Add pre-commit for code linting

.flake8

@@ -0,0 +1,16 @@
+[flake8]
+# https://pep8.readthedocs.io/en/latest/intro.html#error-codes
+ignore =
+    # line break after operator
+    W504
+# Max width of Github code review is 79 characters
+max-line-length = 79
+max-complexity = 18
+per-file-ignores =
+    */__init__.py: F401
+exclude =
+    .git,
+    docs,
+    .idea,
+    .mypy_cache,
+    .pytest_cache,

.github/workflows/build_workflow.yml

@@ -16,6 +16,34 @@ env:
   PATHS_IGNORE: '["**/README.md", "**/docs/**"]'
 
 jobs:
+  pre-commit-hooks:
+    name: lint with pre-commit
+    runs-on: ubuntu-latest
+    timeout-minutes: 5
+    steps:
+      - id: skip_check
+        uses: fkirc/skip-duplicate-actions@master
+        with:
+          cancel_others: ${{ env.CANCEL_OTHERS }}
+          paths_ignore: ${{ env.PATHS_IGNORE }}
+
+      - if: ${{ steps.skip_check.outputs.should_skip != 'true' }}
+        name: Checkout Code Repository
+        uses: actions/checkout@v4
+
+      - if: ${{ steps.skip_check.outputs.should_skip != 'true' }}
+        name: Set up Python 3.10
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.10"
+
+      - if: ${{ steps.skip_check.outputs.should_skip != 'true' }}
+        # Run all pre-commit hooks on all the files.
+        # Getting only staged files can be tricky in case a new PR is opened
+        # since the action is run on a branch in detached head state
+        name: Install and Run Pre-commit
+        uses: pre-commit/[email protected]
+
   build:
     name: test geometric_features - python ${{ matrix.python-version }}
     runs-on: ubuntu-latest

.github/workflows/docs_workflow.yml

@@ -8,6 +8,9 @@ on:
   release:
     types: [published]
 
+env:
+  PYTHON_VERSION: "3.10"
+
 jobs:
   publish-docs:
     runs-on: ubuntu-latest
@@ -40,14 +43,14 @@ jobs:
           channels: conda-forge
           channel-priority: strict
           auto-update-conda: true
-          python-version: ${{ matrix.python-version }}
+          python-version: ${{ env.PYTHON_VERSION }}
 
       - if: ${{ steps.skip_check.outputs.should_skip != 'true' }}
         name: Install geometric_features
         run: |
           git config --global url."https://github.com/".insteadOf "[email protected]:"
           conda create -n geometric_features_dev --file dev-spec.txt \
-            python=${{ matrix.python-version }}
+            python=${{ env.PYTHON_VERSION }}
           conda activate geometric_features_dev
           python -m pip install -vv --no-deps --no-build-isolation -e .
 

.pre-commit-config.yaml

@@ -0,0 +1,44 @@
+exclude: "docs|.git|geometric_data|geometric_features/features_and_tags.json"
+default_stages: [pre-commit]
+fail_fast: true
+
+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v5.0.0
+    hooks:
+      - id: trailing-whitespace
+      - id: end-of-file-fixer
+
+  # Can run individually with `pre-commit run isort --all-files`
+  - repo: https://github.com/PyCQA/isort
+    rev: 5.13.2
+    hooks:
+      - id: isort
+        exclude: "geometric_features/__init__.py"
+
+  # Can run individually with `flynt [file]` or `flynt [source]`
+  - repo: https://github.com/ikamensh/flynt
+    rev: '1.0.1'
+    hooks:
+      - id: flynt
+        args: ["--fail-on-change", "--verbose"]
+        require_serial: true
+
+  # Can run individually with `pre-commit run flake8 --all-files`
+  # Need to use flake8 GitHub mirror due to CentOS git issue with GitLab
+  # https://github.com/pre-commit/pre-commit/issues/1206
+  - repo: https://github.com/pycqa/flake8
+    rev: 7.1.1
+    hooks:
+      - id: flake8
+        args: ["--config=.flake8"]
+        additional_dependencies: [flake8-isort]
+
+  # Can run individually with `pre-commit run mypy --all-files`
+  - repo: https://github.com/pre-commit/mirrors-mypy
+    rev: v1.13.0
+    hooks:
+      - id: mypy
+        args: ["--config=pyproject.toml", "--show-error-codes"]
+        verbose: true
+        additional_dependencies: ['types-requests', 'types-PyYAML']

LICENSE

@@ -1,7 +1,7 @@
 Copyright (c) 2013-2018,  Los Alamos National Security, LLC (LANS) (Ocean: LA-CC-13-047;
 Land Ice: LA-CC-13-117) and the University Corporation for Atmospheric Research (UCAR).
 
-All rights reserved. 
+All rights reserved.
 
 LANS is the operator of the Los Alamos National Laboratory under Contract No.
 DE-AC52-06NA25396 with the U.S. Department of Energy.  UCAR manages the National

contributors/CONTRIBUTORS_HEADER

@@ -2,4 +2,3 @@
 
 Data sources and authors of the regions may be updated from the repository via
 this [script](list_contributors.py):
-

contributors/list_contributors.py

@@ -7,11 +7,11 @@
 02/23/2019
 """
 
-import os
-import subprocess
-import shutil
 import datetime
+import os
 import re
+import shutil
+import subprocess
 
 
 def append_to_file(aline, afile):
@@ -37,8 +37,7 @@ def build_contrib_file():
     shutil.copyfile(contribdir + '/CONTRIBUTORS_HEADER', contribfile)
 
     append_to_file(
-        'List populated on {}:'.format(
-            datetime.datetime.now().strftime("%Y-%m-%d %H:%M")),
+        f"List populated on {datetime.datetime.now().strftime('%Y-%m-%d %H:%M')}:",
         contribfile)
     append_to_file('\n', contribfile)
 

dev-spec.txt

@@ -15,6 +15,9 @@ shapely>=2.0,<3.0
 pip
 pytest
 setuptools>=60
+pre-commit
+isort
+flake8
 
 # Documentation
 sphinx

examples/README.md

@@ -3,4 +3,4 @@ python package to perform various operations on the ``geometric_data``
 contained in this repository.  To use these scripts, you should either
 install the ``geometric_features`` conda package (see README.md in the
 root of the repo) or copy the scripts into the root directory. Each script
-includes detailed comments that should help you adapt them to your own needs.
+includes detailed comments that should help you adapt them to your own needs.

examples/setup_antarctic_basins.py

@@ -4,13 +4,13 @@
 """
 
 # stuff to make scipts work for python 2 and python 3
-from __future__ import absolute_import, division, print_function, \
-    unicode_literals
-
-from geometric_features import GeometricFeatures
+from __future__ import (absolute_import, division, print_function,
+                        unicode_literals)
 
 import matplotlib.pyplot as plt
 
+from geometric_features import GeometricFeatures
+
 plot = True
 
 # create a GeometricFeatures object that points to a local cache of geometric

examples/setup_extended_antarctic_basins.py

@@ -5,13 +5,13 @@
 """
 
 # stuff to make scipts work for python 2 and python 3
-from __future__ import absolute_import, division, print_function, \
-    unicode_literals
-
-from geometric_features import GeometricFeatures, FeatureCollection
+from __future__ import (absolute_import, division, print_function,
+                        unicode_literals)
 
 import matplotlib.pyplot as plt
 
+from geometric_features import FeatureCollection, GeometricFeatures
+
 plot = True
 
 # create a GeometricFeatures object that points to a local cache of geometric
@@ -23,8 +23,8 @@
 # 27 IMBIE basin tags tags
 fc = FeatureCollection()
 for basin in range(1, 28):
-    print('Adding feature from IMBIE basin {:d}'.format(basin))
-    basinName = 'Antarctica_IMBIE{:d}'.format(basin)
+    print(f'Adding feature from IMBIE basin {basin:d}')
+    basinName = f'Antarctica_IMBIE{basin:d}'
     tags = [basinName]
     # load the iceshelf regions for one IMBIE basin
     fcBasin = gf.read(componentName='iceshelves', objectType='region',

examples/setup_ice_shelves.py

@@ -4,13 +4,13 @@
 """
 
 # stuff to make scipts work for python 2 and python 3
-from __future__ import absolute_import, division, print_function, \
-    unicode_literals
-
-from geometric_features import GeometricFeatures, FeatureCollection
+from __future__ import (absolute_import, division, print_function,
+                        unicode_literals)
 
 import matplotlib.pyplot as plt
 
+from geometric_features import FeatureCollection, GeometricFeatures
+
 plot = True
 
 iceShelfNames = ['Abbot',
@@ -125,8 +125,8 @@
 
 nIMBIEBasins = 27
 for basinNumber in range(1, nIMBIEBasins+1):
-    basinName = 'Antarctica_IMBIE{}'.format(basinNumber)
-    combinedIceShelves['IMBIE{}'.format(basinNumber)] = [basinName]
+    basinName = f'Antarctica_IMBIE{basinNumber}'
+    combinedIceShelves[f'IMBIE{basinNumber}'] = [basinName]
 
 # create a GeometricFeatures object that points to a local cache of geometric
 # data and knows which branch of geometric_feature to use to download

examples/setup_ocean_critical_passages.py

@@ -4,8 +4,8 @@
 """
 
 # stuff to make scipts work for python 2 and python 3
-from __future__ import absolute_import, division, print_function, \
-    unicode_literals
+from __future__ import (absolute_import, division, print_function,
+                        unicode_literals)
 
 from geometric_features import GeometricFeatures
 

examples/setup_ocean_land_coverage.py

@@ -8,13 +8,13 @@
 """
 
 # stuff to make scipts work for python 2 and python 3
-from __future__ import absolute_import, division, print_function, \
-    unicode_literals
-
-from geometric_features import GeometricFeatures
+from __future__ import (absolute_import, division, print_function,
+                        unicode_literals)
 
 import matplotlib.pyplot as plt
 
+from geometric_features import GeometricFeatures
+
 plot = True
 withCavities = False
 

examples/setup_ocean_region_groups.py

@@ -12,14 +12,15 @@
 """
 
 # stuff to make scipts work for python 2 and python 3
-from __future__ import absolute_import, division, print_function, \
-    unicode_literals
+from __future__ import (absolute_import, division, print_function,
+                        unicode_literals)
 
-import matplotlib.pyplot as plt
 import copy
+
+import matplotlib.pyplot as plt
 import shapely
 
-from geometric_features import GeometricFeatures, FeatureCollection
+from geometric_features import FeatureCollection, GeometricFeatures
 
 
 def build_ocean_basins(gf, plot):
@@ -50,7 +51,7 @@ def build_ocean_basins(gf, plot):
     for oceanName in ['Atlantic', 'Pacific', 'Indian', 'Arctic',
                       'Southern_Ocean', 'Mediterranean']:
 
-        basinName = '{}_Basin'.format(oceanName)
+        basinName = f'{oceanName}_Basin'
         print(oceanName)
 
         print(' * merging features')
@@ -111,19 +112,19 @@ def build_MOC_basins(gf):
     # build MOC basins from regions with the appropriate tags
     for basinName in MOCSubBasins:
 
-        print('{} MOC'.format(basinName))
+        print(f'{basinName} MOC')
 
         print(' * merging features')
-        tags = ['{}_Basin'.format(basin) for basin in MOCSubBasins[basinName]]
+        tags = [f'{basin}_Basin' for basin in MOCSubBasins[basinName]]
 
         fcBasin = gf.read(componentName='ocean', objectType='region',
                           tags=tags, allTags=False)
 
         print(' * combining features')
-        fcBasin = fcBasin.combine(featureName='{}_MOC'.format(basinName))
+        fcBasin = fcBasin.combine(featureName=f'{basinName}_MOC')
 
         print(' * masking out features south of MOC region')
-        maskName = 'MOC mask {}'.format(MOCSouthernBoundary[basinName])
+        maskName = f'MOC mask {MOCSouthernBoundary[basinName]}'
         fcMask = gf.read(componentName='ocean', objectType='region',
                          featureNames=[maskName])
         # mask out the region covered by the mask
@@ -219,10 +220,9 @@ def remove_small_polygons(fc, minArea):
         if add:
             fcOut.add_feature(copy.deepcopy(feature))
         else:
-            print("{} has been removed.".format(
-                    feature['pproperties']['name']))
+            print(f"{feature['pproperties']['name']} has been removed.")
 
-    print(' * Removed {} small polygons'.format(removedCount))
+    print(f' * Removed {removedCount} small polygons')
 
     return fcOut
 

examples/setup_ocean_standard_transport_sections.py

@@ -5,12 +5,11 @@
 """
 
 # stuff to make scipts work for python 2 and python 3
-from __future__ import absolute_import, division, print_function, \
-    unicode_literals
+from __future__ import (absolute_import, division, print_function,
+                        unicode_literals)
 
 from geometric_features import GeometricFeatures
 
-
 # create a GeometricFeatures object that points to a local cache of geometric
 # data and knows which branch of geometric_feature to use to download
 # missing data