Backmerge: #2512 - Equilibrium Half Arrows are displayed incorrect when saved to PNG (svg) by default size

.github/workflows/indigo-ci.yaml

@@ -29,7 +29,7 @@ jobs:
              git fetch --tags -f
       - name: Check
         run: |
-          python3 -m pip install -r api/python/requirements_dev.txt
+          python3 -m pip install -r api/python/requirements_dev.txt --break-system-packages
           .ci/static_analysis_check.sh
 
   build_indigo_libs_x86_64:
@@ -208,7 +208,7 @@ jobs:
           name: indigo-libs-macos-aarch64
           path: dist/
       - name: Install Python test dependencies
-        run: python3 -m pip install -r api/python/requirements_dev.txt
+        run: python3 -m pip install -r api/python/requirements_dev.txt --break-system-packages
       - name: Build wrappers
         run: |
           mkdir build
@@ -267,16 +267,16 @@ jobs:
           name: indigo-python
           path: dist/
       - name: Install Pillow
-        run: python3 -m pip install Pillow==9.5.0
+        run: python -m pip install Pillow --break-system-packages
       - name: Install wrappers Linux
         if: ${{ startsWith(matrix.os, 'ubuntu') }}
-        run: python3 -m pip install dist/*manylinux1_x86_64*.whl
+        run: python3 -m pip install dist/*manylinux1_x86_64*.whl --break-system-packages
       - name: Install wrappers Windows
         if: ${{ startsWith(matrix.os, 'windows') }}
         run: Get-ChildItem dist -Filter *win_amd64*.whl -Recurse | % { python3 -m pip install $_.FullName }
       - name: Install wrappers macOS
         if: ${{ startsWith(matrix.os, 'macos') }}
-        run: python3 -m pip install dist/*macosx_10_7_intel*.whl
+        run: python3 -m pip install dist/*macosx_10_7_intel*.whl --break-system-packages
       - name: Test
         run: python3 -Wignore api/tests/integration/test.py -t 1 -j junit_report.xml
       - name: Publish Test Report
@@ -322,7 +322,7 @@ jobs:
           run: |
             apt update
             apt install -y --no-install-recommends python3 python3-pip
-            python3 -m pip install Pillow==9.5.0
+            apt install -y python3-pil
             python3 -m pip install dist/*manylinux2014_aarch64*.whl
             python3 api/tests/integration/test.py -p basic/basic.py -t 1 -j junit_report.xml
       - name: Publish Test Report
@@ -361,13 +361,13 @@ jobs:
       - name: Set up Python
         uses: actions/setup-python@v2
         with:
-          python-version: 3.7
+          python-version: '3.9'
           architecture: x86
       - name: Install Pillow
-        run: python -m pip install Pillow==9.5.0
+        run: python -m pip install Pillow --break-system-packages
       - name: Install wrappers Windows
         if: ${{ startsWith(matrix.os, 'windows') }}
-        run: Get-ChildItem dist -Filter *win32*.whl -Recurse | % { python -m pip install $_.FullName }
+        run: Get-ChildItem dist -Filter *win32*.whl -Recurse | % { python -m pip install $_.FullName --break-system-packages }
       - name: Test
         run: python api/tests/integration/test.py -t 1 -p basic/basic.py -j junit_report.xml
       - name: Publish Test Report
@@ -516,7 +516,8 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        os: [ macos-13, ubuntu-latest, windows-latest ]
+        # os: [ macos-13, ubuntu-latest, windows-latest ]
+        os: [ macos-13, windows-latest ]
     runs-on: ${{ matrix.os }}
     needs: build_indigo_wrappers
     steps:
@@ -547,6 +548,11 @@ jobs:
         run: |
           curl -Lo dotnet.tar.gz https://download.visualstudio.microsoft.com/download/pr/270b615f-5281-4c58-980f-d9f7a08db642/3e874492a9cb0d5b87195c596b46d609/dotnet-sdk-6.0.421-osx-x64.tar.gz
           mkdir -p ${{ github.workspace }}/tmp/dotnet && tar zxf dotnet.tar.gz -C ${{ github.workspace }}/tmp/dotnet
+      - name: Install dotnet 6 linux
+        if: ${{ startsWith(matrix.os, 'ubuntu') }}
+        run: |
+          sudo apt update
+          sudo apt install -y dotnet-host dotnet-sdk-6.0
       - name: Prepare UNIX
         if: ${{ !startsWith(matrix.os, 'windows') }}
         run: |
@@ -649,7 +655,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: [ '3.7', '3.10' ]
+        python-version: [ '3.9', '3.10' ]
     needs: build_indigo_wrappers
     steps:
       - uses: actions/checkout@v3
@@ -667,10 +673,10 @@ jobs:
           name: indigo-python
           path: dist/
       - name: Install latest indigo version
-        run: pip install ${GITHUB_WORKSPACE}/dist/epam.indigo-*manylinux1_x86_64.whl
+        run: pip install ${GITHUB_WORKSPACE}/dist/epam.indigo-*manylinux1_x86_64.whl --break-system-packages
         working-directory: bingo/bingo-elastic/python
       - name: Install dev dependencies
-        run: pip install ".[dev]"
+        run: pip install ".[dev]" --break-system-packages
         working-directory: bingo/bingo-elastic/python
       - name: Setup elasticsearch
         run: docker run -d -p 9200:9200 -p 9300:9300 -e "discovery.type=single-node" -e "indices.query.bool.max_clause_count=4096" docker.elastic.co/elasticsearch/elasticsearch:7.16.2
@@ -679,7 +685,7 @@ jobs:
       - name: Build wheel
         working-directory: bingo/bingo-elastic/python
         run: |
-          pip install ".[async]"
+          pip install ".[async]" --break-system-packages
           python setup.py bdist_wheel
           cp dist/*.whl ${GITHUB_WORKSPACE}/dist/
       - name: Run pylint
@@ -1000,7 +1006,7 @@ jobs:
       - name: Set up Python
         uses: actions/setup-python@v2
         with:
-          python-version: 3.7
+          python-version: '3.9'
       - name: Git fetch tags
         run: |
              git config --global --add safe.directory '*'
@@ -1036,7 +1042,7 @@ jobs:
           docker run --rm -d -p 5432:5432 -e "POSTGRES_PASSWORD=password" -v /home:/home epmlsop/bingo-postgres:${{ matrix.postgres_major_version }}-latest
       - name: Install dev dependencies
         run: |
-          pip install -r bingo/tests/requirements.txt
+          pip install -r bingo/tests/requirements.txt --break-system-packages
       - name: Run Bingo tests
         run: |
           export PYTHONPATH=${{ github.workspace }}/bingo/bingo-elastic/python

api/tests/integration/common/rendering/__init__.py

@@ -87,7 +87,7 @@ def average_hash_and_sizes(self):
             self.image = Image.open(self.image_path)
             width, height = self.image.size
             image = self.image.resize(
-                (self.hash_size, self.hash_size), Image.ANTIALIAS
+                (self.hash_size, self.hash_size), Image.LANCZOS
             )
             # image.show()
             allchannelpixels = [

api/tests/integration/ref/rendering/render_reactions.py.out

@@ -11,3 +11,5 @@ issue 2457 wrong chiral label position
 issue_2457.png rendering status: OK
 issue 2444 wrong arrow and plus width
 issue_2444.png rendering status: OK
+issue 2512 two short equilibrium half arrows
+issue_2512.png rendering status: OK

api/tests/integration/tests/rendering/reactions/issue_2512.ket

@@ -0,0 +1,141 @@
+{
+    "root": {
+        "nodes": [
+            {
+                "$ref": "mol0"
+            },
+            {
+                "$ref": "mol1"
+            },
+            {
+                "type": "arrow",
+                "data": {
+                    "mode": "unbalanced-equilibrium-filled-half-triangle",
+                    "pos": [
+                        {
+                            "x": 13.700000000000001,
+                            "y": -7.95,
+                            "z": 0
+                        },
+                        {
+                            "x": 14.700000000000001,
+                            "y": -7.95,
+                            "z": 0
+                        }
+                    ]
+                }
+            }
+        ],
+        "connections": [],
+        "templates": []
+    },
+    "mol0": {
+        "type": "molecule",
+        "atoms": [
+            {
+                "label": "C",
+                "location": [
+                    12.549374214363931,
+                    -8.432470415521406,
+                    0
+                ]
+            },
+            {
+                "label": "C",
+                "location": [
+                    13.55062578563607,
+                    -8.432470415521406,
+                    0
+                ]
+            },
+            {
+                "label": "C",
+                "location": [
+                    13.050050188048687,
+                    -7.567529584478595,
+                    0
+                ]
+            }
+        ],
+        "bonds": [
+            {
+                "type": 1,
+                "atoms": [
+                    0,
+                    1
+                ]
+            },
+            {
+                "type": 1,
+                "atoms": [
+                    1,
+                    2
+                ]
+            },
+            {
+                "type": 1,
+                "atoms": [
+                    2,
+                    0
+                ]
+            }
+        ],
+        "stereoFlagPosition": {
+            "x": 13.55062578563607,
+            "y": 6.567529584478595,
+            "z": 0
+        }
+    },
+    "mol1": {
+        "type": "molecule",
+        "atoms": [
+            {
+                "label": "C",
+                "location": [
+                    14.774374214363931,
+                    -8.482470415521407,
+                    0
+                ]
+            },
+            {
+                "label": "C",
+                "location": [
+                    15.77562578563607,
+                    -8.482470415521407,
+                    0
+                ]
+            },
+            {
+                "label": "C",
+                "location": [
+                    15.275050188048686,
+                    -7.6175295844785955,
+                    0
+                ]
+            }
+        ],
+        "bonds": [
+            {
+                "type": 1,
+                "atoms": [
+                    0,
+                    1
+                ]
+            },
+            {
+                "type": 1,
+                "atoms": [
+                    1,
+                    2
+                ]
+            },
+            {
+                "type": 1,
+                "atoms": [
+                    2,
+                    0
+                ]
+            }
+        ]
+    }
+}

api/tests/integration/tests/rendering/render_reactions.py

@@ -93,6 +93,18 @@ def renderRxnfile(filename, outfile):
 renderer.renderToFile(rxn, joinPathPy("out/" + png_fname, __file__))
 print(checkImageSimilarity(png_fname))
 
+print("issue 2512 two short equilibrium half arrows")
+indigo.resetOptions()
+indigo.setOption("ignore-stereochemistry-errors", "true")
+indigo.setOption("render-background-color", "255, 255, 255")
+indigo.setOption("render-output-format", "png")
+fname = "issue_2512"
+png_fname = fname + ".png"
+ket_fname = joinPathPy("reactions/%s.ket" % fname, __file__)
+rxn = indigo.loadReactionFromFile(ket_fname)
+renderer.renderToFile(rxn, joinPathPy("out/" + png_fname, __file__))
+print(checkImageSimilarity(png_fname))
+
 if isIronPython():
     renderer.Dispose()
     indigo.Dispose()

bingo/bingo-elastic/python/setup.py

@@ -39,7 +39,7 @@
     extras_require={
         "async": ["elasticsearch[async]==7.16.2"],
         "dev": [
-            'pylint==2.17.7; python_version=="3.7"',
+            'pylint==2.17.7; python_version=="3.9"',
             'pylint==3.1.0; python_version>="3.10"',
             "pytest",
             "wheel",

core/render2d/src/render_context.cpp

@@ -1337,11 +1337,20 @@ void RenderContext::drawEquillibriumHalf(const Vec2f& p1, const Vec2f& p2, const
     n.negate();
     pa.addScaled(n, headwidth);
     pb.addScaled(n, headwidth);
+    const float default_shift = headsize * 2.0f;
+    float shift = default_shift;
+    if ((len - shift * 2.0f) < default_shift)
+    {
+        if (len < default_shift * 2.0f)
+            shift = len / 4.0f; // too short arrow - shift will be 1/4 of arrow length, short part - 1/2
+        else
+            shift = (len - default_shift) / 2.0f; // short part of arrow will be headsize*2
+    }
     if (is_unbalanced)
-        pa.addScaled(d, headsize * 2);
+        pa.addScaled(d, shift);
     d.negate();
     if (is_unbalanced)
-        pb.addScaled(d, headsize * 2);
+        pb.addScaled(d, shift);
     drawHalfArrowHeader(pa, d, width, headwidth * width_scale, headsize, arrow_type);
     drawBar(pb, pa, width, margin);
     checkPathNonEmpty();

utils/indigo-service/backend/service/tests/api/indigo_test.py

@@ -484,7 +484,7 @@ def test_headers_wrong(self):
             "ValidationError: {'input_format': ['Must be one of: %s']}"
             % formats
         )
-        self.assertEquals(
+        self.assertEqual(
             expected_text,
             result.text,
         )
@@ -502,7 +502,7 @@ def test_headers_wrong(self):
             "ValidationError: {'output_format': ['Must be one of: %s']}"
             % formats
         )
-        self.assertEquals(
+        self.assertEqual(
             expected_text,
             result.text,
         )
@@ -2163,7 +2163,7 @@ def test_calculate(self):
         # )
         self.assertEqual(200, result.status_code)
         result_data = json.loads(result.text)
-        self.assertEquals("16.0424604", result_data["molecular-weight"])
+        self.assertEqual("16.0424604", result_data["molecular-weight"])
 
     def test_calculate_components_mol(self):
         headers, data = self.get_headers(