🐛fix pypi deployment (#16)

* 🐛 fix pypi deployment
* 🎨 minor style change
* ✅ update toil_container version

.travis.yml

@@ -10,7 +10,7 @@ install:
 matrix:
   include:
   - python: 2.7
-    env: DEPLOY_TOIL_EXAMPLE=true DEPLOY_PYPI=true
+    env: DEPLOY_TOIL_EXAMPLE=true
   - python: 3.6
     env: SKIP_TOIL_TEST=true
 
@@ -30,7 +30,7 @@ deploy:
     tags: true
     repo: leukgen/cookiecutter-toil
     branch: master
-    condition: $DEPLOY_PYPI = true
+    python: 2.7
 
 env:
   global:

setup.json

@@ -26,6 +26,7 @@
     ],
     "license": "BSD",
     "name": "cookiecutter-toil",
+    "description": "🍪 A cookiecutter for the creation of toil pipelines.",
     "long_description": "📘 learn more on `GitHub <https://github.com/leukgen/cookiecutter-toil>`_!",
     "url": "https://github.com/leukgen/cookiecutter-toil"
 }

{{cookiecutter.project_slug}}/.coveragerc

@@ -1,7 +1,7 @@
 [paths]
 source =
    {{cookiecutter.project_slug}}
-   /test/{{cookiecutter.project_slug}}
+   */{{cookiecutter.project_slug}}
 
 [run]
 source =

{{cookiecutter.project_slug}}/.isort.cfg

@@ -3,4 +3,4 @@ force_single_line=true
 from_first=true
 known_future_library=future,pies
 known_standard_library=std,std2
-known_third_party=click,pandas,numpy,toil
+known_third_party=click,pandas,numpy,toil,toil_container

{{cookiecutter.project_slug}}/.travis.yml

@@ -1,7 +1,7 @@
 language: python
 
 python:
-  - 3.6
+  - {% if cookiecutter.cli_type == 'toil' %}2.7{% else %}3.6{% endif %}
 
 services:
   - docker

{{cookiecutter.project_slug}}/Dockerfile

@@ -1,4 +1,4 @@
-FROM {% if cookiecutter.cli_type == "toil" %} python:2.7-jessie {% elif cookiecutter.cli_type == "click" %} python:3.6-jessie {% endif %}
+FROM {% if cookiecutter.cli_type == "toil" %}python:2.7-jessie{% elif cookiecutter.cli_type == "click" %}python:3.6-jessie{% endif %}
 
 RUN \
     # install packages dependencies

{{cookiecutter.project_slug}}/setup.json

@@ -20,14 +20,15 @@
     "install_requires": [
         "Click>=6.7",
         "docker==2.5.1"{% if cookiecutter.cli_type == 'toil' %},
-        "toil_container>=0.2.3"{% endif %}
+        "toil_container>=0.2.4"{% endif %}
     ],
     "extras_require": {
         "test": [
             "coverage>=4.4.2",
             "pydocstyle>=2.1.1",
             "pytest-cov>=2.5.1",
             "pytest-env==0.6.2",
+            "pytest-sugar>=0.9.1",
             "pylint>=1.8.1",
             "tox==2.9.1"
         ]

{{cookiecutter.project_slug}}/test-container.sh

@@ -6,11 +6,13 @@ echo "testing container..."
 # make sure current dir is repo dir
 cd $( dirname "${BASH_SOURCE[0]}" )
 
+TEST_IMAGE="{{cookiecutter.project_slug}}_test_image"
+
 if [ "$1" = "--skip-build" ]; then
     echo "skipping build..."
 else
     echo "building image, to skip run with --skip-build..."
-    docker build -q -t test-image .
+    docker build -q -t $TEST_IMAGE .
 fi
 
 # see https://explainshell.com/explain?cmd=set+-euxo%20pipefail
@@ -20,9 +22,11 @@ set -euxo pipefail
 echo "testing docker image..."
 find . -name '*.pyc' -exec rm {} +
 find . -name '__pycache__' -exec rm -rf {} +
-docker run --rm test-image --version
+
+# run tox inside the container
+docker run --rm $TEST_IMAGE --version
 docker run --rm --entrypoint "" -v `pwd`:/test -w /test \
-    test-image bash -c "cp -r /test /tmp && cd /tmp/test/ && pip install tox && tox && cp .coverage /test"
+    $TEST_IMAGE bash -c "cp -r /test /{{cookiecutter.project_slug}} && cd /{{cookiecutter.project_slug}} && pip install tox && tox && cp .coverage /test"
 
 # move container coverage paths to local, see .coveragerc [paths] and this comment:
 # https://github.com/pytest-dev/pytest-cov/issues/146#issuecomment-272971136

{{cookiecutter.project_slug}}/{{cookiecutter.project_slug}}/commands.py

@@ -33,22 +33,14 @@ def run(self, fileStore):
         fileStore.logToMaster(output)
 
 
-def run_toil(options):
-    """Toil implementation for {{cookiecutter.project_slug}}."""
-    head = Hello(cores=1, memory="1G", options=options)
-    child = HelloMessage(cores=1, memory="1G", options=options)
-    head.addChild(child)
-    ContainerJob.Runner.startToil(head, options)
-
-
 def get_parser():
     """Get pipeline configuration using toil's."""
     parser = ContainerArgumentParser(
         version=__version__,
-        description="{{cookiecutter.project_slug}} pipeline",
+        description="A hello world toil pipeline.",
         )
 
-    settings = parser.add_argument_group("{{cookiecutter.project_slug}} arguments")
+    settings = parser.add_argument_group("pipeline arguments")
 
     settings.add_argument(
         "--message",
@@ -79,6 +71,14 @@ def process_parsed_options(options):
     return options
 
 
+def run_toil(options):
+    """Run toil pipeline give an options namespace."""
+    head = Hello(cores=1, memory="1G", options=options)
+    child = HelloMessage(cores=1, memory="1G", options=options)
+    head.addChild(child)
+    ContainerJob.Runner.startToil(head, options)
+
+
 def main():
     """
     Parse options and run toil.