Add missing dependencies (#533)

david4096 · jsstevenson · korikuzma · web-flow · commit 27567b6e9054 · 2025-04-03T14:11:08.000-04:00
Was working on the annotator and these dependencies were missing. `uv
sync --extra extras`

---------

Co-authored-by: James Stevenson &lt;james.sharpsteen@gmail.com&gt;
Co-authored-by: Kori Kuzma &lt;korikuzma@gmail.com&gt;
diff --git a/pyproject.toml b/pyproject.toml
@@ -40,6 +40,7 @@ dependencies = [
     "bioutils",
     "requests",
     "canonicaljson",
+    "setuptools>=78.1.0", # TODO remove this pin caused by HGVS issue
 ]
 
 [project.optional-dependencies]
@@ -50,6 +51,7 @@ extras = [
     "hgvs>=1.4",
     "dill~=0.3.7",
     "click",
+    "pysam>=0.23.0",
 ]
 dev = [
     # tests

Original file line number	Diff line number	Diff line change
`@@ -40,6 +40,7 @@ dependencies = [`
`40`	`40`	`"bioutils",`
`41`	`41`	`"requests",`
`42`	`42`	`"canonicaljson",`
	`43`	`+ "setuptools>=78.1.0", # TODO remove this pin caused by HGVS issue`
`43`	`44`	`]`
`44`	`45`
`45`	`46`	`[project.optional-dependencies]`
`@@ -50,6 +51,7 @@ extras = [`
`50`	`51`	`"hgvs>=1.4",`
`51`	`52`	`"dill~=0.3.7",`
`52`	`53`	`"click",`
	`54`	`+ "pysam>=0.23.0",`
`53`	`55`	`]`
`54`	`56`	`dev = [`
`55`	`57`	`# tests`