ayenpure · ayenpure · Aug 22, 2025 · Aug 19, 2025 · Aug 19, 2025 · Aug 19, 2025
diff --git a/.bumpversion.cfg b/.bumpversion.cfg
@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 0.1.15
+current_version = 0.1.16
 commit = True
 tag = True
 

diff --git a/README.md b/README.md
@@ -3,132 +3,48 @@
 [![Test](https://github.com/ayenpure/QuickView/actions/workflows/test.yml/badge.svg)](https://github.com/ayenpure/QuickView/actions/workflows/test.yml)
 [![Package and Release](https://github.com/ayenpure/QuickView/actions/workflows/package-and-release.yml/badge.svg)](https://github.com/ayenpure/QuickView/actions/workflows/package-and-release.yml)
 
-**QuickView** is an interactive visualization tool for atmospheric scientists
-working with E3SM (Energy Exascale Earth System Model) data. It provides an
-intuitive interface for exploring atmospheric simulation outputs without the
-steep learning curve of general-purpose visualization tools.
-
-![quickview](docs/images/main.png)
-
-## Quick Start
-
-### Installation
-
-Download the latest release from the
-[releases page](https://github.com/ayenpure/QuickView/releases):
-
-- **macOS**: `QuickView-{version}.dmg` - Double-click to install
-- **Linux**: Coming soon
-- **Windows**: Coming soon
-
-Pre-built binaries include all dependencies - no Python or ParaView required.
-
-## Data
-
-QuickView works with E3SM Atmosphere Model (EAM) output files in NetCDF format.
-Sample data files and their corresponding connectivity files are available at
-[Zenodo](https://zenodo.org/records/16895849).
-
-### Data Files
-
-QuickView supports EAM output files from different model versions:
-
-- **EAM Version 2**: Standard atmospheric simulation outputs (e.g.,
-  `EAMv2_ne30pg2_F2010.eam.h0.nc`)
-- **EAM Version 4 (interim)**: Newer format outputs (e.g.,
-  `EAMxx_ne4pg2_202407.nc`)
-
-These files contain atmospheric variables such as temperature, pressure, wind
-fields, and other model diagnostics on finite-volume physics grids.
-
-### Connectivity Files
-
-Each data file requires a corresponding connectivity file that describes the
-horizontal grid structure:
-
-- Connectivity files follow the naming pattern:
-  `connectivity_{resolution}_TEMPEST.scrip.nc`
-- These files are generated using TempestRemap and contain grid topology
-  information
-- **Important**: The connectivity file resolution must match the data file
-  resolution for proper visualization
-
-For example:
-
-- Data file: `EAMv2_ne30pg2_F2010.eam.h0.nc`
-- Connectivity file: `connectivity_ne30pg2_TEMPEST.scrip.nc`
-
-Both files use the same `ne30pg2` grid resolution and must be loaded together
-for the application to function correctly.
-
-## Documentation
-
-- **[Installation Guide](docs/setup/requirements.md)** - Detailed setup
-  instructions
-- **[User Guide](docs/userguide/launch.md)** - How to use QuickView
-- **[Data Requirements](docs/data-requirements.md)** - NetCDF file format
-  specifications
-- **[Control Panel Reference](docs/userguide/control_panel.md)** - UI components
-  and features
+**EAM QuickView** is an interactive visualization tool
+tailored for scientists working with the atmospheric component of the
+[Energy Exascale Earth System Model (E3SM)](https://e3sm.org/), the
+E3SM Atmosphere Model (EAM). 
+The Graphical User Interface (GUI) built with Python and
+powered by [Trame](https://www.kitware.com/trame/)
+gives users intuitive access to the powerful visualization capabilities of
+[ParaView](https://www.paraview.org/) without requiring a steep learning curve.
 
 ## Key Features
 
-- Clean, minimalist interface tailored for atmospheric modeling
-- Multi-variable visualization with drag-and-drop layout
-- Geographic projections (Plate Carrée, Robinson, etc.)
-- Persistent sessions - pick up where you left off
-- Support for EAM v2, v3, and upcoming v4 data formats
-
-## Development
-
-### Python Development Installation
-
-```bash
-# Clone the repository
-git clone https://github.com/ayenpure/QuickView.git
-cd QuickView
-
-# Set up conda environment
-conda env create -f quickview-env.yml
-conda activate quickview
-
-# Install QuickView
-pip install -e .
-```
-
-### Running from Source
-
-```bash
-python -m quickview.app --data /path/to/your/data.nc --conn /path/to/connectivity.nc
+- Intuitive, minimalist interface tailored for atmospheric modeling.
+- Multi-variable visualization with drag-and-drop layout.
+- Persistent sessions - pick up where you left off.
+- Support for EAM v2, v3, and upcoming v4 output formats.
 
-# Launch server only (no browser popup)
-python --server -m quickview.app --data /path/to/your/data.nc --conn /path/to/connectivity.nc
-```
-
-The application starts a web server at `http://localhost:8080`
-
-### Development Utilities
-
-```bash
-# Run linter
-ruff check quickview/
-
-# Run tests
-python -m quickview.app --help
+## Quick Start
 
-# Bump version
-bumpversion patch
-```
+- Install and launch the app for [end users](docs/setup/for_end_users.md)
+  and [app developers](docs/setup/for_app_developers.md).
+- Download connectivity files of EAM's cubed-sphere grids from
+  [Zenodo](https://doi.org/10.5281/zenodo.16908567).
+- Optional: download [sample simulation output](https://zenodo.org/records/16922608)
+  to test the app.
+- For EAMv2 and v3 developers and users: if your simulation data files
+  are *not* the original files written out by the model,
+  i.e., if your files were generated by NCO, CDO, etc.
+  check QuickView's [data format requirements](docs/userguide/data_requirements.md).
+- For EAMxx developers and users: EAMxx's most recent output format
+  updates might not have been accommodated. If your run into issues
+  opening your data files, please contact our
+  [lead developer](https://www.kitware.com/abhishek-yenpure/).
 
 ## About
 
 QuickView is developed by [Kitware, Inc.](https://www.kitware.com/) in
 collaboration with
 [Pacific Northwest National Laboratory](https://www.pnnl.gov/), supported by the
 U.S. Department of Energy's
-[BER](https://www.energy.gov/science/ber/biological-and-environmental-research)
-and
 [ASCR](https://www.energy.gov/science/ascr/advanced-scientific-computing-research)
+and
+[BER](https://www.energy.gov/science/ber/biological-and-environmental-research)
 programs via [SciDAC](https://www.scidac.gov/).
 
 ### Contributors

diff --git a/app-icon.png b/app-icon.png
diff --git a/docs/README.md b/docs/README.md
@@ -1,12 +1,23 @@
-# EAM QuickView
+# QuickView Homepage
 
 ![eam-quickview-full](../images/eam-quickview-full.png)
 
-## Overview
+## What is QuickView?
 
-EAM QuickView is an open-source, Python-based application for interactive
-visualization of simulation data produced by the atmosphere component of the
-[Energy Exascale Earth System Model](https://e3sm.org/), EAM.
+
+**EAM QuickView** is an interactive visualization tool
+tailored for scientists working with the atmospheric component of the 
+[Energy Exascale Earth System Model](https://e3sm.org/) (EAM,
+[Rasch et al., 2019](https://doi.org/10.1029/2019MS001629);
+[Golaz et al., 2022](https://doi.org/10.1029/2022MS003156); 
+[Donahue et al., 2024](10.1029/2024MS004314)).
+The Graphical User Interface (GUI) built with Python and
+powered by [Trame](https://www.kitware.com/trame/) 
+gives users intuitive access to the powerful visualization capabilities of
+[ParaView](https://www.paraview.org/)
+without requiring a steep learning curve.
+
+## Why QuickView?
 
 While comprehensive tools like [ParaView](https://www.paraview.org/) and
 [VisIt](https://visit-dav.github.io/visit-website/index.html) are widely used in
@@ -32,12 +43,11 @@ multivariate visualization and is currently focused on the EAM model.
 
 ## Key Features
 
-- Clean and minimalist user interface tailored for atmosphere modeling
-  workflows.
+- Minimalist user interface tailored for atmosphere modeling workflows.
 - Push-button visualization of multiple variables.
 - Persistent state: "Pick up where you left off".
 - Supports EAM simulation data from current (EAMv2, v3) and upcoming (v4)
-  versions
+  versions.
 
 ## Further Reading
 
@@ -58,17 +68,13 @@ For information about data file requirements and supported formats, see the
 
 The lead developer of EAM QuickView is
 [Abhishek Yenpure (abhi.yenpure@kitware.com)](https://www.kitware.com/abhishek-yenpure/)
-at [Kitware, Inc.](https://www.kitware.com/).
-
-Other key contributors include Berk Geveci (and Sebastien Jourdain?) at
-[Kitware, Inc.](https://www.kitware.com/); Hui Wan and Kai Zhang at
-[Pacific Northwest National Laboratory](https://www.pnnl.gov/atmospheric-climate-and-earth-sciences-division).
+at [Kitware, Inc.](https://www.kitware.com/). Other key contributors at Kitware, Inc. include [Berk Geveci](https://www.kitware.com/berk-geveci/) and [Sebastien Jourdain](https://www.kitware.com/sebastien-jourdain/). Key contributors on the atmospheric science side are Hui Wan and Kai Zhang at [Pacific Northwest National Laboratory](https://www.pnnl.gov/atmospheric-climate-and-earth-sciences-division).
 
 EAM QuickView is a product of an interdisciplinary collaboration supported by
-the U.S. Department of Energy’s
-[Biological and Environmental Research (BER)](https://www.energy.gov/science/ber/biological-and-environmental-research)
-and
+the U.S. Department of Energy Office of Science’s
 [Advanced Scientific Computing Research (ASCR)](https://www.energy.gov/science/ascr/advanced-scientific-computing-research)
+and
+[Biological and Environmental Research (BER)](https://www.energy.gov/science/ber/biological-and-environmental-research)
 via the
 [Scientific Discovery through Advanced Computing (SciDAC](https://www.scidac.gov/))
 program.
diff --git a/docs/future.md b/docs/future.md
@@ -0,0 +1,11 @@
+# Planned Improvements
+
+Below is a list of improvements that are being worked on or have been planned.
+Addional suggestions are welcome. Bug reports and feature requests
+can be made by opening new
+[issues](https://github.com/ayenpure/QuickView/issues) on GitHub.
+
+
+1. Server-client model and deployment of servers to Department of Energy's Leadership Computing Facilities.
+
+1.  
diff --git a/docs/images/tool-bar.png b/docs/images/tool-bar.png
diff --git a/docs/images/toolbar.png b/docs/images/toolbar.png
diff --git a/docs/images/toolbar_conn_and_data_load.png b/docs/images/toolbar_conn_and_data_load.png
diff --git a/docs/images/toolbar_misc.png b/docs/images/toolbar_misc.png
diff --git a/docs/images/toolbar_state_save_and_load.png b/docs/images/toolbar_state_save_and_load.png
diff --git a/docs/setup/for_app_developers.md b/docs/setup/for_app_developers.md
@@ -0,0 +1,62 @@
+# Installation and Launch for App Developers
+
+At version 1.0, QuickView is expected to be installed and used from a personal computer with the data files also being local. Future versions will support the server-client model allowing access to remote data files.
+
+Releases so far have focused on MacOS. Support for Linux and Windows systems can be provided upon request.
+
+----
+## Cloning the repo
+
+```
+git clone https://github.com/ayenpure/QuickView.git
+cd QuickView
+```
+
+----
+## Installing basic requirements
+
+```
+# Set up conda environment
+conda env create -f quickview-env.yml
+conda activate quickview
+
+# Install QuickView
+pip install -e .
+```
+
+----
+## Additional requirements
+
+Additional requirements for the app are satisfied once the app is launched
+for the very first time using Python virtual environments `venv`. An additional
+step for the use is to provide the path to ParaView's Python client that is
+distributed with the ParaView binaries. The `pvpython` binary is present in the
+`bin` directory of ParaView, on macOS the path is something like
+`/Applications/ParaView-5.13.0.app/Contents/bin/pvpython`
+
+----
+## Launching the app from command line
+
+To launch the EAM QuickView GUI in its dedicated window, use
+```
+python -m quickview.app --data /path/to/your/data.nc --conn /path/to/connectivity.nc
+```
+
+To launch server only (no browser popup), use
+```
+python --server -m quickview.app --data /path/to/your/data.nc --conn /path/to/connectivity.nc
+```
+
+----
+## Development utilities
+
+```
+# Run linter
+ruff check quickview/
+
+# Run tests
+python -m quickview.app --help
+
+# Bump version
+bumpversion patch
+```
diff --git a/docs/setup/for_end_users.md b/docs/setup/for_end_users.md
@@ -0,0 +1,23 @@
+# Installation and Launch for End Users
+
+
+At version 1.0, QuickView is expected to be installed and used from a personal computer with the data files also being local. Future versions will support the server-client model allowing access to remote data files.
+
+Releases so far have focused on MacOS. Installers for Linux and Windows systems can be provided upon request.
+
+---
+# Installation
+
+For end users, we provide pre-built binaries that can be installed using just a few clicks.
+
+1. Download the latest installer from the [releases page](https://github.com/ayenpure/QuickView/releases/tag/v0.1.13). Mac users with Apple Silicon chips should download `QuickView_{version}_aarch64.dmg`, and those with Intel chips should download a `*_x64.dmg` file.
+2. Double-click the downloaded `.dmg` file. In the pop-up window, drag the QuickView icon into the Applications folder.
+
+
+The pre-built binaries include all dependencies needed to start the app on a local computer.
+Additional dependencies needed for data processing and visualization are downloaded and installed automatically when the app is launched for the first time.
+
+---
+# Launch
+
+To launch the EAM QuickView GUI, simply double-click the app icon in your Applications folder.
diff --git a/docs/userguide/camera.md b/docs/userguide/camera.md
@@ -0,0 +1 @@
+# Camera Widget