GH-49397: [Python] Fix PYARROW_GENERATE_COVERAGE end-to-end flow

- Add pytest_configure hook in conftest.py to activate Cython.Coverage
  plugin before any pyarrow modules are imported
- Complete .coveragerc with source, branch, report and html sections

Closes: #49397

Author: omertt27

python/.coveragerc

@@ -17,3 +17,15 @@
 
 [run]
 plugins = Cython.Coverage
+source =
+    pyarrow
+branch = True
+
+[report]
+omit =
+    */tests/*
+    */benchmarks/*
+show_missing = True
+
+[html]
+directory = coverage_html_report

python/pyarrow/conftest.py

@@ -18,6 +18,27 @@
 import pytest
 
 import os
+def pytest_configure(config):
+    """Activate the Cython coverage plugin when PYARROW_GENERATE_COVERAGE is set.
+
+    This must run before any pyarrow modules are imported so that the
+    Cython line-tracing hooks embedded at build time are picked up by
+    coverage.py.  The flag is set by building pyarrow with
+    PYARROW_GENERATE_COVERAGE=1 (see CMakeLists.txt).
+    """
+    if os.environ.get("PYARROW_GENERATE_COVERAGE"):
+        try:
+            import Cython.Coverage  # noqa: F401
+            import coverage
+            coverage.process_startup()
+        except ImportError as e:
+            import warnings
+            warnings.warn(
+                f"PYARROW_GENERATE_COVERAGE is set but required package "
+                f"is not available: {e}. Install it with: "
+                f"pip install coverage Cython",
+                stacklevel=1,
+            )
 import pyarrow as pa
 from pyarrow import Codec
 from pyarrow import fs