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):