Fix CI

paulsengroup · Nov 13, 2024 · 098f3e3 · 098f3e3
1 parent 1f145db
commit 098f3e3
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Showing 3 changed files with 13 additions and 22 deletions.
diff --git a/.github/workflows/codecov.yml b/.github/workflows/codecov.yml
@@ -127,15 +127,6 @@ jobs:
 
           cmake -DCMAKE_BUILD_TYPE=RelWithDebInfo             \
                 -DCMAKE_PREFIX_PATH="$PWD/conan-env"          \
-                -DENABLE_DEVELOPER_MODE=ON                    \
-                -DOPT_ENABLE_INTERPROCEDURAL_OPTIMIZATION=OFF \
-                -DOPT_ENABLE_SANITIZER_ADDRESS=OFF            \
-                -DOPT_ENABLE_SANITIZER_LEAK=OFF               \
-                -DOPT_ENABLE_SANITIZER_POINTER_COMPARE=OFF    \
-                -DOPT_ENABLE_SANITIZER_POINTER_SUBTRACT=OFF   \
-                -DOPT_ENABLE_SANITIZER_UNDEFINED_BEHAVIOR=OFF \
-                -DOPT_ENABLE_CPPCHECK=OFF                     \
-                -DOPT_ENABLE_CLANG_TIDY=OFF                   \
                 -DNCHG_ENABLE_TESTING=ON                      \
                 -DNCHG_DOWNLOAD_TEST_DATASET=OFF              \
                 -DCMAKE_C_FLAGS="$cov_flags"                  \
@@ -385,7 +376,7 @@ jobs:
 
           sudo -u devel                                        \
           -E env "LLVM_PROFILE_FILE=$LLVM_PROFILE_FILE"        \
-          build/src/NCHG cartesian-product                     \
+          build/src/nchg/NCHG cartesian-product                \
             test/data/ENCFF447ERX.1000000.compartments.bed     \
             > "$OUT_PREFIX.bedpe"
 
@@ -401,7 +392,7 @@ jobs:
 
           sudo -u devel                                        \
           -E env "LLVM_PROFILE_FILE=$LLVM_PROFILE_FILE"        \
-          build/src/NCHG cartesian-product                     \
+          build/src/nchg/NCHG cartesian-product                \
             --cis-only                                         \
             test/data/ENCFF447ERX.1000000.compartments.bed     \
             > domains.bedpe
@@ -418,8 +409,8 @@ jobs:
 
           sudo -u devel                                        \
           -E env "LLVM_PROFILE_FILE=$LLVM_PROFILE_FILE"        \
-          build/src/NCHG cartesian-product                     \
-            --cis-only                                         \
+          build/src/nchg/NCHG cartesian-product                \
+            --trans-only                                       \
             test/data/ENCFF447ERX.1000000.compartments.bed     \
             > domains.bedpe
 
@@ -435,9 +426,9 @@ jobs:
 
           sudo -u devel                                        \
           -E env "LLVM_PROFILE_FILE=$LLVM_PROFILE_FILE"        \
-          build/src/NCHG cartesian-product                     \
+          build/src/nchg/NCHG cartesian-product                \
             --chrom1 chr1                                      \
-            --chrom1 chr3                                      \
+            --chrom2 chr3                                      \
             test/data/ENCFF447ERX.1000000.compartments.bed     \
             > domains.bedpe
 
@@ -492,7 +483,7 @@ jobs:
             test/data/ENCFF447ERX.1000000.cool                 \
             "$OUT_PREFIX"                                      \
             --threads "$(nproc)"                               \
-            --domains test/data/ENCFF447ERX.1000000.compartments.bed
+            --domains "$DATA_DIR/cartesian_product/$OUT_PREFIX.gw-domains.bedpe"
 
           test/scripts/validate_nchg_output.py compute \
             "$OUT_PREFIX"                              \

diff --git a/.github/workflows/macos-ci.yml b/.github/workflows/macos-ci.yml
@@ -483,7 +483,7 @@ jobs:
       - name: Test NCHG cartesian-product (trans)
         run: |
           bin/NCHG cartesian-product                           \
-            --cis-only                                         \
+            --trans-only                                       \
             test/data/ENCFF447ERX.1000000.compartments.bed     \
             > domains.bedpe
 
@@ -497,7 +497,7 @@ jobs:
         run: |
           bin/NCHG cartesian-product                           \
             --chrom1 chr1                                      \
-            --chrom1 chr3                                      \
+            --chrom2 chr3                                      \
             test/data/ENCFF447ERX.1000000.compartments.bed     \
             > domains.bedpe
 
@@ -540,7 +540,7 @@ jobs:
             test/data/ENCFF447ERX.1000000.cool                 \
             "$OUT_PREFIX"                                      \
             --threads "$NPROC"                               \
-            --domains test/data/ENCFF447ERX.1000000.compartments.bed
+            --domains "$DATA_DIR/cartesian_product/$OUT_PREFIX.gw-domains.bedpe"
 
           test/scripts/validate_nchg_output.py compute \
             "$OUT_PREFIX"                              \

diff --git a/.github/workflows/ubuntu-ci.yml b/.github/workflows/ubuntu-ci.yml
@@ -530,7 +530,7 @@ jobs:
         run: |
           sudo -u devel                                        \
           bin/NCHG cartesian-product                           \
-            --cis-only                                         \
+            --trans-only                                       \
             test/data/ENCFF447ERX.1000000.compartments.bed     \
             > domains.bedpe
 
@@ -545,7 +545,7 @@ jobs:
           sudo -u devel                                        \
           bin/NCHG cartesian-product                           \
             --chrom1 chr1                                      \
-            --chrom1 chr3                                      \
+            --chrom2 chr3                                      \
             test/data/ENCFF447ERX.1000000.compartments.bed     \
             > domains.bedpe
 
@@ -591,7 +591,7 @@ jobs:
             test/data/ENCFF447ERX.1000000.cool                 \
             "$OUT_PREFIX"                                      \
             --threads "$(nproc)"                               \
-            --domains test/data/ENCFF447ERX.1000000.compartments.bed
+            --domains "$DATA_DIR/cartesian_product/$OUT_PREFIX.gw-domains.bedpe"
 
           test/scripts/validate_nchg_output.py compute \
             "$OUT_PREFIX"                              \