Merge pull request #52 from Sage-Bionetworks-Workflows/bwmac/ORCA-288…

…/test_object_refactor

[ORCA-288] Test Object Naming Refactor

.github/workflows/ci.yml

@@ -36,8 +36,10 @@ jobs:
         with: {python-version: "3.11"}
       - name: Run static analysis and format checkers
         run: pipx run pre-commit run --all-files --show-diff-on-failure
+      - name: Install tox-gh plugin
+        run: python -m pip install tox-gh>=1.2
       - name: Build package distribution files
-        run: pipx run --spec 'tox~=3.0' tox -e clean,build
+        run: tox -e clean,build
       - name: Record the paths of wheel and source tarball distributions
         id: distribution-paths
         run: |
@@ -58,7 +60,7 @@ jobs:
     strategy:
       matrix:
         python:
-        - "3.8"
+        - "3.9" # oldest Python that is supported
         - "3.11"  # newest Python that is stable
         platform:
         - ubuntu-latest
@@ -76,12 +78,15 @@ jobs:
           python-version: ${{ matrix.python }}
       - uses: actions/download-artifact@v3
         with: {name: python-distribution-files, path: dist/}
+      - name: Install tox-gh plugin
+        run: python -m pip install tox-gh>=1.2
+      - name: Setup test suite
+        run: tox -vv --notest
       - name: Run tests
         env:
           SYNAPSE_AUTH_TOKEN: ${{ secrets.SYNAPSE_AUTH_TOKEN }}
         run: >-
-          pipx run --spec 'tox~=3.0' tox
-          --installpkg '${{ needs.prepare.outputs.wheel-path }}'
+          tox --installpkg '${{ needs.prepare.outputs.wheel-path }}'
           -- -rFEx --durations 10 --color yes
       - name: Upload coverage to Codecov
         uses: codecov/codecov-action@v3

.readthedocs.yml

@@ -17,7 +17,7 @@ formats:
   - pdf
 
 python:
-  version: 3.8
+  version: 3.9
   install:
     - requirements: docs/requirements.txt
     - {path: ., method: pip}

setup.cfg

@@ -41,7 +41,7 @@ package_dir =
     =src
 
 # Require a min/specific Python version (comma-separated conditions)
-python_requires = >=3.8
+python_requires = >=3.9, <3.12
 
 # Add here dependencies of your project (line-separated), e.g. requests>=2.2,<3.0.
 # Version specifiers like >=2.2,<3.0 avoid problems due to API changes in
@@ -82,7 +82,6 @@ testing =
 # Dependencies for development (used by Pipenv)
 dev =
     pre-commit~=2.0
-    tox~=3.0
     sphinx-rtd-theme~=1.0
     black~=22.0
     flake8~=5.0

tests/conftest.py

@@ -100,19 +100,19 @@ def test_files(get_data):
     }
     test_files = {
         "date_in_tag_tiff": File(tiff_date_in_tag_path.as_posix(), tiff_metadata),
-        "good": File(txt_path.as_posix(), good_metadata),
-        "date_txt": File(date_path.as_posix(), date_txt_metadata),
-        "ome_tiff": File(ome_tiff_path.as_posix(), ome_tiff_metadata),
+        "good_txt": File(txt_path.as_posix(), good_metadata),
+        "date_string_txt": File(date_path.as_posix(), date_txt_metadata),
+        "good_ome_tiff": File(ome_tiff_path.as_posix(), ome_tiff_metadata),
         "invalid_xml_tiff": File(
             invalid_xml_ome_tiff_path.as_posix(), invalid_xml_metadata
         ),
-        "bad": File(txt_path.as_posix(), bad_metadata),
-        "tiff": File(tiff_path.as_posix(), tiff_metadata),
-        "fastq1": File(fastq1_path.as_posix(), fastq_metadata),
-        "fastq2": File(fastq2_path.as_posix(), fastq_metadata),
-        "jsonld": File(jsonld_path.as_posix(), jsonld_metadata),
-        "synapse": File(syn_path, good_metadata),
-        "tiff_dirty_datetime": File(
+        "wrong_file_type_and_md5_txt": File(txt_path.as_posix(), bad_metadata),
+        "good_tiff": File(tiff_path.as_posix(), tiff_metadata),
+        "good_fastq": File(fastq1_path.as_posix(), fastq_metadata),
+        "good_compressed_fastq": File(fastq2_path.as_posix(), fastq_metadata),
+        "good_jsonld": File(jsonld_path.as_posix(), jsonld_metadata),
+        "good_synapse": File(syn_path, good_metadata),
+        "dirty_datetime_in_tag_tiff": File(
             tiff_dirty_datetime_path.as_posix(), tiff_dirty_datetime_metadata
         ),
     }
@@ -127,18 +127,16 @@ def test_files(get_data):
 
 @pytest.fixture
 def test_targets(test_files):
-    test_targets = dict()
-    for name, file in test_files.items():
-        test_targets[name] = SingleTarget(file)
+    test_targets = {name: SingleTarget(file) for name, file in test_files.items()}
     yield test_targets
 
 
 @pytest.fixture
 def test_suites(test_targets):
-    test_suites = dict()
-    for name, target in test_targets.items():
-        test_suites[name] = SuiteABC.from_target(target)
-    yield test_suites
+    test_suites_dict = {
+        name: SuiteABC.from_target(target) for name, target in test_targets.items()
+    }
+    return test_suites_dict
 
 
 @pytest.fixture
@@ -171,6 +169,7 @@ def mocked_suites_single_targets():
     return mocked_suites
 
 
+# TODO: Add this once we have multi-targets
 # @pytest.fixture
 # def mocked_suites_multi_targets():
 #     mock_dict_multi = {