Add linting including gh action

.github/workflows/lint.yml

@@ -0,0 +1,23 @@
+# Lint tests run on PR
+# but should not run after push to main because reporting
+# these after push is meaningless to the building of the package
+name: lint
+
+on:
+  pull_request:
+    branches: [main]
+
+jobs:
+  lint:
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v3
+    - name: Set up Python
+      uses: actions/setup-python@v4
+      with:
+        python-version: "3.10"
+    - run: pip install tox
+
+    - name: Test Lint
+      run: tox -e lint

README.rst

@@ -5,12 +5,17 @@ COSMO Software Cookbook
 
 .. marker-intro-start
 
-The COSMO cookbook contains recipes for atomic-scale modelling for materials and molecules, with a particular focus on machine learning and statistical sampling methods.
-Rather than focusing on the usage of a specific package (see the `COSMO github page <https://github.com/lab-cosmo>`_ for a list of available tools, and their documentations) this cookbook provides concrete examples of the solution of modeling problems using a combination of the various tools.  
+The COSMO cookbook contains recipes for atomic-scale modelling for materials and
+molecules, with a particular focus on machine learning and statistical sampling methods.
+Rather than focusing on the usage of a specific package (see the `COSMO github page
+<https://github.com/lab-cosmo>`_ for a list of available tools, and their
+documentations) this cookbook provides concrete examples of the solution of modeling
+problems using a combination of the various tools.
 
 .. marker-intro-end
 
 Contributors
 ------------
 
-If you want contribute an example, recipe or tutorial that combines multiple software tools together, check out the `contributing guidelines <CONTRIBUTING.rst>`_ first. 
+If you want contribute an example, recipe or tutorial that combines multiple software
+tools together, check out the `contributing guidelines <CONTRIBUTING.rst>`_ first.

docs/src/index.rst

@@ -0,0 +1,14 @@
+
+COSMO Software Cookbook
+=======================
+
+.. include:: ../../README.rst
+   :start-after: marker-intro-start
+   :end-before: marker-intro-end
+
+.. toctree::
+   :caption: Table of Contents
+
+   mlp_models/index
+   uncategorized/index
+   sample_selection/index

examples/mlp_models/linear_model.py

@@ -10,11 +10,10 @@
 
 
 import numpy as np
-import matplotlib.pyplot as plt
 
 # %%
 # Explanation
 
-X = np.random.rand(10000)*400
-Y = 0.1*X+10.1
-Y_p = Y + np.random.randn(10000)*1.5
+X = np.random.rand(10000) * 400
+Y = 0.1 * X + 10.1
+Y_p = Y + np.random.randn(10000) * 1.5

examples/sample_selection/sample_selection_librascal.py

@@ -12,13 +12,9 @@
 # First, import all the necessary packages
 import ase.io
 import numpy as np
-from sklearn.decomposition import PCA
-
-import chemiscope
 from rascal.representations import SphericalInvariants
-from rascal.utils import FPSFilter
-from skmatter import sample_selection, feature_selection
-
+from sklearn.decomposition import PCA
+from skmatter import feature_selection, sample_selection
 
 # %%
 # Load molecular data
@@ -70,7 +66,8 @@
 # Generate a SOAP spherical expansion
 soap = SphericalInvariants(**soap_hypers)
 
-# Perform a data trasnformation and get the descriptor with samples as atomic environments
+# Perform a data trasnformation and get the descriptor with samples as atomic
+# environments
 atom_dscrptr = soap.transform(frames).get_features(soap)
 
 # Calculate the stucture features as the mean over the atomic features for each

tox.ini

@@ -1,13 +1,57 @@
 [tox]
 min_version = 4.0
 envlist =
+    lint
     docs
 
-[testenv:docs]
+lint_folders = "{toxinidir}/examples"
+
+[testenv:lint]
+skip_install = true
+deps =
+    black
+    blackdoc
+    flake8
+    flake8-bugbear
+    isort
+    flake8-sphinx-links
+    sphinx-lint
+commands =
+    flake8 {[tox]lint_folders}
+    black --check --diff {[tox]lint_folders}
+    blackdoc --check --diff {[tox]lint_folders}
+    isort --check-only --diff {[tox]lint_folders}
+    sphinx-lint --enable line-too-long --max-line-length 88 \
+        -i "{toxinidir}/docs/src" \
+        {[tox]lint_folders} "{toxinidir}/README.rst"
 
+[testenv:docs]
+deps =
+    -r docs/requirements.txt
 commands =
-    pip install -r docs/requirements.txt
+    # tox's can not handle our custom requirement files in the deps section.
     pip install -r docs/requirements-rascal.txt
     pip install -r docs/requirements-equistore.txt
 
     sphinx-build {posargs:-E} -W -b html docs/src docs/build/html
+
+[testenv:format]
+# Abuse tox to do actual formatting. Users can call `tox -e format` to run
+# formatting on all files
+skip_install = true
+deps =
+    black
+    blackdoc
+    isort
+commands =
+    black {[tox]lint_folders}
+    blackdoc {[tox]lint_folders}
+    isort {[tox]lint_folders}
+
+[flake8]
+max_line_length = 88
+exclude =
+    docs/src/examples/
+per-file-ignores =
+    # D205 and D400 are incompatible with the requirements of sphinx-gallery
+    examples/**:D205, D400