Remove bed_reader dep and add pandas

jeromekelleher · jeromekelleher · commit 2b3b40fd1c32 · 2025-05-23T10:12:01.000Z
diff --git a/pyproject.toml b/pyproject.toml
@@ -23,6 +23,8 @@ dependencies = [
   # cyvcf2 also pulls in coloredlogs and click
   "coloredlogs",
   "click",
+  # Using pandas for reading plink files, but will be useful more generally
+  "pandas"
 ]
 requires-python = ">=3.10"
 classifiers = [
@@ -68,11 +70,9 @@ dev = [
 ]
 # TODO Using dev version of tskit for CI, FIXME before release
 tskit = ["tskit @ git+https://github.com/tskit-dev/tskit.git@main#subdirectory=python"]
-plink = ["bed_reader"]
 vcf = ["cyvcf2"]
 all = [
   "tskit @ git+https://github.com/tskit-dev/tskit.git@main#subdirectory=python", 
-  "bed_reader", 
   "cyvcf2"
   ]
 

Original file line number	Diff line number	Diff line change
`@@ -23,6 +23,8 @@ dependencies = [`
`23`	`23`	`# cyvcf2 also pulls in coloredlogs and click`
`24`	`24`	`"coloredlogs",`
`25`	`25`	`"click",`
	`26`	`+ # Using pandas for reading plink files, but will be useful more generally`
	`27`	`+ "pandas"`
`26`	`28`	`]`
`27`	`29`	`requires-python = ">=3.10"`
`28`	`30`	`classifiers = [`
`@@ -68,11 +70,9 @@ dev = [`
`68`	`70`	`]`
`69`	`71`	`# TODO Using dev version of tskit for CI, FIXME before release`
`70`	`72`	`tskit = ["tskit @ git+https://github.com/tskit-dev/tskit.git@main#subdirectory=python"]`
`71`		`-plink = ["bed_reader"]`
`72`	`73`	`vcf = ["cyvcf2"]`
`73`	`74`	`all = [`
`74`	`75`	`"tskit @ git+https://github.com/tskit-dev/tskit.git@main#subdirectory=python",`
`75`		`- "bed_reader",`
`76`	`76`	`"cyvcf2"`
`77`	`77`	`]`
`78`	`78`