Various updates to testing and CI infrastructure.

.github/workflows/ci.yaml

@@ -0,0 +1,48 @@
+name: Python CI
+on: [pull_request]
+env:
+  PGPASSWORD: postgres
+  PGHOST: localhost
+jobs:
+  test:
+    runs-on: ubuntu-latest
+    timeout-minutes: 90
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ['3.6']
+        tox-action:
+          - lint
+          - pytest
+          - integration
+    services:
+      postgres:
+        image: postgres:10.8
+        env:
+          POSTGRES_USER: postgres
+          POSTGRES_PASSWORD: postgres
+          POSTGRES_DB: postgres
+        ports:
+        - 5432:5432
+        # needed because the postgres container does not provide a healthcheck
+        options: --health-cmd pg_isready --health-interval 10s --health-timeout 5s --health-retries 5
+    steps:
+      - uses: actions/checkout@v1
+        with:
+          fetch-depth: 1
+          submodules: true
+      - uses: actions/setup-python@v1
+        with:
+          python-version: ${{ matrix.python-version }}
+      - name: Test psql
+        run: |
+          psql --tuples-only --username postgres -P pager=off --list
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install tox coveralls
+      - name: Test with tox
+        run: |
+          TOXENV=$(echo $TOXENV | sed 's/\.//') tox
+        env:
+          TOXENV: py${{ matrix.python-version }}-${{ matrix.tox-action }}

.travis.yml

@@ -5,12 +5,8 @@ env:
     - secure: 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
 matrix:
   include:
-    - python: 2.7
-      env: TOX_ENV=py27-lint
     - python: 3.5
       env: TOX_ENV=py35-lint
-    - python: 2.7
-      env: TOX_ENV=py27-lint-readme
     - python: 3.5
       env: TOX_ENV=py35-pytest
       install:
@@ -23,15 +19,6 @@ matrix:
         # Only run if CODACY_PROJECT_TOKEN is defined.
         # This is not the case for pull requests outside of galaxyproject/ephemeris
         - bash -c 'if [[ -v CODACY_PROJECT_TOKEN ]]  ; then  python-codacy-coverage -r coverage.xml; fi'
-
-    - python: 2.7
-      env: TOX_ENV=py27-pytest
-      services:
-      - docker
-    - python: 2.7
-      env: TOX_ENV=py27
-      services:
-        - docker
     - python: 3.5
       env: TOX_ENV=py35
       services:

Makefile

@@ -111,6 +111,7 @@ open-project:
 
 dist: clean
 	$(IN_VENV) python setup.py sdist bdist_egg bdist_wheel
+	$(IN_VENV) twine check dist/*
 	ls -l dist
 
 release-test-artifacts: dist

README.rst

@@ -14,7 +14,7 @@
 .. image:: https://api.codacy.com/project/badge/Grade/e12102174b4e452c871cd2bafedaec60
    :target: https://www.codacy.com/app/galaxyproject/ephemeris?utm_source=github.com&utm_medium=referral&utm_content=galaxyproject/ephemeris&utm_campaign=Badge_Grade
 
-Ephemeris is a small Python library and set of scripts for managing the
+Ephemeris is a small Python 3 library and set of scripts for managing the
 bootstrapping of Galaxy_ plugins - tools, index data, and workflows.
 
 * Free software: Academic Free License version 3.0

dev-requirements.txt

@@ -11,8 +11,6 @@ sphinx-argparse
 sphinx
 CommonMark
 
-# Used to check readme.
-readme
 # Used for code checking.
 pyflakes
 flake8

requirements.txt

@@ -2,6 +2,5 @@ six>=1.9.0
 PyYAML
 bioblend>=0.10.0
 Jinja2
-galaxy-tool-util>=20.5.0.dev1
-galaxy-util>=20.1.0.dev0  # temporarily needed because this is a pre-release and https://github.com/pypa/pip/issues/988
-futures ; python_version < '3'
+galaxy-tool-util>=20.9.1
+galaxy-util>=20.9.0

setup.py

@@ -87,8 +87,10 @@ def get_var(var_name):
         'Topic :: Software Development :: Code Generators',
         'Topic :: Software Development :: Testing',
         'Natural Language :: English',
-        "Programming Language :: Python :: 2",
-        'Programming Language :: Python :: 2.7',
+        "Programming Language :: Python :: 3",
+        'Programming Language :: Python :: 3.6',
+        'Programming Language :: Python :: 3.7',
+        'Programming Language :: Python :: 3.8',
     ],
     test_suite=TEST_DIR,
     tests_require=test_requirements

src/ephemeris/shed_tools.py

@@ -46,6 +46,7 @@
 from bioblend.galaxy.client import ConnectionError
 from bioblend.galaxy.toolshed import ToolShedClient
 from galaxy.tool_util.verify.interactor import (
+    DictClientTestConfig,
     GalaxyInteractorApi,
     verify_tool,
 )
@@ -231,6 +232,7 @@ def test_tools(self,
                    test_user="ephemeris@galaxyproject.org",
                    parallel_tests=1,
                    test_all_versions=False,
+                   client_test_config_path=None,
                    ):
         """Run tool tests for all tools in each repository in supplied tool list or ``self.installed_repositories()``.
         """
@@ -252,6 +254,13 @@ def test_tools(self,
 
         all_test_results = []
         galaxy_interactor = self._get_interactor(test_user, test_user_api_key)
+        if client_test_config_path is not None:
+            with open(client_test_config_path, "r") as f:
+                client_test_config_dict = yaml.full_load(f)
+            client_test_config = DictClientTestConfig(client_test_config_dict.get("tools"))
+        else:
+            client_test_config = None
+
         test_history = galaxy_interactor.new_history()
 
         with ThreadPoolExecutor(max_workers=parallel_tests) as executor:
@@ -265,6 +274,7 @@ def test_tools(self,
                                     tool_test_results=all_test_results,
                                     tests_passed=tests_passed,
                                     test_exceptions=test_exceptions,
+                                    client_test_config=client_test_config,
                                     )
             finally:
                 # Always write report, even if test was cancelled.
@@ -325,25 +335,34 @@ def _test_tool(executor,
                    test_exceptions,
                    log,
                    test_history=None,
+                   client_test_config=None,
                    ):
         if test_history is None:
             test_history = galaxy_interactor.new_history()
         tool_id = tool["id"]
         tool_version = tool["version"]
+        # If given a tool_id with a version suffix, strip it off so we can treat tool_version
+        # correctly at least in client_test_config.
+        if tool_version and tool_id.endswith("/" + tool_version):
+            tool_id = tool_id[:-len("/" + tool_version)]
+
+        label_base = tool_id
+        if tool_version:
+            label_base += "/" + str(tool_version)
         try:
             tool_test_dicts = galaxy_interactor.get_tool_tests(tool_id, tool_version=tool_version)
         except Exception as e:
             if log:
-                log.warning("Fetching test definition for tool '%s' failed", tool_id, exc_info=True)
-            test_exceptions.append((tool_id, e))
+                log.warning("Fetching test definition for tool '%s' failed", label_base, exc_info=True)
+            test_exceptions.append((label_base, e))
             Results = namedtuple("Results", ["tool_test_results", "tests_passed", "test_exceptions"])
             return Results(tool_test_results=tool_test_results,
                            tests_passed=tests_passed,
                            test_exceptions=test_exceptions)
         test_indices = list(range(len(tool_test_dicts)))
 
         for test_index in test_indices:
-            test_id = tool_id + "-" + str(test_index)
+            test_id = label_base + "-" + str(test_index)
 
             def run_test(index, test_id):
 
@@ -360,6 +379,7 @@ def register(job_data):
                     verify_tool(
                         tool_id, galaxy_interactor, test_index=index, tool_version=tool_version,
                         register_job_data=register, quiet=True, test_history=test_history,
+                        client_test_config=client_test_config,
                     )
                     tests_passed.append(test_id)
                     if log:
@@ -606,6 +626,7 @@ def main():
             test_user=args.test_user,
             parallel_tests=args.parallel_tests,
             test_all_versions=args.test_all_versions,
+            client_test_config_path=args.client_test_config,
         )
     else:
         raise NotImplementedError("This point in the code should not be reached. Please contact the developers.")
@@ -623,6 +644,7 @@ def main():
                 test_user_api_key=args.test_user_api_key,
                 test_user=args.test_user,
                 parallel_tests=args.parallel_tests,
+                client_test_config_path=args.client_test_config
             )
 
 

src/ephemeris/shed_tools_args.py

@@ -33,6 +33,7 @@ def parser():
         test_json="tool_test_output.json",
         test_existing=False,
         parallel_tests=1,
+        client_test_config=None,
     )
 
     # SUBPARSERS
@@ -240,5 +241,11 @@ def parser():
              "apply for tools where revisions have not been provided through "
              "the --revisions arg, --tool_file or --tool_yaml."
     )
+    test_command_parser.add_argument(
+        "--client_test_config",
+        dest="client_test_config",
+        help="Annotate expectations about tools in client testing YAML "
+             "configuration file."
+    )
 
     return shed_parser