diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml index 1029b838..7e40d60a 100644 --- a/.github/workflows/main.yml +++ b/.github/workflows/main.yml @@ -42,9 +42,8 @@ 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: loc run: | sudo apt-get install -y cloc @@ -52,7 +51,7 @@ jobs: 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: diff --git a/HISTORY.md b/HISTORY.md index 527a58d4..276ced01 100644 --- a/HISTORY.md +++ b/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) diff --git a/LICENSE b/LICENSE index 004db309..9be1b822 100644 --- a/LICENSE +++ b/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: diff --git a/README.md b/README.md index 16f2a597..2d247fbc 100644 --- a/README.md +++ b/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. diff --git a/docs/development.md b/docs/development.md index f98fab38..6efbc60a 100644 --- a/docs/development.md +++ b/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 +``` diff --git a/logs/.gitkeep b/logs/.gitkeep deleted file mode 100644 index e69de29b..00000000 diff --git a/pyproject.toml b/pyproject.toml index cc3951da..0aa569ab 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,9 +1,11 @@ [project] name = "bmds_ui" license = {text = "MIT License"} -authors = [{name = "Andy Shapiro", email = "shapiro.andy@epa.gov"}] +authors = [ + {name = "Andy Shapiro", email = "shapiro.andy@epa.gov"} +] 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"