Genbank parser rewrite

.devcontainer/devcontainer.json

@@ -2,15 +2,8 @@
 {
 	"name": "poly-devcontainer",
 	// Or use a Dockerfile or Docker Compose file. More info: https://containers.dev/guide/dockerfile
-	"image": "mcr.microsoft.com/devcontainers/base:bullseye",
+	"image": "mcr.microsoft.com/devcontainers/go:1.23-bookworm",
 
-	"features": {
-		"ghcr.io/devcontainers/features/go:1": {
-			"version": "latest",
-			"golangciLintVersion": "latest"
-		},
-	},
-
 	"extensions": ["golang.go"],
 
 	// Use 'forwardPorts' to make a list of ports inside the container available locally.

.golangci.yml

@@ -20,7 +20,6 @@ linters:
     - stylecheck
     - unconvert
     - unparam
-    - whitespace
 linters-settings:
   stylecheck:
     # https://staticcheck.io/docs/options#checks

CHANGELOG.md

@@ -7,6 +7,25 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ## [Unreleased]
 
+### Fixed
+ - Made it possible to simulate primers shorter than design minimum.
+
+## [0.31.1] - 2024-01-31
+
+### Added
+- Fixed package level doc strings for search and bwt packages.
+
+[0.31.1]: https://github.com/TimothyStiles/poly/releases/tag/v0.31.0
+
+## [0.31.0] - 2024-01-31
+
+### Added
+- Basic BWT for sub-sequence count and offset for sequence alignment. Only supports exact matches for now.
+- Moved `BWT`, `align`, and `mash` packages to new `search` sub-directory.
+- Implemented Run-Length Burrows Wheeler Transform.
+
+[0.31.0]: https://github.com/TimothyStiles/poly/releases/tag/v0.31.0
+
 
 ## [0.30.0] - 2023-12-18
 Oops, we weren't keeping a changelog before this tag!

LICENSE

@@ -1,4 +1,4 @@
-Copyright (c) 2023 Timothy Stiles
+Copyright (c) 2024 Timothy Stiles
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal

README.md

@@ -1,4 +1,4 @@
-# (Poly)merase <img align="right" src="https://cdn.discordapp.com/attachments/766785755305213953/777596834734145546/ProfileFrameArtboard_1.png" width="100">
+# (Poly)merase <img align="right" src="https://raw.githubusercontent.com/bebop/presskit/main/gopher.png" width="100">
 
 [![PkgGoDev](https://pkg.go.dev/badge/github.com/bebop/poly)](https://pkg.go.dev/github.com/bebop/poly)
 [![GitHub license](https://img.shields.io/badge/license-MIT-blue.svg)](https://github.com/bebop/poly/blob/main/LICENSE) 
@@ -47,4 +47,4 @@ Poly is a Go package for engineering organisms.
 
 * [MIT](LICENSE)
 
-* Copyright (c) 2023 Timothy Stiles
+* Copyright (c) 2024 Timothy Stiles

fold/fold_test.go

@@ -1,6 +1,7 @@
 package fold
 
 import (
+	"fmt"
 	"math"
 	"strings"
 	"testing"
@@ -201,3 +202,13 @@ func TestFold(t *testing.T) {
 		assert.InDelta(t, struc.energy, -4.2, 0.2)
 	})
 }
+func TestZuker_ErrorCreatingFoldingContext(t *testing.T) {
+	seq := "ATGGATTTAGATAGATADFQ#(RSDOFIA)"
+	temp := 4000.0
+
+	expectedErr := fmt.Errorf("error creating folding context: the sequence ATGGATTTAGATAGATADFQ#(RSDOFIA) is not RNA or DNA")
+
+	_, err := Zuker(seq, temp)
+	require.Error(t, err)
+	assert.Equal(t, expectedErr.Error(), err.Error())
+}

fold/seqfold_test.go

@@ -0,0 +1,43 @@
+package fold
+
+import (
+	"fmt"
+	"math"
+	"testing"
+)
+
+func TestResult_MinimumFreeEnergy_LengthZero(t *testing.T) {
+	result := Result{} // Create a Result instance with empty structs
+
+	expectedEnergy := math.Inf(1)
+	actualEnergy := result.MinimumFreeEnergy()
+
+	if actualEnergy != expectedEnergy {
+		t.Errorf("expected energy to be %f, but got %f", expectedEnergy, actualEnergy)
+	}
+}
+
+func TestResult_DotBracket_LengthZero(t *testing.T) {
+	result := Result{} // Create a Result instance with empty structs
+
+	expectedDotBracket := ""
+	actualDotBracket := result.DotBracket()
+
+	if actualDotBracket != expectedDotBracket {
+		t.Errorf("expected dot bracket to be %s, but got %s", expectedDotBracket, actualDotBracket)
+	}
+}
+
+func TestNewFoldingContext_InvalidSequence(t *testing.T) {
+	seq := "XYZ"
+	temp := 37.0
+
+	_, err := newFoldingContext(seq, temp)
+	if err == nil {
+		t.Errorf("expected error, but got nil")
+	}
+	expectedError := fmt.Errorf("the sequence %s is not RNA or DNA", seq)
+	if err.Error() != expectedError.Error() {
+		t.Errorf("expected error message to be %q, but got %q", expectedError.Error(), err.Error())
+	}
+}