Release 24.1 (#82)

* add pypi links

* remove gitlab configuration

* update documentation

* update version numbers

* added Cody

* fix case

* update documentation link

docs/source/history.md

@@ -4,7 +4,7 @@
 
 ### Version 24.1
 
-*Released on 2024-XX-XX.*
+*Released on 2024-11-25.*
 
 * Added BMDS Desktop mode for execution
 * Added support for Multitumor modeling
@@ -13,16 +13,14 @@
 * Minimum `pybmds` version increased to version `24.1`
 * Initial release of `bmds-ui`; project was originally forked from [shapiromatron/bmds-server](https://github.com/shapiromatron/bmds-server)
 
-Released on 2024-XX-XX.
-
 ## pybmds
 
 ### Version 24.1
 
-*Released on 2024-XX-XX.*
+*Released on 2024-11-25.*
 
 * Added Multitumor and Multistage Cancer model
 * Add Nested Dichotomous models
 * Updated `bmdscore` library; integration now uses [pybind11](https://pybind11.readthedocs.io/) for direct integration instead of using a shared library. This should improve performance and stability and make it easier to develop moving forward.
 * Build distributions for windows, mac, and linux using [cibuildwheel](https://cibuildwheel.pypa.io/)
-* Initial release of `pybmds`; project was originally forked from [shapiromatron/bmds](https://github.com/shapiromatron/bmds)
+* Initial release of `pybmds`; the python components of the package were originally taken from [shapiromatron/bmds](https://github.com/shapiromatron/bmds)

docs/source/index.md

@@ -17,19 +17,12 @@ The Python package **pybmds** enables execution of dose-response models in a scr
 * Reporting in Microsoft Excel and Microsoft Word reports
 * Batch execution for multiple datasets or option set configuration
 
-
 **If you are experienced with installing Python packages**, then enter the following command to install **BMDS Desktop** (which includes `pybmds`):
 
 ```bash
 pip install bmds-ui
 ```
 
-:::{admonition} NOTE - this will not work until we officially release!
-:class: caution
-
-The above command will not work until we are cleared for public release; please follow the detailed [installation guide](./installation.md). This message will be removed prior to official release.
-:::
-
 **If you are new to installing Python packages** and wish to BMDS Desktop or `pybmds`, then please follow the detailed [installation guide](./installation.md). The installation guide makes it easy to configure your computer, and describes possible issues and solutions that may arise during installation.
 
 

docs/source/installation.md

@@ -224,30 +224,6 @@ You'll need to activate the environment **every time** you want to run BMDS Desk
 
 With Python installed and a virtual environment created, you're ready to install BMDS Desktop and `pybmds`.  You'll need to [activate your environment](activate-venv), and then install the packages using Python's package installer, [pip](https://pip.pypa.io/), which is included with Python.
 
-(internal-epa)=
-:::{admonition} NOTE - for internal EPA testing
-:class: tip
-
-This portion of the guide should be used as we develop pre-release versions. Recommended for EPA staff. Please check the FAQ below with any questions, or reach out to [Andy Shapiro](mailto:[email protected]) for any feedback.  If anything is missing from the guide or anything is confusing, please let us know! This will be removed when we can officially release.
-
----
-
-While connected to the EPA VPN install the packages:
-
-```bash
-python -m pip install pybmds --index-url https://gitlab.epa.gov/api/v4/projects/1508/packages/pypi/simple
-python -m pip install bmds-ui --index-url https://gitlab.epa.gov/api/v4/projects/1508/packages/pypi/simple
-```
-
-:::
-
-:::{admonition} NOTE - this will not work until we officially release!
-:class: caution
-
-The content below will not work until we are cleared for public release; please follow the [EPA installation guide](internal-epa). This message will be removed prior to official release.
-
----
-
 To install **BMDS Desktop**, which includes `pybmds`:
 
 ```bash
@@ -262,8 +238,6 @@ python -m pip install bmds-ui==24.1
 
 If no version is specified, `pip` will install the latest version.
 
-:::
-
 After installation, you're ready to use BMDS Desktop and `pybmds`.
 
 (desktop-shortcut)=
@@ -502,32 +476,9 @@ To fix, [activate](activate-venv) your Python virtual environment after successf
 
 After [activating your environment](activate-venv), you can upgrade to the latest version:
 
-:::{admonition} NOTE - this will not work until we officially release!
-:class: caution
-
-The content below will not work until we are cleared for public release; please follow the [EPA installation guide](internal-epa). This message will be removed prior to official release.
-
----
-
 ```bash
 python -m pip install --upgrade bmds-ui
 ```
-:::
-
-:::{admonition} NOTE - for internal EPA testing
-:class: tip
-
-Use this guide instead until we are cleared for release.
-
----
-
-While connected to the EPA VPN, install the packages:
-
-```bash
-python -m pip install --upgrade bmds-ui --index-url https://gitlab.epa.gov/api/v4/projects/1508/packages/pypi/simple
-```
-
-:::
 
 (multiple-versions)=
 ### Installing Multiple Versions of BMDS Desktop

pyproject.toml

@@ -2,8 +2,9 @@
 name = "pybmds"
 license = {text = "MIT License"}
 authors = [
-  {name = "BMDS development team"},
+  {name = "BMDS Development Team"},
   {name = "Andy Shapiro", email = "[email protected]"},
+  {name = "Cody Simmons", email = "[email protected]"},
 ]
 readme = "README.md"
 description = "U.S. EPA Dose Response Modeling Software"
@@ -29,6 +30,12 @@ dependencies = [
   "tqdm",
 ]
 
+[project.urls]
+"Source" = "https://github.com/USEPA/BMDS"
+"Changes" = "https://github.com/USEPA/BMDS/blob/main/docs/source/history.md"
+"Issue Tracker" = "https://github.com/USEPA/BMDS/issues"
+"Documentation" = "https://usepa.github.io/BMDS/"
+
 [project.optional-dependencies]
 dev = [
   "coverage~=7.6.4",

src/bmdscore/bmds_helper.cpp

@@ -15,7 +15,7 @@
 #include "bmds_helper.h"
 
 // calendar versioning; see https://peps.python.org/pep-0440/#pre-releases
-std::string BMDS_VERSION = "24.1a6";
+std::string BMDS_VERSION = "24.1";
 
 double python_dichotomous_model_result::getSRAtDose(double targetDose, std::vector<double> doses) {
   std::vector<double> diff;

src/pybmds/__init__.py

@@ -1,4 +1,4 @@
-__version__ = "24.1a6"  # see docs/development for versioning
+__version__ = "24.1"  # see docs/development for versioning
 
 from .batch import BatchResponse, BatchSession  # noqa: F401
 from .constants import DistType as ContinuousDistType  # noqa: F401