Merge pull request #25 from derb12/development

Merge development for v1.0.0

.bumpversion.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 0.8.0
+current_version = 1.0.0
 commit = False
 tag = False
 
@@ -14,3 +14,11 @@ replace = __version__ = '{new_version}'
 [bumpversion:file:docs/conf.py]
 search = version = '{current_version}'
 replace = version = '{new_version}'
+
+[bumpversion:file:CITATION.cff]
+search = version: {current_version}
+replace = version: {new_version}
+
+[bumpversion:file:docs/citing.rst]
+search = version = {{{current_version}}}
+replace = version = {{{new_version}}}

.github/workflows/python-test.yml

@@ -31,13 +31,13 @@ jobs:
       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']
+        python-version: ['3.6', '3.7', '3.8', '3.9', '3.10', '3.11']
 
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v3
 
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v2
+      uses: actions/setup-python@v4
       with:
         python-version: ${{ matrix.python-version }}
 
@@ -66,11 +66,12 @@ jobs:
 
     - name: Install optional dependencies
       id: install-optional
-      # skip optional depedencies for python 3.10 until numba is available
-      if: matrix.python-version != '3.10'
+      # 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"
 
     - name: Test with optional dependencies
+      # uncomment below in case this step ever needs skipped again
       if: steps.install-optional.outcome == 'success'
       run: pytest .
 
@@ -84,10 +85,10 @@ jobs:
         python-version: ['3.6']
 
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v3
 
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v2
+      uses: actions/setup-python@v4
       with:
         python-version: ${{ matrix.python-version }}
 

CHANGELOG.rst

@@ -2,6 +2,61 @@
 Changelog
 =========
 
+Version 1.0.0 (2022-10-26)
+--------------------------
+
+This is a major version with new features, bug fixes, deprecations,
+and documentation improvements.
+
+New Features
+~~~~~~~~~~~~
+
+* Added a new class-based api for all algorithms, which can be accessed by using
+  the `pybaselines.api.Baseline` class. All algorithms are available as methods of
+  the `Baseline` class. The functional api from earlier versions is also maintained
+  for backwards compatibility.
+* All functions now allow inputting an `x_data` keyword, even if it is not used within
+  the function, to allow for a more consistent api. Likewise, `pybaselines.misc.interp_pts`
+  added an unused `data` keyword. Now, all algorithms can be called with
+  the signature `baseline_algorithm(data=y_data, x_data=x_data, ...)`.
+* Added a function for Whittaker smoothing to pybaselines.utils,
+  `pybaselines.utils.whittaker_smooth`.
+* whittaker.iasls and spline.psline_iasls now allow inputting a `diff_order` parameter.
+
+Bug Fixes
+~~~~~~~~~
+
+* Fixed the addition of the penalty difference diagonals in spline.pspline_drpls, which
+  was incorrectly treating the penalty diagonals as lower banded rather than fully banded.
+
+Other Changes
+~~~~~~~~~~~~~
+
+* Officially list Python 3.11 as supported.
+* Added default `half_window` values for snip and noise_median.
+* collab_pls accomodates `alpha` for aspls and pspline_aspls; the `alpha` parameter is
+  calculated for the entire dataset in the same way as the weights and is then fixed when
+  fitting each of the individual data entries.
+* Improved input validation.
+* Improved testing base classes to reduce copied code and improve test coverage.
+* Improved code handling for banded systems and penalized splines to simplify internal code.
+
+Deprecations/Breaking Changes
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+* Removed the ability to pass addtional keyword arguments to algorithms in
+  pybaselines.optimizers, which was deprecated in version 0.8.0.
+* Removed the deprecated pybaselines.window module, which was formally deprecated in version 0.8.
+* Moved the `PENTAPY_SOLVER` constant from pybaselines.utils to the new pybaselines.config module.
+
+Documentation/Examples
+~~~~~~~~~~~~~~~~~~~~~~
+
+* Added citation guidelines to make it easier to cite pybaselines.
+* Added new examples showing how to use the new `Baseline` class.
+* Added a new example examining the `beads` algorithm.
+
+
 Version 0.8.0 (2021-12-07)
 --------------------------
 

CITATION.cff

@@ -0,0 +1,29 @@
+abstract: pybaselines is a Python library that provides many different algorithms for
+  performing baseline correction on data from experimental techniques such as Raman,
+  FTIR, NMR, XRD, etc.
+authors:
+  - family-names: Erb
+    given-names: Donald
+cff-version: 1.2.0
+identifiers:
+  - type: doi
+    value: 10.5281/zenodo.5608581
+    description: "Persistent DOI for all versions of pybaselines"
+  - type: url
+    value: https://github.com/derb12/pybaselines
+    description: "URL for the pybaselines source code repository"
+  - type: url
+    value: https://pypi.org/project/pybaselines
+    description: "URL for the PyPI upload of pybaselines"
+keywords:
+  - "baseline correction"
+  - "materials characterization"
+  - spectroscopy
+  - Python
+license: BSD-3-Clause
+message: "If citing this software, consider using this metadata."
+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

LICENSE.txt

@@ -1,6 +1,6 @@
 BSD 3-Clause License
 
-Copyright (c) 2021, Donald Erb
+Copyright (c) 2021-2022, Donald Erb
 All rights reserved.
 
 Redistribution and use in source and binary forms, with or without

README.rst

@@ -132,14 +132,17 @@ pybaselines's documentation. For examples of their usage, refer to the `examples
 
 .. _examples section: https://pybaselines.readthedocs.io/en/latest/examples/index.html
 
-A simple example is shown below.
+A simple example is shown below (if using a version earlier than 1.0, see the `quickstart`_ in
+the documentation for the old version).
+
+.. _quickstart: https://pybaselines.readthedocs.io/en/latest/quickstart.html#pre-version-1-0-0-quick-start
+
 
 .. code-block:: python
 
     import matplotlib.pyplot as plt
     import numpy as np
-    import pybaselines
-    from pybaselines import utils
+    from pybaselines import Baseline, utils
 
     x = np.linspace(1, 1000, 1000)
     # a measured signal containing several Gaussian peaks
@@ -159,10 +162,12 @@ A simple example is shown below.
 
     y = signal + true_baseline + noise
 
-    bkg_1 = pybaselines.polynomial.modpoly(y, x, poly_order=3)[0]
-    bkg_2 = pybaselines.whittaker.asls(y, lam=1e7, p=0.02)[0]
-    bkg_3 = pybaselines.morphological.mor(y, half_window=30)[0]
-    bkg_4 = pybaselines.smooth.snip(
+    baseline_fitter = Baseline(x_data=x)
+
+    bkg_1 = baseline_fitter.modpoly(y, poly_order=3)[0]
+    bkg_2 = baseline_fitter.asls(y, lam=1e7, p=0.02)[0]
+    bkg_3 = baseline_fitter.mor(y, half_window=30)[0]
+    bkg_4 = baseline_fitter.snip(
         y, max_half_window=40, decreasing=True, smooth_half_window=3
     )[0]
 
@@ -211,6 +216,14 @@ For more information, refer to the license_.
 .. _license: https://github.com/derb12/pybaselines/tree/main/LICENSE.txt
 
 
+Citing
+------
+
+If you use pybaselines for published research, please consider citing
+by following the `guidelines in the documentation
+<https://pybaselines.readthedocs.io/en/latest/citing.html>`_.
+
+
 Author
 ------
 

docs/_templates/autoapi/python/module.rst

@@ -5,11 +5,6 @@
 {{ obj.name }}
 {{ "=" * obj.name|length }}
 
-{% if obj.name == "pybaselines.window" %}
-{{ "This module was renamed in version 0.6.0. Use :mod:`pybaselines.smooth` instead." }}
-
-{% endif %}
-
 .. py:module:: {{ obj.name }}