[pull] main from AlphaGenes:main

.flake8

@@ -4,5 +4,8 @@ max-line-length = 88
 extend-ignore = 
     # also the Black's default, whitespace before ':'
     E203,
+    # for the missing whitespace after ',', csv files need to have no whitespace after the comma
+    # also for the missing whitespace after ':', which is used in website links and f-string formatting
+    E231,
     # this is for the line length, all the lines too long are comments now
     E501

.github/workflows/publish.yml

@@ -11,9 +11,9 @@ jobs:
         environment: release
 
         steps:
-            - uses: actions/checkout@v3
+            - uses: actions/checkout@v6
             - name: Set up Python
-              uses: actions/setup-python@v4
+              uses: actions/setup-python@v6
               with:
                 python-version: "3.x"
 
@@ -31,14 +31,14 @@ jobs:
             - name: Build SDist and wheel
               run: python3 -m build
 
-            - uses: actions/upload-artifact@v4
+            - uses: actions/upload-artifact@v6
               with:
                 path: dist/*
 
             - name: Check metadata
               run: pipx run twine check dist/*
 
-            - uses: actions/download-artifact@v4
+            - uses: actions/download-artifact@v7
               with:
                 name: artifact
                 path: dist
@@ -47,4 +47,3 @@ jobs:
               if: startsWith(github.ref, 'refs/tags')
               uses: pypa/gh-action-pypi-publish@release/v1
 
-

.github/workflows/tests.yml

@@ -4,22 +4,36 @@ on: [push, pull_request]
 jobs:
     pre-commit_and_pytest:
         name: Run pre-commit and pytest
+        env:
+          PIP_DISABLE_PIP_VERSION_CHECK: "1"
         strategy:
           matrix:
-            os: [ubuntu-latest, Windows-latest, macos-latest]
+            os: [ubuntu-latest, windows-latest, macos-latest]
+            python-version: ["3.8", "3.9", "3.10", "3.11", "3.12", "3.13"]
         runs-on: ${{ matrix.os }}
         permissions:
             contents: read
 
         steps:
-            - uses: actions/checkout@v3
-            - name: Set up Python
-              uses: actions/setup-python@v4
+            - uses: actions/checkout@v5
               with:
-                python-version: "3.11.x"
-
-            - uses: pre-commit/action@v3.0.0
-              name: Run pre-commit
+                fetch-depth: 1
+                fetch-tags: false
+                show-progress: false
+            - name: Set up Python ${{ matrix.python-version }}
+              uses: actions/setup-python@v6
+              with:
+                python-version: ${{ matrix.python-version }}
+                pip-version: "25.0.1"
+
+            - name: Upgrade pip
+              run: python -m pip install --upgrade pip
+
+            - name: Install pre-commit
+              run: python -m pip install pre-commit
+
+            - name: Run pre-commit
+              run: pre-commit run --show-diff-on-failure --color=always --all-files
 
             - name: Install pypa/build
               run: >-
@@ -36,7 +50,7 @@ jobs:
               run: python3 -m build
 
             - name: Install AlphaPeel
-              run: pip install dist/alphapeel-1.3.0-py3-none-any.whl
+              run: pip install dist/alphapeel-1.4.0-py3-none-any.whl
 
             - name: Install pytest
               run: |
@@ -45,4 +59,4 @@ jobs:
 
             - name: Run pytest
               run: |
-                pytest
+                pytest

.gitignore

@@ -1,25 +1,29 @@
-*.pyo
-*.pyc
-dist
-bin
 __pycache__/
-*.py[cod]
+.Rproj.user
+.pytest_cache
 *.DS_Store
 *.egg-info/
+*.py[cod]
+*.pyo
+*.pyc
+**/.RData
+**/.Rhistory
+**/*.Rproj
+**/segfile.txt
+.vscode
 AlphaPeel
+AlphaPeel_env
+bin
+dist
 build/
 docs/build/
 example/outputs
-AlphaPeel_env
-tests/functional_tests/**/outputs/
-tests/functional_tests/**/outputs/**
+example/simple_*/*_output.*
+tests/accuracy_tests/accu_report.txt
+tests/accuracy_tests/outputs*
+tests/accuracy_tests/reports*
 tests/accuracy_tests/outputs/
 tests/accuracy_tests/outputs/**
-.pytest_cache
-tests/accuracy_tests/accu_report.txt
-.Rproj.user
-**/.RData
-**/.Rhistory
-**/*.Rproj
-**/segfile.txt
 tests/accuracy_tests/sim_for_alphapeel_accu_test/seg_file.txt
+tests/functional_tests/**/outputs/
+tests/functional_tests/**/outputs/**

README.md

@@ -12,6 +12,16 @@ Whalen, A, Ros-Freixedes, R, Wilson, DL, Gorjanc, G, Hickey, JM. (2018). Hybrid
 
 See https://alphapeel.readthedocs.io/en/latest
 
+Quick links:
+
+- [Installation](https://alphapeel.readthedocs.io/en/latest/get_started.html#install-software)
+
+- [Simple example](https://alphapeel.readthedocs.io/en/latest/get_started.html#an-example)
+
+- [How to use](https://alphapeel.readthedocs.io/en/latest/usage.html)
+
+- [Algorithm](https://alphapeel.readthedocs.io/en/latest/algorithm.html)
+
 ## Conditions of use
 
 AlphaPeel is fully and freely available for all use under the MIT License.