Added black (#31)

* update dev reqs

* added black

* added black to travis

* update docs

* added pre-commit config

.pre-commit-config.yaml

@@ -0,0 +1,58 @@
+default_language_version:
+    python: python3.8
+
+repos:
+-   repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v2.5.0
+    hooks:
+    -   id: trailing-whitespace
+        language_version: python3
+    -   id: end-of-file-fixer
+        language_version: python3
+    -   id: check-yaml
+        language_version: python3
+    -   id: debug-statements
+        language_version: python3
+-   repo: https://github.com/ambv/black
+    rev: 20.8b1
+    hooks:
+    -   id: black
+        language_version: python3
+        args: ["--target-version", "py38"]
+-   repo: https://github.com/pycqa/flake8
+    rev: 3.8.3
+    hooks:
+    -   id: flake8
+        language_version: python3
+        args: ['--config=setup.cfg']
+#-   repo: https://github.com/pre-commit/mirrors-autopep8
+#    rev: v1.4.4
+#    hooks:
+#    -   id: autopep8
+#        args: ['--global-config=setup.cfg','--in-place']
+# -   repo: https://github.com/timothycrosley/isort
+#     rev: 5.0.7
+#     hooks:
+#     -   id: isort
+#         language_version: python3
+#         args: ['--profile', 'black']
+#-   repo: https://github.com/pycqa/pydocstyle
+#    rev: 5.0.2
+#    hooks:
+#    -   id: pydocstyle
+#        args: ["--conventions=numpy"]
+# -   repo: https://github.com/asottile/pyupgrade
+#     rev: v2.4.1
+#     hooks:
+#     -   id: pyupgrade
+#         language_version: python3
+# -   repo: meta
+#     hooks:
+#     -   id: check-hooks-apply
+#     -   id: check-useless-excludes
+# -   repo: https://github.com/kynan/nbstripout
+#     rev: 0.3.7
+#     hooks:
+#     -   id: nbstripout
+#         language_version: python3
+#         files: ".ipynb"

.travis.yml

@@ -27,6 +27,7 @@ matrix:
       env:
         - CONDA_FN="Miniconda3-latest-Linux-x86_64.sh"
         - PEP8=true
+        - BLACK=true
         - PYTHON_DESIRED=3.8
 
 sudo: false
@@ -47,10 +48,11 @@ install:
   - conda env update -f environment.yml
   - source activate rooki
   # Packages for testing
-  - pip install pytest nbval flake8
+  - pip install pytest nbval flake8 black
   # Install package
   - python setup.py install
 script:
   - make test
   - make test-nb
   - if [[ $PEP8 == true ]]; then flake8 rooki tests; fi
+  - if [[ $BLACK == true ]]; then black --check --target-version py38 rooki tests; fi

docs/source/development.rst

@@ -20,11 +20,12 @@ Install additional dependencies:
 
   $ pip install -r requirements_dev.txt
 
-When you're done making changes, check that your changes pass `flake8` and the tests:
+When you're done making changes, check that your changes pass `black`, `flake8` and the tests:
 
 .. code-block:: console
 
-    $ flake8 rooki
+    $ black rooki tests
+    $ flake8 rooki tests
     $ pytest tests
 
 Or use the Makefile:
@@ -34,6 +35,19 @@ Or use the Makefile:
      $ make lint
      $ make test
 
+
+Add pre-commit hooks
+--------------------
+
+Before committing your changes, we ask that you install `pre-commit` in your environment.
+`Pre-commit` runs git hooks that ensure that your code resembles that of the project
+and catches and corrects any small errors or inconsistencies when you `git commit`:
+
+.. code-block:: console
+
+     $ conda install -c conda-forge pre_commit
+     $ pre-commit install
+
 Write Documentation
 -------------------
 

requirements_dev.txt

@@ -1,4 +1,4 @@
-pip>=18.1
+pip>=20.0
 bumpversion>=0.5.3
 wheel>=0.32.1
 watchdog>=0.9.0
@@ -8,7 +8,8 @@ coverage>=4.5.1
 Sphinx>=1.8.1
 nbsphinx>=0.7.0
 twine>=1.12.1
-
+pre-commit>=2.7.1
+black>=20.0
 pytest>=3.8.2
 pytest-runner>=4.2
 nbval>=0.9.6

rooki/__init__.py

@@ -6,5 +6,5 @@
 
 
 __all__ = [
-    'rooki',
+    "rooki",
 ]

rooki/client.py

@@ -9,10 +9,10 @@
 
 class Rooki(WPSClient):
     def __init__(self, url=None, mode=None, verify=None):
-        self._url = url or config.get_config_value('service', 'url')
-        self._mode = mode or config.get_config_value('service', 'mode')
+        self._url = url or config.get_config_value("service", "url")
+        self._mode = mode or config.get_config_value("service", "mode")
         if verify is None:
-            self._verify = config.get_config_value('service', 'ssl_verify')
+            self._verify = config.get_config_value("service", "ssl_verify")
         else:
             self._verify = verify
         progress = self.mode == ASYNC

rooki/config.py

@@ -3,9 +3,11 @@
 import logging
 
 ROOKI_HOME = os.path.abspath(os.path.dirname(__file__))
-DEFAULT_CFG = os.path.join(ROOKI_HOME, 'default.cfg')
+DEFAULT_CFG = os.path.join(ROOKI_HOME, "default.cfg")
 
-RAW_OPTIONS = [('logging', 'format'), ]
+RAW_OPTIONS = [
+    ("logging", "format"),
+]
 
 CONFIG = None
 LOGGER = logging.getLogger("ROOKI")
@@ -23,7 +25,7 @@ def get_config_value(section, option):
     if not CONFIG:
         load_configuration()
 
-    value = ''
+    value = ""
 
     if CONFIG.has_section(section):
         if CONFIG.has_option(section, option):
@@ -47,32 +49,32 @@ def load_configuration(cfgfiles=None):
     """
     global CONFIG
 
-    LOGGER.info('loading configuration')
+    LOGGER.info("loading configuration")
     CONFIG = configparser.ConfigParser(os.environ)
 
-    LOGGER.debug('setting default values')
-    CONFIG.add_section('service')
-    CONFIG.set('service', 'url', 'http://localhost:5000/wps')
+    LOGGER.debug("setting default values")
+    CONFIG.add_section("service")
+    CONFIG.set("service", "url", "http://localhost:5000/wps")
 
     config_files = _get_default_config_files_location()
     if cfgfiles:
         config_files.extend(cfgfiles)
 
-    if 'ROOKI_CFG' in os.environ:
-        config_files.append(os.environ['ROOKI_CFG'])
+    if "ROOKI_CFG" in os.environ:
+        config_files.append(os.environ["ROOKI_CFG"])
 
     loaded_files = CONFIG.read(config_files)
     if loaded_files:
-        LOGGER.info('Configuration file(s) {} loaded'.format(loaded_files))
+        LOGGER.info("Configuration file(s) {} loaded".format(loaded_files))
     else:
-        LOGGER.info('No configuration files loaded. Using default values')
+        LOGGER.info("No configuration files loaded. Using default values")
     # dirty hack to set rook url on binder
-    if 'ROOK_URL' in os.environ:
-        CONFIG.set('service', 'url', os.environ['ROOK_URL'])
-    if 'ROOK_MODE' in os.environ:
-        CONFIG.set('service', 'mode', os.environ['ROOK_MODE'])
-    if 'ROOK_SSL_VERIFY' in os.environ:
-        CONFIG.set('service', 'ssl_verify', os.environ['ROOK_SSL_VERIFY'])
+    if "ROOK_URL" in os.environ:
+        CONFIG.set("service", "url", os.environ["ROOK_URL"])
+    if "ROOK_MODE" in os.environ:
+        CONFIG.set("service", "mode", os.environ["ROOK_MODE"])
+    if "ROOK_SSL_VERIFY" in os.environ:
+        CONFIG.set("service", "ssl_verify", os.environ["ROOK_SSL_VERIFY"])
 
 
 def _get_default_config_files_location():
@@ -83,8 +85,11 @@ def _get_default_config_files_location():
     :returns: configuration files
     :rtype: list of strings
     """
-    LOGGER.debug('trying to estimate the default location')
-    cfgfiles = [DEFAULT_CFG, "/etc/rooki.cfg", ]
-    if 'HOME' in os.environ:
-        cfgfiles.append(os.path.join(os.environ['HOME'], ".rooki.cfg"))
+    LOGGER.debug("trying to estimate the default location")
+    cfgfiles = [
+        DEFAULT_CFG,
+        "/etc/rooki.cfg",
+    ]
+    if "HOME" in os.environ:
+        cfgfiles.append(os.path.join(os.environ["HOME"], ".rooki.cfg"))
     return cfgfiles

rooki/operators.py

@@ -7,27 +7,26 @@
 
 
 class Operator:
-
     def __init__(self, *args, **kwargs):
         self.args = args
         self.kwargs = kwargs
 
     def _tree(self, tree=defaultdict(dict)):
         # args = [arg._tree(tree) for arg in self.args]
         [arg._tree(tree) for arg in self.args]
-        tree['steps'][self.method_key] = {
-            'run': self.METHOD,
-            'in': {
-                'collection': _unpack_if_single([arg.collection for arg in self.args]),
+        tree["steps"][self.method_key] = {
+            "run": self.METHOD,
+            "in": {
+                "collection": _unpack_if_single([arg.collection for arg in self.args]),
                 **self.kwargs,
-            }
+            },
         }
-        tree['outputs']['output'] = self.collection
+        tree["outputs"]["output"] = self.collection
         return tree
 
-    def _serialise(self, doc='workflow'):
+    def _serialise(self, doc="workflow"):
         tree = self._tree()
-        tree['doc'] = doc
+        tree["doc"] = doc
         return json.dumps(tree)
 
     def orchestrate(self):
@@ -36,7 +35,7 @@ def orchestrate(self):
     @property
     def method_key(self):
         methods = self._get_methods([])
-        return f'{self.METHOD}_{self.variable}_{methods.count(self.METHOD)}'
+        return f"{self.METHOD}_{self.variable}_{methods.count(self.METHOD)}"
 
     def _get_methods(self, methods):
         # method_names = [arg._get_methods(methods) for arg in self.args]
@@ -46,67 +45,66 @@ def _get_methods(self, methods):
 
     @property
     def collection(self):
-        return f'{self.method_key}/output'
+        return f"{self.method_key}/output"
 
     @property
     def variable(self):
         return _unpack_if_single([arg.variable for arg in self.args])
 
 
 class Input:
-
     def __init__(self, variable, dataset):
         self.variable = variable
         self.dataset = dataset
 
-    def _serialise(self, doc='workflow'):
+    def _serialise(self, doc="workflow"):
         tree = self._tree()
-        tree['doc'] = doc
+        tree["doc"] = doc
         return json.dumps(tree)
 
     def orchestrate(self):
         return rooki.orchestrate(workflow=self._serialise())
 
     def _tree(self, tree=defaultdict(dict)):
-        tree['inputs'][self.variable] = self.dataset
+        tree["inputs"][self.variable] = self.dataset
         return tree
 
     def _get_methods(self, methods):
         return methods
 
     @property
     def collection(self):
-        return f'inputs/{self.variable}'
+        return f"inputs/{self.variable}"
 
 
 class Average(Operator):
-    METHOD = 'average'
+    METHOD = "average"
 
 
 class Subset(Operator):
-    METHOD = 'subset'
+    METHOD = "subset"
 
 
 class Diff(Operator):
-    METHOD = 'diff'
+    METHOD = "diff"
 
     def _tree(self, tree=defaultdict(dict)):
         # args = [arg._tree(tree) for arg in self.args]
         [arg._tree(tree) for arg in self.args]
-        tree['steps'][self.method_key] = {
-            'run': self.METHOD,
-            'in': {
-                'collection_a': _unpack_if_single([self.args[0].collection]),
-                'collection_b': _unpack_if_single([self.args[1].collection]),
+        tree["steps"][self.method_key] = {
+            "run": self.METHOD,
+            "in": {
+                "collection_a": _unpack_if_single([self.args[0].collection]),
+                "collection_b": _unpack_if_single([self.args[1].collection]),
                 **self.kwargs,
-            }
+            },
         }
-        tree['outputs']['output'] = self.collection
+        tree["outputs"]["output"] = self.collection
         return tree
 
     @property
     def variable(self):
-        return 'var'
+        return "var"
 
 
 def _unpack_if_single(list):