Merge branch 'add-version-notes' of github.com:Avogadro/two.avogadro.…

…cc into add-version-notes

_sources/api/index.md.txt

@@ -1,6 +1,6 @@
 (api)=
 
-# Library API
+# Develop
 
 Avogadro libraries can be used from both C++ and Python interfaces.
 

_sources/install/index.md.txt

@@ -4,8 +4,7 @@
 
 In addition to installing the latest release ({{release}}), there are nightly builds and anyone can build Avogadro from source code.
 
-::::{grid} 3
-:::{grid-item-card}
+:::{card}
 :text-align: center
 :class-header: sd-font-weight-bold sd-bg-light
 {fab}`apple;fa-2x` MacOS
@@ -15,7 +14,7 @@ In addition to installing the latest release ({{release}}), there are nightly bu
 <a class="sd-sphinx-override sd-btn sd-text-wrap sd-btn-outline-primary reference external" href="https://nightly.link/OpenChemistry/avogadrolibs/workflows/build_cmake/master/macOS.dmg.zip"><span>Download Nightly Build</span></a>
 :::
 
-:::{grid-item-card}
+:::{card}
 :text-align: center
 :class-header: sd-font-weight-bold sd-bg-light
 {fab}`windows;fa-2x` Windows
@@ -25,25 +24,31 @@ In addition to installing the latest release ({{release}}), there are nightly bu
 <a class="sd-sphinx-override sd-btn sd-text-wrap sd-btn-outline-primary reference external" href="https://nightly.link/OpenChemistry/avogadrolibs/workflows/build_cmake/master/Win64.exe.zip"><span>Download Nightly Build</span></a>
 :::
 
-:::{grid-item-card}
+:::{card}
 :text-align: center
 :class-header: sd-font-weight-bold sd-bg-light
 {fab}`linux;fa-2x` Linux
 ^^^
-{{ '<a class="sd-sphinx-override sd-btn sd-text-wrap sd-btn-outline-primary reference external" href="' + appurl + '"><span>Download AppImage</span></a>'}}
-<a class="sd-sphinx-override sd-btn sd-text-wrap sd-btn-outline-primary reference external" href="https://dl.flathub.org/repo/appstream/org.openchemistry.Avogadro2.flatpakref"><span>Download Flatpak</span></a>
+{{ '<a class="sd-sphinx-override sd-btn sd-text-wrap sd-btn-outline-primary reference external" href="' + appurl + '"><span>Download AppImage</span></a>'}} <a class="sd-sphinx-override sd-btn sd-text-wrap sd-btn-outline-primary reference external" href="https://dl.flathub.org/repo/appstream/org.openchemistry.Avogadro2.flatpakref"><span>Download Flatpak</span></a>
 ++++
 <a class="sd-sphinx-override sd-btn sd-text-wrap sd-btn-outline-primary reference external" href="https://nightly.link/OpenChemistry/avogadrolibs/workflows/build_cmake/master/Avogadro2.AppImage.zip"><span>Download Nightly AppImage</span></a>
 <a class="sd-sphinx-override sd-btn sd-text-wrap sd-btn-outline-primary reference external" href="build.html"><span>Build from source</span></a>
 :::
 
-::::
+:::{card} 
+:text-align: center
+:class-header: sd-font-weight-bold sd-bg-light sd-text-danger
+{fab}`freebsd;fa-2x` FreeBSD
+^^^
+<a class="sd-sphinx-override sd-btn sd-text-wrap sd-btn-outline-primary reference external" href="https://www.freshports.org/science/avogadro2/"><span>`pkg install avogadro2`</span></a>
+:::
 
 ```{toctree}
 ---
 hidden: true
 caption: Installation
 ---
-
+self
 build
+versions/index
 ```

_sources/install/versions/index.md.txt

@@ -0,0 +1,15 @@
+(versions)=
+
+# Version History
+
+```{toctree}
+---
+caption: Version History
+---
+v198
+v197
+v196
+v1951
+v195
+v194
+```

_sources/install/versions/v194.md.txt

@@ -0,0 +1,94 @@
+(v194)=
+
+# Release Notes v1.94.0
+
+June 2, 2021
+
+We are pleased to announce the latest release of Avogadro, including piles of
+bug fixes and feature enhancements.
+
+As part of the release, we've made it easier to download scripts and data,
+including new input generators, molecule fragments, and build and analysis
+commands. These scripts make it much easier to integrate Avogadro with many
+open source chemistry Python tools, including RDKit, ASE, etc.
+
+Draft developer documentation can be found at https://two.avogadro.cc
+
+If you have comments or suggestions, please join us at https://discuss.avogadro.cc
+
+We anticipate several more releases over the summer and early fall 2021.
+
+## Features
+
+- Bring back "insert framgent" builder from Avogadro v1 @ghutchis (#591)
+- New docs on http://two.avogadro.cc @ghutchis (#568)
+- Remove dependency on MoleQueue @cryos (#596)
+- Initial Flatpak package @kevinsmia1939
+- Improved download widget @ghutchis (#534)
+- Reorganize menus - fix #474 @ghutchis (#564)
+- Export to SVG @serk12 (#588)
+- Symmetry enhancements @ghutchis (#553)
+- Added yaehmop with band structure calc @psavery (#339)
+- Cp2k input @ghutchis (#383)
+- OpenMM script builder plugin @badarsh2 (#343)
+- Handle drag-and-drop of files to the window @ghutchis
+- Use native message / dialog boxes on Mac @ghutchis
+- Download entries from PDB @ghutchis (#575)
+- Allow manipulate to rotate selected fragments @ghutchis (#594)
+- Add bestFitPlane on Molecule @dvermd (#500)
+- Add centerOfGeometry, centerOfMass and radius methods on Molecule @dvermd (#499)
+- Reset view (camera) @serk12 (#450)
+- Transparent support for ASE "extended XYZ" files @ghutchis (#603)
+
+## 🐛 Bug Fixes
+
+- Switch to using Python 3, fixing #431 @ghutchis (#462)
+- Switch Open Babel calls to use CML and non-local numeric format (#471)
+- Save background color across sessions and set bg alpha for export @ghutchis
+- Add support for cut/copy/clear selected atoms @ghutchis (#510)
+- Label toolbar windows for context menu @ghutchis
+- Make sure to send Extensions the setActiveWidget call @ghutchis
+- Make sure to install Qt image plugins on Mac and Windows @ghutchis
+- Fix #483 through stream-specific locale @ghutchis (#549)
+- Fix a pile of rendering bugs on high-res by saving viewport @ghutchis (#556)
+- Adjust font size for 2D measure labels on hires screens @ghutchis (#548)
+- Make sure to check movie sizes for high-dpi screens @ghutchis (#570)
+- Fixes silent export on save bug #439 @anubh4v (#517)
+- Switch to the navigate tool after pasting coordinates over empty @ghutchis (#593)
+- Fix #571 - ensure we read Gaussian files from file, not stream @ghutchis (#592)
+- Fix symmetry detection with dummy atoms (e.g, ferrocene example) @ghutchis (#595)
+
+## 🐍 Python Improvements
+
+- Add support for a JSON list of selected atoms @ghutchis (#440)
+- Simplify wheel building @psavery (#520)
+- Update example Avogadro RPC script @ghutchis
+
+## 🧰 Maintenance
+
+- Switch to using GitHub actions for continual builds @ghutchis (#461)
+- Translations update from Weblate @weblate
+- Get rid of bits/stdc++ headers - non-portable GCC header @ghutchis (#463)
+- Add fedora patches @ghutchis (#460)
+- Allow use of HDF5 >= 1.12.0 @berquist (#488)
+- Remove exit calls from qtaim code @ghutchis (#475)
+- Switch to include spglib.h with no subdir - fixes build issues @ghutchis (#533)
+- Update residues from LigandExpo @ghutchis (#572)
+- Make VtkPlot more object-oriented @psavery (#379)
+
+## Credits
+
+Thanks to many contributors, including: @Andre870-hub, @ImgBotApp, 
+@KovalevArtem, @NathanBnm, @Padanian,
+@Pietro026, @SantosSi, @SoftwareByRedline, @VeryTastyTomato, @Z-Fikar,
+@Zaryob, @adreasnow, @ahmadubuntu, @akyunus, @amandadumi,
+@andhikapangestu29, @anubh4v, @badarsh2, @berquist, @borisfaure,
+@comradekingu, @crlambda, @cryos, @dnandz, @dvermd, @ghutchis,
+@grsousajunior, @hello-malaysia, @imgbot, @joanavieira8,
+@kevinsmia1939, @koffevar, @ludovicobesana, @mirosnik1, @niskala5570,
+@psavery, @rezaalmanda, @serk12, @shivupa, @tacostea, @tiagomalho,
+@udopton, @weblate, @willow88, @yavgech, Alex, Apostol Penkov, Editor
+Do Sonic BR, Irina Puscas, J. Lavoie, Jacque Fresco, Jörg S, Kavin
+Teenakul, Liu Tao, Michalis, My Random Thoughts, Oğuz Ersen, RIDHO
+NURUL ADILLA, Szabolcs Kalapos, Talking Panda, Thomas Koller, Tymofij
+Lytvynenko, fikril Ha, phlostically, rahul bahuguna

_sources/install/versions/v195.md.txt

@@ -0,0 +1,78 @@
+(v195)=
+
+# Release Notes v1.95.0
+
+Aug 16, 2021
+
+## Changes
+
+We are pleased to announce the latest release of Avogadro, including piles of bug fixes and feature enhancements.
+Thanks to many for suggestions, bug reports, and discussions.
+
+This release includes many new features, including new protein ribbon / cartoon renderings and the new "Layer"
+system as part of Google Summer of Code by @serk12.
+
+Draft developer documentation can be found at https://two.avogadro.cc
+
+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.**
+
+We anticipate several more releases over fall 2021.
+
+## ✨ Features
+
+- New "Layer" system, including custom rendering, locking and hiding parts of the molecule @serk12 (#709)
+- Atom and residue labels @serk12 (#715)
+- New protein cartoon / ribbon display @serk12 (#660 #694 #716)
+- Update render options for Wireframe and Ball-and-Sticks @ghutchis (#700 #720)
+- Use MMTF downloads - more efficient than PDB format @ghutchis (#699)
+- Add back support for importing crystals @ghutchis (#658 #659)
+- Add CJSON support for save/load residues and atom colors @ghutchis (#646)
+- Refactor of Python command and input generators, including tabs @ghutchis (#667)
+- New View => Apply Colors menu @ghutchis (#640 #723)
+- Apply color schemes for residues @ghutchis (#638 #688)
+- Add more selection commands, including select by residue @ghutchis (#632 #634)
+- Render selected atoms in VdW and licorice modes @ghutchis (#702)
+- Detect secondary structure from residues / backbones @ghutchis (#685)
+- Save enabled / disabled state of scene / rendering plugins on quit @ghutchis
+- Should now download and install translations for @ghutchis
+
+## 🐛 Bug Fixes
+
+- Fix Mac builds by turning off COORDGEN library @ghutchis (#606)
+- Fix Windows installer to include all needed files @ghutchis
+- Save projection type on close #682 @ghutchis
+- Add a pass to fix OB plugin library paths on Mac @ghutchis (#627 #628)
+- Fix odd behavior on 'Center' command @serk12 (#728)
+- Fix several crashes with proteins @ghutchis (#724 #726 #727)
+- Fix crash in CJSON reading file without labels @ghutchis (#722)
+- Fix bug deleting selected atoms #650 @ghutchis (#672 #677)
+- Fix "delete last atom" bug @ghutchis (#691)
+- When dragging to create a new atom, use starting coords @ghutchis (#690)
+- Fix #679 - incorrect PDB unit cells @ghutchis (#689)
+- Fixed problems inserting SMILES without coordinates @ghutchis (#661)
+- Fix for transparent widgets @ghutchis (#656)
+- Fix #602 - use Molden order for f-orbitals @ghutchis (#649)
+- If a chain ID is missing / invalid, skip (to read non-standard PDB) @ghutchis (#647)
+- Make sure to reset colors when changing elements @ghutchis (#708)
+
+## 🧰 Maintenance
+
+- Make sure to install crystals directory even when it exists @ghutchis (#613)
+- Replace NULL/0 with nullptr @e-kwsm (#617)
+- Add support for reading partial charge models from obabel @ghutchis (#626)
+- Replace obsolescent `LINK_(PRIVATE|PUBLIC)` with `(PRIVATE|PUBLIC)` @e-kwsm (#629)
+- Refactor Molecules class  @serk12 (#648)
+- Don't install cclib script - which was removed @ghutchis (#662 #663)
+
+## 📚 Translations
+
+- Fix fuzzy entry for Nihonium (not Zirconium!) @e-kwsm (#618)
+- Fix all incorrect fuzzy entries #619 @e-kwsm (#643)
+- Remove wrong entries which were fuzzy @e-kwsm (#644)
+- Translations update from Weblate @weblate (#625)
+- Add a workflow which should update the translation template continuously @ghutchis (#624)
+
+## Credits
+
+Thanks to many contributors, including: @12emin34, @GicoProgram, @LihanzUpenn, @NathanBnm, @San4ito, @acunm, @alexrsoares, @danialk03, @dillonschultz93, @e-kwsm, @ghutchis, @grsousajunior, @psavery, @rezaalmanda, @serk12, @tacitcoast, @weblate, Eisuke Kawashima, Jacque Fresco and phlostically

_sources/install/versions/v1951.md.txt

@@ -0,0 +1,35 @@
+(v1951)=
+
+# Release Notes v1.95.1
+
+Aug 26, 2021
+
+This release fixes several bugs in the recent [1.95.0 release](#v195) and is recommended for all users.
+
+Thanks to @drew-parsons and @yurivict for prompt bug reports!
+
+## 🐛 Bug Fixes
+
+- Fix disabled "Balls and Sticks" rendering on a fresh install @serk12 (#744)
+- Fix for loading settings @serk12 (#732)
+- Add "..." to all input generators to indicate opening a dialog @ghutchis (#743)
+- Fix reference axes menu item @ghutchis (#705)
+- Continue rendering cartoons even if residues aren't found @ghutchis (#736)
+- Enable script formats like cclib to ask for bond perception on read @ghutchis (#738)
+
+## ✨ Features
+
+- Initial display-only property tables @ghutchis (#711)
+- Improve selection tool for layers @serk12 (#729)
+
+## 🧰 Maintenance
+
+- Make sure to run tests in avogadrolibs (including some fix for test failures) @ghutchis (#739)
+
+## 📚 Translations
+
+- Translations update from Weblate @weblate (#721)
+
+## Credits
+
+Thanks to many contributors, including: @drew-parsons, @ghutchis, @mrmrcl, @ovari, @serk12 @yurivict, and @weblate

_sources/install/versions/v196.md.txt

@@ -0,0 +1,83 @@
+(v196)=
+
+# Release Notes v1.96.0
+
+June 2, 2022
+
+## 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](https://appimage.github.io/apps/) 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