switch to github actions to python 312 (#63)

* switch to py312

* add software disclaimer

* update frontmatter for release; following USEPA/open-source-projects

* update pyproject.toml authors

.github/workflows/main.yml

@@ -42,17 +42,16 @@ jobs:
         token: ${{ secrets.USEPA_BMDS_PRIVATE_PAT }}
     - uses: actions/setup-python@v5
       with:
-        python-version: '3.11'
-        architecture: 'x64'
-        cache: 'pip'
+        python-version: "3.12"
+        cache: pip
     - name: loc
       run: |
         sudo apt-get install -y cloc
         echo "# Lines of Code Report" >> $GITHUB_STEP_SUMMARY
         make loc >> $GITHUB_STEP_SUMMARY
     - name: Install pybmds
       run: |
-        python -m pip install -U pip wheel
+        python -m pip install -U pip wheel setuptools
         cd venv
         source ./tools/linux_ci_setup.sh
         source ./tools/linux_ci_env.sh
@@ -155,9 +154,8 @@ jobs:
         token: ${{ secrets.USEPA_BMDS_PRIVATE_PAT }}
     - uses: actions/setup-python@v5
       with:
-        python-version: '3.11'
-        architecture: 'x64'
-        cache: 'pip'
+        python-version: "3.12"
+        cache: pip
     - name: Download webpack build
       uses: actions/download-artifact@v4
       with:

HISTORY.md

@@ -2,4 +2,11 @@
 
 ## v24.1 (TBD)
 
-* ...
+*Released on 2024-XX-XX.*
+
+* Added BMDS Desktop mode for execution
+* Added support for Multitumor modeling
+* Added support for Nested Dichotomous modeling
+* Added poly-k adjustment for dichotomous datasets
+* 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)

LICENSE

@@ -1,6 +1,6 @@
 The MIT License (MIT)
 
-Copyright (c) 2020 Andrew J Shapiro
+Copyright (c) 2024 U.S Federal Government (in countries where recognized)
 
 Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:
 

README.md

@@ -1,9 +1,9 @@
 # BMDS UI
 
-BMDS UI is a user interface for running [pybmds](https://pypi.org/project/pybmds/), a python package for dose-response modeling using the US EPA's Benchmark Dose Modeling Software ([BMDS](https://www.epa.gov/bmds)).  The user interface is a web application, but has two different deployment options:
+BMDS UI is a user interface for running [pybmds](https://pypi.org/project/pybmds/), a Python package for dose-response modeling using the US EPA's Benchmark Dose Modeling Software ([BMDS](https://www.epa.gov/bmds)).  The user interface is a web application, but has two different deployment options:
 
+* It can be deployed locally as a desktop application, which we call **BMDS Desktop**
 * It can deployed as a web application, such as [BMDS Online](https://bmdsonline.epa.gov)
-* It can be deployed locally as a desktop application, which we call **BMDS Desktop**.
 
 **BMDS Desktop application home screen:**
 ![](./docs/img/bmds-desktop.jpg)
@@ -28,11 +28,6 @@ Database technology|Uses a sqlite database file (single file)|Uses a PostgreSQL
 The BMDS Desktop has a startup screen where you can select which database file you'd like to use in your application. You can have multiple databases on your computer, one per project for example:
 ![](./docs/img/desktop-startup.jpg)
 
-## Build Notes
+## Disclaimer
 
-To build containers for deployment:
-
-```bash
-make build
-docker compose -f compose/build.yml --project-directory . build
-```
+The United States Environmental Protection Agency (EPA) GitHub project code is provided on an "as is" basis and the user assumes responsibility for its use.  EPA has relinquished control of the information and no longer has responsibility to protect the integrity , confidentiality, or availability of the information.  Any reference to specific commercial products, processes, or services by service mark, trademark, manufacturer, or otherwise, does not constitute or imply their endorsement, recommendation or favoring by EPA.  The EPA seal and logo shall not be used in any manner to imply endorsement of any commercial product or activity by EPA or the United States Government.  Any reference to specific commercial products, processes, or services by service mark, trademark, manufacturer, or otherwise, does not constitute or imply their endorsement, recommendation or favoring by EPA.  The EPA seal and logo shall not be used in any manner to imply endorsement of any commercial product or activity by EPA or the United States Government.

docs/development.md

@@ -171,3 +171,12 @@ py.test -sv tests/integration/test_dichotomous.py --pdb
 ```bash
 textual run --dev bmds_ui.desktop.cli:main
 ```
+
+## Deployment
+
+To build containers for deployment:
+
+```bash
+make build
+docker compose -f compose/build.yml --project-directory . build
+```

pyproject.toml

@@ -1,9 +1,11 @@
 [project]
 name = "bmds_ui"
 license = {text = "MIT License"}
-authors = [{name = "Andy Shapiro", email = "[email protected]"}]
+authors = [
+  {name = "Andy Shapiro", email = "[email protected]"}
+]
 readme = "README.md"
-description = "US EPA Dose Response Modeling Software"
+description = "U.S. EPA Dose Response Modeling Software User Interface"
 dynamic = ["version"]
 keywords = [
   "dose response",
@@ -78,13 +80,16 @@ prod = [
 ]
 
 [project.urls]
-Source = "https://github.com/USEPA/bmds-online-private"
+"Source" = "https://github.com/USEPA/bmds-ui"
+"Changes" = "https://github.com/USEPA/bmds-ui/blob/main/HISTORY.md"
+"Issue Tracker" = "https://github.com/USEPA/bmds-ui/issues"
+"Download" = "https://pypi.org/project/bmds-ui/"
 
 [project.scripts]
 "manage.py" = "bmds_ui:manage"
-manage = "bmds_ui:manage"
-bmds = "bmds_ui.desktop.cli:main"
-bmdsdesktop = "bmds_ui.desktop.cli:main"
+"manage" = "bmds_ui:manage"
+"bmds" = "bmds_ui.desktop.cli:main"
+"bmdsdesktop" = "bmds_ui.desktop.cli:main"
 "bmds_desktop" = "bmds_ui.desktop.cli:main"
 "bmds-desktop" = "bmds_ui.desktop.cli:main"