🚀 deploy toil_example on every new commit (#10)

* 🚀 add logic to deploy toil example
* 🐛 fix git command
* 📝 add credits to generated README
* 🔧 skip example deployment if GH_TOKEN is unset
* 🔧 make sure toil_example starts from scratch
* 🔧 symlink .gitmessage
* 🔧 no need for -f with cookiecutter
* 🐛 force branch and push in example deployment

.gitmessage

@@ -0,0 +1 @@
+{{cookiecutter.project_slug}}/.gitmessage

.travis.yml

@@ -2,28 +2,36 @@ language: python
 
 cache:
   pip: true
-  directories: $TRAVIS_BUILD_DIR/.tox
+  directories: "$TRAVIS_BUILD_DIR/.tox"
 
 install:
   - cd $TRAVIS_BUILD_DIR && pip install -U -r requirements.txt
   - pip install -U tox-travis
 
 matrix:
   include:
-    - python: 2.7
-    - python: 3.6
-      env: SKIP_TOIL_TEST=true
+  - python: 2.7
+    env: DEPLOY_TOIL_EXAMPLE=true
+  - python: 3.6
+    env: SKIP_TOIL_TEST=true
 
 script:
   - pytest -s tests
 
+after_success:
+  - bash $TRAVIS_BUILD_DIR/.travis/deploy_toil_example.sh
+
 deploy:
   provider: pypi
   distributions: sdist bdist_wheel
   user: leukgen
   password:
-    secure: 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
+    secure: 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
   on:
     tags: true
     repo: leukgen/cookiecutter-toil
     branch: master
+
+env:
+  global:
+    secure: uzWd7bdnaSw5q8r7s5iS/OWPJXHGNgM7FuISux+/SlpLU0E7g+boJo9/IlwrnjDirczw9hOHP6ndGussJEjxLTNfSZ5yqO6JmQW3P4yE3N6tByg32WPsLaEvmRx71tDPBWV3kylQC1Wnw8Lc0MIsPnKU1fTWI/LpD+SGzBNGxpEI2telboILmayVOez1v/E/8Uxx2+CjKT30XKKZvKlyflOrP1K8+QrHbu8G075M+/mwLHk4NFfRB0b2GJR6dZyre0+RSHRaK2ibGwXQlYKyx23qjeP++1w2Q3Sbatau8d1KA4jrlPw6Jyv7OEyfInAIMBOW2G59BfJW8jvqtUFrLs9224aeAWSMGub243l3BRMdZEXx8OLltcclDBPgO+W6SeU4Wm4gIS4lInwdNDnkaLpolsd09JUHqX1StEh28FqAt3QmIcW+sq8YWBS9i87VeUrnpzIWVLYby5dhFN15twhuV1oFcPHWVbmiBbPwhIzASadTnU0UPE6j6Y1De78Qe55pvGv9FGVR4T8wytWxIoxSQY/1HBGB6+b1fmKHnY9e+MH+BrFaxpF45k1im1BlzEEG9dDvNk4bQjIWrM6sYkFDrsqLvC1kMyRG83Hz/dJLVXpo/ese8KDZ/4Gmo+kreRqWMC1Kw2nwAXr+U27gg0y6+2i1ys2cxv3lu+M0MxY=

.travis/deploy_toil_example.sh

@@ -0,0 +1,35 @@
+if [ -z "$GH_TOKEN" ]; then
+    echo "No GH token available, skipping toil_example deployment..."
+    exit 0
+fi
+
+DEPLOY_REPO_URL=https://${GH_TOKEN}@github.com/leukgen/toil_example.git
+DEPLOY_BASE_DIR=/tmp/toil_example_deploy
+DEPLOY_TEMP_DIR=/tmp/toil_example_deploy/_toil_example
+DEPLOY_REPO_DIR=/tmp/toil_example_deploy/toil_example
+DEPLOY_REPO_BRA=${TRAVIS_PULL_REQUEST_BRANCH:="$TRAVIS_BRANCH"}
+
+git config --global user.email "travis@travis-ci.org"
+git config --global user.name "Travis CI"
+
+if [ "$DEPLOY_TOIL_EXAMPLE" = "true" ]; then
+    mkdir $DEPLOY_BASE_DIR && cd $DEPLOY_BASE_DIR
+    git clone $DEPLOY_REPO_URL $DEPLOY_REPO_DIR
+
+    echo "checking out to current branch: $DEPLOY_REPO_BRA"
+    cd $DEPLOY_REPO_DIR && git checkout -B $DEPLOY_REPO_BRA
+
+    echo "force creating cookiecutter..."
+    cd $DEPLOY_BASE_DIR && mv $DEPLOY_REPO_DIR $DEPLOY_TEMP_DIR
+    cookiecutter $TRAVIS_BUILD_DIR --no-input -o $DEPLOY_BASE_DIR
+
+    echo "moving back .git directory to repo..."
+    mv $DEPLOY_TEMP_DIR/.git $DEPLOY_REPO_DIR
+    cd $DEPLOY_REPO_DIR && git add .
+
+    echo "pushing changes: 🤖 travis build $TRAVIS_BUILD_NUMBER..."
+    git commit --message "🤖 travis build $TRAVIS_BUILD_NUMBER"
+    git push -u --force origin $DEPLOY_REPO_BRA
+else
+    echo "DEPLOY_TOIL_EXAMPLE not set to true, skipping..."
+fi

README.md

@@ -9,6 +9,12 @@ A [cookiecutter] for the creation of [toil] and [click] Command Line Interfaces
     pip install cookiecutter-toil
     cookiecutter cookiecutter-toil
 
+# Live Example
+
+[![travis badge][example_travis_badge]][example_travis_base]
+[![codecov badge][example_codecov_badge]][example_codecov_base]
+
+Check out [toil_example], this project is updated automatically with every new commit on cookiecutter-toil.
 
 # Features
 
@@ -69,8 +75,9 @@ A [cookiecutter] for the creation of [toil] and [click] Command Line Interfaces
 
 * 🌀   **Continuous Integration**
 
-    [Travis CI] configuration with automatic deployment to `PyPi` with tags on `master`. To encrypt your `PyPi` password replace the field `deploy.password` in the `.travis.yml` configuration file and run:
+    [Travis CI] configuration with automatic deployment to `PyPi` with tags on `master`. To encrypt your `PyPi` password simply run:
 
+        # you need travis (e.g. brew install travis)
         travis encrypt --add deploy.password
 
     Check out this [tutorial][travis_deploy] if you want to learn more about deployment.
@@ -84,6 +91,7 @@ A [cookiecutter] for the creation of [toil] and [click] Command Line Interfaces
 Please see the [CONTRIBUTING.md](CONTRIBUTING.md) in this repository!
 
 <!-- References -->
+[toil_example]: https://github.com/leukgen/toil_example
 [`VERSION`]: https://packaging.python.org/guides/single-sourcing-package-version/
 [click]: http://click.pocoo.org/6/
 [covenant]: http://contributor-covenant.org/version/1/4/
@@ -107,3 +115,9 @@ Please see the [CONTRIBUTING.md](CONTRIBUTING.md) in this repository!
 [pyup_base]: https://pyup.io/repos/github/leukgen/cookiecutter-toil/
 [travis_badge]: https://img.shields.io/travis/leukgen/cookiecutter-toil.svg
 [travis_base]: https://travis-ci.org/leukgen/cookiecutter-toil
+
+<!-- toil example badges -->
+[example_codecov_badge]: https://codecov.io/gh/leukgen/toil_example/branch/master/graph/badge.svg
+[example_codecov_base]: https://codecov.io/gh/leukgen/toil_example
+[example_travis_badge]: https://img.shields.io/travis/leukgen/toil_example.svg
+[example_travis_base]: https://travis-ci.org/leukgen/toil_example

cookiecutter.json

@@ -1,9 +1,9 @@
 {
-    "full_name": "John Smith",
-    "email": "smithj@mskcc.org",
+    "full_name": "Juan S. Medina, Juan E. Arango",
+    "email": "medinaj@mskcc.org",
     "github_account": "leukgen",
     "cli_type": ["toil", "click"],
-    "project_name": "test_project",
+    "project_name": "toil_example",
     "project_slug": "{{ cookiecutter.project_name.lower()|replace(' ', '_')|replace('-', '_') }}",
-    "project_description": "An awesome python package."
+    "project_description": "A Command Line Interface created with [cookiecutter-toil](https://github.com/leukgen/cookiecutter-toil)."
 }

setup.json

@@ -26,5 +26,6 @@
     ],
     "license": "BSD",
     "name": "cookiecutter-toil",
-    "url": "github.com/leukgen/cookiecutter-toil"
+    "long_description": "📘 learn more on `GitHub <https://github.com/leukgen/cookiecutter-toil>`_!",
+    "url": "https://github.com/leukgen/cookiecutter-toil"
 }

setup.py

@@ -3,28 +3,19 @@
 from os.path import join
 from os.path import abspath
 from os.path import dirname
-import io
 import json
 
 from setuptools import find_packages
 from setuptools import setup
 
 
-def read(path, **kwargs):
-    """Return content of a file."""
-    return io.open(path, encoding=kwargs.get("encoding", "utf8")).read()
-
-
 ROOT = abspath(dirname(__file__))
 
 # please put setup keywords in the setup.json to keep this file clean
 with open(join(ROOT, "setup.json"), "r") as f:
     SETUP = json.load(f)
 
 setup(
-    # load description from README
-    long_description=read(join(ROOT, "README.md")),
-
     # the version is only defined in one place
     version="0.1.0",
 

{{cookiecutter.project_slug}}/README.md

@@ -4,23 +4,19 @@
 [![travis badge][travis_badge]][travis_base]
 [![codecov badge][codecov_badge]][codecov_base]
 
-An awesome pipeline called {{cookiecutter.project_slug}}.
+{{cookiecutter.project_description}}
 
 # Features
 
-* 📦   **Installation**
+* 📦   **Easy Installation**
 
-        # local
-        pip install --editable .
-
-        # pypi (if available)
         pip install {{cookiecutter.project_slug}}
 
-* 🍉   **Usage**
+* 🍉   **Usage Documentation**
 
         {{cookiecutter.project_slug}} --help
 
-* 🐳   **Container Usage**
+* 🐳   **Containers Support**
 
     Check our docker hub for {{cookiecutter.project_slug}} images. Alternatively clone this repo and build the image yourself.
 
@@ -44,9 +40,17 @@ An awesome pipeline called {{cookiecutter.project_slug}}.
 
 Contributions are welcome, and they are greatly appreciated, check our [contributing guidelines](CONTROBUTING.md)!
 
+# Credits
+
+This package was created using [Cookiecutter] and the
+[leukgen/cookiecutter-toil] project template.
+
+
 <!-- References -->
 [singularity]: http://singularity.lbl.gov/
 [docker2singularity]: https://github.com/singularityware/docker2singularity
+[cookiecutter]: https://github.com/audreyr/cookiecutter
+[leukgen/cookiecutter-toil]: https://github.com/leukgen/cookiecutter-toil
 
 <!-- Badges -->
 [codecov_badge]: https://codecov.io/gh/{{cookiecutter.github_account}}/{{cookiecutter.project_slug}}/branch/master/graph/badge.svg

{{cookiecutter.project_slug}}/setup.json

@@ -33,10 +33,11 @@
         ]
     },
     "author": "{{cookiecutter.full_name}}",
-    "description": "{{cookiecutter.project_description}}",
     "keywords": [],
     "license": "BSD",
     "name": "{{cookiecutter.project_slug}}",
     "test_suite": "tests",
+    "long_description": "📘 learn more on `GitHub <https://github.com/{{cookiecutter.github_account}}/{{cookiecutter.project_slug}}>`_!",
+    "description": "{{cookiecutter.project_description}}",
     "url": "https://github.com/{{cookiecutter.github_account}}/{{cookiecutter.project_slug}}"
 }

{{cookiecutter.project_slug}}/setup.py

@@ -3,34 +3,28 @@
 from os.path import join
 from os.path import abspath
 from os.path import dirname
-import io
 import json
 
 from setuptools import find_packages
 from setuptools import setup
 
-
-def read(path, **kwargs):
-    """Return content of a file."""
-    return io.open(path, encoding=kwargs.get("encoding", "utf8")).read()
-
-
 ROOT = abspath(dirname(__file__))
 
 # please put setup keywords in the setup.json to keep this file clean
 with open(join(ROOT, "setup.json"), "r") as f:
     SETUP = json.load(f)
 
-setup(
-    # load description from README
-    long_description=read(join(ROOT, "README.md")),
+# see 4 > https://packaging.python.org/guides/single-sourcing-package-version/
+with open(join(ROOT, "{{cookiecutter.project_slug}}", "VERSION"), "r") as f:
+    VERSION = f.read().strip()
 
-    # the version is only defined in one place
-    version=read(join(ROOT, "{{cookiecutter.project_slug}}", "VERSION")).strip(),
+setup(
+    # single source package version
+    version=VERSION,
 
     # in combination with recursive-includes in MANIFEST.in, non-python files
-    # included inside the {{cookiecutter.project_slug}} will be copied to the
-    # site-packages installation directory
+    # within the {{cookiecutter.project_slug}} will be copied into the
+    # site-packages and wheels installation directories
     include_package_data=True,
 
     # return a list all Python packages found within the ROOT directory

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

@@ -48,8 +48,8 @@ def run(self, fileStore):
 
 def run_toil(options):
     """Toil implementation for {{cookiecutter.project_slug}}."""
-    head = Hello(cores=4, memory="12G", options=options)
-    child = HelloMessage(cores=4, memory="12G", options=options)
+    head = Hello(cores=1, memory="1G", options=options)
+    child = HelloMessage(cores=1, memory="1G", options=options)
     head.addChild(child)
     ContainerCallJob.Runner.startToil(head, options)