From 2ebce2bc32cdeb7e250f97965579bb5d092af1a3 Mon Sep 17 00:00:00 2001
From: Chris Markiewicz <effigies@gmail.com>
Date: Fri, 22 Mar 2024 22:15:45 -0400
Subject: [PATCH 1/4] MNT: Do not omit tests from coverage

---
 .coveragerc | 1 -
 codecov.yml | 3 ---
 2 files changed, 4 deletions(-)

diff --git a/.coveragerc b/.coveragerc
index f65ec5e..e207ce9 100644
--- a/.coveragerc
+++ b/.coveragerc
@@ -2,4 +2,3 @@
 branch = True
 omit =
     */_version.py
-    */tests/*
diff --git a/codecov.yml b/codecov.yml
index bbf806c..f45bbe4 100644
--- a/codecov.yml
+++ b/codecov.yml
@@ -1,10 +1,7 @@
 coverage:
   range: "50...100"
   ignore:          # files and folders that will be removed during processing
-    - "**/tests"
     - "**/_version.py"
-    - "setup.py"
-    - "versioneer.py"
   status:
     project:
       default:

From cc8a2786e529d0e7f359eaf6524b92f5dc9a3148 Mon Sep 17 00:00:00 2001
From: Chris Markiewicz <effigies@gmail.com>
Date: Fri, 22 Mar 2024 22:17:59 -0400
Subject: [PATCH 2/4] MNT: Set fallback __version__, ignore coverage

---
 pydra/tasks/nipype1/__init__.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/pydra/tasks/nipype1/__init__.py b/pydra/tasks/nipype1/__init__.py
index 090acf5..94ee228 100644
--- a/pydra/tasks/nipype1/__init__.py
+++ b/pydra/tasks/nipype1/__init__.py
@@ -5,8 +5,8 @@
 
 try:
     from ._version import __version__
-except ImportError:
-    pass
+except ImportError:  # pragma: no cover
+    __version__ = "0+unknown"
 
 from .utils import Nipype1Task
 

From 374bc1e0892f05583689d46d45d2b92177bda4f2 Mon Sep 17 00:00:00 2001
From: Chris Markiewicz <effigies@gmail.com>
Date: Fri, 22 Mar 2024 22:21:50 -0400
Subject: [PATCH 3/4] CI: Do not submit etelemetry during tests

---
 .github/workflows/pythonpackage.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.github/workflows/pythonpackage.yml b/.github/workflows/pythonpackage.yml
index 5178511..aca88a8 100644
--- a/.github/workflows/pythonpackage.yml
+++ b/.github/workflows/pythonpackage.yml
@@ -7,6 +7,7 @@ name: Python package
 env:
   SUBPACKAGE: nipype1
   FSLCONDA: https://fsl.fmrib.ox.ac.uk/fsldownloads/fslconda/public/
+  NO_ET: 1  # etelemetry causes order-of-magnitude slowdowns
 
 on:
   push:

From 4dd12219fcddcc9fa097574a465c8f2533774972 Mon Sep 17 00:00:00 2001
From: Chris Markiewicz <effigies@gmail.com>
Date: Fri, 22 Mar 2024 22:28:10 -0400
Subject: [PATCH 4/4] CI: Update pytest invocation to get test coverage

---
 .coveragerc                         | 5 +++++
 .github/workflows/pythonpackage.yml | 4 ++--
 2 files changed, 7 insertions(+), 2 deletions(-)

diff --git a/.coveragerc b/.coveragerc
index e207ce9..dd05c95 100644
--- a/.coveragerc
+++ b/.coveragerc
@@ -2,3 +2,8 @@
 branch = True
 omit =
     */_version.py
+
+[paths]
+source =
+    pydra/tasks
+    /**/pydra/tasks
diff --git a/.github/workflows/pythonpackage.yml b/.github/workflows/pythonpackage.yml
index aca88a8..47984d1 100644
--- a/.github/workflows/pythonpackage.yml
+++ b/.github/workflows/pythonpackage.yml
@@ -87,8 +87,8 @@ jobs:
           python -c "import pydra as m; print(f'{m.__name__} {m.__version__} @ {m.__file__}')"
       - name: Test with pytest
         run: |
-          pytest -sv --doctest-modules pydra/tasks/$SUBPACKAGE \
-              --cov pydra.tasks.$SUBPACKAGE --cov-report xml
+          pytest -sv --doctest-modules --pyargs pydra.tasks.$SUBPACKAGE \
+              --cov pydra.tasks.$SUBPACKAGE --cov-report xml --cov-report term-missing
       - uses: codecov/codecov-action@v4
         if: ${{ always() }}
         with: