Merge branch 'master' of ssh://github.com/GMOD/JBrowse

.gitignore

@@ -3,14 +3,10 @@
 .#*
 \#*\#
 *.index
-/bin/wig2png
 *.pyc
 *TODO.txt
 Makefile
 /sample_data/json
-/src/wig2png/config.log
-/src/wig2png/config.status
-/src/wig2png/src/config.h
 /docs/jsdoc/
 /*-debug.html
 /extlib*
@@ -46,10 +42,11 @@ _Inline
 .DS_Store
 blib
 pm_to_blib
-bin/wig2png.dSYM
 bower_components
 src/dojo-themes
 themes/*/css
 .sass-cache
 .vscode/
 *driver.log
+JBrowse-*/
+JBrowse-*.zip

.travis.yml

@@ -1,44 +1,80 @@
 sudo: false
 dist: trusty
 language: perl
-python: "2.7.10"
+python: 2.7.10
 perl:
-  - "5.26"
-  - "5.14"
+- '5.26'
+- '5.14'
 addons:
   apt:
     packages:
     - libdb-dev
     - libgd2-noxpm-dev
-  firefox: "58.0"
+  firefox: '58.0'
 cache:
+  directories:
   - extlib/
-  - $HOME/perl5/
-before_install:
-  #install geckodriver for the selenium tests :-P
-  - wget https://github.com/mozilla/geckodriver/releases/download/v0.19.1/geckodriver-v0.19.1-linux64.tar.gz
-  - mkdir geckodriver
-  - tar -xzf geckodriver-v0.19.1-linux64.tar.gz -C geckodriver
-  - export PATH=$PATH:$PWD/geckodriver
-  # install perl deps
-  - cpanm --notest GD::Image Text::Markdown DateTime
-  #- cpanm --notest git://github.com/bioperl/[email protected]
-  # and jshint for the JS code
-  - npm install -g jshint
+  - "$HOME/perl5/"
+  - node_modules/
+  - "$HOME/python/"
+  - "$HOME/.nvm/"
+  - "$HOME/geckodriver"
 install:
-  - virtualenv ~/python
-  - source ~/python/bin/activate
-  - pip install nose selenium
-  - bash setup.sh legacy
-before_script:
-  - ./jb_run.js -p 9000 &
+- |
+  if [[ ! -f ~/geckodriver/geckodriver ]]; then
+    rm -rf ~/geckodriver;
+    mkdir ~/geckodriver;
+    wget -O - https://github.com/mozilla/geckodriver/releases/download/v0.19.1/geckodriver-v0.19.1-linux64.tar.gz | tar -xzf - -C ~/geckodriver;
+  fi
+- export PATH=$PATH:$HOME/geckodriver
+- cpanm --notest GD::Image Text::Markdown DateTime JSON
+- npm install -g jshint
+# only init the python virtualenv if it did not show up in our build cache
+- if [[ ! -f ~/python/bin/activate ]]; then virtualenv ~/python; fi
+- source ~/python/bin/activate
+- pip install nose selenium
 script:
-  - jshint src/JBrowse/
-  - prove -j4 -Isrc/perl5 -lr tests/perl_tests
-  - MOZ_HEADLESS=1 SELENIUM_BROWSER=firefox JBROWSE_URL=http://localhost:9000/index.html nosetests tests/selenium_tests/
-  # only run `make release` for builds on master, or on a tag, or on a pull request
-  - if [[ "x$TRAVIS_TAG" != "x" || $TRAVIS_BRANCH = "master" || $TRAVIS_PULL_REQUEST != "false" ]]; then make -f build/Makefile release; fi
+- jshint src/JBrowse/
+- if [[ "x$TRAVIS_TAG" != "x" ]]; then build/set_package_versions.pl $TRAVIS_TAG src/JBrowse/package.json package.json; fi
+- RELEASE_VERSION=`node -e 'require("fs").readFile("src/JBrowse/package.json", (e,d)=>console.log(JSON.parse(d).version))'`
+- BUILD_DIR=$PWD
+# if we are building for inclusion into the `dev` branch, run the minification and test against that
+- |
+  if [[ "x$TRAVIS_TAG" != "x" || $TRAVIS_BRANCH = "master" || $TRAVIS_BRANCH = "dev" || $TRAVIS_PULL_REQUEST != "false" ]]; then
+    make -f build/Makefile release;
+    rm -rf JBrowse-*/;
+    unzip -q JBrowse-$RELEASE_VERSION.zip;
+    cp -r tests/ JBrowse-$RELEASE_VERSION/;
+    cd JBrowse-$RELEASE_VERSION/;
+  fi
+- ./setup.sh legacy;
+- prove -Isrc/perl5 -r -j3 tests/perl_tests;
+- utils/jb_run.js -p 9000 &
+- MOZ_HEADLESS=1 SELENIUM_BROWSER=firefox JBROWSE_URL=http://localhost:9000/index.html tests/selenium_tests/travis_wrapper.sh;
+- cd $BUILD_DIR
 after_failure:
-  - cat JBrowse-1.x.x-dev/setup.log 
-  - find JBrowse-1.x.x-dev/extlib/lib/perl5
-  - cat JBrowse-1.x.x-dev/src/build-report.txt
+- cat JBrowse-*/setup.log
+- find JBrowse-*/extlib/lib/perl5
+- cat JBrowse-*/src/build-report.txt
+deploy:
+# upload both minified and non-minified builds to GitHub releases
+- provider: releases
+  api_key:
+    secure: BuOD7rqrcGKT3g0hVY5AGpJI/Kkko4DhSIYSUQ28sS2AOdoNyTD0t5doL/Kiq4BC41q198tbFFt1dnXGdo8YKpBSXO/uGUuuiGtMFHM++I84oLq20p49iyrenNZ4m/jy/Q4YtizIYLs83DVzVdQzhJ5hrTx6f+d1gc9EgaMeBF4=
+  file: JBrowse-1.*.zip
+  file_glob: true
+  skip_cleanup: true
+  on:
+    repo: GMOD/jbrowse
+    perl: 5.26
+    tags: true
+# upload regular non-minified version to npm
+- provider: npm
+  email: [email protected]
+  skip_cleanup: true
+  api_key:
+    secure: mgvlVdeMAR35C69+NERuYK4YGwbBAQsnSXS7IJhn3CRNgbtWh2zqaVV8NbHWitD9RJmocTbkIe94MfD8HfI3zBAgIVewckQ0QWMyjAJuWJR2Zw91R309aIQpbsix4kNCP9RDDrtfzovptBJ6JS8UwEk5CsQ7Wfohctek59+UnyU=
+  on:
+    repo: GMOD/jbrowse
+    perl: 5.26
+    tags: true

README.md

@@ -1,4 +1,4 @@
-[![Build status](https://travis-ci.org/GMOD/jbrowse.svg?branch=master)](https://travis-ci.org/GMOD/jbrowse)
+[![Build status](https://travis-ci.org/GMOD/jbrowse.svg?branch=dev)](https://travis-ci.org/GMOD/jbrowse)
 
 # Installing JBrowse
 
@@ -35,8 +35,7 @@ This allows JBrowse to be easily integrated into other applications.  `jb_setup.
 
 You can also optionally run build steps to create the minimized codebase. Extra perl dependencies Text::Markdown and DateTime are required to run the build step.
 
-    make -f build/Makefile release-notest
-    make -f build/Makefile release # alternate build with full test suite
+    make -f build/Makefile release
 
 To build the Electron app (JBrowse desktop app), run the following
 
@@ -72,29 +71,25 @@ eggs for `selenium` and `nose` installed.  Run the tests with:
 
     MOZ_HEADLESS=1 SELENIUM_BROWSER=firefox JBROWSE_URL='http://localhost/jbrowse/index.html' nosetests
 
-Supported browsers are 'firefox', 'chrome', 'phantom', and 'travis_saucelabs'.  The Sauce Labs + Travis one will only work properly in a properly configured Travis CI build environment.
+Supported browsers are 'firefox', 'chrome', 'phantom', and 'travis_saucelabs'.  The Sauce Labs + Travis
+one will only work in a properly configured Travis CI build environment.
 
 # Cutting a JBrowse release
 
-1. Edit the JBrowse `package.json` file and change 'version' to the version you are releasing.  *Don't commit this change to the repository, it should stay as `dev` in git so that it shows up in analytics as a development version.*
+NOTE: Beginning in 1.12.4, 
 
-2. Build the release packages: `make -f build/Makefile release`.  The files produced during the build should not be committed to the repository either. There is also `make -f build/Makefile release-notest` for releases that don't need perl tests to be run. NOTE: you may need to use the command `ulimit -n 1000` to avoid "spawn EMFILE" build errors.
+1. Make a tag in the repository for the release, named, e.g. `1.6.3-release`.  This should cause Travis CI
+to create a release on GitHub under https://github.com/GMOD/jbrowse/releases
 
-3. Make a tag in the repository for the release, named, e.g. `1.6.3-release`.
+1. Add release notes to the new release that Travis created.
 
-4. `scp` the release .zip files (min and full) to jbrowse.org.
+1. Write a blog post announcing the release, with links to the built releases on GitHub.
 
-5. Add them to the Wordpress Downloads list so that we can track how
-many times they are downloaded.
+1. Update the "Install" page on the site to point to the newest release.
 
-6. Write a blog post announcing the release.  The `release-notes.html`
-file made during the build might be useful for this.
+1. Update the latest-release code checkout on the site, which the "Latest Release" demo on the jbrowse.org points to, to be an unzipped-and-set-up copy of the latest release.
 
-7. Update the "Install" page on the site to point to the newest release.
-
-8. Update the latest-release code checkout on the site, which the "Latest Release" demo on the jbrowse.org points to, to be an unzipped-and-set-up copy of the latest release.
-
-9. Write an email announcing the release, sending to gmod-ajax,
+1. Write an email announcing the release, sending to gmod-ajax,
 jbrowse-dev.  If it is a major release, add gmod-announce and make a GMOD news item.
 
 As you can tell, this process could really use some more streamlining and automation.