[BFX-758] Switch to pbtestutils

PacificBiosciences · Nov 2, 2023 · d0838d6 · d0838d6
1 parent 39c263e
commit d0838d6
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Showing 23 changed files with 17 additions and 1,332 deletions.
diff --git a/.clang-format b/.clang-format
diff --git a/bamboo_build.sh b/bamboo_build.sh
diff --git a/include/pbmm2/MM2Helper.h b/include/pbmm2/MM2Helper.h
@@ -164,7 +164,8 @@ struct CompatMappedRead : public Data::MappedRead
 {
     CompatMappedRead(Data::MappedRead mr, const int32_t refIdArg)
         : Data::MappedRead{std::move(mr)}, refId{refIdArg}
-    {}
+    {
+    }
 
     int32_t refId = 0;
     bool primaryAln = true;
@@ -190,10 +191,12 @@ struct CompatMappedRead : public Data::MappedRead
     void RemoveTag(const char*) const {}
     template <typename... Args>
     void EditTag(const char*, Args...) const
-    {}
+    {
+    }
     template <typename... Args>
     void AddTag(const char*, Args...) const
-    {}
+    {
+    }
 };
 
 struct AlignedRead : public AlignedRecordImpl<CompatMappedRead>

diff --git a/meson.build b/meson.build
@@ -95,12 +95,11 @@ subdir('include')
 subdir('src')
 
 # tests
-if not meson.is_subproject()
-  if get_option('tests')
-    pbmm2_clang_formatter = find_program('tools/check-formatting')
-    pbmm2_cram_script = find_program('scripts/cram')
-    subdir('tests')
-  endif
+if (not meson.is_subproject()) and get_option('tests')
+  pbmm2_pbtestutils_dep = dependency('pbtestutils', fallback : ['pbtestutils', 'pbtestutils_dep'])
+  pbmm2_cram_script = subproject('pbtestutils').get_variable('cram_script')
+
+  subdir('tests')
 endif
 
 # dependency info

diff --git a/scripts/cram b/scripts/cram
diff --git a/src/StreamWriters.cpp b/src/StreamWriters.cpp
@@ -276,7 +276,8 @@ StreamWriters::StreamWriters(BAM::BamHeader& header, const std::string& outPrefi
     , sortThreads_(sortThreads)
     , numThreads_(numThreads)
     , sortMemory_(sortMemory)
-{}
+{
+}
 
 StreamWriter& StreamWriters::at(const std::string& infix, const std::string& sample)
 {

diff --git a/subprojects/pbtestutils.wrap b/subprojects/pbtestutils.wrap
@@ -0,0 +1,4 @@
+[wrap-git]
+directory=pbtestutils
+url=ssh://git@bitbucket.nanofluidics.com:7999/bfx/pbtestutils.git
+revision=develop
diff --git a/tests/meson.build b/tests/meson.build
@@ -1,10 +1,3 @@
-test(
-  'pbmm2 formatting check',
-  pbmm2_clang_formatter,
-  args : [
-    '--all'],
-  workdir : meson.project_source_root())
-
 subdir('unit')
 
 pbmm2_cram_test = [

diff --git a/third-party/cram-0.7/cram/__init__.py b/third-party/cram-0.7/cram/__init__.py
diff --git a/third-party/cram-0.7/cram/__main__.py b/third-party/cram-0.7/cram/__main__.py
diff --git a/third-party/cram-0.7/cram/_cli.py b/third-party/cram-0.7/cram/_cli.py