Clean code

.github/workflows/ci.yml

@@ -17,7 +17,11 @@ jobs:
                python -m pip install --upgrade pip
                pip install .
                pip install pytest
+               pip install coverage
         - name: Run tests
           run: |
-               pytest test/test_core.py
-               pytest test/test_cli.py
+              make coverage
+        - name: Upload coverage reports to Codecov
+          uses: codecov/[email protected]
+          with:
+            token: ${{ secrets.CODECOV_TOKEN }}

.gitignore

@@ -29,4 +29,5 @@ site/
 # Tests
 test/test_protein_L/tmp/
 ## pytest
-.pytest_cache
+.pytest_cache
+.coverage

.pre-commit-config.yaml

@@ -0,0 +1,14 @@
+# See https://pre-commit.com for more information
+# See https://pre-commit.com/hooks.html for more hooks
+repos:
+-   repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v3.2.0
+    hooks:
+    -   id: trailing-whitespace
+    -   id: end-of-file-fixer
+    -   id: check-yaml
+    -   id: check-added-large-files
+-   repo: https://github.com/psf/black
+    rev: 24.1.1
+    hooks:
+    -   id: black

Makefile

@@ -0,0 +1,17 @@
+.PHONY: coverage
+
+coverage:
+	coverage run -m pytest test/test_fitting.py \
+	                       test/test_lineshapes.py \
+						   test/test_io.py \
+						   test/test_utils.py \
+						   test/test_main.py \
+						   test/test_cli.py \
+						   test/test_simulation.py \
+						   test/test_plotting.py
+
+coverage-html:
+	coverage html
+	firefox htmlcov/index.html
+
+test: coverage coverage-html

README.md

@@ -1,6 +1,8 @@
 # Peakipy - NMR peak integration/deconvolution using python
 
 ![Test](https://github.com/j-brady/peakipy/actions/workflows/ci.yml/badge.svg)
+[![codecov](https://codecov.io/gh/j-brady/peakipy/graph/badge.svg?token=1F90QI5WMS)](https://codecov.io/gh/j-brady/peakipy)
+
 
 [peakipy documentation](https://j-brady.github.io/peakipy)
 
@@ -26,7 +28,7 @@ should have been added to your path.
 
 ## Inputs
 
-1. Peak list (NMRPipe, Analysis v2.4, Sparky) 
+1. Peak list (NMRPipe, Analysis v2.4, Sparky)
 2. NMRPipe frequency domain dataset (2D or Pseudo 3D)
 
 There are four main commands:

ccpn_macros/selected_to_peakipy.py

@@ -1,4 +1,5 @@
 """ Export selected peaks to TSV file """
+
 import os
 from pathlib import Path
 import pandas as pd
@@ -84,7 +85,6 @@ def peakipy_check():
 
 
 if __name__ == "__main__":
-
     peaks = current.peaks
     df = PeaksToDataFrame(peaks)
     column_order = [

docs/quickstart.md

@@ -95,7 +95,7 @@ Requirements
 
 === "Latest"
 
-    The latest version (1.1.2) of `peakipy` requires Python 3.10 or above (see `pyproject.toml` for details).
+    The latest version (1.1.3) of `peakipy` requires Python 3.10 or above (see `pyproject.toml` for details).
 
 === "0.2.0"