v1.0.10

CHANGELOG.md

@@ -1,4 +1,4 @@
-## [1.0.10] - tbd
+## [1.0.10] - 2024-04-08
 
 ### Added
 - CosMX reader with image stitching (experimental)
@@ -8,6 +8,7 @@
 - Minimum number of transcripts per patch set to 4000 (#41)
 - Config files refactoring (configs added or renamed)
 - Readers refactoring
+- Section with error during report are not displayed (instead of throwing an error)
 
 ## [1.0.9] - 2024-04-03
 

pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "sopa"
-version = "1.0.9"
+version = "1.0.10"
 description = "Spatial-omics pipeline and analysis"
 documentation = "https://gustaveroussy.github.io/sopa"
 homepage = "https://gustaveroussy.github.io/sopa"

sopa/io/report/generate.py

@@ -54,6 +54,14 @@ def _kdeplot_vmax_quantile(values: np.ndarray, quantile: float = 0.95):
 
 
 class SectionBuilder:
+    SECTION_NAMES = [
+        "general_section",
+        "cell_section",
+        "channel_section",
+        "transcripts_section",
+        "representation_section",
+    ]
+
     def __init__(self, sdata: SpatialData):
         self.sdata = sdata
         self.adata = self.sdata.tables.get(SopaKeys.TABLE)
@@ -64,8 +72,6 @@ def _table_has(self, key, default=False):
         return self.adata.uns[SopaKeys.UNS_KEY].get(key, default)
 
     def general_section(self):
-        log.info("Writing general section")
-
         return Section(
             "General",
             [
@@ -82,8 +88,6 @@ def general_section(self):
         )
 
     def cell_section(self):
-        log.info("Writing cell section")
-
         shapes_key, _ = get_boundaries(self.sdata, return_key=True)
         coord_system = get_intrinsic_cs(self.sdata, shapes_key)
 
@@ -111,8 +115,6 @@ def cell_section(self):
         )
 
     def channel_section(self):
-        log.info("Writing channel section")
-
         image = get_spatial_image(self.sdata)
 
         subsections = [
@@ -154,8 +156,6 @@ def transcripts_section(self):
         if not self._table_has(SopaKeys.UNS_HAS_TRANSCRIPTS):
             return None
 
-        log.info("Writing transcript section")
-
         mean_transcript_count = self.adata.X.mean(0).A1
         low_average = mean_transcript_count < LOW_AVERAGE_COUNT
 
@@ -183,8 +183,6 @@ def transcripts_section(self):
         return Section("Transcripts", [SubSection("Quality controls", QC_subsubsections)])
 
     def representation_section(self, max_obs: int = 400_000):
-        log.info("Writing representation section")
-
         if self._table_has(SopaKeys.UNS_HAS_TRANSCRIPTS):
             sc.pp.normalize_total(self.adata)
             sc.pp.log1p(self.adata)
@@ -209,11 +207,14 @@ def representation_section(self, max_obs: int = 400_000):
         )
 
     def compute_sections(self) -> list[Section]:
-        sections = [
-            self.general_section(),
-            self.cell_section(),
-            self.channel_section(),
-            self.transcripts_section(),
-            self.representation_section(),
-        ]
+        sections = []
+
+        for name in self.SECTION_NAMES:
+            try:
+                log.info(f"Writing {name}")
+                section = getattr(self, name)()
+                sections.append(section)
+            except Exception as e:
+                log.warn(f"Section {name} failed with error {e}")
+
         return [section for section in sections if section is not None]

sopa/utils/data.py

@@ -21,7 +21,7 @@ def uniform(
     *_,
     length: int = 2_048,
     cell_density: float = 1e-4,
-    n_points_per_cell: int = 50,
+    n_points_per_cell: int = 100,
     c_coords: list[str] = ["DAPI", "CK", "CD3", "CD20"],
     genes: int | list[str] = ["EPCAM", "CD3E", "CD20", "CXCL4", "CXCL10"],
     sigma_factor: float = 0.05,