Documentation updates from tech review

docs/source/desktop.md

@@ -4,11 +4,11 @@ BMDS Desktop is a graphical user interface to execute dose-response modeling on
 
 BMDS Desktop is identical to [BMDS Online](https://bmdsonline.epa.gov), with a few additional features:
 
-* Analyses (dose response analyses) and data storage is fully offline
+* Analyses (dose response analyses) and data storage are fully offline
 * Database files (projects) are single files containing all analyses
 * Within a project, analyses can be labelled and organized
 
-Follow the [installation](installation.md) guide to install the software. Make sure to create the [BMDS Desktop Manager](./installation.md#the-bmds-desktop-manager) shortcut. To start BMDS Desktop, double-click the shortcut and then enter option `1` to start the application:
+Follow the [installation](installation.md) guide to install the software. Make sure to create the [BMDS Desktop Manager](./installation.md#create-the-bmds-desktop-manager-shortcut) shortcut. To start BMDS Desktop, double-click the shortcut and then enter option `1` to start the application:
 
 ```{figure} _static/img/bmds-desktop-manager.jpg
 :alt: BMDS Desktop Manager
@@ -29,7 +29,7 @@ The BMDS Desktop Startup Interface is the gateway to create a BMDS project and s
 ```{figure} _static/img/desktop-startup.jpg
 :alt: Screenshot of BMDS Desktop Startup
 
-BMDS Desktop Startup Interface. On startup, you see a list existing projects that have been run with BMDS Desktop; you can create new projects from this screen as well. Navigate the interface using your keyboard or mouse.
+BMDS Desktop Startup Interface. On startup, you see a list of existing projects that have been run with BMDS Desktop. You can create new projects from this screen as well. Navigate the interface using your keyboard or mouse.
 ```
 
 Each project in BMDS Desktop contains all of that project's analyses stored in a single file. You can create a single project and store all of your analyses in a single file, or multiple projects - one project per chemical, for example.
@@ -43,7 +43,7 @@ BMDS Desktop Project Creation. Create a new project by specifying a path and a d
 ```
 
 :::{important}
-Creating a new project creates an accompanying database file at the path and filename specified if it does not already exist. Database files should have the `.db` extension. BMDS Desktop also creates other files with different extensions in that directory- `.db-shm` and `.db-wal`. **Do not delete those files -** they allow multiple users to work with the same project concurrently.
+Creating a new project creates an accompanying database file at the path and filename specified if it does not already exist. Database files should have the `.db` extension. BMDS Desktop also creates other files with different extensions in that directory, such as `.db-shm` and `.db-wal`. **Do not delete those files -** they allow multiple users to work with the same project concurrently.
 :::
 
 You can also update a database's location, in the event that you moved the database to a new directory. Updating the database refreshes the path/location so BMDS Desktop can find it again; the updating process does not change the file's contents.
@@ -52,8 +52,7 @@ Deleting a project from the BMDS Desktop Startup Interface deletes its entry in
 
 ## BMDS Desktop Application
 
-After at least one project has been created, press the "Start"
- button to run the project. Starting a project will open a new BMDS Desktop tab in your default browser. For a new project, initial startup may take up to a minute for the browser tab to appear.
+After at least one project has been created, select the "Start" button to run the project. Starting a project will open a new BMDS Desktop tab in your default browser. For a new project, initial startup may take up to a minute before the browser tab appears.
 
 You can run only one BMDS Desktop project at a time.
 

docs/source/development.md

@@ -1,6 +1,6 @@
 # Development
 
-Like layers of an onion, there are multiple BMDS products that can be developed, each of which require slightly different build steps and tooling. A description of each of the environments is described below.
+BMDS consists of multiple products, each of which requires slightly different build steps and tooling. The following sections describe each of those environments.
 
 ## Building and testing `pybmds`
 
@@ -21,11 +21,11 @@ python -m pip install -U pip
 python -m pip install -e ".[dev,docs]"
 ```
 
-This will install the package and all dependencies, including building the C++ `bmdscore` shared object which will require a compiler and related dependencies installed and configured for your local setup.
+This will install the package and all dependencies, including building the C++ `bmdscore` shared object, which will require a compiler and related dependencies to be installed and configured for your local setup.
 
 :::{tip}
 
-If you want to skip building `bmdscore` locally, you can set an environment variable `SKIP_BUILD=1` in your python environment; this will allow you to install the package but skip compilation of the shared object.
+If you want to skip building `bmdscore` locally, you can set the environment variable `SKIP_BUILD=1` in your Python environment. Setting this variable will allow you to install the package but skip compilation of the shared object.
 
 :::
 
@@ -39,9 +39,9 @@ py.test
 py.test -k test_my_special_test_name
 ```
 
-There is a built-in Makefile, ``make``, that runs many common utility methods for developing the application. You can run tests by running `make test`, run code formatting using `make format`, or build documentation using `make docs`. For more details or other built-in actions, view the `Makefile` (or the `make.bat` file for Windows).
+There is a built-in Makefile, ``make``, that runs many common utility methods for developing the application. You can run tests by running `make test`, run code formatting using `make format`, or build documentation using `make docs`. For more details on other built-in actions, view the `Makefile` (or the `make.bat` file for Windows).
 
-Github Actions are in place to execute whenever code a pull-request is submitted to check code formatting and successful tests. When code is merged into the `main` branch, a wheel artifact is created and stored on github. We use [cibuildwheel](https://cibuildwheel.pypa.io/en/stable/) to build wheel packages in Windows, Mac, and Linux using Github Actions.
+Github Actions are in place to execute whenever a pull-request is submitted to check code formatting and successful tests. When code is merged into the `main` branch, a wheel artifact is created and stored on github. We use [cibuildwheel](https://cibuildwheel.pypa.io/en/stable/) to build wheel packages in Windows, macOS, and Linux using Github Actions.
 
 ## Build and testing in `bmdscore`
 
@@ -68,7 +68,7 @@ See [documentation](https://github.com/USEPA/BMDS-UI/blob/main/docs/development.
 
 ## Documentation
 
-Documentation is generated using [Sphinx](https://www.sphinx-doc.org/). Narrative text is written in markdown; any examples of using `pybmds` are written in jupyter notebooks and are executing when building documentation; the returned notebook with any output (such as figures or output tables) are rendered directly in the documentation.
+Documentation is generated using [Sphinx](https://www.sphinx-doc.org/). Narrative text is written in Markdown; any examples of using `pybmds` are written in jupyter notebooks and are executing when building documentation; the returned notebook with any output (such as figures or output tables) are rendered directly in the documentation.
 
 To build documentation, there are a few different commands available in the `make` file:
 

docs/source/index.md

@@ -3,13 +3,15 @@
   <img src="_static/img/pybmds-identifier.png" width="210px">
 </p>
 
-The U.S. EPA [BMDS Online](https://bmdsonline.epa.gov) is a web application which allows users to execute the Benchmark Dose Modeling Software using a using a Graphical User Interface (GUI) on your web browser, no installation required.  If you'd prefer to run the software on your computer, **BMDS Desktop** is the same application running locally. The Python package **bmds-ui** installs BMDS Desktop.
+The U.S. EPA [BMDS Online](https://bmdsonline.epa.gov) is a web application that enables users to execute the Benchmark Dose Modeling Software using a Graphical User Interface (GUI) on your web browser, no installation required.
 
-The Python package **pybmds** allows execution of dose-response models in a scripting environment. The package includes dose-response models for multiple types of dose-response data, including dichotomous, continuous, nested dichotomous, and cancer (including multitumor modeling). It is the underlying execution engine for BMDS Online and BMDS Desktop.
+If you'd prefer to run the software on your computer, **BMDS Desktop** is the same application running locally. The Python package **bmds-ui** installs BMDS Desktop.
+
+The Python package **pybmds** enables execution of dose-response models in a scripting environment. The package includes dose-response models for multiple types of dose-response data, including dichotomous, continuous, nested dichotomous, and cancer (including multitumor modeling). `pybmds` is the underlying execution engine for BMDS Online and BMDS Desktop.
 
 **Highlights:**
 
-* Dose response modeling for multiple dataset types (continuous, dichotomous, nested dichotomous, cancer, multitumor)
+* Dose-response modeling for multiple dataset types (continuous, dichotomous, nested dichotomous, cancer, multitumor)
 * Plotting and summary table capabilities
 * Model recommendation logic
 * Reporting in Microsoft Excel and Microsoft Word reports
@@ -28,7 +30,7 @@ pip install bmds-ui
 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 use `pybmds` or BMDS Desktop for multiple projects, then please follow the detailed [installation guide](./installation.md). The installation guide makes it easy to configure your computer including adding a shortcut to start and update the application. It also describes possible issues and solutions that may arise during installation.
+**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.
 
 
 An example dose-response modeling session using `pybmds`: