Fix Indigo CI

.github/workflows/indigo-ci.yaml

@@ -267,16 +267,16 @@ jobs:
           name: indigo-python
           path: dist/
       - name: Install Pillow
-        run: python3 -m pip install Pillow==9.5.0
+        run: python3 -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 
       - 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:
@@ -649,7 +650,7 @@ 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 +668,10 @@ 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 +680,7 @@ 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 +1001,7 @@ 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 '*'

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 = [

bingo/bingo-elastic/python/setup.py

@@ -33,13 +33,13 @@
         "Source Code": "https://github.com/epam/indigo/",
     },
     download_url="https://pypi.org/project/bingo_elastic",
-    python_requires=">=3.7",
+    python_requires=">=3.9",
     packages=["bingo_elastic", "bingo_elastic.model"],
     install_requires=["epam.indigo==1.25.0.rc1", "elasticsearch==7.16.2"],
     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",

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(

utils/indigo-service/backend/service/v2/bingo_ql/test.py

@@ -9,88 +9,88 @@ def setUp(self):
 
     def testQueryByPropName(self):
         query = self.builder.build_query('"monoisotopic_weight"')
-        self.assertEquals("(elems->>'y' = %(property_term_0)s)", query)
-        self.assertEquals(
+        self.assertEqual("(elems->>'y' = %(property_term_0)s)", query)
+        self.assertEqual(
             {"property_term_0": "monoisotopic_weight"},
             self.builder.bind_params,
         )
 
         query = self.builder.build_query('"BBB log([brain]:[blood])"')
-        self.assertEquals("(elems->>'y' = %(property_term_0)s)", query)
-        self.assertEquals(
+        self.assertEqual("(elems->>'y' = %(property_term_0)s)", query)
+        self.assertEqual(
             {"property_term_0": "bbb log([brain]:[blood])"},
             self.builder.bind_params,
         )
 
         query = self.builder.build_query('~"count"')
-        self.assertEquals("(elems->>'y' LIKE %(property_term_0)s)", query)
-        self.assertEquals(
+        self.assertEqual("(elems->>'y' LIKE %(property_term_0)s)", query)
+        self.assertEqual(
             {"property_term_0": "%count%"}, self.builder.bind_params
         )
 
         query = self.builder.build_query("count")
-        self.assertEquals("(elems->>'y' LIKE %(property_term_0)s)", query)
-        self.assertEquals(
+        self.assertEqual("(elems->>'y' LIKE %(property_term_0)s)", query)
+        self.assertEqual(
             {"property_term_0": "%count%"}, self.builder.bind_params
         )
 
     def testQueryPropWithValue(self):
         query = self.builder.build_query('"atom_count" != 30')
-        self.assertEquals(
+        self.assertEqual(
             "(elems->>'x' = %(property_term_0)s AND jsonb_typeof(elems->'y') = 'number' AND (elems->>'y')::float != %(property_value_0)s)",
             query,
         )
-        self.assertEquals(
+        self.assertEqual(
             {"property_term_0": "atom_count", "property_value_0": "30"},
             self.builder.bind_params,
         )
 
         query = self.builder.build_query('"weight" > 0.537')
-        self.assertEquals(
+        self.assertEqual(
             "(elems->>'x' = %(property_term_0)s AND jsonb_typeof(elems->'y') = 'number' AND (elems->>'y')::float > %(property_value_0)s)",
             query,
         )
-        self.assertEquals(
+        self.assertEqual(
             {"property_term_0": "weight", "property_value_0": "0.537"},
             self.builder.bind_params,
         )
 
         query = self.builder.build_query("count > 25")
-        self.assertEquals(
+        self.assertEqual(
             "(elems->>'x' LIKE %(property_term_0)s AND jsonb_typeof(elems->'y') = 'number' AND (elems->>'y')::float > %(property_value_0)s)",
             query,
         )
-        self.assertEquals(
+        self.assertEqual(
             {"property_term_0": "%count%", "property_value_0": "25"},
             self.builder.bind_params,
         )
 
         query = self.builder.build_query('"formula" = "C14H21N3O2"')
-        self.assertEquals(
+        self.assertEqual(
             "(elems->>'x' = %(property_term_0)s AND elems->>'y' = %(property_value_0)s)",
             query,
         )
-        self.assertEquals(
+        self.assertEqual(
             {"property_term_0": "formula", "property_value_0": "c14h21n3o2"},
             self.builder.bind_params,
         )
 
         query = self.builder.build_query("'formula' != " + '"C14H21N3O2"')
-        self.assertEquals(
+        self.assertEqual(
             "(elems->>'x' = %(property_term_0)s AND elems->>'y' != %(property_value_0)s)",
             query,
         )
-        self.assertEquals(
+        self.assertEqual(
             {"property_term_0": "formula", "property_value_0": "c14h21n3o2"},
             self.builder.bind_params,
         )
 
         query = self.builder.build_query('~"molecular formula" = "C14H21N3O2"')
-        self.assertEquals(
+        self.assertEqual(
             "(elems->>'x' LIKE %(property_term_0)s AND elems->>'y' = %(property_value_0)s)",
             query,
         )
-        self.assertEquals(
+        self.assertEqual(
             {
                 "property_term_0": "%molecular formula%",
                 "property_value_0": "c14h21n3o2",
@@ -99,11 +99,11 @@ def testQueryPropWithValue(self):
         )
 
         query = self.builder.build_query('formula = "C14H21N3O2"')
-        self.assertEquals(
+        self.assertEqual(
             "(elems->>'x' LIKE %(property_term_0)s AND elems->>'y' = %(property_value_0)s)",
             query,
         )
-        self.assertEquals(
+        self.assertEqual(
             {
                 "property_term_0": "%formula%",
                 "property_value_0": "c14h21n3o2",
@@ -112,11 +112,11 @@ def testQueryPropWithValue(self):
         )
 
         query = self.builder.build_query("'formula' ~ 'C14H21N3O2'")
-        self.assertEquals(
+        self.assertEqual(
             "(elems->>'x' = %(property_term_0)s AND elems->>'y' LIKE %(property_value_0)s)",
             query,
         )
-        self.assertEquals(
+        self.assertEqual(
             {
                 "property_term_0": "formula",
                 "property_value_0": "%c14h21n3o2%",
@@ -125,11 +125,11 @@ def testQueryPropWithValue(self):
         )
 
         query = self.builder.build_query("formula !~ C14H21N3O2")
-        self.assertEquals(
+        self.assertEqual(
             "(elems->>'x' LIKE %(property_term_0)s AND elems->>'y' NOT LIKE %(property_value_0)s)",
             query,
         )
-        self.assertEquals(
+        self.assertEqual(
             {
                 "property_term_0": "%formula%",
                 "property_value_0": "%c14h21n3o2%",
@@ -138,11 +138,11 @@ def testQueryPropWithValue(self):
         )
 
         query = self.builder.build_query('"P-gp category_Probability" ~ "no"')
-        self.assertEquals(
+        self.assertEqual(
             "(elems->>'x' = %(property_term_0)s AND elems->>'y' LIKE %(property_value_0)s)",
             query,
         )
-        self.assertEquals(
+        self.assertEqual(
             {
                 "property_term_0": "p-gp category_probability",
                 "property_value_0": "%no%",
@@ -153,11 +153,11 @@ def testQueryPropWithValue(self):
         query = self.builder.build_query(
             '"PPB90 category_Probability" ~ "high = 0.18;"'
         )
-        self.assertEquals(
+        self.assertEqual(
             "(elems->>'x' = %(property_term_0)s AND elems->>'y' LIKE %(property_value_0)s)",
             query,
         )
-        self.assertEquals(
+        self.assertEqual(
             {
                 "property_term_0": "ppb90 category_probability",
                 "property_value_0": "%high = 0.18;%",
@@ -166,11 +166,11 @@ def testQueryPropWithValue(self):
         )
 
         query = self.builder.build_query('"molecular_formula" !~ "C14H21N3O2"')
-        self.assertEquals(
+        self.assertEqual(
             "(elems->>'x' = %(property_term_0)s AND elems->>'y' NOT LIKE %(property_value_0)s)",
             query,
         )
-        self.assertEquals(
+        self.assertEqual(
             {
                 "property_term_0": "molecular_formula",
                 "property_value_0": "%c14h21n3o2%",
@@ -182,11 +182,11 @@ def testQueryCompound(self):
         query = self.builder.build_query(
             '"mass" > 30 OR ~"probability" !~ "LOW"'
         )
-        self.assertEquals(
+        self.assertEqual(
             "(elems->>'x' = %(property_term_0)s AND jsonb_typeof(elems->'y') = 'number' AND (elems->>'y')::float > %(property_value_0)s) OR (elems->>'x' LIKE %(property_term_1)s AND elems->>'y' NOT LIKE %(property_value_1)s)",
             query,
         )
-        self.assertEquals(
+        self.assertEqual(
             {
                 "property_term_0": "mass",
                 "property_value_0": "30",
@@ -197,11 +197,11 @@ def testQueryCompound(self):
         )
 
         query = self.builder.build_query('"STATUS" or ~"NAME" or "CODE"')
-        self.assertEquals(
+        self.assertEqual(
             "(elems->>'y' = %(property_term_0)s) OR (elems->>'y' LIKE %(property_term_1)s) OR (elems->>'y' = %(property_term_2)s)",
             query,
         )
-        self.assertEquals(
+        self.assertEqual(
             {
                 "property_term_0": "status",
                 "property_term_1": "%name%",
@@ -211,11 +211,11 @@ def testQueryCompound(self):
         )
 
         query = self.builder.build_query("logP > 2 and StdDev < 0.5")
-        self.assertEquals(
+        self.assertEqual(
             "(elems->>'x' LIKE %(property_term_0)s AND jsonb_typeof(elems->'y') = 'number' AND (elems->>'y')::float > %(property_value_0)s))\n                    inner join {1} t1 on str.s = t1.s\n                    inner join jsonb_array_elements(t1.p) elems_t1 on ((elems_t1->>'x' LIKE %(property_term_1)s AND jsonb_typeof(elems_t1->'y') = 'number' AND (elems_t1->>'y')::float < %(property_value_1)s)",
             query,
         )
-        self.assertEquals(
+        self.assertEqual(
             {
                 "property_term_0": "%logp%",
                 "property_term_1": "%stddev%",