Run tests with a realistic version of git

.github/workflows/pytest-frozen-ubuntu-20.04.yml

@@ -0,0 +1,52 @@
+name: Python tests Ubuntu-20.04 (frozen)
+# This workflow is triggered on pushes and PRs to the repository.
+# Only run if we changed a Python file
+on:
+  push:
+    branches:
+      - dev
+  pull_request:
+  release:
+    types: [published]
+
+# Cancel if a newer run is started
+concurrency:
+  group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  pytest:
+    runs-on: ubuntu-20.04
+    steps:
+      - uses: actions/checkout@v3
+        name: Check out source-code repository
+
+      - name: Set up Python 3.8
+        uses: actions/setup-python@v3
+        with:
+          python-version: "3.8"
+
+      - name: Install python dependencies
+        run: |
+          python -m pip install --upgrade pip -r requirements-dev.txt
+          pip install -e .
+
+      - name: Downgrade git to the Ubuntu official repository's version
+        run: |
+          sudo apt remove git git-man
+          sudo add-apt-repository --remove ppa:git-core/ppa
+          sudo apt install git
+
+      - name: Install Nextflow
+        uses: nf-core/setup-nextflow@v1
+        with:
+          version: "latest-everything"
+
+      - name: Test with pytest
+        run: python3 -m pytest tests/ --color=yes --cov-report=xml --cov-config=.github/.coveragerc --cov=nf_core
+
+      - uses: codecov/codecov-action@v1
+        name: Upload code coverage report
+        with:
+          if: success()
+          token: ${{ secrets.CODECOV_TOKEN }}

CHANGELOG.md

@@ -31,6 +31,7 @@
 - Add file `versions.yml` when generating `test.yml` with `nf-core modules create-test-yml` but don't check for md5sum [#1963](https://github.com/nf-core/tools/pull/1963)
 - Mock biocontainers and anaconda api calls in modules and subworkflows tests [#1967](https://github.com/nf-core/tools/pull/1967)
 - Run tests with Python 3.11 ([#1970](https://github.com/nf-core/tools/pull/1970))
+- Run test with a realistic version of git ([#2043](https://github.com/nf-core/tools/pull/2043))
 - Bump promoted Python version from 3.7 to 3.8 ([#1971](https://github.com/nf-core/tools/pull/1971))
 - Fix incorrect file deletion in `nf-core launch` when `--params_in` has the same name as `--params_out`
 - Updated GitHub actions ([#1998](https://github.com/nf-core/tools/pull/1998), [#2001](https://github.com/nf-core/tools/pull/2001))

nf_core/create.py

@@ -528,10 +528,10 @@ def git_init_pipeline(self):
 
         log.info("Initialising pipeline git repository")
         repo = git.Repo.init(self.outdir)
-        if default_branch:
-            repo.active_branch.rename(default_branch)
         repo.git.add(A=True)
         repo.index.commit(f"initial template build from nf-core/tools, version {nf_core.__version__}")
+        if default_branch:
+            repo.active_branch.rename(default_branch)
         repo.git.branch("TEMPLATE")
         repo.git.branch("dev")
         log.info(

tests/test_sync.py

@@ -32,7 +32,9 @@ def setUp(self):
         self.create_obj.init_pipeline()
         self.remote_path = os.path.join(self.tmp_dir, "remote_repo")
         self.remote_repo = git.Repo.init(self.remote_path, bare=True)
-        self.remote_repo.active_branch.rename(default_branch)
+
+        if self.remote_repo.active_branch.name != "master":
+            self.remote_repo.active_branch.rename(default_branch)
 
     def tearDown(self):
         if os.path.exists(self.tmp_dir):