Bump dependencies and switch to conanfile.py

.github/workflows/build-docker-image.yml

@@ -16,7 +16,7 @@ on:
       - "CMakeLists.txt"
       - ".dockerignore"
       - "Dockerfile"
-      - "conanfile.txt"
+      - "conanfile.py"
     tags:
       - 'v*.*.*'
 
@@ -31,7 +31,7 @@ on:
       - "CMakeLists.txt"
       - "Dockerfile"
       - ".dockerignore"
-      - "conanfile.txt"
+      - "conanfile.py"
 
 # https://stackoverflow.com/a/72408109
 concurrency:

.github/workflows/build-portable-binaries-linux.yml

@@ -14,7 +14,7 @@ on:
       - "test/**"
       - "!test/scripts/devel/**"
       - "CMakeLists.txt"
-      - "conanfile.txt"
+      - "conanfile.py"
     tags:
       - 'v*.*.*'
 
@@ -62,7 +62,7 @@ jobs:
 
           os="centos-7"
           compiler="gcc-11"
-          hash="${{ hashFiles('conanfile.txt', '.github/workflows/build-portable-binary-ubuntu.yml') }}"
+          hash="${{ hashFiles('conanfile.py', '.github/workflows/build-portable-binary-ubuntu.yml') }}"
 
           # This can be used by to always update a cache entry (useful e.g. for ccache)
           current_date="$(date '+%s')"
@@ -92,11 +92,11 @@ jobs:
           conan cache clean "*" --source
           conan remove --confirm "*"
 
-      - name: Build conanfile.txt
+      - name: Build conanfile.py
         run: |
           # We need to rebuild b2 to workaround GLIBCXX incompatibilities
           PATH="/opt/rh/devtoolset-11/root/usr/bin/:$PATH" \
-          conan install conanfile.txt              \
+          conan install conanfile.py              \
                --build=missing                     \
                --build="b2*"                       \
                -pr:b="$CONAN_DEFAULT_PROFILE_PATH" \

.github/workflows/macos-ci.yml

@@ -14,7 +14,7 @@ on:
       - "test/**"
       - "!test/scripts/devel/**"
       - "CMakeLists.txt"
-      - "conanfile.txt"
+      - "conanfile.py"
     tags:
       - 'v*.*.*'
 
@@ -27,7 +27,7 @@ on:
       - "test/**"
       - "!test/scripts/devel/**"
       - "CMakeLists.txt"
-      - "conanfile.txt"
+      - "conanfile.py"
 
 # https://stackoverflow.com/a/72408109
 concurrency:
@@ -114,9 +114,9 @@ jobs:
           compiler="${{ matrix.compiler_name }}"
           build_type="${{ matrix.build_type }}"
 
-          conanfile_hash="${{ hashFiles('conanfile.txt') }}"
+          conanfile_hash="${{ hashFiles('conanfile.py') }}"
           workflow_hash="${{ hashFiles('.github/workflows/macos-ci.yml') }}"
-          combined_hash="${{ hashFiles('conanfile.txt', '.github/workflows/macos-ci.yml') }}"
+          combined_hash="${{ hashFiles('conanfile.py', '.github/workflows/macos-ci.yml') }}"
 
           # This can be used by to always update a cache entry (useful e.g. for ccache)
           current_date="$(date '+%s')"
@@ -150,9 +150,9 @@ jobs:
           conan cache clean "*" --source
           conan remove --confirm "*"
 
-      - name: Build conanfile.txt
+      - name: Build conanfile.py
         run: |
-          conan install conanfile.txt                 \
+          conan install conanfile.py                 \
                --build=missing                        \
                -pr default                            \
                -s build_type=${{ matrix.build_type }} \

.github/workflows/ubuntu-ci.yml

@@ -14,7 +14,7 @@ on:
       - "test/**"
       - "!test/scripts/devel/**"
       - "CMakeLists.txt"
-      - "conanfile.txt"
+      - "conanfile.py"
     tags:
       - 'v*.*.*'
 
@@ -27,7 +27,7 @@ on:
       - "test/**"
       - "!test/scripts/devel/**"
       - "CMakeLists.txt"
-      - "conanfile.txt"
+      - "conanfile.py"
 
 # https://stackoverflow.com/a/72408109
 concurrency:
@@ -182,9 +182,9 @@ jobs:
           generator="${{ matrix.generator }}"
           build_type="${{ matrix.build_type }}"
 
-          conanfile_hash="${{ hashFiles('conanfile.txt') }}"
+          conanfile_hash="${{ hashFiles('conanfile.py') }}"
           workflow_hash="${{ hashFiles('.github/workflows/ubuntu-ci.yml') }}"
-          combined_hash="${{ hashFiles('conanfile.txt', '.github/workflows/ubuntu-ci.yml') }}"
+          combined_hash="${{ hashFiles('conanfile.py', '.github/workflows/ubuntu-ci.yml') }}"
 
           # This can be used by to always update a cache entry (useful e.g. for ccache)
           current_date="$(date '+%s')"
@@ -214,9 +214,9 @@ jobs:
           conan cache clean "*" --source
           conan remove --confirm "*"
 
-      - name: Build conanfile.txt
+      - name: Build conanfile.py
         run: |
-          conan install conanfile.txt                 \
+          conan install conanfile.py                 \
                --build=missing                        \
                -pr:b="$CONAN_DEFAULT_PROFILE_PATH"    \
                -pr:h="$CONAN_DEFAULT_PROFILE_PATH"    \

CMakeLists.txt

@@ -30,8 +30,8 @@ include(FetchContent)
 # cmake-format: off
 FetchContent_Declare(
         _project_options
-        URL ${CMAKE_CURRENT_SOURCE_DIR}/external/project_options-v0.28.0.tar.xz
-        URL_HASH SHA512=216d0970ace00e3176788a2b5abb7b92490c005111d26365e7807a5e86c6323e38b33e2e5b01f4ee43438a8f8e96cacf16cedc6f905a7e0ad58752905b260b38
+        URL ${CMAKE_CURRENT_SOURCE_DIR}/external/project_options-v0.33.0.tar.xz
+        URL_HASH SHA512=d652ff0b6fe4833dfd340ff9687358e7b39dc85157924a855cfc51079446d249b2ea58713a2dc430dd1b65b459399fd26dddecddbcb1b7f896082987bee46489
 )
 # cmake-format: on
 
@@ -191,7 +191,6 @@ endif()
 target_compile_definitions(
   project_options
   INTERFACE SPDLOG_CLOCK_COARSE
-            SPDLOG_DISABLE_DEFAULT_LOGGER
             SPDLOG_NO_ATOMIC_LEVELS
             SPDLOG_PREVENT_CHILD_FD)
 
@@ -222,6 +221,4 @@ endif()
 
 add_subdirectory(src)
 
-include(cmake/FetchExternalDeps.cmake)
-
 # include(cmake/Packaging.cmake)

Dockerfile

@@ -46,9 +46,9 @@ RUN if [ $(uname -m) != x86_64 ]; then \
     -pr:h="$CONAN_DEFAULT_PROFILE_PATH"; \
 fi
 
-COPY conanfile.txt "$src_dir"
+COPY conanfile.py "$src_dir"
 RUN cd "$build_dir"                                  \
-&& conan install "$src_dir/conanfile.txt"            \
+&& conan install "$src_dir/conanfile.py"             \
                  --build=missing                     \
                  -pr:b="$CONAN_DEFAULT_PROFILE_PATH" \
                  -pr:h="$CONAN_DEFAULT_PROFILE_PATH" \

conanfile.py

@@ -0,0 +1,135 @@
+# Copyright (C) 2024 Roberto Rossini <[email protected]>
+#
+# SPDX-License-Identifier: MIT
+
+from conan import ConanFile
+from conan.tools.build import check_min_cppstd
+
+required_conan_version = ">=1.53.0"
+
+
+class MoDLEConan(ConanFile):
+    name = "modle"
+    description = "High-performance stochastic modeling of DNA loop extrusion interactions."
+    license = "MIT"
+    topics = ("modle", "bioinformatics")
+    homepage = "https://github.com/paulsengroup/modle"
+    url = "https://github.com/paulsengroup/modle"
+    package_type = "application"
+    settings = "os", "arch", "compiler", "build_type"
+
+    options = {
+        "shared": [True, False],
+        "fPIC": [True, False],
+    }
+
+    default_options = {
+        "shared": False,
+        "fPIC": True,
+    }
+
+    generators = "CMakeDeps"
+
+    @property
+    def _min_cppstd(self):
+        return 17
+
+    def requirements(self):
+        self.requires("abseil/20240116.2#932ead913d27bb5087303c2880a7b06d")
+        self.requires("bitflags/1.5.0#626da9d1913161321841f30caf9b994e")
+        self.requires("boost/1.85.0#7926babdab0a9779cc164d0af6c28d5e")
+        self.requires("bshoshany-thread-pool/4.1.0#be1802a8768416a6c9b1393cf0ce5e9c")
+        self.requires("bzip2/1.0.8#457c272f7da34cb9c67456dd217d36c4")
+        self.requires("catch2/3.6.0#819bc5a82c2cb626916fc18ee1dbc45f")
+        self.requires("cli11/2.4.2#1b431bda2fb2cd3efed633899abcd8cc")
+        self.requires("concurrentqueue/1.0.4#1e48e1c712bcfd892087c9c622a51502")
+        self.requires("cpp-sort/1.15.0#a48647a61f03d08b77d15fb5a8bfbe5e")
+        self.requires("fast_float/6.1.1#e29acaa3d0543dee343abe3f6815346e")
+        self.requires("fmt/10.2.1#9199a7a0611866dea5c8849a77467b25")
+        self.requires("hictk/0.0.12#8e413cd45528da38b5a41ccffee41d6d")
+        self.requires("libarchive/3.7.4#db39e5a5cddfd3a1884daaab4b7942fb")
+        self.requires("libbigwig/0.4.7#3f34dc76212124688b984b781e6f853d")
+        self.requires("libcuckoo/0.3.1#7e514d4c23a9aba3d8d80758824e9dc0")
+        self.requires("lz4/1.9.4#1217a03c990b79aa34ed0faede18f534")
+        self.requires("lzo/2.10#5725914235423c771cb1c6b607109b45")
+        self.requires("range-v3/0.12.0#4c05d91d7b40e6b91b44b5345ac64408")
+        self.requires("readerwriterqueue/1.0.6#aaa5ff6fac60c2aee591e9e51b063b83")
+        self.requires("spdlog/1.14.1#972bbf70be1da4bc57ea589af0efde03", force=True)
+        self.requires("tomlplusplus/3.4.0#92c93d4de6b0a6a2d0ae9b4430e09c9b")
+        self.requires("xoshiro-cpp/1.1#20f566efb3e2bf6e1b813d4abfc5e62c")
+        self.requires("xxhash/0.8.2#03fd1c9a839b3f9cdf5ea9742c312187")
+        self.requires("xz_utils/5.4.5#51e5a6e6564f4ea3afd79def01f035ad", force=True)
+        self.requires("zlib/1.3.1#f52e03ae3d251dec704634230cd806a2")
+        self.requires("zstd/1.5.6#afefe79a309bc2a7b9f56c2093504c8b", force=True)
+
+    def validate(self):
+        if self.settings.get_safe("compiler.cppstd"):
+            check_min_cppstd(self, self._min_cppstd)
+
+    def configure(self):
+        if self.settings.compiler in ["clang", "gcc"]:
+            self.settings.compiler.libcxx = "libstdc++11"
+
+        self.options["boost"].system_no_deprecated = True
+        self.options["boost"].asio_no_deprecated = True
+        self.options["boost"].filesystem_no_deprecated = True
+        self.options["boost"].filesystem_version = 4
+        self.options["boost"].zlib = True
+        self.options["boost"].bzip2 = True
+        self.options["boost"].lzma = True
+        self.options["boost"].zstd = True
+        self.options["boost"].without_atomic = False
+        self.options["boost"].without_charconv = True
+        self.options["boost"].without_chrono = True
+        self.options["boost"].without_container = True
+        self.options["boost"].without_context = True
+        self.options["boost"].without_contract = True
+        self.options["boost"].without_coroutine = True
+        self.options["boost"].without_date_time = True
+        self.options["boost"].without_exception = False
+        self.options["boost"].without_fiber = True
+        self.options["boost"].without_filesystem = False
+        self.options["boost"].without_graph = True
+        self.options["boost"].without_graph_parallel = True
+        self.options["boost"].without_iostreams = False
+        self.options["boost"].without_json = True
+        self.options["boost"].without_locale = True
+        self.options["boost"].without_log = True
+        self.options["boost"].without_math = False
+        self.options["boost"].without_mpi = True
+        self.options["boost"].without_nowide = True
+        self.options["boost"].without_program_options = True
+        self.options["boost"].without_python = True
+        self.options["boost"].without_random = False
+        self.options["boost"].without_regex = False
+        self.options["boost"].without_serialization = False
+        self.options["boost"].without_stacktrace = True
+        self.options["boost"].without_system = False
+        self.options["boost"].without_test = True
+        self.options["boost"].without_thread = True
+        self.options["boost"].without_timer = True
+        self.options["boost"].without_type_erasure = True
+        self.options["boost"].without_url = True
+        self.options["boost"].without_wave = True
+        self.options["bzip2"].enable_executable = True
+        self.options["fmt"].header_only = True
+        self.options["hdf5"].enable_cxx = False
+        self.options["hdf5"].hl = False
+        self.options["hdf5"].threadsafe = False
+        self.options["hdf5"].parallel = False
+        # self.options["hictk"].with_arrow = False
+        self.options["hictk"].with_eigen = False
+        self.options["highfive"].with_boost = False
+        self.options["highfive"].with_eigen = False
+        self.options["highfive"].with_opencv = False
+        self.options["highfive"].with_xtensor = False
+        self.options["libarchive"].with_zlib = True
+        self.options["libarchive"].with_bzip2 = True
+        self.options["libarchive"].with_lz4 = True
+        self.options["libarchive"].with_lzo = True
+        self.options["libarchive"].with_lzma = True
+        self.options["libarchive"].with_zstd = True
+        self.options["libbigwig"].with_curl = False
+        self.options["spdlog"].header_only = True
+        self.options["xxhash"].utility = False
+        self.options["zstd"].build_programs = False