Merge branch 'main' into simon-comp-fig-1

naobservatory · Nov 28, 2023 · 2c9c2de · 2c9c2de
2 parents 77700b9 + 66c052c
commit 2c9c2de
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Showing 3 changed files with 6 additions and 7 deletions.
diff --git a/figures/counts-by-pathogen-and-study.py b/figures/counts-by-pathogen-and-study.py
@@ -15,7 +15,7 @@
 
 def start():
     branch = "simon-validation-exclusion-run"
-    #ref = "ref"
+    # ref = "ref"
     mgs_data = mgs.MGSData.from_repo(ref=branch)
     pathogen_taxids_by_name = defaultdict(list)
     for (
@@ -151,7 +151,7 @@ def start():
         cellLoc="center",
         loc="upper left",
     )
-    fig.show() 
+    fig.show()
     fig.savefig(f"matching-reads-table_from{branch}.png", dpi=180)
     plt.clf()
 

diff --git a/fit.py b/fit.py
@@ -23,7 +23,7 @@ def summarize_output(coeffs: pd.DataFrame) -> pd.DataFrame:
 
 def start(num_samples: int, plot: bool) -> None:
     branch = "simon-validation-exclusion-run"
-    print("Using mgs-pipeline branch simon-validation-exclusion-run") 
+    print("Using mgs-pipeline branch simon-validation-exclusion-run")
     figdir = Path("fig")
     if plot:
         figdir.mkdir(exist_ok=True)

diff --git a/mgs.py b/mgs.py
@@ -68,18 +68,17 @@ class SampleAttributes(BaseModel):
     country: str
     state: Optional[str] = None
     county: Optional[str] = None
-    location: Optional[str] = None #FIX ME
+    location: str
     fine_location: Optional[str] = None
     # Fixme: Not all the dates are real dates
     date: date | str
-    reads: Optional[int] = None #FIX ME 
+    reads: int
     enrichment: Optional[Enrichment] = None
     method: Optional[str] = None
 
 
 def load_sample_attributes(repo: GitHubRepo) -> dict[Sample, SampleAttributes]:
     data = json.loads(repo.get_file("dashboard/metadata_samples.json"))
-    print("Changed SampleAttributes in mgs.py to not require location or reads. Needs fixing.")
     return {
         Sample(s): SampleAttributes(**attribs) for s, attribs in data.items()
     }
@@ -139,7 +138,7 @@ def from_repo(
         ref=MGS_REPO_DEFAULTS["ref"],
     ):
         repo = GitHubRepo(user, repo, ref)
-        print(repo, type(repo)) #FIX ME
+        print(repo, type(repo))
         return MGSData(
             bioprojects=load_bioprojects(repo),
             sample_attrs=load_sample_attributes(repo),