Merge pull request #28 from derb12/development

Merge development for v1.1.0

.github/PULL_REQUEST_TEMPLATE.md

@@ -5,9 +5,8 @@
 are required and/or what problems they fix. Link or add the issue number
 for any existing issues that the pull request solves.
 
-Note that unsolicited pull requests will most likely be closed.
-Please file an issue first, so that details can be discussed/finalized
-before a pull request is created.-->
+Note that it is preferred to file an issue first, so that details can be
+discussed/finalized before a pull request is created.-->
 
 
 ### Type of Pull Request
@@ -24,9 +23,9 @@ before a pull request is created.-->
 To run tests locally, type the following command within the pybaselines
 directory: pytest .
 
-To lint files using flake8 to see if they pass PEP 8 standards and that
+To lint files using ruff to see if they pass PEP 8 standards and that
 docstrings are okay, run the following command within the pybaselines
-directory: flake8 .
+directory: ruff check .
 
 To build documentation locally, type the following command within the
 docs directory: make html

.github/workflows/python-test-latest.yml

@@ -0,0 +1,54 @@
+# For testing the nightly builds of numpy and scipy so that any new changes will not be
+# a surprise.
+
+# Will only trigger if there is a change within pybaselines or tests directories.
+
+name: test-latest-dependencies
+
+on:
+  # allow manually activating the workflow
+  workflow_dispatch:
+
+  push:
+    branches: [ main ]
+    paths:
+    - 'pybaselines/**'
+    - 'tests/**'
+    - '.github/workflows/**'
+
+  pull_request:
+    # always trigger on a pull request, regardless of the branch
+    paths:
+    - 'pybaselines/**'
+    - 'tests/**'
+    - '.github/workflows/**'
+
+jobs:
+  test-nightly:
+
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        # Choose the latest stable python version
+        python-version: ['3.12']
+
+    steps:
+    - uses: actions/checkout@v4
+
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v5
+      with:
+        python-version: ${{ matrix.python-version }}
+
+    - name: Install required dependencies
+      run: |
+        python -m pip install --upgrade pip
+        python -m pip install pytest
+        python -m pip install -i https://pypi.anaconda.org/scientific-python-nightly-wheels/simple numpy
+        python -m pip install -i https://pypi.anaconda.org/scientific-python-nightly-wheels/simple scipy
+
+    - name: Test with required dependencies
+      # use -Werror so that any warnings will show up as errors -> want to be as stringent
+      # as possible
+      run: python -Werror -m pytest .

.github/workflows/python-test.yml

@@ -26,87 +26,88 @@ on:
 jobs:
   test:
 
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-latest
     strategy:
       fail-fast: false
       matrix:
         # Use strings since yaml considers 3.10 equal to 3.1
-        python-version: ['3.6', '3.7', '3.8', '3.9', '3.10', '3.11']
+        python-version: ['3.8', '3.9', '3.10', '3.11', '3.12']
 
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
 
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v4
+      uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
 
     - name: Install required dependencies
       run: |
         python -m pip install --upgrade pip
-        python -m pip install "numpy>=1.14" "scipy>=1.0" pytest
-
-    # Only lint a single version; pick a recent, stable version
-    - name: Install linting dependencies
-      id: install-linters
-      if: matrix.python-version == '3.9'
-      run: |
-        python -m pip install flake8 flake8-comprehensions flake8-docstrings
-
-    - name: Lint
-      if: steps.install-linters.outcome == 'success'
-      run: |
-        # stop the build if there are Python syntax errors or undefined names
-        flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
-        # exit-zero treats all errors as warnings.
-        flake8 . --count --exit-zero --statistics
+        python -m pip install "numpy>=1.20" "scipy>=1.5" pytest
 
     - name: Test with required dependencies
       run: pytest .
 
     - name: Install optional dependencies
       id: install-optional
-      # uncomment below in case this step ever needs skipped again
-      #if: matrix.python-version != '3.11'
-      run: python -m pip install "pentapy>=1.0" "numba>=0.45"
+      # uncomment below to allow skipping future versions
+      #if: matrix.python-version != '3.13'
+      run: python -m pip install "pentapy>=1.1" "numba>=0.49"
 
     - name: Test with optional dependencies
-      # uncomment below in case this step ever needs skipped again
       if: steps.install-optional.outcome == 'success'
       run: pytest .
 
 
   test-min-dependencies:
 
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-latest
     strategy:
       fail-fast: false
       matrix:
-        python-version: ['3.6']
+        python-version: ['3.8']
 
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
 
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v4
+      uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
 
     - name: Install minimum dependencies
-      # Use numpy 1.14.5 rather than 1.14.0 since the optional
-      # dependency pentapy requires numpy>=1.14.5; no relevant difference
-      # between 1.14.0 and 1.14.5.
       run: |
         python -m pip install --upgrade pip
-        python -m pip install numpy==1.14.5 scipy==1.0 pytest
+        python -m pip install "numpy==1.20" "scipy==1.5" pytest
 
     - name: Test with minimum required dependencies
       run: pytest .
 
     - name: Install minimum optional dependencies
-    # Have to pin llvmlite to 0.30.0 since it otherwise gets a more recent
-    # version that is imcompatible with numba v0.45
-      run: python -m pip install pentapy==1.0 numba==0.45 llvmlite==0.30.0
+      run: python -m pip install "pentapy==1.1" "numba==0.49"
 
     - name: Test with minimum optional dependencies
       run: pytest .
+
+  lint:
+
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ['3.11']
+
+    steps:
+    - uses: actions/checkout@v4
+
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v5
+      with:
+        python-version: ${{ matrix.python-version }}
+
+    - name: Install linting dependencies
+      run: python -m pip install ruff
+
+    - name: Lint
+      run: ruff check .

.gitignore

@@ -50,6 +50,7 @@ docs/_build/
 
 # sphinx-gallery output
 docs/examples/
+sg_execution_times.rst
 
 # sphinx-autoapi output
 docs/api

.readthedocs.yaml

@@ -8,7 +8,7 @@ version: 2
 build:
   os: ubuntu-22.04
   tools:
-    python: "3.9"
+    python: "3.11"
 
 # Path to sphinx's configuration file
 sphinx:

CHANGELOG.rst

@@ -2,6 +2,62 @@
 Changelog
 =========
 
+Version 1.1.0 (2024-02-18)
+--------------------------
+
+This is a minor version with new features, deprecations,
+and documentation improvements.
+
+New Features
+~~~~~~~~~~~~
+
+* Added two dimensional versions of various baseline correction algorithms,
+  with the focus on Whittaker-smoothing-based, spline, and polynomial methods.
+  These can be accessed using the new `Baseline2D` class.
+* Added the `Baseline2D.individual_axes` method, which allows fitting each row and/or
+  column in two dimensional data with any one dimensional method in pybaselines.
+* Added a version of the rubberband method to pybaselines.misc which allows fitting
+  individual segments within data to better fit concave-shaped data.
+* Added the Customized Baseline Correction (custom_bc) method to
+  pybaselines.optimizers, which allows fitting baselines with controllable
+  levels of stiffness in different regions.
+* Added a penalized version of mpls (pspline_mpls) to pybaselines.spline.
+* Updated spline.mixture_model to use expectation-maximization rather than the previous
+  nieve approach of fitting the histogram of the residuals with the probability density
+  function. Should reduce calculation times.
+* Added a function for penalized spline (P-spline) smoothing to pybaselines.utils,
+  `pybaselines.utils.pspline_smooth`, which will return a tuple of the smoothed input and
+  the knots, spline coefficients, and spline degree for any further use with
+  SciPy's BSpline.
+
+Other Changes
+~~~~~~~~~~~~~
+
+* Officially list Python 3.12 as supported.
+* Updated lowest supported Python version to 3.8
+* Updated lowest supported dependency versions: NumPy 1.20, SciPy 1.5,
+  pentapy 1.1, and Numba 0.49
+* Use SciPy's sparse arrays when the installed SciPy version is 1.12 or newer. This
+  only affects user codes if using functions from the pybaselines.utils module.
+* Vendor SciPy's cwt and ricker functions, which were deprecated from SciPy in version 1.12.
+
+Deprecations/Breaking Changes
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+* Deprecated passing `num_bins` to spline.mixture_model. The keyword argument will
+  be removed in version 1.3.
+* Removed the pybaselines.config module, which was simply used to set the pentapy solver.
+  The same behavior can be done by setting the `pentapy_solver` attribute of a `Baseline`
+  object after initialization.
+
+Documentation/Examples
+~~~~~~~~~~~~~~~~~~~~~~
+
+* Added a section of the documentation explaining the extension of baseline correction for
+  two dimensional data.
+* Added new examples for 2D baseline correction and for custom_bc.
+
+
 Version 1.0.0 (2022-10-26)
 --------------------------
 

CITATION.cff

@@ -26,4 +26,4 @@ repository-artifact: https://pypi.org/project/pybaselines
 repository-code: https://github.com/derb12/pybaselines
 title: "pybaselines: A Python library of algorithms for the baseline correction of experimental data"
 type: software
-version: 1.0.0
+version: 1.1.0

LICENSE.txt

@@ -1,6 +1,6 @@
 BSD 3-Clause License
 
-Copyright (c) 2021-2023, Donald Erb
+Copyright (c) 2021-2024, Donald Erb
 All rights reserved.
 
 Redistribution and use in source and binary forms, with or without

LICENSES_bundled.txt

@@ -162,11 +162,11 @@ FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
 OTHER DEALINGS IN THE SOFTWARE.
 
 
-Source: SciPy (https://github.com/scipy/scipy, last accessed November 6, 2021)
-File: pybaselines._spline_utils.py
+Source: SciPy (https://github.com/scipy/scipy, last accessed December 28, 2023)
+Files: pybaselines._spline_utils.py, pybaselines.classification.py
 License: 3-clause BSD
 
-Copyright (c) 2001-2002 Enthought, Inc.  2003-2019, SciPy Developers.
+Copyright (c) 2001-2002 Enthought, Inc.  2003-2023, SciPy Developers.
 All rights reserved.
 
 Redistribution and use in source and binary forms, with or without