From ef01264cad54058f00b8e930b1d4f050dda59a98 Mon Sep 17 00:00:00 2001
From: Roberto Rossini <71787608+robomics@users.noreply.github.com>
Date: Sat, 26 Oct 2024 17:48:57 +0200
Subject: [PATCH] Suppress C++23 deprecated decl. warnings

Suppress -Wdeprecated-declarations raised due to deprecated usage of
std::aligned_storage inside <parallel_hashmap/phmap.h>
---
 src/hictk/cli/cli_zoomify.cpp                         |  9 ++++++++-
 .../balancing/include/hictk/balancing/weights.hpp     |  5 +++++
 src/libhictk/cooler/include/hictk/cooler/dataset.hpp  | 11 +++++++----
 src/libhictk/cooler/include/hictk/cooler/group.hpp    | 10 +++++++---
 .../include/hictk/cooler/impl/file_accessors_impl.hpp |  9 ++++++++-
 .../include/hictk/expected_values_aggregator.hpp      |  6 ++++++
 src/libhictk/hic/include/hictk/hic/cache.hpp          |  6 ++++++
 src/libhictk/hic/include/hictk/hic/footer_cache.hpp   |  6 ++++++
 src/libhictk/hic/include/hictk/hic/header.hpp         |  6 ++++++
 .../hic/include/hictk/hic/impl/file_reader_impl.hpp   |  9 ++++++++-
 .../hic/include/hictk/hic/impl/file_writer_impl.hpp   |  9 ++++++++-
 .../hic/include/hictk/hic/impl/index_impl.hpp         |  9 ++++++++-
 src/libhictk/hic/include/hictk/hic/index.hpp          |  6 ++++++
 .../include/hictk/hic/interaction_to_block_mapper.hpp |  7 +++++++
 src/libhictk/hic/include/hictk/hic/pixel_selector.hpp |  6 ++++++
 .../reference/include/hictk/impl/reference_impl.hpp   |  9 ++++++++-
 src/libhictk/reference/include/hictk/reference.hpp    |  6 ++++++
 .../include/hictk/transformers/coarsen.hpp            |  6 ++++++
 18 files changed, 122 insertions(+), 13 deletions(-)

diff --git a/src/hictk/cli/cli_zoomify.cpp b/src/hictk/cli/cli_zoomify.cpp
index 5f8dd85f4..490e1b7c0 100644
--- a/src/hictk/cli/cli_zoomify.cpp
+++ b/src/hictk/cli/cli_zoomify.cpp
@@ -2,8 +2,15 @@
 //
 // SPDX-License-Identifier: MIT
 
-#include <fmt/format.h>
+// clang-format off
+#include "hictk/suppress_warnings.hpp"
+HICTK_DISABLE_WARNING_PUSH
+HICTK_DISABLE_WARNING_DEPRECATED_DECLARATIONS
 #include <parallel_hashmap/phmap.h>
+HICTK_DISABLE_WARNING_POP
+// clang-format on
+
+#include <fmt/format.h>
 #include <spdlog/spdlog.h>
 
 #include <algorithm>
diff --git a/src/libhictk/balancing/include/hictk/balancing/weights.hpp b/src/libhictk/balancing/include/hictk/balancing/weights.hpp
index 59329dee4..1f6efa216 100644
--- a/src/libhictk/balancing/include/hictk/balancing/weights.hpp
+++ b/src/libhictk/balancing/include/hictk/balancing/weights.hpp
@@ -4,7 +4,12 @@
 
 #pragma once
 
+// clang-format off
+#include "hictk/suppress_warnings.hpp"
+HICTK_DISABLE_WARNING_PUSH
+HICTK_DISABLE_WARNING_DEPRECATED_DECLARATIONS
 #include <parallel_hashmap/phmap.h>
+HICTK_DISABLE_WARNING_POP
 
 #include <cstddef>
 #include <cstdint>
diff --git a/src/libhictk/cooler/include/hictk/cooler/dataset.hpp b/src/libhictk/cooler/include/hictk/cooler/dataset.hpp
index 1621415bc..a99383a5e 100644
--- a/src/libhictk/cooler/include/hictk/cooler/dataset.hpp
+++ b/src/libhictk/cooler/include/hictk/cooler/dataset.hpp
@@ -8,16 +8,19 @@
 
 // clang-format off
 #include "hictk/suppress_warnings.hpp"
-// clang-format on
-
+HICTK_DISABLE_WARNING_PUSH
+HICTK_DISABLE_WARNING_DEPRECATED_DECLARATIONS
 #include <parallel_hashmap/phmap.h>
+HICTK_DISABLE_WARNING_POP
 
-#include <cstddef>
-#include <cstdint>
 HICTK_DISABLE_WARNING_PUSH
 HICTK_DISABLE_WARNING_NULL_DEREFERENCE
 #include <highfive/H5DataSet.hpp>
 HICTK_DISABLE_WARNING_POP
+// clang-format on
+
+#include <cstddef>
+#include <cstdint>
 #include <highfive/H5DataSpace.hpp>
 #include <highfive/H5DataType.hpp>
 #include <highfive/H5PropertyList.hpp>
diff --git a/src/libhictk/cooler/include/hictk/cooler/group.hpp b/src/libhictk/cooler/include/hictk/cooler/group.hpp
index f78b4ec79..43dfa4db1 100644
--- a/src/libhictk/cooler/include/hictk/cooler/group.hpp
+++ b/src/libhictk/cooler/include/hictk/cooler/group.hpp
@@ -8,15 +8,19 @@
 
 // clang-format off
 #include "hictk/suppress_warnings.hpp"
-// clang-format on
-
-#include <fmt/format.h>
+HICTK_DISABLE_WARNING_PUSH
+HICTK_DISABLE_WARNING_DEPRECATED_DECLARATIONS
 #include <parallel_hashmap/phmap.h>
+HICTK_DISABLE_WARNING_POP
 
 HICTK_DISABLE_WARNING_PUSH
 HICTK_DISABLE_WARNING_NULL_DEREFERENCE
 #include <highfive/H5File.hpp>
 HICTK_DISABLE_WARNING_POP
+// clang-format on
+
+#include <fmt/format.h>
+
 #include <highfive/H5Group.hpp>
 #include <optional>
 #include <string>
diff --git a/src/libhictk/cooler/include/hictk/cooler/impl/file_accessors_impl.hpp b/src/libhictk/cooler/include/hictk/cooler/impl/file_accessors_impl.hpp
index 57e346237..844942ef4 100644
--- a/src/libhictk/cooler/include/hictk/cooler/impl/file_accessors_impl.hpp
+++ b/src/libhictk/cooler/include/hictk/cooler/impl/file_accessors_impl.hpp
@@ -4,8 +4,15 @@
 
 #pragma once
 
-#include <fmt/format.h>
+// clang-format off
+#include "hictk/suppress_warnings.hpp"
+HICTK_DISABLE_WARNING_PUSH
+HICTK_DISABLE_WARNING_DEPRECATED_DECLARATIONS
 #include <parallel_hashmap/phmap.h>
+HICTK_DISABLE_WARNING_POP
+// clang-format on
+
+#include <fmt/format.h>
 
 #include <cassert>
 #include <cstdint>
diff --git a/src/libhictk/expected_values_aggregator/include/hictk/expected_values_aggregator.hpp b/src/libhictk/expected_values_aggregator/include/hictk/expected_values_aggregator.hpp
index 3b69859ff..5851ff25a 100644
--- a/src/libhictk/expected_values_aggregator/include/hictk/expected_values_aggregator.hpp
+++ b/src/libhictk/expected_values_aggregator/include/hictk/expected_values_aggregator.hpp
@@ -4,8 +4,14 @@
 
 #pragma once
 
+// clang-format off
+#include "hictk/suppress_warnings.hpp"
+HICTK_DISABLE_WARNING_PUSH
+HICTK_DISABLE_WARNING_DEPRECATED_DECLARATIONS
 #include <parallel_hashmap/btree.h>
 #include <parallel_hashmap/phmap.h>
+HICTK_DISABLE_WARNING_POP
+// clang-format on
 
 #include <cstddef>
 #include <memory>
diff --git a/src/libhictk/hic/include/hictk/hic/cache.hpp b/src/libhictk/hic/include/hictk/hic/cache.hpp
index beb32444a..4caca2e0c 100644
--- a/src/libhictk/hic/include/hictk/hic/cache.hpp
+++ b/src/libhictk/hic/include/hictk/hic/cache.hpp
@@ -6,7 +6,13 @@
 
 // IWYU pragma: private, include "hictk/hic.hpp"
 
+// clang-format off
+#include "hictk/suppress_warnings.hpp"
+HICTK_DISABLE_WARNING_PUSH
+HICTK_DISABLE_WARNING_DEPRECATED_DECLARATIONS
 #include <parallel_hashmap/phmap.h>
+HICTK_DISABLE_WARNING_POP
+// clang-format on
 
 #include <cstddef>
 #include <cstdint>
diff --git a/src/libhictk/hic/include/hictk/hic/footer_cache.hpp b/src/libhictk/hic/include/hictk/hic/footer_cache.hpp
index c64487d56..dcb7cae19 100644
--- a/src/libhictk/hic/include/hictk/hic/footer_cache.hpp
+++ b/src/libhictk/hic/include/hictk/hic/footer_cache.hpp
@@ -6,7 +6,13 @@
 
 // IWYU pragma: private, include "hictk/hic.hpp"
 
+// clang-format off
+#include "hictk/suppress_warnings.hpp"
+HICTK_DISABLE_WARNING_PUSH
+HICTK_DISABLE_WARNING_DEPRECATED_DECLARATIONS
 #include <parallel_hashmap/phmap.h>
+HICTK_DISABLE_WARNING_POP
+// clang-format on
 
 #include <cstddef>
 #include <memory>
diff --git a/src/libhictk/hic/include/hictk/hic/header.hpp b/src/libhictk/hic/include/hictk/hic/header.hpp
index 67985c09d..43e4a9486 100644
--- a/src/libhictk/hic/include/hictk/hic/header.hpp
+++ b/src/libhictk/hic/include/hictk/hic/header.hpp
@@ -6,7 +6,13 @@
 
 // IWYU pragma: private, include "hictk/hic.hpp"
 
+// clang-format off
+#include "hictk/suppress_warnings.hpp"
+HICTK_DISABLE_WARNING_PUSH
+HICTK_DISABLE_WARNING_DEPRECATED_DECLARATIONS
 #include <parallel_hashmap/phmap.h>
+HICTK_DISABLE_WARNING_POP
+// clang-format on
 
 #include <cstdint>
 #include <string>
diff --git a/src/libhictk/hic/include/hictk/hic/impl/file_reader_impl.hpp b/src/libhictk/hic/include/hictk/hic/impl/file_reader_impl.hpp
index 37d5c3448..8a80cf949 100644
--- a/src/libhictk/hic/include/hictk/hic/impl/file_reader_impl.hpp
+++ b/src/libhictk/hic/include/hictk/hic/impl/file_reader_impl.hpp
@@ -4,10 +4,17 @@
 
 #pragma once
 
+// clang-format off
+#include "hictk/suppress_warnings.hpp"
+HICTK_DISABLE_WARNING_PUSH
+HICTK_DISABLE_WARNING_DEPRECATED_DECLARATIONS
+#include <parallel_hashmap/phmap.h>
+HICTK_DISABLE_WARNING_POP
+// clang-format on
+
 #include <fmt/compile.h>
 #include <fmt/format.h>
 #include <libdeflate.h>
-#include <parallel_hashmap/phmap.h>
 
 #include <algorithm>
 #include <cassert>
diff --git a/src/libhictk/hic/include/hictk/hic/impl/file_writer_impl.hpp b/src/libhictk/hic/include/hictk/hic/impl/file_writer_impl.hpp
index 87c778e15..5ede9ce3f 100644
--- a/src/libhictk/hic/include/hictk/hic/impl/file_writer_impl.hpp
+++ b/src/libhictk/hic/include/hictk/hic/impl/file_writer_impl.hpp
@@ -4,6 +4,14 @@
 
 #pragma once
 
+// clang-format off
+#include "hictk/suppress_warnings.hpp"
+HICTK_DISABLE_WARNING_PUSH
+HICTK_DISABLE_WARNING_DEPRECATED_DECLARATIONS
+#include <parallel_hashmap/phmap.h>
+HICTK_DISABLE_WARNING_POP
+// clang-format on
+
 #if __has_include(<blockingconcurrentqueue.h>)
 #include <blockingconcurrentqueue.h>
 #else
@@ -12,7 +20,6 @@
 #include <fmt/compile.h>
 #include <fmt/format.h>
 #include <libdeflate.h>
-#include <parallel_hashmap/phmap.h>
 #if __has_include(<readerwriterqueue.h>)
 #include <readerwriterqueue.h>
 #else
diff --git a/src/libhictk/hic/include/hictk/hic/impl/index_impl.hpp b/src/libhictk/hic/include/hictk/hic/impl/index_impl.hpp
index b944e64d8..847c1e99f 100644
--- a/src/libhictk/hic/include/hictk/hic/impl/index_impl.hpp
+++ b/src/libhictk/hic/include/hictk/hic/impl/index_impl.hpp
@@ -4,8 +4,15 @@
 
 #pragma once
 
-#include <fmt/format.h>
+// clang-format off
+#include "hictk/suppress_warnings.hpp"
+HICTK_DISABLE_WARNING_PUSH
+HICTK_DISABLE_WARNING_DEPRECATED_DECLARATIONS
 #include <parallel_hashmap/phmap.h>
+HICTK_DISABLE_WARNING_POP
+// clang-format on
+
+#include <fmt/format.h>
 
 #include <algorithm>
 #include <cassert>
diff --git a/src/libhictk/hic/include/hictk/hic/index.hpp b/src/libhictk/hic/include/hictk/hic/index.hpp
index dc8a33768..c3b7c5146 100644
--- a/src/libhictk/hic/include/hictk/hic/index.hpp
+++ b/src/libhictk/hic/include/hictk/hic/index.hpp
@@ -6,7 +6,13 @@
 
 // IWYU pragma: private, include "hictk/hic.hpp"
 
+// clang-format off
+#include "hictk/suppress_warnings.hpp"
+HICTK_DISABLE_WARNING_PUSH
+HICTK_DISABLE_WARNING_DEPRECATED_DECLARATIONS
 #include <parallel_hashmap/phmap.h>
+HICTK_DISABLE_WARNING_POP
+// clang-format on
 
 #include <cstddef>
 #include <cstdint>
diff --git a/src/libhictk/hic/include/hictk/hic/interaction_to_block_mapper.hpp b/src/libhictk/hic/include/hictk/hic/interaction_to_block_mapper.hpp
index d477d8929..fc212fba6 100644
--- a/src/libhictk/hic/include/hictk/hic/interaction_to_block_mapper.hpp
+++ b/src/libhictk/hic/include/hictk/hic/interaction_to_block_mapper.hpp
@@ -6,8 +6,15 @@
 
 // IWYU pragma: private, include "hictk/hic.hpp"
 
+// clang-format off
+#include "hictk/suppress_warnings.hpp"
+HICTK_DISABLE_WARNING_PUSH
+HICTK_DISABLE_WARNING_DEPRECATED_DECLARATIONS
 #include <parallel_hashmap/btree.h>
 #include <parallel_hashmap/phmap.h>
+HICTK_DISABLE_WARNING_POP
+// clang-format on
+
 #if __has_include(<readerwriterqueue.h>)
 #include <readerwriterqueue.h>
 #else
diff --git a/src/libhictk/hic/include/hictk/hic/pixel_selector.hpp b/src/libhictk/hic/include/hictk/hic/pixel_selector.hpp
index 2aeb0fb2a..4a734b120 100644
--- a/src/libhictk/hic/include/hictk/hic/pixel_selector.hpp
+++ b/src/libhictk/hic/include/hictk/hic/pixel_selector.hpp
@@ -6,7 +6,13 @@
 
 // IWYU pragma: private, include "hictk/hic.hpp"
 
+// clang-format off
+#include "hictk/suppress_warnings.hpp"
+HICTK_DISABLE_WARNING_PUSH
+HICTK_DISABLE_WARNING_DEPRECATED_DECLARATIONS
 #include <parallel_hashmap/phmap.h>
+HICTK_DISABLE_WARNING_POP
+// clang-format on
 
 #include <cstddef>
 #include <cstdint>
diff --git a/src/libhictk/reference/include/hictk/impl/reference_impl.hpp b/src/libhictk/reference/include/hictk/impl/reference_impl.hpp
index 4ceec8f41..e6545fa74 100644
--- a/src/libhictk/reference/include/hictk/impl/reference_impl.hpp
+++ b/src/libhictk/reference/include/hictk/impl/reference_impl.hpp
@@ -4,9 +4,16 @@
 
 #pragma once
 
+// clang-format off
+#include "hictk/suppress_warnings.hpp"
+HICTK_DISABLE_WARNING_PUSH
+HICTK_DISABLE_WARNING_DEPRECATED_DECLARATIONS
+#include <parallel_hashmap/phmap.h>
+HICTK_DISABLE_WARNING_POP
+// clang-format on
+
 #include <fmt/format.h>
 #include <fmt/std.h>
-#include <parallel_hashmap/phmap.h>
 
 #include <algorithm>
 #include <cassert>
diff --git a/src/libhictk/reference/include/hictk/reference.hpp b/src/libhictk/reference/include/hictk/reference.hpp
index d157fcd1d..5d9b4f4b1 100644
--- a/src/libhictk/reference/include/hictk/reference.hpp
+++ b/src/libhictk/reference/include/hictk/reference.hpp
@@ -4,7 +4,13 @@
 
 #pragma once
 
+// clang-format off
+#include "hictk/suppress_warnings.hpp"
+HICTK_DISABLE_WARNING_PUSH
+HICTK_DISABLE_WARNING_DEPRECATED_DECLARATIONS
 #include <parallel_hashmap/phmap.h>
+HICTK_DISABLE_WARNING_POP
+// clang-format on
 
 #include <cstddef>
 #include <cstdint>
diff --git a/src/libhictk/transformers/include/hictk/transformers/coarsen.hpp b/src/libhictk/transformers/include/hictk/transformers/coarsen.hpp
index b85727467..423ff53ae 100644
--- a/src/libhictk/transformers/include/hictk/transformers/coarsen.hpp
+++ b/src/libhictk/transformers/include/hictk/transformers/coarsen.hpp
@@ -4,7 +4,13 @@
 
 #pragma once
 
+// clang-format off
+#include "hictk/suppress_warnings.hpp"
+HICTK_DISABLE_WARNING_PUSH
+HICTK_DISABLE_WARNING_DEPRECATED_DECLARATIONS
 #include <parallel_hashmap/phmap.h>
+HICTK_DISABLE_WARNING_POP
+// clang-format on
 
 #include <cstddef>
 #include <cstdint>