Merge pull request #38 from pysat/flake8

TST: Add pytest-flake8 to travis tests

.travis.yml

@@ -14,6 +14,7 @@ addons:
 
 before_install:
   - pip install pytest-cov
+  - pip install pytest-flake8
   - pip install coveralls
   - pip install future
   - pip install numpy
@@ -41,7 +42,7 @@ install:
   - python setup.py install
 
 script:
-  - pytest -vs --cov=pysatModels/
+  - pytest -vs --cov=pysatModels/  --flake8
 
 after_success:
   - coveralls

CONTRIBUTING.md

@@ -2,18 +2,20 @@ Contributing
 ============
 
 Bug reports, feature suggestions and other contributions are greatly
-appreciated!  pysatModels is a community-driven project and welcomes both feedback and contributions.
+appreciated!  pysatModels is a community-driven project and welcomes both
+feedback and contributions.
 
 Short version
 =============
 
-* Submit bug reports and feature requests at `GitHub <https://github.com/pysat/pysatModels/issues>`_
+* Submit bug reports and feature requests at
+  [GitHub Issues](https://github.com/pysat/pysatModels/issues)
 * Make pull requests to the ``develop`` branch
 
 Bug reports
 ===========
 
-When `reporting a bug <https://github.com/pysat/pysatModels/issues>`_ please
+When [reporting a bug](https://github.com/pysat/pysatModels/issues) please
 include:
 
 * Your operating system name and version
@@ -24,7 +26,7 @@ Feature requests and feedback
 =============================
 
 The best way to send feedback is to file an issue at
-`GitHub <https://github.com/pysat/pysatModels/issues>`_.
+[GitHub Issues](https://github.com/pysat/pysatModels/issues).
 
 If you are proposing a feature:
 
@@ -38,40 +40,48 @@ Development
 
 To set up `pysatModels` for local development:
 
-1. `Fork pysat on GitHub <https://github.com/pysat/pysatModels/fork>`_.
+1. Fork pysat on [GitHub](https://github.com/pysat/pysatModels/fork).
 2. Clone your fork locally::
 
 
-    git clone [email protected]:your_name_here/pysatModels.git
+       git clone [email protected]:your_name_here/pysatModels.git
 
 3. Create a branch for local development::
 
 
-    git checkout -b name-of-your-bugfix-or-feature
+       git checkout -b name-of-your-bugfix-or-feature
 
    Now you can make your changes locally. Tests for new instruments are
    performed automatically.  Tests for custom functions should be added to the
-   appropriately named file in ``pysatModels/tests``.  For example, the averaging routines in avg.py are tested in ``pysatModels/tests/test_avg.py``.  If no
-   test file exists, then you should create one.  This testing uses pytest, which
-   will run tests on any python file in the test directory that starts with
-   ``test_``.
+   appropriately named file in ``pysatModels/tests``.  For example, the
+   averaging routines in avg.py are tested in
+   ``pysatModels/tests/test_avg.py``.  If no test file exists, then you should
+   create one.  This testing uses pytest, which will run tests on any python
+   file in the test directory that starts with ``test_``.
 
-4. When you're done making changes, run all the checks to ensure that nothing
-   is broken on your local system::
+4. When you're done making changes, run all the checks from the
+   ``pysatModels/tests`` directory to ensure that nothing is broken on your
+   local system.  You may need to install
+   [pytest](https://docs.pytest.org/en/latest/) and
+   [pytest-flake8](https://pypi.org/project/pytest-flake8/) first. ::
 
 
-    pytest -vs
+       python -m pytest -vs --flake8
 
-5. Update/add documentation (in ``docs``), if relevant
+5. Update or add documentation (in ``docs``), if relevant.  If you have added
+   a new routine, you will need to add an example in the ``docs/examples``
+   folder.
 
-5. Commit your changes and push your branch to GitHub::
+6. Commit your changes and push your branch to GitHub.  Our commit statements
+   follow the basic rules in the
+   [Numpy/SciPy workflow](https://docs.scipy.org/doc/numpy-1.15.1/dev/gitwash/development_workflow.html)::
 
 
-    git add .
-    git commit -m "Brief description of your changes"
-    git push origin name-of-your-bugfix-or-feature
+       git add .
+       git commit -m "TYPE: Brief description of your changes"
+       git push origin name-of-your-bugfix-or-feature
 
-6. Submit a pull request through the GitHub website. Pull requests should be
+7. Submit a pull request through the GitHub website. Pull requests should be
    made to the ``develop`` branch.
 
 Pull Request Guidelines
@@ -85,10 +95,10 @@ For merging, you should:
 1. Include an example for use
 2. Add a note to ``CHANGELOG.md`` about the changes
 3. Ensure that all checks passed (current checks include Scrutinizer, Travis-CI,
-   and Coveralls) [1]_
+   and Coveralls).
 
-.. [1] If you don't have all the necessary Python versions available locally or
-       have trouble building all the testing environments, you can rely on
-       Travis to run the tests for each change you add in the pull request.
-       Because testing here will delay tests by other developers, please ensure
-       that the code passes all tests on your local system first.
+   If you don't have all the necessary Python versions available locally or
+   have trouble building all the testing environments, you can rely on
+   Travis to run the tests for each change you add in the pull request.
+   Because testing here will delay tests by other developers, please ensure
+   that the code passes all tests on your local system first.

pysatModels/__init__.py

@@ -5,7 +5,7 @@
 # -----------------------------------------------------------------------------
 """
 pysatModels
-===============
+===========
 
 Model utilities designed to facilitate studies that integrate observational
 and modelled data sets.
@@ -18,8 +18,9 @@
 import logging
 import os
 
-from pysatModels import (utils)
-from pysatModels import (models)
+# Import key modules and skip F401 testing in flake8
+from pysatModels import (utils)  # noqa: F401
+from pysatModels import (models)  # noqa: F401
 
 # set the version
 here = os.path.abspath(os.path.dirname(__file__))

pysatModels/models/__init__.py

@@ -14,4 +14,5 @@
 from __future__ import absolute_import
 from __future__ import unicode_literals
 
-from pysatModels.models import ucar_tiegcm
+# Import key modules and skip F401 testing in flake8
+from pysatModels.models import ucar_tiegcm  # noqa: F401

pysatModels/tests/test_utils_extract.py

@@ -87,7 +87,8 @@ def test_bad_arg_input(self, bad_index, bad_input, err_msg):
                                "interpn only understands the methods"),
                               ("model_label", 1, "Unknown format code "),
                               ("time_method", "fun", "unknown time method"),
-                              ("pair_method", "fun", "unknown pairing method")])
+                              ("pair_method", "fun",
+                               "unknown pairing method")])
     def test_bad_kwarg_input(self, bad_key, bad_val, err_msg):
         """ Test for expected failure with bad kwarg input """
         kwargs = {bad_key: bad_val}

pysatModels/tests/test_utils_match.py

@@ -8,7 +8,6 @@
 
 import pysat
 
-import pysatModels as ps_mod
 import pysatModels.utils.match as match
 
 
@@ -77,12 +76,16 @@ def teardown(self):
         del self.input_args, self.required_kwargs, self.inst, self.model
 
     @pytest.mark.parametrize("del_key,err_msg",
-                             [("inst_lon_name", "Need longitude name for inst"),
-                              ("mod_lon_name", "Need longitude name for model"),
-                              ("inst_name", "Must provide instrument location"),
+                             [("inst_lon_name",
+                               "Need longitude name for inst"),
+                              ("mod_lon_name",
+                               "Need longitude name for model"),
+                              ("inst_name",
+                               "Must provide instrument location"),
                               ("mod_name", "Must provide the same number"),
                               ("mod_units", "Must provide units for each "),
-                              ("mod_datetime_name", "Need datetime coordinate"),
+                              ("mod_datetime_name",
+                               "Need datetime coordinate"),
                               ("mod_time_name", "Need time coordinate"),
                               ("inst_clean_rout", "Need routine to clean")])
     def test_input_failure(self, del_key, err_msg):

pysatModels/utils/__init__.py

@@ -5,14 +5,15 @@
 # -----------------------------------------------------------------------------
 """
 pysatModels.utils
-=====================
+=================
 
 Utilities designed to extract, match, and compare modelled and observed data
 
 """
 
-from __future__ import absolute_import,  unicode_literals
+from __future__ import absolute_import, unicode_literals
 
-from pysatModels.utils import extract
-from pysatModels.utils import match
-from pysatModels.utils import compare
+# Import key modules and skip F401 testing in flake8
+from pysatModels.utils import extract  # noqa: F401
+from pysatModels.utils import match  # noqa: F401
+from pysatModels.utils import compare  # noqa: F401

pysatModels/utils/compare.py

@@ -116,8 +116,8 @@ def compare_model_and_inst(pairs=None, inst_name=[], mod_name=[],
         raise ValueError('must provide Dataset of paired observations')
 
     if len(inst_name) != len(mod_name):
-        raise ValueError('must provide equal number of instrument and model ' +
-                         'data names for comparison')
+        raise ValueError(''.join(['must provide equal number of instrument ',
+                                  'and model data names for comparison']))
 
     if not np.all([iname in pairs.data_vars.keys() for iname in inst_name]):
         raise ValueError('unknown instrument data value supplied')
@@ -130,9 +130,9 @@ def compare_model_and_inst(pairs=None, inst_name=[], mod_name=[],
         known_methods.extend(list(grouped_methods.keys()))
         unknown_methods = [mm for mm in methods
                            if mm not in list(method_rout.keys())]
-        raise ValueError('unknown statistical method(s) requested:\n' +
-                         '{:}\nuse only:\n{:}'.format(unknown_methods,
-                                                      known_methods))
+        raise ValueError(''.join(['unknown statistical method(s) requested:\n',
+                                  '{:}\nuse only:\n'.format(unknown_methods),
+                                  '{:}'.format(unknown_methods)]))
 
     # Initialize the output
     stat_dict = {iname: dict() for iname in inst_name}
@@ -170,6 +170,6 @@ def compare_model_and_inst(pairs=None, inst_name=[], mod_name=[],
                 # instead of stopping processing.  Only valid statistics will
                 # be included in output
                 ps_mod.logger.info("{:s} can't use {:s}: {:}".format(iname,
-                                                                       mm, err))
+                                                                     mm, err))
 
     return stat_dict, data_units