[TEST] Update tests

seqan · Sep 25, 2024 · 6a23ffb · 6a23ffb
1 parent 8b8bb49
commit 6a23ffb
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Showing 14 changed files with 686 additions and 848 deletions.
diff --git a/test/api/count_test.cpp b/test/api/count_test.cpp
@@ -5,33 +5,31 @@
 
 #include "ibf.h"
 #include "shared.h"
+#include "../app_test.hpp"
 
-#ifndef DATA_INPUT_DIR
-#  define DATA_INPUT_DIR @DATA_INPUT_DIR@
-#endif
-
-using seqan3::operator""_shape;
-std::filesystem::path tmp_dir = std::filesystem::temp_directory_path(); // get the temp directory
-
-void initialization_args(estimate_ibf_arguments & args)
+// To prevent issues when running multiple CLI tests in parallel, give each CLI test unique names:
+struct count_test : public app_test
 {
-    args.compressed = true;
-    args.k = 4;
-    args.shape = seqan3::ungapped{args.k};
-    args.w_size = seqan3::window_size{4};
-    args.s = seqan3::seed{0};
-    args.path_out = tmp_dir/"Count_Test_";
-}
+    void initialization_args(estimate_ibf_arguments & args)
+    {
+        args.compressed = true;
+        args.k = 4;
+        args.shape = seqan3::ungapped{args.k};
+        args.w_size = seqan3::window_size{4};
+        args.s = seqan3::seed{0};
+        args.path_out = "Count_Test_";
+    }
+};
 
-TEST(count, small_example)
+TEST_F(count_test, small_example)
 {
     estimate_ibf_arguments args{};
     initialization_args(args);
 
-    count(args, {std::string(DATA_INPUT_DIR) + "mini_example.fasta"}, std::string(DATA_INPUT_DIR) + "mini_gen.fasta",
-          std::string(DATA_INPUT_DIR) + "mini_gen.genome", false);
+    count(args, {data("mini_example.fasta")}, data("mini_gen.fasta"),
+          data("mini_gen.genome"), false);
 
-    std::ifstream output_file(tmp_dir/"mini_example.count.out");
+    std::ifstream output_file("mini_example.count.out");
     std::string line;
     std::string expected{"gen1\t3"};
     if (output_file.is_open())
@@ -42,18 +40,17 @@ TEST(count, small_example)
         }
         output_file.close();
     }
-    std::filesystem::remove(tmp_dir/"Count_Test_mini_example.count.out");
 }
 
-TEST(count, small_example_paired)
+TEST_F(count_test, small_example_paired)
 {
     estimate_ibf_arguments args{};
     initialization_args(args);
 
-    count(args, {std::string(DATA_INPUT_DIR) + "mini_example.fasta", std::string(DATA_INPUT_DIR) + "mini_example.fasta"},
-          std::string(DATA_INPUT_DIR) + "mini_gen.fasta", std::string(DATA_INPUT_DIR) + "mini_gen.genome", true);
+    count(args, {data("mini_example.fasta"), data("mini_example.fasta")},
+          data("mini_gen.fasta"), data("mini_gen.genome"), true);
 
-    std::ifstream output_file(tmp_dir/"mini_example.count.out");
+    std::ifstream output_file("mini_example.count.out");
     std::string line;
     std::string expected{"gen1\t6"};
     if (output_file.is_open())
@@ -64,18 +61,17 @@ TEST(count, small_example_paired)
         }
         output_file.close();
     }
-    std::filesystem::remove(tmp_dir/"Count_Test_mini_example.count.out");
 }
 
-TEST(count, small_example_exclude)
+TEST_F(count_test, small_example_exclude)
 {
     estimate_ibf_arguments args{};
     initialization_args(args);
 
-    count(args, {std::string(DATA_INPUT_DIR) + "mini_example.fasta"}, std::string(DATA_INPUT_DIR) + "mini_gen.fasta",
-                 std::string(DATA_INPUT_DIR) + "mini_gen2.genome", false);
+    count(args, {data("mini_example.fasta")}, data("mini_gen.fasta"),
+                 data("mini_gen2.genome"), false);
 
-    std::ifstream output_file(tmp_dir/"mini_example.count.out");
+    std::ifstream output_file("mini_example.count.out");
     std::string line;
     std::string expected{"gen1\t3"};
     if (output_file.is_open())
@@ -86,19 +82,19 @@ TEST(count, small_example_exclude)
         }
         output_file.close();
     }
-    std::filesystem::remove(tmp_dir/"Count_Test_mini_example.count.out");
+
 }
 
-TEST(genome, small_example)
+TEST_F(count_test, genome_small_example)
 {
     estimate_ibf_arguments args{};
     initialization_args(args);
 
-    count_genome(args, std::string(DATA_INPUT_DIR) + "mini_gen.fasta", std::string(DATA_INPUT_DIR) + "mini_gen2.fasta");
+    count_genome(args, data("mini_gen.fasta"), data("mini_gen2.fasta"));
 
     std::ifstream output_file;
     uint64_t expected{192};
-    output_file.open(tmp_dir/"mini_gen.genome", std::ios::binary);
+    output_file.open("mini_gen.genome", std::ios::binary);
     uint64_t minimiser;
     while(output_file.read((char*)&minimiser, sizeof(minimiser)))
     {