Add pre-commit hooks with black code formatting (ARM-DOE#419)

* use black for formatting

* add pre-commit to deps

* add pre-commit to dev req

* update contributing docs

.pre-commit-config.yaml

@@ -0,0 +1,35 @@
+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.1.0
+    hooks:
+      - id: trailing-whitespace
+      - id: end-of-file-fixer
+      - id: check-docstring-first
+      - id: check-json
+      - id: check-yaml
+      - id: double-quote-string-fixer
+      - id: debug-statements
+      - id: mixed-line-ending
+
+  - repo: https://github.com/asottile/pyupgrade
+    rev: v2.31.0
+    hooks:
+      - id: pyupgrade
+        args:
+          - '--py38-plus'
+
+  - repo: https://github.com/psf/black
+    rev: 22.1.0
+    hooks:
+      - id: black
+      - id: black-jupyter
+
+  - repo: https://github.com/PyCQA/flake8
+    rev: 4.0.1
+    hooks:
+      - id: flake8
+
+  - repo: https://github.com/PyCQA/isort
+    rev: 5.10.1
+    hooks:
+      - id: isort

CONTRIBUTING.rst

@@ -66,8 +66,7 @@ to `act`.
 
 4. Create or modified code so that it produces doc string and follows standards.
 
-5. PEP8 check using `flake8 <https://pypi.org/project/flake8/>`_.  The command we 
-   use in testing is flake8 --max-line-length=115 --ignore=F401,E402,W504,W605
+5. Install your `pre-commit <https://pre-commit.com>` hooks, by using `pre-commit install`
 
 6. Local unit testing using Pytest.
 
@@ -129,7 +128,7 @@ To delete a branch both locally and remotely, if done with it::
                 git branch -d <branch_name>
 
 or in this case::
-                
+
                 git push origin --delete wind_rose_plot
                 git branch -d wind_rose_plot
 
@@ -176,13 +175,13 @@ For example:
 
 .. code-block:: python
 
-        import glob
-        import os
-         
-        import numpy as np
-        import numpy.ma as ma
+    import glob
+    import os
+
+    import numpy as np
+    import numpy.ma as ma
 
-        from .dataset import ACTAccessor
+    from .dataset import ACTAccessor
 
 Following the main function def line, but before the code within it, a doc
 string is needed to explain arguments, returns, references if needed, and
@@ -197,38 +196,38 @@ An example:
 
 .. code-block:: python
 
-        def read_netcdf(filenames, variables=None):
+    def read_netcdf(filenames, variables=None):
 
-            """
-            Returns `xarray.Dataset` with stored data and metadata from a
-            user-defined query of standard netCDF files from a single
-            datastream.
+        """
+        Returns `xarray.Dataset` with stored data and metadata from a
+        user-defined query of standard netCDF files from a single
+        datastream.
 
-            Parameters
-            ----------
-            filenames : str or list
-                Name of file(s) to read
-            variables : list, optional
-                List of variable name(s) to read
+        Parameters
+        ----------
+        filenames : str or list
+            Name of file(s) to read
+        variables : list, optional
+            List of variable name(s) to read
 
-            Returns
-            -------
-            act_obj : Object
-                ACT dataset
+        Returns
+        -------
+        act_obj : Object
+            ACT dataset
 
-            Examples
-            --------
-            This example will load the example sounding data used for unit
-            testing.
+        Examples
+        --------
+        This example will load the example sounding data used for unit
+        testing.
 
-            .. code-block:: python
+        .. code-block:: python
 
-                import act
+            import act
 
-                the_ds, the_flag = act.io.armfiles.read_netcdf(
-                    act.tests.sample_files.EXAMPLE_SONDE_WILDCARD)
-                print(the_ds.act.datastream)
-            """
+            the_ds, the_flag = act.io.armfiles.read_netcdf(
+                act.tests.sample_files.EXAMPLE_SONDE_WILDCARD)
+            print(the_ds.act.datastream)
+        """
 
 As seen, each argument has what type of object it is, an explanation of
 what it is, mention of units, and if an argument has a default value, a
@@ -240,8 +239,8 @@ An example:
 
 .. code-block:: python
 
-        def _get_value(self):
-        """ Gets a value that is used in a public function. """
+    def _get_value(self):
+        """Gets a value that is used in a public function."""
 
 Code Style
 ----------
@@ -269,7 +268,7 @@ To install pylint::
 
 To use pylint::
 
-        pylint path/to/code/to/check.py 
+        pylint path/to/code/to/check.py
 
 Both of these tools are highly configurable to suit a user's taste. Refer to
 the tools documentation for details on this process.
@@ -294,21 +293,21 @@ An example:
 
 .. code-block:: python
 
-        import act
-        import numpy as np
-        import xarray as xr
+    import act
+    import numpy as np
+    import xarray as xr
 
 
-        def test_correct_ceil():
-            # Make a fake dataset to test with, just an array with 1e-7
-            # for half of it.
-            fake_data = 10 * np.ones((300, 20))
-            fake_data[:, 10:] = -1
-            arm_obj = {}
-            arm_obj['backscatter'] = xr.DataArray(fake_data)
-            arm_obj = act.corrections.ceil.correct_ceil(arm_obj)
-            assert np.all(arm_obj['backscatter'].data[:, 10:] == -7)
-            assert np.all(arm_obj['backscatter'].data[:, 1:10] == 1)
+    def test_correct_ceil():
+        # Make a fake dataset to test with, just an array with 1e-7
+        # for half of it.
+        fake_data = 10 * np.ones((300, 20))
+        fake_data[:, 10:] = -1
+        arm_obj = {}
+        arm_obj["backscatter"] = xr.DataArray(fake_data)
+        arm_obj = act.corrections.ceil.correct_ceil(arm_obj)
+        assert np.all(arm_obj["backscatter"].data[:, 10:] == -7)
+        assert np.all(arm_obj["backscatter"].data[:, 1:10] == 1)
 
 Pytest is used to run unit tests in ACT.
 
@@ -344,7 +343,7 @@ filename is the filename and location, such as::
         pytest /home/user/act/act/tests/test_correct.py
 
 Relative paths can also be used::
-        
+
         cd ACT
         pytest ./act/tests/test_correct.py
 

LICENSE.txt

@@ -1,7 +1,7 @@
 Copyright © 2019, UChicago Argonne, LLC
 All Rights Reserved
  Software Name: Atmospheric data Community Toolkit (ACT)
-By: Argonne National Laboratory, University of Oklahoma, and 
+By: Argonne National Laboratory, University of Oklahoma, and
 Oak Ridge National Laboratory
 OPEN SOURCE LICENSE
 

README.rst

@@ -94,8 +94,8 @@ When installing with pip, the ACT dependencies found in
     pip install act-atmos
 
 The easiest method for installing ACT is to use the conda packages from
-the latest release. To do this you must download and install 
-`Anaconda <https://www.anaconda.com/download/#>`_ or 
+the latest release. To do this you must download and install
+`Anaconda <https://www.anaconda.com/download/#>`_ or
 `Miniconda <https://conda.io/miniconda.html>`_.
 With Anaconda or Miniconda install, it is recommended to create a new conda
 environment when using ACT or even other packages. To create a new
@@ -117,7 +117,7 @@ To update an older version of ACT to the latest release use::
     conda update -c conda-forge act-atmos
 
 If you do not wish to use Anaconda or Miniconda as a Python environment or want
-to use the latest, unreleased version of ACT see the section below on 
+to use the latest, unreleased version of ACT see the section below on
 **Installing from source**.
 
 Installing from Source
@@ -148,7 +148,7 @@ ACT is an open source, community software project. Contributions to the
 package are welcomed from all users.
 
 The latest source code can be obtained with the command::
- 
+
     git clone https://github.com/ARM-DOE/ACT.git
 
 If you are planning on making changes that you would like included in ACT,

act/__init__.py

@@ -4,20 +4,14 @@
 
 """
 
-from . import io
-from . import plotting
-from . import corrections
-from . import utils
-from . import tests
-from . import discovery
-from . import retrievals
-from . import qc
-from ._version import get_versions
-
 # No more pandas warnings
 from pandas.plotting import register_matplotlib_converters
+
+from . import corrections, discovery, io, plotting, qc, retrievals, tests, utils
+from ._version import get_versions
+
 register_matplotlib_converters()
 
 # Version for source builds
 vdict = get_versions()
-__version__ = vdict["version"]
+__version__ = vdict['version']