Merge pull request #23 from clara-genomics/cga_to_claragenomics_namec…

…hange cga to claragenomics namechange
NVIDIA-Genomics-Research · Jul 2, 2019 · 6dc3061 · 6dc3061
2 parents 9749d2c + a90fdd8
commit 6dc3061
Show file tree

Hide file tree

Showing 86 changed files with 197 additions and 197 deletions.
diff --git a/ci/common/test-pycga.sh → ci/common/test-pyclaragenomics.sh b/ci/common/test-pycga.sh → ci/common/test-pyclaragenomics.sh
diff --git a/ci/cpu/build.sh b/ci/cpu/build.sh
@@ -44,10 +44,10 @@ logger "Build SDK..."
 source ci/common/build-test-sdk.sh ${WORKSPACE} ${CMAKE_COMMON_VARIABLES} ${PARALLEL_LEVEL} 0
 
 ################################################################################
-# Pycga tests
+# Pyclaragenomics tests
 ################################################################################
 
 cd ${WORKSPACE}
 if [ "${TEST_PYCLARAGENOMICSANALYSIS}" == '1' ]; then
-    source ci/common/test-pycga.sh $WORKSPACE/pycga
+    source ci/common/test-pyclaragenomics.sh $WORKSPACE/pyclaragenomics
 fi
diff --git a/common/cudautils/include/cudautils/cudautils.hpp b/common/cudautils/include/cudautils/cudautils.hpp
@@ -21,14 +21,14 @@
 /// \ingroup cudautils
 /// \def CGA_CU_CHECK_ERR
 /// \brief Log on CUDA error in enclosed expression
-#define CGA_CU_CHECK_ERR(ans)                                 \
-    {                                                         \
-        cga::cudautils::gpuAssert((ans), __FILE__, __LINE__); \
+#define CGA_CU_CHECK_ERR(ans)                                           \
+    {                                                                   \
+        claragenomics::cudautils::gpuAssert((ans), __FILE__, __LINE__); \
     }
 
 /// \}
 
-namespace cga
+namespace claragenomics
 {
 
 namespace cudautils
@@ -63,4 +63,4 @@ inline void gpuAssert(cudaError_t code, const char* file, int line, bool abort =
 
 } // namespace cudautils
 
-} // namespace cga
+} // namespace claragenomics
diff --git a/common/logging/include/logging/logging.hpp b/common/logging/include/logging/logging.hpp
@@ -71,7 +71,7 @@
 // MUST come after the defines of the logging level!
 #include <spdlog/spdlog.h>
 
-namespace cga
+namespace claragenomics
 {
 namespace logging
 {
@@ -134,6 +134,6 @@ LoggingStatus SetHeader(bool logTime, bool logLocation);
 #define CGA_LOG_CRITICAL(...) SPDLOG_CRITICAL(__VA_ARGS__)
 
 } // namespace logging
-} // namespace cga
+} // namespace claragenomics
 
 /// \}
diff --git a/common/logging/src/logging.cpp b/common/logging/src/logging.cpp
@@ -13,7 +13,7 @@
 #include <spdlog/sinks/basic_file_sink.h>
 #include <spdlog/sinks/stdout_sinks.h>
 
-namespace cga
+namespace claragenomics
 {
 namespace logging
 {
@@ -78,4 +78,4 @@ LoggingStatus SetHeader(bool logTime, bool logLocation)
     return LoggingStatus::success;
 }
 } // namespace logging
-} // namespace cga
+} // namespace claragenomics
diff --git a/common/utils/include/utils/genomeutils.hpp b/common/utils/include/utils/genomeutils.hpp
@@ -12,7 +12,7 @@
 
 #include <random>
 
-namespace cga
+namespace claragenomics
 {
 
 namespace genomeutils
@@ -92,4 +92,4 @@ inline std::vector<std::string> generate_random_sequences(std::string backbone,
 
 } // namespace genomeutils
 
-} // namespace cga
+} // namespace claragenomics
diff --git a/common/utils/include/utils/signed_integer_utils.hpp b/common/utils/include/utils/signed_integer_utils.hpp
@@ -15,7 +15,7 @@
 #include <stdexcept>
 #include <type_traits>
 
-namespace cga
+namespace claragenomics
 {
 
 template <class Container>
@@ -36,4 +36,4 @@ T throw_on_negative(T x, const char* message)
     return x;
 }
 
-} // namespace cga
+} // namespace claragenomics
diff --git a/common/utils/include/utils/stringutils.hpp b/common/utils/include/utils/stringutils.hpp
@@ -13,7 +13,7 @@
 #include <string>
 #include <stdint.h>
 
-namespace cga
+namespace claragenomics
 {
 
 namespace stringutils
@@ -33,4 +33,4 @@ inline std::string array_to_string(T* arr, size_t len, std::string delim = "-")
 
 } //namespace stringutils
 
-} // namespace cga
+} // namespace claragenomics
diff --git a/cudaaligner/benchmarks/singlealignment/main.cpp b/cudaaligner/benchmarks/singlealignment/main.cpp
@@ -14,7 +14,7 @@
 #include "cudautils/cudautils.hpp"
 #include "cudaaligner/aligner.hpp"
 
-namespace cga
+namespace claragenomics
 {
 
 namespace cudaaligner
@@ -26,8 +26,8 @@ static void BM_SingleAlignment(benchmark::State& state)
 
     // Generate random sequences
     std::minstd_rand rng(1);
-    std::string genome_1 = cga::genomeutils::generate_random_genome(genome_size, rng);
-    std::string genome_2 = cga::genomeutils::generate_random_genome(genome_size, rng);
+    std::string genome_1 = claragenomics::genomeutils::generate_random_genome(genome_size, rng);
+    std::string genome_2 = claragenomics::genomeutils::generate_random_genome(genome_size, rng);
 
     // Create aligner object
     std::unique_ptr<Aligner> aligner = create_aligner(genome_size,
@@ -53,6 +53,6 @@ BENCHMARK(BM_SingleAlignment)
     ->RangeMultiplier(10)
     ->Range(100, 1000000);
 } // namespace cudaaligner
-} // namespace cga
+} // namespace claragenomics
 
 BENCHMARK_MAIN();
diff --git a/cudaaligner/benchmarks/singlebatchalignment/main.cpp b/cudaaligner/benchmarks/singlebatchalignment/main.cpp
@@ -16,7 +16,7 @@
 #include "cudautils/cudautils.hpp"
 #include "cudaaligner/aligner.hpp"
 
-namespace cga
+namespace claragenomics
 {
 
 namespace cudaaligner
@@ -54,8 +54,8 @@ static void BM_SingleBatchAlignment(benchmark::State& state)
     for (int32_t i = 0; i < alignments_per_batch; i++)
     {
         // TODO: generate genomes with indels as well
-        std::string genome_1 = cga::genomeutils::generate_random_genome(genome_size, rng);
-        std::string genome_2 = cga::genomeutils::generate_random_genome(genome_size, rng);
+        std::string genome_1 = claragenomics::genomeutils::generate_random_genome(genome_size, rng);
+        std::string genome_2 = claragenomics::genomeutils::generate_random_genome(genome_size, rng);
 
         aligner->add_alignment(genome_1.c_str(), genome_1.length(),
                                genome_2.c_str(), genome_2.length());
@@ -76,6 +76,6 @@ BENCHMARK(BM_SingleBatchAlignment)
     ->Ranges({{32, 512}, {500, 10000}});
 
 } // namespace cudaaligner
-} // namespace cga
+} // namespace claragenomics
 
 BENCHMARK_MAIN();
diff --git a/cudaaligner/include/cudaaligner/aligner.hpp b/cudaaligner/include/cudaaligner/aligner.hpp
@@ -17,7 +17,7 @@
 
 #include "cudaaligner/cudaaligner.hpp"
 
-namespace cga
+namespace claragenomics
 {
 
 namespace cudaaligner
@@ -87,4 +87,4 @@ std::unique_ptr<Aligner> create_aligner(int32_t max_query_length, int32_t max_su
 
 /// \}
 } // namespace cudaaligner
-} // namespace cga
+} // namespace claragenomics
diff --git a/cudaaligner/include/cudaaligner/alignment.hpp b/cudaaligner/include/cudaaligner/alignment.hpp
@@ -16,7 +16,7 @@
 
 #include "cudaaligner/cudaaligner.hpp"
 
-namespace cga
+namespace claragenomics
 {
 
 namespace cudaaligner
@@ -69,4 +69,4 @@ class Alignment
 
 /// \}
 } // namespace cudaaligner
-} // namespace cga
+} // namespace claragenomics
diff --git a/cudaaligner/include/cudaaligner/cudaaligner.hpp b/cudaaligner/include/cudaaligner/cudaaligner.hpp
@@ -14,7 +14,7 @@
 /// Base docs for the cudaaligner package (tbd)
 /// \{
 
-namespace cga
+namespace claragenomics
 {
 
 namespace cudaaligner
@@ -48,5 +48,5 @@ enum class AlignmentState
 
 StatusType Init();
 } // namespace cudaaligner
-} // namespace cga
+} // namespace claragenomics
 /// \}
diff --git a/cudaaligner/src/aligner.cpp b/cudaaligner/src/aligner.cpp
@@ -11,7 +11,7 @@
 #include "cudaaligner/aligner.hpp"
 #include "aligner_global.hpp"
 
-namespace cga
+namespace claragenomics
 {
 
 namespace cudaaligner
@@ -29,4 +29,4 @@ std::unique_ptr<Aligner> create_aligner(int32_t max_query_length, int32_t max_su
     }
 }
 } // namespace cudaaligner
-} // namespace cga
+} // namespace claragenomics
diff --git a/cudaaligner/src/aligner_global.cpp b/cudaaligner/src/aligner_global.cpp
@@ -22,7 +22,7 @@
 #include <logging/logging.hpp>
 #include "batched_device_matrices.cuh"
 
-namespace cga
+namespace claragenomics
 {
 
 namespace cudaaligner
@@ -188,4 +188,4 @@ void AlignerGlobal::reset()
     alignments_.clear();
 }
 } // namespace cudaaligner
-} // namespace cga
+} // namespace claragenomics
diff --git a/cudaaligner/src/aligner_global.hpp b/cudaaligner/src/aligner_global.hpp
@@ -15,7 +15,7 @@
 #include "device_storage.cuh"
 #include <thrust/system/cuda/experimental/pinned_allocator.h>
 
-namespace cga
+namespace claragenomics
 {
 
 namespace cudaaligner
@@ -82,4 +82,4 @@ class AlignerGlobal : public Aligner
     int32_t device_id_;
 };
 } // namespace cudaaligner
-} // namespace cga
+} // namespace claragenomics
diff --git a/cudaaligner/src/alignment_impl.cpp b/cudaaligner/src/alignment_impl.cpp
@@ -11,7 +11,7 @@
 #include "alignment_impl.hpp"
 #include <utils/signed_integer_utils.hpp>
 
-namespace cga
+namespace claragenomics
 {
 
 namespace cudaaligner
@@ -105,4 +105,4 @@ FormattedAlignment AlignmentImpl::format_alignment() const
     return output;
 }
 } // namespace cudaaligner
-} // namespace cga
+} // namespace claragenomics
diff --git a/cudaaligner/src/alignment_impl.hpp b/cudaaligner/src/alignment_impl.hpp
@@ -12,7 +12,7 @@
 
 #include "cudaaligner/alignment.hpp"
 
-namespace cga
+namespace claragenomics
 {
 
 namespace cudaaligner
@@ -111,4 +111,4 @@ class AlignmentImpl : public Alignment
     std::string alignment_state_to_cigar_state(AlignmentState) const;
 };
 } // namespace cudaaligner
-} // namespace cga
+} // namespace claragenomics
diff --git a/cudaaligner/src/batched_device_matrices.cuh b/cudaaligner/src/batched_device_matrices.cuh
@@ -16,7 +16,7 @@
 #include "device_storage.cuh"
 #include "matrix_cpu.hpp"
 
-namespace cga
+namespace claragenomics
 {
 namespace cudaaligner
 {
@@ -151,4 +151,4 @@ private:
 };
 
 } // end namespace cudaaligner
-} // end namespace cga
+} // end namespace claragenomics
diff --git a/cudaaligner/src/cudaaligner.cpp b/cudaaligner/src/cudaaligner.cpp
@@ -11,7 +11,7 @@
 #include "cudaaligner/cudaaligner.hpp"
 #include <logging/logging.hpp>
 
-namespace cga
+namespace claragenomics
 {
 
 namespace cudaaligner
@@ -25,4 +25,4 @@ StatusType Init()
     return StatusType::success;
 }
 } // namespace cudaaligner
-} // namespace cga
+} // namespace claragenomics
diff --git a/cudaaligner/src/device_storage.cuh b/cudaaligner/src/device_storage.cuh
@@ -12,7 +12,7 @@
 
 #include <cudautils/cudautils.hpp>
 
-namespace cga
+namespace claragenomics
 {
 
 template <typename T>
@@ -45,4 +45,4 @@ private:
     int32_t device_id_;
 };
 
-} // end namespace cga
+} // end namespace claragenomics
diff --git a/cudaaligner/src/matrix_cpu.hpp b/cudaaligner/src/matrix_cpu.hpp
@@ -13,7 +13,7 @@
 #include <vector>
 #include <cassert>
 
-namespace cga
+namespace claragenomics
 {
 
 namespace cudaaligner
@@ -113,4 +113,4 @@ inline bool operator!=(matrix<T> const& a, matrix<T> const& b)
     return !(a == b);
 }
 } // namespace cudaaligner
-} // namespace cga
+} // namespace claragenomics
diff --git a/cudaaligner/src/needleman_wunsch_cpu.hpp b/cudaaligner/src/needleman_wunsch_cpu.hpp
@@ -16,7 +16,7 @@
 #include <string>
 #include <cassert>
 
-namespace cga
+namespace claragenomics
 {
 
 namespace cudaaligner
@@ -185,4 +185,4 @@ std::vector<int8_t> needleman_wunsch_cpu(std::string const& text, std::string co
 
 } // end namespace nw_cpu
 } // namespace cudaaligner
-} // namespace cga
+} // namespace claragenomics
diff --git a/cudaaligner/src/ukkonen_cpu.hpp b/cudaaligner/src/ukkonen_cpu.hpp
@@ -15,7 +15,7 @@
 #include <limits>
 #include <cassert>
 
-namespace cga
+namespace claragenomics
 {
 
 namespace cudaaligner
@@ -245,4 +245,4 @@ std::vector<int8_t> ukkonen_cpu(std::string const& target, std::string const& qu
 }
 } // namespace nw_cpu
 } // namespace cudaaligner
-} // namespace cga
+} // namespace claragenomics
diff --git a/cudaaligner/src/ukkonen_gpu.cu b/cudaaligner/src/ukkonen_gpu.cu
@@ -18,7 +18,7 @@
 
 #define CGA_UKKONEN_MAX_THREADS_PER_BLOCK 1024
 
-namespace cga
+namespace claragenomics
 {
 namespace cudaaligner
 {
@@ -319,4 +319,4 @@ size_t ukkonen_max_score_matrix_size(int32_t max_query_length, int32_t max_targe
 }
 
 } // end namespace cudaaligner
-} // end namespace cga
+} // end namespace claragenomics