Merge pull request #976 from mvdbeek/gh_workflow

Implement github workflow and fix profile commands if psql unavailable

Author: jmchilton

.github/workflows/ci.yaml

@@ -0,0 +1,38 @@
+name: Python CI
+on: [push, pull_request]
+env:
+  PLANEMO_SKIP_REDUNDANT_TESTS: 1
+  PLANEMO_ENABLE_POSTGRES_TESTS: 1
+  PLANEMO_SKIP_GALAXY_CWL_TESTS: 1
+  PLANEMO_TEST_WORKFLOW_RUN_PROFILE: 1
+jobs:
+  test:
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: [2.7, 3.7]
+        tox-action:
+          - lint
+          - lint_readme
+          - lint_docs
+          - quick
+          - unit
+    steps:
+    - uses: actions/checkout@v1
+      with:
+        fetch-depth: 1
+        submodules: true
+    - uses: actions/setup-python@v1
+      with:
+        python-version: ${{ matrix.python-version }}
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install tox coveralls
+    - name: Test with tox
+      run: |
+        export TOXENV=$(echo $TOXENV | sed 's/\.//') && tox
+      env:
+        TOXENV: py${{ matrix.python-version }}-${{ matrix.tox-action }}
+

.travis.yml

@@ -1,38 +1,12 @@
 language: python
-env:
-  global:
-    - PLANEMO_SKIP_REDUNDANT_TESTS=1
-    - PLANEMO_ENABLE_POSTGRES_TESTS=1
-    - PLANEMO_SKIP_GALAXY_CWL_TESTS=1
-    - PLANEMO_TEST_WORKFLOW_RUN_PROFILE=travisworkflowtests
 matrix:
   include:
-    - python: 2.7
-      env: TOX_ENV=py27-lint
-    - python: 3.7
-      env: TOX_ENV=py37-lint_readme
-    - python: 3.7
-      env: TOX_ENV=py37-lint_docs
     - python: 3.7
       env: TOX_ENV=py37-lint_docstrings
-    - python: 3.7
-      env: TOX_ENV=py37-lint
-    - python: 3.7
-      env: TOX_ENV=py37-quick
-    - python: 2.7
-      env: TOX_ENV=py27-unit
-    - python: 3.7
-      env: TOX_ENV=py37-unit
   allow_failures:
     - env: TOX_ENV=py37-lint_docstrings
 
 install:
-  - pip install tox coveralls
+  - pip install tox
 
 script: tox -e $TOX_ENV
-
-after_success:
-  - coveralls
-
-services:
-  - postgresql

planemo/commands/cmd_database_create.py

@@ -10,7 +10,8 @@
 
 @click.command('database_create')
 @options.database_identifier_argument()
-@options.database_source_options()
+@options.profile_database_options()
+@options.docker_config_options()
 @command_function
 def cli(ctx, identifier, **kwds):
     """Create a *development* database.

planemo/commands/cmd_database_delete.py

@@ -9,7 +9,8 @@
 
 @click.command('database_delete')
 @options.database_identifier_argument()
-@options.database_source_options()
+@options.profile_database_options()
+@options.docker_config_options()
 @command_function
 def cli(ctx, identifier, **kwds):
     """Delete a *development* database.

planemo/commands/cmd_database_list.py

@@ -9,7 +9,8 @@
 
 
 @click.command('database_create')
-@options.database_source_options()
+@options.profile_database_options()
+@options.docker_config_options()
 @command_function
 def cli(ctx, **kwds):
     """List databases in configured database source.

planemo/commands/cmd_profile_delete.py

@@ -11,6 +11,7 @@
 @click.command('profile_delete')
 @options.profile_name_argument()
 @options.profile_database_options()
+@options.docker_config_options()
 @command_function
 def cli(ctx, profile_name, **kwds):
     """Delete a profile."""

planemo/database/postgres_docker.py

@@ -4,6 +4,7 @@
 from galaxy.tools.deps import docker_util
 from galaxy.tools.deps import dockerfiles
 from galaxy.tools.deps.commands import execute
+from galaxy.util import unicodify
 
 from .interface import DatabaseSource
 from .postgres import _CommandBuilder, ExecutesPostgresSqlMixin
@@ -23,7 +24,7 @@ def docker_exec(name, commands=[], **kwds):
 
 def is_running_container(name=DEFAULT_CONTAINER_NAME, **kwds):
     ps_command = docker_ps(["--format", "{{.Names}}"], **kwds)
-    running_containers = execute(ps_command)
+    running_containers = unicodify(execute(ps_command))
     containers = running_containers.splitlines()
     return name in containers
 
@@ -37,6 +38,15 @@ def start_postgres_docker(name=DEFAULT_CONTAINER_NAME, password=DEFAULT_POSTGRES
     execute(run_command)
 
 
+def stop_postgres_docker(name=DEFAULT_CONTAINER_NAME, **kwds):
+    stop_command = docker_util.command_list(
+        "stop",
+        [name],
+        **kwds
+    )
+    execute(stop_command)
+
+
 class DockerPostgresDatabaseSource(ExecutesPostgresSqlMixin, DatabaseSource):
     """Postgres database running inside a Docker container."""
 

tests/test_cmd_serve.py

@@ -121,6 +121,7 @@ def test_serve_profile(self):
 
     @skip_if_environ("PLANEMO_SKIP_GALAXY_TESTS")
     @skip_unless_environ("PLANEMO_ENABLE_POSTGRES_TESTS")
+    @skip_unless_executable("psql")
     def test_serve_postgres_profile(self):
         self._test_serve_profile("--database_type", "postgres")
 

tests/test_database_commands.py

@@ -1,19 +1,33 @@
+from planemo.database.postgres_docker import stop_postgres_docker
 from .test_utils import (
     CliTestCase,
     skip_unless_environ,
+    skip_unless_executable,
 )
 
 
 class DatabaseCommandsTestCase(CliTestCase):
 
     @skip_unless_environ("PLANEMO_ENABLE_POSTGRES_TESTS")
-    def test_database_commands(self):
+    def _database_commands(self, database_type="postgres"):
         with self._isolate():
             result = self._check_exit_code(["database_list"])
             assert "test1234" not in result.output
-            self._check_exit_code(["database_create", "test1234"])
+            self._check_exit_code(["database_create", "test1234", "--database_type", database_type])
             result = self._check_exit_code(["database_list"])
             assert "test1234" in result.output
             self._check_exit_code(["database_delete", "test1234"])
             result = self._check_exit_code(["database_list"])
             assert "test1234" not in result.output
+
+    @skip_unless_environ("PLANEMO_ENABLE_POSTGRES_TESTS")
+    @skip_unless_executable("psql")
+    def test_database_commands(self):
+        self._database_commands()
+
+    @skip_unless_executable("docker")
+    def test_database_commands_docker(self):
+        try:
+            self._database_commands(database_type="postgres_docker")
+        finally:
+            stop_postgres_docker()

tests/test_profile_commands.py

@@ -1,19 +1,32 @@
+from planemo.database.postgres_docker import stop_postgres_docker
 from .test_utils import (
     CliTestCase,
     skip_unless_environ,
+    skip_unless_executable
 )
 
 
 class ProfileCommandsTestCase(CliTestCase):
 
-    @skip_unless_environ("PLANEMO_ENABLE_POSTGRES_TESTS")
-    def test_profile_commands(self):
+    def _profile_commands(self, database_type="postgresql"):
         with self._isolate():
             result = self._check_exit_code(["profile_list"])
             assert "profile1234" not in result.output
-            self._check_exit_code(["profile_create", "profile1234"])
+            self._check_exit_code(["profile_create", "profile1234", "--database_type", database_type])
             result = self._check_exit_code(["profile_list"])
             assert "profile1234" in result.output
             self._check_exit_code(["profile_delete", "profile1234"])
             result = self._check_exit_code(["profile_list"])
             assert "profile1234" not in result.output, result.output
+
+    @skip_unless_environ("PLANEMO_ENABLE_POSTGRES_TESTS")
+    @skip_unless_executable("psql")
+    def test_profile_commands(self):
+        self._profile_commands()
+
+    @skip_unless_executable("docker")
+    def test_profile_commands_docker(self):
+        try:
+            self._profile_commands(database_type="postgres_docker")
+        finally:
+            stop_postgres_docker()