From aea21052cff3766e9e9e46f29d54393181e91d89 Mon Sep 17 00:00:00 2001
From: Chris Markiewicz <effigies@gmail.com>
Date: Fri, 22 Mar 2024 22:02:56 -0400
Subject: [PATCH 1/3] CI: Add Publish environment to deploy step

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

diff --git a/.github/workflows/pythonpackage.yml b/.github/workflows/pythonpackage.yml
index b4412ac..5178511 100644
--- a/.github/workflows/pythonpackage.yml
+++ b/.github/workflows/pythonpackage.yml
@@ -108,6 +108,7 @@ jobs:
     permissions:
       id-token: write
     if: github.repository_owner == 'nipype' && github.event.action == 'published'
+    environment: Publish
     steps:
       - uses: actions/download-artifact@v4
         with:

From d03363373746212b3391a46acd195469b4045ce1 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Fri, 22 Mar 2024 22:03:23 -0400
Subject: [PATCH 2/3] [pre-commit.ci] pre-commit autoupdate (#34)
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

updates:
- [github.com/pre-commit/pre-commit-hooks: v4.4.0 → v4.5.0](https://github.com/pre-commit/pre-commit-hooks/compare/v4.4.0...v4.5.0)
- [github.com/psf/black: 23.3.0 → 24.3.0](https://github.com/psf/black/compare/23.3.0...24.3.0)

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
---
 .pre-commit-config.yaml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index 1336a23..7a0fcb1 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -2,13 +2,13 @@
 # See https://pre-commit.com/hooks.html for more hooks
 repos:
 -   repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.4.0
+    rev: v4.5.0
     hooks:
     -   id: trailing-whitespace
     -   id: end-of-file-fixer
     -   id: check-yaml
     -   id: check-added-large-files
 -   repo: https://github.com/psf/black
-    rev: 23.3.0
+    rev: 24.3.0
     hooks:
     -   id: black

From 4c08fabae17bf03f7d44e796732fd97d2c120fa0 Mon Sep 17 00:00:00 2001
From: Chris Markiewicz <markiewicz@stanford.edu>
Date: Fri, 22 Mar 2024 23:09:32 -0400
Subject: [PATCH 3/3] MNT: Coverage updates (#36)

* MNT: Do not omit tests from coverage

* MNT: Set fallback __version__, ignore coverage

* CI: Do not submit etelemetry during tests

* CI: Update pytest invocation to get test coverage
---
 .coveragerc                         | 6 +++++-
 .github/workflows/pythonpackage.yml | 5 +++--
 codecov.yml                         | 3 ---
 pydra/tasks/nipype1/__init__.py     | 4 ++--
 4 files changed, 10 insertions(+), 8 deletions(-)

diff --git a/.coveragerc b/.coveragerc
index f65ec5e..dd05c95 100644
--- a/.coveragerc
+++ b/.coveragerc
@@ -2,4 +2,8 @@
 branch = True
 omit =
     */_version.py
-    */tests/*
+
+[paths]
+source =
+    pydra/tasks
+    /**/pydra/tasks
diff --git a/.github/workflows/pythonpackage.yml b/.github/workflows/pythonpackage.yml
index 5178511..47984d1 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:
@@ -86,8 +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:
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:
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