diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 0cf1cdae9bf..14cbfcba60e 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -86,7 +86,7 @@ jobs:
       - name: Install changed files test dependencies
         run: dev_tools/conf/pip-install-minimal-for-pytest-changed-files.sh
       - name: Changed files test
-        run: check/pytest-changed-files
+        run: check/pytest-changed-files -n auto
   lint:
     name: Lint check
     runs-on: ubuntu-20.04
@@ -168,7 +168,7 @@ jobs:
       - name: Run Quil dependencies
         run: docker-compose -f cirq-rigetti/docker-compose.test.yaml up -d
       - name: Pytest check
-        run: check/pytest --ignore=cirq-core/cirq/contrib --actually-quiet --rigetti-integration
+        run: check/pytest -n auto --ignore=cirq-core/cirq/contrib --actually-quiet --rigetti-integration
       - name: Stop Quil dependencies
         run: docker-compose -f cirq-rigetti/docker-compose.test.yaml down
   build_docs:
@@ -221,7 +221,7 @@ jobs:
       - name: Run Quil dependencies
         run: docker-compose -f cirq-rigetti/docker-compose.test.yaml up -d
       - name: Coverage check
-        run: check/pytest-and-incremental-coverage --actually-quiet
+        run: check/pytest-and-incremental-coverage -n auto
       - name: Stop Quil dependencies
         run: docker-compose -f cirq-rigetti/docker-compose.test.yaml down
   windows:
@@ -245,7 +245,7 @@ jobs:
       - name: Pytest Windows
         run: |
           source dev_tools/pypath
-          check/pytest --ignore=cirq-core/cirq/contrib --actually-quiet
+          check/pytest -n auto --ignore=cirq-core/cirq/contrib --actually-quiet
         shell: bash
   macos:
     name: Pytest MacOS
@@ -266,7 +266,7 @@ jobs:
       - name: Install requirements
         run: pip install --upgrade --upgrade-strategy eager -r dev_tools/requirements/no-contrib.env.txt
       - name: Pytest check
-        run: check/pytest --ignore=cirq-core/cirq/contrib
+        run: check/pytest -n auto --ignore=cirq-core/cirq/contrib
   notebooks-stable:
     name: Changed Notebooks Isolated Test against Cirq stable
     env:
diff --git a/check/pytest-and-incremental-coverage b/check/pytest-and-incremental-coverage
index b8ace83ebd4..027c2260fa1 100755
--- a/check/pytest-and-incremental-coverage
+++ b/check/pytest-and-incremental-coverage
@@ -4,7 +4,7 @@
 # Finds changed uncovered lines.
 #
 # Usage:
-#     check/pytest-and-incremental-coverage [BASE_REVISION]
+#     check/pytest-and-incremental-coverage [BASE_REVISION] [PYTEST_ARGS]
 #
 # You can specify a base git revision to compare against (i.e. to use when
 # determining whether or not a line is considered to have "changed"). To make
@@ -26,13 +26,30 @@
 cd "$( dirname "${BASH_SOURCE[0]}" )" || exit 1
 cd "$(git rev-parse --show-toplevel)" || exit 1
 
+PYTEST_ARGS=()
+ANALYZE_COV=1
+BASEREV=""
+
+if [[ "$1" == [^-]* ]]; then
+    BASEREV="$1"
+    shift
+fi
+
+for arg in "$@"; do
+    if [[ "${arg}" == "--no-analyze" ]]; then
+        ANALYZE_COV=0
+    else
+        PYTEST_ARGS+=("${arg}")
+    fi
+done
+
 # Figure out which revision to compare against.
-if [ ! -z "$1" ] && [[ $1 != -* ]]; then
-    if [ "$(git cat-file -t $1 2> /dev/null)" != "commit" ]; then
-        echo -e "\033[31mNo revision '$1'.\033[0m" >&2
+if [ -n "${BASEREV}" ]; then
+    if [ "$(git cat-file -t "${BASEREV}" 2> /dev/null)" != "commit" ]; then
+        echo -e "\033[31mNo revision '${BASEREV}'.\033[0m" >&2
         exit 1
     fi
-    rev=$1
+    rev="${BASEREV}"
 elif [ "$(git cat-file -t upstream/master 2> /dev/null)" == "commit" ]; then
     rev=upstream/master
 elif [ "$(git cat-file -t origin/master 2> /dev/null)" == "commit" ]; then
@@ -57,19 +74,27 @@ source dev_tools/pypath
 check/pytest --actually-quiet \
              --rigetti-integration \
              --cov \
-             --cov-report=annotate \
-             --cov-config=dev_tools/conf/.coveragerc
+             --cov-config=dev_tools/conf/.coveragerc \
+             "${PYTEST_ARGS[@]}"
 pytest_result=$?
 
-# Analyze coverage files.
-python dev_tools/check_incremental_coverage_annotations.py "${rev}"
-cover_result=$?
 
-# Clean up generated coverage files.
-find . | grep "\.py,cover$" | xargs rm -f
+# assume succesful cover_result in case coverage is not run
+cover_result=0
+if (( $ANALYZE_COV )); then
+    # Convert to .py,cover files.
+    coverage annotate
+
+    # Analyze coverage files.
+    python dev_tools/check_incremental_coverage_annotations.py "${rev}"
+    cover_result=$?
+
+    # Clean up generated coverage files.
+    git clean --force --quiet -x -- "*.py,cover"
+fi
 
 # Report result.
-if [ "${pytest_result}" -ne "0" ] || [ "${cover_result}" -ne "0" ]; then
-  exit 1
+if (( ${pytest_result} || ${cover_result} )); then
+    exit 1
 fi
 exit 0
diff --git a/check/pytest-changed-files-and-incremental-coverage b/check/pytest-changed-files-and-incremental-coverage
index f4fa9f721ac..200a1fc22a7 100755
--- a/check/pytest-changed-files-and-incremental-coverage
+++ b/check/pytest-changed-files-and-incremental-coverage
@@ -101,7 +101,7 @@ python dev_tools/check_incremental_coverage_annotations.py "${rev}"
 cover_result=$?
 
 # Clean up generated coverage files.
-find . | grep "\.py,cover$" | xargs rm -f
+git clean --force --quiet -x -- "*.py,cover"
 
 # Report result.
 if [ "${pytest_result}" -ne "0" ] || [ "${cover_result}" -ne "0" ]; then
diff --git a/dev_tools/bash_scripts_test.py b/dev_tools/bash_scripts_test.py
index f7dadabc368..c63530d68af 100644
--- a/dev_tools/bash_scripts_test.py
+++ b/dev_tools/bash_scripts_test.py
@@ -351,8 +351,11 @@ def test_pytest_and_incremental_coverage_branch_selection(tmpdir_factory):
     assert result.exit_code == 0
     assert result.out == (
         'INTERCEPTED check/pytest '
-        '--actually-quiet --rigetti-integration --cov --cov-report=annotate '
+        '--actually-quiet --rigetti-integration --cov '
         '--cov-config=dev_tools/conf/.coveragerc\n'
+        'The annotate command will be removed in a future version.\n'
+        'Get in touch if you still use it: ned@nedbatchelder.com\n'
+        'No data to report.\n'
         'INTERCEPTED '
         'python dev_tools/check_incremental_coverage_annotations.py HEAD\n'
     )
@@ -375,10 +378,13 @@ def test_pytest_and_incremental_coverage_branch_selection(tmpdir_factory):
     assert result.exit_code == 0
     assert result.out == (
         'INTERCEPTED check/pytest '
-        '--actually-quiet --rigetti-integration --cov --cov-report=annotate '
+        '--actually-quiet --rigetti-integration --cov '
         '--cov-config=dev_tools/conf/.coveragerc\n'
-        'INTERCEPTED python '
-        'dev_tools/check_incremental_coverage_annotations.py master\n'
+        'The annotate command will be removed in a future version.\n'
+        'Get in touch if you still use it: ned@nedbatchelder.com\n'
+        'No data to report.\n'
+        'INTERCEPTED '
+        'python dev_tools/check_incremental_coverage_annotations.py master\n'
     )
     assert result.err == "Comparing against revision 'master'.\n"
 
@@ -391,10 +397,13 @@ def test_pytest_and_incremental_coverage_branch_selection(tmpdir_factory):
     assert result.exit_code == 0
     assert result.out == (
         'INTERCEPTED check/pytest '
-        '--actually-quiet --rigetti-integration --cov --cov-report=annotate '
+        '--actually-quiet --rigetti-integration --cov '
         '--cov-config=dev_tools/conf/.coveragerc\n'
-        'INTERCEPTED python '
-        'dev_tools/check_incremental_coverage_annotations.py origin/master\n'
+        'The annotate command will be removed in a future version.\n'
+        'Get in touch if you still use it: ned@nedbatchelder.com\n'
+        'No data to report.\n'
+        'INTERCEPTED '
+        'python dev_tools/check_incremental_coverage_annotations.py origin/master\n'
     )
     assert result.err == "Comparing against revision 'origin/master'.\n"
 
@@ -407,10 +416,13 @@ def test_pytest_and_incremental_coverage_branch_selection(tmpdir_factory):
     assert result.exit_code == 0
     assert result.out == (
         'INTERCEPTED check/pytest '
-        '--actually-quiet --rigetti-integration --cov --cov-report=annotate '
+        '--actually-quiet --rigetti-integration --cov '
         '--cov-config=dev_tools/conf/.coveragerc\n'
-        'INTERCEPTED python '
-        'dev_tools/check_incremental_coverage_annotations.py upstream/master\n'
+        'The annotate command will be removed in a future version.\n'
+        'Get in touch if you still use it: ned@nedbatchelder.com\n'
+        'No data to report.\n'
+        'INTERCEPTED '
+        'python dev_tools/check_incremental_coverage_annotations.py upstream/master\n'
     )
     assert result.err == "Comparing against revision 'upstream/master'.\n"
 
@@ -423,10 +435,13 @@ def test_pytest_and_incremental_coverage_branch_selection(tmpdir_factory):
     assert result.exit_code == 0
     assert result.out == (
         'INTERCEPTED check/pytest '
-        '--actually-quiet --rigetti-integration --cov --cov-report=annotate '
+        '--actually-quiet --rigetti-integration --cov '
         '--cov-config=dev_tools/conf/.coveragerc\n'
-        'INTERCEPTED python '
-        'dev_tools/check_incremental_coverage_annotations.py upstream/master\n'
+        'The annotate command will be removed in a future version.\n'
+        'Get in touch if you still use it: ned@nedbatchelder.com\n'
+        'No data to report.\n'
+        'INTERCEPTED '
+        'python dev_tools/check_incremental_coverage_annotations.py upstream/master\n'
     )
     assert result.err == "Comparing against revision 'upstream/master'.\n"
 
@@ -451,10 +466,13 @@ def test_pytest_and_incremental_coverage_branch_selection(tmpdir_factory):
     assert result.exit_code == 0
     assert result.out == (
         'INTERCEPTED check/pytest '
-        '--actually-quiet --rigetti-integration --cov --cov-report=annotate '
+        '--actually-quiet --rigetti-integration --cov '
         '--cov-config=dev_tools/conf/.coveragerc\n'
-        'INTERCEPTED python '
-        'dev_tools/check_incremental_coverage_annotations.py HEAD\n'
+        'The annotate command will be removed in a future version.\n'
+        'Get in touch if you still use it: ned@nedbatchelder.com\n'
+        'No data to report.\n'
+        'INTERCEPTED '
+        'python dev_tools/check_incremental_coverage_annotations.py HEAD\n'
     )
     assert result.err == "Comparing against revision 'HEAD'.\n"
 
@@ -467,10 +485,13 @@ def test_pytest_and_incremental_coverage_branch_selection(tmpdir_factory):
     assert result.exit_code == 0
     assert result.out == (
         'INTERCEPTED check/pytest '
-        '--actually-quiet --rigetti-integration --cov --cov-report=annotate '
+        '--actually-quiet --rigetti-integration --cov '
         '--cov-config=dev_tools/conf/.coveragerc\n'
-        'INTERCEPTED python '
-        'dev_tools/check_incremental_coverage_annotations.py master\n'
+        'The annotate command will be removed in a future version.\n'
+        'Get in touch if you still use it: ned@nedbatchelder.com\n'
+        'No data to report.\n'
+        'INTERCEPTED '
+        'python dev_tools/check_incremental_coverage_annotations.py master\n'
     )
     assert result.err == "Comparing against revision 'master'.\n"
 
@@ -490,10 +511,13 @@ def test_pytest_and_incremental_coverage_branch_selection(tmpdir_factory):
     assert result.exit_code == 0
     assert result.out.startswith(
         'INTERCEPTED check/pytest '
-        '--actually-quiet --rigetti-integration --cov --cov-report=annotate '
+        '--actually-quiet --rigetti-integration --cov '
         '--cov-config=dev_tools/conf/.coveragerc\n'
-        'INTERCEPTED python '
-        'dev_tools/check_incremental_coverage_annotations.py '
+        'The annotate command will be removed in a future version.\n'
+        'Get in touch if you still use it: ned@nedbatchelder.com\n'
+        'No data to report.\n'
+        'INTERCEPTED '
+        'python dev_tools/check_incremental_coverage_annotations.py '
     )
     assert result.err.startswith("Comparing against revision 'master' (merge base ")