Merge branch 'dev/embedding' of https://github.com/OpenProteinAI/openprotein-python into release

Author: mbarber

openprotein/api/jobs.py

@@ -42,9 +42,9 @@ class Job(BaseModel):
     start_date: Optional[datetime]
     end_date: Optional[datetime]
     prerequisite_job_id: Optional[str]
-    progress_message: Optional[str]
+    progress_message: Optional[str] = None
     progress_counter: Optional[int] = 0
-    num_records: Optional[int]
+    num_records: Optional[int] = None
 
     def refresh(self, session: APISession):
         """refresh job status"""
@@ -62,10 +62,11 @@ def _update_progress(self, job) -> int:
         """update rules for jobs without counters"""
         progress = job.progress_counter
         #if progress is not None:  # Check None before comparison
-        if job.status == JobStatus.PENDING and progress is None:
-            progress = 5
-        if job.status == JobStatus.RUNNING and progress is None:
-            progress = 25
+        if progress is None:
+            if job.status == JobStatus.PENDING:
+                progress = 5
+            if job.status == JobStatus.RUNNING:
+                progress = 25
         if job.status in [JobStatus.SUCCESS, JobStatus.FAILURE]:
             progress = 100
         return progress or 0 # never None

openprotein/models.py

@@ -59,7 +59,7 @@ class SVDMetadata(BaseModel):
     model_id: str
     n_components: int
     reduction: Optional[str]
-    sequence_length: Optional[int]
+    sequence_length: Optional[int] = None
 
     def is_done(self):
         return self.status.done()

tests/conftest.py

@@ -0,0 +1,19 @@
+def pytest_addoption(parser):
+    # adapted from https://stackoverflow.com/a/33181491
+    parser.addoption('--longrun', action='store_true', dest="longrun",
+                 default=False, help="enable longrundecorated tests")
+
+
+def pytest_configure(config):
+    config.addinivalue_line(
+        "markers", "longrun: mark tests that take a long time to run"
+    )
+    if not config.option.longrun:
+        if config.option.markexpr != "":
+            setattr(
+                config.option,
+                'markexpr',
+                config.option.markexpr + ' and not longrun',
+            )
+        else:
+            setattr(config.option, 'markexpr', 'not longrun')