ifilot · ifilot · Feb 28, 2026 · Feb 27, 2026 · Feb 27, 2026 · Feb 27, 2026
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -10,8 +10,19 @@ env:
   PROGNAME: managlyph
 
 jobs:
+  version-sync:
+    name: Version sync check
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Verify application version consistency
+        run: ./scripts/check-version-sync.sh
+
   linux:
     name: Linux (Ubuntu)
+    needs: version-sync
     runs-on: ubuntu-latest
 
     steps:
@@ -45,6 +56,7 @@ jobs:
 # --------------------------------------------------
   windows-mingw:
     name: Windows (MSYS2 MinGW64)
+    needs: version-sync
     runs-on: windows-latest
 
     defaults:

diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -45,7 +45,7 @@ add_executable(managlyph
     src/data/orbitals/wavefunction.cpp
     src/gui/anaglyph_widget.cpp
     src/gui/interface_window.cpp
-    src/gui/lighting_settings_dialog.cpp
+    src/gui/visualisation_settings_dialog.cpp
     src/gui/logwindow.cpp
     src/gui/mainwindow.cpp
     src/gui/orbital_widget.cpp

diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md
@@ -0,0 +1,92 @@
+# Contributing
+
+When contributing to this repository, please first discuss the change you wish to make via issue,
+email, or any other method with the owners of this repository before making a change.
+
+Please note we have a code of conduct, please follow it in all your interactions with the project.
+
+## Pull Request Process
+
+1. Ensure any install or build dependencies are removed before the end of the layer when doing a
+   build.
+2. Update the README.md with details of changes to the interface, this includes new environment
+   variables, exposed ports, useful file locations and container parameters.
+3. Increase the version numbers in any examples files and the README.md to the new version that this
+   Pull Request would represent. The versioning scheme we use is [SemVer](http://semver.org/).
+4. You may merge the Pull Request in once you have the sign-off of two other developers, or if you
+   do not have permission to do that, you may request the second reviewer to merge it for you.
+
+## Code of Conduct
+
+### Our Pledge
+
+In the interest of fostering an open and welcoming environment, we as
+contributors and maintainers pledge to making participation in our project and
+our community a harassment-free experience for everyone, regardless of age, body
+size, disability, ethnicity, gender identity and expression, level of experience,
+nationality, personal appearance, race, religion, or sexual identity and
+orientation.
+
+### Our Standards
+
+Examples of behavior that contributes to creating a positive environment
+include:
+
+* Using welcoming and inclusive language
+* Being respectful of differing viewpoints and experiences
+* Gracefully accepting constructive criticism
+* Focusing on what is best for the community
+* Showing empathy towards other community members
+
+Examples of unacceptable behavior by participants include:
+
+* The use of sexualized language or imagery and unwelcome sexual attention or
+advances
+* Trolling, insulting/derogatory comments, and personal or political attacks
+* Public or private harassment
+* Publishing others' private information, such as a physical or electronic
+  address, without explicit permission
+* Other conduct which could reasonably be considered inappropriate in a
+  professional setting
+
+### Our Responsibilities
+
+Project maintainers are responsible for clarifying the standards of acceptable
+behavior and are expected to take appropriate and fair corrective action in
+response to any instances of unacceptable behavior.
+
+Project maintainers have the right and responsibility to remove, edit, or
+reject comments, commits, code, wiki edits, issues, and other contributions
+that are not aligned to this Code of Conduct, or to ban temporarily or
+permanently any contributor for other behaviors that they deem inappropriate,
+threatening, offensive, or harmful.
+
+### Scope
+
+This Code of Conduct applies both within project spaces and in public spaces
+when an individual is representing the project or its community. Examples of
+representing a project or community include using an official project e-mail
+address, posting via an official social media account, or acting as an appointed
+representative at an online or offline event. Representation of a project may be
+further defined and clarified by project maintainers.
+
+### Enforcement
+
+Instances of abusive, harassing, or otherwise unacceptable behavior may be
+reported by contacting the project team at [INSERT EMAIL ADDRESS]. All
+complaints will be reviewed and investigated and will result in a response that
+is deemed necessary and appropriate to the circumstances. The project team is
+obligated to maintain confidentiality with regard to the reporter of an incident.
+Further details of specific enforcement policies may be posted separately.
+
+Project maintainers who do not follow or enforce the Code of Conduct in good
+faith may face temporary or permanent repercussions as determined by other
+members of the project's leadership.
+
+### Attribution
+
+This Code of Conduct is adapted from the [Contributor Covenant][homepage], version 1.4,
+available at [http://contributor-covenant.org/version/1/4][version]
+
+[homepage]: http://contributor-covenant.org
+[version]: http://contributor-covenant.org/version/1/4/
diff --git a/README.md b/README.md
@@ -5,47 +5,51 @@
 [![License: GPL v3](https://img.shields.io/badge/License-GPLv3-blue.svg)](https://www.gnu.org/licenses/gpl-3.0)
 
 ## Overview
-Managlyph is a powerful educational tool for visualizing atomic and molecular
-structures in 3D. It enables students and educators to explore atomic orbitals,
-reaction mechanisms, and molecular properties interactively, enhancing learning
-through dynamic 3D visualizations using red/cyan glasses or 3D monitors. Its
-versatility and ease of use make it an invaluable resource for teaching complex
-chemical concepts.
-
-> [!TIP]
-> * Download the Windows 64 bit installer [via this link](https://github.com/ifilot/managlyph/releases/latest/download/managlyph-installer-win64.exe)
-> * Detailed information on how to use Managlyph can be found in the [online manual](https://ifilot.github.io/managlyph/).
-
-## Features
-
-- **Anaglyph Projection**: Immerse yourself in stunning 3D visualizations with
-  just a simple pair of red/cyan anaglyph glasses, bringing depth and realism to
-  your viewing experience. For those with specialized 3D equipment, the system
-  also supports interlacing, enabling seamless compatibility with a wide range
-  of 3D monitors and projectors. Whether you're exploring 3D content on basic
-  setups or advanced displays, this feature ensures accessibility and enhanced
-  visual performance for everyone.
-
-  ![red/cyan stereographic projection](img/screenshot-anaglyph.png)
-- **Molecular Orbitals**: Managlyph leverages the versatile 'Atom Bond Object'
-  (ABO) file format, a powerful tool for embedding and managing multiple
-  atomistic structures. These files can encapsulate complex details, such as
-  molecular geometries, chemical bonding, and even molecular orbitals
-  represented as isosurfaces. This flexibility allows for the seamless
-  integration and visualization of intricate structural and electronic
-  properties, making it an invaluable resource for advanced scientific modeling
-  and analysis. 
-
-  ![molecular orbitals](img/screenshot-molecular-orbitals.png)
-- **Atomic Orbitals**: Create, project, and rotate atomic orbitals up to the 4f
-  subshell, providing an unparalleled opportunity to explore the intricate
-  details of atomic structures. This capability allows users to visualize and
-  analyze the shapes, orientations, and complexities of orbitals in 3D, offering
-  a deeper understanding of quantum mechanics and atomic interactions.
-
-  ![molecular orbitals](img/screenshot-atomic-orbitals.png)
-
-## Boost
-
-**Managlyph** was developed with the generous financial support of the
-[TU/e boost program](https://boost.tue.nl/projects/3d-visualization-with-artificial-intelligence-and-projection/).
+Managlyph is a desktop application for 3D visualization of atomic and molecular
+structures.
+
+The application supports stereoscopic rendering via red/cyan anaglyph projection
+and interlaced output for compatible 3D displays. Typical use cases include
+classroom demonstrations, self-study, and interactive exploration of molecular
+models.
+
+## Documentation and Downloads
+- Windows 64-bit installer:
+  https://github.com/ifilot/managlyph/releases/latest/download/managlyph-installer-win64.exe
+- User manual:
+  https://ifilot.github.io/managlyph/
+
+## Capabilities
+
+### Stereoscopic Rendering
+Managlyph provides red/cyan anaglyph rendering and interlaced stereo output.
+These modes are intended for use with either anaglyph glasses or supported 3D
+monitors/projectors.
+
+![red/cyan stereographic projection](img/screenshot-anaglyph.png)
+
+### ABO File Support and Molecular Orbitals
+Managlyph uses the Atom Bond Object (ABO) format to store atomistic structures
+and related metadata. ABO datasets can include molecular geometries, bonding
+information, and molecular-orbital isosurfaces for visualization.
+
+![molecular orbitals](img/screenshot-molecular-orbitals.png)
+
+### Atomic Orbitals
+The application can generate and render atomic orbitals up to the 4f subshell,
+including rotation and inspection in 3D.
+
+![atomic orbitals](img/screenshot-atomic-orbitals.png)
+
+### Reaction Pathway Visualization
+Managlyph can visualize elementary reaction pathways by interpolating between
+structures (for example: reactants, intermediates, transition states, and
+products). This allows stepwise inspection of geometry changes during a
+reaction.
+
+![reaction pathway](img/screenshot-reaction.png)
+
+## Project Support
+Development of Managlyph received financial support from the TU/e Boost
+program:
+https://boost.tue.nl/projects/3d-visualization-with-artificial-intelligence-and-projection/
diff --git a/assets/containers/catalysis/co1121_ch_hydrogenation.abo b/assets/containers/catalysis/co1121_ch_hydrogenation.abo
diff --git a/assets/containers/catalysis/co1121_co_dissociation.abo b/assets/containers/catalysis/co1121_co_dissociation.abo
diff --git a/assets/shaders/phong.fs b/assets/shaders/phong.fs
@@ -12,6 +12,7 @@ uniform float specular_strength;
 uniform float shininess;             // specular exponent (e.g. 16–128)
 uniform float edge_strength;
 uniform float edge_power;
+uniform int camera_mode;
 
 out vec4 fragColor;
 
@@ -21,6 +22,9 @@ void main()
     vec3 N = normalize(normal_eyespace);
     vec3 L = normalize(lightdirection_eyespace);
     vec3 V = normalize(vertex_direction_eyespace);
+    if (camera_mode == 1) {
+        V = vec3(0.0, 0.0, 1.0);
+    }
 
     // --- Ambient ---
     vec3 ambient = ambient_strength * light_color;

diff --git a/assets/shaders/simplecanvas.fs b/assets/shaders/simplecanvas.fs
@@ -9,10 +9,5 @@ layout(origin_upper_left, pixel_center_integer) in vec4 gl_FragCoord;
 
 void main()
 {
-    vec3 col = texture(regular_texture, TexCoords).rgb;
-    if(length(col) > .1) {
-        FragColor = vec4(col, 1.0f);
-    } else {
-        FragColor = vec4(col, 0.0f);
-    }
+    FragColor = texture(regular_texture, TexCoords);
 }
diff --git a/docs/source/_static/custom.css b/docs/source/_static/custom.css
@@ -30,4 +30,15 @@
     background: #24292e;
     padding: 6px 10px;
     border-radius: 4px;
+}
+
+/* Disable horizontal scrolling for tables */
+.wy-table-responsive {
+    overflow-x: visible !important;
+}
+
+/* Allow table cells to wrap normally */
+.wy-table-responsive table td,
+.wy-table-responsive table th {
+    white-space: normal !important;
 }
diff --git a/docs/source/_static/img/screenshot_4dz2.png b/docs/source/_static/img/screenshot_4dz2.png
diff --git a/docs/source/_static/img/screenshot_anaglyph.png b/docs/source/_static/img/screenshot_anaglyph.png
diff --git a/docs/source/_static/img/screenshot_checkerboard.png b/docs/source/_static/img/screenshot_checkerboard.png
diff --git a/docs/source/_static/img/screenshot_select_anaglyph.png b/docs/source/_static/img/screenshot_select_anaglyph.png
diff --git a/docs/source/_static/img/screenshot_visualisation_settings.png b/docs/source/_static/img/screenshot_visualisation_settings.png
diff --git a/docs/source/building_models.rst b/docs/source/building_models.rst
@@ -0,0 +1,40 @@
+Building Models
+===============
+
+Managlyph renders 3D geometry stored inside ABO containers. These models can
+represent molecular orbitals, isosurfaces, or general 3D meshes. Models are
+typically prepared using **AboBuilder**, a companion tool for constructing ABO
+files compatible with Managlyph.
+
+Using AboBuilder
+----------------
+
+AboBuilder provides tools for constructing atomic structures and generating
+renderable geometry for use in Managlyph. It supports:
+
+- construction of molecular and atomic structures
+- generation of orbital and isosurface meshes
+- export of frame data and geometry to the ABO container format
+
+AboBuilder is available at: `https://ifilot.github.io/abobuilder/ <https://ifilot.github.io/abobuilder/>`_
+
+Generated ABO files can be opened directly in Managlyph.
+
+Integration with PyQInt
+-----------------------
+
+AboBuilder can integrate with **PyQInt**, a quantum chemistry library used to
+compute electronic structure properties such as molecular orbitals and electron
+density distributions.
+
+PyQInt project page: `https://github.com/ifilot/pyqint <https://github.com/ifilot/pyqint>`_
+
+This integration enables the generation of orbital surfaces and related data
+for visualization.
+
+Typical workflow:
+
+1. Compute molecular orbitals or electron density using PyQInt.
+2. Use AboBuilder (in conjunction with PyTessel) to convert computed data into isosurfaces or meshes.
+3. Export the result to an ABO container.
+4. Open the ABO file in Managlyph for stereographic visualization.
diff --git a/docs/source/community_guidelines.rst b/docs/source/community_guidelines.rst
@@ -0,0 +1,13 @@
+.. index:: Community Guidelines
+
+Community guidelines
+====================
+
+* Contributions to :program:`Managlyph` are always welcome and appreciated. Before doing
+  so, please first read the `CONTRIBUTING <https://github.com/ifilot/managlyph/blob/master/CONTRIBUTING.md>`_
+  guide.
+* For reporting issues or problems with the software, you are kindly invited to
+  `to open a new issue on Github with the bug tag <https://github.com/ifilot/managlyph/issues/new?labels=bug>`_.
+* If you seek support in using :program:`Managlyph`, please
+  `open an issue with the question tag <https://github.com/ifilot/managlyph/issues/new?labels=question>`_.
+* If you wish to contact the developers, please send an e-mail to ivo@ivofilot.nl.