theochem · FanwangM · Sep 7, 2024 · Sep 7, 2024 · Sep 7, 2024 · Sep 7, 2024
diff --git a/.github/workflows/ci_codecov.yml → .github/workflows/ci_codecov.yaml b/.github/workflows/ci_codecov.yml → .github/workflows/ci_codecov.yaml
@@ -27,7 +27,7 @@ jobs:
     strategy:
       matrix:
         os: [ubuntu-latest]
-        python-version: [3.11]
+        python-version: ["3.11"]
 
     steps:
     - uses: actions/checkout@v4

diff --git a/.github/workflows/ci_tox.yml → .github/workflows/ci_tox.yaml b/.github/workflows/ci_tox.yml → .github/workflows/ci_tox.yaml
@@ -26,7 +26,7 @@ jobs:
       matrix:
         # os: [macOS-latest, windows-latest, ubuntu-latest]
         os: [macos-13, windows-latest, ubuntu-latest]
-        python-version: ["3.9", "3.10", "3.11"]
+        python-version: ["3.9", "3.10", "3.11", "3.12"]
 
     steps:
     - uses: actions/checkout@v4

diff --git a/.github/workflows/release.yaml → .github/workflows/pypi_release.yaml b/.github/workflows/release.yaml → .github/workflows/pypi_release.yaml
diff --git a/HEADER b/HEADER
@@ -1,22 +1,21 @@
-# -*- coding: utf-8 -*-
-# The Selector library provides a set of tools for selecting a
-# subset of the dataset and computing diversity.
-#
-# Copyright (C) 2023 The QC-Devs Community
-#
-# This file is part of Selector.
-#
-# Selector is free software; you can redistribute it and/or
-# modify it under the terms of the GNU General Public License
-# as published by the Free Software Foundation; either version 3
-# of the License, or (at your option) any later version.
-#
-# Selector is distributed in the hope that it will be useful,
-# but WITHOUT ANY WARRANTY; without even the implied warranty of
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-# GNU General Public License for more details.
-#
-# You should have received a copy of the GNU General Public License
-# along with this program; if not, see <http://www.gnu.org/licenses/>
-#
-# --
+
+The Selector is a Python library of algorithms for selecting diverse
+subsets of data for machine-learning.
+
+Copyright (C) 2022-2024 The QC-Devs Community
+
+This file is part of Selector.
+
+Selector is free software; you can redistribute it and/or
+modify it under the terms of the GNU General Public License
+as published by the Free Software Foundation; either version 3
+of the License, or (at your option) any later version.
+
+Selector is distributed in the hope that it will be useful,
+but WITHOUT ANY WARRANTY; without even the implied warranty of
+MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+GNU General Public License for more details.
+
+You should have received a copy of the GNU General Public License
+along with this program; if not, see <http://www.gnu.org/licenses/>
+
diff --git a/MANIFEST.in b/MANIFEST.in
@@ -3,5 +3,8 @@ include MANIFEST.in
 include CODE_OF_CONDUCT.md
 include versioneer.py
 
+prune notebooks
+prune book
+
 graft selector
 global-exclude *.py[cod] __pycache__ *.so
diff --git a/README.md b/README.md
@@ -1,6 +1,10 @@
-# The `selector` Library
+<!-- # The Selector Library -->
+<h1>
+  The Selector Library
+  <img src="book/content/selector_logo.png" alt="Logo" align="right" width="180">
+</h1>
 
-[![This project supports Python 3.7+](https://img.shields.io/badge/Python-3.7+-blue.svg)](https://python.org/downloads)
+[![This project supports Python 3.9+](https://img.shields.io/badge/Python-3.9+-blue.svg)](https://python.org/downloads)
 [![GPLv3 License](https://img.shields.io/badge/License-GPL%20v3-yellow.svg)](https://opensource.org/licenses/)
 [![GitHub Actions CI Tox Status](https://github.com/theochem/Selector/actions/workflows/ci_tox.yml/badge.svg?branch=main)](https://github.com/theochem/Selector/actions/workflows/ci_tox.yml)
 [![codecov](https://codecov.io/gh/theochem/Selector/graph/badge.svg?token=0UJixrJfNJ)](https://codecov.io/gh/theochem/Selector)
@@ -38,12 +42,13 @@ To install `selector` with `pip`, we can install the latest stable release from
     pip install qc-selector
 ```
 
+To download the prebuilt wheel files, visit the [PyPI page](https://pypi.org/project/qc-selector/)
+and [GitHub releases](https://github.com/theochem/Selector/tags).
+
 In addition, we can install the latest development version from the GitHub repository as follows:
 
 ```bash
-    # Install the latest development version.
-
-    # install the development version
+    # install the latest development version
     pip install git+https://github.com/theochem/Selector.git
 
 ```

diff --git a/pyproject.toml b/pyproject.toml
@@ -24,9 +24,8 @@
 [project]
 # https://packaging.python.org/en/latest/specifications/declaring-project-metadata/
 name = "qc-selector"
-version = "0.0.2b4"
 description = "Subset selection with maximum diversity."
-readme = "README.md"
+readme = {file = 'README.md', content-type='text/markdown'}
 #requires-python = ">=3.9,<4.0"
 requires-python = ">=3.9"
 # "LICENSE" is name of the license file, which must be in root of project folder
@@ -53,6 +52,7 @@ classifiers = [
     "Natural Language :: English",
     "Operating System :: MacOS",
     "Operating System :: Microsoft :: Windows",
+    "Operating System :: Unix",
     "Operating System :: POSIX",
     "Operating System :: POSIX :: Linux",
     "Programming Language :: Python",
@@ -61,9 +61,17 @@ classifiers = [
     "Programming Language :: Python :: 3.10",
     "Programming Language :: Python :: 3.11",
     "Programming Language :: Python :: 3.12",
+    "Topic :: Scientific/Engineering",
+    "Topic :: Sociology",
+
 ]
 
-dynamic = ["dependencies", "optional-dependencies"]
+# version = "0.0.2b4"
+dynamic = [
+    "dependencies",
+    "optional-dependencies",
+    "version",
+    ]
 
 # not using this section now but it's here for reference
 # # Required dependencies for install/usage of your package or application
@@ -167,13 +175,16 @@ repository = "https://github.com/theochem/Selector"
 
 [build-system]
 # Minimum requirements for the build system to execute.
-requires = ["setuptools", "wheel"]
+requires = ["setuptools>=64", "setuptools-scm>=8", "wheel"]
 build-backend = "setuptools.build_meta"
 
 [tool.setuptools.dynamic]
 dependencies = {file = ["requirements.txt"]}
 optional-dependencies = {dev = { file = ["requirements_dev.txt"] }}
 
+[tool.setuptools_scm]
+# can be empty if no extra settings are needed, presence enables setuptools-scm
+
 [tool.setuptools]
 # https://setuptools.pypa.io/en/latest/userguide/pyproject_config.html
 platforms = ["Linux", "Windows", "MacOS"]
@@ -189,7 +200,7 @@ selector = ["*.xml"]
 # Python modules and packages that are included in the
 # distribution package (and therefore become importable)
 [tool.setuptools.packages.find]
-exclude = ["*/*/tests", "tests_*", "examples", "book"]
+exclude = ["*/*/tests", "tests_*", "examples", "book/content", "notebooks"]
 
 
 # PDM example

diff --git a/requirements_dev.txt b/requirements_dev.txt
@@ -7,6 +7,7 @@ pytest>=7.4.0
 pytest-cov>=3.0.0
 scikit-learn>=1.0.1
 scipy>=1.11.1
-setuptools>=62.6
+setuptools>=64.0.0
 tomli
 xdoctest
+setuptools-scm>=8.0.0
diff --git a/selector/__init__.py b/selector/__init__.py
@@ -1,7 +1,9 @@
-# The Selector library provides a set of tools for selecting a
-# subset of the dataset and computing diversity.
+# -*- coding: utf-8 -*-
 #
-# Copyright (C) 2023 The QC-Devs Community
+# The Selector is a Python library of algorithms for selecting diverse
+# subsets of data for machine-learning.
+#
+# Copyright (C) 2022-2024 The QC-Devs Community
 #
 # This file is part of Selector.
 #

diff --git a/selector/measures/init.py → selector/measures/__init__.py b/selector/measures/init.py → selector/measures/__init__.py
@@ -1,7 +1,9 @@
-# The Selector library provides a set of tools for selecting a
-# subset of the dataset and computing diversity.
+# -*- coding: utf-8 -*-
 #
-# Copyright (C) 2023 The QC-Devs Community
+# The Selector is a Python library of algorithms for selecting diverse
+# subsets of data for machine-learning.
+#
+# Copyright (C) 2022-2024 The QC-Devs Community
 #
 # This file is part of Selector.
 #

diff --git a/selector/measures/converter.py b/selector/measures/converter.py
@@ -1,7 +1,9 @@
-# The Selector library provides a set of tools for selecting a
-# subset of the dataset and computing diversity.
+# -*- coding: utf-8 -*-
 #
-# Copyright (C) 2023 The QC-Devs Community
+# The Selector is a Python library of algorithms for selecting diverse
+# subsets of data for machine-learning.
+#
+# Copyright (C) 2022-2024 The QC-Devs Community
 #
 # This file is part of Selector.
 #

diff --git a/selector/measures/diversity.py b/selector/measures/diversity.py
@@ -1,7 +1,9 @@
-# The Selector library provides a set of tools for selecting a
-# subset of the dataset and computing diversity.
+# -*- coding: utf-8 -*-
 #
-# Copyright (C) 2023 The QC-Devs Community
+# The Selector is a Python library of algorithms for selecting diverse
+# subsets of data for machine-learning.
+#
+# Copyright (C) 2022-2024 The QC-Devs Community
 #
 # This file is part of Selector.
 #

diff --git a/selector/measures/similarity.py b/selector/measures/similarity.py
@@ -1,7 +1,9 @@
-# The Selector library provides a set of tools for selecting a
-# subset of the dataset and computing diversity.
+# -*- coding: utf-8 -*-
 #
-# Copyright (C) 2023 The QC-Devs Community
+# The Selector is a Python library of algorithms for selecting diverse
+# subsets of data for machine-learning.
+#
+# Copyright (C) 2022-2024 The QC-Devs Community
 #
 # This file is part of Selector.
 #

diff --git a/selector/measures/tests/__init__.py b/selector/measures/tests/__init__.py
@@ -1,7 +1,9 @@
-# The Selector library provides a set of tools for selecting a
-# subset of the dataset and computing diversity.
+# -*- coding: utf-8 -*-
 #
-# Copyright (C) 2023 The QC-Devs Community
+# The Selector is a Python library of algorithms for selecting diverse
+# subsets of data for machine-learning.
+#
+# Copyright (C) 2022-2024 The QC-Devs Community
 #
 # This file is part of Selector.
 #

diff --git a/selector/measures/tests/common.py b/selector/measures/tests/common.py
@@ -1,7 +1,9 @@
-# The Selector library provides a set of tools for selecting a
-# subset of the dataset and computing diversity.
+# -*- coding: utf-8 -*-
 #
-# Copyright (C) 2023 The QC-Devs Community
+# The Selector is a Python library of algorithms for selecting diverse
+# subsets of data for machine-learning.
+#
+# Copyright (C) 2022-2024 The QC-Devs Community
 #
 # This file is part of Selector.
 #

diff --git a/selector/measures/tests/test_converter.py b/selector/measures/tests/test_converter.py
@@ -1,7 +1,9 @@
-# The Selector library provides a set of tools for selecting a
-# subset of the dataset and computing diversity.
+# -*- coding: utf-8 -*-
 #
-# Copyright (C) 2023 The QC-Devs Community
+# The Selector is a Python library of algorithms for selecting diverse
+# subsets of data for machine-learning.
+#
+# Copyright (C) 2022-2024 The QC-Devs Community
 #
 # This file is part of Selector.
 #

diff --git a/selector/measures/tests/test_diversity.py b/selector/measures/tests/test_diversity.py
@@ -1,7 +1,9 @@
-# The Selector library provides a set of tools for selecting a
-# subset of the dataset and computing diversity.
+# -*- coding: utf-8 -*-
 #
-# Copyright (C) 2023 The QC-Devs Community
+# The Selector is a Python library of algorithms for selecting diverse
+# subsets of data for machine-learning.
+#
+# Copyright (C) 2022-2024 The QC-Devs Community
 #
 # This file is part of Selector.
 #

diff --git a/selector/methods/__init__.py b/selector/methods/__init__.py
@@ -1,7 +1,9 @@
-# The Selector library provides a set of tools for selecting a
-# subset of the dataset and computing diversity.
+# -*- coding: utf-8 -*-
 #
-# Copyright (C) 2023 The QC-Devs Community
+# The Selector is a Python library of algorithms for selecting diverse
+# subsets of data for machine-learning.
+#
+# Copyright (C) 2022-2024 The QC-Devs Community
 #
 # This file is part of Selector.
 #

diff --git a/selector/methods/base.py b/selector/methods/base.py
@@ -1,7 +1,9 @@
-# The Selector library provides a set of tools for selecting a
-# subset of the dataset and computing diversity.
+# -*- coding: utf-8 -*-
 #
-# Copyright (C) 2023 The QC-Devs Community
+# The Selector is a Python library of algorithms for selecting diverse
+# subsets of data for machine-learning.
+#
+# Copyright (C) 2022-2024 The QC-Devs Community
 #
 # This file is part of Selector.
 #

diff --git a/selector/methods/distance.py b/selector/methods/distance.py
@@ -1,7 +1,9 @@
-# The Selector library provides a set of tools for selecting a
-# subset of the dataset and computing diversity.
+# -*- coding: utf-8 -*-
 #
-# Copyright (C) 2023 The QC-Devs Community
+# The Selector is a Python library of algorithms for selecting diverse
+# subsets of data for machine-learning.
+#
+# Copyright (C) 2022-2024 The QC-Devs Community
 #
 # This file is part of Selector.
 #

diff --git a/selector/methods/partition.py b/selector/methods/partition.py
@@ -1,7 +1,9 @@
-# The Selector library provides a set of tools for selecting a
-# subset of the dataset and computing diversity.
+# -*- coding: utf-8 -*-
 #
-# Copyright (C) 2023 The QC-Devs Community
+# The Selector is a Python library of algorithms for selecting diverse
+# subsets of data for machine-learning.
+#
+# Copyright (C) 2022-2024 The QC-Devs Community
 #
 # This file is part of Selector.
 #

diff --git a/selector/methods/similarity.py b/selector/methods/similarity.py
@@ -1,5 +1,7 @@
-# The Selector library provides a set of tools for selecting a
-# subset of the dataset and computing diversity.
+# -*- coding: utf-8 -*-
+#
+# The Selector is a Python library of algorithms for selecting diverse
+# subsets of data for machine-learning.
 #
 # Copyright (C) 2022-2024 The QC-Devs Community
 #

diff --git a/selector/methods/tests/__init__.py b/selector/methods/tests/__init__.py
@@ -1,7 +1,9 @@
-# The Selector library provides a set of tools for selecting a
-# subset of the dataset and computing diversity.
+# -*- coding: utf-8 -*-
 #
-# Copyright (C) 2023 The QC-Devs Community
+# The Selector is a Python library of algorithms for selecting diverse
+# subsets of data for machine-learning.
+#
+# Copyright (C) 2022-2024 The QC-Devs Community
 #
 # This file is part of Selector.
 #

diff --git a/selector/methods/tests/common.py b/selector/methods/tests/common.py
@@ -1,7 +1,9 @@
-# The Selector library provides a set of tools for selecting a
-# subset of the dataset and computing diversity.
+# -*- coding: utf-8 -*-
 #
-# Copyright (C) 2023 The QC-Devs Community
+# The Selector is a Python library of algorithms for selecting diverse
+# subsets of data for machine-learning.
+#
+# Copyright (C) 2022-2024 The QC-Devs Community
 #
 # This file is part of Selector.
 #

diff --git a/selector/methods/tests/test_distance.py b/selector/methods/tests/test_distance.py
@@ -1,7 +1,9 @@
-# The Selector library provides a set of tools for selecting a
-# subset of the dataset and computing diversity.
+# -*- coding: utf-8 -*-
 #
-# Copyright (C) 2023 The QC-Devs Community
+# The Selector is a Python library of algorithms for selecting diverse
+# subsets of data for machine-learning.
+#
+# Copyright (C) 2022-2024 The QC-Devs Community
 #
 # This file is part of Selector.
 #