Merge branch 'master' into 2748_backwards_substituents

epam · Feb 20, 2025 · 86f42d1 · 86f42d1
2 parents 1ee3db5 + 6bf742c
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diff --git a/.ci/version.txt b/.ci/version.txt
@@ -1,5 +1,5 @@
-1.29.0
+1.30.0
 dev
 2
 
-f8cca60fc0f22fd07fb4842fefbc4277ce2ac10e181c357e6585da30c2da7899
+b3178f37128cd9ff392394f299a2b92d2eed1a0be48bbe06155570c92633a223
diff --git a/.github/workflows/indigo-ci.yaml b/.github/workflows/indigo-ci.yaml
@@ -738,7 +738,7 @@ jobs:
         with:
           java-version: ${{ matrix.java-version }}
       - name: Cache Maven packages
-        uses: actions/cache@v2
+        uses: actions/cache@v4
         with:
           path: ~/.m2
           key: ${{ runner.os }}-m2-${{ hashFiles('**/pom.xml') }}

diff --git a/CHANGELOG.md b/CHANGELOG.md
diff --git a/README.md b/README.md
@@ -1,4 +1,3 @@
-![Build Status](https://github.com/epam/indigo/workflows/CI/badge.svg)
 [![License](https://img.shields.io/badge/License-Apache%202.0-blue.svg)](https://opensource.org/licenses/Apache-2.0)
 
 # EPAM Indigo projects #
@@ -28,7 +27,7 @@ Changelog could be found in [CHANGELOG.md](/CHANGELOG.md).
 
 
 ## Download ##
-<https://lifescience.opensource.epam.com/download/indigo/index.html>
+<https://lifescience.opensource.epam.com/download/indigo.html>
 
 ### Bindings in public repositories:
 * .NET: <https://www.nuget.org/packages/Indigo.Net>
@@ -52,50 +51,137 @@ correct references you need to use CMake configurations from the build_scripts d
 
 To build the project from the sources, the following tools should be installed:
 
+>Required:
 * GIT 1.8.2+
 * C/C++ compilers with C++14 support (GCC, Clang and MSVC are officially supported)
 * CMake 3.4+
 * Python 3.6+
+
+>Required to build all targets:
 * JDK 1.8+
 * .NET Standard 2.0+
+
+>Required to build Indigo-WASM:
 * Emscripten SDK
 * Ninja
 
+
+#### **Dependencies:**
+
+> **Python**
+- wheel package installed. Command: `python -m pip install wheel`
+- setuptools version less than 72.0.0 package installed. Command: `python -m pip install setuptools==68.0.0`
+- waitress package installed (to run backend API test). Command: `python -m pip install waitress`
+- flasgger package installed (to run backend API test). Command: `python -m pip install flasgger`
+- psycopg2 package installed (to run backend API test). Command: `python -m pip install psycopg2`
+- sqlalchemy package installed (to run backend API test). Command: `python -m pip install sqlalchemy`
+- numpy package installed (to run backend API test). Command: `python -m pip install numpy`
+- celery package installed (to run backend API test). Command: `python -m pip install celery`
+- marshmallow package installed (to run backend API test). Command: `python -m pip install marshmallow`
+- redis package installed (to run backend API test). Command: `python -m pip install redis`
+- flask_httpauth package installed (to run backend API test). Command: `python -m pip install flask_httpauth`
+- pyparsing package installed (to run backend API test). Command: `python -m pip install pyparsing`
+- requests package installed (to run backend API test). Command: `python -m pip install requests`
+
+> On Linux use python3 insted of python. Using virtual environment might be required as well.
+
+
 ## Build instruction ##
 
-Create build folder and use cmake with desired options. For instance:
+>On Windows use cmd  to run the commands.
 
-```
-Indigo/build>cmake .. -DBUILD_INDIGO=ON -DBUILD_INDIGO_WRAPPERS=ON -DBUILD_INDIGO_UTILS=ON
-```
+1) Create build folder
+    ```
+    mkdir build
+    ```
+2) Move to build folder
+    ```
+    cd build
+    ```
 
-To build Indigo from console:
-```
-Indigo/build>cmake --build . --config Release --target all
-```
+2) Run CMake to configure the project with desired options. For instance:
+    ```
+    cmake .. -DBUILD_INDIGO=ON -DBUILD_INDIGO_WRAPPERS=ON -DBUILD_INDIGO_UTILS=ON
+    ```
 
-or any of the following targets could be specified: --target { indigo-dotnet | indigo-java | indigo-python }
-Build results could be collected from Indigo/dist folder.
+3) Build Indigo from console:
+    ```
+    cmake --build . --config Release --target <target name>
+    ```
 
-## Run tests ##
+Replace _**\<target name\>**_ with any of the following targets you need:
+
+- **ALL_BUILD** (on Windows)
+- **all** (on Linux)
+- **indigo-dotnet**
+- **indigo-java**
+- **indigo-python**
 
-Befo run any test you have to build and install indigo-python
-1) Build indigo-python using '--target all' or '--target indigo=python'.
-   Package should be in 'build' directory, it will be named like 'epam.indigo-version-arch.whl'
-3) Install package using pip `python -m pip uninstall epam.indigo -y ; python -m pip install dist/epam.indigo-version-arch.whl`
+> Build results could be collected from Indigo/dist folder.
 
-Run integration test using `python api/tests/integration/test.py -t 1` for all test, or `python api/tests/integration/test.py -t 1 -p test_name` to run tests by mask `test_name`.
+> 'indigo-python' target is commonly used.
 
-To run backend API test:
-1) Install epam-indigo
-2) Install waitress `python pip install waitress`
+## Run tests ##
+Befor running any test you have to build and install indigo-python
+
+1) Build indigo-python using `--target indigo-python` or `--target ALL_BUILD`(on Windows) or `--target all`(on Linux). See Build instruction above.
+    > - On Windows the package should be in 'Indigo/api/python/dist' folder
+    > - On Linux it is located in 'Indigo\dist' folder
+
+
+> Package will be named like 'epam.indigo-*\<version-arch\>*.whl'. For instance: *epam.indigo-1.29.0.dev2-py3-none-win_amd64.whl*
+   
+2) Install package using pip
+    > - If Indigo package has been already installed, uninstall it with the following command: `python -m pip uninstall <path-to-.whl-file> -y`
+
+    ```
+    python -m pip install <path-to-.whl-file>
+    ```
+    
+    > Replace _**\<path-to-.whl-file>**_ with the right path to .whl package. For instance: `python -m pip install ../api/python/dist/epam.indigo-1.29.0.dev2-py3-none-win_amd64.whl`
+
+3) Run integration test
+
+    >to run all test
+
+    ```
+    python api/tests/integration/test.py -t 1
+    ```
+    
+    >to run tests by mask use `test_name`
+    ```
+    python api/tests/integration/test.py -t 1 -p test_name
+    ```
+
+### To run backend API test:
+1) Build and install indigo-python
+2) Set environment variable by running this command:
+
+    > for Linux
+    ```
+    export INDIGO_SERVICE_URL=http://localhost:5000/v2
+    ```
+    > for Windows in PowerShell
+    ```
+    $env:INDIGO_SERVICE_URL="http://localhost:5000/v2"
+    ```
 3) Run backend service :
-  * `cd utils/indigo-service/backend/service`
-  * `cp v2/common/config.py .`
-  * `waitress-serve --listen="127.0.0.1:5000 [::1]:5000"  app:app` you may use any port instead of 5000
+    ```
+    cd utils/indigo-service/backend/service
+    ```
+    ```
+    cp v2/common/config.py .
+    ```
+    ```
+    waitress-serve --listen="127.0.0.1:5000 [::1]:5000"  app:app
+    ```
+    > you may use any port instead of 5000
+
 4) Run backend API test:
-  * set environment variable `export INDIGO_SERVICE_URL=http://localhost:5000/v2` (in powershell `$env:INDIGO_SERVICE_URL="http://localhost:5000/v2"`)
-  * run test `python utils/indigo-service/backend/service/tests/api/indigo_test.py` use `-k test_name` to run test by pattern.
+    ```
+    python utils/indigo-service/backend/service/tests/api/indigo_test.py`
+    ```
+    > use `-k test_name` to run test by pattern.
 
 ## How to build Indigo-WASM ##
 
@@ -137,11 +223,20 @@ Make sure it's running from path:
 * Install emscripten sdk (https://github.com/emscripten-core/emsdk)
 
 ```
->git clone https://github.com/emscripten-core/emsdk.git
->cd emsdk
->./emsdk install latest
->./emsdk activate latest
->source ./emsdk_env.sh
+git clone https://github.com/emscripten-core/emsdk.git
+```
+```
+cd emsdk
+```
+```
+./emsdk install latest
+```
+
+```
+./emsdk activate latest
+```
+```
+source ./emsdk_env.sh
 ```
 
 Note: On Windows, run `emsdk` instead of `./emsdk`, and `emsdk_env.bat` instead of source `./emsdk_env.sh`, use `cmd` instead of `powershell`.
@@ -172,4 +267,4 @@ Now build:
 ```
 >emcmake cmake .. -DCMAKE_BUILD_TYPE=Debug -G Ninja
 >ninja indigo-ketcher-js-test
-```
+```
diff --git a/api/c/indigo/src/indigo_match.cpp b/api/c/indigo/src/indigo_match.cpp
@@ -985,7 +985,7 @@ int indigoIterateMatches(int target_matcher, int query)
         {
             IndigoMoleculeSubstructureMatcher& matcher = IndigoMoleculeSubstructureMatcher::cast(obj);
 
-            if (matcher.tau_params.method != BASIC && matcher.mode == IndigoMoleculeSubstructureMatcher::TAUTOMER)
+            if (matcher.mode == IndigoMoleculeSubstructureMatcher::TAUTOMER && matcher.tau_params.method != BASIC)
             {
                 std::unique_ptr<IndigoTautomerSubstructureMatchIter> match_iter(
                     matcher.getTautomerMatchIterator(self, query, true, self.max_embeddings, matcher.tau_params.method));

diff --git a/api/dotnet/src/Indigo.Net.csproj b/api/dotnet/src/Indigo.Net.csproj
@@ -2,7 +2,7 @@
 
 	<PropertyGroup>
 		<TargetFrameworks>netstandard2.0</TargetFrameworks>
-		<Version>1.29.0-dev.2</Version>
+		<Version>1.30.0-dev.2</Version>
 		<Authors>EPAM Systems Life Science Department</Authors>
 		<Company>EPAM Systems</Company>
 		<Description>Universal cheminformatics toolkit</Description>

diff --git a/api/http/requirements.txt b/api/http/requirements.txt
@@ -1,7 +1,7 @@
 anyio==3.7.0
 asgiref==3.7.1
 click==8.1.3
-epam.indigo==1.29.0.dev2
+epam.indigo==1.30.0.dev2
 fastapi==0.95.2
 h11==0.14.0
 idna==3.7

diff --git a/api/http/setup.py b/api/http/setup.py
@@ -20,7 +20,7 @@
 
 setup_kwargs = {
     "name": "indigo-service",
-    "version": "1.29.0.dev2",
+    "version": "1.30.0.dev2",
     "description": "",
     "long_description": None,
     "author": "Ruslan Khyurri",

diff --git a/api/indigo-version.cmake b/api/indigo-version.cmake
@@ -1,4 +1,4 @@
-set(INDIGO_DEFAULT_VERSION "1.29.0-dev.2")
+set(INDIGO_DEFAULT_VERSION "1.30.0-dev.2")
 set(INDIGO_MAX_REVISION 1000)
 find_package(Git)
 if(GIT_EXECUTABLE)

diff --git a/api/java/pom.xml b/api/java/pom.xml
@@ -17,7 +17,7 @@
         <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
         <maven.compiler.source>1.8</maven.compiler.source>
         <maven.compiler.target>${maven.compiler.source}</maven.compiler.target>
-        <revision>1.29.0-dev.2</revision>
+        <revision>1.30.0-dev.2</revision>
     </properties>
 
     <licenses>

diff --git a/api/python/indigo/__init__.py b/api/python/indigo/__init__.py
@@ -3,4 +3,4 @@
 from .indigo.indigo_exception import IndigoException  # noqa
 from .indigo.indigo_object import IndigoObject  # noqa
 
-__version__ = "1.29.0.dev2"
+__version__ = "1.30.0.dev2"
diff --git a/api/python/setup.py b/api/python/setup.py
@@ -98,7 +98,7 @@
 
 setup(
     name="epam.indigo",
-    version="1.29.0.dev2",
+    version="1.30.0.dev2",
     description="Indigo universal cheminformatics toolkit",
     author="EPAM Systems Life Science Department",
     author_email="lifescience.opensource@epam.com",

diff --git a/api/r/DESCRIPTION b/api/r/DESCRIPTION
@@ -1,5 +1,5 @@
 Package: rindigo
-Version: 1.29.0-dev.2
+Version: 1.30.0-dev.2
 Date: 2020-12-10
 Title: R Package for Indigo Toolkit
 Authors@R: c(person(given = "Mikhail", family = "Kviatkovskii", role = c("cre"),

diff --git a/api/tests/integration/ref/basic/test_smiles.py.out b/api/tests/integration/ref/basic/test_smiles.py.out
@@ -365,3 +365,97 @@ M  END
 
 C1c2cc3cc4ccc5cc6Cc7cc8ccc1c1c9c%10c%11c(c6c7c%10c81)c5c4c%11c3c29
 C1c2cc3cc4ccc5cc6Cc7cc8ccc1c1c9c%10c%11c(c6c7c%10c81)c5c4c%11c3c29
+*Cl |$_AV:;3$,$R1;$|
+*Cl |$R1;$|
+
+  -INDIGO-01000000002D
+
+  2  1  0  0  0  0  0  0  0  0999 V2000
+    0.0000    0.0000    0.0000 R1  0  0  0  0  0  0  0  0  0  0  0  0
+    0.0000    0.0000    0.0000 Cl  0  0  0  0  0  0  0  0  0  0  0  0
+  1  2  1  0  0  0  0
+M  END
+
+C*CC |$;;;R$|
+C*CC |$;A;;R$|
+
+  -INDIGO-01000000002D
+
+  4  3  0  0  0  0  0  0  0  0999 V2000
+    0.0000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    0.0000    0.0000    0.0000 A   0  0  0  0  0  0  0  0  0  0  0  0
+    0.0000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    0.0000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+  1  2  1  0  0  0  0
+  2  3  1  0  0  0  0
+  3  4  1  0  0  0  0
+A    4
+R
+M  END
+
+C*CC |$;;R$|
+C*CC |$;A;R;$|
+
+  -INDIGO-01000000002D
+
+  4  3  0  0  0  0  0  0  0  0999 V2000
+    0.0000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    0.0000    0.0000    0.0000 A   0  0  0  0  0  0  0  0  0  0  0  0
+    0.0000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    0.0000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+  1  2  1  0  0  0  0
+  2  3  1  0  0  0  0
+  3  4  1  0  0  0  0
+A    3
+R
+M  END
+
+C*CC |$;R$|
+C*CC |$;R;;$|
+
+  -INDIGO-01000000002D
+
+  4  3  0  0  0  0  0  0  0  0999 V2000
+    0.0000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    0.0000    0.0000    0.0000 R   0  0  0  0  0  0  0  0  0  0  0  0
+    0.0000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    0.0000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+  1  2  1  0  0  0  0
+  2  3  1  0  0  0  0
+  3  4  1  0  0  0  0
+M  END
+
+C*CC |$R$|
+C*CC |$R;A;;$|
+
+  -INDIGO-01000000002D
+
+  4  3  0  0  0  0  0  0  0  0999 V2000
+    0.0000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    0.0000    0.0000    0.0000 A   0  0  0  0  0  0  0  0  0  0  0  0
+    0.0000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    0.0000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+  1  2  1  0  0  0  0
+  2  3  1  0  0  0  0
+  3  4  1  0  0  0  0
+A    1
+R
+M  END
+
+C*CC |$R$|
+C*CC |$R;A;;$|
+
+  -INDIGO-01000000002D
+
+  4  3  0  0  0  0  0  0  0  0999 V2000
+    0.0000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    0.0000    0.0000    0.0000 A   0  0  0  0  0  0  0  0  0  0  0  0
+    0.0000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    0.0000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+  1  2  1  0  0  0  0
+  2  3  1  0  0  0  0
+  3  4  1  0  0  0  0
+A    1
+R
+M  END
+