bump to 24.1 - Single-container setup

.github/workflows/compose.yml

@@ -2,6 +2,7 @@ name: build-and-test
 on: [push]
 jobs:
   build_container_base:
+    if: false  # Temporarily disable workflow 
     runs-on: ubuntu-20.04
     steps:
       - name: Checkout

.github/workflows/lint.yml

@@ -5,18 +5,18 @@ jobs:
     runs-on: ubuntu-latest
     steps:
     - name: Checkout
-      uses: actions/checkout@v2
-    - name: Cleanup to only use compose
-      run: rm -R docs galaxy test
+      uses: actions/checkout@v4
+    # - name: Cleanup to only use compose
+    #   run: rm -R docs galaxy test
     - name: Run shellcheck with reviewdog
-      uses: reviewdog/action-shellcheck@v1.1.3
+      uses: reviewdog/action-shellcheck@v1.27.0
       with:
         github_token: ${{ secrets.GITHUB_TOKEN }}
         reporter: github-check
         level: warning
         pattern: "*.sh"
     - name: Run hadolint with reviewdog
-      uses: reviewdog/action-hadolint@v1.16.0
+      uses: reviewdog/action-hadolint@v1.46.0
       with:
         github_token: ${{ secrets.GITHUB_TOKEN }}
         reporter: github-check

.github/workflows/pull-request.yml

@@ -2,6 +2,7 @@ name: pr-test
 on: pull_request
 jobs:
   test:
+    if: false  # Temporarily disable workflow 
     runs-on: ubuntu-20.04
     strategy:
       matrix:

.github/workflows/single.sh

@@ -18,7 +18,6 @@ docker --version
 docker info
 
 # start building this repo
-git submodule update --init --recursive
 sudo chown 1450 /tmp && sudo chmod a=rwx /tmp
 
 ## define a container size check function, first parameter is the container name, second the max allowed size in MB
@@ -50,8 +49,8 @@ docker run -d -p 8080:80 -p 8021:21 -p 8022:22 \
     --privileged=true \
     -v "$(pwd)/local_folder:/export/" \
     -e GALAXY_CONFIG_ALLOW_USER_DATASET_PURGE=True \
-    -e GALAXY_CONFIG_ALLOW_LIBRARY_PATH_PASTE=True \
-    -e GALAXY_CONFIG_ENABLE_USER_DELETION=True \
+    -e GALAXY_CONFIG_ALLOW_PATH_PASTE=True \
+    -e GALAXY_CONFIG_ALLOW_USER_DELETION=True \
     -e GALAXY_CONFIG_ENABLE_BETA_WORKFLOW_MODULES=True \
     -v /tmp/:/tmp/ \
     quay.io/bgruening/galaxy
@@ -82,15 +81,15 @@ cd "${WORKING_DIR}/test/slurm/" && bash test.sh && cd "$WORKING_DIR"
 # - cd $WORKING_DIR/test/gridengine/ && bash test.sh && cd $WORKING_DIR
 
 echo 'Waiting for Galaxy to come up.'
-galaxy-wait -g $BIOBLEND_GALAXY_URL --timeout 300
+galaxy-wait -g $BIOBLEND_GALAXY_URL --timeout 600
 
 curl -v --fail $BIOBLEND_GALAXY_URL/api/version
 
 # Test self-signed HTTPS
 docker_run -d --name httpstest -p 443:443 -e "USE_HTTPS=True" $DOCKER_RUN_CONTAINER
-# TODO 19.05
-# - sleep 90s && curl -v -k --fail https://127.0.0.1:443/api/version
-#- echo | openssl s_client -connect 127.0.0.1:443 2>/dev/null | openssl x509 -issuer -noout| grep selfsigned
+
+sleep 180s && curl -v -k --fail https://127.0.0.1:443/api/version
+echo | openssl s_client -connect 127.0.0.1:443 2>/dev/null | openssl x509 -issuer -noout| grep localhost
 
 docker logs httpstest && docker stop httpstest && docker rm httpstest
 
@@ -124,7 +123,7 @@ cd "$WORKING_DIR/test/bioblend/" && . ./test.sh && cd "$WORKING_DIR/"
 #  then
 #    # Test without install-repository wrapper
 #      sleep 10
-#      docker_exec_run bash -c 'cd $GALAXY_ROOT && python ./scripts/api/install_tool_shed_repositories.py --api admin -l http://localhost:80 --url https://toolshed.g2.bx.psu.edu -o devteam --name cut_columns --panel-section-name BEDTools'
+#      docker_exec_run bash -c 'cd $GALAXY_ROOT_DIR && python ./scripts/api/install_tool_shed_repositories.py --api admin -l http://localhost:80 --url https://toolshed.g2.bx.psu.edu -o devteam --name cut_columns --panel-section-name BEDTools'
 #  fi
 
 

.github/workflows/single_container.yml

@@ -1,15 +1,15 @@
 name: Single Container Test
-on: [push]
+on: [push, pull_request]
 jobs:
   build_and_test:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: [3.7]
+        python-version: ['3.10']
     steps:
     - name: Checkout
-      uses: actions/checkout@v2
-    - uses: actions/setup-python@v1
+      uses: actions/checkout@v4
+    - uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
     - name: Build and Test

.travis.yml

@@ -1,14 +1,14 @@
 sudo: required
 
 language: python
-python: 3.6
+python: 3.10
 
 services:
   - docker
 
 env:
   matrix:
-    - TOX_ENV=py36
+    - TOX_ENV=py310
   global:
     - secure: "SEjcKJQ0NGXdpFxFhLVlyJmiBvgiLtR5Uufg90Vm3owKlMy0NSfIrOR+2dwNniqOp7QI3eVepnqjid/Ka0QStzVqMCe55OLkJ/TbTHnMLpbtY63mpGfogVRvxMMAVpzLpcQqtJFORZmO/MIWSLlBiXMMzOg3+tbXvQXmL17Rbmw="
 
@@ -38,7 +38,6 @@ before_install:
 
 
   # start building this repo
-  - git submodule update --init --recursive
   - sudo chown 1450 /tmp && sudo chmod a=rwx /tmp
   - export WORKING_DIR="$TRAVIS_BUILD_DIR"
   - export DOCKER_RUN_CONTAINER="quay.io/bgruening/galaxy"
@@ -68,8 +67,8 @@ before_install:
         --privileged=true \
         -v `pwd`/local_folder:/export/ \
         -e GALAXY_CONFIG_ALLOW_USER_DATASET_PURGE=True \
-        -e GALAXY_CONFIG_ALLOW_LIBRARY_PATH_PASTE=True \
-        -e GALAXY_CONFIG_ENABLE_USER_DELETION=True \
+        -e GALAXY_CONFIG_ALLOW_PATH_PASTE=True \
+        -e GALAXY_CONFIG_ALLOW_USER_DELETION=True \
         -e GALAXY_CONFIG_ENABLE_BETA_WORKFLOW_MODULES=True \
         -v /tmp/:/tmp/ \
         quay.io/bgruening/galaxy
@@ -101,15 +100,16 @@ script:
   # - cd $TRAVIS_BUILD_DIR/test/gridengine/ && bash test.sh && cd $WORKING_DIR
 
   - echo 'Waiting for Galaxy to come up.'
-  - galaxy-wait -g $BIOBLEND_GALAXY_URL --timeout 300
+  - galaxy-wait -g $BIOBLEND_GALAXY_URL --timeout 600
 
   - curl -v --fail $BIOBLEND_GALAXY_URL/api/version
 
   # Test self-signed HTTPS
   - docker_run -d --name httpstest -p 443:443 -e "USE_HTTPS=True" $DOCKER_RUN_CONTAINER
-  # TODO 19.05
-  # - sleep 90s && curl -v -k --fail https://127.0.0.1:443/api/version
-  #- echo | openssl s_client -connect 127.0.0.1:443 2>/dev/null | openssl x509 -issuer -noout| grep selfsigned
+
+  - sleep 180s && curl -v -k --fail https://127.0.0.1:443/api/version
+  - echo | openssl s_client -connect 127.0.0.1:443 2>/dev/null | openssl x509 -issuer -noout| grep localhost
+
   - docker logs httpstest && docker stop httpstest && docker rm httpstest
 
   # Test FTP Server upload
@@ -140,7 +140,7 @@ script:
   #  then
   #      # Test without install-repository wrapper
   #      sleep 10
-  #      docker_exec_run bash -c 'cd $GALAXY_ROOT && python ./scripts/api/install_tool_shed_repositories.py --api admin -l http://localhost:80 --url https://toolshed.g2.bx.psu.edu -o devteam --name cut_columns --panel-section-name BEDTools'
+  #      docker_exec_run bash -c 'cd $GALAXY_ROOT_DIR && python ./scripts/api/install_tool_shed_repositories.py --api admin -l http://localhost:80 --url https://toolshed.g2.bx.psu.edu -o devteam --name cut_columns --panel-section-name BEDTools'
   #  fi