Prepare v1.0.1 (#103) [ci full]

.github/ISSUE_TEMPLATE/bug.yml

@@ -33,7 +33,7 @@ body:
         Example:
         - modle simulate ...
         - modle_tools transform ...
-        - docker run ghcr.io/paulsengroup/modle:1.0.0 ...
+        - docker run ghcr.io/paulsengroup/modle:1.0.1 ...
     validations:
       required: false
   - type: textarea

.gitignore

@@ -26,3 +26,4 @@ gmon.out
 perf.*
 
 compile_commands.json
+CMakeUserPresets.json

CMakeLists.txt

@@ -80,6 +80,7 @@ include(${CMAKE_CURRENT_SOURCE_DIR}/cmake/CompilerWarnings.cmake)
 
 set(ENABLE_CACHE_DEFAULT ON)
 set(ENABLE_CLANG_TIDY_DEFAULT OFF)
+set(ENABLE_COMPILE_COMMANDS_SYMLINK_DEFAULT OFF)
 set(ENABLE_CONAN_DEFAULT OFF)
 set(ENABLE_CPPCHECK_DEFAULT OFF)
 set(ENABLE_DOXYGEN_USER OFF)
@@ -120,6 +121,8 @@ option(
   "Enable assertions and various other runtime checks (this is done regardless of the type passed to CMAKE_BUILD_TYPE)"
   OFF)
 option(MODLE_DOWNLOAD_TEST_DATASET "Download datasets required by unit and integration tests" ON)
+option(MODLE_ENABLE_TESTING "Build MoDLE's unit tests" ON)
+option(MODLE_ENABLE_GIT_VERSION_TRACKING "Retrieve project version and metadata from git" ON)
 
 target_compile_features(project_options INTERFACE cxx_std_${CMAKE_CXX_STANDARD})
 

cmake/FetchExternalDeps.cmake

@@ -10,8 +10,8 @@ endif()
 # cmake-format: off
 FetchContent_Declare(
         coolerpp
-        GIT_REPOSITORY https://github.com/robomics/coolerpp.git
-        GIT_TAG eef184a7d56a12b0691e8d9cb0437746e7645682
+        URL ${CMAKE_CURRENT_SOURCE_DIR}/external/coolerpp-0b19a5b.tar.xz
+        URL_HASH SHA512=b8df4b89afba941851573033ddf72a5725faadc3476ff4ac9a1d9abb7070d6a503be4bdf91ace0fa0ec9b87239d801d45f0bc6170b284cc21b99f45dda55e507
 )
 # cmake-format: on
 

cmake/Versioning.cmake

@@ -4,11 +4,11 @@
 
 set(MODLE_PROJECT_VERSION_MAJOR 1)
 set(MODLE_PROJECT_VERSION_MINOR 0)
-set(MODLE_PROJECT_VERSION_PATCH 0)
+set(MODLE_PROJECT_VERSION_PATCH 1)
 set(MODLE_PROJECT_VERSION_SUFFIX "")
 
 function(ConfigureVersioning input_config_folder output_config_folder)
-  if(EXISTS "${CMAKE_CURRENT_SOURCE_DIR}/.git")
+  if(MODLE_ENABLE_GIT_VERSION_TRACKING AND EXISTS "${CMAKE_CURRENT_SOURCE_DIR}/.git")
     # cmake-format: off
     FetchContent_Declare(
             _modle_cmake-git-version-tracking
@@ -66,4 +66,4 @@ function(ConfigureVersioning input_config_folder output_config_folder)
   configure_file("${input_config_folder}/version.cpp.in" "${output_config_folder}/version.cpp" @ONLY)
 endfunction()
 
-configureversioning("${CMAKE_CURRENT_SOURCE_DIR}/src/config" "${CMAKE_CURRENT_BINARY_DIR}/src/config")
+ConfigureVersioning("${CMAKE_CURRENT_SOURCE_DIR}/src/config" "${CMAKE_CURRENT_BINARY_DIR}/src/config")

external/checksums.sha512

@@ -1,2 +1,3 @@
 aa339b9fb5f147c5d88341ed4abf85e88b78173714c3a994860aa81f3b558b674829c17a1567d04642ae9df3ce6ed0e88001ba143bb152e91ed7e75bc607a86b  cmake-git-version-tracking.20221027.tar.xz
+b8df4b89afba941851573033ddf72a5725faadc3476ff4ac9a1d9abb7070d6a503be4bdf91ace0fa0ec9b87239d801d45f0bc6170b284cc21b99f45dda55e507  coolerpp-0b19a5b.tar.xz
 216d0970ace00e3176788a2b5abb7b92490c005111d26365e7807a5e86c6323e38b33e2e5b01f4ee43438a8f8e96cacf16cedc6f905a7e0ad58752905b260b38  project_options-v0.28.0.tar.xz

src/modle/cli.cpp

@@ -130,7 +130,8 @@ static std::vector<CLI::App*> add_common_options(CLI::App& subcommand, modle::Co
       "Example: running modle sim -o /tmp/my_simulation ... yields the following files:\n"
       "         - /tmp/my_simulation.cool\n"
       "         - /tmp/my_simulation.log\n"
-      "         - /tmp/my_simulation_config.toml")
+      "         - /tmp/my_simulation_config.toml\n"
+      "         - /tmp/my_simulation_lef_1d_occupancy.bw")
       ->required();
 
   io.add_option(
@@ -588,7 +589,8 @@ static std::vector<CLI::App*> add_common_options(CLI::App& subcommand, modle::Co
 
   // Deprecated options
   deprecated.add_option("--chrom-subranges", c.path_to_genomic_intervals)->check(CLI::ExistingFile);
-  deprecated.get_option("--chrom-subranges")->excludes(io.get_option("--genomic-intervals"));
+  // We do not want this exclusion to show up in the help message
+  // deprecated.get_option("--chrom-subranges")->excludes(io.get_option("--genomic-intervals"));
 
   std::array<std::reference_wrapper<CLI::App>, 10> option_groups{
       io, lefbar, cgen, stopping, misc, io_adv, lef_adv, barr_adv, cgen_adv, burnin_adv};

test/units/contact_matrix/contact_matrix_dense_test.cpp

@@ -108,13 +108,13 @@ TEST_CASE("ContactMatrixDense in/decrement", "[cmatrix][short]") {
   if constexpr (utils::ndebug_not_defined()) {
     CHECK_THROWS_WITH(m.increment(25, 25),
                       Catch::Matchers::ContainsSubstring(
-                          "Detected an out-of-bound read: attempt to access item at"));
+                          "detected an out-of-bound read: attempt to access item at"));
     CHECK(m.get_n_of_missed_updates() == 1);
     CHECK(m.get_tot_contacts() == 1);
 
     CHECK_THROWS_WITH(m.decrement(25, 25),
                       Catch::Matchers::ContainsSubstring(
-                          "Detected an out-of-bound read: attempt to access item at"));
+                          "detected an out-of-bound read: attempt to access item at"));
     CHECK(m.get_n_of_missed_updates() == 1);
     CHECK(m.get_tot_contacts() == 1);
   }

test/units/contact_matrix/contact_matrix_sparse_test.cpp

@@ -47,13 +47,13 @@ TEST_CASE("CMatrixSparse in/decrement", "[cmatrix][short]") {
   if constexpr (utils::ndebug_not_defined()) {
     CHECK_THROWS_WITH(m.increment(25, 25),
                       Catch::Matchers::ContainsSubstring(
-                          "Detected an out-of-bound read: attempt to access item at"));
+                          "detected an out-of-bound read: attempt to access item at"));
     CHECK(m.get_n_of_missed_updates() == 1);
     CHECK(m.get_tot_contacts() == 1);
 
     CHECK_THROWS_WITH(m.decrement(25, 25),
                       Catch::Matchers::ContainsSubstring(
-                          "Detected an out-of-bound read: attempt to access item at"));
+                          "detected an out-of-bound read: attempt to access item at"));
     CHECK(m.get_n_of_missed_updates() == 1);
     CHECK(m.get_tot_contacts() == 1);
   }