Improve coverage (#263)

Switch to using clang's source-based code coverage.
paulsengroup · Sep 30, 2024 · 124d606 · 124d606
1 parent 3c04ff4
commit 124d606
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Showing 14 changed files with 437 additions and 94 deletions.
diff --git a/.github/workflows/codecov.yml b/.github/workflows/codecov.yml
diff --git a/test/integration/src/hictk_integration_suite/runners/hictk/common.py b/test/integration/src/hictk_integration_suite/runners/hictk/common.py
@@ -2,12 +2,17 @@
 #
 # SPDX-License-Identifier: MIT
 
+import os
 import pathlib
 import subprocess as sp
 
 
 def version(hictk: pathlib.Path) -> str:
-    ver = sp.check_output([str(hictk), "--version"], encoding="utf-8").strip()
+    env_variables = os.environ.copy()
+    if "LLVM_PROFILE_FILE" in env_variables:
+        env_variables["LLVM_PROFILE_FILE"] = env_variables["LLVM_PROFILE_FILE"].replace("%id", "%p")
+
+    ver = sp.check_output([str(hictk), "--version"], encoding="utf-8", env=env_variables).strip()
     if ver.startswith("hictk"):
         return ver.removeprefix("hictk-")
 

diff --git a/test/integration/src/hictk_integration_suite/runners/hictk/harness.py b/test/integration/src/hictk_integration_suite/runners/hictk/harness.py
@@ -2,6 +2,7 @@
 #
 # SPDX-License-Identifier: MIT
 
+import os
 import pathlib
 from datetime import timedelta
 from timeit import default_timer as timer
@@ -131,6 +132,14 @@ def run(
         self._args = args
         self._expect_failure = expect_failure
 
+        if env_variables is None:
+            env_variables = os.environ.copy()
+        else:
+            env_variables = dict(env_variables.copy())
+
+        if "LLVM_PROFILE_FILE" in env_variables:
+            env_variables["LLVM_PROFILE_FILE"] = env_variables["LLVM_PROFILE_FILE"].replace("%id", str(id))
+
         t0 = timer()
         self._run_hictk(args, timeout=timeout, env_variables=env_variables, max_attempts=max_attempts)
         t1 = timer()

diff --git a/test/integration/src/hictk_integration_suite/tests/balance.py b/test/integration/src/hictk_integration_suite/tests/balance.py
@@ -3,6 +3,7 @@
 # SPDX-License-Identifier: MIT
 
 import logging
+import os
 import pathlib
 from timeit import default_timer as timer
 from typing import Any, Dict, List
@@ -137,6 +138,14 @@ def run(  # noqa
         self._args = args
         self._expect_failure = expect_failure
 
+        if env_variables is None:
+            env_variables = os.environ.copy()
+        else:
+            env_variables = dict(env_variables.copy())
+
+        if "LLVM_PROFILE_FILE" in env_variables:
+            env_variables["LLVM_PROFILE_FILE"] = env_variables["LLVM_PROFILE_FILE"].replace("%id", str(id))
+
         t0 = timer()
         try:
             self._run_hictk(args, timeout=timeout, env_variables=env_variables, max_attempts=max_attempts)

diff --git a/test/integration/src/hictk_integration_suite/tests/convert.py b/test/integration/src/hictk_integration_suite/tests/convert.py
@@ -2,6 +2,7 @@
 #
 # SPDX-License-Identifier: MIT
 import logging
+import os
 from timeit import default_timer as timer
 from typing import Any, Dict, List
 
@@ -107,6 +108,14 @@ def run(  # noqa
         self._args = args
         self._expect_failure = expect_failure
 
+        if env_variables is None:
+            env_variables = os.environ.copy()
+        else:
+            env_variables = dict(env_variables.copy())
+
+        if "LLVM_PROFILE_FILE" in env_variables:
+            env_variables["LLVM_PROFILE_FILE"] = env_variables["LLVM_PROFILE_FILE"].replace("%id", str(id))
+
         t0 = timer()
         try:
             self._run_hictk(args, timeout=timeout, env_variables=env_variables, max_attempts=max_attempts)

diff --git a/test/integration/src/hictk_integration_suite/tests/dump.py b/test/integration/src/hictk_integration_suite/tests/dump.py
@@ -2,6 +2,7 @@
 #
 # SPDX-License-Identifier: MIT
 import logging
+import os
 from timeit import default_timer as timer
 from typing import Any, Dict, List
 
@@ -138,6 +139,14 @@ def run(  # noqa
         else:
             colnames = None
 
+        if env_variables is None:
+            env_variables = os.environ.copy()
+        else:
+            env_variables = dict(env_variables.copy())
+
+        if "LLVM_PROFILE_FILE" in env_variables:
+            env_variables["LLVM_PROFILE_FILE"] = env_variables["LLVM_PROFILE_FILE"].replace("%id", str(id))
+
         t0 = timer()
         try:
             self._run_hictk(

diff --git a/test/integration/src/hictk_integration_suite/tests/fix_mcool.py b/test/integration/src/hictk_integration_suite/tests/fix_mcool.py
@@ -4,6 +4,7 @@
 
 import json
 import logging
+import os
 import pathlib
 from timeit import default_timer as timer
 from typing import Any, Dict, List
@@ -67,6 +68,14 @@ def run(  # noqa
         self._args = args
         self._expect_failure = expect_failure
 
+        if env_variables is None:
+            env_variables = os.environ.copy()
+        else:
+            env_variables = dict(env_variables.copy())
+
+        if "LLVM_PROFILE_FILE" in env_variables:
+            env_variables["LLVM_PROFILE_FILE"] = env_variables["LLVM_PROFILE_FILE"].replace("%id", str(id))
+
         t0 = timer()
         try:
             self._run_hictk(args, timeout=timeout, env_variables=env_variables, max_attempts=max_attempts)

diff --git a/test/integration/src/hictk_integration_suite/tests/load.py b/test/integration/src/hictk_integration_suite/tests/load.py
@@ -3,6 +3,7 @@
 # SPDX-License-Identifier: MIT
 
 import logging
+import os
 import pathlib
 from timeit import default_timer as timer
 from typing import Any, Dict, List
@@ -78,6 +79,14 @@ def run(  # noqa
         self._args = args
         self._expect_failure = expect_failure
 
+        if env_variables is None:
+            env_variables = os.environ.copy()
+        else:
+            env_variables = dict(env_variables.copy())
+
+        if "LLVM_PROFILE_FILE" in env_variables:
+            env_variables["LLVM_PROFILE_FILE"] = env_variables["LLVM_PROFILE_FILE"].replace("%id", str(id))
+
         t0 = timer()
         try:
             self._run_hictk(args, timeout=timeout, env_variables=env_variables, max_attempts=max_attempts)

diff --git a/test/integration/src/hictk_integration_suite/tests/merge.py b/test/integration/src/hictk_integration_suite/tests/merge.py
@@ -3,6 +3,7 @@
 # SPDX-License-Identifier: MIT
 
 import logging
+import os
 import pathlib
 from timeit import default_timer as timer
 from typing import Any, Dict, List
@@ -91,6 +92,14 @@ def run(  # noqa
         self._args = args
         self._expect_failure = expect_failure
 
+        if env_variables is None:
+            env_variables = os.environ.copy()
+        else:
+            env_variables = dict(env_variables.copy())
+
+        if "LLVM_PROFILE_FILE" in env_variables:
+            env_variables["LLVM_PROFILE_FILE"] = env_variables["LLVM_PROFILE_FILE"].replace("%id", str(id))
+
         t0 = timer()
         try:
             self._run_hictk(args, timeout=timeout, env_variables=env_variables, max_attempts=max_attempts)

diff --git a/test/integration/src/hictk_integration_suite/tests/metadata.py b/test/integration/src/hictk_integration_suite/tests/metadata.py
@@ -4,6 +4,7 @@
 
 import json
 import logging
+import os
 import tomllib
 from timeit import default_timer as timer
 from typing import Any, Dict, List
@@ -123,6 +124,14 @@ def run(  # noqa
         self._args = args
         self._expect_failure = expect_failure
 
+        if env_variables is None:
+            env_variables = os.environ.copy()
+        else:
+            env_variables = dict(env_variables.copy())
+
+        if "LLVM_PROFILE_FILE" in env_variables:
+            env_variables["LLVM_PROFILE_FILE"] = env_variables["LLVM_PROFILE_FILE"].replace("%id", str(id))
+
         t0 = timer()
         try:
             self._run_hictk(args, timeout=timeout, env_variables=env_variables, max_attempts=max_attempts)

diff --git a/test/integration/src/hictk_integration_suite/tests/rename_chromosomes.py b/test/integration/src/hictk_integration_suite/tests/rename_chromosomes.py
@@ -3,6 +3,7 @@
 # SPDX-License-Identifier: MIT
 
 import logging
+import os
 import pathlib
 from timeit import default_timer as timer
 from typing import Any, Dict, List
@@ -146,6 +147,14 @@ def run(  # noqa
         self._args = args
         self._expect_failure = expect_failure
 
+        if env_variables is None:
+            env_variables = os.environ.copy()
+        else:
+            env_variables = dict(env_variables.copy())
+
+        if "LLVM_PROFILE_FILE" in env_variables:
+            env_variables["LLVM_PROFILE_FILE"] = env_variables["LLVM_PROFILE_FILE"].replace("%id", str(id))
+
         t0 = timer()
         try:
             self._run_hictk(args, timeout=timeout, env_variables=env_variables, max_attempts=max_attempts)

diff --git a/test/integration/src/hictk_integration_suite/tests/validate.py b/test/integration/src/hictk_integration_suite/tests/validate.py
@@ -3,6 +3,7 @@
 # SPDX-License-Identifier: MIT
 
 import logging
+import os
 from timeit import default_timer as timer
 from typing import Any, Dict, List
 
@@ -73,6 +74,14 @@ def run(  # noqa
         self._args = args
         self._expect_failure = expect_failure
 
+        if env_variables is None:
+            env_variables = os.environ.copy()
+        else:
+            env_variables = dict(env_variables.copy())
+
+        if "LLVM_PROFILE_FILE" in env_variables:
+            env_variables["LLVM_PROFILE_FILE"] = env_variables["LLVM_PROFILE_FILE"].replace("%id", str(id))
+
         t0 = timer()
         try:
             self._run_hictk(args, timeout=timeout, env_variables=env_variables, max_attempts=max_attempts)

diff --git a/test/integration/src/hictk_integration_suite/tests/zoomify.py b/test/integration/src/hictk_integration_suite/tests/zoomify.py
@@ -3,6 +3,7 @@
 # SPDX-License-Identifier: MIT
 
 import logging
+import os
 import pathlib
 from timeit import default_timer as timer
 from typing import Any, Dict, List
@@ -112,6 +113,14 @@ def run(  # noqa
         self._args = args
         self._expect_failure = expect_failure
 
+        if env_variables is None:
+            env_variables = os.environ.copy()
+        else:
+            env_variables = dict(env_variables.copy())
+
+        if "LLVM_PROFILE_FILE" in env_variables:
+            env_variables["LLVM_PROFILE_FILE"] = env_variables["LLVM_PROFILE_FILE"].replace("%id", str(id))
+
         t0 = timer()
         try:
             self._run_hictk(args, timeout=timeout, env_variables=env_variables, max_attempts=max_attempts)