Merge branch 'main' into tolerance

.github/workflows/codeql-analysis.yml

@@ -46,7 +46,7 @@ jobs:
 
     # Initializes the CodeQL tools for scanning.
     - name: Initialize CodeQL
-      uses: github/codeql-action/init@v1
+      uses: github/codeql-action/init@v3
       with:
         languages: ${{ matrix.language }}
         # If you wish to specify custom queries, you can do so here or in a config file.
@@ -57,7 +57,7 @@ jobs:
     # Autobuild attempts to build any compiled languages  (C/C++, C#, or Java).
     # If this step fails, then you should remove it and run the build manually (see below)
     - name: Autobuild
-      uses: github/codeql-action/autobuild@v1
+      uses: github/codeql-action/autobuild@v3
 
     # ℹ️ Command-line programs to run using the OS shell.
     # 📚 https://git.io/JvXDl
@@ -71,4 +71,4 @@ jobs:
     #   make release
 
     - name: Perform CodeQL Analysis
-      uses: github/codeql-action/analyze@v1
+      uses: github/codeql-action/analyze@v3

.github/workflows/linting.yml

@@ -0,0 +1,33 @@
+name: linting
+
+on:
+  push:
+  pull_request:
+  workflow_dispatch:
+
+jobs:
+  pre-job:
+    runs-on: ubuntu-latest
+    outputs:
+      should_skip: ${{ steps.skip_check.outputs.should_skip }}
+    steps:
+      - id: skip_check
+        uses: fkirc/skip-duplicate-actions@master
+        with:
+          concurrent_skipping: 'same_content'
+          skip_after_successful_duplicate: 'false'
+          do_not_skip: '["workflow_dispatch", "schedule"]'
+  linting:
+    needs: pre-job
+    runs-on: ubuntu-latest
+    if: ${{ needs.pre-job.outputs.should_skip != 'true' }}
+    steps:
+      - name: Cancel Previous Runs
+        uses: styfle/[email protected]
+        with:
+          access_token: ${{ github.token }}
+      - uses: actions/checkout@v2
+      - uses: actions/setup-python@v4
+        with:
+          python-version: '3.10'
+      - uses: pre-commit/[email protected]

CONTRIBUTING.rst

@@ -247,39 +247,22 @@ An example:
 Code Style
 ----------
 
-ACT follows PEP8 coding standards. To make sure your code follows the
-PEP8 style, you can use a variety of tools that can check for you. Two
-popular PEP8 check modules are flake8 and pylint. (Note: ACT's continuous
-integration uses flake8).
+Py-ART uses pre-commit for linting, which applies a variety of pep8 and other
+code style rules.
 
 For more on pep8 style:
 
 - https://www.python.org/dev/peps/pep-0008/
 
-To install flake8::
+To install pre-commit hooks for the Py-ART repo::
 
-        conda install -c conda-forge flake8
+        pre-commit install
 
-To use flake8::
+Afterwards, pre-commit will run on every commit to the repository. It will
+re-format files as neccessary.
 
-        flake8 path/to/code/to/check.py
-
-To install pylint::
-
-        conda install pylint
-
-To use pylint::
-
-        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.
-
-- https://flake8.pycqa.org/en/latest/
-- https://www.pylint.org/
-
-Naming Convenction
-----------------------------------------
+Naming Convention
+-----------------
 
 Discovery
 ~~~~~~~~~

README.rst

@@ -38,16 +38,14 @@ Please report any issues or feature requests by sumitting an `Issue <https://git
 Version 2.0
 ~~~~~~~~~~~
 
-ACT will soon have a version 2.0 release. This release will contain many function
+ACT now has a version 2.0 release. This release contains many function
 naming changes such as IO and Discovery module function naming changes. To
 prepare for this release, a `v2.0 <https://arm-doe.github.io/ACT/userguide/GUIDE_V2.html>`_
 has been provided that explains the changes and how to work with the new syntax.
 
-To test out the release candidate 2.0.0-rc.0 of ACT, use::
+The new release is available on both PyPI and conda-forge.
 
-    pip install git+https://github.com/ARM-DOE/[email protected]
-
-Please report any bugs of the release candidate to the Issue Tracker mentioned in
+Please report any bugs of the 2.0 release to the Issue Tracker mentioned in
 the Important Links section below.
 
 Important Links

act/__init__.py

@@ -14,7 +14,7 @@
 register_matplotlib_converters()
 
 # Import early so these classes are available to the object
-from .qc import QCFilter, QCTests, clean
+from .qc import QCFilter, QCTests, clean  # noqa
 
 # Import the lazy loaded modules
 submodules = [

act/io/hysplit.py

@@ -95,7 +95,8 @@ def read_hysplit(filename, base_year=2000):
             var_list.append(variable)
 
     input_df = pd.read_csv(
-        filename, sep='\s+', index_col=False, names=var_list, skiprows=12)  # noqa W605
+        filename, sep=r'\s+', index_col=False, names=var_list, skiprows=12
+    )  # noqa W605
     input_df['year'] = base_year + input_df['year']
     input_df['time'] = pd.to_datetime(
         input_df[["year", "month", "day", "hour", "minute"]], format='%y%m%d%H%M'

act/plotting/__init__.py

@@ -17,10 +17,10 @@
 import lazy_loader as lazy
 
 # Load colormaps
-import cmweather
+import cmweather  # noqa
 
 # Eagerly load in common
-from . import common
+from . import common  # noqa
 
 __getattr__, __dir__, __all__ = lazy.attach(
     __name__,

act/utils/data_utils.py

@@ -35,8 +35,13 @@ def __init__(self, ds):
         self._ds = ds
 
     def change_units(
-        self, variables=None, desired_unit=None, skip_variables=None, skip_standard=True,
-        verbose=False, raise_error=False
+        self,
+        variables=None,
+        desired_unit=None,
+        skip_variables=None,
+        skip_standard=True,
+        verbose=False,
+        raise_error=False,
     ):
         """
         Parameters
@@ -111,10 +116,14 @@ def change_units(
                 np.core._exceptions.UFuncTypeError,
             ):
                 if raise_error:
-                    raise ValueError(f"Unable to convert '{var_name}' to units of '{desired_unit}'.")
+                    raise ValueError(
+                        f"Unable to convert '{var_name}' to units of '{desired_unit}'."
+                    )
                 elif verbose:
-                    print(f"\n    Unable to convert '{var_name}' to units of '{desired_unit}'. "
-                          f"Skipping unit converstion for '{var_name}'.\n")
+                    print(
+                        f"\n    Unable to convert '{var_name}' to units of '{desired_unit}'. "
+                        f"Skipping unit converstion for '{var_name}'.\n"
+                    )
 
         return self._ds
 

continuous_integration/environment_actions.yml

@@ -24,11 +24,12 @@ dependencies:
   - coveralls
   - pandas
   - shapely
-  - pip
   - lazy_loader
   - cmweather
   - arm-test-data
   - moviepy
+  - ruff
+  - pip
   - pip:
     - mpl2nc
     - metpy

docs/source/conf.py

@@ -91,7 +91,7 @@
 # |version| and |release|, also used in various other places throughout the
 # built documents.
 #
-import act
+import act  # noqa
 
 # The short X.Y version.
 version = act.__version__

examples/plotting/plot_daytime_averages.py

@@ -33,7 +33,7 @@
 ds = ds.where(ds['sun_variable'] == 1)
 
 # Take daily mean using xarray features
-ds = ds.resample(time='1d', skipna=True, keep_attrs=True).mean()
+ds = ds.resample(time='1d', skipna=True).mean()
 
 # Creat Plot Display
 display = act.plotting.TimeSeriesDisplay(ds, figsize=(15, 10))

examples/plotting/plot_scatter.py

@@ -32,7 +32,7 @@
     'ground_speed',
     m_field='ambient_temp',
     marker='x',
-    cbar_label=r'Ambient Temperature ($^\circ$C)', # noqa W605
+    cbar_label=r'Ambient Temperature ($^\circ$C)',  # noqa W605
 )
 
 # Set the range of the field on the x-axis
@@ -47,7 +47,7 @@
 display.axes[0].plot(ds['true_airspeed'], p(ds['true_airspeed']), 'r', linewidth=2)
 
 # Display the line equation
-display.axes[0].text(45, 135, "y = {:.3f}x + ({:.3f})".format(z[0], z[1]), color='r', fontsize=12)
+display.axes[0].text(45, 135, f"y = {z[0]:.3f}x + ({z[1]:.3f})", color='r', fontsize=12)
 
 # Calculate Pearson Correlation Coefficient
 cc_conc = pearsonr(ds['true_airspeed'], ds['ground_speed'])

examples/qc/plot_arm_qc.py

@@ -145,7 +145,7 @@
 # to give to other users.
 # There is a file in the same directory called sgpmfrsr7nchE11.b1.yaml with times of
 # incorrect or suspect values that can be read and applied to the Dataset.
-from act.qc.add_supplemental_qc import apply_supplemental_qc
+from act.qc.add_supplemental_qc import apply_supplemental_qc  # noqa
 
 apply_supplemental_qc(ds, 'sgpmfrsr7nchE11.b1.yaml')
 

pyproject.toml

@@ -6,3 +6,9 @@ ignore = ["act/io/arm.py"]
 
 [tool.check-manifest]
 ignore = ["docs/*", "ci/*"]
+
+[tool.ruff]
+target-version = "py39"
+ignore = [
+    "E501",
+]

tests/plotting/test_geodisplay.py

@@ -7,6 +7,7 @@
 from act.tests import sample_files
 
 try:
+    import cartopy  # noqa
     CARTOPY_AVAILABLE = True
 except ImportError:
     CARTOPY_AVAILABLE = False

tests/plotting/test_xsectiondisplay.py

@@ -7,6 +7,7 @@
 from act.tests import sample_files
 
 try:
+    import cartopy  # noqa
     CARTOPY_AVAILABLE = True
 except ImportError:
     CARTOPY_AVAILABLE = False

tests/qc/test_qcfilter.py

@@ -13,7 +13,7 @@
 from act.tests import EXAMPLE_MET1, EXAMPLE_METE40, EXAMPLE_IRT25m20s
 
 try:
-    import scikit_posthocs
+    import scikit_posthocs  # noqa
 
     SCIKIT_POSTHOCS_AVAILABLE = True
 except ImportError:

tests/retrievals/test_sp2_retrievals.py

@@ -4,7 +4,7 @@
 import act
 
 try:
-    import pysp2
+    import pysp2  # noqa
 
     PYSP2_AVAILABLE = True
 except ImportError:

tests/utils/test_data_utils.py

@@ -152,8 +152,10 @@ def test_convert_units():
     with redirect_stdout(f):
         ds.utils.change_units('home_signal_15', 'not_a_real_unit_string', verbose=True)
     s = f.getvalue()
-    assert s.strip() == f"Unable to convert '{var_name}' to units of '{unit}'. Skipping unit converstion for '{var_name}'."
-
+    assert (
+        s.strip()
+        == f"Unable to convert '{var_name}' to units of '{unit}'. Skipping unit converstion for '{var_name}'."
+    )
     ds.close()
     del ds
 

tests/utils/test_io_utils.py

@@ -12,7 +12,8 @@
 from act.tests import sample_files
 
 try:
-    import moviepy.video.io.ImageSequenceClip
+    import moviepy.video.io.ImageSequenceClip  # noqa
+
     MOVIEPY_AVAILABLE = True
 except ImportError:
     MOVIEPY_AVAILABLE = False