New upstream version 5.7.4

SINGULARITY_VER=3.3.0

version: 2

jobs:

  build:

    machine: true

    environment:

      - GCLOUD: /opt/google-cloud-sdk/bin/gcloud

      - GSUTIL: /opt/google-cloud-sdk/bin/gsutil

      - BOTO_CONFIG: /dev/null

    steps:

      - checkout

      - restore_cache:

          keys:

            - snakemake-{{ .Environment.CACHE_VERSION }}-{{ checksum ".circleci/setup.sh" }}-{{ checksum "test-environment.yml" }}-{{ checksum ".circleci/common.sh" }}

      - run:

          name: Update PATH

          command: echo 'export PATH="`pwd`/miniconda/bin:$PATH"' >> $BASH_ENV

      - run:

          name: Setup Conda

          command: .circleci/setup.sh

      - save_cache:

          key: snakemake-{{ .Environment.CACHE_VERSION }}-{{ checksum ".circleci/setup.sh" }}-{{ checksum "test-environment.yml" }}-{{ checksum ".circleci/common.sh" }}

          paths:

            - miniconda

      - run:

          name: Setup singularity

          command: |

            # TODO only install if singularity is not yet present

            # if type singularity > /dev/null; then exit 0; fi

            source .circleci/common.sh

            sudo add-apt-repository ppa:gophers/archive

            sudo apt-get update

            sudo apt-get install build-essential libssl-dev uuid-dev libgpgme11-dev libseccomp-dev wget pkg-config squashfs-tools libarchive-dev golang-1.11

            export PATH=/usr/lib/go-1.11/bin:$PATH

            wget https://github.com/sylabs/singularity/releases/download/v${SINGULARITY_VER}/singularity-${SINGULARITY_VER}.tar.gz

            tar -xvf singularity-$SINGULARITY_VER.tar.gz

            cd singularity

            ./mconfig

            make -C builddir

            sudo make -C builddir install

      - run:

          name: Setup Snakemake

          command: |

            source activate snakemake

            pip install -e .

      - run:

          name: Setup iRODS Docker image

          command: |

            docker build -t irods-server tests/test_remote_irods

            docker run -d -p 1247:1247 --name provider irods-server -i run_irods

            sleep 10

            docker exec -u irods provider iput /incoming/infile

            cp -r tests/test_remote_irods/setup-data ~/.irods

      - run:

          name: Setup gcloud

          command: |

            # skip if key is unset

            if [ -z $GCLOUD_SERVICE_KEY ]; then exit 0; fi

            # otherwise init cloud

            echo $GCLOUD_SERVICE_KEY | base64 --decode --ignore-garbage > ${HOME}/gcloud-service-key.json

            sudo $GCLOUD components install kubectl

            sudo chown -R $USER:$USER /home/circleci/.config/gcloud

            $GCLOUD auth activate-service-account --key-file=${HOME}/gcloud-service-key.json

            $GCLOUD config set project snakemake-testing

      - run:

          name: Run tests

          no_output_timeout: 60m

          command: |

            export GCLOUD_CLUSTER=t-`uuidgen`

            export GOOGLE_APPLICATION_CREDENTIALS=${HOME}/gcloud-service-key.json

            source activate snakemake

            py.test tests/test*.py -v -x

#!/bin/bash

set -euo pipefail

if type conda > /dev/null; then exit 0; fi

wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh

bash miniconda.sh -b -p miniconda

conda env create --name snakemake --file test-environment.yml

[run]

source = snakemake

parallel = True

[report]

omit = tests/*

snakemake/_version.py export-subst

snakemake/report/report.html linguist-vendored=true

snakemake/gui.html linguist-vendored=true

snakemake/report/table.html linguist-vendored=true

tests/test_issue1046/expected-results/test_report.html linguist-vendored=true