Merge branch 'release/0.37.0'

* release/0.37.0: (23 commits) Update Changelog Version 0.37.0 Projection base implementation derivatives performance/encapsulation … (#185) atlas_io is an adaptor library when eckit_codec is available (#181) Fix build for configuration setting ATLAS_BITS_LOCAL=64 (#184) Revert "Avoid linker warnings on macOS about 'ld: warning: could not create compact unwind for ...'" Cosmetic: readability braces Initialize std::array values to zero because valgrind complains, even though c++ standard mandates it should be default-initialized to zero Fix bug in TraceT caused by typo where the title was wrong Avoid linker warnings on macOS about 'ld: warning: could not create compact unwind for ...' Use new LocalConfiguration baseclass functions in util::Config and util::Metadata instead of eckit::Value backdoor Removed leftover code missed in PR #175 Update `SphericalVector` to work with StructuredColumns as source functionspace. (#175) Bugfix for regional grids with ny > nx Refactoring of interpolation::method::SphericalVector and implementation of adjoint methods. (#168) Added test with empty integer sequence. Added arrayForEachDim method. Add docs build workflow Github Actions: Fix macOS MPI slots Fix for elements that might have unassigned partition via parallel Delaunay meshgenerator ...
ecmwf · Apr 9, 2024 · 986938e · 986938e
2 parents 24d175a + d6f45e7
commit 986938e
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diff --git a/.github/docs-config.yml b/.github/docs-config.yml
@@ -0,0 +1,14 @@
+# note: each step is executed in own process
+build-steps:
+  - git clone --depth 1 https://github.com/ecmwf/atlas-docs.git $RUNNER_TEMP/atlas-docs
+  - sudo apt install -y -q doxygen texlive-full
+  - | 
+    cd $RUNNER_TEMP/atlas-docs
+    make PUBLIC=1 WITH_ECKIT=1 WITH_DOXYGEN=1 ATLAS_SOURCE_DIR=$GITHUB_WORKSPACE clean html
+    echo "DOC_BUILD_PATH=$RUNNER_TEMP/atlas-docs/build/html" >> "$GITHUB_ENV"
+
+hosts:
+  ecmwf-sites:
+    space: docs
+    name: atlas
+
diff --git a/.github/workflows/docs.yml b/.github/workflows/docs.yml
@@ -0,0 +1,15 @@
+name: docs
+
+on:
+  push:
+    tags:
+      - '**'
+
+  workflow_dispatch: ~
+
+jobs:
+  publish:
+    uses: ecmwf-actions/reusable-workflows/.github/workflows/cd-docs.yml@v2
+    secrets: inherit
+    with:
+      config: .github/docs-config.yml
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -7,6 +7,19 @@ This project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.html
 
 ## [Unreleased]
 
+## [0.37.0] - 2024-04-09
+### Added
+- Add SphericalVector interpolation method using parallel transport (#163)
+- Added arrayForEachDim method
+
+### Fixed
+- Bugfix for regional grids with ny > nx
+- Fix build for configuration setting ATLAS_BITS_LOCAL=64
+
+### Changed
+- Use new LocalConfiguration baseclass functions in util::Config and util::Metadata instead of eckit::Value backdoor
+- atlas_io is an adaptor library when eckit_codec is available (#181)
+
 ## [0.36.0] - 2023-12-11
 ### Added
 - Add TriangularMeshBuilder with Fortran API, so far for serial meshes only
@@ -514,6 +527,7 @@ Fix StructuredInterpolation2D with retry for failed stencils
 ## 0.13.0 - 2018-02-16
 
 [Unreleased]: https://github.com/ecmwf/atlas/compare/master...develop
+[0.37.0]: https://github.com/ecmwf/atlas/compare/0.36.0...0.37.0
 [0.36.0]: https://github.com/ecmwf/atlas/compare/0.35.1...0.36.0
 [0.35.1]: https://github.com/ecmwf/atlas/compare/0.35.0...0.35.1
 [0.35.0]: https://github.com/ecmwf/atlas/compare/0.34.0...0.35.0

diff --git a/VERSION b/VERSION
@@ -1 +1 @@
-0.36.0
+0.37.0
diff --git a/atlas_io/CMakeLists.txt b/atlas_io/CMakeLists.txt
@@ -28,6 +28,20 @@ ecbuild_debug( "   eckit_FEATURES : [${eckit_FEATURES}]" )
 ################################################################################
 # Features that can be enabled / disabled with -DENABLE_<FEATURE>
 
+ecbuild_add_option( FEATURE ECKIT_DEVELOP
+                    DESCRIPTION "Used to enable new features or API depending on eckit develop branch, not yet in a tagged release"
+                    DEFAULT OFF )
+
+set( eckit_HAVE_ECKIT_CODEC 0 )
+if( TARGET eckit_codec )
+  set( eckit_HAVE_ECKIT_CODEC 1 )
+endif()
+
+ecbuild_add_option( FEATURE ECKIT_CODEC
+                    DEFAULT ON
+                    DESCRIPTION "Use eckit::codec with adaptor"
+                    CONDITION eckit_HAVE_ECKIT_CODEC )
+
 ################################################################################
 # sources
 
@@ -47,8 +61,12 @@ else()
   set( ATLAS_IO_LITTLE_ENDIAN 1 )
 endif()
 
-
-add_subdirectory( src )
+if( HAVE_ECKIT_CODEC )
+  ecbuild_info("atlas_io is configured to be an adaptor library which delegates calls to eckit_codec")
+  add_subdirectory(eckit_codec_adaptor)
+else()
+  add_subdirectory( src )
+endif()
 add_subdirectory( tests )
 
 ################################################################################

diff --git a/atlas_io/eckit_codec_adaptor/CMakeLists.txt b/atlas_io/eckit_codec_adaptor/CMakeLists.txt
@@ -0,0 +1 @@
+add_subdirectory(src)
diff --git a/atlas_io/eckit_codec_adaptor/src/CMakeLists.txt b/atlas_io/eckit_codec_adaptor/src/CMakeLists.txt
@@ -0,0 +1,2 @@
+add_subdirectory(atlas_io)
+
diff --git a/atlas_io/eckit_codec_adaptor/src/atlas_io/CMakeLists.txt b/atlas_io/eckit_codec_adaptor/src/atlas_io/CMakeLists.txt
@@ -0,0 +1,19 @@
+
+ecbuild_add_library( TARGET atlas_io
+
+    INSTALL_HEADERS    ALL
+    HEADER_DESTINATION include/atlas_io
+    PUBLIC_LIBS        eckit_codec
+    PUBLIC_INCLUDES
+      $<BUILD_INTERFACE:${PROJECT_SOURCE_DIR}/eckit_codec_adaptor/src>
+
+    SOURCES
+        atlas-io.h
+        Trace.cc
+        Trace.h
+        detail/BlackMagic.h
+    LINKER_LANGUAGE CXX
+)
+
+target_compile_features( atlas_io PUBLIC cxx_std_17 )
+
diff --git a/atlas_io/eckit_codec_adaptor/src/atlas_io/Trace.cc b/atlas_io/eckit_codec_adaptor/src/atlas_io/Trace.cc
@@ -0,0 +1,43 @@
+/*
+ * (C) Copyright 2020 ECMWF.
+ *
+ * This software is licensed under the terms of the Apache Licence Version 2.0
+ * which can be obtained at http://www.apache.org/licenses/LICENSE-2.0.
+ * In applying this licence, ECMWF does not waive the privileges and immunities
+ * granted to it by virtue of its status as an intergovernmental organisation
+ * nor does it submit to any jurisdiction.
+ */
+
+#include "Trace.h"
+
+#include "eckit/log/CodeLocation.h"
+
+namespace atlas {
+namespace io {
+
+atlas::io::Trace::Trace(const eckit::CodeLocation& loc) {
+    for (size_t id = 0; id < TraceHookRegistry::size(); ++id) {
+        if (TraceHookRegistry::enabled(id)) {
+            hooks_.emplace_back(TraceHookRegistry::hook(id)(loc, loc.func()));
+        }
+    }
+}
+
+Trace::Trace(const eckit::CodeLocation& loc, const std::string& title) {
+    for (size_t id = 0; id < TraceHookRegistry::size(); ++id) {
+        if (TraceHookRegistry::enabled(id)) {
+            hooks_.emplace_back(TraceHookRegistry::hook(id)(loc, title));
+        }
+    }
+}
+
+Trace::Trace(const eckit::CodeLocation& loc, const std::string& title, const Labels& labels) {
+    for (size_t id = 0; id < TraceHookRegistry::size(); ++id) {
+        if (TraceHookRegistry::enabled(id)) {
+            hooks_.emplace_back(TraceHookRegistry::hook(id)(loc, title));
+        }
+    }
+}
+
+}  // namespace io
+}  // namespace atlas
diff --git a/atlas_io/eckit_codec_adaptor/src/atlas_io/Trace.h b/atlas_io/eckit_codec_adaptor/src/atlas_io/Trace.h
@@ -0,0 +1,77 @@
+/*
+ * (C) Copyright 2020 ECMWF.
+ *
+ * This software is licensed under the terms of the Apache Licence Version 2.0
+ * which can be obtained at http://www.apache.org/licenses/LICENSE-2.0.
+ * In applying this licence, ECMWF does not waive the privileges and immunities
+ * granted to it by virtue of its status as an intergovernmental organisation
+ * nor does it submit to any jurisdiction.
+ */
+
+#pragma once
+
+
+#include <functional>
+#include <memory>
+#include <string>
+#include <vector>
+#include <limits>
+
+namespace eckit {
+class CodeLocation;
+}
+
+namespace atlas {
+namespace io {
+
+struct TraceHook {
+    TraceHook()          = default;
+    virtual ~TraceHook() = default;
+};
+
+struct TraceHookRegistry {
+    using TraceHookBuilder = std::function<std::unique_ptr<TraceHook>(const eckit::CodeLocation&, const std::string&)>;
+    std::vector<TraceHookBuilder> hooks;
+    std::vector<int> enabled_;
+    static TraceHookRegistry& instance() {
+        static TraceHookRegistry instance;
+        return instance;
+    }
+    static size_t add(TraceHookBuilder&& hook) {
+        instance().hooks.emplace_back(hook);
+        instance().enabled_.emplace_back(true);
+        return instance().hooks.size() - 1;
+    }
+    static size_t add(const TraceHookBuilder& hook) {
+        instance().hooks.emplace_back(hook);
+        instance().enabled_.emplace_back(true);
+        return instance().hooks.size() - 1;
+    }
+    static void enable(size_t id) { instance().enabled_[id] = true; }
+    static void disable(size_t id) { instance().enabled_[id] = false; }
+    static bool enabled(size_t id) { return instance().enabled_[id]; }
+    static size_t size() { return instance().hooks.size(); }
+    static TraceHookBuilder& hook(size_t id) { return instance().hooks[id]; }
+    static size_t invalidId() { return std::numeric_limits<size_t>::max(); }
+
+private:
+    TraceHookRegistry() = default;
+};
+
+struct Trace {
+    using Labels = std::vector<std::string>;
+    Trace(const eckit::CodeLocation& loc);
+    Trace(const eckit::CodeLocation& loc, const std::string& title);
+    Trace(const eckit::CodeLocation& loc, const std::string& title, const Labels& labels);
+
+private:
+    std::vector<std::unique_ptr<TraceHook>> hooks_;
+};
+
+}  // namespace io
+}  // namespace atlas
+
+#include "atlas_io/detail/BlackMagic.h"
+
+#define ATLAS_IO_TRACE(...) __ATLAS_IO_TYPE(::atlas::io::Trace, Here() __ATLAS_IO_COMMA_ARGS(__VA_ARGS__))
+#define ATLAS_IO_TRACE_SCOPE(...) __ATLAS_IO_TYPE_SCOPE(::atlas::io::Trace, Here() __ATLAS_IO_COMMA_ARGS(__VA_ARGS__))
diff --git a/atlas_io/eckit_codec_adaptor/src/atlas_io/atlas-io.h b/atlas_io/eckit_codec_adaptor/src/atlas_io/atlas-io.h
@@ -0,0 +1,99 @@
+/*
+ * (C) Copyright 2023- ECMWF.
+ *
+ * This software is licensed under the terms of the Apache Licence Version 2.0
+ * which can be obtained at http://www.apache.org/licenses/LICENSE-2.0.
+ * In applying this licence, ECMWF does not waive the privileges and immunities
+ * granted to it by virtue of its status as an intergovernmental organisation
+ * nor does it submit to any jurisdiction.
+ */
+
+#pragma once
+
+#include "eckit/codec/codec.h"
+
+namespace atlas::io {
+
+    // Encoding/Decoding
+    using Metadata = ::eckit::codec::Metadata;
+    using DataType = ::eckit::codec::DataType;
+    using Data     = ::eckit::codec::Data;
+    using Encoder  = ::eckit::codec::Encoder;
+    using Decoder  = ::eckit::codec::Decoder;
+
+    // Record
+    using Record           = ::eckit::codec::Record;
+    using RecordWriter     = ::eckit::codec::RecordWriter;
+    using RecordPrinter    = ::eckit::codec::RecordPrinter;
+    using RecordItemReader = ::eckit::codec::RecordItemReader;
+    using RecordReader     = ::eckit::codec::RecordReader;
+
+    // I/O
+    using Session          = ::eckit::codec::Session;
+    using Mode             = ::eckit::codec::Mode;
+    using Stream           = ::eckit::codec::Stream;
+    using FileStream       = ::eckit::codec::FileStream;
+    using InputFileStream  = ::eckit::codec::InputFileStream;
+    using OutputFileStream = ::eckit::codec::OutputFileStream;
+
+    // Array
+    using ArrayReference = ::eckit::codec::ArrayReference;
+    using ArrayMetadata  = ::eckit::codec::ArrayMetadata;
+    using ArrayShape     = ::eckit::codec::ArrayShape;
+
+    // Exceptions
+    using Exception      = ::eckit::codec::Exception;
+    using NotEncodable   = ::eckit::codec::NotEncodable;
+    using NotDecodable   = ::eckit::codec::NotDecodable;
+    using InvalidRecord  = ::eckit::codec::InvalidRecord;
+    using DataCorruption = ::eckit::codec::DataCorruption;
+    using WriteError     = ::eckit::codec::WriteError;
+
+    // Type traits
+    template <class T, class A>
+    static constexpr bool is_interpretable() {
+        return ::eckit::codec::is_interpretable<T,A>();
+    }
+    template <typename T>
+    static constexpr bool is_encodable() {
+        return ::eckit::codec::is_encodable<T>();
+    }
+    template <typename T>
+    static constexpr bool is_decodable() {
+        return ::eckit::codec::is_decodable<T>();
+    }
+    template <typename T>
+    static constexpr bool can_encode_metadata() {
+        return ::eckit::codec::can_encode_metadata<T>();
+    }
+    template <typename T>
+    static constexpr bool can_encode_data() {
+        return ::eckit::codec::can_encode_metadata<T>();
+    }
+
+    namespace tag {
+        using disable_static_assert = ::eckit::codec::tag::disable_static_assert;
+        using enable_static_assert  = ::eckit::codec::tag::enable_static_assert;
+    }
+
+    // Functions
+    using ::eckit::codec::ref;
+    using ::eckit::codec::copy;
+    using ::eckit::codec::encode;
+    using ::eckit::codec::decode;
+    using ::eckit::codec::interprete;
+    using ::eckit::codec::link;
+    using ::eckit::codec::make_datatype;
+    // template <typename DATATYPE>
+    // using make_datatype = eckit::codec::make_datatype<DATATYPE>;
+
+    namespace defaults {
+        using ::eckit::codec::defaults::compression_algorithm;
+        using ::eckit::codec::defaults::checksum_algorithm;
+        using ::eckit::codec::defaults::checksum_read;
+        using ::eckit::codec::defaults::checksum_write;
+    }
+}
+
+#define ATLAS_IO_ASSERT(X) ASSERT(X)
+#define ATLAS_IO_ASSERT_MSG(X, M) ASSERT_MSG(X, M)