Merge pull request #31 from paulsengroup/fix-unit-tests

Various changes to CI and unit tests [ci full]
paulsengroup · Jun 18, 2022 · ad556a9 · ad556a9
2 parents a50b4b6 + 20b40f4
commit ad556a9
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Showing 29 changed files with 486 additions and 550 deletions.
diff --git a/.github/workflows/build-docker-image.yml b/.github/workflows/build-docker-image.yml
@@ -6,7 +6,7 @@ name: Build Docker image
 on:
   create:
     branches-ignore:
-      - "*"
+      - "**"
     tags:
       - 'v*.*.*'
 

diff --git a/.github/workflows/unit-tests-macos.yml b/.github/workflows/unit-tests-macos.yml
@@ -47,9 +47,18 @@ jobs:
     steps:
       - uses: actions/checkout@v3
 
-      - run: |
+      - name: Detect number available CPUs
+        run: |
+          ncpus=$(python -c 'import multiprocessing as mp; print(mp.cpu_count())')
+
+          echo "CMAKE_BUILD_PARALLEL_LEVEL=$ncpus" >> $GITHUB_ENV
+          echo "CTEST_PARALLEL_LEVEL=$ncpus" >> $GITHUB_ENV
+
+      - name: Generate requirements.txt for pip
+        run: |
           echo 'conan==${{ matrix.conan-ver }}' > requirements.txt
           echo 'cmake==${{ matrix.cmake-ver }}' >> requirements.txt
+          echo 'scipy' >> requirements.txt
 
       - uses: actions/setup-python@v4
         with:
@@ -104,19 +113,34 @@ jobs:
                 -B "${{ github.workspace }}/build"
 
       - name: Build project
-        run: cmake --build ${{ github.workspace }}/build -j $(nproc)
+        run: cmake --build ${{ github.workspace }}/build
+
+      - name: Generate R package requirement list
+        run: |
+          printf 'Package: foo\nVersion: 0.0.1\nLicense: MIT\nDescription: foo\n"' >> DESCRIPTION
+          printf 'Title: foo\nAuthor: me\nMaintainer: me\nImports: wCorr' >> DESCRIPTION
+
+      - name: Install setup-r action dependencies
+        run: brew install imagemagick@6 libgit2
+
+      - name: Setup R
+        uses: r-lib/actions/setup-r@v2
+        with:
+          r-version: '4.2.0'
+
+      - name: Install R packages
+        uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          cache: true
 
       - name: Run unit tests
         working-directory: ${{ github.workspace }}/build
         run: |
-          ctest --test-dir .             \
-                --schedule-random        \
-                --output-on-failure      \
-                --no-tests=error         \
-                --timeout 120            \
-                --repeat after-timeout:3 \
-                -E '(SciPy)|(wCorr)'     \
-                -j $(nproc)
+          ctest --test-dir .        \
+                --schedule-random   \
+                --output-on-failure \
+                --no-tests=error    \
+                --timeout 60
 
       - name: Inspect MoDLE version
         run: |

diff --git a/.github/workflows/unit-tests-ubuntu.yml b/.github/workflows/unit-tests-ubuntu.yml
@@ -234,7 +234,6 @@ jobs:
                 --output-on-failure      \
                 --no-tests=error         \
                 --timeout 120            \
-                --repeat after-timeout:3 \
                 -j $(nproc)
 
       - name: Run integration tests
@@ -359,12 +358,11 @@ jobs:
       - name: Run unit tests
         working-directory: ${{ github.workspace }}/build
         run: |
-          ctest --test-dir .             \
-                --schedule-random        \
-                --output-on-failure      \
-                --no-tests=error         \
-                --timeout 120            \
-                --repeat after-timeout:3 \
+          ctest --test-dir .        \
+                --schedule-random   \
+                --output-on-failure \
+                --no-tests=error    \
+                --timeout 60        \
                 -j $(nproc)
 
       - name: Run integration tests

diff --git a/Dockerfile b/Dockerfile
@@ -117,7 +117,6 @@ RUN cd "$src_dir/build"           \
          --output-on-failure      \
          --no-tests=error         \
          --timeout 60             \
-         --repeat after-timeout:3 \
 && rm -rf "$src_dir/test/Testing"
 
 ARG FINAL_BASE_IMAGE

diff --git a/conanfile.py b/conanfile.py
@@ -17,7 +17,7 @@ class MoDLE(ConanFile):
   requires = ["abseil/20211102.0",
               "boost/1.79.0",
               "bzip2/1.0.8",
-              "catch2/2.13.9",
+              "catch2/3.0.1",
               "cli11/2.2.0",
               "concurrentqueue/1.0.3",
               "cpp-sort/1.13.0",

diff --git a/test/CMakeLists.txt b/test/CMakeLists.txt
@@ -16,8 +16,7 @@ add_executable(test_main)
 
 target_sources(
   test_main
-  PRIVATE ${CMAKE_CURRENT_SOURCE_DIR}/test_main.cpp
-          ${CMAKE_CURRENT_SOURCE_DIR}/units/common/cli_utils_test.cpp
+  PRIVATE ${CMAKE_CURRENT_SOURCE_DIR}/units/common/cli_utils_test.cpp
           ${CMAKE_CURRENT_SOURCE_DIR}/units/common/const_map_test.cpp
           ${CMAKE_CURRENT_SOURCE_DIR}/units/common/dna_test.cpp
           ${CMAKE_CURRENT_SOURCE_DIR}/units/contact_matrix/contact_matrix_test.cpp
@@ -32,7 +31,6 @@ target_sources(
           ${CMAKE_CURRENT_SOURCE_DIR}/units/simulation_cpu/simulation_complex_unit_test.cpp
           ${CMAKE_CURRENT_SOURCE_DIR}/units/simulation_cpu/simulation_simple_unit_test.cpp
           ${CMAKE_CURRENT_SOURCE_DIR}/units/simulation_internal/extrusion_barriers_test.cpp
-          ${CMAKE_CURRENT_SOURCE_DIR}/units/stats/common.hpp
           ${CMAKE_CURRENT_SOURCE_DIR}/units/stats/correlation_test.cpp
           ${CMAKE_CURRENT_SOURCE_DIR}/units/stats/correlation_utils_test.cpp
           ${CMAKE_CURRENT_SOURCE_DIR}/units/stats/descriptive_test.cpp
@@ -67,7 +65,7 @@ target_link_system_libraries(
   absl::strings
   Boost::filesystem
   Boost::headers
-  Catch2::Catch2
+  Catch2::Catch2WithMain
   fmt::fmt
   HDF5::HDF5
   spdlog::spdlog
@@ -85,12 +83,8 @@ catch_discover_tests(
   " - SHORT"
   WORKING_DIRECTORY
   ${CMAKE_CURRENT_SOURCE_DIR}/../
-  REPORTER
-  xml
   OUTPUT_DIR
   ${CMAKE_CURRENT_SOURCE_DIR}/Testing/
-  OUTPUT_SUFFIX
-  .xml
   EXTRA_ARGS
   --success)
 
@@ -102,12 +96,8 @@ catch_discover_tests(
   " - MEDIUM"
   WORKING_DIRECTORY
   ${CMAKE_CURRENT_SOURCE_DIR}/../
-  REPORTER
-  xml
   OUTPUT_DIR
   ${CMAKE_CURRENT_SOURCE_DIR}/Testing/
-  OUTPUT_SUFFIX
-  .xml
   EXTRA_ARGS
   --success)
 
@@ -119,7 +109,7 @@ catch_discover_tests(
   " - LONG"
   WORKING_DIRECTORY
   ${CMAKE_CURRENT_SOURCE_DIR}/../
-  REPORTER
-  compact # This dramatically speeds up the test suit
+  OUTPUT_DIR
+  ${CMAKE_CURRENT_SOURCE_DIR}/Testing/
   EXTRA_ARGS
   --success)
diff --git a/test/test_main.cpp b/test/test_main.cpp
diff --git a/test/units/common/cli_utils_test.cpp b/test/units/common/cli_utils_test.cpp
@@ -2,7 +2,7 @@
 //
 // SPDX-License-Identifier: MIT
 
-#include <catch2/catch.hpp>  // for operator""_catch_sr, AssertionHandler
+#include <catch2/catch_test_macros.hpp>
 // clang-format off
 #include "modle/common/suppress_compiler_warnings.hpp"
 DISABLE_WARNING_PUSH

diff --git a/test/units/common/const_map_test.cpp b/test/units/common/const_map_test.cpp
@@ -4,7 +4,7 @@
 
 #include "modle/common/const_map.hpp"
 
-#include <catch2/catch.hpp>
+#include <catch2/catch_test_macros.hpp>
 #include <string_view>
 
 namespace modle::test::utils {

diff --git a/test/units/common/dna_test.cpp b/test/units/common/dna_test.cpp
@@ -4,7 +4,7 @@
 
 #include "modle/common/dna.hpp"
 
-#include <catch2/catch.hpp>
+#include <catch2/catch_test_macros.hpp>
 
 #include "modle/common/common.hpp"
 

diff --git a/test/units/contact_matrix/contact_matrix_test.cpp b/test/units/contact_matrix/contact_matrix_test.cpp
@@ -8,7 +8,9 @@
 #include <algorithm>                                // for generate, max
 #include <boost/dynamic_bitset/dynamic_bitset.hpp>  // for dynamic_bitset, dynamic_bitset<>::ref...
 #include <boost/process.hpp>
-#include <catch2/catch.hpp>             // for operator""_catch_sr, AssertionHandler
+#include <catch2/catch_approx.hpp>
+#include <catch2/catch_test_macros.hpp>
+#include <catch2/matchers/catch_matchers_string.hpp>
 #include <filesystem>                   // for path
 #include <stdexcept>                    // for runtime_error
 #include <string>                       // for string
@@ -171,12 +173,14 @@ TEST_CASE("CMatrix in/decrement", "[cmatrix][short]") {
 
   if constexpr (utils::ndebug_not_defined()) {
     CHECK_THROWS_WITH(m.increment(25, 25),
-                      Catch::Contains("Detected an out-of-bound read: attempt to access item at"));
+                      Catch::Matchers::ContainsSubstring(
+                          "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::Contains("Detected an out-of-bound read: attempt to access item at"));
+                      Catch::Matchers::ContainsSubstring(
+                          "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);
   }
@@ -368,7 +372,7 @@ TEST_CASE("CMatrix blur (SciPy)", "[cmatrix][long]") {
 
     for (usize j = 4; j < input_matrix.nrows(); ++j) {
       for (auto k = j; k < input_matrix.ncols() - 4; ++k) {
-        CHECK(Approx(reference_matrix.get(j, k)) == blurred_matrix.get(j, k));
+        CHECK(Catch::Approx(reference_matrix.get(j, k)) == blurred_matrix.get(j, k));
       }
     }
   }
@@ -408,7 +412,7 @@ TEST_CASE("CMatrix blur parallel (SciPy)", "[cmatrix][long]") {
 
     for (usize j = 4; j < input_matrix.nrows(); ++j) {
       for (auto k = j; k < input_matrix.ncols() - 4; ++k) {
-        CHECK(Approx(reference_matrix.get(j, k)) == blurred_matrix.get(j, k));
+        CHECK(Catch::Approx(reference_matrix.get(j, k)) == blurred_matrix.get(j, k));
       }
     }
   }
@@ -450,8 +454,8 @@ TEST_CASE("CMatrix difference of gaussians (SciPy)", "[cmatrix][long]") {
 
   for (usize j = 4; j < input_matrix.nrows(); ++j) {
     for (auto k = j; k < input_matrix.ncols() - 4; ++k) {
-      CHECK(Approx(reference_matrix.get(j, k)) == gauss_diff_matrix.get(j, k));
-      CHECK(Approx(m1.get(j, k) - m2.get(j, k)) == gauss_diff_matrix.get(j, k));
+      CHECK(Catch::Approx(reference_matrix.get(j, k)) == gauss_diff_matrix.get(j, k));
+      CHECK(Catch::Approx(m1.get(j, k) - m2.get(j, k)) == gauss_diff_matrix.get(j, k));
     }
   }
 }
@@ -496,8 +500,8 @@ TEST_CASE("CMatrix difference of gaussians - parallel (SciPy)", "[cmatrix][long]
 
   for (usize j = 4; j < input_matrix.nrows(); ++j) {
     for (auto k = j; k < input_matrix.ncols() - 4; ++k) {
-      CHECK(Approx(reference_matrix.get(j, k)) == gauss_diff_matrix.get(j, k));
-      CHECK(Approx(m1.get(j, k) - m2.get(j, k)) == gauss_diff_matrix.get(j, k));
+      CHECK(Catch::Approx(reference_matrix.get(j, k)) == gauss_diff_matrix.get(j, k));
+      CHECK(Catch::Approx(m1.get(j, k) - m2.get(j, k)) == gauss_diff_matrix.get(j, k));
     }
   }
 }

diff --git a/test/units/include/modle/test/self_deleting_folder.hpp b/test/units/include/modle/test/self_deleting_folder.hpp
@@ -27,8 +27,6 @@ class SelfDeletingFolder {
       tmpdir = std::filesystem::temp_directory_path();
     } catch (const std::filesystem::filesystem_error& e) {
       // Workaround spurious CI failures due to missing /tmp folder exception
-      assert(absl::StartsWith(e.what(), "std::filesystem::temp_directory_path: Not a directory"));
-      assert(absl::EndsWith(e.what(), "\"/tmp\""));
       tmpdir = "test/data/unit_tests/scratch";
     }
 

diff --git a/test/units/interval_tree/interval_tree_test.cpp b/test/units/interval_tree/interval_tree_test.cpp
@@ -7,12 +7,12 @@
 #include <absl/strings/str_split.h>  // for StrSplit, Splitter, ByAnyChar
 #include <fmt/format.h>              // for format
 
-#include <algorithm>         // for max
-#include <catch2/catch.hpp>  // for AssertionHandler, operator""_catch_sr, SourceLineInfo
-#include <filesystem>        // for path
-#include <string>            // for string, basic_string, operator==
-#include <string_view>       // for string_view
-#include <vector>            // for vector, allocator
+#include <algorithm>  // for max
+#include <catch2/catch_test_macros.hpp>
+#include <filesystem>   // for path
+#include <string>       // for string, basic_string, operator==
+#include <string_view>  // for string_view
+#include <vector>       // for vector, allocator
 
 #include "modle/common/numeric_utils.hpp"         // for parse_numeric_or_throw
 #include "modle/compressed_io/compressed_io.hpp"  // for Reader

diff --git a/test/units/libmodle_io/bed_parser_test.cpp b/test/units/libmodle_io/bed_parser_test.cpp
@@ -5,12 +5,12 @@
 #include <absl/strings/str_split.h>  // for StrSplit, Splitter
 #include <fmt/format.h>              // for to_string
 
-#include <algorithm>         // for sort, max
-#include <catch2/catch.hpp>  // for AssertionHandler, operator""_catch_sr, SourceLineInfo
-#include <filesystem>        // for path
-#include <string>            // for string, basic_string, operator==, char_traits, stoull
-#include <string_view>       // for operator!=, basic_string_view, string_view, operator<
-#include <vector>            // for vector
+#include <algorithm>  // for sort, max
+#include <catch2/catch_test_macros.hpp>
+#include <filesystem>   // for path
+#include <string>       // for string, basic_string, operator==, char_traits, stoull
+#include <string_view>  // for operator!=, basic_string_view, string_view, operator<
+#include <vector>       // for vector
 
 #include "absl/strings/match.h"                   // for StrContains
 #include "modle/bed/bed.hpp"                      // for BED, Parser, formatter<>::format, BED::BED3

diff --git a/test/units/libmodle_io/bed_tree_test.cpp b/test/units/libmodle_io/bed_tree_test.cpp
@@ -6,12 +6,12 @@
 #include <absl/types/span.h>         // for Span
 #include <fmt/format.h>              // for format
 
-#include <algorithm>         // for max, min
-#include <catch2/catch.hpp>  // for AssertionHandler, operator""_catch_sr, SourceLineInfo
-#include <filesystem>        // for path
-#include <string>            // for basic_string, operator==, string
-#include <string_view>       // for string_view
-#include <vector>            // for vector
+#include <algorithm>  // for max, min
+#include <catch2/catch_test_macros.hpp>
+#include <filesystem>   // for path
+#include <string>       // for basic_string, operator==, string
+#include <string_view>  // for string_view
+#include <vector>       // for vector
 
 #include "modle/bed/bed.hpp"        // for BED, BED_tree, BED_tree::contains, BED_tree::count_...
 #include "modle/common/common.hpp"  // for usize, u8

diff --git a/test/units/libmodle_io/compressed_io_test.cpp b/test/units/libmodle_io/compressed_io_test.cpp
@@ -4,11 +4,11 @@
 
 #include "modle/compressed_io/compressed_io.hpp"  // for Reader
 
-#include <catch2/catch.hpp>  // for AssertionHandler, operator""_catch_sr, Source...
-#include <filesystem>        // for path, operator/
-#include <fstream>           // for ifstream, basic_ios, basic_istream, operator<<
-#include <iostream>          // for cerr
-#include <string>            // for operator==, string, basic_string, getline
+#include <catch2/catch_test_macros.hpp>
+#include <filesystem>  // for path, operator/
+#include <fstream>     // for ifstream, basic_ios, basic_istream, operator<<
+#include <iostream>    // for cerr
+#include <string>      // for operator==, string, basic_string, getline
 
 #include "modle/test/self_deleting_folder.hpp"  // for SelfDeletingFolder