From 8c2b7c774507237a439d96a48f2e46c3f0b5a740 Mon Sep 17 00:00:00 2001 From: blakeaw Date: Sun, 14 Jul 2024 15:11:18 -0500 Subject: [PATCH 1/4] Changes to the pyproject.toml to make sure the subpackages are installed, as well as other corresponding updates to version numbers, etc. --- CHANGELOG.md | 6 ++++++ README.md | 14 +++++++------- pyproject.toml | 2 +- src/pysb/pkpd/__init__.py | 2 +- 4 files changed, 15 insertions(+), 9 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 1d5612e..bb32b89 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -4,6 +4,12 @@ All notable changes to this project will be documented in this file. The format is based on [Keep a Changelog](http://keepachangelog.com/) and this project adheres to [Semantic Versioning](http://semver.org/). +## [0.3.1] - 2024-07-03 + +### Fixed + +- Missing sub-packages problem when installing with pip from the repo; Fix for Issue https://github.com/blakeaw/pysb-pkpd/issues/16 + ## [0.3.0] - 2024-07-01 ### Added diff --git a/README.md b/README.md index f4b3afb..d5c3c91 100644 --- a/README.md +++ b/README.md @@ -3,8 +3,8 @@ ![Python version badge](https://img.shields.io/badge/python-3.11.3-blue.svg) [![PySB version badge](https://img.shields.io/badge/PySB->%3D1.15.0-9cf.svg)](https://pysb.org/) [![license](https://img.shields.io/github/license/blakeaw/pysb-pkpd.svg)](LICENSE) -![version](https://img.shields.io/badge/version-0.3.0-orange.svg) -[![release](https://img.shields.io/github/release-pre/blakeaw/pysb-pkpd.svg)](https://github.com/blakeaw/pysb-pkpd/releases/tag/v0.3.0) +![version](https://img.shields.io/badge/version-0.3.1-orange.svg) +[![release](https://img.shields.io/github/release-pre/blakeaw/pysb-pkpd.svg)](https://github.com/blakeaw/pysb-pkpd/releases/tag/v0.3.1) __`pysb-pkpd` enables you to efficiently program and simulate dynamic PK/PD and QSP models in Python using the PySB modeling framework.__ @@ -56,27 +56,27 @@ Note that `pysb-pkpd` has the following core dependencies: ### pip install -You can install `pysb-pkpd` version 0.3.0 with `pip` sourced from the GitHub repo: +You can install `pysb-pkpd` version 0.3.1 with `pip` sourced from the GitHub repo: ##### with git installed: Fresh install: ``` -pip install git+https://github.com/blakeaw/pysb-pkpd@v0.3.0 +pip install git+https://github.com/blakeaw/pysb-pkpd@v0.3.1 ``` Or to upgrade from an older version: ``` -pip install --upgrade git+https://github.com/blakeaw/pysb-pkpd@v0.3.0 +pip install --upgrade git+https://github.com/blakeaw/pysb-pkpd@v0.3.1 ``` ##### without git installed: Fresh install: ``` -pip install https://github.com/blakeaw/pysb-pkpd/archive/refs/tags/v0.3.0.zip +pip install https://github.com/blakeaw/pysb-pkpd/archive/refs/tags/v0.3.1.zip ``` Or to upgrade from an older version: ``` -pip install --upgrade https://github.com/blakeaw/pysb-pkpd/archive/refs/tags/v0.3.0.zip +pip install --upgrade https://github.com/blakeaw/pysb-pkpd/archive/refs/tags/v0.3.1.zip ``` ### Manual install diff --git a/pyproject.toml b/pyproject.toml index 876c39a..02e1485 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -45,7 +45,7 @@ Changelog = "https://github.com/blakeaw/pysb-pkpd/blob/main/CHANGELOG.md" # Find namespace package [tool.setuptools.packages.find] where = ["src"] -include = ["pysb.pkpd"] +include = ["pysb.pkpd", "pysb.pkpd.models", "pysb.pkpd.pk_models"] namespaces = true # Set the dynamic version diff --git a/src/pysb/pkpd/__init__.py b/src/pysb/pkpd/__init__.py index 31f2014..c2e1742 100644 --- a/src/pysb/pkpd/__init__.py +++ b/src/pysb/pkpd/__init__.py @@ -5,4 +5,4 @@ from .macros import * from .util import simulate -__version__ = '0.3.0' \ No newline at end of file +__version__ = '0.3.1' \ No newline at end of file From 19c085358b33c16ef8882a83728fb81253c247b7 Mon Sep 17 00:00:00 2001 From: blakeaw Date: Thu, 18 Jul 2024 17:00:02 -0500 Subject: [PATCH 2/4] Updated the Sponsor bullet under Supporting section. --- README.md | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/README.md b/README.md index d5c3c91..01fe9ea 100644 --- a/README.md +++ b/README.md @@ -246,7 +246,9 @@ I'm very happy that you've chosen to use __pysb-pkpd__. This add-on is a project * **Star** :star: : Show your support by starring the [pysb-pkpd GitHub repository](https://github.com/blakeaw/pysb-pkpd). It helps increase the project's visibility and lets others know it's useful. It also benefits my motivation to continue improving the package! * **Share** :mega: : Sharing `pysb-pkpd` on your social media, forums, or with your network is another great way to support the project. It helps more people discover `pysb-pkpd`, which in turn motivates me to keep developing! * **Cite** :books: : Citing or mentioning this software in your work, publications, or projects is another valuable way to support it. It helps spread the word and acknowledges the effort put into its development, which is greatly appreciated! -* **Sponsor** :dollar: : Even small contributions through my Ko-fi page, [ko-fi.com/blakeaw](https://ko-fi.com/blakeaw), can make a big difference. Every little bit can help me continue developing this and other open-source projects, and I truly appreciate your support! +* **Sponsor** :dollar: : Even small financial contributions, such as spotting me the cost of a tea through Ko-fi so I can get my caffeine fix, can make a big difference! Every little bit can help me continue developing this and other open-source projects. + +[![ko-fi](https://ko-fi.com/img/githubbutton_sm.svg)](https://ko-fi.com/J3J4ZUCVU) ----- From 128f1b117b43a8033a361cbc246880c6594d00b7 Mon Sep 17 00:00:00 2001 From: blakeaw Date: Thu, 18 Jul 2024 17:00:21 -0500 Subject: [PATCH 3/4] A couple of extra spaces. --- src/pysb/pkpd/macros.py | 2 ++ 1 file changed, 2 insertions(+) diff --git a/src/pysb/pkpd/macros.py b/src/pysb/pkpd/macros.py index 7161b9a..6896336 100644 --- a/src/pysb/pkpd/macros.py +++ b/src/pysb/pkpd/macros.py @@ -4,6 +4,8 @@ import sympy from sympy import Piecewise + + __all__ = [ "drug_monomer", "one_compartment", From f084294515755ec040503016af553049ad9d62b7 Mon Sep 17 00:00:00 2001 From: blakeaw Date: Thu, 18 Jul 2024 17:04:44 -0500 Subject: [PATCH 4/4] Added an explicit install of pysb.pkpd.macros in the pyproject.toml --- pyproject.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pyproject.toml b/pyproject.toml index 02e1485..c0275cf 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -45,7 +45,7 @@ Changelog = "https://github.com/blakeaw/pysb-pkpd/blob/main/CHANGELOG.md" # Find namespace package [tool.setuptools.packages.find] where = ["src"] -include = ["pysb.pkpd", "pysb.pkpd.models", "pysb.pkpd.pk_models"] +include = ["pysb.pkpd", "pysb.pkpd.macros", "pysb.pkpd.models", "pysb.pkpd.pk_models"] namespaces = true # Set the dynamic version