Merge pull request #2 from sodascience/new_r_functionality

Align Python ReMoDe with R outputs and update packaging/CI

Author: jgarciab

.github/workflows/ci.yml

@@ -1,6 +1,9 @@
 name: CI
 
-on: [push, pull_request]
+on:
+  push:
+  pull_request:
+  workflow_dispatch:
 
 jobs:
   build:
@@ -14,27 +17,28 @@ jobs:
     steps:
     - name: Check out repository
       uses: actions/checkout@v4
+      with:
+        fetch-depth: 0
 
     - name: Set up Python ${{ matrix.python-version }}
       uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
+        cache: pip
 
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip
-        pip install .
-        pip install ruff mypy pytest
+        python -m pip install ".[test]"
 
     - name: Lint with ruff
       run: |
-        ruff .
-      continue-on-error: true
+        python -m ruff check remode tests
 
     - name: Check types with mypy
       run: |
-        mypy remode/remode.py 
+        python -m mypy remode/remode.py
 
     - name: Run tests with pytest
       run: |
-        pytest
+        python -m pytest -q

.github/workflows/python-publish.yml

@@ -3,6 +3,7 @@ name: Upload Python Package
 on:
   release:
     types: [published]
+  workflow_dispatch:
 
 permissions:
   contents: read
@@ -17,15 +18,19 @@ jobs:
         uses: actions/setup-python@v5
         with:
           python-version: '3.x'
+          cache: pip
 
       - name: Install build tools
         run: |
           python -m pip install --upgrade pip
-          pip install build
+          python -m pip install build twine
 
       - name: Build package
         run: python -m build
 
+      - name: Validate package metadata
+        run: python -m twine check dist/*
+
       - name: Publish package
         uses: pypa/gh-action-pypi-publish@db8f07d3871a0a180efa06b95d467625c19d5d5f
         with:

.gitignore

@@ -158,3 +158,6 @@ cython_debug/
 #  and can be added to the global gitignore or merged into this file.  For a more nuclear
 #  option (not recommended) you can uncomment the following to ignore the entire idea folder.
 #.idea/
+
+# macOS
+.DS_Store

README.md

@@ -5,6 +5,7 @@
 ### Features
 - Mode Detection: Identifies all potential local maxima in the dataset.
 - Statistical Tests: Implements Fisher's exact test and binomial tests to validate modes.
+- Mode Statistics: Returns per-mode p-values and approximate Bayes factors.
 - Data Formatting: Converts raw data into histogram format for analysis.
 - Stability Analysis: Includes functionality to assess the stability of detected modes using jackknife resampling.
 - Visualization: Provides methods to plot the histogram of data along with identified modes.
@@ -26,21 +27,28 @@ from remode import ReMoDe
 xt_count = [8, 20, 5, 2, 6, 2, 30]
 
 # Create an instance of ReMoDe
-detector = ReMoDe()
+detector = ReMoDe(alpha_correction="descriptive_peaks")  # default
 
 # Fit model
 results = detector.fit(xt_count)
+# results contains:
+# - nr_of_modes
+# - modes
+# - p_values
+# - approx_bayes_factors
 
 # Plot the results
 detector.plot_maxima()
 
 # Perform stability analysis
-stability_info = detector.evaluate_stability(percentage_steps=50)
+stability_info = detector.remode_stability(percentage_steps=50)
 
 ```
 
+
 See also the tutorial [here](https://github.com/sodascience/remode/blob/main/tutorial.ipynb).
 
+
 ### Citation
 
 Please cite the following paper:

pyproject.toml

@@ -1,9 +1,5 @@
 [build-system]
-requires = [
-  "setuptools>=42",
-  "wheel",
-  "setuptools_scm[toml]>=6.0"
-]
+requires = ["setuptools>=61", "setuptools-scm>=8", "wheel"]
 build-backend = "setuptools.build_meta"
 
 [project]
@@ -31,7 +27,6 @@ dynamic = ["version"]
 
 
 classifiers = [
-    "License :: OSI Approved :: MIT License",
     "Programming Language :: Python :: 3",
     "Programming Language :: Python :: 3.8",
     "Programming Language :: Python :: 3.9",
@@ -41,16 +36,19 @@ classifiers = [
     "Operating System :: OS Independent",
 ]
 
-
-[tool.setuptools_scm]
-write_to = "remode/_version.py"
-
-
 [project.optional-dependencies]
 test = [
     "ruff", "pytest", "mypy"
 ]
 
+[tool.setuptools_scm]
+write_to = "remode/_version.py"
+tag_regex = "^(?:v)?(?P<version>\\d+\\.\\d+(?:\\.\\d+)?)$"
+local_scheme = "no-local-version"
+
+[tool.setuptools.packages.find]
+include = ["remode*"]
+
 [project.urls]
 homepage = "https://github.com/sodascience/remode"
 repository = "https://github.com/sodascience/remode"

remode/__init__.py

@@ -1,5 +1,15 @@
 """Import ReMoDe class and statistical tests."""
 
-__all__ = ['ReMoDe', 'perform_fisher_test', 'perform_binomial_test']
+from importlib.metadata import PackageNotFoundError, version
+
+__all__ = ['ReMoDe', 'perform_fisher_test', 'perform_binomial_test', '__version__']
 
 from .remode import ReMoDe, perform_fisher_test, perform_binomial_test
+
+try:
+    __version__ = version('ReMoDe')
+except PackageNotFoundError:
+    try:
+        from ._version import version as __version__
+    except ImportError:
+        __version__ = '0+unknown'