINIO_URL s3 cp spim_report.pdf $S3TARGET/spim_report.pdf

Dockerfile

+FROM debian:latest
+
+# Hack for Gitlab CI bug with Debian /bin/sh --> dash
+RUN ln -snf /bin/bash /bin/sh
+
+
+# Python and LaTeX
+RUN apt-get update
+RUN apt-get install -y texlive-latex-recommended texlive-latex-extra
+RUN apt-get install -y python3-pip curl
+
+# Install Python requirements
+COPY requirements.txt /data/requirements.txt
+RUN pip3 install -r /data/requirements.txt
+
+# Install AWS CLI
+RUN curl "https://awscli.amazonaws.com/awscli-exe-linux-x86_64.zip" -o "/data/awscliv2.zip"
+RUN cd data && unzip awscliv2.zip && ./aws/install && cd ..
+
+CMD [ '/bin/bash', '-c' ]