Issue #613 - update conda env setup for CI images (#636)

* update conda env setup

* init conda after env create

* switch to conda run, add full-trace flag to sge pytests

Author: kaelancotter

ci/htcondor.sh

@@ -21,13 +21,13 @@ function jobqueue_before_install {
 
 function jobqueue_install {
     cd ./ci/htcondor
-    docker-compose exec -T submit /bin/bash -c "cd /dask-jobqueue; pip3 install -e .;chown -R submituser ."
+    docker-compose exec -T submit conda run -n dask-jobqueue /bin/bash -c "cd /dask-jobqueue; pip3 install -e .;chown -R submituser ."
     cd -
 }
 
 function jobqueue_script {
     cd ./ci/htcondor
-    docker-compose exec -T --user submituser submit /bin/bash -c "cd; pytest /dask-jobqueue/dask_jobqueue --log-cli-level DEBUG --capture=tee-sys --verbose -E htcondor "
+    docker-compose exec -T --user submituser submit conda run -n dask-jobqueue /bin/bash -c "cd; pytest /dask-jobqueue/dask_jobqueue --log-cli-level DEBUG --capture=tee-sys --verbose -E htcondor "
     cd -
 }
 

ci/htcondor/Dockerfile

@@ -7,7 +7,8 @@ RUN curl -o miniconda.sh https://repo.anaconda.com/miniconda/Miniconda3-latest-L
 ENV PATH /opt/anaconda/bin:$PATH
 # environment.yml file is copied by CI script. If manually building, you should copy it too from parent directory
 COPY environment.yml .
-RUN conda env update -n base --file environment.yml
+RUN conda env create --file environment.yml
+SHELL ["conda", "run", "-n", "dask-jobqueue", "/bin/bash", "-c"]
 
 FROM  htcondor/execute:el7 as execute
 

ci/pbs.sh

@@ -20,11 +20,11 @@ function jobqueue_before_install {
 }
 
 function jobqueue_install {
-    docker exec pbs_master /bin/bash -c "cd /dask-jobqueue; pip install -e .; chown -R pbsuser ."
+    docker exec pbs_master conda run -n dask-jobqueue /bin/bash -c "cd /dask-jobqueue; pip install -e .; chown -R pbsuser ."
 }
 
 function jobqueue_script {
-    docker exec -u pbsuser pbs_master /bin/bash -c "cd; pytest /dask-jobqueue/dask_jobqueue --verbose -s -E pbs"
+    docker exec -u pbsuser pbs_master conda run -n dask-jobqueue /bin/bash -c "cd; pytest /dask-jobqueue/dask_jobqueue --verbose -s -E pbs"
 }
 
 function jobqueue_after_script {

ci/pbs/Dockerfile

@@ -32,7 +32,8 @@ RUN curl -o miniconda.sh https://repo.anaconda.com/miniconda/Miniconda3-latest-L
     rm -f miniconda.sh
 # environment.yml file is copied by CI script. If manually building, you should copy it too from parent directory
 COPY environment.yml .
-RUN conda env update -n base --file environment.yml
+RUN conda env create --file environment.yml
+SHELL ["conda", "run", "-n", "dask-jobqueue", "/bin/bash", "-c"]
 
 # Copy entrypoint and other needed scripts
 COPY ./*.sh /

ci/sge.sh

@@ -19,11 +19,11 @@ function jobqueue_before_install {
 }
 
 function jobqueue_install {
-    docker exec sge_master /bin/bash -c "cd /dask-jobqueue; pip install -e ."
+    docker exec sge_master conda run -n dask-jobqueue /bin/bash -c "cd /dask-jobqueue; pip install -e ."
 }
 
 function jobqueue_script {
-    docker exec sge_master /bin/bash -c "cd; pytest /dask-jobqueue/dask_jobqueue --verbose -s -E sge"
+    docker exec sge_master conda run -n dask-jobqueue /bin/bash -c "cd; pytest /dask-jobqueue/dask_jobqueue --verbose --full-trace -s -E sge"
 }
 
 function jobqueue_after_script {

ci/sge/Dockerfile

@@ -11,7 +11,8 @@ RUN curl -o miniconda.sh https://repo.anaconda.com/miniconda/Miniconda3-latest-L
 ENV PATH /opt/anaconda/bin:$PATH
 # environment.yml file is copied by CI script. If manually building, you should copy it too from parent directory
 COPY environment.yml .
-RUN conda env update -n base --file environment.yml
+RUN conda env create --file environment.yml
+SHELL ["conda", "run", "-n", "dask-jobqueue", "/bin/bash", "-c"]
 
 COPY ./*.sh /
 COPY ./*.txt /

ci/sge/run-master.sh

@@ -9,13 +9,12 @@ while ! ping -c1 slave_one &>/dev/null; do :; done
 while ! qconf -sconf &>/dev/null; do sleep 0.1; done
 cat /var/lib/gridengine//default/common/act_qmaster
 
-qconf -Msconf /scheduler.txt
-qconf -Ahgrp /hosts.txt
-qconf -Aq /queue.txt
+qconf -Msconf /dask-jobqueue/ci/sge/scheduler.txt
+qconf -Ahgrp /dask-jobqueue/ci/sge/hosts.txt
+qconf -Aq /dask-jobqueue/ci/sge/queue.txt
 
 qconf -ah slave_one
 qconf -ah slave_two
-qconf -ah slave_three
 
 qconf -as $HOSTNAME
 bash add_worker.sh dask.q slave_one 4

ci/slurm.sh

@@ -22,17 +22,17 @@ function show_network_interfaces {
     for c in slurmctld c1 c2; do
         echo '------------------------------------------------------------'
         echo docker container: $c
-        docker exec $c python -c 'import psutil; print(psutil.net_if_addrs().keys())'
+        docker exec $c conda run -n dask-jobqueue python -c 'import psutil; print(psutil.net_if_addrs().keys())'
         echo '------------------------------------------------------------'
     done
 }
 
 function jobqueue_install {
-    docker exec slurmctld /bin/bash -c "cd /dask-jobqueue; pip install -e ."
+    docker exec slurmctld conda run -n dask-jobqueue /bin/bash -c "cd /dask-jobqueue; pip install -e ."
 }
 
 function jobqueue_script {
-    docker exec slurmctld /bin/bash -c "cd; pytest /dask-jobqueue/dask_jobqueue --verbose -E slurm -s"
+    docker exec slurmctld conda run -n dask-jobqueue /bin/bash -c "cd; pytest /dask-jobqueue/dask_jobqueue --verbose -E slurm -s"
 }
 
 function jobqueue_after_script {

ci/slurm/Dockerfile

@@ -9,7 +9,8 @@ RUN curl -o miniconda.sh https://repo.anaconda.com/miniconda/Miniconda3-latest-L
 ENV PATH /opt/anaconda/bin:$PATH
 # environment.yml file is copied by CI script. If manually building, you should copy it too from parent directory
 COPY environment.yml .
-RUN conda env update -n base --file environment.yml
+RUN conda env create --file environment.yml
+SHELL ["conda", "run", "-n", "dask-jobqueue", "/bin/bash", "-c"]
 
 ENV LC_ALL en_US.UTF-8