From e1974086e5e2ea6626148636aaf57b1767a9859b Mon Sep 17 00:00:00 2001 From: Padraig Gleeson Date: Fri, 9 Apr 2021 13:12:24 +0100 Subject: [PATCH 01/12] Move to v0.9.2 --- .openworm.yml | 4 ++-- Dockerfile | 8 ++++---- build.cmd | 2 +- build.sh | 2 +- build2.sh | 2 +- master_openworm.py | 2 +- rebuild.sh | 2 +- run-shell-only.cmd | 6 +++--- run-shell-only.sh | 2 +- run.cmd | 2 +- run.sh | 2 +- run2-shell-only.sh | 2 +- run2.sh | 2 +- 13 files changed, 19 insertions(+), 19 deletions(-) diff --git a/.openworm.yml b/.openworm.yml index 1940a04..ac77156 100644 --- a/.openworm.yml +++ b/.openworm.yml @@ -1,5 +1,5 @@ repo: openworm/OpenWorm shortDescription: "Project Home repo for Central Dockerfile and Project-wide issues" -contributor-guide: "http://docs.openworm.org/en/latest/community/#contribution-best-practices" +contributor-guide: "http://docs.openworm.org/community/#contribution-best-practices" coordinator: stephen@openworm.org -documentation: "http://docs.openworm.org/en/latest/" \ No newline at end of file +documentation: "http://docs.openworm.org" diff --git a/Dockerfile b/Dockerfile index 15ae0f6..6deef83 100644 --- a/Dockerfile +++ b/Dockerfile @@ -43,7 +43,7 @@ RUN apt-get update && apt-get install -y --no-install-recommends apt-utils \ maven openjdk-8-jdk \ python3-setuptools python3-yaml libnuma1 \ openmpi-bin libopenmpi-dev \ - libgl1-mesa-glx libgl1-mesa-dri libfreetype6-dev \ + libgl1-mesa-glx libgl1-mesa-dri libfreetype6-dev \ libxft-dev python3-matplotlib unzip ffmpeg xvfb tmux #RUN sudo pip install --upgrade pip @@ -77,7 +77,7 @@ RUN mkdir neuron && \ cd src/nrnpython && \ sudo python3 setup.py install - + ################################################################################ ######## Install pyNeuroML for handling NeuroML network model @@ -101,7 +101,7 @@ RUN git clone https://github.com/openworm/PyOpenWorm.git && \ ################################################################################ ######## Install c302 for building neuronal network models -RUN git clone https://github.com/openworm/c302.git && \ +RUN git clone https://github.com/openworm/c302.git && \ cd c302 && \ git checkout ow-0.9.1 && \ sudo python3 setup.py install @@ -187,4 +187,4 @@ RUN sudo update-alternatives --install /usr/bin/python python /usr/bin/python3 RUN echo '\n\nalias cd..="cd .."\nalias h=history\nalias ll="ls -alt"' >> ~/.bashrc -RUN echo "Built the OpenWorm Docker image!" \ No newline at end of file +RUN echo "Built the OpenWorm Docker image!" diff --git a/build.cmd b/build.cmd index a3bdc44..5b02483 100644 --- a/build.cmd +++ b/build.cmd @@ -1 +1 @@ -docker build -t "openworm/openworm:0.9.1" . +docker build -t "openworm/openworm:0.9.2" . diff --git a/build.sh b/build.sh index bcc4afd..11718a3 100755 --- a/build.sh +++ b/build.sh @@ -1,3 +1,3 @@ #!/bin/bash -docker build "$@" -t "openworm/openworm:0.9.1" . +docker build "$@" -t "openworm/openworm:0.9.2" . diff --git a/build2.sh b/build2.sh index 7519a0b..b1ba7c7 100755 --- a/build2.sh +++ b/build2.sh @@ -4,4 +4,4 @@ # Note: Python 2 is no longer officially supported and this Docker image will # probably stop working eventually... -docker build "$@" -t "openworm/openworm:0.9.1_py2" -f Dockerfile2 . +docker build "$@" -t "openworm/openworm:0.9.2_py2" -f Dockerfile2 . diff --git a/master_openworm.py b/master_openworm.py index 5e4635c..e18a9fe 100644 --- a/master_openworm.py +++ b/master_openworm.py @@ -13,7 +13,7 @@ import math print("*****************************") -print("OpenWorm Master Script v0.9.1") +print("OpenWorm Master Script v0.9.2") print("*****************************") print("") print("This script attempts to run a full pass through the OpenWorm scientific libraries.") diff --git a/rebuild.sh b/rebuild.sh index dcf5f5b..edd5d85 100755 --- a/rebuild.sh +++ b/rebuild.sh @@ -1,3 +1,3 @@ #!/bin/bash -docker build "$@" -t "openworm/openworm:0.9.1" --no-cache . +docker build "$@" -t "openworm/openworm:0.9.2" --no-cache . diff --git a/run-shell-only.cmd b/run-shell-only.cmd index d0fe5c1..3fc432a 100644 --- a/run-shell-only.cmd +++ b/run-shell-only.cmd @@ -1,10 +1,10 @@ SET OW_OUT_DIR=/home/ow/shared SET HOST_OUT_DIR=%~dp0 - + docker run -it ^ --name openworm ^ -e OW_OUT_DIR=%OW_OUT_DIR% ^ --privileged ^ -v %HOST_OUT_DIR%:%OW_OUT_DIR%:rw ^ - openworm/openworm:0.9 ^ - /bin/bash \ No newline at end of file + openworm/openworm:0.9.2 ^ + /bin/bash diff --git a/run-shell-only.sh b/run-shell-only.sh index 1d8b6bb..aef4e70 100755 --- a/run-shell-only.sh +++ b/run-shell-only.sh @@ -13,5 +13,5 @@ docker run -ti \ -v /tmp/.X11-unix:/tmp/.X11-unix:rw \ --privileged \ -v $HOST_OUT_DIR:$OW_OUT_DIR:rw \ - openworm/openworm:0.9.1 \ + openworm/openworm:0.9.2 \ bash diff --git a/run.cmd b/run.cmd index 078107f..5c26a90 100644 --- a/run.cmd +++ b/run.cmd @@ -20,7 +20,7 @@ docker run -d ^ -e DURATION=%DURATION% ^ --privileged ^ -v %HOST_OUT_DIR%:%OW_OUT_DIR%:rw ^ - openworm/openworm:0.9.1 ^ + openworm/openworm:0.9.2 ^ /bin/bash -c "python master_openworm.py" docker logs -f openworm diff --git a/run.sh b/run.sh index de016d2..f1ea535 100755 --- a/run.sh +++ b/run.sh @@ -33,7 +33,7 @@ $DURATION_PART \ -v /tmp/.X11-unix:/tmp/.X11-unix:rw \ --privileged \ -v $HOST_OUT_DIR:$OW_OUT_DIR:rw \ -openworm/openworm:0.9.1 \ +openworm/openworm:0.9.2 \ bash -c "DISPLAY=:44 python master_openworm.py" docker logs -f openworm diff --git a/run2-shell-only.sh b/run2-shell-only.sh index 8cf68b5..edb6f72 100755 --- a/run2-shell-only.sh +++ b/run2-shell-only.sh @@ -17,5 +17,5 @@ docker run -ti \ -v /tmp/.X11-unix:/tmp/.X11-unix:rw \ --privileged \ -v $HOST_OUT_DIR:$OW_OUT_DIR:rw \ - openworm/openworm:0.9.1 \ + openworm/openworm:0.9.2 \ bash diff --git a/run2.sh b/run2.sh index 2464b76..9d550ae 100755 --- a/run2.sh +++ b/run2.sh @@ -37,7 +37,7 @@ $DURATION_PART \ -v /tmp/.X11-unix:/tmp/.X11-unix:rw \ --privileged \ -v $HOST_OUT_DIR:$OW_OUT_DIR:rw \ -openworm/openworm:0.9.1_py2 \ +openworm/openworm:0.9.2_py2 \ bash -c "DISPLAY=:44 python master_openworm.py" docker logs -f openworm2 From 52780f7e758ecbf860e1f7c68bebf5c046120cfb Mon Sep 17 00:00:00 2001 From: Padraig Gleeson Date: Thu, 3 Jun 2021 10:08:53 +0100 Subject: [PATCH 02/12] Install Neuron via pip For https://github.com/openworm/OpenWorm/issues/310 --- Dockerfile | 26 +------------------------- 1 file changed, 1 insertion(+), 25 deletions(-) diff --git a/Dockerfile b/Dockerfile index 6deef83..1b35d36 100644 --- a/Dockerfile +++ b/Dockerfile @@ -58,24 +58,7 @@ WORKDIR $HOME ################################################################################ ######## Install NEURON simulator -RUN mkdir neuron && \ - cd neuron && \ - git clone https://github.com/nrnhines/iv.git && \ - git clone https://github.com/nrnhines/nrn.git && \ - cd iv && \ - git checkout 76c123b && \ - ./build.sh && \ - ./configure --prefix=`pwd` && \ - make -j3 && \ - sudo make install && \ - cd ../nrn && \ - git checkout e0950a1 && \ - ./build.sh && \ - ./configure --prefix=`pwd` --with-iv=$HOME/neuron/iv --with-nrnpython=/usr/bin/python3 --with-paranrn && \ - make -j3 && \ - sudo make install && \ - cd src/nrnpython && \ - sudo python3 setup.py install +RUN sudo pip3 install neuron==7.8.1 ################################################################################ @@ -120,13 +103,6 @@ RUN cp c302/pyopenworm.conf sibernetic/ # Temp step until PyOpenWorm can be ru ################################################################################ ######## Set some paths//environment variables -ENV JNML_HOME=$HOME/jNeuroML -ENV PATH=$PATH:$JNML_HOME -ENV IV=$HOME/neuron/iv -ENV N=$HOME/neuron/nrn -ENV CPU=x86_64 -ENV PATH=$PATH:$IV/$CPU/bin:$N/$CPU/bin -ENV NEURON_HOME=$N/$CPU ENV C302_HOME=$HOME/c302/c302 ENV SIBERNETIC_HOME=$HOME/sibernetic ENV PYTHONPATH=$PYTHONPATH:$HOME/c302:$SIBERNETIC_HOME From 8c2887504e8700c643af507b02bb13221f84ba4e Mon Sep 17 00:00:00 2001 From: Padraig Gleeson Date: Fri, 29 Oct 2021 12:27:44 +0100 Subject: [PATCH 03/12] Simplify installation & use latest c302 & owmeta --- Dockerfile | 44 +++++++++++++++----------------------------- 1 file changed, 15 insertions(+), 29 deletions(-) diff --git a/Dockerfile b/Dockerfile index 0234357..cb24671 100644 --- a/Dockerfile +++ b/Dockerfile @@ -26,7 +26,6 @@ RUN mkdir -p /etc/sudoers.d && \ ENV DEBIAN_FRONTEND noninteractive # TODO: change - #RUN useradd -ms /bin/bash $USER @@ -55,46 +54,37 @@ USER $USER ENV HOME /home/$USER WORKDIR $HOME -################################################################################ -######## Install NEURON simulator - -RUN sudo pip3 install neuron==7.8.1 +#### TODO: check that this is the best way to switch to py3... +RUN sudo update-alternatives --install /usr/bin/python python /usr/bin/python3 10 +RUN sudo update-alternatives --install /usr/bin/pip pip /usr/bin/pip3 10 ################################################################################ -######## Install pyNeuroML for handling NeuroML network model +######## Install NEURON simulator -RUN git clone https://github.com/NeuroML/pyNeuroML.git && \ - cd pyNeuroML && \ - git checkout master && \ - sudo python3 setup.py install +RUN sudo pip install neuron==7.8.1 ################################################################################ -######## Install PyOpenWorm +######## Install c302 for building neuronal network models + # TODO remove this line after we have better dependency management. The # current version of gitpython requires python >= 3.7, which is newer than the # python included in the base image. Therefore, we manually install an older # gitpython to be used with OpenWormData. # See https://github.com/openworm/OpenWorm/pull/316 -RUN sudo pip3 install 'gitpython==2.1.15' - -RUN git clone https://github.com/openworm/PyOpenWorm.git && \ - cd PyOpenWorm && \ - git checkout ow-0.9 && \ - sudo apt-get install -y python3-cffi && \ - sudo python3 setup.py install && \ - pow clone https://github.com/openworm/OpenWormData.git - - -################################################################################ -######## Install c302 for building neuronal network models +RUN sudo pip install 'gitpython==2.1.15' RUN git clone https://github.com/openworm/c302.git && \ cd c302 && \ - git checkout ow-0.9.1 && \ - sudo python3 setup.py install + git checkout ow-0.9.2 && \ + sudo python setup.py install + +# Note: owmeta, owmeta-core and pyNeuroML installed with the above library + +RUN owm bundle remote --user add ow 'https://raw.githubusercontent.com/openworm/owmeta-bundles/master/index.json' + ################################################################################ @@ -164,10 +154,6 @@ RUN cd sibernetic && \ # ./Release/Sibernetic -f worm -no_g device=GPU 37ms - -#### TODO: check that this is the best way to switch to py3... -RUN sudo update-alternatives --install /usr/bin/python python /usr/bin/python3 10 - RUN echo '\n\nalias cd..="cd .."\nalias h=history\nalias ll="ls -alt"' >> ~/.bashrc RUN echo "Built the OpenWorm Docker image!" From 23701e2e0ff79ab11461154c2a0674ca7beec856 Mon Sep 17 00:00:00 2001 From: Padraig Gleeson Date: Fri, 29 Oct 2021 12:38:42 +0100 Subject: [PATCH 04/12] Additionally test running the image --- .github/workflows/docker-image.yml | 4 +++- Dockerfile | 2 +- 2 files changed, 4 insertions(+), 2 deletions(-) diff --git a/.github/workflows/docker-image.yml b/.github/workflows/docker-image.yml index d380414..dc52498 100644 --- a/.github/workflows/docker-image.yml +++ b/.github/workflows/docker-image.yml @@ -15,4 +15,6 @@ jobs: steps: - uses: actions/checkout@v2 - name: Build the Docker image - run: docker build . --file Dockerfile --tag openworm:$(date +%s) + run: | + docker build . --file Dockerfile --tag openworm:$(date +%s) + ./run.sh diff --git a/Dockerfile b/Dockerfile index cb24671..5a67ebf 100644 --- a/Dockerfile +++ b/Dockerfile @@ -79,7 +79,7 @@ RUN sudo pip install 'gitpython==2.1.15' RUN git clone https://github.com/openworm/c302.git && \ cd c302 && \ git checkout ow-0.9.2 && \ - sudo python setup.py install + sudo pip install . # Note: owmeta, owmeta-core and pyNeuroML installed with the above library From d79b7e466eb7097374f8c58a47c72821464a63c4 Mon Sep 17 00:00:00 2001 From: Padraig Gleeson Date: Fri, 29 Oct 2021 12:56:15 +0100 Subject: [PATCH 05/12] Use build and run scripts --- .github/workflows/docker-image.yml | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/.github/workflows/docker-image.yml b/.github/workflows/docker-image.yml index dc52498..659b077 100644 --- a/.github/workflows/docker-image.yml +++ b/.github/workflows/docker-image.yml @@ -16,5 +16,8 @@ jobs: - uses: actions/checkout@v2 - name: Build the Docker image run: | - docker build . --file Dockerfile --tag openworm:$(date +%s) + ./build.sh + - name: Run the Docker image + run: | ./run.sh + ls -alt output From 10c36196173ad52f28d9495cd8270415dc4c7848 Mon Sep 17 00:00:00 2001 From: Padraig Gleeson Date: Fri, 29 Oct 2021 16:56:28 +0100 Subject: [PATCH 06/12] Improved output of run --- master_openworm.py | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/master_openworm.py b/master_openworm.py index e18a9fe..1a851a1 100644 --- a/master_openworm.py +++ b/master_openworm.py @@ -1,4 +1,3 @@ -from __future__ import print_function import errno import matplotlib matplotlib.use('Agg') @@ -23,7 +22,7 @@ print("") print("****************************") -print("Step 1: Rebuild c302 from the latest PyOpenWorm") +print("Step 1: Rebuild c302 from the latest owmeta") print("****************************") print("Not yet implemented. See https://github.com/openworm/c302/issues/10") @@ -80,7 +79,7 @@ def execute_with_realtime_output(command, directory, env=None): p = Popen(shlex.split(command), stdout=PIPE, bufsize=1, cwd=directory, env=env) with p.stdout: for line in iter(p.stdout.readline, b''): - print(line, end="") + print(line.decode('utf-8'), end='') p.wait() # wait for the subprocess to exit except KeyboardInterrupt as e: print("Caught CTRL+C") From 16317d4a86fa0e755d8bf0ffbc902c66e2a44880 Mon Sep 17 00:00:00 2001 From: Padraig Gleeson Date: Sat, 11 Dec 2021 10:56:52 +0000 Subject: [PATCH 07/12] Update docker-image.yml --- .github/workflows/docker-image.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/docker-image.yml b/.github/workflows/docker-image.yml index 659b077..7789c2a 100644 --- a/.github/workflows/docker-image.yml +++ b/.github/workflows/docker-image.yml @@ -20,4 +20,4 @@ jobs: - name: Run the Docker image run: | ./run.sh - ls -alt output + ls -alt output/C2* From 10c190800281380b973c6471b00f140583d2fdc0 Mon Sep 17 00:00:00 2001 From: Padraig Gleeson Date: Fri, 14 Jan 2022 14:54:44 +0000 Subject: [PATCH 08/12] Update README.md --- README.md | 2 ++ 1 file changed, 2 insertions(+) diff --git a/README.md b/README.md index 7b27a42..9ea258a 100644 --- a/README.md +++ b/README.md @@ -111,3 +111,5 @@ Find out more about OpenWorm. Documentation is available at [http://docs.openwo This repository references: * Project-wide tracking via high-level [issues](https://github.com/openworm/OpenWorm/issues?labels=&milestone=&page=1&state=open) and [milestones](https://github.com/openworm/OpenWorm/milestones) + +[![Docker Image CI](https://github.com/openworm/OpenWorm/actions/workflows/docker-image.yml/badge.svg)](https://github.com/openworm/OpenWorm/actions/workflows/docker-image.yml) From e82b872dac9c3e8e6ed7eeaf9dc65f32c6689172 Mon Sep 17 00:00:00 2001 From: Padraig Gleeson Date: Fri, 8 Apr 2022 14:11:55 +0100 Subject: [PATCH 09/12] Pin version of neuromllite for py3.6 --- Dockerfile | 2 ++ 1 file changed, 2 insertions(+) diff --git a/Dockerfile b/Dockerfile index 08b8619..14e7516 100644 --- a/Dockerfile +++ b/Dockerfile @@ -76,6 +76,8 @@ RUN sudo pip install neuron==7.8.1 # See https://github.com/openworm/OpenWorm/pull/316 RUN sudo pip install 'gitpython==2.1.15' markupsafe +RUN sudo pip install 'NeuroMLlite<0.5.0' # for python 3.6... + RUN git clone https://github.com/openworm/c302.git && \ cd c302 && \ git checkout ow-0.9.2 && \ From 522fe9878b649bb90d5f408ce427364c82329d12 Mon Sep 17 00:00:00 2001 From: Padraig Gleeson Date: Mon, 16 May 2022 15:52:35 +0100 Subject: [PATCH 10/12] Move to v0.9.3 --- LICENSE | 2 +- build.cmd | 2 +- build.sh | 2 +- build2.sh | 2 +- master_openworm.py | 4 ++-- rebuild.sh | 2 +- run-shell-only.cmd | 2 +- run-shell-only.sh | 2 +- run.cmd | 2 +- run.sh | 2 +- run2-shell-only.sh | 2 +- run2.sh | 2 +- 12 files changed, 13 insertions(+), 13 deletions(-) diff --git a/LICENSE b/LICENSE index 9195599..3d59acb 100644 --- a/LICENSE +++ b/LICENSE @@ -1,4 +1,4 @@ -Copyright (c) 2012-2021 Individual Authors of code +Copyright (c) 2012-2022 Individual Authors of code Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal diff --git a/build.cmd b/build.cmd index 5b02483..6ba0e30 100644 --- a/build.cmd +++ b/build.cmd @@ -1 +1 @@ -docker build -t "openworm/openworm:0.9.2" . +docker build -t "openworm/openworm:0.9.3" . diff --git a/build.sh b/build.sh index 11718a3..e0150be 100755 --- a/build.sh +++ b/build.sh @@ -1,3 +1,3 @@ #!/bin/bash -docker build "$@" -t "openworm/openworm:0.9.2" . +docker build "$@" -t "openworm/openworm:0.9.3" . diff --git a/build2.sh b/build2.sh index b1ba7c7..6f09776 100755 --- a/build2.sh +++ b/build2.sh @@ -4,4 +4,4 @@ # Note: Python 2 is no longer officially supported and this Docker image will # probably stop working eventually... -docker build "$@" -t "openworm/openworm:0.9.2_py2" -f Dockerfile2 . +docker build "$@" -t "openworm/openworm:0.9.3_py2" -f Dockerfile2 . diff --git a/master_openworm.py b/master_openworm.py index 1a851a1..7bfcaa8 100644 --- a/master_openworm.py +++ b/master_openworm.py @@ -12,7 +12,7 @@ import math print("*****************************") -print("OpenWorm Master Script v0.9.2") +print("OpenWorm Master Script v0.9.3") print("*****************************") print("") print("This script attempts to run a full pass through the OpenWorm scientific libraries.") @@ -79,7 +79,7 @@ def execute_with_realtime_output(command, directory, env=None): p = Popen(shlex.split(command), stdout=PIPE, bufsize=1, cwd=directory, env=env) with p.stdout: for line in iter(p.stdout.readline, b''): - print(line.decode('utf-8'), end='') + print(line.decode('utf-8'), end='') p.wait() # wait for the subprocess to exit except KeyboardInterrupt as e: print("Caught CTRL+C") diff --git a/rebuild.sh b/rebuild.sh index edd5d85..414ae4d 100755 --- a/rebuild.sh +++ b/rebuild.sh @@ -1,3 +1,3 @@ #!/bin/bash -docker build "$@" -t "openworm/openworm:0.9.2" --no-cache . +docker build "$@" -t "openworm/openworm:0.9.3" --no-cache . diff --git a/run-shell-only.cmd b/run-shell-only.cmd index 3fc432a..64fe0d5 100644 --- a/run-shell-only.cmd +++ b/run-shell-only.cmd @@ -6,5 +6,5 @@ docker run -it ^ -e OW_OUT_DIR=%OW_OUT_DIR% ^ --privileged ^ -v %HOST_OUT_DIR%:%OW_OUT_DIR%:rw ^ - openworm/openworm:0.9.2 ^ + openworm/openworm:0.9.3 ^ /bin/bash diff --git a/run-shell-only.sh b/run-shell-only.sh index aef4e70..dba930d 100755 --- a/run-shell-only.sh +++ b/run-shell-only.sh @@ -13,5 +13,5 @@ docker run -ti \ -v /tmp/.X11-unix:/tmp/.X11-unix:rw \ --privileged \ -v $HOST_OUT_DIR:$OW_OUT_DIR:rw \ - openworm/openworm:0.9.2 \ + openworm/openworm:0.9.3 \ bash diff --git a/run.cmd b/run.cmd index 5c26a90..8168273 100644 --- a/run.cmd +++ b/run.cmd @@ -20,7 +20,7 @@ docker run -d ^ -e DURATION=%DURATION% ^ --privileged ^ -v %HOST_OUT_DIR%:%OW_OUT_DIR%:rw ^ - openworm/openworm:0.9.2 ^ + openworm/openworm:0.9.3 ^ /bin/bash -c "python master_openworm.py" docker logs -f openworm diff --git a/run.sh b/run.sh index f1ea535..89c3510 100755 --- a/run.sh +++ b/run.sh @@ -33,7 +33,7 @@ $DURATION_PART \ -v /tmp/.X11-unix:/tmp/.X11-unix:rw \ --privileged \ -v $HOST_OUT_DIR:$OW_OUT_DIR:rw \ -openworm/openworm:0.9.2 \ +openworm/openworm:0.9.3 \ bash -c "DISPLAY=:44 python master_openworm.py" docker logs -f openworm diff --git a/run2-shell-only.sh b/run2-shell-only.sh index edb6f72..1dee7ef 100755 --- a/run2-shell-only.sh +++ b/run2-shell-only.sh @@ -17,5 +17,5 @@ docker run -ti \ -v /tmp/.X11-unix:/tmp/.X11-unix:rw \ --privileged \ -v $HOST_OUT_DIR:$OW_OUT_DIR:rw \ - openworm/openworm:0.9.2 \ + openworm/openworm:0.9.3 \ bash diff --git a/run2.sh b/run2.sh index 9d550ae..6078f69 100755 --- a/run2.sh +++ b/run2.sh @@ -37,7 +37,7 @@ $DURATION_PART \ -v /tmp/.X11-unix:/tmp/.X11-unix:rw \ --privileged \ -v $HOST_OUT_DIR:$OW_OUT_DIR:rw \ -openworm/openworm:0.9.2_py2 \ +openworm/openworm:0.9.3_py2 \ bash -c "DISPLAY=:44 python master_openworm.py" docker logs -f openworm2 From 904f02304ec1c7cc36003c33d1e5339d89a7f9c5 Mon Sep 17 00:00:00 2001 From: pgleeson Date: Tue, 12 Sep 2023 17:27:44 +0100 Subject: [PATCH 11/12] Add docker pull test - no build --- .github/workflows/docker-image-quickrun.yml | 2 +- .github/workflows/docker-image.yml | 2 +- .github/workflows/docker-pull.yml | 32 +++++++++++++++++++++ 3 files changed, 34 insertions(+), 2 deletions(-) create mode 100644 .github/workflows/docker-pull.yml diff --git a/.github/workflows/docker-image-quickrun.yml b/.github/workflows/docker-image-quickrun.yml index 4db6cb8..aa4a273 100644 --- a/.github/workflows/docker-image-quickrun.yml +++ b/.github/workflows/docker-image-quickrun.yml @@ -13,7 +13,7 @@ jobs: runs-on: ubuntu-latest steps: - - uses: actions/checkout@v2 + - uses: actions/checkout@v3 - name: Build the Docker image run: | chmod a+w output/ diff --git a/.github/workflows/docker-image.yml b/.github/workflows/docker-image.yml index aa785ef..a601406 100644 --- a/.github/workflows/docker-image.yml +++ b/.github/workflows/docker-image.yml @@ -13,7 +13,7 @@ jobs: runs-on: ubuntu-latest steps: - - uses: actions/checkout@v2 + - uses: actions/checkout@v3 - name: Build the Docker image run: | chmod a+w output/ diff --git a/.github/workflows/docker-pull.yml b/.github/workflows/docker-pull.yml new file mode 100644 index 0000000..dc0e2a4 --- /dev/null +++ b/.github/workflows/docker-pull.yml @@ -0,0 +1,32 @@ +name: Docker Pull Test + +on: + push: + branches: [ master, dev* ] + pull_request: + branches: [ master, dev* ] + +jobs: + + build: + + runs-on: ubuntu-latest + + steps: + - uses: actions/checkout@v3 + + - name: Run the Docker image + run: | + # Don't build. Will be pulled when run below + ./run-quick.sh + + - name: Info on Docker images + run: | + docker -v + docker images + + - name: Info on generated files + run: | + ls -alt + ls -alt output + ls -alt output/* From a1fe2ff492895ad2c3903a9f2424ee208b6a9d98 Mon Sep 17 00:00:00 2001 From: pgleeson Date: Thu, 16 Nov 2023 11:50:04 +0000 Subject: [PATCH 12/12] Also test run.sh --- .github/workflows/docker-pull.yml | 11 +++++++++++ 1 file changed, 11 insertions(+) diff --git a/.github/workflows/docker-pull.yml b/.github/workflows/docker-pull.yml index dc0e2a4..6cfe606 100644 --- a/.github/workflows/docker-pull.yml +++ b/.github/workflows/docker-pull.yml @@ -18,6 +18,17 @@ jobs: - name: Run the Docker image run: | # Don't build. Will be pulled when run below + ./run.sh + + - name: Info on Docker images + run: | + docker -v + docker images + + - name: Run the Docker image - no c302 + run: | + # Shouldn't need to pull again. + ./stop.sh ./run-quick.sh - name: Info on Docker images