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Merged
johanneskoester merged 5 commits into from
Sep 22, 2026
Merged

feat: add --commit flag to deploy-workflow #127

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0e1e13f
Add --commit flag to deploy-workflow
Jun 24, 2026
ec11a28
fix: make --tag, --branch, and --commit mutually exclusive
ntnn19 Sep 7, 2026
c98520d
fixed conflicts caused by introducing changes to main instead of the …
ntnn19 Sep 7, 2026
90b154a
Merge branch 'main' into feature/deploy-workflow-commit-flag
johanneskoester Sep 22, 2026
c6cae6f
Change commit parameter type to str | None
johanneskoester Sep 22, 2026
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18 changes: 18 additions & 0 deletions docs/workflow_users/workflow_deployment.rst
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Original file line number Diff line number Diff line change
Expand Up @@ -41,6 +41,24 @@ Further, the workflow definition Snakefile can be arbitrarily extended and modif

It is highly advisable to put the deployed workflow into a new (perhaps private) git repository (e.g., see `here <https://docs.github.com/en/github/importing-your-projects-to-github/adding-an-existing-project-to-github-using-the-command-line>`_ for instructions how to do that with Github).

If you want to pin the deployment to an exact commit (e.g. for full reproducibility independent of any future changes to a branch or tag), use ``--commit`` instead of ``--tag``/``--branch``:

.. code-block:: console

$ snakedeploy deploy-workflow https://github.com/snakemake-workflows/dna-seq-varlociraptor /tmp/dest --commit 87709354b54391aee5dbb01a64cacfc20aed5ec3

This will generate a module declaration pinned to that exact commit:

.. code-block:: python

module dna_seq_varlociraptor:
snakefile:
github("snakemake-workflows/dna-seq-varlociraptor", path="workflow/Snakefile", commit="87709354b54391aee5dbb01a64cacfc20aed5ec3")
config:
config

Note that ``--commit``, ``--tag``, and ``--branch`` are mutually exclusive: exactly one of them has to be specified.

For more options and details, run

.. code-block:: console
Expand Down
14 changes: 10 additions & 4 deletions snakedeploy/client.py
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Original file line number Diff line number Diff line change
Expand Up @@ -78,16 +78,23 @@ def get_parser():
help="Path to create the deploying workflow in.",
)

deploy_workflow_parser.add_argument(
ref_group = deploy_workflow_parser.add_mutually_exclusive_group(required=True)

ref_group.add_argument(
"--tag",
help="Git tag to deploy from (e.g. a certain release).",
)

deploy_workflow_parser.add_argument(
ref_group.add_argument(
"--branch",
help="Git branch to deploy from.",
)

ref_group.add_argument(
"--commit",
help="Git commit (SHA) to deploy from and pin the resulting module to.",
)

deploy_group.add_argument(
"--name",
help="The name for the module in the resulting Snakefile (default: repository name).",
Expand Down Expand Up @@ -290,13 +297,12 @@ def help(return_code=0):

try:
if args.subcommand == "deploy-workflow":
if not (args.tag or args.branch):
raise UserError("Please specify either --tag or --branch")
deploy(
args.repo,
name=args.name,
tag=args.tag,
branch=args.branch,
commit=args.commit,
dest_path=Path(args.dest),
force=args.force,
)
Expand Down
30 changes: 27 additions & 3 deletions snakedeploy/deploy.py
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Original file line number Diff line number Diff line change
Expand Up @@ -19,6 +19,7 @@ def __init__(
dest: Path,
tag: str | None = None,
branch: str | None = None,
commit: str | None = None,
force=False,
):
self.provider = get_provider(source)
Expand All @@ -28,6 +29,7 @@ def __init__(
self._cloned = None
self.tag = tag
self.branch = branch
self.commit = commit

def __enter__(self):
return self
Expand Down Expand Up @@ -137,7 +139,9 @@ def repo_clone(self):
logger.info("Obtaining source repository...")
self._cloned = tempfile.TemporaryDirectory()
self.provider.clone(self._cloned.name)
if self.tag is not None:
if self.commit is not None:
self.provider.checkout(self._cloned.name, self.commit)
elif self.tag is not None:
self.provider.checkout(self._cloned.name, self.tag)
elif self.branch is not None:
self.provider.checkout(self._cloned.name, self.branch)
Expand Down Expand Up @@ -225,7 +229,7 @@ def deploy_snakefile(self, tmpdir: str, name: str):
module_deployment = template.render(
name=name,
snakefile=self.provider.get_source_file_declaration(
snakefile, self.tag, self.branch
snakefile, self.tag, self.branch, self.commit
),
repo=self.provider.source_url,
config=config,
Expand All @@ -250,6 +254,7 @@ def deploy(
tag: str | None,
branch: str | None,
dest_path: Path,
commit: str | None = None,
force=False,
):
"""
Expand All @@ -271,8 +276,27 @@ def deploy(
force=True
)

Instead of a tag or branch, a specific commit can be pinned (the three
are mutually exclusive):

.. code-block:: python

from snakedeploy.deploy import deploy
deploy(
"https://github.com/snakemake-workflows/dna-seq-varlociraptor",
dest_path="/tmp/dest",
name="dna_seq",
commit="a1b2c3d4e5f6...",
force=True
)

"""
with WorkflowDeployer(
source=source_url, dest=dest_path, tag=tag, branch=branch, force=force
source=source_url,
dest=dest_path,
tag=tag,
branch=branch,
commit=commit,
force=force,
) as sd:
sd.deploy(name=name)
21 changes: 16 additions & 5 deletions snakedeploy/providers.py
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Original file line number Diff line number Diff line change
Expand Up @@ -71,7 +71,9 @@ def get_raw_file(self, path: str, tag: str):
)
return f"{self.source_url}/{path}"

def get_source_file_declaration(self, path: str, tag: str, branch: str):
def get_source_file_declaration(
self, path: str, tag: str, branch: str, commit: str | None = None
):
relative_path = path.replace(self.source_url, "").strip(os.sep)
Comment on lines +74 to 77

@coderabbitai coderabbitai Bot Jul 14, 2026

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🎯 Functional Correctness | 🟠 Major | 🏗️ Heavy lift

Do not silently ignore --commit for local repositories.

repo_clone invokes provider.checkout(..., commit), but Local.checkout() is a no-op and this declaration cannot encode the commit. A local deployment therefore copies the current working tree rather than the requested snapshot. Either implement commit checkout for Git-backed local sources or reject --commit for the Local provider.

🤖 Prompt for AI Agents 
Verify each finding against current code. Fix only still-valid issues, skip the
rest with a brief reason, keep changes minimal, and validate.

In `@snakedeploy/providers.py` around lines 77 - 80, Ensure the Local provider
does not silently ignore a requested commit: either implement commit-aware
checkout in Local.checkout or explicitly reject --commit for Local before
deployment proceeds. Update the related get_source_file_declaration flow only as
needed to preserve the requested snapshot behavior.

return f'"{relative_path}"'

Expand Down Expand Up @@ -103,11 +105,20 @@ def checkout(self, path: str, ref: str):
def get_raw_file(self, path: str, tag: str):
return f"{self.source_url}/raw/{tag}/{path}"

def get_source_file_declaration(self, path: str, tag: str, branch: str):
def get_source_file_declaration(
self, path: str, tag: str, branch: str, commit: str | None = None
):
owner_repo = "/".join(self.source_url.split("/")[-2:])
if not (tag or branch):
raise UserError("Either tag or branch has to be specified for deployment.")
ref_arg = f'tag="{tag}"' if tag is not None else f'branch="{branch}"'
if not (tag or branch or commit):
raise UserError(
"Either tag, branch, or commit has to be specified for deployment."
)
if commit is not None:
ref_arg = f'commit="{commit}"'
elif tag is not None:
ref_arg = f'tag="{tag}"'
else:
ref_arg = f'branch="{branch}"'
return f'{self.name}("{owner_repo}", path="{path}", {ref_arg})'


Expand Down
9 changes: 9 additions & 0 deletions tests/test_client.sh
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Original file line number Diff line number Diff line change
Expand Up @@ -46,6 +46,15 @@ dest=$tmpdir/gitlab-testing
repo="https://gitlab.com/nate-d-olson/snaketestworkflow"
runTest 0 $output snakedeploy deploy-workflow "${repo}" "${dest}" --name snake-test --branch master

echo
echo "#### Testing snakedeploy deployment pinned to a specific commit"
dest=$tmpdir/commit-testing
repo="https://github.com/snakemake-workflows/dna-seq-varlociraptor"
commit_sha="87709354b54391aee5dbb01a64cacfc20aed5ec3"
runTest 0 $output snakedeploy deploy-workflow "${repo}" "${dest}" --commit ${commit_sha} --name dna-seq-commit
runTest 0 $output grep "commit=\"${commit_sha}\"" ${dest}/workflow/Snakefile
runTest 2 $output snakedeploy deploy-workflow "${repo}" "${dest}" --branch master --commit ${commit_sha}

echo
echo "#### Testing snakedeploy local deployment"
local=$tmpdir/rna-seq-star-deseq2
Expand Down
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