update documentation (#54)

* switch to furo?

* remove sphinx docx

.gitignore

@@ -12,7 +12,6 @@ build/
 /data/
 coverage_report/
 dist/
-docs/site/
 node_modules/
 scripts/private
 /public/

HISTORY.md

@@ -0,0 +1,5 @@
+# History
+
+## v24.1 (TBD)
+
+* ...

Makefile

@@ -1,4 +1,4 @@
-.PHONY: build docs docs-clean docs-serve docs-all clean clean-test clean-pyc clean-build loc help lint lint-py lint-js format format-py format-js sync-dev
+.PHONY: build clean clean-test clean-pyc clean-build loc help lint lint-py lint-js format format-py format-js sync-dev
 .DEFAULT_GOAL := help
 
 define BROWSER_PYSCRIPT
@@ -60,29 +60,6 @@ coverage: ## Generate test coverage report
 	coverage html -d coverage_report
 	$(BROWSER) coverage_report/index.html
 
-docs: ## Build documentation {html}
-	@$(MAKE) -C docs clean
-	@$(MAKE) -C docs html
-	@echo "HTML: \"docs/build/html/index.html\""
-
-docs-clean: ## Clean documentation
-	@$(MAKE) -C docs clean
-
-docs-serve: ## Realtime documentation preview
-	sphinx-autobuild -b html docs/source docs/build/html --port 5555
-
-docs-all: ## Build documentation {html, pdf, docx}
-	@$(MAKE) -C docs clean
-	@$(MAKE) -C docs html
-	@$(MAKE) -C docs singlehtml
-	@$(MAKE) -C docs latexpdf
-	@mkdir -p docs/build/docx
-	@cd docs/build/singlehtml; pandoc -s index.html -o ../docx/pybmds.docx
-	@echo "HTML: \"docs/build/html/index.html\""
-	@echo "Single Page HTML: \"docs/build/singlehtml/index.html\""
-	@echo "Microsoft Word:  \"docs/build/docx/pybmds.docx\""
-	@echo "PDF: \"docs/build/latex/pybmds.pdf\""
-
 loc: ## Generate lines of code report
 	@cloc \
 		--exclude-dir=build,dist,migrations,node_modules,logs,private,public,scripts,vendor,venv \

README.md

@@ -1,33 +1,4 @@
-# BMDS webserver
+# BMDS UI
 
-Run a webserver that will batch process dose-response data using the US EPA's
-benchmark dose modeling software [BMDS](https://www.epa.gov/bmds).  Under the hood, this web application
-uses the [BMDS Python interface](https://pypi.python.org/pypi/bmds).
+A user interface foe execution of dose-response data using the US EPA's Benchmark Dose Modeling Software [BMDS](https://www.epa.gov/bmds). Under the hood, this web application uses the [BMDS Python interface](https://pypi.python.org/pypi/bmds).
 
-To use the webserver, specify a new BMDS Job using a input file formatted like this.
-
-```json
-{
-    "dataset_type": "D",
-    "bmds_version": "BMDS2601",
-    "datasets": [
-        {
-            "doses": [0, 1.96, 5.69, 29.75],
-            "ns": [75, 49, 50, 49],
-            "incidences": [5, 1, 3, 14]
-        },
-        {
-            "doses": [0, 1.96, 5.69, 29.75],
-            "ns": [75, 49, 50, 49],
-            "incidences": [0, 0, 11, 27]
-        }
-    ]
-}
-```
-
-You'll receive a Job ID back, and you can check the website to see when the job is complete. Then, results can be downloaded. Results include:
-
-* The dfile created for each model
-* The outfile created for each model
-* The parsed output file for each model
-* A recommended best-fitting model, using guidance from [Wignall et al. 2014](https://dx.doi.org/10.1289/ehp.1307539) (optional)

bmds_ui/analysis/fixtures/initial_data.json

@@ -6,7 +6,7 @@
             "content_type": 1,
             "subject": "Homepage",
             "content": {
-                "template": "<div class=\"row\">\n    <div class=\"col-sm-12\">\n        <h1>Welcome to BMDS online.</h1>\n    </div>\n</div>\n<div class=\"row\">\n    <div class=\"col-md-8\">\n        <div class=\"col-lg\">\n            <p>\n                This web-application executes the US EPA's benchmark dose modeling software (<a href=\"https://www.epa.gov/bmds\">BMDS</a>).\n            </p>\n            <ul>\n                <li>Load example datasets below to view example input files; for more information, see the <a  href=\"http://bmds-ui.readthedocs.io/en/latest/\">documentation</a>\n                </li>\n                <li>Software is designed for automated BMDS execution using a\n                    programming language such as Python, R, or Java. To take\n                    advantage of automation, use the <a href=\"/api/v1/\">API</a>,\n                    and see the <a href=\"http://bmds-ui.readthedocs.io/en/latest/quickstart.html\">quickstart</a> section.\n                </li>\n            </ul>\n        </div>\n    </div>\n    <div class=\"col-md-4\">\n        <form  action=\"{% url 'analysis_create' %}\" method=\"post\">\n            {% csrf_token %}\n            <label for=\"id_id\">Create a new analysis:</label>\n            <button type=\"submit\" class=\"btn btn-primary btn-block mb-1\">Create a new BMDS analysis</button>\n            <p class=\"text-muted\">Analyses are deleted after {{days_to_keep_analyses}}.</p>\n        </form>\n    </div>\n</div>\n"
+                "template": "<div class=\"row\">\n    <div class=\"col-sm-12\">\n        <h1>Welcome to BMDS online.</h1>\n    </div>\n</div>\n<div class=\"row\">\n    <div class=\"col-md-8\">\n        <div class=\"col-lg\">\n            <p>\n                This web-application executes the US EPA's benchmark dose modeling software (<a href=\"https://www.epa.gov/bmds\">BMDS</a>).\n            </p>\n            <ul>\n                <li>Load example datasets below to view example input files; for more information, see the documentation\n                </li>\n                <li>Software is designed for automated BMDS execution using a\n                    programming language such as Python, R, or Java. To take\n                    advantage of automation, use the <a href=\"/api/v1/\">API</a>,\n                    and see the quickstart section.\n                </li>\n            </ul>\n        </div>\n    </div>\n    <div class=\"col-md-4\">\n        <form  action=\"{% url 'analysis_create' %}\" method=\"post\">\n            {% csrf_token %}\n            <label for=\"id_id\">Create a new analysis:</label>\n            <button type=\"submit\" class=\"btn btn-primary btn-block mb-1\">Create a new BMDS analysis</button>\n            <p class=\"text-muted\">Analyses are deleted after {{days_to_keep_analyses}}.</p>\n        </form>\n    </div>\n</div>\n"
             },
             "created": "2021-01-31 08:00:00.123456+00:00",
             "last_updated": "2021-01-31 08:00:00.123456+00:00"

docs/source/development.md → docs/development.md

@@ -8,7 +8,7 @@ Make sure you have the following applications installed locally:
 - [Yarn](https://yarnpkg.com/)
 - [PostgreSQL](https://www.postgresql.org/) >= 16
 
-If installing on Windows, all requirements are available using [miniconda](https://docs.conda.io/en/latest/miniconda.html), and do not require administrative access.
+If installing on Windows, these packages are available using [miniconda](https://docs.conda.io/en/latest/miniconda.html).
 
 ## Initial setup
 
@@ -79,7 +79,7 @@ npm start
 If you navigate to [localhost](http://127.0.0.1:8000/) and see a website, you're ready to begin coding!
 
 
-## Visual Studio Code settings
+## Visual Studio Code
 
 [Visual Studio Code](https://code.visualstudio.com/) is the recommended editor for this project.
 
@@ -89,35 +89,6 @@ Recommended extensions:
 - [Eslint](https://marketplace.visualstudio.com/items?itemName=dbaeumer.vscode-eslint)
 - [Ruff](https://marketplace.visualstudio.com/items?itemName=charliermarsh.ruff)
 
-Recommended workspace settings:
-
-```json
-{
-    "restructuredtext.linter.disabled": true,
-    "[html]": {
-        "editor.formatOnSave": false
-    },
-    "[python]": {
-        "editor.formatOnSave": true,
-        "editor.formatOnPaste": false,
-        "editor.codeActionsOnSave": {
-            "source.fixAll": true
-        }
-    },
-    "[javascript]": {
-        "editor.formatOnSave": false,
-        "editor.codeActionsOnSave": {
-            "source.fixAll.eslint": true
-        }
-    },
-    "editor.formatOnSave": true,
-    "python.linting.flake8Enabled": false,
-    "python.pythonPath": "./venv/bin/python",
-    "eslint.workingDirectories": [
-        "./frontend"
-    ]
-}
-```
 ## Additional settings
 
 ### Feature flags (frontend)
@@ -134,14 +105,10 @@ Future mode can also be enabled via the local setting `ALWAYS_SHOW_FUTURE`. This
 
 ```python
 # bmds_ui\main\settings\local.py
-    ...
-    # Shows future-flagged items without login/url parameter
-    ALWAYS_SHOW_FUTURE = True
-    ...
-```
 
-
-That's it! Now you should be able to view content that's coming soon!
+# Shows future-flagged items without login/url parameter
+ALWAYS_SHOW_FUTURE = True
+```
 
 ### Building a test database
 

docs/index.md

@@ -0,0 +1,18 @@
+# BMDS UI
+
+BMDS UI is a user interface for running `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, and it is desgined for running as a web application (such as [BMDS Online](https://bmdsonline.epa.gov)) or a desktop model, which we call BMDS Desktop.
+
+## BMDS Desktop Capabilities
+
+BMDS Desktop is designed to run locally on your desktop computer in fully offline mode; it does not interact with any resources on the internet after initial installation.
+
+
+*Screenshot of TUI*
+
+*Create database*
+
+*BMDS Desktop User Interface w/ Runs*
+
+*Dose Response Setup*
+
+*Dose Response Plot*

make.bat

@@ -4,9 +4,6 @@ if "%~1" == "" goto :help
 if /I %1 == help goto :help
 if /I %1 == sync-dev goto :sync-dev
 if /I %1 == build goto :build
-if /I %1 == docs goto :docs
-if /I %1 == docs-serve goto :docs-serve
-if /I %1 == docs-all goto :docs-all
 if /I %1 == test goto :test
 if /I %1 == lint goto :lint
 if /I %1 == format goto :format
@@ -23,9 +20,6 @@ goto :help
 echo.Please use `make ^<target^>` where ^<target^> is one of
 echo.  sync-dev     sync dev environment after code checkout
 echo.  build        build application (python wheel)
-echo.  docs         Build documentation {html}
-echo.  docs-serve   Realtime documentation preview
-echo.  docs-all     Build documentation {html, docx}
 echo.  test         perform both test-py and test-js
 echo.  coverage     generate test coverage report
 echo.  test-py      run python tests
@@ -52,25 +46,6 @@ python manage.py set_git_commit
 flit build --no-use-vcs --format=wheel
 goto :eof
 
-:docs
-rmdir /s /q docs\build
-sphinx-build -b html docs/source docs/build/html
-goto :eof
-
-:docs-serve
-rmdir /s /q docs\build
-sphinx-autobuild -b html docs/source docs/build/html --port 5555
-goto :eof
-
-:docs-all
-rmdir /s /q docs\build
-sphinx-build -b html docs/source docs/build/html
-sphinx-build -b singlehtml docs/source docs/build/singlehtml
-cd docs\build\singlehtml
-pandoc -s index.html -o pybmds.docx
-cd ../../..
-goto :eof
-
 :lint
 ruff format . --check && ruff check .
 npm --prefix .\frontend run lint

pyproject.toml

@@ -54,11 +54,6 @@ dev = [
   "django_extensions==3.2.3",
   "django-browser-reload==1.12.1",
 
-  # docs
-  "Sphinx~=7.3.7",
-  "myst-parser~=2.0.0",
-  "pydata-sphinx-theme~=0.15.2",
-
   # tests
   "pytest~=8.2.1",
   "pytest-django~=4.8.0",

tests/data/db.yaml

@@ -5161,11 +5161,11 @@
         \       <div class=\"col-lg\">\n            <p>\n                This web-application
         executes the US EPA's benchmark dose modeling software (<a href=\"https://www.epa.gov/bmds\">BMDS</a>).\n
         \           </p>\n            <ul>\n                <li>Load example datasets
-        below to view example input files; for more information, see the <a  href=\"http://bmds-ui.readthedocs.io/en/latest/\">documentation</a>\n
+        below to view example input files; for more information, see the documentation\n
         \               </li>\n                <li>Software is designed for automated
         BMDS execution using a\n                    programming language such as Python,
         R, or Java. To take\n                    advantage of automation, use the
-        <a href=\"/api/v1/\">API</a>,\n                    and see the <a href=\"http://bmds-ui.readthedocs.io/en/latest/quickstart.html\">quickstart</a>
+        <a href=\"/api/v1/\">API</a>,\n                    and see the quickstart
         section.\n                </li>\n            </ul>\n        </div>\n    </div>\n
         \   <div class=\"col-md-4\">\n        <form  action=\"{% url 'analysis_create' %}\" method=\"post\">\n            {%
         csrf_token %}\n            <label for=\"id_id\">Create a new analysis:</label>\n