Fix: Make annorefine import optional for CI compatibility

- Make annorefine import optional in log.py with try/except
- Add ANNOREFINE_AVAILABLE flag to check if module is installed
- Update system_info() to conditionally include annorefine version
- Add annorefine to macOS CI workflow dependencies
- Fixes ImportError in unit tests when annorefine is not installed

This allows the test suite to run even when annorefine is not available,
while still supporting the full functionality when it is installed.

Author: Jon Palmer

.github/workflows/tests.yml

@@ -55,7 +55,7 @@ jobs:
         if [[ "${{ matrix.use_conda }}" == "true" ]]; then
           # Use conda for macOS to avoid mappy build issues
           conda install -c conda-forge -c bioconda mappy numpy pytest pytest-cov -y
-          pip install natsort gfftk buscolite gapmm2 pyhmmer pyfastx requests gb-io json-repair pytantan
+          pip install natsort gfftk buscolite gapmm2 pyhmmer pyfastx requests gb-io json-repair pytantan annorefine
           pip install -e . --no-deps
         else
           # Linux - use pip as normal

funannotate2/log.py

@@ -5,7 +5,12 @@
 
 import buscolite
 import gfftk
-import annorefine
+
+try:
+    import annorefine
+    ANNOREFINE_AVAILABLE = True
+except ImportError:
+    ANNOREFINE_AVAILABLE = False
 
 from .__init__ import __version__
 from .utilities import human_readable_size
@@ -110,15 +115,25 @@ def system_info(log):
     Returns:
     - None
     """
-    log(
-        "Python v{}; funannotate2 v{}; gfftk v{}; buscolite v{}; annorefine v{}".format(
-            platform.python_version(),
-            __version__,
-            gfftk.__version__,
-            buscolite.__version__,
-            annorefine.__version__,
+    if ANNOREFINE_AVAILABLE:
+        log(
+            "Python v{}; funannotate2 v{}; gfftk v{}; buscolite v{}; annorefine v{}".format(
+                platform.python_version(),
+                __version__,
+                gfftk.__version__,
+                buscolite.__version__,
+                annorefine.__version__,
+            )
+        )
+    else:
+        log(
+            "Python v{}; funannotate2 v{}; gfftk v{}; buscolite v{}".format(
+                platform.python_version(),
+                __version__,
+                gfftk.__version__,
+                buscolite.__version__,
+            )
         )
-    )
 
 
 def finishLogging(log, module):