From caea16ef8b96d69c4e47e4fde713d6fc8b8609bc Mon Sep 17 00:00:00 2001
From: Philip Cook <cookpa@pennmedicine.upenn.edu>
Date: Sun, 18 Feb 2024 16:26:30 -0500
Subject: [PATCH 1/3] ENH: Set path to source for coverage tests

---
 .github/workflows/code-coverage.yml | 10 +++++++++-
 tests/run_tests.sh                  |  5 ++++-
 2 files changed, 13 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/code-coverage.yml b/.github/workflows/code-coverage.yml
index 7515958b..49861e5f 100644
--- a/.github/workflows/code-coverage.yml
+++ b/.github/workflows/code-coverage.yml
@@ -24,8 +24,16 @@ jobs:
       - name: Install coverage
         run: python -m pip install coverage
 
+      - name: Find installed package path
+        id: find_package_path
+        run: >
+          echo "PACKAGE_PATH=$(python -c 'import importlib.util;
+          package_name=\"ants\"; package_spec=importlib.util.find_spec(package_name);
+          print(package_spec.submodule_search_locations[0] if package_spec else \"\")')"
+          >> $GITHUB_ENV
+
       - name: Unit tests
-        run: tests/run_tests.sh -c
+        run: tests/run_tests.sh -c -s ${PACKAGE_PATH}
 
       - name: Coveralls
         uses: coverallsapp/github-action@v2
diff --git a/tests/run_tests.sh b/tests/run_tests.sh
index fa6c947c..a43cdb2f 100755
--- a/tests/run_tests.sh
+++ b/tests/run_tests.sh
@@ -3,10 +3,12 @@ set -e
 
 PYCMD=${PYCMD:="python3"}
 COVERAGE=0
+SOURCE="ants"
 while [[ "$#" -gt 0 ]]; do
     case "$1" in
         -p|--python) PYCMD=$2; shift 2 ;;
         -c|--coverage) COVERAGE=1; shift 1;;
+        -s|--source) SOURCE=$2; shift 2 ;;
         --) shift; break ;;
         *) echo "Invalid argument: $1!" ; exit 1 ;;
     esac
@@ -14,7 +16,7 @@ done
 
 if [[ $COVERAGE -eq 1 ]]; then
     coverage erase
-    PYCMD="coverage run --parallel-mode --source ants "
+    PYCMD="coverage run --parallel-mode --source $SOURCE "
     echo "coverage flag found. Setting command to: \"$PYCMD\""
 fi
 
@@ -50,6 +52,7 @@ $PYCMD test_bugs.py $@
 if [[ $COVERAGE -eq 1 ]]; then
     coverage combine
     coverage html
+    coverage xml
 fi
 
 

From 5b6d69bb33f7423cbfcaa0a685839c4b50859e72 Mon Sep 17 00:00:00 2001
From: Philip Cook <cookpa@pennmedicine.upenn.edu>
Date: Sun, 18 Feb 2024 16:31:32 -0500
Subject: [PATCH 2/3] [skip ci] ENH: Remove unnecessary parameter

Github already lets you choose the branch to run on, seems there's no need to do it explicitly
---
 .github/workflows/code-coverage.yml | 4 ----
 1 file changed, 4 deletions(-)

diff --git a/.github/workflows/code-coverage.yml b/.github/workflows/code-coverage.yml
index 49861e5f..ea2f66ba 100644
--- a/.github/workflows/code-coverage.yml
+++ b/.github/workflows/code-coverage.yml
@@ -4,10 +4,6 @@ on:
       - master
 
   workflow_dispatch:
-    inputs:
-      branch:
-        description: 'Branch name'
-        required: true
 
 name: codecov
 

From f90e610308f8aadd63c6bf1ccee040fcde0e6bdc Mon Sep 17 00:00:00 2001
From: Philip Cook <cookpa@pennmedicine.upenn.edu>
Date: Sun, 18 Feb 2024 17:31:04 -0500
Subject: [PATCH 3/3] [skip ci] BUG: Attempt at inline python script didn't
 work so well

---
 .github/workflows/code-coverage.yml | 7 ++-----
 tests/find_package_path.py          | 7 +++++++
 2 files changed, 9 insertions(+), 5 deletions(-)
 create mode 100644 tests/find_package_path.py

diff --git a/.github/workflows/code-coverage.yml b/.github/workflows/code-coverage.yml
index ea2f66ba..844e0789 100644
--- a/.github/workflows/code-coverage.yml
+++ b/.github/workflows/code-coverage.yml
@@ -22,11 +22,8 @@ jobs:
 
       - name: Find installed package path
         id: find_package_path
-        run: >
-          echo "PACKAGE_PATH=$(python -c 'import importlib.util;
-          package_name=\"ants\"; package_spec=importlib.util.find_spec(package_name);
-          print(package_spec.submodule_search_locations[0] if package_spec else \"\")')"
-          >> $GITHUB_ENV
+        run: |
+          echo "PACKAGE_PATH=$(python tests/find_package_path.py)" >> $GITHUB_ENV
 
       - name: Unit tests
         run: tests/run_tests.sh -c -s ${PACKAGE_PATH}
diff --git a/tests/find_package_path.py b/tests/find_package_path.py
new file mode 100644
index 00000000..23b3e253
--- /dev/null
+++ b/tests/find_package_path.py
@@ -0,0 +1,7 @@
+import importlib.util
+
+# This is used for CI scripts to find the location of the installed package
+
+package_name = 'ants'
+package_spec = importlib.util.find_spec(package_name)
+print(package_spec.submodule_search_locations[0] if package_spec else '')
\ No newline at end of file