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* testing docker from github * minor fix to travis-ci * changed branch to $TRAVIS_BRANCH * adding env variables * adding env variables * double checking that travis variables are set up * double checking that travis variables are set up * double checking that travis variables are set up * changing from deploy tag to after_success tag * lowercase slug * trying to fix the build tag name * trying to fix the build tag name * chewbbaca with python3 * chewbbaca with python3 * debugging docker tag * debugging docker tag * debugging docker tag * debugging docker tag * debugging docker tag * debugging docker tag * fixing docker tag * fixing docker login * explicitly giving lskatz for username * secret variable space * trying to get secret env variables for docker login * trying out docker caching * Update .travis.yml * fix "docker save" * trying the other kind of caching * fixed single quote * view dockerImages.stdout * added cache folder * test for size of dockerImages.stdout * from xargs to bash loop * fixed a quote * a quick rm cache * Update .travis.yml * after removing all cache * rm cache * checking if file exists * rm cache * back to normal * Create travis-docker.yml * Update travis-docker.yml * Update travis-docker.yml * docker login * passwordless login * docker build * updating run commands for variable printing * updating run commands for variable printing * updating run commands for variable printing * more debugging; switching build directory to HOME * more debugging * more debugging * more debugging * actions/checkout@v2 * actions/checkout on this branch * actions/checkout on this branch * actions/checkout on this branch * actions/checkout on this branch * fixed space typo * fixed working directory during docker build * fixed working directory during docker build * fixing docker build * fixing docker build * fixing docker build * fixing docker build * fixing docker build * trying docker push * using a more appropriate env variable * fixed case on docker tag * moving env out of job and to global * separating out to multiple jobs that depend on each other, in preparation for any concurrency * some concurrency * m * m * added some debugging * m * added init and debugging jobs * init needs debugging * exporting REMOTE_TAG * figuring out variable continuity * figuring out variable continuity * passing outputs between jobs * passing outputs between jobs * passing outputs between jobs * debugging more * debugging more * debugging more with JSON * debugging more with JSON * debugging more with JSON2 * moved git checkout to init job * maybe I needed to do fromJSON. And moved git checkout back. * JSON3 * JSON3 * JSON4 * JSON5 * JSON6 * test slug * removed all underscores and dashes in this output chain * export slug * export slug2 * just trying to make env work at all * env2 * env3 * making the env work properly with format() * env2 * env3 * env4 * env5 * env6 * trying things out * trying things out * trying things out * trying things out * trying things out * just making the variables work * docker cache action * docker cache action * Trying to follow satackey more closely * Update travis-docker.yml * added docker login * login before tagging * Rename travis-docker.yml to travis-docker.yml.bak * Create github-docker.yml * removed needs:init * corrected the docker repo * pushing to both docker and github https://docs.github.com/en/actions/guides/publishing-docker-images * renamed the github container name from my-image to sneakernet * tags: latest * adding extra LC_ALL to the end * newer blast in Dockerfile * blast library COPY statements * reverting blast libs * getting blast from mlst container * manual installation of staramr * manual installation of staramr2 * tag with hashsum values too * trying to invoke the sha sum * adding apt-get packages for staramr * trying out docker push v2 * trying docker action v2 * fixed newline error * removed ipython-notebook * Update github-docker.yml * Update Dockerfile * numpy installation through pip now * Removing multistage for pip-based images * fixed apt-get command syntax * changed tags to a value instead a list * updated the tag docker/build-push-action#160 * list of tags * pushing to the github registry (?) * one space before pipe * Not sending to github packages; yes sending multiple tags to dockerhub * removed list again * Rename github-docker.yml to github-docker.yml.bak * Create build-and-push-container.yml * added this branch for github actions * added libpython3.5-dev ``` #130 [linux/386 stage-11 34/47] RUN pip3 install poetry && git clone https:/... #130 11.73 building '_openssl' extension #130 11.73 creating build/temp.linux-x86_64-3.6/build #130 11.73 creating build/temp.linux-x86_64-3.6/build/temp.linux-x86_64-3.6 #130 11.73 i686-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.6m -c build/temp.linux-x86_64-3.6/_openssl.c -o build/temp.linux-x86_64-3.6/build/temp.linux-x86_64-3.6/_openssl.o -Wconversion -Wno-error=sign-conversion #130 11.73 build/temp.linux-x86_64-3.6/_openssl.c:50:14: fatal error: pyconfig.h: No such file or directory #130 11.73 # include <pyconfig.h> #130 11.73 ^~~~~~~~~~~~ #130 11.73 compilation terminated. #130 11.73 error: command 'i686-linux-gnu-gcc' failed with exit status 1 #130 11.73 ---------------------------------------- #130 11.73 ERROR: Failed building wheel for cryptography #130 11.73 Failed to build cryptography #130 11.74 ERROR: Could not build wheels for cryptography which use PEP 517 and cannot be installed directly #130 ERROR: executor failed running [/bin/sh -c pip3 install poetry && git clone https://github.com/hcdenbakker/SalmID.git --branch 0.1.23 --single-branch && cd SalmID && poetry build -vvv && pip3 install dist/salmid*.whl]: buildkit-runc did not terminate successfully ``` * fixed libpython-dev * libpython3-dev * newline. Does it make things work * separate some pip3 installations for staramr; removed numpy pip3 * removing staramr and salmid for right now * removed all platforms except linux/amd64 * uncomment pip commands * combined some pip commands for fewer layers * Combined some chewbbaca steps into single layers * RUN echo "LC_ALL=C" >> /etc/environment * switched to UTF-8 per instructions * apt-get install locales Co-authored-by: Lee Katz - Aspen <gzu2@cdc.gov>
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