Merge branch 'dev/ci' into 'release/1.2'

Merge dev/ci into release/1.2

Updated the CI testing.

See merge request !25

Author: ericenns

.ci/Dockerfile

@@ -0,0 +1,90 @@
+FROM debian:jessie
+
+USER root
+ARG DEBIAN_FRONTEND=noninteractive
+
+#==============================================================================
+# BASIC UTILITIES
+#==============================================================================
+RUN apt-get update -qqy \
+  && apt-get -qqy install \
+    apt-utils\
+    dialog\
+    less\
+    vim\
+    make\
+    build-essential\
+    git\
+    wget\
+    man-db\
+  && rm -rf /var/lib/apt/lists/*
+
+#==============================================================================
+# SLURM
+#==============================================================================
+RUN apt-get update -qqy \
+  && apt-get -qqy install \
+    slurm-llnl\
+    munge\
+    heirloom-mailx\
+    libslurm-dev\
+    slurm-drmaa-dev\
+  && rm -rf /var/lib/apt/lists/*
+
+# Make necessary directories:
+RUN mkdir /var/log/slurm/ /var/run/slurm-llnl/ \
+  /var/lib/slurm/ /var/lib/slurm/slurmctld/
+
+# Make necessary files:
+RUN touch /var/log/slurm/slurmctld.log /var/run/slurm-llnl/slurmctld.pid
+
+# Permissions:
+RUN chown -R slurm /var/lib/slurm/ /var/log/slurm/ /var/run/slurm-llnl/
+
+# Configuration file:
+ADD slurm.conf /etc/slurm-llnl/slurm.conf
+
+# Slurm setup:
+ADD slurm.sh /root/
+
+#==============================================================================
+# Python / Python-DRMAA Bindings
+#==============================================================================
+RUN apt-get update -qqy \
+  && apt-get -qqy install \
+    python-dev\
+    python-pip\
+  && rm -rf /var/lib/apt/lists/*
+
+RUN pip install drmaa
+
+ENV SGE_ROOT=/var/lib/slurm
+ENV SGE_CELL=default
+ENV DRMAA_LIBRARY_PATH=/usr/lib/libdrmaa.so
+
+#==============================================================================
+# BLAST+
+#==============================================================================
+RUN apt-get update -qqy \
+  && apt-get -qqy install \
+    blast2\
+    ncbi-blast+\
+  && rm -rf /var/lib/apt/lists/*
+
+#==============================================================================
+# NEPTUNE
+#==============================================================================
+RUN pip install --upgrade pip
+
+RUN pip install numpy
+RUN pip install scipy
+RUN pip install biopython
+
+RUN pip install tox
+
+#==============================================================================
+# FINISH
+#==============================================================================
+WORKDIR /root/
+
+

.ci/run_flake8.sh

@@ -1,9 +1,3 @@
 #!/bin/bash -e
 
-printf "setenv = \n    DRMAA_LIBRARY_PATH = /usr/lib/gridengine-drmaa/lib/libdrmaa.so.1.0\n" >> tox.ini
-printf "    SGE_ROOT = /opt/gridengine\n" >> tox.ini
-printf "    SGE_CELL=default\n" >> tox.ini
-printf "    SGE_QMASTER_PORT=536\n" >> tox.ini
-printf "    SGE_EXECD_PORT=537\n" >> tox.ini
-printf "    SGE_ARCH=linux-x64\n" >> tox.ini
 tox -r -e flake8

.ci/run_tests.sh

@@ -1,9 +1,5 @@
 #!/bin/bash -e
 
-printf "setenv = \n    DRMAA_LIBRARY_PATH = /usr/lib/gridengine-drmaa/lib/libdrmaa.so.1.0\n" >> tox.ini
-printf "    SGE_ROOT = /opt/gridengine\n" >> tox.ini
-printf "    SGE_CELL=default\n" >> tox.ini
-printf "    SGE_QMASTER_PORT=536\n" >> tox.ini
-printf "    SGE_EXECD_PORT=537\n" >> tox.ini
-printf "    SGE_ARCH=linux-x64\n" >> tox.ini
+/root/slurm.sh
+
 tox -r

.ci/slurm.conf

@@ -0,0 +1,52 @@
+# slurm.conf file generated by configurator easy.html.
+# Put this file on all nodes of your cluster.
+# See the slurm.conf man page for more information.
+#
+ControlMachine=localhost
+#ControlAddr=
+#
+#MailProg=/bin/mail
+MpiDefault=none
+#MpiParams=ports=#-#
+ProctrackType=proctrack/pgid
+ReturnToService=1
+SlurmctldPidFile=/var/run/slurm-llnl/slurmctld.pid
+#SlurmctldPort=6817
+SlurmdPidFile=/var/run/slurm-llnl/slurmd.pid
+#SlurmdPort=6818
+SlurmdSpoolDir=/var/lib/slurm/slurmd
+SlurmUser=slurm
+#SlurmdUser=root
+StateSaveLocation=/var/lib/slurm/slurmctld
+SwitchType=switch/none
+TaskPlugin=task/none
+#
+#
+# TIMERS
+#KillWait=30
+#MinJobAge=300
+#SlurmctldTimeout=120
+#SlurmdTimeout=300
+#
+#
+# SCHEDULING
+FastSchedule=1
+SchedulerType=sched/backfill
+#SchedulerPort=7321
+SelectType=select/linear
+#
+#
+# LOGGING AND ACCOUNTING
+AccountingStorageType=accounting_storage/none
+ClusterName=cluster
+#JobAcctGatherFrequency=30
+JobAcctGatherType=jobacct_gather/none
+#SlurmctldDebug=3
+SlurmctldLogFile=/var/log/slurm/slurmctld.log
+#SlurmdDebug=3
+SlurmdLogFile=/var/log/slurm/slurmd.log
+#
+#
+# COMPUTE NODES
+NodeName=localhost CPUs=4 State=UNKNOWN
+PartitionName=debug Nodes=localhost Default=YES MaxTime=INFINITE State=UP

.ci/slurm.sh

@@ -0,0 +1,6 @@
+#!/usr/bin/env bash
+
+/etc/init.d/slurmd start
+/etc/init.d/munge start
+/etc/init.d/slurmctld start
+

.gitlab-ci.yml

@@ -1,4 +1,7 @@
+image: docker.corefacility.ca:5000/marinier/neptune_deps:latest
+
 tests:
   script: ".ci/run_tests.sh"
+
 flake8:
   script: ".ci/run_flake8.sh"

tox.ini

@@ -9,7 +9,7 @@ commands=
 
 [flake8]
 ignore=E302, E402
-exclude=tests/*,setup.py
+exclude=tests/*,setup.py,.tox/*
 filename=*.py
 
 [testenv]