Partial implementation: replace MultiMap in MoleculeRGroupsComposition class - Part 2, remove MultiMap completely

.ci/docker/indigo-tester/Dockerfile

@@ -2,10 +2,10 @@ FROM debian:stable-slim
 
 ARG JDK_VERSION_MAJOR=8u342
 ARG JDK_VERSION_MINOR=b07
-ARG MAVEN_VERSION=3.8.6
+ARG MAVEN_VERSION=3.8.7
 ARG JYTHON_VERSION=2.7.2
 ARG DOTNET_VERSION=6.0
-ARG IRONPYTHON_VERSION=3.4.0-beta1
+ARG IRONPYTHON_VERSION=3.4.0
 
 RUN set -eux && \
     apt update && \

.ci/version.txt

@@ -1,5 +1,5 @@
 1.9.0
-dev
-0
+rc
+1
 
-61934d47141baa775cf6b3f9e02f8ad132b3c364ad613e4c4df45497e2278cbd
+db544139e56560177275ed6d7e8525f955e4949d53bbae0a47d13c807e1374f5

.github/workflows/indigo-ci.yaml

@@ -515,28 +515,20 @@ jobs:
           mkdir IronPython
           mkdir tmp
           cd IronPython
-          curl -OL https://github.com/IronLanguages/ironpython2/releases/download/ipy-2.7.12/IronPython.2.7.12.zip
+          curl -OL https://github.com/IronLanguages/ironpython3/releases/download/v3.4.0/IronPython.3.4.0.zip
       - name: Prepare UNIX
         if: ${{ matrix.os != 'windows' }}
         run: |
           cd IronPython
-          unzip IronPython.2.7.12.zip
+          unzip IronPython.3.4.0.zip
           cd ../tmp
           unzip ../dist/Indigo.Net.*.nupkg
           chmod -R a+rw .
-      - name: Prepare macOS
-        if: ${{ matrix.os == 'macos' }}
-        run: |
-          brew install mono-libgdiplus
-      - name: Prepare Linux
-        if: ${{ matrix.os == 'ubuntu' }}
-        run: |
-          sudo apt install -y libgdiplus
       - name: Prepare Windows
         if: ${{ matrix.os == 'windows' }}
         run: |
           cd IronPython
-          Expand-Archive IronPython.2.7.12.zip .
+          Expand-Archive IronPython.3.4.0.zip .
           cd ../tmp
           Expand-Archive ../dist/Indigo.Net.*.nupkg .
       - name: Test Linux
@@ -545,20 +537,20 @@ jobs:
           INDIGO_PATH: ${{ github.workspace }}/tmp/lib/netstandard2.0/Indigo.Net.dll
           LD_LIBRARY_PATH: ${{ github.workspace }}/tmp/runtimes/linux-x64/native
         run: |
-          dotnet IronPython/netcoreapp3.1/ipy.dll -X:ExceptionDetail api/tests/integration/test.py -t 1 -j junit_report.xml
+          dotnet IronPython/net6.0/ipy.dll api/tests/integration/test.py -t 1 -j junit_report.xml
       - name: Test macOS
         if: ${{ matrix.os == 'macos' }}
         env:
           INDIGO_PATH: ${{ github.workspace }}/tmp/lib/netstandard2.0/Indigo.Net.dll
         run: |
           export DYLD_LIBRARY_PATH=${PWD}/tmp/runtimes/osx-x64/native
-          dotnet IronPython/netcoreapp3.1/ipy.dll -X:ExceptionDetail api/tests/integration/test.py -t 1 -j junit_report.xml -platform mac
+          dotnet IronPython/net6.0/ipy.dll api/tests/integration/test.py -t 1 -j junit_report.xml
       - name: Test Windows
         if: ${{ matrix.os == 'windows' }}
         env:
           INDIGO_PATH: ${{ github.workspace }}/tmp/lib/netstandard2.0/Indigo.Net.dll
           PATH: ${{ env.PATH }};${{ github.workspace }}/tmp/runtimes/win-x64/native
-        run: ./IronPython/net45/ipy.exe -X:ExceptionDetail api/tests/integration/test.py -t 1 -j junit_report.xml -platform ironwin
+        run: ./IronPython/net462/ipy.exe api/tests/integration/test.py -t 1 -j junit_report.xml
       - name: Publish Test Report
         if: always()
         uses: mikepenz/action-junit-report@v1
@@ -595,20 +587,20 @@ jobs:
           mkdir IronPython
           mkdir tmp
           cd IronPython
-          curl -OL https://github.com/IronLanguages/ironpython2/releases/download/ipy-2.7.12/IronPython.2.7.12.zip
+          curl -OL https://github.com/IronLanguages/ironpython3/releases/download/v3.4.0/IronPython.3.4.0.zip
       - name: Prepare Windows
         if: ${{ matrix.os == 'windows' }}
         run: |
           cd IronPython
-          Expand-Archive IronPython.2.7.12.zip .
+          Expand-Archive IronPython.3.4.0.zip .
           cd ../tmp
           Expand-Archive ../dist/Indigo.Net.*.nupkg .
       - name: Test Windows
         if: ${{ matrix.os == 'windows' }}
         env:
           INDIGO_PATH: ${{ github.workspace }}/tmp/lib/netstandard2.0/Indigo.Net.dll
           PATH: ${{ env.PATH }};${{ github.workspace }}/tmp/runtimes/win-x86/native
-        run: ./IronPython/net45/ipy32.exe -X:ExceptionDetail api/tests/integration/test.py -t 1 -p basic/basic.py -j junit_report.xml -platform ironwin
+        run: ./IronPython/net462/ipy32.exe api/tests/integration/test.py -t 1 -p basic/basic.py -j junit_report.xml
       - name: Publish Test Report
         if: always()
         uses: mikepenz/action-junit-report@v1

CMakeLists.txt

@@ -15,6 +15,7 @@ option(WITH_STATIC "Build Indigo static library as well as shared" OFF)
 
 # Indigo API options
 option(BUILD_INDIGO "Build indigo shared library" ON)
+option(USE_FONT_MANAGER "Build indigo render with font_face_manager" OFF)
 
 # Indigo API Wrappers options
 option(BUILD_INDIGO_WRAPPERS "Build all existing Indigo API wrappers" ON)
@@ -82,6 +83,7 @@ if (EMSCRIPTEN)
     set(BUILD_BINGO_SQLSERVER OFF)
     set(BUILD_BINGO_ORACLE OFF)
     set(BUILD_BINGO_ELASTIC OFF)
+    set(USE_FONT_MANAGER ON)
 endif()
 
 if (BUILD_INDIGO OR BUILD_INDIGO_UTILS OR BUILD_BINGO_SQLSERVER OR BUILD_BINGO_ORACLE OR BUILD_BINGO_POSTGRES OR EMSCRIPTEN)

api/c/indigo/indigo.h

@@ -206,7 +206,13 @@ CEXPORT const char* indigoCml(int object);
 
 // accepts molecules and reactions
 CEXPORT int indigoSaveCdxml(int object, int output);
+CEXPORT int indigoSaveCdx(int item, int output);
+
+CEXPORT const char* indigoCdxml(int item);
+
 CEXPORT int indigoSaveCdxmlToFile(int object, const char* filename);
+CEXPORT int indigoSaveCdxToFile(int item, const char* filename);
+
 CEXPORT const char* indigoCdxml(int object);
 
 // the output must be a file or a buffer, but not a string

api/c/indigo/src/indigo_layout.cpp

@@ -101,6 +101,7 @@ CEXPORT int indigoLayout(int object)
             bool no_layout = rxn.catalystCount() || rxn.intermediateCount() || rxn.specialConditionsCount() || rxn.meta().getNonChemicalMetaCount();
             if (!no_layout)
             {
+                rxn.meta().resetMetaData();
                 ReactionLayout rl(rxn, self.smart_layout);
                 rl.max_iterations = self.layout_max_iterations;
                 rl.layout_orientation = (layout_orientation_value)self.layout_orientation;

api/c/indigo/src/indigo_macros.c

@@ -202,6 +202,20 @@ CEXPORT int indigoSaveCdxmlToFile(int item, const char* filename)
     return res;
 }
 
+CEXPORT int indigoSaveCdxToFile(int item, const char* filename)
+{
+    int f = indigoWriteFile(filename);
+    int res;
+
+    if (f == -1)
+        return -1;
+
+    res = indigoSaveCdx(item, f);
+
+    indigoFree(f);
+    return res;
+}
+
 CEXPORT const char* indigoCdxml(int item)
 {
     int b = indigoWriteBuffer();

api/c/indigo/src/indigo_savers.cpp

@@ -735,3 +735,47 @@ CEXPORT int indigoSaveCdxml(int item, int output)
     }
     INDIGO_END(-1);
 }
+
+CEXPORT int indigoSaveCdx(int item, int output)
+{
+    INDIGO_BEGIN
+    {
+        IndigoObject& obj = self.getObject(item);
+        Output& out = IndigoOutput::get(self.getObject(output));
+
+        if (IndigoBaseMolecule::is(obj))
+        {
+            MoleculeCdxmlSaver saver(out, true);
+            if (obj.type == IndigoObject::MOLECULE)
+            {
+                Molecule& mol = obj.getMolecule();
+                saver.saveMolecule(mol);
+            }
+            else if (obj.type == IndigoObject::QUERY_MOLECULE)
+            {
+                QueryMolecule& mol = obj.getQueryMolecule();
+                saver.saveMolecule(mol);
+            }
+            out.flush();
+            return 1;
+        }
+        if (IndigoBaseReaction::is(obj))
+        {
+            ReactionCdxmlSaver saver(out, true);
+            if (obj.type == IndigoObject::REACTION)
+            {
+                Reaction& rxn = obj.getReaction();
+                saver.saveReaction(rxn);
+            }
+            else if (obj.type == IndigoObject::QUERY_REACTION)
+            {
+                QueryReaction& rxn = obj.getQueryReaction();
+                saver.saveReaction(rxn);
+            }
+            out.flush();
+            return 1;
+        }
+        throw IndigoError("indigoSaveCdxml(): expected molecule or reaction, got %s", obj.debugInfo());
+    }
+    INDIGO_END(-1);
+}

api/dotnet/src/Indigo.Net.csproj

@@ -2,7 +2,7 @@
 
 	<PropertyGroup>
 		<TargetFrameworks>netstandard2.0</TargetFrameworks>
-		<Version>1.9.0-dev.0</Version>
+		<Version>1.9.0-rc.1</Version>
 		<Authors>EPAM Systems Life Science Department</Authors>
 		<Company>EPAM Systems</Company>
 		<Description>Universal cheminformatics toolkit</Description>

api/dotnet/src/Indigo.cs

@@ -301,13 +301,13 @@ public void setOption(string name, int value)
         public void setOption(string name, float valuer, float valueg, float valueb)
         {
             setSessionID();
-            checkResult(IndigoLib.indigoSetOptionColor(name, valuer / 255.0f, valueg / 255.0f, valueb / 255.0f));
+            checkResult(IndigoLib.indigoSetOptionColor(name, valuer, valueg, valueb));
         }
 
         public void setOption(string name, double valuer, double valueg, double valueb)
         {
             setSessionID();
-            checkResult(IndigoLib.indigoSetOptionColor(name, (float) valuer / 255.0f, (float) valueg / 255.0f, (float) valueb / 255.0f));
+            checkResult(IndigoLib.indigoSetOptionColor(name, (float) valuer, (float) valueg, (float) valueb));
         }
 
         public void setOption(string name, Color value)

api/http/requirements.txt

@@ -1,7 +1,7 @@
 anyio==3.3.4
 asgiref==3.4.1
 click==8.0.3
-epam.indigo==1.9.0.dev0
+epam.indigo==1.9.0.rc1
 fastapi==0.70.0
 h11==0.12.0
 idna==3.3

api/http/setup.py

@@ -19,7 +19,7 @@
 
 setup_kwargs = {
     "name": "indigo-service",
-    "version": "1.9.0.dev0",
+    "version": "1.9.0.rc1",
     "description": "",
     "long_description": None,
     "author": "Ruslan Khyurri",

api/indigo-version.cmake

@@ -1,6 +1,5 @@
-set(INDIGO_DEFAULT_VERSION "1.9.0-dev.0")
-set(INDIGO_MAX_REVISION 500)
-
+set(INDIGO_DEFAULT_VERSION "1.9.0-rc.1")
+set(INDIGO_MAX_REVISION 1000)
 find_package(Git)
 if(GIT_EXECUTABLE)
    EXECUTE_PROCESS(COMMAND ${GIT_EXECUTABLE} describe --long --tags --match indigo-*

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>1.9.0-dev.0</revision>
+        <revision>1.9.0-rc.1</revision>
     </properties>
 
     <licenses>
@@ -52,7 +52,7 @@
         <dependency>
             <groupId>org.junit.jupiter</groupId>
             <artifactId>junit-jupiter</artifactId>
-            <version>5.7.1</version>
+            <version>5.9.1</version>
             <scope>test</scope>
         </dependency>
     </dependencies>
@@ -73,7 +73,7 @@
          <plugin>
       <groupId>org.codehaus.mojo</groupId>
       <artifactId>flatten-maven-plugin</artifactId>
-      <version>1.1.0</version>
+      <version>1.3.0</version>
       <configuration>
         <updatePomFile>true</updatePomFile>
         <flattenMode>resolveCiFriendliesOnly</flattenMode>
@@ -98,7 +98,7 @@
             <plugin>
                 <groupId>org.apache.maven.plugins</groupId>
                 <artifactId>maven-compiler-plugin</artifactId>
-                <version>3.8.1</version>
+                <version>3.10.1</version>
             </plugin>
             <plugin>
                 <artifactId>maven-surefire-plugin</artifactId>
@@ -107,7 +107,7 @@
             <plugin>
                 <groupId>org.apache.maven.plugins</groupId>
                 <artifactId>maven-source-plugin</artifactId>
-                <version>3.2.0</version>
+                <version>3.2.1</version>
                 <executions>
                     <execution>
                         <id>attach-sources</id>
@@ -121,7 +121,7 @@
             <plugin>
                 <groupId>org.apache.maven.plugins</groupId>
                 <artifactId>maven-javadoc-plugin</artifactId>
-                <version>3.2.0</version>
+                <version>3.4.1</version>
                 <executions>
                     <execution>
                         <id>attach-javadocs</id>
@@ -135,7 +135,7 @@
             <plugin>
                 <groupId>org.apache.maven.plugins</groupId>
                 <artifactId>maven-jar-plugin</artifactId>
-                <version>3.2.0</version>
+                <version>3.3.0</version>
                 <configuration>
                     <archive>
                         <addMavenDescriptor>true</addMavenDescriptor>
@@ -175,7 +175,7 @@
                     <plugin>
                         <groupId>org.apache.maven.plugins</groupId>
                         <artifactId>maven-gpg-plugin</artifactId>
-                        <version>1.6</version>
+                        <version>3.0.1</version>
                         <configuration>
                             <passphrase>${gpg.passhprase}</passphrase>
                             <gpgArguments>

api/python/indigo/__init__.py

@@ -3,4 +3,4 @@
 from .indigo.indigo_exception import IndigoException  # noqa
 from .indigo.indigo_object import IndigoObject  # noqa
 
-__version__ = "1.9.0.dev0"
+__version__ = "1.9.0.rc1"

api/python/setup.py

@@ -98,7 +98,7 @@
 
 setup(
     name="epam.indigo",
-    version="1.9.0.dev0",
+    version="1.9.0.rc1",
     description="Indigo universal cheminformatics toolkit",
     author="EPAM Systems Life Science Department",
     author_email="[email protected]",

api/r/DESCRIPTION

@@ -1,5 +1,5 @@
 Package: rindigo
-Version: 1.9.0-dev.0
+Version: 1.9.0-rc.1
 Date: 2020-12-10
 Title: R Package for Indigo Toolkit
 Authors@R: c(person(given = "Mikhail", family = "Kviatkovskii", role = c("cre"),

api/tests/integration/common/env_indigo.py

@@ -122,7 +122,7 @@ def rmdir(path):
                 jars.insert(0, jar_path)
             else:
                 jars.append(jar_path)
-    for jar in jars:
+    for jar in sorted(jars):
         sys.path.append(jar)
     from com.epam.indigo import (
         Bingo,