pre-commit formatting

.github/scripts/generate_pip_deps_from_conda.py

@@ -15,15 +15,16 @@
     $ python scripts/generate_pip_deps_from_conda.py --compare
 
 """
+
 import argparse
 import pathlib
 import re
 import sys
 
 if sys.version_info >= (3, 11):
-    import tomllib
+    pass
 else:
-    import tomli as tomllib
+    pass
 import yaml
 
 EXCLUDE = {"python"}

.github/workflows/main.yml

@@ -17,23 +17,23 @@ jobs:
           environment-file: environment.yml
           use-mamba: true
           python-version: "3.9"
-          
+
       - shell: bash -l {0}
         run: |
           conda info
           conda list
-          
+
       - name: Install snowlaps-emulator
         shell: bash -l {0}
         run: |
             pip install -e .
-            
+
       - name: Checkout code
         uses: actions/checkout@v4
         with:
           # Full git history is needed to get a proper list of changed files within `super-linter`
-          fetch-depth: 0 
-          
+          fetch-depth: 0
+
       - name: Run tests and generate coverage report
         shell: bash -l {0}
         run: |
@@ -58,4 +58,3 @@ jobs:
       #     snyk test --file=dev-requirements.txt --package-manager=pip --severity-threshold=high
       #   env:
       #     SNYK_TOKEN: ${{ secrets.SNYK_TOKEN }}
-

.pre-commit-config.yaml

@@ -0,0 +1,77 @@
+ci:
+    autofix_prs: false
+    autoupdate_schedule: quarterly
+repos:
+        - repo: https://github.com/pre-commit/pre-commit-hooks
+          rev: v5.0.0
+          hooks:
+                - id: check-yaml
+                - id: end-of-file-fixer
+                  exclude: \.txt$
+                - id: trailing-whitespace  # Remove trailing
+                                           # whitespaces
+                - id: check-merge-conflict
+        # Fix common spelling mistakes
+        - repo: https://github.com/codespell-project/codespell
+          rev: v2.3.0
+          hooks:
+                - id: codespell
+                  args: [
+                  '--ignore-words-list', 'alos,inout,vor',
+                    '--ignore-regex', '\bnin\b',
+                    '--'
+                  ]
+                  types_or: [python, markdown] # rst, 
+                  files: ^(snowlaps|tests)/ # docs
+
+        # Replace relative imports
+        - repo: https://github.com/astral-sh/ruff-pre-commit
+          # Ruff version.
+          rev: v0.8.1
+          hooks:
+            # Run the linter.
+            - id: ruff
+              types_or: [ python, pyi ]
+              args: ["check", "--fix" ]
+            # Run the formatter.
+            - id: ruff-format
+              types_or: [ python, pyi ]
+
+        # Format the code aggressively using black
+        - repo: https://github.com/psf/black
+          rev: 24.10.0
+          hooks:
+                  - id: black
+                    args: [--line-length=88]
+
+        # Automatically upgrade syntax to a minimum version
+        - repo: https://github.com/asottile/pyupgrade
+          rev: v3.19.0
+          hooks:
+                - id: pyupgrade
+                  args: [--py37-plus]
+
+        # Various formattings
+        - repo: https://github.com/pre-commit/pygrep-hooks
+          rev: v1.10.0
+          hooks:
+                # Eval should never be used (can do arbitrary code
+                # execution)
+                - id: python-no-eval
+                # Enforce the use of type annotations instead of
+                # docstring type comments
+                - id: python-use-type-annotations
+
+
+        - repo: local
+          hooks:
+            # Generate pip's dev-requirements.txt from conda's
+            # dev-environment.yml to run snyk (snyk doesn't currently
+            # support conda)
+            - id: pip-to-conda
+              name: Generate pip dependency from conda
+              language: python
+              entry: .github/scripts/generate_pip_deps_from_conda.py
+              files: ^(dev-environment.yml|requirements-dev.txt)$
+              pass_filenames: false
+              additional_dependencies: [tomli, pyyaml]

README.org

@@ -76,11 +76,10 @@ cd snowlaps
 
 * Contributions
 
-Any contribution to =snowlaps= is welcome! Feel free to add new issues, open pull requests or ask questions in the discussion forum. 
+Any contribution to =snowlaps= is welcome! Feel free to add new issues, open pull requests or ask questions in the discussion forum.
 
 * Citation
 
-If you use this code, please cite the associated publication: 
-
-Chevrollier, L.-A., Wehrlé, A., Cook, J. M., Pirk, N., Benning, L. G., Anesio, A. M., and Tranter, M.: Separating the albedo reducing effect of different light absorbing particles on snow using deep learning, EGUsphere [preprint], https://doi.org/10.5194/egusphere-2024-2583, 2024. 
+If you use this code, please cite the associated publication:
 
+Chevrollier, L.-A., Wehrlé, A., Cook, J. M., Pirk, N., Benning, L. G., Anesio, A. M., and Tranter, M.: Separating the albedo reducing effect of different light absorbing particles on snow using deep learning, EGUsphere [preprint], https://doi.org/10.5194/egusphere-2024-2583, 2024.

data/inputs/snicar_config_for_emulator.yaml

@@ -54,13 +54,13 @@ IMPURITIES:
     COATED: False
     UNIT: 0
     CONC: [0 ,0]
-  
+
   SA:
     NAME: "sa"
     FILE: "snow_algae_empirical_Chevrollier2023.nc"
     COATED: False
     UNIT: 1
-    CONC: [0 ,0]  
+    CONC: [0 ,0]
 
   DUST:
     NAME: "dust"
@@ -85,7 +85,7 @@ PLOT:
     SAVE: False
     SAVEPATH: "./"
 
-BIOOPTICAL: 
+BIOOPTICAL:
     WET_DENSITY: 1060
     DRY_DENSITY: 684
     ABS_CFF_CALC: True
@@ -130,4 +130,3 @@ BIOOPTICAL:
     SAVE_PATH_NETCDF: "Data/OP_data/480band/lap/"
     INFO_NETCDF: "info"
     FILENAME_NETCDF: "alg"
-

examples/snowlaps_ex03_compare_with_biosnicar.py

@@ -2,7 +2,7 @@
 
 """
 
-NOTE: this script requires an installation of the main branch of the biosnicar 
+NOTE: this script requires an installation of the main branch of the biosnicar
 model (https://github.com/jmcook1186/biosnicar-py/tree/master)
 
 """

ruff.toml

@@ -0,0 +1,18 @@
+# let Black deal with line length, Ruff currently doesn't autofix E501
+line-length = 150
+
+[lint]
+select = [
+    # pycodestyle
+    "E",
+    # Pyflakes
+    "F",
+    # pyupgrade
+    "UP",
+    # flake8-bugbear
+    "B",
+    # flake8-simplify
+    "SIM",
+    # isort
+    "I",
+]

setup.cfg

@@ -14,4 +14,4 @@ exclude = test*
 
 [options.entry_points]
 console_scripts =
-    snowlaps-cli = snowlaps.snowlaps:SnowLapsEmulator
+    snowlaps-cli = snowlaps.snowlaps:SnowLapsEmulator

tests/test_snowlaps.py

@@ -8,6 +8,7 @@
 
 from snowlaps.snowlaps import SnowlapsEmulator
 
+
 class TestSnowlapsEmulator:
     my_emulator = SnowlapsEmulator()