sync hamming (#569)

Author: keiravillekode

exercises/practice/hamming/.docs/instructions.md

@@ -1,26 +1,15 @@
 # Instructions
 
-Calculate the Hamming Distance between two DNA strands.
+Calculate the Hamming distance between two DNA strands.
 
-Your body is made up of cells that contain DNA.
-Those cells regularly wear out and need replacing, which they achieve by dividing into daughter cells.
-In fact, the average human body experiences about 10 quadrillion cell divisions in a lifetime!
-
-When cells divide, their DNA replicates too.
-Sometimes during this process mistakes happen and single pieces of DNA get encoded with the incorrect information.
-If we compare two strands of DNA and count the differences between them we can see how many mistakes occurred.
-This is known as the "Hamming Distance".
-
-We read DNA using the letters C,A,G and T.
+We read DNA using the letters C, A, G and T.
 Two strands might look like this:
 
     GAGCCTACTAACGGGAT
     CATCGTAATGACGGCCT
     ^ ^ ^  ^ ^    ^^
 
-They have 7 differences, and therefore the Hamming Distance is 7.
-
-The Hamming Distance is useful for lots of things in science, not just biology, so it's a nice phrase to be familiar with :)
+They have 7 differences, and therefore the Hamming distance is 7.
 
 ## Implementation notes
 

exercises/practice/hamming/.docs/introduction.md

@@ -0,0 +1,12 @@
+# Introduction
+
+Your body is made up of cells that contain DNA.
+Those cells regularly wear out and need replacing, which they achieve by dividing into daughter cells.
+In fact, the average human body experiences about 10 quadrillion cell divisions in a lifetime!
+
+When cells divide, their DNA replicates too.
+Sometimes during this process mistakes happen and single pieces of DNA get encoded with the incorrect information.
+If we compare two strands of DNA and count the differences between them, we can see how many mistakes occurred.
+This is known as the "Hamming distance".
+
+The Hamming distance is useful in many areas of science, not just biology, so it's a nice phrase to be familiar with :)

exercises/practice/hamming/.meta/config.json

@@ -20,7 +20,7 @@
       ".meta/example.lua"
     ]
   },
-  "blurb": "Calculate the Hamming difference between two DNA strands.",
+  "blurb": "Calculate the Hamming distance between two DNA strands.",
   "source": "The Calculating Point Mutations problem at Rosalind",
   "source_url": "https://rosalind.info/problems/hamm/"
 }

exercises/practice/hamming/.meta/example.lua

@@ -1,9 +1,7 @@
 local Hamming = {}
 
 function Hamming.compute(a, b)
-  if #a ~= #b then
-    return -1
-  end
+  assert(#a == #b, 'strands must be of equal length')
   local distance = 0
   for i = 1, a:len() do
     if (a:sub(i, i) ~= b:sub(i, i)) then

exercises/practice/hamming/.meta/spec_generator.lua

@@ -0,0 +1,17 @@
+return {
+  module_name = 'hamming',
+
+  generate_test = function(case)
+    if type(case.expected) == 'number' then
+      local template = [[
+        assert.are.equal(%s, hamming.compute("%s", "%s"))]]
+      return template:format(case.expected, case.input.strand1, case.input.strand2)
+    else
+      local template = [[
+        assert.has_error(function()
+          hamming.compute("%s", "%s")
+        end, "%s")]]
+      return template:format(case.input.strand1, case.input.strand2, case.expected.error)
+    end
+  end
+}

exercises/practice/hamming/.meta/tests.toml

@@ -1,6 +1,13 @@
-# This is an auto-generated file. Regular comments will be removed when this
-# file is regenerated. Regenerating will not touch any manually added keys,
-# so comments can be added in a "comment" key.
+# This is an auto-generated file.
+#
+# Regenerating this file via `configlet sync` will:
+# - Recreate every `description` key/value pair
+# - Recreate every `reimplements` key/value pair, where they exist in problem-specifications
+# - Remove any `include = true` key/value pair (an omitted `include` key implies inclusion)
+# - Preserve any other key/value pair
+#
+# As user-added comments (using the # character) will be removed when this file
+# is regenerated, comments can be added via a `comment` key.
 
 [f6dcb64f-03b0-4b60-81b1-3c9dbf47e887]
 description = "empty strands"
@@ -19,12 +26,42 @@ description = "long different strands"
 
 [919f8ef0-b767-4d1b-8516-6379d07fcb28]
 description = "disallow first strand longer"
+include = false
+
+[b9228bb1-465f-4141-b40f-1f99812de5a8]
+description = "disallow first strand longer"
+reimplements = "919f8ef0-b767-4d1b-8516-6379d07fcb28"
 
 [8a2d4ed0-ead5-4fdd-924d-27c4cf56e60e]
 description = "disallow second strand longer"
+include = false
+
+[dab38838-26bb-4fff-acbe-3b0a9bfeba2d]
+description = "disallow second strand longer"
+reimplements = "8a2d4ed0-ead5-4fdd-924d-27c4cf56e60e"
 
 [5dce058b-28d4-4ca7-aa64-adfe4e17784c]
 description = "disallow left empty strand"
+include = false
+
+[db92e77e-7c72-499d-8fe6-9354d2bfd504]
+description = "disallow left empty strand"
+include = false
+reimplements = "5dce058b-28d4-4ca7-aa64-adfe4e17784c"
+
+[b764d47c-83ff-4de2-ab10-6cfe4b15c0f3]
+description = "disallow empty first strand"
+reimplements = "db92e77e-7c72-499d-8fe6-9354d2bfd504"
 
 [38826d4b-16fb-4639-ac3e-ba027dec8b5f]
 description = "disallow right empty strand"
+include = false
+
+[920cd6e3-18f4-4143-b6b8-74270bb8f8a3]
+description = "disallow right empty strand"
+include = false
+reimplements = "38826d4b-16fb-4639-ac3e-ba027dec8b5f"
+
+[9ab9262f-3521-4191-81f5-0ed184a5aa89]
+description = "disallow empty second strand"
+reimplements = "920cd6e3-18f4-4143-b6b8-74270bb8f8a3"

exercises/practice/hamming/hamming_spec.lua

@@ -1,63 +1,47 @@
-local compute = require('hamming').compute
+local hamming = require('hamming')
 
 describe('hamming', function()
-  it('identical strands', function()
-    assert.are.equal(0, compute('A', 'A'))
-  end)
-
-  it('long identical strands', function()
-    assert.are.equal(0, compute('GGACTGA', 'GGACTGA'))
-  end)
-
-  it('complete distance in single nucleotide strands', function()
-    assert.are.equal(1, compute('A', 'G'))
-  end)
-
-  it('complete distance in small strands', function()
-    assert.are.equal(2, compute('AG', 'CT'))
-  end)
-
-  it('small distance in small strands', function()
-    assert.are.equal(1, compute('AT', 'CT'))
-  end)
-
-  it('small distance', function()
-    assert.are.equal(1, compute('GGACG', 'GGTCG'))
-  end)
-
-  it('small distance in long strands', function()
-    assert.are.equal(2, compute('ACCAGGG', 'ACTATGG'))
+  it('empty strands', function()
+    assert.are.equal(0, hamming.compute("", ""))
   end)
 
-  it('non unique character in first strand', function()
-    assert.are.equal(1, compute('AGA', 'AGG'))
+  it('single letter identical strands', function()
+    assert.are.equal(0, hamming.compute("A", "A"))
   end)
 
-  it('non unique character in second strand', function()
-    assert.are.equal(1, compute('AGG', 'AGA'))
+  it('single letter different strands', function()
+    assert.are.equal(1, hamming.compute("G", "T"))
   end)
 
-  it('same nucleotides in different positions', function()
-    assert.are.equal(2, compute('TAG', 'GAT'))
+  it('long identical strands', function()
+    assert.are.equal(0, hamming.compute("GGACTGAAATCTG", "GGACTGAAATCTG"))
   end)
 
-  it('large distance', function()
-    assert.are.equal(4, compute('GATACA', 'GCATAA'))
+  it('long different strands', function()
+    assert.are.equal(9, hamming.compute("GGACGGATTCTG", "AGGACGGATTCT"))
   end)
 
-  it('large distance in off-by-one strand', function()
-    assert.are.equal(9, compute('GGACGGATTCTG', 'AGGACGGATTCT'))
+  it('disallow first strand longer', function()
+    assert.has_error(function()
+      hamming.compute("AATG", "AAA")
+    end, "strands must be of equal length")
   end)
 
-  it('empty strands', function()
-    assert.are.equal(0, compute('', ''))
+  it('disallow second strand longer', function()
+    assert.has_error(function()
+      hamming.compute("ATA", "AGTG")
+    end, "strands must be of equal length")
   end)
 
-  it('disallow first strand longer', function()
-    assert.are.equal(-1, compute('AATG', 'AAA'))
+  it('disallow empty first strand', function()
+    assert.has_error(function()
+      hamming.compute("", "G")
+    end, "strands must be of equal length")
   end)
 
-  it('disallow second strand longer', function()
-    assert.are.equal(-1, compute('ATA', 'AGTG'))
+  it('disallow empty second strand', function()
+    assert.has_error(function()
+      hamming.compute("G", "")
+    end, "strands must be of equal length")
   end)
 end)