switch to ubuntu only for test

Sage-Bionetworks-Workflows · Oct 30, 2023 · 2cda95c · 2cda95c
1 parent 5492955
commit 2cda95c
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diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -61,8 +61,8 @@ jobs:
         - "3.8"
         - "3.11"  # newest Python that is stable
         platform:
-        #- ubuntu-latest
-        - macos-latest
+        - ubuntu-latest
+        # - macos-latest
         # TODO: Debug the Windows issues
         # - windows-latest
     env:
@@ -79,16 +79,7 @@ jobs:
       - name: Run tests
         env:
           SYNAPSE_AUTH_TOKEN: ${{ secrets.SYNAPSE_AUTH_TOKEN }}
-        run: |
-          codesign --sign - --entitlements entitlements.xml \
-          --force /usr/local/bin/qemu-system-x86_64
-          brew install docker colima
-          colima start
-          while ! docker info > /dev/null 2>&1; do
-            echo "Waiting for docker daemon to start..."
-            sleep 5
-            done
-          echo "Docker daemon is running"
+        run: >-
           pipx run --spec 'tox~=3.0' tox \
           --installpkg '${{ needs.prepare.outputs.wheel-path }}' \
           -- -rFEx --durations 10 --color yes

diff --git a/tests/test_external_tests.py b/tests/test_external_tests.py
@@ -181,132 +181,152 @@ def test_that_the_bioformats_info_test_command_is_produced(test_targets):
     assert "showinf" in process.command
 
 
-# def test_that_the_bioformats_info_test_exit_code_is_0_when_it_should_be(test_files):
-#     one_tiff_file = test_files["ome_tiff"]
-#     target = SingleTarget(one_tiff_file)
-#     test = tests.BioFormatsInfoTest(target)
+# def test_that_the_tifftag306datetimetest_command_is_produced(test_targets):
+#     target = test_targets["tiff"]
+#     test = tests.TiffTag306DateTimeTest(target)
+#     process = test.generate_process()
+#     assert "jq" in process.command
+
+
+# def test_that_the_tifftag306datetimetest_exit_code_is_0_when_it_should_be(test_files):
+#     tiff_file = test_files["tiff"]
+#     target = SingleTarget(tiff_file)
+#     test = tests.TiffTag306DateTimeTest(target)
 #     process = test.generate_process()
 #     executor = DockerExecutor(process.container, process.command, target.file.url)
 #     executor.execute()
 #     assert executor.exit_code == "0"
 
 
-# def test_that_the_bioformats_info_test_correctly_interprets_exit_code_0_and_1(
+# def test_that_the_tifftag306datetimetest_correctly_interprets_exit_code_0_and_1(
 #     test_files, mocker
 # ):
-#     # 0 is pass, 1 is fail
+#     # 1 is pass, 0 is fail
 #     tiff_file = test_files["tiff"]
 #     target = SingleTarget(tiff_file)
 #     with TemporaryDirectory() as tmp_dir:
 #         path_0 = Path(tmp_dir, "code_0.txt")
 #         path_1 = Path(tmp_dir, "code_1.txt")
 #         path_0.write_text("0")
 #         path_1.write_text("1")
-#         pass_outputs = {"std_out": path_1, "std_err": path_1, "exit_code": path_0}
-#         fail_outputs = {"std_out": path_0, "std_err": path_0, "exit_code": path_1}
+#         fail_outputs = {"std_out": path_1, "std_err": path_1, "exit_code": path_0}
+#         pass_outputs = {"std_out": path_0, "std_err": path_0, "exit_code": path_1}
 
-#         test = tests.BioFormatsInfoTest(target)
+#         test = tests.TiffTag306DateTimeTest(target)
 #         mocker.patch.object(test, "_find_process_outputs", return_value=pass_outputs)
 #         test_status = test.get_status()
 #         assert test_status == TestStatus.PASS
 
-#         test = tests.BioFormatsInfoTest(target)
+#         test = tests.TiffTag306DateTimeTest(target)
 #         mocker.patch.object(test, "_find_process_outputs", return_value=fail_outputs)
 #         test_status = test.get_status()
 #         assert test_status == TestStatus.FAIL
 
 
-# def test_that_the_ome_xml_schema_test_command_is_produced(test_targets):
+# def test_that_the_tiffdatetimetest_command_is_produced(test_targets):
 #     target = test_targets["tiff"]
-#     test = tests.OmeXmlSchemaTest(target)
+#     test = tests.TiffDateTimeTest(target)
 #     process = test.generate_process()
-#     assert "xmlvalid" in process.command
+#     assert "grep" in process.command
 
 
-# def test_that_the_ome_xml_info_test_correctly_interprets_exit_code_0_and_1(
+# def test_that_the_tiffdatetimetest_correctly_interprets_exit_code_0_and_1(
 #     test_files, mocker
 # ):
-#     # 0 is pass, 1 is fail
+#     # 1 is pass, 0 is fail
 #     tiff_file = test_files["tiff"]
 #     target = SingleTarget(tiff_file)
 #     with TemporaryDirectory() as tmp_dir:
 #         path_0 = Path(tmp_dir, "code_0.txt")
 #         path_1 = Path(tmp_dir, "code_1.txt")
 #         path_0.write_text("0")
 #         path_1.write_text("1")
-#         pass_outputs = {"std_out": path_1, "std_err": path_1, "exit_code": path_0}
-#         fail_outputs = {"std_out": path_0, "std_err": path_0, "exit_code": path_1}
+#         fail_outputs = {"std_out": path_1, "std_err": path_1, "exit_code": path_0}
+#         pass_outputs = {"std_out": path_0, "std_err": path_0, "exit_code": path_1}
 
-#         test = tests.OmeXmlSchemaTest(target)
+#         test = tests.TiffDateTimeTest(target)
 #         mocker.patch.object(test, "_find_process_outputs", return_value=pass_outputs)
 #         test_status = test.get_status()
 #         assert test_status == TestStatus.PASS
 
-#         test = tests.OmeXmlSchemaTest(target)
+#         test = tests.TiffDateTimeTest(target)
 #         mocker.patch.object(test, "_find_process_outputs", return_value=fail_outputs)
 #         test_status = test.get_status()
 #         assert test_status == TestStatus.FAIL
 
 
-# def test_that_the_tifftag306datetimetest_command_is_produced(test_targets):
-#     target = test_targets["tiff"]
-#     test = tests.TiffTag306DateTimeTest(target)
+# def test_that_the_bioformats_info_test_exit_code_is_0_when_it_should_be(test_files):
+#     one_tiff_file = test_files["ome_tiff"]
+#     target = SingleTarget(one_tiff_file)
+#     test = tests.BioFormatsInfoTest(target)
 #     process = test.generate_process()
-#     assert "jq" in process.command
+#     executor = DockerExecutor(process.container, process.command, target.file.url)
+#     executor.execute()
+#     assert executor.exit_code == "0"
 
 
-# def test_that_the_tifftag306datetimetest_correctly_interprets_exit_code_0_and_1(
+# def test_that_the_bioformats_info_test_correctly_interprets_exit_code_0_and_1(
 #     test_files, mocker
 # ):
-#     # 1 is pass, 0 is fail
+#     # 0 is pass, 1 is fail
 #     tiff_file = test_files["tiff"]
 #     target = SingleTarget(tiff_file)
 #     with TemporaryDirectory() as tmp_dir:
 #         path_0 = Path(tmp_dir, "code_0.txt")
 #         path_1 = Path(tmp_dir, "code_1.txt")
 #         path_0.write_text("0")
 #         path_1.write_text("1")
-#         fail_outputs = {"std_out": path_1, "std_err": path_1, "exit_code": path_0}
-#         pass_outputs = {"std_out": path_0, "std_err": path_0, "exit_code": path_1}
+#         pass_outputs = {"std_out": path_1, "std_err": path_1, "exit_code": path_0}
+#         fail_outputs = {"std_out": path_0, "std_err": path_0, "exit_code": path_1}
 
-#         test = tests.TiffTag306DateTimeTest(target)
+#         test = tests.BioFormatsInfoTest(target)
 #         mocker.patch.object(test, "_find_process_outputs", return_value=pass_outputs)
 #         test_status = test.get_status()
 #         assert test_status == TestStatus.PASS
 
-#         test = tests.TiffTag306DateTimeTest(target)
+#         test = tests.BioFormatsInfoTest(target)
 #         mocker.patch.object(test, "_find_process_outputs", return_value=fail_outputs)
 #         test_status = test.get_status()
 #         assert test_status == TestStatus.FAIL
 
 
-# def test_that_the_tiffdatetimetest_command_is_produced(test_targets):
+# def test_that_the_ome_xml_schema_test_command_is_produced(test_targets):
 #     target = test_targets["tiff"]
-#     test = tests.TiffDateTimeTest(target)
+#     test = tests.OmeXmlSchemaTest(target)
 #     process = test.generate_process()
-#     assert "grep" in process.command
+#     assert "xmlvalid" in process.command
 
 
-# def test_that_the_tiffdatetimetest_correctly_interprets_exit_code_0_and_1(
+# def test_that_the_ome_xml_schema_test_exit_code_is_0_when_it_should_be(test_files):
+#     tiff_file = test_files["ome_tiff"]
+#     target = SingleTarget(tiff_file)
+#     test = tests.OmeXmlSchemaTest(target)
+#     process = test.generate_process()
+#     executor = DockerExecutor(process.container, process.command, target.file.url)
+#     executor.execute()
+#     assert executor.exit_code == "0"
+
+
+# def test_that_the_ome_xml_info_test_correctly_interprets_exit_code_0_and_1(
 #     test_files, mocker
 # ):
-#     # 1 is pass, 0 is fail
+#     # 0 is pass, 1 is fail
 #     tiff_file = test_files["tiff"]
 #     target = SingleTarget(tiff_file)
 #     with TemporaryDirectory() as tmp_dir:
 #         path_0 = Path(tmp_dir, "code_0.txt")
 #         path_1 = Path(tmp_dir, "code_1.txt")
 #         path_0.write_text("0")
 #         path_1.write_text("1")
-#         fail_outputs = {"std_out": path_1, "std_err": path_1, "exit_code": path_0}
-#         pass_outputs = {"std_out": path_0, "std_err": path_0, "exit_code": path_1}
+#         pass_outputs = {"std_out": path_1, "std_err": path_1, "exit_code": path_0}
+#         fail_outputs = {"std_out": path_0, "std_err": path_0, "exit_code": path_1}
 
-#         test = tests.TiffDateTimeTest(target)
+#         test = tests.OmeXmlSchemaTest(target)
 #         mocker.patch.object(test, "_find_process_outputs", return_value=pass_outputs)
 #         test_status = test.get_status()
 #         assert test_status == TestStatus.PASS
 
-#         test = tests.TiffDateTimeTest(target)
+#         test = tests.OmeXmlSchemaTest(target)
 #         mocker.patch.object(test, "_find_process_outputs", return_value=fail_outputs)
 #         test_status = test.get_status()
 #         assert test_status == TestStatus.FAIL