Merge pull request #34 from jungtaekkim/0.5.5

0.5.5
jungtaekkim · Nov 21, 2023 · 700dd3a · 700dd3a
2 parents 1a73f64 + 43252ff
commit 700dd3a
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diff --git a/.readthedocs.yml b/.readthedocs.yml
@@ -1,5 +1,10 @@
 version: 2
 
+build:
+  os: ubuntu-22.04
+  tools:
+    python: "3.11"
+
 sphinx:
   builder: html
   configuration: docs/conf.py
@@ -9,7 +14,6 @@ formats:
   - pdf
 
 python:
-  version: 3.8
   install:
     - requirements: requirements.txt
     - requirements: requirements-optional.txt

diff --git a/CITATION.cff b/CITATION.cff
@@ -0,0 +1,32 @@
+cff-version: "1.2.0"
+authors:
+- family-names: Kim
+  given-names: Jungtaek
+  orcid: "https://orcid.org/0000-0002-1905-1399"
+- family-names: Choi
+  given-names: Seungjin
+  orcid: "https://orcid.org/0000-0002-7873-4616"
+doi: 10.5281/zenodo.8419023
+message: If you use this software, please cite our article in the
+  Journal of Open Source Software.
+preferred-citation:
+  authors:
+  - family-names: Kim
+    given-names: Jungtaek
+    orcid: "https://orcid.org/0000-0002-1905-1399"
+  - family-names: Choi
+    given-names: Seungjin
+    orcid: "https://orcid.org/0000-0002-7873-4616"
+  date-published: 2023-10-09
+  doi: 10.21105/joss.05320
+  issn: 2475-9066
+  issue: 90
+  journal: Journal of Open Source Software
+  publisher:
+    name: Open Journals
+  start: 5320
+  title: "BayesO: A Bayesian optimization framework in Python"
+  type: article
+  url: "https://joss.theoj.org/papers/10.21105/joss.05320"
+  volume: 8
+title: "BayesO: A Bayesian optimization framework in Python"
diff --git a/README.md b/README.md
@@ -1,16 +1,17 @@
 <p align="center">
-<img src="docs/_static/assets/logo_bayeso_capitalized.svg" width="400" />
+<img src="https://raw.githubusercontent.com/jungtaekkim/bayeso/main/docs/_static/assets/logo_bayeso_capitalized.svg" width="400" />
 </p>
 
 # BayesO: A Bayesian Optimization Framework in Python
+[![DOI](https://joss.theoj.org/papers/10.21105/joss.05320/status.svg)](https://doi.org/10.21105/joss.05320)
 [![Build Status](https://github.com/jungtaekkim/bayeso/actions/workflows/pytest.yml/badge.svg)](https://github.com/jungtaekkim/bayeso/actions/workflows/pytest.yml)
 [![Coverage Status](https://coveralls.io/repos/github/jungtaekkim/bayeso/badge.svg?branch=main)](https://coveralls.io/github/jungtaekkim/bayeso?branch=main)
 [![PyPI - Python Version](https://img.shields.io/pypi/pyversions/bayeso)](https://pypi.org/project/bayeso/)
 [![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/licenses/MIT)
 [![Documentation Status](https://readthedocs.org/projects/bayeso/badge/?version=main)](https://bayeso.readthedocs.io/en/main/?badge=main)
 
 <p align="center">
-<img src="docs/_static/steps/ei.gif" width="600" />
+<img src="https://raw.githubusercontent.com/jungtaekkim/bayeso/main/docs/_static/steps/ei.gif" width="600" />
 </p>
 
 Simple, but essential Bayesian optimization package.
@@ -79,11 +80,14 @@ We provide a [list of examples](EXAMPLES.md) and a [list of tests](TESTS.md).
 
 ## Citation
 ```
-@misc{KimJ2017bayeso,
+@article{KimJ2023joss,
     author={Kim, Jungtaek and Choi, Seungjin},
     title={{BayesO}: A {Bayesian} optimization framework in {Python}},
-    howpublished={\url{https://bayeso.org}},
-    year={2017}
+    journal={Journal of Open Source Software},
+    volume={8},
+    number={90},
+    pages={5320},
+    year={2023}
 }
 ```
 

diff --git a/bayeso/__init__.py b/bayeso/__init__.py
@@ -6,4 +6,4 @@
 package, implemented in Python."""
 
 
-__version__ = '0.5.4'
+__version__ = '0.5.5'
diff --git a/create_wheels_source.txt b/create_wheels_source.txt
diff --git a/docs/about/about_bayeso.rst b/docs/about/about_bayeso.rst
@@ -123,11 +123,14 @@ Citation
 
 .. code-block:: latex
 
-    @misc{KimJ2017bayeso,
+    @article{KimJ2023joss,
         author={Kim, Jungtaek and Choi, Seungjin},
         title={{BayesO}: A {Bayesian} optimization framework in {Python}},
-        howpublished={\url{https://bayeso.org}},
-        year={2017}
+        journal={Journal of Open Source Software},
+        volume={8},
+        number={90},
+        pages={5320},
+        year={2023}
     }
 
 License

diff --git a/docs/conf.py b/docs/conf.py
@@ -24,7 +24,7 @@
 author = 'Jungtaek Kim and Seungjin Choi'
 
 # The short X.Y version
-version = '0.5.4'
+version = '0.5.5'
 # The full version, including alpha/beta/rc tags
 release = '{} alpha'.format(version)
 

diff --git a/publish_new_release.txt b/publish_new_release.txt
@@ -0,0 +1,29 @@
+# 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.
+
+# 6. Upload wheel and source files to the PyPI repository.
+twine upload dist/*
+
+# 7. (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.
+## 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.
+## To upload the release, download a ZIP file from a particular tag.
diff --git a/requirements-dev.txt b/requirements-dev.txt
@@ -7,3 +7,4 @@ sphinx_rtd_theme
 jupyter
 pylint
 jupytext
+twine
diff --git a/setup.py b/setup.py
@@ -31,7 +31,7 @@
 
 setup(
     name='bayeso',
-    version='0.5.4',
+    version='0.5.5',
     author='Jungtaek Kim',
     author_email='jtkim@postech.ac.kr',
     url='https://bayeso.org',

diff --git a/tests/common/test_version.py b/tests/common/test_version.py
@@ -5,7 +5,7 @@
 """test_import"""
 
 
-STR_VERSION = '0.5.4'
+STR_VERSION = '0.5.5'
 
 def test_version_bayeso():
     import bayeso