Update travis testing definitions

Author: bgruening

.travis.yml

@@ -2,53 +2,50 @@ sudo: false
 language: python
 python: 2.7
 
+# This is a big repository so break Travis CI work into 2 CI jobs.
 env:
-  - CHUNK=xaa
-  - CHUNK=xab
-  - CHUNK=xac
-  - CHUNK=xad
+  - CHUNK=0
+  - CHUNK=1
 
 before_install:
   - export GALAXY_REPO=https://github.com/galaxyproject/galaxy
   - export GALAXY_RELEASE=release_16.10
   - export PLANEMO_CONDA_PREFIX="$HOME/conda"
-  - unset JAVA_HOME  # Interferes with java tools installed through conda
 
 install:
-  # html5lib (planemo dep) requires setuptools >= 18.5
-  - pip install -q flake8 planemo
+  - pip install flake8 planemo
   - planemo conda_init
   - export PATH="$PLANEMO_CONDA_PREFIX/bin:$PATH"
+  - conda update -y conda
   - conda create -y -q -c bioconda --name iuc_conda samtools=0.1.19 bcftools
   - . activate iuc_conda
   - planemo --version
   - conda --version
-  - echo $TRAVIS_COMMIT_RANGE
-  - git diff --name-only $TRAVIS_COMMIT_RANGE | xargs -n1 dirname | ./filter_directories.py | sort -u > changed_repositories.list
-  - cat changed_repositories.list
-
-script:
-  - cd "$TRAVIS_BUILD_DIR" ## && flake8 -v --exclude=.git .
+  - git diff --quiet "$TRAVIS_COMMIT_RANGE" -- ; GIT_DIFF_EXIT_CODE=$?
   - |
-    if [ -s changed_repositories.list ]
-    then
-      split -n l/4 changed_repositories.list
+    if [ "$GIT_DIFF_EXIT_CODE" -gt 1 ] ; then
+      git remote set-branches --add origin master;
+      git fetch;
+      TRAVIS_COMMIT_RANGE=origin/master...;
     fi
-  - echo "$CHUNK"
+  - echo $TRAVIS_COMMIT_RANGE
   - |
-    if [ "${CHUNK}" ] && [ -s "${CHUNK}" ]
-    then
-      cat "$CHUNK"
-      export PLANEMO_TEST_RUN=True
-      while read -r DIR; do planemo shed_lint --report_level warn --tools --fail_level error --recursive "$DIR"; done < "$CHUNK"
-      while read -r DIR; do planemo conda_install "$DIR"; done < "$CHUNK"
-      while read -r DIR; do planemo test --conda_dependency_resolution --galaxy_branch $GALAXY_RELEASE --galaxy_source $GALAXY_REPO "$DIR" || exit 1; done < "$CHUNK"
-    fi
+      planemo ci_find_repos --exclude_from .tt_blacklist \
+                            --exclude packages --exclude data_managers \
+                            --changed_in_commit_range "$TRAVIS_COMMIT_RANGE" \
+                            --chunk_count 2 --chunk "${CHUNK}" \
+                            --output changed_repositories_chunk.list
+  - cat changed_repositories_chunk.list
+
+script:
+  - cd "$TRAVIS_BUILD_DIR" ## && flake8 --exclude=.git .
+  - while read -r DIR; do planemo shed_lint --tools --ensure_metadata --urls --report_level warn --fail_level error --recursive "$DIR" || exit 1; done < changed_repositories_chunk.list
+  - while read -r DIR; do planemo conda_install "$DIR"; done < changed_repositories_chunk.list
+  - while read -r DIR; do planemo test --conda_dependency_resolution --galaxy_branch "$GALAXY_RELEASE" --galaxy_source "$GALAXY_REPO" "$DIR" || exit 1; done < changed_repositories_chunk.list
 
 after_success:
   - |
-    if [ "$TRAVIS_PULL_REQUEST" == "false" -a "$TRAVIS_BRANCH" == "master" -a "$PLANEMO_TEST_RUN" == 'True' ]
-    then
-      while read -r DIR; do planemo shed_update --shed_target testtoolshed --shed_email $SHED_EMAIL --shed_password $SHED_PASSWORD --force_repository_creation "$DIR" || exit 1; done < "$CHUNK"
-      while read -r DIR; do planemo shed_update --shed_target toolshed --shed_email $SHED_EMAIL --shed_password $SHED_PASSWORD --force_repository_creation "$DIR" || exit 1; done < "$CHUNK"
+    if [ "$TRAVIS_PULL_REQUEST" == "false" -a "$TRAVIS_BRANCH" == "master" ]; then
+      while read -r DIR; do planemo shed_update --shed_target testtoolshed --shed_email "$SHED_EMAIL" --shed_password "$SHED_PASSWORD" --force_repository_creation "$DIR" || exit 1; done < changed_repositories_chunk.list
+      while read -r DIR; do planemo shed_update --shed_target toolshed --shed_email "$SHED_EMAIL" --shed_password "$SHED_PASSWORD" --force_repository_creation "$DIR" || exit 1; done < changed_repositories_chunk.list
     fi