build: cleaner build process

.github/workflows/upload-to-pypi.yml

@@ -2,10 +2,36 @@ name: Upload package to Pypi
 
 on:
   workflow_dispatch:
-  release:
-    types: [created]
+    inputs:
+      overrideVersion:
+        description: Manually force a version
+
+env:
+  SETUPTOOLS_SCM_PRETEND_VERSION: ${{ github.event.inputs.overrideVersion }}
+  CIBW_BUILD_VERBOSITY: 1
 
 jobs:
+  make_sdist:
+    name: Make SDist
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v2
+      with:
+        fetch-depth: 0
+    - name: Setup Python
+      uses: actions/setup-python@v2
+      with:
+        python-version: '3.8'
+    - name: Install deps
+      run: python -m pip install build twine
+    - name: Build SDist
+      run: python -m build --sdist
+    - uses: actions/upload-artifact@v2
+      with:
+        path: dist/*.tar.gz
+    - name: Check metadata
+      run: twine check dist/*
+
   build_wheels:
     name: Build wheels on ${{ matrix.os }}
     runs-on: ${{ matrix.os }}
@@ -36,52 +62,35 @@ jobs:
             bitness: 32
           - os: windows-latest
             python: 39
-
     steps:
       - uses: actions/checkout@v2
-
+        with:
+          fetch-depth: 0
       - uses: actions/setup-python@v2
         name: Install Python
         with:
           python-version: '3.8'
-
-      - name: Install cibuildwheel and dependencies
+      - name: Install cibuildwheel
         run: |
           python -m pip install --upgrade pip
-          python -m pip install cibuildwheel twine
-
+          python -m pip install cibuildwheel
       - name: Build wheels
         env:
           CIBW_BUILD: cp${{ matrix.python }}-${{ matrix.platform_id }}
-          TWINE_USERNAME: ${{ secrets.PYPI_USERNAME }}
-          TWINE_PASSWORD: ${{ secrets.PYPI_PASSWORD }}
-        run: |
-          python -m cibuildwheel --output-dir wheelhouse
-          python -m twine upload wheelhouse/*.whl
-
+        run: python -m cibuildwheel --output-dir wheelhouse
       - uses: actions/upload-artifact@v2
         with:
           path: wheelhouse/*.whl
 
-  deploy_sdist:
+  upload_all:
+    needs: [build_wheels, make_sdist]
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v2
-      - name: Set up Python 3.8
-        uses: actions/setup-python@v2
-        with:
-          python-version: '3.8'
-      - name: Install dependencies
-        run: |
-          python -m pip install --upgrade pip
-          pip install setuptools wheel twine
-      - name: Build
-        env:
-          TWINE_USERNAME: ${{ secrets.PYPI_USERNAME }}
-          TWINE_PASSWORD: ${{ secrets.PYPI_PASSWORD }}
-        run: |
-          python setup.py sdist
-          python -m twine upload dist/*.tar.gz
-      - uses: actions/upload-artifact@v2
-        with:
-          path: dist/*.tar.gz
+    - uses: actions/download-artifact@v2
+      with:
+        name: artifact
+        path: dist
+    - uses: pypa/[email protected]
+      with:
+        user: ${{ secrets.PYPI_USERNAME }}
+        password: ${{ secrets.PYPI_PASSWORD }}

.gitignore

@@ -82,4 +82,5 @@ docs/build/*
 .Trashes
 ehthumbs.db
 Thumbs.db
-site/
+site/
+src/ruptures/version.py

.pre-commit-config.yaml

@@ -1,43 +1,43 @@
 repos:
 - repo: https://github.com/psf/black
-  rev: stable
+  rev: 20.8b1
   hooks:
     - id: black
       language_version: python3
 - repo: https://github.com/pre-commit/pre-commit-hooks
-  rev: v3.2.0
+  rev: v3.4.0
   hooks:
     - id: trailing-whitespace  # This hook trims trailing whitespace.
     - id: check-docstring-first  # Checks a common error of defining a docstring after code.
     - id: check-merge-conflict  # Check for files that contain merge conflict strings.
     - id: check-yaml  # This hook checks yaml files for parseable syntax.
     - id: detect-private-key  # Detects the presence of private keys.
-    - id: requirements-txt-fixer  # Sorts entries in requirements.txt.
+    - id: check-symlinks
+    - id: check-toml
 - repo: https://github.com/pre-commit/pygrep-hooks
-  rev: v1.6.0
+  rev: v1.7.0
   hooks:
     - id: python-no-eval  # A quick check for the eval() built-in function.
 - repo: https://github.com/myint/docformatter
-  rev: v1.3.1
+  rev: v1.4
   hooks:
     - id: docformatter
       args: [--in-place]
 - repo: https://gitlab.com/pycqa/flake8
-  rev: 3.8.3
+  rev: 3.8.4
   hooks:
     - id: flake8
       # additional_dependencies: [flake8-docstrings, flake8-bugbear, flake8-spellcheck, flake8-import-order]
 - repo: https://github.com/kynan/nbstripout
-  rev: master
+  rev: 0.3.9
   hooks:
     - id: nbstripout
 -   repo: https://github.com/asottile/blacken-docs
-    rev: v1.8.0
+    rev: v1.9.1
     hooks:
     - id: blacken-docs
 - repo: https://github.com/nbQA-dev/nbQA
-  rev: 0.4.1
+  rev: 0.5.6
   hooks:
     - id: nbqa-black
-      args: [--nbqa-mutate]
-      # additional_dependencies: [black==20.8b1]
+      args: [--nbqa-mutate]

CONTRIBUTING.md

@@ -4,6 +4,11 @@
 ## Before contributing
 
 In all following steps, it is highly recommended to use a virtual environment.
+Build and installation are performed using `pip` so be sure to have the latest version available.
+
+```
+python -m pip install --upgrade pip
+```
 
 ### Install the development version
 
@@ -22,7 +27,7 @@ python -m pip install --editable .[dev]
 ```
 
 Note that `python -m` can be omitted most of the times, but within virtualenvs, it can prevent certain errors.
-Also, in certain terminals (such as zsh), the square brackets must be escaped, e.g. replace `.[dev]` by `.\[dev\]`.
+Also, in certain terminals (such as `zsh`), the square brackets must be escaped, e.g. replace `.[dev]` by `.\[dev\]`.
 
 In addition to `numpy`, `scipy` and `ruptures`, this command will install all packages needed to develop `ruptures`.
 The exact list of librairies can be found in the [`setup.cfg` file](https://github.com/deepcharles/ruptures/blob/master/setup.cfg) (section `[options.extras_require]`).
@@ -37,7 +42,6 @@ To activate the hooks, simply run the following command in your terminal.
 pre-commit install
 ```
 
-
 If you try to commit a non-compliant (i.e. badly formatted) file, `pre-commit` will modify this file and make the commit fail.
 However you need to stage the new changes **yourself** as `pre-commit` will not do that for you (this is by design; see [here](https://github.com/pre-commit/pre-commit/issues/806) or [here](https://github.com/pre-commit/pre-commit/issues/747)).
 Fortunately, `pre-commit` outputs useful messages.

MANIFEST.in

@@ -1 +1,7 @@
-include pyproject.toml
+prune *
+graft src
+graft tests
+
+include LICENSE README.md pyproject.toml setup.py setup.cfg
+exclude CHANGELOG.md CONTRIBUTING.md mkdocs.yml mkdocs_macros.py
+global-exclude __pycache__ *.py[cod] .*

README.md

@@ -2,6 +2,7 @@
 ![build](https://github.com/deepcharles/ruptures/workflows/build/badge.svg)
 ![python](https://img.shields.io/badge/python-3.6%20|%203.7%20|%203.8%20|%203.9-blue)
 [![PyPI version](https://badge.fury.io/py/ruptures.svg)](https://badge.fury.io/py/ruptures)
+[![Conda Version](https://img.shields.io/conda/vn/conda-forge/ruptures.svg)](https://anaconda.org/conda-forge/ruptures)
 ![docs](https://github.com/deepcharles/ruptures/workflows/docs/badge.svg)
 ![PyPI - License](https://img.shields.io/pypi/l/ruptures)
 [![Downloads](https://pepy.tech/badge/ruptures)](https://pepy.tech/project/ruptures)
@@ -30,22 +31,7 @@ If you use `ruptures` in a scientific publication, we would appreciate citations
 
 # Dependencies and install
 
-`ruptures` is tested to work under Python >= 3.6.
-It is written in pure Python and depends on the following libraries: `numpy`, `scipy` and `matplotlib` (optional).
-
-- With **pip**:
-    > pip3 install ruptures
-
-- With **conda**:
-    > conda install -c conda-forge ruptures
-
-- From source: download the archive and run from inside the **ruptures** directory:
-
-    > python3 setup.py install
-
-    or
-
-    > python3 setup.py develop
+Installation instructions can be found [here](https://centre-borelli.github.io/ruptures-docs/install/).
 
 # Basic usage
 

docs/install.md

@@ -1,6 +1,6 @@
 # Installation
 
-This library requires Python3 and the following packages: `numpy`, `scipy` and `matplotlib` (the last one is optional and only for display purposes).
+This library requires Python >=3.6 and the following packages: `numpy`, `scipy` and `matplotlib` (the last one is optional and only for display purposes).
 You can either install the latest stable release or the development version.
 
 ## Stable release
@@ -13,6 +13,7 @@ To install the latest stable release, use `pip` or `conda`.
     ```
 
 === "With conda"
+    `ruptures` can be installed from the `conda-forge` channel (run `conda config --add channels conda-forge` to add it):
     ```
     conda install ruptures
     ```

docs/user-guide/costs/costlinear.md

@@ -6,7 +6,7 @@ Let $0 < t_1 < t_2 < \dots < n$ be unknown change points indexes.
 Consider the following multiple linear regression model
 
 $$
-y_t = z_t' \delta_j + \varepsilon_t, \quad \forall t=t_j,\dots,t_{j+1}-1
+y_t = x_t' \delta_j + \varepsilon_t, \quad \forall t=t_j,\dots,t_{j+1}-1
 $$
 
 for $j>1$.
@@ -17,7 +17,7 @@ The least-squares estimates of the break dates is obtained by minimizing the sum
 Formally, the associated cost function on an interval $I$ is
 
 $$
-c(y_{I}) = \min_{\delta\in\mathbb{R}^p} \sum_{t\in I} \|y_t - \delta' z_t \|_2^2.
+c(y_{I}) = \min_{\delta\in\mathbb{R}^p} \sum_{t\in I} \|y_t - \delta' x_t \|_2^2.
 $$
 
 ## Usage
@@ -31,7 +31,7 @@ import ruptures as rpt
 
 # creation of data
 n, n_reg = 2000, 3  # number of samples, number of regressors (including intercept)
-n_bkps, sigma = 3, 5  # number of change points, noise standart deviation
+n_bkps = 3  # number of change points
 # regressors
 tt = np.linspace(0, 10 * np.pi, n)
 X = np.vstack((np.sin(tt), np.sin(5 * tt), np.ones(n))).T
@@ -74,4 +74,4 @@ algo = rpt.Dynp(model="linear")
 ## References
 
 <a id="Bai2003">[Bai2003]</a>
-J. Bai and P. Perron. Critical values for multiple structural change tests. Econometrics Journal, 6(1):72–78, 2003.
+J. Bai and P. Perron. Critical values for multiple structural change tests. Econometrics Journal, 6(1):72–78, 2003.

pyproject.toml

@@ -1,9 +1,10 @@
 [build-system]
 # Minimum requirements for the build system to execute.
 requires = [
-    "setuptools>=38.3.0",  # version with most `setup.cfg` bugfixes
+    "setuptools>=42",  # https://github.com/deepcharles/ruptures/pull/100#discussion_r553700339
     "wheel",
     "Cython>=0.28.5",
+    "setuptools_scm[toml]>=3.4",  # https://scikit-hep.org/developer/packaging#git-tags-official-pypa-method
 
     # PyPy needs numpy >= 1.14.0
     # platform_python_implementation!='CPython' not needed >= Python 3.7 which is numpy 1.14.5
@@ -36,4 +37,7 @@ build-backend = "setuptools.build_meta"
 [tool.pytest.ini_options]
 minversion = "6.0"
 addopts = "--cov-report=xml --cov-report=term:skip-covered --cov=ruptures"
-testpaths = ["tests"]
+testpaths = ["tests"]
+
+[tool.setuptools_scm]
+write_to = "src/ruptures/version.py"

src/ruptures/__init__.py

@@ -5,4 +5,5 @@
 from .exceptions import NotEnoughPoints
 from .show import display
 
-__version__ = "1.1.2"
+# Convenient access to the version number
+from .version import version as __version__

src/ruptures/costs/costclinear.py

@@ -55,5 +55,7 @@ def error(self, start, end) -> float:
         sub = self.signal[start:end]
         slope = (self.signal[end - 1] - self.signal[start - 1]) / (end - start)
         intercept = self.signal[start - 1]
-        approx = slope * (np.arange(1, end - start + 1)) + intercept
-        return np.sum((sub - approx) ** 2)
+        approx = slope.reshape(-1, 1) * np.arange(
+            1, end - start + 1
+        ) + intercept.reshape(-1, 1)
+        return np.sum((sub - approx.transpose()) ** 2)