UIP-47: Simplify narrative installation #3559
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| NAR_NAME="kbase/narrative" | ||
| NAR_VER_NAME="kbase/narrative_version" # Image for serving up the narrative version | ||
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| # Get the current branch, so that we can tag images to branch | ||
| BRANCH=${TRAVIS_BRANCH:-`git symbolic-ref --short HEAD`} | ||
| BRANCH=${GIT_BRANCH:-`git symbolic-ref --short HEAD`} |
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TRAVIS_BRANCH was annoying me
| npm install 2>&1 | tee -a ${logfile} | ||
| npm run install-npm | ||
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| # Install Narrative requirements | ||
| # ------------------------------ | ||
| log "Installing biokbase requirements from src/requirements.txt" | ||
| cd "$NARRATIVE_ROOT_DIR/src" | ||
| cat requirements.txt | sed -e '/^\s*#.*$/d' -e '/^\s*$/d' | xargs -n 1 pip --no-cache-dir install 2>&1 | tee -a "${logfile}" | ||
| cat $NARRATIVE_ROOT_DIR/src/requirements.txt | sed -e '/^\s*#.*$/d' -e '/^\s*$/d' | xargs -n 1 pip --no-cache-dir install 2>&1 | tee -a "${logfile}" |
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this command is what the install_docker_narrative.sh script uses
| # Install Narrative code | ||
| # ---------------------- | ||
| log "Installing biokbase modules" | ||
| cd "$NARRATIVE_ROOT_DIR/src" | ||
| log "Running local 'setup.py'" | ||
| python setup.py install 2>&1 | tee -a "${logfile}" | ||
| log "Done installing biokbase." | ||
| cd "$NARRATIVE_ROOT_DIR" | ||
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Begone foul setup.py!
| @@ -110,7 +101,6 @@ then | |||
| cd nbextensions | |||
| sh install.sh | |||
| cd ../.. | |||
| jupyter nbextension enable --py --sys-prefix widgetsnbextension | |||
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this line is in the install.sh script
| # Install Narrative code | ||
| # ---------------------- | ||
| console "Installing biokbase modules" | ||
| cd $NARRATIVE_ROOT_DIR/src | ||
| console "Running local 'setup.py'" | ||
| ${PYTHON} setup.py install | ||
| console "Done installing biokbase." |
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Begone again foul setup.py!
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| cp $NARRATIVE_DIR/src/config.json $JUPYTER_CONFIG_DIR/static/kbase/config/ | ||
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| python /kb/dev_container/narrative/src/biokbase/narrative/exporter/run_narrative.py "$@" |
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this script does not exist. I meant to delete this file in the last PR but must have forgotten
| @@ -6,6 +6,7 @@ export JUPYTER_RUNTIME_DIR=/tmp/jupyter_runtime | |||
| export JUPYTER_DATA_DIR=/tmp/jupyter_data | |||
| export JUPYTER_PATH=$NARRATIVE_DIR/kbase-extension | |||
| export IPYTHONDIR=$NARRATIVE_DIR/kbase-extension/ipython | |||
| export PYTHONPATH=$NARRATIVE_DIR/src/:$PYTHONPATH | |||
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cool new PYTHONPATH
| @@ -1,6 +1,6 @@ | |||
| #!/bin/bash | |||
| export NARRATIVE_DIR=$(pwd) | |||
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| export PYTHONPATH=$NARRATIVE_DIR/src:$PYTHONPATH | |||
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amend the PYTHONPATH
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Codecov ReportAll modified and coverable lines are covered by tests ✅
Additional details and impacted files@@ Coverage Diff @@
## develop #3559 +/- ##
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- Coverage 25.72% 25.71% -0.02%
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Files 461 461
Lines 46694 46694
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- Hits 12014 12007 -7
- Misses 34680 34687 +7 see 3 files with indirect coverage changes Continue to review full report in Codecov by Sentry.
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Description of PR purpose/changes
Removing antiquated
setup.pyand adding thesrc/directory to thePYTHONPATHenv var to simplify narrative installation and use.Jira Ticket / Issue
Related Jira ticket: https://kbase-jira.atlassian.net/browse/UIP-47
DATAUP-69 Adds a PR template)Testing Instructions
Dev Checklist:
formatandcheckon changed Python code manually or with a git precommit hookUpdating Version and Release Notes (if applicable)
N/A