From d011679c57c1bde57959f1d0dd7e90992b13cdb8 Mon Sep 17 00:00:00 2001
From: chrisbarnettster <chrisbarnettster@gmail.com>
Date: Fri, 24 Jul 2020 16:49:26 +0200
Subject: [PATCH] more updates for github actions, initial was added directly
 to master by github (#77)

---
 .travis.yml           | 127 ------------------------------------------
 .tt_biocontainer_skip |   1 +
 .tt_blacklist         |   1 -
 .tt_skip              |   1 +
 4 files changed, 2 insertions(+), 128 deletions(-)
 delete mode 100644 .travis.yml
 create mode 100644 .tt_biocontainer_skip
 delete mode 100644 .tt_blacklist
 create mode 100644 .tt_skip

diff --git a/.travis.yml b/.travis.yml
deleted file mode 100644
index 696f5a67..00000000
--- a/.travis.yml
+++ /dev/null
@@ -1,127 +0,0 @@
-# 'sudo required' will give us 7,5 GB memory, but has slower startup times, as we start a VM instead of a Container
-sudo: required
-language: python
-cache: pip
-
-python: 2.7
-
-jobs:
-  include:
-    - stage: lint
-      addons: {}
-      before_install: skip
-      install:
-        - pip install flake8 flake8-import-order planemo
-        - planemo --version
-        - git diff --quiet "$TRAVIS_COMMIT_RANGE" -- ; GIT_DIFF_EXIT_CODE=$?
-        - |
-          if [ "$GIT_DIFF_EXIT_CODE" -gt 1 ] ; then
-              git remote set-branches --add origin master
-              git fetch
-              TRAVIS_COMMIT_RANGE=origin/master...
-          fi
-        - echo $TRAVIS_COMMIT_RANGE
-        - |
-          planemo ci_find_repos --exclude_from .tt_blacklist \
-                                --changed_in_commit_range "$TRAVIS_COMMIT_RANGE" \
-                                --output changed_repositories.list
-        - cat changed_repositories.list
-      script:
-        - set -e
-        - cd "$TRAVIS_BUILD_DIR" && flake8 --exclude=.git,./deprecated/ .
-        - while read -r DIR; do planemo shed_lint --tools --ensure_metadata --urls --report_level warn --fail_level error --recursive "$DIR"; done < changed_repositories.list
-
-    - stage: test
-      env: CHUNK=0
-
-    - stage: test
-      env: CHUNK=1
-
-    - stage: test
-      env: CHUNK=2
-
-    - stage: test
-      env: CHUNK=3
-
-    - stage: deploy
-      if: (type = push) AND (branch = master)
-      addons: {}
-      before_install: skip
-      install:
-        - pip install planemo
-        - planemo --version
-        - git diff --quiet "$TRAVIS_COMMIT_RANGE" -- ; GIT_DIFF_EXIT_CODE=$?
-        - |
-          if [ "$GIT_DIFF_EXIT_CODE" -gt 1 ] ; then
-              git remote set-branches --add origin master
-              git fetch
-              TRAVIS_COMMIT_RANGE=origin/master...
-          fi
-        - echo $TRAVIS_COMMIT_RANGE
-        - |
-          planemo ci_find_repos --exclude_from .tt_blacklist \
-                                --changed_in_commit_range "$TRAVIS_COMMIT_RANGE" \
-                                --output changed_repositories.list
-        - cat changed_repositories.list
-      script:
-        - set -e
-        - |
-          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 "$DIR" || exit 1; done < changed_repositories.list
-              while read -r DIR; do planemo shed_update --shed_target toolshed --shed_email "$SHED_EMAIL" --shed_password "$SHED_PASSWORD" --force_repository_creation "$DIR" || exit 1; done < changed_repositories.list
-          fi
-
-before_install:
-  - export GALAXY_REPO=https://github.com/galaxyproject/galaxy
-  - export GALAXY_RELEASE=release_20.01
-  - export PLANEMO_CONDA_PREFIX="$HOME/conda"
-  - unset JAVA_HOME
-
-install:
-  - pip install planemo
-  - planemo conda_init
-  - export PATH="$PLANEMO_CONDA_PREFIX/bin:$PATH"
-  - conda install -y -c conda-forge conda=4.3.34 
-  - planemo --version
-  - conda --version
-  - git diff --quiet "$TRAVIS_COMMIT_RANGE" -- ; GIT_DIFF_EXIT_CODE=$?
-  - |
-    if [ "$GIT_DIFF_EXIT_CODE" -gt 1 ] ; then
-        git remote set-branches --add origin master
-        git fetch
-        TRAVIS_COMMIT_RANGE=origin/master...
-    fi
-  - echo $TRAVIS_COMMIT_RANGE
-  - |
-    planemo ci_find_repos --exclude data_managers \
-                          --exclude packages \
-                          --exclude_from .tt_blacklist \
-                          --changed_in_commit_range "$TRAVIS_COMMIT_RANGE" \
-                          --output changed_repositories.list
-  - touch changed_repositories_chunk.list changed_tools_chunk.list
-  - |
-    if [ -s changed_repositories.list ]; then
-        if [ $(wc -l < changed_repositories.list) -eq 1 ]; then
-            planemo ci_find_tools --chunk_count 4 --chunk "${CHUNK}" \
-                                  --output changed_tools_chunk.list \
-                                  $(cat changed_repositories.list)
-        else
-            planemo ci_find_repos --chunk_count 4 --chunk "${CHUNK}" \
-                                  --output changed_repositories_chunk.list \
-                                  $(cat changed_repositories.list)
-        fi
-    fi
-  - cat changed_repositories.list
-  - cat changed_repositories_chunk.list
-  - cat changed_tools_chunk.list
-
-script:
-  - set -e
-  - |
-    if [ -s changed_tools_chunk.list ]; then
-        planemo test --conda_dependency_resolution --conda_auto_install --conda_channels iuc,conda-forge,bioconda,defaults --galaxy_branch "$GALAXY_RELEASE" --galaxy_source "$GALAXY_REPO" $(cat changed_tools_chunk.list)
-    elif [ -s changed_repositories_chunk.list ]; then
-        while read -r DIR; do
-            planemo test --conda_dependency_resolution --conda_auto_install --conda_channels iuc,conda-forge,bioconda,defaults --galaxy_branch "$GALAXY_RELEASE" --galaxy_source "$GALAXY_REPO" "$DIR"
-        done < changed_repositories_chunk.list
-    fi
diff --git a/.tt_biocontainer_skip b/.tt_biocontainer_skip
new file mode 100644
index 00000000..5b3bda6f
--- /dev/null
+++ b/.tt_biocontainer_skip
@@ -0,0 +1 @@
+data_managers/
diff --git a/.tt_blacklist b/.tt_blacklist
deleted file mode 100644
index 1ccb63f3..00000000
--- a/.tt_blacklist
+++ /dev/null
@@ -1 +0,0 @@
-# tools on this list will not be tested
diff --git a/.tt_skip b/.tt_skip
new file mode 100644
index 00000000..5b3bda6f
--- /dev/null
+++ b/.tt_skip
@@ -0,0 +1 @@
+data_managers/