Implement script to test library against actual tool tests.

Script installs planemo into a virtualenv, setups "a Galaxy package" around a new virtualenv for this library, clones tools-devteam, and runs planemo test against fastq tools and the ad-hoc Galaxy package.

This script may be executed with "make tool-tests" or using the tox environment "tool-tests".

Author: jmchilton

.travis.yml

@@ -8,6 +8,7 @@ env:
   - TOX_ENV=py27
   - TOX_ENV=py34
   - TOX_ENV=py27-lint-docstrings
+  - TOX_ENV=tool-tests
 
 install:
   # Setup git to allow git operations.

Makefile

@@ -70,7 +70,10 @@ lint-readme: ## check README formatting for PyPI
 test: ## run tests with the default Python (faster than tox)
 	$(IN_VENV) nosetests $(NOSE_TESTS)
 
-tox:
+tool-tests: ## Run tools-devteam tool tests against library in current state
+	bash tests/planemo_test.bash
+
+tox: ## run tests with tox in the specified ENV, defaults to py27
 	$(IN_VENV) tox -e $(ENV) -- $(ARGS)
 
 _coverage-report: ## build coverage report with the default Python

tests/planemo_test.bash

@@ -0,0 +1,57 @@
+#!/bin/bash
+
+set -e
+
+shopt -s nullglob
+
+# This directory.
+SCRIPT_DIR="$( cd "$(dirname "$0")" ; pwd )"
+
+# Planemo to install for test.
+PLANEMO_INSTALL_TARGET="${PLANEMO_INSTALL_TARGET:-planemo==0.37.0}"
+
+# By default use pyton setup.py install to install the library.
+SETUP_COMMAND="${SETUP_COMMAND:-install}"
+
+TOOLS_DEVTEAM="${TOOLS_DEVTEAM:-}"
+
+# Initialize a temp directory for testing.
+TEMP_DIR=`mktemp -d`
+echo "Setting up test directory $TEMP_DIR"
+cd "$TEMP_DIR"
+
+PLANEMO_VIRTUAL_ENV="${PLANEMO_VIRTUAL_ENV:-$TEMP_DIR/planemo-venv}"
+virtualenv "$PLANEMO_VIRTUAL_ENV"
+. "$PLANEMO_VIRTUAL_ENV/bin/activate"
+pip install "$PLANEMO_INSTALL_TARGET"
+deactivate
+
+ENV_DIR="$TEMP_DIR/dependencies/galaxy_sequence_utils/dev"
+mkdir -p "$ENV_DIR"
+cat "$SCRIPT_DIR/planemo_test_env.sh" | sed -e "s#_temp_dir_#/$TEMP_DIR#" > "$ENV_DIR/env.sh"
+ln -s dev "$TEMP_DIR/dependencies/galaxy_sequence_utils/default"
+
+virtualenv "$ENV_DIR/venv"
+. "$ENV_DIR/venv/bin/activate"
+
+cd $SCRIPT_DIR/..
+python setup.py "$SETUP_COMMAND"
+
+## TODO: Add option to test a wheel instead.
+# pip install $SCRIPT_DIR/../dist/*whl
+
+cat "$SCRIPT_DIR/planemo_test_dependency_resolvers_conf_template.xml" | sed -e "s#_temp_dir_#$TEMP_DIR#" > "$TEMP_DIR/dependency_resolvers_conf.xml"
+
+
+. "$PLANEMO_VIRTUAL_ENV/bin/activate"
+
+if [ -z "$TOOLS_DEVTEAM" ];
+then
+    TOOLS_DEVTEAM="$TEMP_DIR/tools-devteam"
+    git clone https://github.com/galaxyproject/tools-devteam.git "$TOOLS_DEVTEAM"
+fi
+
+for tool_dir in tools/fastq_trimmer_by_quality tool_collections/galaxy_sequence_utils/fastq_combiner
+do
+    planemo test --dependency_resolvers_config_file "$TEMP_DIR/dependency_resolvers_conf.xml" "$TOOLS_DEVTEAM/$tool_dir"
+done

tests/planemo_test_dependency_resolvers_conf_template.xml

@@ -0,0 +1,3 @@
+<dependency_resolvers>
+  <galaxy_packages versionless="true" base_path="_temp_dir_/dependencies" />
+</dependency_resolvers>

tests/planemo_test_env.sh

@@ -0,0 +1,3 @@
+#!/bin/bash
+
+. "_temp_dir_/dependencies/galaxy_sequence_utils/dev/venv/bin/activate"

tox.ini

@@ -1,6 +1,6 @@
 # TODO: implement doc linting
 [tox]
-envlist = py34-lint, py27-lint, py27-lint-readme, py27, py34, py27-lint-docstring, py27-lint-docstring-include-list
+envlist = py34-lint, py27-lint, py27-lint-readme, py27, py34, py27-lint-docstring, py27-lint-docstring-include-list, tool-tests
 source_dir = galaxy_utils
 test_dir = tests
 
@@ -36,3 +36,8 @@ skip_install = True
 deps =
     flake8
     flake8-docstrings
+
+[testenv:tool-tests]
+commands = make tool-tests
+whitelist_externals = bash
+skip_install = True