Update indigo to 1.36.0 (#163)

Author: AliaksandrDziarkach

rst/download/bingo.rst

@@ -15,7 +15,7 @@ Latest release
 .. toctree::
     :maxdepth: 1
 
-    bingo/bingo-1.35.0.rst
+    bingo/bingo-1.36.0.rst
 
 
 Older releases
@@ -24,6 +24,7 @@ Older releases
 .. toctree::
     :maxdepth: 1
 
+    bingo/bingo-1.35.0.rst
     bingo/bingo-1.34.0.rst
     bingo/bingo-1.33.0.rst
     bingo/bingo-1.32.0.rst

rst/download/bingo/bingo-1.36.0.rst

@@ -0,0 +1,49 @@
+Bingo 1.36.0
+------------
+
+The changelog is available `on this page <../../indigo/release-notes/indigo-1.36.0.html>`__
+
+.. list-table:: 
+   :header-rows: 1
+   :stub-columns: 1
+   :widths: 28 24 24 24
+
+   * - 
+     - |image0| Linux
+     - |image1| Windows
+     - |image2| Mac OS
+   * - Oracle
+     - `64-bit <https://lifescience.opensource.epam.com/downloads/bingo-1.36.0/bingo-oracle-linux-x86_64.zip>`__
+     - `64-bit <https://lifescience.opensource.epam.com/downloads/bingo-1.36.0/bingo-oracle-windows-msvc-x86_64.zip>`__
+     - binaries upon request.
+   * - PostgreSQL 17
+     - `64-bit <https://lifescience.opensource.epam.com/downloads/bingo-1.36.0/bingo-postgres-17-linux-x86_64.zip>`__
+     - \-
+     - `64-bit <https://lifescience.opensource.epam.com/downloads/bingo-1.36.0/bingo-postgres-17-macos-x86_64.zip>`__  
+   * - PostgreSQL 16
+     - `64-bit <https://lifescience.opensource.epam.com/downloads/bingo-1.36.0/bingo-postgres-16-linux-x86_64.zip>`__
+     - `64-bit <https://lifescience.opensource.epam.com/downloads/bingo-1.36.0/bingo-postgres-16-windows-x86_64.zip>`__
+     - `64-bit <https://lifescience.opensource.epam.com/downloads/bingo-1.36.0/bingo-postgres-16-macos-x86_64.zip>`__  
+   * - PostgreSQL 15
+     - `64-bit <https://lifescience.opensource.epam.com/downloads/bingo-1.36.0/bingo-postgres-15-linux-x86_64.zip>`__
+     - `64-bit <https://lifescience.opensource.epam.com/downloads/bingo-1.36.0/bingo-postgres-15-windows-x86_64.zip>`__
+     - `64-bit <https://lifescience.opensource.epam.com/downloads/bingo-1.36.0/bingo-postgres-15-macos-x86_64.zip>`__  
+   * - PostgreSQL 14
+     - `64-bit <https://lifescience.opensource.epam.com/downloads/bingo-1.36.0/bingo-postgres-14-linux-x86_64.zip>`__
+     - `64-bit <https://lifescience.opensource.epam.com/downloads/bingo-1.36.0/bingo-postgres-14-windows-x86_64.zip>`__
+     - `64-bit <https://lifescience.opensource.epam.com/downloads/bingo-1.36.0/bingo-postgres-14-macos-x86_64.zip>`__  
+   * - PostgreSQL 13
+     - `64-bit <https://lifescience.opensource.epam.com/downloads/bingo-1.36.0/bingo-postgres-13-linux-x86_64.zip>`__
+     - `64-bit <https://lifescience.opensource.epam.com/downloads/bingo-1.36.0/bingo-postgres-13-windows-x86_64.zip>`__
+     - `64-bit <https://lifescience.opensource.epam.com/downloads/bingo-1.36.0/bingo-postgres-13-macos-x86_64.zip>`__
+   * - Microsoft SQL Server
+     - \-
+     - `64-bit <https://lifescience.opensource.epam.com/downloads/bingo-1.36.0/bingo-sqlserver-windows-latest-x86_64.zip>`__
+     - \-
+
+`Source code on GitHub <http://github.com/epam/indigo>`__
+
+
+.. |image0| image:: ../../assets/Linux.png
+.. |image1| image:: ../../assets/Windows.png
+.. |image2| image:: ../../assets/AppleSZ.png

rst/download/indigo.rst

@@ -15,14 +15,15 @@ Latest release
 .. toctree::
     :maxdepth: 1
 
-    indigo/indigo-1.35.0.rst
+    indigo/indigo-1.36.0.rst
 
 Older releases
 --------------
 
 .. toctree::
     :maxdepth: 1
 
+    indigo/indigo-1.35.0.rst
     indigo/indigo-1.34.0.rst
     indigo/indigo-1.33.0.rst
     indigo/indigo-1.32.0.rst

rst/download/indigo/indigo-1.36.0.rst

@@ -0,0 +1,98 @@
+
+.. toctree::
+  :hidden:
+  :includehidden:
+
+  ../../indigo/release-notes/index.rst
+
+
+Indigo 1.36.0
+-------------
+
+Language Bindings
+~~~~~~~~~~~~~~~~~
+
+.. list-table:: 
+   :header-rows: 0
+   :stub-columns: 1
+
+   * - |p-icon| Python 
+     - `indigo-python.zip <https://lifescience.opensource.epam.com/downloads/indigo-1.36.0/indigo-python.zip>`__
+   * - |j-icon| Java 
+     - `indigo-java.zip <https://lifescience.opensource.epam.com/downloads/indigo-1.36.0/indigo-java.zip>`__
+   * - |c-icon| .NET 
+     - `indigo-dotnet.zip <https://lifescience.opensource.epam.com/downloads/indigo-1.36.0/indigo-dotnet.zip>`__
+   * - |n-icon| Native Libraries in one archive
+     - `indigo-native-shared-libs.zip <https://lifescience.opensource.epam.com/downloads/indigo-1.36.0/indigo-native-shared-libs.zip>`__
+
+
+Platform/CPU Bindings
+~~~~~~~~~~~~~~~~~~~~~
+
+.. list-table:: 
+   :header-rows: 1
+   :stub-columns: 1
+
+   * - 
+     - |image0| Linux
+     - |image1| Windows
+     - |image2| Mac OS
+   * - |n-icon| Native Libraries x64
+     - `indigo-libs-linux-x86_64.zip <https://lifescience.opensource.epam.com/downloads/indigo-1.36.0/indigo-libs-linux-x86_64.zip>`__
+     - `indigo-libs-windows-x86_64.zip <https://lifescience.opensource.epam.com/downloads/indigo-1.36.0/indigo-libs-windows-x86_64.zip>`__
+     - `indigo-libs-macos-x86_64.zip <https://lifescience.opensource.epam.com/downloads/indigo-1.36.0/indigo-libs-macos-x86_64.zip>`__
+   * - 
+     -
+     - `indigo-libs-windows-mingw-x86_64.zip <https://lifescience.opensource.epam.com/downloads/indigo-1.36.0/indigo-libs-windows-mingw-x86_64.zip>`__
+     -
+   * - |n-icon| Native Libraries ARM64
+     - `indigo-libs-linux-aarch64.zip <https://lifescience.opensource.epam.com/downloads/indigo-1.36.0/indigo-libs-linux-aarch64.zip>`__
+     - \-
+     - `indigo-libs-macos-aarch64.zip <https://lifescience.opensource.epam.com/downloads/indigo-1.36.0/indigo-libs-macos-aarch64.zip>`__
+   * - |n-icon| Native Libraries i386
+     - \-
+     - `indigo-libs-windows-i386.zip <https://lifescience.opensource.epam.com/downloads/indigo-1.36.0/indigo-libs-windows-i386.zip>`__
+     - \-
+   * - |n-icon| Utilities x64
+     - `indigo-utils-linux-x86_64.zip <https://lifescience.opensource.epam.com/downloads/indigo-1.36.0/indigo-utils-linux-x86_64.zip>`__
+     - `indigo-utils-windows-x86_64.zip <https://lifescience.opensource.epam.com/downloads/indigo-1.36.0/indigo-utils-windows-x86_64.zip>`__
+     - `indigo-utils-macos-x86_64.zip <https://lifescience.opensource.epam.com/downloads/indigo-1.36.0/indigo-utils-macos-x86_64.zip>`__
+
+Source code
+~~~~~~~~~~~
+
+`Source code zip <https://github.com/epam/Indigo/archive/indigo-1.36.0.zip>`__
+
+`Repository on GitHub <https://github.com/epam/Indigo>`__
+
+
+NuGet Repository
+~~~~~~~~~~~~~~~~
+
+Indigo .NET packages available at `Nuget <https://www.nuget.org/packages/Indigo.Net/>`__
+
+Just add ``Indigo.Net`` as a dependency into the project.
+
+PyPi package
+~~~~~~~~~~~~
+
+Indigo Python SDK can be found at `PyPi <https://pypi.org/project/epam.indigo/>`__
+
+One can install the Indigo library using *pip* utility
+
+
+.. code-block:: xml
+
+    pip install epam.indigo
+
+
+
+.. |image0| image:: ../../assets/Linux.png
+.. |image1| image:: ../../assets/Windows.png
+.. |image2| image:: ../../assets/AppleSZ.png
+.. |image3| image:: ../../assets/globe.png
+.. |p-icon| image:: ../../assets/indigo/python-icon.png
+.. |j-icon| image:: ../../assets/indigo/java-icon.png
+.. |c-icon| image:: ../../assets/indigo/csharp-icon.png
+.. |n-icon| image:: ../../assets/indigo/native-icon.png
+.. |w-icon| image:: ../../assets/indigo/wasm-icon.png

rst/indigo/release-notes/index.rst

@@ -7,6 +7,7 @@ Contents:
 .. toctree::
     :maxdepth: 2
 
+    indigo-1.36.0
     indigo-1.35.0
     indigo-1.34.0
     indigo-1.33.0

rst/indigo/release-notes/indigo-1.36.0.md

@@ -0,0 +1,31 @@
+# Indigo 1.36.0
+Released 2025-10-16
+
+## Features
+* [905](https://github.com/epam/Indigo/issues/905) Support for pagination in Bingo Elastic
+* [3092](https://github.com/epam/Indigo/issues/3092) Avoid overwriting cmake output directories variables
+* [3099](https://github.com/epam/Indigo/issues/3099) Support dev container
+* [2893](https://github.com/epam/Indigo/issues/2893) Reaction data support in KET-format 
+* [3136](https://github.com/epam/Indigo/issues/3136) No attachment points check should be performed for terminal CHEMs on IDT import/export
+* [3135](https://github.com/epam/Indigo/issues/3135) Mark undefined stereocenters using the standardize function
+* [3085](https://github.com/epam/Indigo/issues/3085) HELM annotations support
+
+## Bugfixes and improvements
+* [3065](https://github.com/epam/Indigo/issues/3065) Indigo build fails when trying to build indigo-depict
+* [3060](https://github.com/epam/Indigo/issues/3060) CH labels are recognised as pseudo-atoms when parsing cdxml
+* [3096](https://github.com/epam/Indigo/issues/3096) Expand monomer works wrong with selection
+* [3105](https://github.com/epam/Indigo/issues/3105) bingo-elastic-python filter broken for exact/substructure
+* [3130](https://github.com/epam/Indigo/issues/3130) Bingo-postrgress-fingerprints tests are failing
+* [3071](https://github.com/epam/Indigo/issues/3071) Export to RDF V2000 doesn't work if "star" atom on the canvas. System throws exception: Convert error! std::bad_cast
+* [3067](https://github.com/epam/Indigo/issues/3067) System can't load HELM with inline SMILES if it has r-site star atom without square brackets
+* [3120](https://github.com/epam/Indigo/issues/3120) bingo-elastic-python reaction exact search do not use postprocess actions
+* [3150](https://github.com/epam/Indigo/issues/3150) Exception during molecules loading in test fixture
+* [3123](https://github.com/epam/Indigo/issues/3123) Unable to paste FASTA content from clipcoard
+* [3159](https://github.com/epam/Indigo/issues/3159) Export to HELM works wrong for custom monomers imported from HELM with inline SMILES
+* [3068](https://github.com/epam/Indigo/issues/3068), [3080](https://github.com/epam/Indigo/issues/3080), [3082](https://github.com/epam/Indigo/issues/3082), [3086](https://github.com/epam/Indigo/issues/3086), [3087](https://github.com/epam/Indigo/issues/3087), [3088](https://github.com/epam/Indigo/issues/3088), [3090](https://github.com/epam/Indigo/issues/3090), [3084](https://github.com/epam/Indigo/issues/3084) System can't load atom properties (Charge, Isotope and Valence) in SMARTS with "star" atom. System throws exception. 
+* [3144](https://github.com/epam/Indigo/issues/3144), [3147](https://github.com/epam/Indigo/issues/3147) Export to IDT baseless preset and modified phosphate
+* [3148](https://github.com/epam/Indigo/issues/3148) Export to IDT shouldn't work if monomer at the end has no 3' position IDT code
+* [3169](https://github.com/epam/Indigo/issues/3169) Export to IDT doesn't work if R1-only CHEM stays on five prime position
+
+
+**Full Changelog**: https://github.com/epam/Indigo/compare/indigo-1.35.0-rc.1...indigo-1.36.0

rst/newsfeed.rst

@@ -7,6 +7,31 @@ News
     newsfeed
     release-notes/index
 
+Indigo and Bingo 1.36.0 released
+--------------------------------
+
+*16 October 2025*
+
+We are happy to announce that a new version 1.36.0 of Indigo toolkit and Bingo is released.
+
+* |indigo_1_36_0_notes|
+
+* |indigo_1_36_0_downloads|
+
+* |bingo_1_36_0_downloads|
+
+.. |indigo_1_36_0_notes| raw:: html
+
+   <a href="indigo/release-notes/indigo-1.36.0.html" target="_blank">Release Notes</a>
+
+.. |indigo_1_36_0_downloads| raw:: html
+
+   <a href="download/indigo/indigo-1.36.0.html" target="_blank">Indigo Downloads</a>
+
+.. |bingo_1_36_0_downloads| raw:: html
+
+   <a href="download/bingo/bingo-1.36.0.html" target="_blank">Bingo Downloads</a>
+
 Indigo and Bingo 1.35.0 released
 --------------------------------