Avogadro 1.96.0

Changes

We are pleased to announce the latest release of Avogadro, including piles of bug fixes and feature enhancements, including contributions from @aerkiaga as part of Google Summer of Code.
Thanks to many for suggestions, bug reports, and discussions.

Draft developer documentation can be found at https://two.avogadro.cc

As part of this release, we have an official AppImage build for Linux, as well as a code-signed release for macOS.

If you have comments or suggestions, please join us at https://discuss.avogadro.cc and as always, help and contributions
in many forms are very welcome, particularly if you'd like to help with user documentation or website developement.

✨ Features

• Insert DNA/RNA dialog @ghutchis (#909)
• Render close contacts @aerkiaga (#898)
• Create new layer from selection @ghutchis (#899)
• Tweak the mesh lighting .. now lights "from the top" @ghutchis (#880)
• Add an initial config widget to set mesh colors and opacity @ghutchis (#877)
• Import and retain space group information @ghutchis (#875)
• Write Gaussian cube files @ghutchis (#873)
• Add plugin to focus or unfocus selection @aerkiaga (#868)
• Implement close contact perception logic @aerkiaga (#862)
• Add formal charge to atom property tables @ghutchis (#839)
• Add support for formal charges @aerkiaga (#831)
• Add setting to reverse direction of scroll-to-zoom @ghutchis (#778)
• Tweak icons for label editor and selection @ghutchis (#776)
• Add tooltips to tools @ghutchis (#777)
• Add label editor to create custom labels @serk12 (#740)
• Add a copy graphics action

🚀 Performance Fixes

• Subgraph rewrite @aerkiaga (#878)
• Approximate cartoon B-spline from a small local neighborhood @aerkiaga (#860)
• Bond graph optimization @aerkiaga (#832)
• Faster bond perception @aerkiaga (#829)
• Optimize secondary structure @aerkiaga (#833)

🐛 Bug Fixes

• Add .cjson extension to files if none is present
• Update atomic masses @ghutchis (#894)
• Fix layer memory crash @ghutchis (#876)
• Fix memory leak with OpenGL: Detaching and deleting shaders/programs on updates @octycs (#855)
• Remove call for Core::Molecule rendering to eliminate casting @ghutchis (#871)
• Fix reading generic file formats with Open Babel @ghutchis (#848)
• Fix erratic editing behavior @aerkiaga (#819)
• Solve problems writing files with no extension @ghutchis (#835)
• Convert 2-letter PDB symbols to appropriate case @aerkiaga (#830)
• Fix Manipulation and Bond Centric Manipulation tools @aerkiaga (#825)
• Fall back to Wikipedia method for dihedral angles @ghutchis (#808)
• Be careful about assign or copy from molecules with no layers @ghutchis (#806)
• Disable dynamic bonding during animation @ghutchis (#767)
• Try to use 'python' in the path as a fallback @ghutchis (#746)

🧰 Maintenance

• Fix Valgrind uninitialized errors @aerkiaga (#887)
• Add tests using various sanitizers @ghutchis (#888)
• Make sure to sign and notarize the Mac build @ghutchis (#893) (#885)
• Only build overlayaxes if USE_OPENGL is enabled @ghutchis (#879)
• Try using Windows 2019 to build wheels @ghutchis (#861)
• Create Codacy scans @ghutchis (#850)
• test ">=0" within machine precision (>-EPS) @drew-parsons (#813)
• Add defaultBehavior method to render plugins @serk12 (#807)
• Update setup.py with long description from README.md and URLs @ghutchis (#750)

📚 Translations

• Translations update from Hosted Weblate @weblate
• Automated translation updates @github-actions (#853)
• Minor tweaks to the automated pull request @ghutchis (#761)

Credits

Thanks to many contributors, including: @HoangTuan110, @Lisapple, @M3CG, @SantosSi, @aerkiaga, @comradekingu, @drew-parsons, @ejatjon, @ersen0, @ghutchis, @github-actions, @github-actions[bot], @milotype, @nicolasfella, @octycs, @ovari, @rezaalmanda, @serk12, @urkawa, @weblate, J. Lavoie, Pa, Temuri Doghonadze, phlostically and 刘韬