Enable pre commit and fix code style once (#29)

* Enable linting * Make sure we run on main * Disable interrogate, codespell, mypy * Satisfy linter * Fix isort
MarcoLandtHayen · Jun 9, 2022 · eddcf62 · eddcf62
1 parent 696ebdf
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diff --git a/.github/workflows/linting.yaml b/.github/workflows/linting.yaml
@@ -0,0 +1,16 @@
+name: linting with pre-commit
+
+on:
+  pull_request:
+  push:
+    branches: [main]
+
+jobs:
+  pre-commit:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v2
+      - uses: actions/setup-python@v2
+        with:
+          python-version: "3.8"
+      - uses: pre-commit/action@v2.0.0
diff --git a/.github/workflows/optional/linting.yaml b/.github/workflows/optional/linting.yaml
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -1,61 +1,82 @@
 repos:
+  # - repo: https://github.com/econchick/interrogate
+  #   rev: 1.2.0
+  #   hooks:
+  #     - id: interrogate
+  #       exclude: ^(docs|setup.py|tests)
+  #       args: [--config=pyproject.toml]
 
-- repo: https://github.com/econchick/interrogate
-  rev: 1.2.0
-  hooks:
-    - id: interrogate
-      exclude: ^(docs|setup.py|tests)
-      args: [--config=pyproject.toml]
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v3.1.0
+    hooks:
+      - id: trailing-whitespace
+        exclude: tests/data
+      - id: check-ast
+      - id: debug-statements
+      - id: end-of-file-fixer
+      - id: check-docstring-first
+      - id: check-added-large-files
+      - id: requirements-txt-fixer
+      - id: file-contents-sorter
+        files: requirements-dev.txt
 
-- repo: https://github.com/pre-commit/pre-commit-hooks
-  rev: v3.1.0
-  hooks:
-    - id: trailing-whitespace
-      exclude: tests/data
-    - id: check-ast
-    - id: debug-statements
-    - id: end-of-file-fixer
-    - id: check-docstring-first
-    - id: check-added-large-files
-    - id: requirements-txt-fixer
-    - id: file-contents-sorter
-      files: requirements-dev.txt
+  - repo: https://gitlab.com/pycqa/flake8
+    rev: 3.7.9
+    hooks:
+      - id: flake8
+        exclude: docs/source/conf.py
+        args:
+          [
+            --max-line-length=105,
+            --ignore=E203,
+            E501,
+            W503,
+            --select=select=C,
+            E,
+            F,
+            W,
+            B,
+            B950,
+          ]
 
-- repo: https://gitlab.com/pycqa/flake8
-  rev: 3.7.9
-  hooks:
-    - id: flake8
-      exclude: docs/source/conf.py
-      args: [--max-line-length=105, --ignore=E203,E501,W503, --select=select=C,E,F,W,B,B950]
+  - repo: https://github.com/pre-commit/mirrors-isort
+    rev: v4.3.21
+    hooks:
+      - id: isort
+        additional_dependencies: [toml]
+        args:
+          [
+            --project=gcm_filters,
+            --multi-line=3,
+            --lines-after-imports=2,
+            --lines-between-types=1,
+            --trailing-comma,
+            --force-grid-wrap=0,
+            --use-parentheses,
+            --line-width=88,
+          ]
 
-- repo: https://github.com/pre-commit/mirrors-isort
-  rev: v4.3.21
-  hooks:
-  - id: isort
-    additional_dependencies: [toml]
-    args: [--project=gcm_filters, --multi-line=3, --lines-after-imports=2, --lines-between-types=1, --trailing-comma, --force-grid-wrap=0, --use-parentheses, --line-width=88]
+  - repo: https://github.com/asottile/seed-isort-config
+    rev: v2.1.1
+    hooks:
+      - id: seed-isort-config
 
-- repo: https://github.com/asottile/seed-isort-config
-  rev: v2.1.1
-  hooks:
-    - id: seed-isort-config
+  - repo: https://github.com/psf/black
+    rev: stable
+    hooks:
+      - id: black
+        language_version: python3
 
-- repo: https://github.com/psf/black
-  rev: stable
-  hooks:
-  - id: black
-    language_version: python3
+  # - repo: https://github.com/pre-commit/mirrors-mypy
+  #   rev: v0.770
+  #   hooks:
+  #     - id: mypy
+  #       exclude: docs/source/conf.py
+  #       args: [--ignore-missing-imports]
 
-- repo: https://github.com/pre-commit/mirrors-mypy
-  rev: v0.770
-  hooks:
-  - id: mypy
-    exclude: docs/source/conf.py
-    args: [--ignore-missing-imports]
-
-- repo: https://github.com/codespell-project/codespell
-  rev: v1.16.0
-  hooks:
-    - id: codespell
-      args:
-        - --quiet-level=2
+  # - repo: https://github.com/codespell-project/codespell
+  #   rev: v1.16.0
+  #   hooks:
+  #     - id: codespell
+  #       args:
+  #         - --quiet-level=2
diff --git a/LICENSE.txt b/LICENSE.txt
@@ -7,4 +7,3 @@ Permission is hereby granted, free of charge, to any person obtaining a copy of
 The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.
 
 THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
-
diff --git a/climate_index_collection/__main__.py b/climate_index_collection/__main__.py
@@ -1,4 +1,5 @@
 from .cli import run
 
+
 if __name__ == "__main__":
     run()
diff --git a/climate_index_collection/data_loading.py b/climate_index_collection/data_loading.py
@@ -1,6 +1,7 @@
-import xarray as xr
 from pathlib import Path
 
+import xarray as xr
+
 
 def find_data_files(data_path="data/test_data/", data_source_name="FOCI"):
     """Find all files for given data source.

diff --git a/climate_index_collection/indices.py b/climate_index_collection/indices.py
@@ -3,19 +3,19 @@
 
 def southern_annular_mode(data_set, slp_name="sea-level-pressure"):
     """Calculate the southern annular mode index.
-    
+
     Parameters
     ----------
     data_set: xarray.DataSet
         Dataset containing a SLP field.
     slp_name: str
         Name of the Sea-Level Pressure field. Defaults to "sea-level-pressure".
-    
+
     Returns
     -------
     xarray.DataArray
         Time series containing the SAM index.
-        
+
     """
     slp = data_set[slp_name]
 

diff --git a/climate_index_collection/reductions.py b/climate_index_collection/reductions.py
@@ -1,6 +1,6 @@
 def mean_unweighted(dobj, dim=None):
     """Calculate an unweighted mean for one or more dimensions.
-    
+
     Parameters
     ----------
     dobj: xarray.Dataset or xarray.DataArray
@@ -12,14 +12,14 @@ def mean_unweighted(dobj, dim=None):
     -------
     xarray.Dataset or xarray.DataArray
         Averaged data. Has the same variable name(s) as dobj.
-    
+
     """
     return dobj.mean(dim)
 
 
 def mean_weighted(dobj, weights=None, dim=None):
     """Calculate a weighted mean.
-    
+
     Parameters
     ----------
     dobj: xarray.Dataset or xarray.DataArray
@@ -33,7 +33,7 @@ def mean_weighted(dobj, weights=None, dim=None):
     -------
     xarray.Dataset or xarray.DataArray
         Averaged data. Has the same variable name(s) as dobj.
-    
+
     """
     numerator = (dobj * weights).sum(dim)
     denominator = weights.where(~dobj.isnull()).sum(dim)
@@ -46,7 +46,7 @@ def variance_weighted(dobj, weights=None, dim=None):
 
     This uses a weighted mean <.>_w and defines variance as
     var[a] = <a**2>_w - (<a>_w)**2.
-    
+
     Parameters
     ----------
     dobj: xarray.Dataset or xarray.DataArray
@@ -60,9 +60,9 @@ def variance_weighted(dobj, weights=None, dim=None):
     -------
     xarray.Dataset or xarray.DataArray
         Variance data. Has the same variable name(s) as dobj.
-    
+
     """
-    mean_of_squares = mean_weighted(dobj ** 2, weights=weights, dim=dim)
+    mean_of_squares = mean_weighted(dobj**2, weights=weights, dim=dim)
     square_of_means = mean_weighted(dobj, weights=weights, dim=dim) ** 2
     variance = mean_of_squares - square_of_means
     return variance
@@ -82,7 +82,7 @@ def variance_unweighted(dobj, dim=None):
     -------
     xarray.Dataset or xarray.DataArray
         Variance data. Has the same variable name(s) as dobj.
-    
+
     """
     return dobj.var(dim)
 
@@ -92,7 +92,7 @@ def stddev_weighted(dobj, weights=None, dim=None):
 
     This uses a weighted mean <.>_w, defines variance as
     var[a] = <a**2>_w - (<a>_w)**2, and std dev as var***0.5.
-    
+
     Parameters
     ----------
     dobj: xarray.Dataset or xarray.DataArray
@@ -106,16 +106,16 @@ def stddev_weighted(dobj, weights=None, dim=None):
     -------
     xarray.Dataset or xarray.DataArray
         Stddev data. Has the same variable name(s) as dobj.
-    
+
     """
     variance = variance_weighted(dobj, weights=weights, dim=dim)
-    std_dev = variance ** 0.5
+    std_dev = variance**0.5
     return std_dev
 
 
 def stddev_unweighted(dobj, dim=None):
     """Calculate an unweighted stddev.
-    
+
     Parameters
     ----------
     dobj: xarray.Dataset or xarray.DataArray
@@ -127,6 +127,6 @@ def stddev_unweighted(dobj, dim=None):
     -------
     xarray.Dataset or xarray.DataArray
         Stddev data. Has the same variable name(s) as dobj.
-    
+
     """
     return dobj.std(dim)
diff --git a/docs/Makefile b/docs/Makefile
@@ -17,4 +17,4 @@ help:
 # Catch-all target: route all unknown targets to Sphinx using the new
 # "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
 %: Makefile
-	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
diff --git a/docs/api.rst b/docs/api.rst
@@ -7,4 +7,4 @@
  .. automodule:: climate_index_collection.dummy
     :members:
     :undoc-members:
-    :show-inheritance:
+    :show-inheritance:
diff --git a/docs/conf.py b/docs/conf.py
@@ -14,6 +14,12 @@
 import pathlib
 import sys
 
+# The version info for the project you're documenting, acts as replacement for
+# |version| and |release|, also used in various other places throughout the
+# built documents.
+# see https://pypi.org/project/setuptools-scm/ for details
+from pkg_resources import get_distribution
+
 
 print("python exec:", sys.executable)
 print("sys.path:", sys.path)
@@ -29,14 +35,9 @@
 copyright = "2021, Marco Landt-Hayen"
 author = "Marco Landt-Hayen"
 
-# The version info for the project you're documenting, acts as replacement for
-# |version| and |release|, also used in various other places throughout the
-# built documents.
-# see https://pypi.org/project/setuptools-scm/ for details
-from pkg_resources import get_distribution
-release = get_distribution('climate_index_collection').version
+release = get_distribution("climate_index_collection").version
 # for example take major/minor
-version = '.'.join(release.split('.')[:2])
+version = ".".join(release.split(".")[:2])
 
 # -- General configuration ---------------------------------------------------
 
@@ -84,4 +85,4 @@
 
 # -- nbsphinx specific options ----------------------------------------------
 # this allows notebooks to be run even if they produce errors.
-nbsphinx_allow_errors = True
+nbsphinx_allow_errors = True
diff --git a/docs/environment.yml b/docs/environment.yml
@@ -20,4 +20,4 @@ dependencies:
      - jupyter_client
      - sphinx_pangeo_theme
      - sphinx-copybutton
-     - sphinxcontrib-srclinks
+     - sphinxcontrib-srclinks
diff --git a/docs/index.rst b/docs/index.rst
@@ -29,4 +29,4 @@ Indices and tables
 * :ref:`modindex`
 * :ref:`search`
 
-.. _reStructuredText: https://www.sphinx-doc.org/en/master/usage/restructuredtext/basics.html
+.. _reStructuredText: https://www.sphinx-doc.org/en/master/usage/restructuredtext/basics.html
diff --git a/docs/new_section.rst b/docs/new_section.rst
@@ -1,2 +1,2 @@
 Some new exciting Section
-=========================
+=========================
diff --git a/docs/new_section_notebook.ipynb b/docs/new_section_notebook.ipynb
@@ -68,4 +68,4 @@
  },
  "nbformat": 4,
  "nbformat_minor": 4
-}
+}