Merge pull request #167 from mmaelicke/pre-commit

Pre commit

.coveragerc

@@ -1,12 +1,12 @@
 [run]
-omit = 
+omit =
     skgstat/tests/*
     skgstat/plotting/*
     docs/*
     setup.py
 
 [report]
-exclude_lines = 
+exclude_lines =
     pragma: no cover
     def __repr__
     def __str__

.github/workflows/main.yml

@@ -13,9 +13,9 @@ jobs:
    name: Run Unittest
    runs-on: ubuntu-20.04
    strategy:
-    matrix: 
+    matrix:
       python: ['3.6', '3.7', '3.8', '3.9', '3.10']
-   
+
    steps:
       - name: Checkout
         uses: actions/checkout@master
@@ -24,7 +24,7 @@ jobs:
         with:
           python-version: ${{ matrix.python }}
       - name: Install SciKit-GStat
-        run: | 
+        run: |
           pip3 install -r requirements.txt
           python3 setup.py install
       - name: Install PyTest requirements
@@ -51,7 +51,7 @@ jobs:
         with:
           python-version: '3.8'
       - name: Install SciKit-GStat
-        run: | 
+        run: |
           pip3 install -r requirements.txt
           python3 setup.py install
       - name: Install Sphinx requirements
@@ -61,13 +61,13 @@ jobs:
       - name: Install pdflatex
         run: sudo apt install texlive-latex-extra texlive-latex-recommended texlive-fonts-recommended pandoc
       - name: make HTML & LaTeX docs
-        run: | 
+        run: |
           cd docs
-          make html 
+          make html
           make latex
         continue-on-error: true
       - name: compile LaTeX
-        run: | 
+        run: |
           cd docs/_build/latex
           pdflatex -interaction=nonstopmode -halt-on-error SciKitGStat.tex
           cd ../..
@@ -79,7 +79,7 @@ jobs:
           target_branch: gh-pages
           build_dir: docs/_build/html
         env:
-          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}  
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
 
   release:
     name: Create Github release
@@ -101,7 +101,7 @@ jobs:
     name: Publish to PyPi
     runs-on: ubuntu-20.04
     needs: test
-    if: startsWith(github.event.ref, 'refs/tags/v')  
+    if: startsWith(github.event.ref, 'refs/tags/v')
 
     steps:
     - uses: actions/checkout@v3
@@ -119,13 +119,13 @@ jobs:
       uses: pypa/gh-action-pypi-publish@27b31702a0e7fc50959f5ad993c78deac1bdfc29
       with:
         user: __token__
-        password: ${{ secrets.PYPI_TOKEN }} 
-    
-  ci_develop:    
+        password: ${{ secrets.PYPI_TOKEN }}
+
+  ci_develop:
     name: Print Github Context for Development
     runs-on: ubuntu-20.04
     if: true
-    
+
     steps:
     - name: Dump GitHub context
       env:

.github/workflows/pre-commit.yml

@@ -0,0 +1,15 @@
+name: Linting and formatting (pre-commit)
+
+on:
+  push:
+    branches: [ main ]
+  pull_request:
+    branches: [ main ]
+
+jobs:
+  pre-commit:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v3
+    - uses: actions/setup-python@v4
+    - uses: pre-commit/[email protected]

.gitignore

@@ -113,4 +113,4 @@ container
 Playground.ipynb
 in_progress
 docs/auto_examples
-docs/gen_modules
+docs/gen_modules

.pre-commit-config.yaml

@@ -0,0 +1,23 @@
+repos:
+  # Fix common spelling mistakes
+  - repo: https://github.com/codespell-project/codespell
+    rev: v2.2.1
+    hooks:
+      - id: codespell
+        args: [
+          #  Verly is a Name, coo references the SciPy coo sparse matrix
+          '--ignore-words-list', 'verly,coo',
+          '--write-changes',
+  #                    'nd,alos,inout',
+  #                    '--ignore-regex', '\bhist\b',
+          '--'
+        ]
+        types_or: [python, rst, markdown]
+        files: ^(skgstat|docs|tutorials)/
+
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v2.3.0
+    hooks:
+      - id: check-yaml
+      - id: end-of-file-fixer
+      - id: trailing-whitespace

Dockerfile

@@ -29,4 +29,4 @@ RUN pip install jupyter
 # open port 8888
 EXPOSE 8888
 
-CMD jupyter notebook --ip "0.0.0.0"
+CMD jupyter notebook --ip "0.0.0.0"

Dockerfile.legacy

@@ -2,7 +2,7 @@
 # use the minimal jupyter notebook
 FROM jupyter/minimal-notebook:ad3574d3c5c7
 
-# build tutorials folder 
+# build tutorials folder
 USER root
 RUN mkdir tutorials
 
@@ -12,15 +12,15 @@ USER $NB_USER
 # copy the tutorials content
 COPY ./docs/tutorials ./tutorials
 
-# install the latest version 
+# install the latest version
 COPY ./ ./scikit-gstat
 
 # use the latest
 RUN cd scikit-gstat && \
     pip install . && \
     cd ..
 
-# the interfaces has two additional 
+# the interfaces has two additional
 # optional dependencies: pykrige and gstools
 RUN pip install pykrige gstools
 

MANIFEST.in

@@ -8,4 +8,4 @@ include .coveragerc
 include Dockerfile
 include Dockerfile.legacy
 graft skgstat/data/rf
-graft skgstat/data/samples
+graft skgstat/data/samples

README.rst

@@ -79,8 +79,8 @@ PyPI
 
   pip install scikit-gstat
 
-**Note:** It can happen that the installation of numba or numpy is failing using pip. Especially on Windows systems. 
-Usually, a missing Dll (see eg. `#31 <https://github.com/mmaelicke/scikit-gstat/issues/31>`_) or visual c++ redistributable is the reason. 
+**Note:** It can happen that the installation of numba or numpy is failing using pip. Especially on Windows systems.
+Usually, a missing Dll (see eg. `#31 <https://github.com/mmaelicke/scikit-gstat/issues/31>`_) or visual c++ redistributable is the reason.
 
 GIT:
 ^^^^

RELEASE.md

@@ -1,6 +1,6 @@
 # Scikit-GStat
 
-SciKit-Gstat is a scipy-styled variogram estimation and analysis module for geostatistics. 
+SciKit-Gstat is a scipy-styled variogram estimation and analysis module for geostatistics.
 It includes classes for variogram estimation and ordinary kriging. More advanced use-cases
 like directional variograms and space-time variograms are included as well.
 
@@ -26,4 +26,4 @@ or bibtex:
     URL = {https://gmd.copernicus.org/articles/15/2505/2022/},
     DOI = {10.5194/gmd-15-2505-2022}
 }
-```
+```

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)