Merge pull request #35 from jungtaekkim/0.6.0

0.6.0
jungtaekkim · Mar 12, 2024 · c098cdb · c098cdb
2 parents 700dd3a + a744dcc
commit c098cdb
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diff --git a/.github/workflows/pylint.yml b/.github/workflows/pylint.yml
@@ -19,11 +19,11 @@ jobs:
       uses: actions/setup-python@v2
       with:
         python-version: ${{ matrix.python-version }}
-    - name: Install dependencies
+    - name: Install this project and its dependencies
       run: |
-        python -m pip install --upgrade pip setuptools
-        pip install pylint
-        pip install .
+        pip install --upgrade pip
+        pip install .[dev]
+        pip list
     - name: Analyze the code with pylint
       run: |
         pylint --rcfile=.pylintrc bayeso/
diff --git a/.github/workflows/pytest.yml b/.github/workflows/pytest.yml
@@ -18,14 +18,13 @@ jobs:
       - uses: actions/setup-python@v2
         with:
           python-version: ${{ matrix.python-version }}
-      - name: Install dependencies
+      - name: Install this project and its dependencies
         run: |
-          python -m pip install --upgrade pip setuptools
-          pip install pytest pytest-cov pytest-timeout
+          pip install --upgrade pip
+          pip install .[dev]
+          pip list
       - name: Run pytest
         run: |
-          set -e
-          pip install -e .[test]
           pytest tests/common --cov
         shell: bash
       - uses: AndreMiras/coveralls-python-action@v20201129

diff --git a/.readthedocs.yml b/.readthedocs.yml
@@ -15,6 +15,5 @@ formats:
 
 python:
   install:
-    - requirements: requirements.txt
-    - requirements: requirements-optional.txt
-    - requirements: requirements-dev.txt
+    - method: pip
+      path: .[dev]
diff --git a/LICENSE b/LICENSE
@@ -1,6 +1,6 @@
 MIT License
 
-Copyright (c) 2017-2023 Jungtaek Kim
+Copyright (c) 2017-2024 Jungtaek Kim
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal

diff --git a/MANIFEST.in b/MANIFEST.in
@@ -1,4 +1,2 @@
 include CODE_OF_CONDUCT.md
 include LICENSE
-include requirements.txt
-include requirements-optional.txt
diff --git a/README.md b/README.md
@@ -33,22 +33,22 @@ $ pip install bayeso
 
 * Using source code (for developer installation)
 
-To install `bayeso` from source code, command
+To install `bayeso` from source code, command the following in the `bayeso` root.
 
 ```shell
-$ pip install .
+pip install .
 ```
-in the `bayeso` root.
 
 * Using source code (for editable development mode)
 
-To use editable development mode, command
+To use editable development mode, command the following in the `bayeso` root.
 
 ```shell
-$ pip install -r requirements.txt
-$ python setup.py develop
+pip install -e .
 ```
-in the `bayeso` root.
+
+If you want to install the packages required for optional features, development, and examples, you can simply add `[optional]`, `[dev]`, and `[examples]`.
+For example, `pip install .[dev]` or `pip install -e .[dev]`.
 
 * Uninstallation
 
@@ -58,14 +58,6 @@ If you would like to uninstall `bayeso`, command it.
 $ pip uninstall bayeso
 ```
 
-## Required Packages
-Mandatory pacakges are inlcuded in `requirements.txt`.
-The following `requirements` files include the package list, the purpose of which is described as follows.
-
-* `requirements-optional.txt`: It is an optional package list, but it needs to be installed to execute some features of `bayeso`.
-* `requirements-dev.txt`: It is for developing the `bayeso` package.
-* `requirements-examples.txt`: It needs to be installed to execute the examples included in the `bayeso` repository.
-
 ## Supported Python Version
 We test our package in the following versions.
 

diff --git a/bayeso/__init__.py b/bayeso/__init__.py
@@ -1,9 +1,9 @@
 #
-# author: Jungtaek Kim (jtkim@postech.ac.kr)
-# last updated: November 28, 2022
+# author: Jungtaek Kim (jungtaek.kim.mail@gmail.com)
+# last updated: January 4, 2024
 #
 """BayesO is a simple, but essential Bayesian optimization
 package, implemented in Python."""
 
 
-__version__ = '0.5.5'
+__version__ = '0.6.0'
diff --git a/docs/conf.py b/docs/conf.py
@@ -20,11 +20,11 @@
 # -- Project information -----------------------------------------------------
 
 project = 'BayesO'
-copyright = '2017-2023, Jungtaek Kim and Seungjin Choi'
+copyright = '2017-2024, Jungtaek Kim and Seungjin Choi'
 author = 'Jungtaek Kim and Seungjin Choi'
 
 # The short X.Y version
-version = '0.5.5'
+version = '0.6.0'
 # The full version, including alpha/beta/rc tags
 release = '{} alpha'.format(version)
 

diff --git a/docs/getting_started/installation.rst b/docs/getting_started/installation.rst
@@ -18,43 +18,41 @@ Compiling from Source
 =====================
 
 It is for developer installation.
-To install **bayeso** from source code, command
+To install **bayeso** from source code, command it in the **bayeso** root.
 
 .. code-block:: console
 
     $ pip install .
 
-in the **bayeso** root.
-
 Compiling from Source (Editable)
 ================================
 
 It is for editable development mode.
-To use editable development mode, command
+To use editable development mode, command it in the **bayeso** root.
 
 .. code-block:: console
 
-    $ pip install -r requirements.txt
-    $ python setup.py develop
+    $ pip install -e .
 
-in the **bayeso** root.
+If you want to install the packages required for optional features, development, and examples,
+you can simply add **[optional]**, **[dev]**, and **[examples]**.
+For example, you can command it for installing the packages required for development.
 
-Uninstalling
-============
+.. code-block:: console
 
-If you would like to uninstall **bayeso**, command it.
+    $ pip install .[dev]
+
+or
 
 .. code-block:: console
 
-    $ pip uninstall bayeso
+    $ pip install -e .[dev]
 
-Required Packages
-=================
+Uninstalling
+============
 
-Mandatory pacakges are inlcuded in **requirements.txt**.
-The following **requirements** files include the package list, the purpose of which is described as follows.
+If you would like to uninstall **bayeso**, command it.
 
-- **requirements-optional.txt**: It is an optional package list, but it needs to be installed to execute some features of **bayeso**.
-- **requirements-dev.txt**: It is for developing the **bayeso** package.
-- **requirements-examples.txt**: It needs to be installed to execute the examples included in the **bayeso** repository.
+.. code-block:: console
 
+    $ pip uninstall bayeso
diff --git a/publish_new_release.txt b/publish_new_release.txt
@@ -1,29 +1,26 @@
+# 0. (If needed) Install setuptools, wheel, build, and twine.
+
 # 1. Merge a working branch to the main branch first.
 
 # 2. Clone the main branch in a new clean directory.
 
-# 3. (If needed) Install setuptools and wheel.
-
-# 4. Create wheel and source files.
-python2 setup.py sdist bdist_wheel (deprecated) 
-python3 setup.py sdist bdist_wheel
-
-# 5. (If needed) Install twine.
+# 3. Create wheel and source files.
+python3 -m build
 
-# 6. Upload wheel and source files to the PyPI repository.
-twine upload dist/*
+# 4. Upload wheel and source files to the PyPI repository.
+python3 -m twine upload dist/*
 
-# 7. (Optional) Upload to Anaconda repository.
+# 5. (Optional) Upload to Anaconda repository.
 ~/anaconda3/bin/anaconda upload dist/*.tar.gz
 # or
 anaconda upload dist/*.tar.gz
 
-# 8. Publish a new release at GitHub.
+# 6. Publish a new release at GitHub.
 ## Create a tag at GitHub.
 ## Make sure that it is created in the main branch.
 ## Assign the tag to a new release.
 ## The name convention of tags is "v0.5.5".
 ## Upload the wheel and source files, which can be downloaded from the PyPI repository, together.
 
-# 9. Check out Zenodo or upload the release on Zenodo.
+# 7. Check out Zenodo or upload the release on Zenodo.
 ## To upload the release, download a ZIP file from a particular tag.
diff --git a/pyproject.toml b/pyproject.toml
@@ -0,0 +1,74 @@
+[build-system]
+build-backend = "setuptools.build_meta"
+requires = [
+    "setuptools",
+]
+
+[tool.setuptools]
+packages = [
+    "bayeso",
+    "bayeso.bo",
+    "bayeso.gp",
+    "bayeso.tp",
+    "bayeso.trees",
+    "bayeso.wrappers",
+    "bayeso.utils",
+]
+
+[project]
+name = "bayeso"
+version = "0.6.0"
+authors = [
+    {name = "Jungtaek Kim", email = "jungtaek.kim.mail@gmail.com"},
+]
+description = "Simple, but essential Bayesian optimization package"
+readme = "README.md"
+requires-python = ">=3.7"
+dependencies = [
+    "numpy",
+    "scipy",
+    "cma",
+    "tqdm",
+]
+license = {text = "MIT"}
+classifiers = [
+    "Programming Language :: Python :: 3",
+    "Intended Audience :: Science/Research",
+    "License :: OSI Approved :: MIT License",
+    "Operating System :: OS Independent",
+    "Topic :: Scientific/Engineering",
+    "Topic :: Scientific/Engineering :: Artificial Intelligence",
+]
+
+[project.urls]
+Homepage = "https://bayeso.org"
+Source = "https://github.com/jungtaekkim/bayeso"
+Issues = "https://github.com/jungtaekkim/bayeso/issues"
+
+[project.optional-dependencies]
+dev = [
+    "pytest",
+    "pytest-benchmark",
+    "pytest-timeout",
+    "pytest-cov",
+    "coveralls",
+    "sphinx",
+    "sphinx_rtd_theme",
+    "jupyter",
+    "jupytext",
+    "pylint",
+    "wheel",
+    "build",
+    "twine",
+]
+
+optional = [
+    "scipydirect",
+    "matplotlib",
+    "bayeso-benchmarks",
+]
+
+examples = [
+    "xgboost",
+    "scikit-learn",
+]
diff --git a/requirements-dev.txt b/requirements-dev.txt
diff --git a/requirements-examples.txt b/requirements-examples.txt
diff --git a/requirements-optional.txt b/requirements-optional.txt
diff --git a/requirements.txt b/requirements.txt
diff --git a/setup.py b/setup.py
diff --git a/tests/common/test_version.py b/tests/common/test_version.py
@@ -1,11 +1,11 @@
 #
-# author: Jungtaek Kim (jtkim@postech.ac.kr)
-# last updated: November 28, 2022
+# author: Jungtaek Kim (jungtaek.kim.mail@gmail.com)
+# last updated: January 4, 2024
 #
 """test_import"""
 
 
-STR_VERSION = '0.5.5'
+STR_VERSION = '0.6.0'
 
 def test_version_bayeso():
     import bayeso