Merge pull request #1 from galaxyproject/dev

update official

Author: gagayuan

.ci/autopep8.sh

@@ -0,0 +1,15 @@
+#!/bin/sh
+TEST=$(mktemp)
+TEST_EXTRA_CLASSES=$(mktemp)
+
+pytest --collect-only --ignore=test/functional lib/galaxy_test/ test/ > "$TEST"
+pytest -o python_classes='Test* *Test *TestCase' --collect-only --ignore=test/functional lib/galaxy_test/ test/ > "$TEST_EXTRA_CLASSES"
+
+n_tests=$(grep 'tests collected' "$TEST" | sed -e 's/[^0-9]*\([0-9]*\) tests collected.*/\1/')
+n_tests_extra_classes=$(grep 'tests collected' "$TEST_EXTRA_CLASSES" | sed -e 's/[^0-9]*\([0-9]*\) tests collected.*/\1/')
+
+if [ "$n_tests_extra_classes" -gt "$n_tests" ]; then
+    echo "New test class with name not starting with Test introduced, change it to have tests collected by pytest"
+    diff "$TEST" "$TEST_EXTRA_CLASSES"
+    exit 1
+fi

.ci/check_py3_compatibility.sh

@@ -5,4 +5,4 @@ set -e
 # Setting NODE_PATH and config appropriately, using dependencies from
 # client/node_modules, run eslint against args passed to this script.
 # Primary use case here is for a pre-commit check.
-NODE_PATH=src/ node client/node_modules/eslint/bin/eslint.js -c client/.eslintrc.json "$@"
+NODE_PATH=src/ node client/node_modules/eslint/bin/eslint.js -c client/.eslintrc.js "$@"

.ci/check_test_class_names.sh

@@ -1,18 +1,16 @@
 .git
 .tox
-.venv
-.venv3
+.venv*
 packages/*/.venv
 packages/*/build
 packages/*/dist
 packages/venv
 node_modules
 database
 doc/build
-doc/source/conf.py
 eggs
-lib/galaxy/util/jstree.py
 lib/galaxy/web/proxy/js/node_modules
+lib/tool_shed/test/test_data/repos
 static/maps
 static/scripts
 test/functional/tools/cwl_tools/v1.?/

.ci/eslint_wrapper.sh

@@ -0,0 +1,3 @@
+hda
+implementors
+purgable

.ci/flake8_ignorelist.txt

@@ -7,5 +7,7 @@ xsd_path="lib/galaxy/tools/xsd/galaxy.xsd"
 xmllint --noout "$xsd_path"
 
 test_tools_path='test/functional/tools'
-tool_files_list=$(ls "$test_tools_path"/*.xml | grep -v '_conf.xml$')
+# test all test tools except upload.xml which uses a non-standard conditional
+# (without param) which does not survive xsd validation
+tool_files_list=$(ls "$test_tools_path"/*.xml | grep -v '_conf.xml$' | grep -v upload.xml)
 sh scripts/validate_tools.sh $tool_files_list

.ci/ignore-spelling.txt

@@ -5,16 +5,6 @@ variables:
     restore_cache:
       keys:
         - v1-repo-{{ .Environment.CIRCLE_SHA1 }}
-  restore_yarn_cache: &restore_yarn_cache
-    restore_cache:
-      keys:
-        - v1-repo-{{ .Environment.CIRCLE_SHA1 }}
-        - yarn-packages-{{ checksum "client/yarn.lock" }}
-  save_yarn_cache: &save_yarn_cache
-    save_cache:
-      key: yarn-packages-{{ checksum "client/yarn.lock" }}
-      paths:
-        - ~/.cache/yarn
   install_tox: &install_tox
     run: pip install tox
   set_workdir: &set_workdir
@@ -25,7 +15,7 @@ variables:
 jobs:
   get_code:
     docker:
-      - image: cimg/python:3.7
+      - image: cimg/python:3.8
     <<: *set_workdir
     steps:
       # Replace standard code checkout with shallow clone to speed things up.
@@ -34,7 +24,7 @@ jobs:
           command: |-
               # Add github.com to known hosts
               mkdir -p ~/.ssh
-              echo 'github.com ssh-rsa AAAAB3NzaC1yc2EAAAABIwAAAQEAq2A7hRGmdnm9tUDbO9IDSwBK6TbQa+PXYPCPy6rbTrTtw7PHkccKrpp0yVhp5HdEIcKr6pLlVDBfOLX9QUsyCOV0wzfjIJNlGEYsdlLJizHhbn2mUjvSAHQqZETYP81eFzLQNnPHt4EVVUh7VfDESU84KezmD5QlWpXLmvU31/yMf+Se8xhHTvKSCZIFImWwoG6mbUoWf9nzpIoaSjB+weqqUUmpaaasXVal72J+UX2B+2RPW3RcT0eOzQgqlJL3RKrTJvdsjE3JEAvGq3lGHSZXy28G3skua2SmVi/w4yCE6gbODqnTWlg7+wC604ydGXA8VJiS5ap43JXiUFFAaQ==
+              echo 'github.com ssh-rsa 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
               ' >> ~/.ssh/known_hosts
 
               # Add the user ssh key and set correct perms
@@ -83,30 +73,18 @@ jobs:
             - ~/repo
   validate_test_tools:
     docker:
-      - image: cimg/python:3.7
+      - image: cimg/python:3.8
     <<: *set_workdir
     steps:
       - *restore_repo_cache
       - run: sudo apt-get update
       - run: sudo apt-get install -y libxml2-utils
       - *install_tox
       - run: tox -e validate_test_tools
-  js_lint:
-    docker:
-      - image: cimg/node:16.15.1
-    <<: *set_workdir
-    steps:
-      - *restore_yarn_cache
-      - run: cd client && yarn install --frozen-lockfile
-      - *save_yarn_cache
-      - run: cd client && yarn run eslint
-      - run: cd client && yarn run format-check
 workflows:
   version: 2
   get_code_and_test:
     jobs:
       - get_code
       - validate_test_tools:
           <<: *requires_get_code
-      - js_lint:
-          <<: *requires_get_code

.ci/validate_test_tools.sh

@@ -3,8 +3,9 @@
 # B008 Do not perform function calls in argument defaults (for FastAPI Depends and Body)
 # E203 is whitespace before ':'; we follow black's formatting here. See https://black.readthedocs.io/en/stable/faq.html#why-are-flake8-s-e203-and-w503-violated
 # E402 module level import not at top of file # TODO, we would like to improve this.
-# E501 is line length
+# E501 is line length (delegated to black)
+# E701,E704 are multiple statements on one line; we follow black's formatting here. See https://black.readthedocs.io/en/stable/guides/using_black_with_other_tools.html#configuration
 # W503 is line breaks before binary operators, which has been reversed in PEP 8.
 # D** are docstring linting - which we mostly ignore except D302. (Hopefully we will solve more over time).
-ignore = B008,E203,E402,E501,W503,D100,D101,D102,D103,D104,D105,D106,D107,D200,D201,D202,D204,D205,D206,D207,D208,D209,D210,D211,D300,D301,D400,D401,D402,D403,D412,D413
-exclude = lib/galaxy/util/jstree.py
+ignore = B008,E203,E402,E501,E701,E704,W503,D100,D101,D102,D103,D104,D105,D106,D107,D200,D201,D202,D204,D205,D206,D207,D208,D209,D210,D211,D300,D301,D400,D401,D402,D403,D412,D413
+exclude = lib/tool_shed/test/test_data/repos

.circleci/config.yml

@@ -14,6 +14,10 @@ A clear and concise description of what the bug is.
 Galaxy Version: (check <galaxy_url>/api/version if you don't know)
 Commit: (run `git rev-parse HEAD` if you run this Galaxy server)
 
+**Browser and Operating System**
+Operating System: Windows, Linux, macOS
+Browser: Firefox, Chrome, Chrome-based, Safari
+
 **To Reproduce**
 Steps to reproduce the behavior:
 1. Go to '...'