rename the project to varistat

Cargo.toml

@@ -1,5 +1,5 @@
 [package]
-name = "popgen"
+name = "varistat"
 version = "0.1.0"
 edition = "2021"
 

examples/from_tskit.rs

@@ -1,6 +1,6 @@
 use std::env;
 
-use popgen::MultiSiteCounts;
+use varistat::MultiSiteCounts;
 
 fn process_ts(ts: &tskit::TreeSequence) {
     let counts = MultiSiteCounts::try_from_tree_sequence(ts, None).unwrap();

examples/from_vcf.rs

@@ -1,5 +1,5 @@
 use noodles::vcf;
-use popgen::{adapter::vcf::record_to_genotypes_adapter, MultiSiteCounts};
+use varistat::{adapter::vcf::record_to_genotypes_adapter, MultiSiteCounts};
 
 static VCF_FILE: &str = r#"##fileformat=VCFv4.5
 ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">

src/adapter.rs

@@ -1,6 +1,6 @@
 #[cfg(feature = "noodles")]
 pub mod vcf {
-    use crate::{AlleleID, PopgenResult};
+    use crate::{AlleleID, VaristatResult};
     use noodles::vcf::variant::record::samples::keys::key;
     use noodles::vcf::variant::record::samples::series::Value;
     use noodles::vcf::variant::record::samples::Sample;
@@ -13,7 +13,7 @@ pub mod vcf {
         record: Record,
         num_samples: usize,
         ploidy: usize,
-    ) -> PopgenResult<Vec<Option<AlleleID>>> {
+    ) -> VaristatResult<Vec<Option<AlleleID>>> {
         let mut genotypes = Vec::with_capacity(ploidy * num_samples);
 
         for sample in record.samples().iter() {

src/from_tree_sequence.rs

@@ -1,4 +1,4 @@
-use crate::{MultiSiteCounts, PopgenResult};
+use crate::{MultiSiteCounts, VaristatResult};
 
 // NOTES:
 // 1. tskit could use Add for all id types!
@@ -42,7 +42,7 @@ fn update_right(
 pub fn try_from_tree_sequence(
     ts: &tskit::TreeSequence,
     _parameters: Option<FromTreeSequenceOptions>,
-) -> PopgenResult<MultiSiteCounts> {
+) -> VaristatResult<MultiSiteCounts> {
     let mut counts = MultiSiteCounts::default();
     let mut left = 0.0;
     // NOTE: we need TreeSequence to be able to provide these

src/lib.rs

@@ -11,7 +11,7 @@ pub mod stats;
 mod test;
 pub(crate) mod util;
 
-pub type PopgenResult<T> = Result<T, PopgenError>;
+pub type VaristatResult<T> = Result<T, VaristatError>;
 
 #[cfg(feature = "tskit")]
 pub use tskit;
@@ -21,7 +21,7 @@ pub use from_tree_sequence::FromTreeSequenceOptions;
 
 #[non_exhaustive]
 #[derive(Debug, thiserror::Error)]
-pub enum PopgenError {
+pub enum VaristatError {
     #[cfg(feature = "noodles")]
     #[error("couldn't handle VCF: {0}")]
     NoodlesVCF(#[from] std::io::Error),
@@ -95,7 +95,7 @@ impl MultiSiteCounts {
     pub fn try_from_tree_sequence(
         ts: &tskit::TreeSequence,
         options: Option<FromTreeSequenceOptions>,
-    ) -> Result<Self, PopgenError> {
+    ) -> Result<Self, VaristatError> {
         from_tree_sequence::try_from_tree_sequence(ts, options)
     }
 

src/test.rs

@@ -16,7 +16,7 @@ mod tests {
     #[cfg(feature = "noodles")]
     mod vcf {
         use crate::adapter::vcf::record_to_genotypes_adapter;
-        use crate::{AlleleID, MultiSiteCounts, PopgenResult};
+        use crate::{AlleleID, MultiSiteCounts, VaristatResult};
         use noodles::vcf::header::record::value::map::{Contig, Format};
         use noodles::vcf::header::record::value::Map;
         use noodles::vcf::variant::io::Write;
@@ -168,7 +168,7 @@ mod tests {
                 .records()
                 .map(Result::unwrap)
                 .map(|rec| record_to_genotypes_adapter(&header, rec, num_samples, ploidy))
-                .collect::<PopgenResult<Vec<_>>>()
+                .collect::<VaristatResult<Vec<_>>>()
                 .unwrap();
             let counts = MultiSiteCounts::from_tabular(all_alleles.iter().cloned());
             (all_alleles, counts)

tests/test_try_from_tree_sequence.rs

@@ -1,8 +1,8 @@
 // NOTE: these tests require compiling
 // with the tskit feature
 
-use popgen::tskit;
-use popgen::tskit::prelude::StreamingIterator;
+use varistat::tskit;
+use varistat::tskit::prelude::StreamingIterator;
 
 #[cfg(test)]
 struct MutationData {
@@ -63,7 +63,7 @@ struct SiteCountContents {
 }
 
 #[cfg(test)]
-fn validate_site_counts(counts: &popgen::iter::SiteCounts, expected: SiteCountContents) {
+fn validate_site_counts(counts: &varistat::iter::SiteCounts, expected: SiteCountContents) {
     let num_alleles = expected
         .derived
         .iter()
@@ -246,7 +246,7 @@ mod naive_details {
 #[cfg(test)]
 fn generate_expected_site_counts_naive(
     ts: &tskit::TreeSequence,
-    options: Option<popgen::FromTreeSequenceOptions>,
+    options: Option<varistat::FromTreeSequenceOptions>,
 ) -> Vec<SiteCountContents> {
     let mut expected = vec![];
     // We have no code depending on options yet
@@ -645,9 +645,9 @@ where
 #[cfg(test)]
 fn generate_counts_and_validate(
     ts: &tskit::TreeSequence,
-    options: Option<popgen::FromTreeSequenceOptions>,
+    options: Option<varistat::FromTreeSequenceOptions>,
 ) {
-    let counts = popgen::MultiSiteCounts::try_from_tree_sequence(ts, None).unwrap();
+    let counts = varistat::MultiSiteCounts::try_from_tree_sequence(ts, None).unwrap();
     let expected = generate_expected_site_counts_naive(ts, options);
     assert_eq!(counts.len(), expected.len());
     for (obs, exp) in counts.iter().zip(expected.into_iter()) {