tskit-dev

Author: benjeffery

README.md

@@ -67,7 +67,7 @@ alignments and metadata stored in
 
 Resources:
 
-- See this [notebook](https://github.com/jeromekelleher/sc2ts-paper/blob/main/notebooks/example_data_processing.ipynb)
+- See this [notebook](https://github.com/tskit-dev/sc2ts-paper/blob/main/notebooks/example_data_processing.ipynb)
 for an example in which we access the data variant-by-variant and
 which explains the low-level data encoding
 - See the [VCF Zarr publication](https://doi.org/10.1093/gigascience/giaf049)

docs/_config.yml

@@ -14,7 +14,7 @@ launch_buttons:
   binderhub_url: ""
 
 repository:
-  url: https://github.com/jeromekelleher/sc2ts
+  url: https://github.com/tskit-dev/sc2ts
   branch: main
   path_to_book: docs
 
@@ -50,7 +50,7 @@ sphinx:
       - deflist
       - substitution
 
-    issues_github_path: jeromekelleher/sc2ts
+    issues_github_path: tskit-dev/sc2ts
     todo_include_todos: true
 
     intersphinx_mapping:

sc2ts/data_import.py

@@ -70,7 +70,7 @@ def get_problematic_regions():
     These regions have been reported to have highly recurrent or unusual
     patterns of deletions.
 
-    https://github.com/jeromekelleher/sc2ts/issues/231#issuecomment-2401405355
+    https://github.com/tskit-dev/sc2ts/issues/231#issuecomment-2401405355
 
     Region: NTD domain
     Coords: [21602-22472)

sc2ts/debug.py

@@ -717,7 +717,7 @@ def _node_summary(self, u, child_mutations=True):
                     strain = "debug missing"
             elif "group_id" in md:
                 # FIXME clipping this artificially for now
-                # see https://github.com/jeromekelleher/sc2ts/issues/434
+                # see https://github.com/tskit-dev/sc2ts/issues/434
                 strain = md["group_id"][:8]
 
         pango = md.get(self.pango_source, None)

tests/sc2ts_fixtures.py

@@ -148,7 +148,7 @@ def fx_ts_map(tmp_path, fx_data_cache, fx_dataset, fx_match_db):
     cache_path = fx_data_cache / f"{dates[-1]}.ts"
     if not cache_path.exists():
         # These sites are masked out in all alignments in the initial data
-        # anyway; https://github.com/jeromekelleher/sc2ts/issues/282
+        # anyway; https://github.com/tskit-dev/sc2ts/issues/282
         last_ts = si.initial_ts([56, 57, 58, 59, 60])
         cache_path = fx_data_cache / "initial.ts"
         last_ts.dump(cache_path)