Merge pull request #78 from Avogadro/v199

Update for 1.99 release including some release note tweaks

source/conf.py

@@ -25,7 +25,7 @@
     response = requests.get("https://api.github.com/repos/openchemistry/avogadrolibs/releases/latest")
     release = response.json()['tag_name']
 except requests.exceptions.ConnectionError:
-    release = "1.97.0"
+    release = "1.99.0"
 version = release
 
 year = date.today().year
@@ -153,7 +153,7 @@
   #'index': []
 }
 
-html_logo = '_images/avogadro2.png'
+html_logo = '_static/avogadro2.png'
 
 # Add any paths that contain custom static files (such as style sheets) here,
 # relative to this directory. They are copied after the builtin static files,

source/install/versions/v195.md

@@ -2,7 +2,7 @@
 
 # Release Notes v1.95.0
 
-Aug 16, 2021
+16 Aug 2021
 
 ## Changes
 

source/install/versions/v1951.md

@@ -2,7 +2,7 @@
 
 # Release Notes v1.95.1
 
-Aug 26, 2021
+26 August 2021
 
 This release fixes several bugs in the recent [1.95.0 release](#v195) and is recommended for all users.
 

source/install/versions/v196.md

@@ -2,7 +2,7 @@
 
 # Release Notes v1.96.0
 
-June 2, 2022
+2 June 2022
 
 ## Changes
 

source/install/versions/v197.md

@@ -2,7 +2,7 @@
 
 # Release Notes v1.97.0
 
-Jul 21, 2022
+21 July 2022
 
 We are pleased to announce the latest release of Avogadro, including piles of bug fixes and many feature enhancements, including contributions from @aerkiaga as part of Google Summer of Code. 
 Thanks to many for suggestions, bug reports, and discussions.

source/install/versions/v198.md

@@ -2,6 +2,8 @@
 
 # Release Notes v1.98.0
 
+26 October 2023
+
 ## 🌟 Highlights (tldr)
 
 - Integration with 3Dconnexion input devices on Mac and Windows

source/install/versions/v1981.md

@@ -0,0 +1,31 @@
+(v1981)=
+
+# Release Notes v1.98.1
+
+2 November 2023
+
+This is a bug-fix release, particularly for Windows users, removing a filename filter that affected opening and saving files.
+
+This also includes the openbabel-3.dll which was left out of Windows releases.
+
+## 🐛 Bug Fixes
+
+- Make sure to grab openbabel*.dll on Windows package @ghutchis 
+- Migrated typedefs and changed const to constexpr @Atharva-Kanherkar
+- Fix Python module install dir @antonio-rojas
+- Revert validation of filenames. @ghutchis
+- Parsing orca output would crash when swapping orbitals @ghutchis
+
+## 🧰 Maintenance
+
+- Add workflow concurrency - should stop builds during quick changes @ghutchis
+- vtk: Add missing OpenGL link target @antonio-rojas
+
+## 📚 Translations
+
+- Translations update from Hosted Weblate @weblate
+- Automated translation updates @github-actions
+
+## Credits
+
+Thanks to many contributors, including: @Atharva-Kanherkar, @antonio-rojas, @atharrrva15, @ghutchis, @github-actions, @ovari, @weblate, Alejandro Díaz-Moscoso and Martin Slavík

source/install/versions/v199.md

@@ -0,0 +1,112 @@
+(v199)=
+
+# Release Notes v1.99.0
+
+10 February 2024
+
+## 🌟 Highlights (tldr)
+
+- Further improvements to the new optimization framework, including default integrated Open Babel force fields (MMFF94, UFF, GAFF)
+- New toolbar icons with light / dark theme from @matterhorn103
+- Significantly faster molecular and orbital surfaces
+- Vibrational spectra plotting
+- Support for installing Python packages with plugins via `pip` or `conda`
+- Improved selection of `conda` environments
+- Conformer search dialog through Open Babel
+- Improved template tool for inserting ligands and functional groups
+	- Significant improvements from @nbehrnd for the ligand library
+- Logging debugging / error messages to a file for Windows users
+
+## ✨ Features
+
+- Add optional energy / optimize code that links Open Babel @ghutchis 
+- Update tool plugins to set icon as light / dark theme @ghutchis
+- Modern tool icons @matterhorn103 
+- Add confirmation dialog to install with conda or pip @ghutchis
+- Add support for first launch dialog and conda environments @ghutchis 
+- Add red = a, blue = b, green = c color axes for unit cells @ghutchis 
+- Vibrational spectra plot @ghutchis
+- Add UniqueID atom label type @ghutchis 
+- Add ethylene, ethyne, and phosphate standard functional groups @ghutchis 
+- Improved python configure dialog @ghutchis 
+- Adding support for bond label in base classes and CJSON @ghutchis 
+- Add "…" indicator for display types with settings @ghutchis
+- Split ligands and functional groups in the template tool @ghutchis 
+- Added copy and export feature to property tables @Surajjalpun2002
+- Add initial support for copy from tables @ghutchis 
+- Add conformer search box @ghutchis
+- Add template library to insert ligands or functional groups @ghutchis (#1456)
+- Add support for Hall number and space group to CJSON read/write @ghutchis (#1440)
+- Add new MessagePack version of CJSON @ghutchis (#1452)
+- Add a message handler to grab debug / warnings on Windows @ghutchis
+- Save and load the camera modelView and projection matrix @ghutchis
+
+## 🐛 Bug Fixes
+
+- Fixed typo in setDefaultPythonInterpretor() @matterhorn103 (#1583)
+- Fix Mac builds @ghutchis (#1522)
+- Fix quantum surface max cutoff for diffuse functions @ghutchis (#1556)
+- Change "Insert fragment" ⇒ "Insert molecule" by popular request @ghutchis (#1519)
+- Fix parsing XYZ files with tabs between columns @ghutchis (#1513)
+- Fix bug with incorrect Unicode characters added to labels @ghutchis (#1588)
+- Fix for Wayland @matterhorn103 (#1577)
+- Fixed crash with angle properties on an empty molecule @secretkontributer (#1566)
+- Fix density color crash @ghutchis (#1537)
+- Fix crash in forcefields - check if method is valid before using it @ghutchis (#1526)
+- Fix for first item in ordered plugin dialog being empty @matterhorn103 (#1523)
+- Fix crash with "copy as" and an empty molecule @ghutchis (#1521)
+- Turn off Color Opacity Map unless a VTK widget is active @ghutchis (#1509)
+- Make sure to automatically load the "Meshes" display type @ghutchis (#1508)
+- If no partial charges are assigned, set them @ghutchis (#1502)
+- Fix potential crashes in selection commands @ghutchis (#1499)
+- Fix vibration animation @ghutchis (#1487)
+- Generate the density matrix if needed for the electron density surface @ghutchis (#1482)
+- Fix empty window showing up for commands without an option dialog @ghutchis (#1468)
+- Save partial charges and properly read them from CJSON @ghutchis (#1467)
+- Don't show PNG files in the filter dialog @ghutchis (#1462)
+- Fix GFN-FF energy - redirect GFN-FF output through a hack @ghutchis (#1454)
+- Fixup PDB reading with non-standard MD files (no element column) @ghutchis (#1450)
+- Fix atomic numbers from Orca - it would read electrons not symbols @ghutchis (#1451)
+- Fix linear molecular template @ghutchis (#1474)
+- Avoid segfaulting while manipulating carbon bonds/hydrogens @Makiah (#1493)
+- Reduce ambiguity of "Export" toolbar button @matterhorn103 (#442)
+- Ensure that title bar correctly displays active molecule file @Makiah (#440)
+
+## 🐍 Scripting / Plugin Improvements
+
+- Allow scripts to add properties (orbitals, vibrations, cubes) @ghutchis 
+- Add support for navigator commands - rotate, translate, zoom @ghutchis 
+- Windows: Standardize plugin location based on forum feedback @ghutchis
+- Add some additional Python classes including cjson and connect @ghutchis 
+- Always supply cjson to scripts @ghutchis 
+- If userOptions specifies an order, use that to sort the form @ghutchis 
+- Check script --menupath for {} priority numbers @ghutchis 
+- Add a "text" option for scripts to add text labels / help @ghutchis 
+
+## 🚀 Performance Improvements
+
+- Skip calculating orbital / surface points too far apart (e.g., negligible) @ghutchis
+    - Leads to 2-3x faster surface generation
+
+## 🧰 Builds / Maintenance
+
+- Package OpenSSL for Windows @ghutchis
+- Update Eigen cmake header references @ghutchis (#1544)
+- Add Qt6 build tests @ghutchis (#1547)
+- Update to cibuildwheel for Python 3.12 @ghutchis (#1546)
+- Fix include of avogadrocoreexport.h @ghutchis (#1504)
+- Add specialization for char\* and MatrixXf types @ghutchis (#1494)
+- Install ligand and functional group fragments @ghutchis (#1460)
+- Make sure to copy libopenbabel on Mac for CPack @ghutchis
+
+## 📚 Translations
+
+- Correct typo @Acylation (#1553)
+- Update Australian and Canadian localization from GB version @ghutchis (#1453)
+- Translations update from Hosted Weblate @weblate
+- Automated translation updates @github-actions
+- Fix a few remaining cases of .. instead of ellipsis character @ghutchis (#1458)
+
+## Credits
+
+Thanks to many contributors, including: @Acylation, @Azaathooth, @IagoEmanuel15, @ImgBotApp, @Makiah, @NorwayFun, @Surajjalpun2002, @alchemistcai, @bitigchi, @dependabot, @dependabot[bot], @ghutchis, @github-actions, @hakkikonu, @imgbot, @imitrichev, @joerivan, @koenr, @matterhorn103, @nbehrnd, @ovari, @research11111, @secretkontributer, @tacitcoast, @weblate, Alejandro Díaz-Moscoso, Eisuke Kawashima, Ivanushka, LibreTranslate, Remus-Gabriel Chelu, Weblate Translation Memory and gallegonovato