From 914c6040ae88bf0ddaf5ebef664743bd92640354 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Dan=20S=C3=B8ndergaard?= <das@genome.au.dk>
Date: Sun, 15 Dec 2024 20:14:12 +0100
Subject: [PATCH] Add --force and --no-deps flags to run command

The --force flag forces submission of targets,  without performing any
IO (so not stat'ing the filesystem).

The --no-deps flag will ignore dependencies, so only the targets
specified (by default the endpoints) will be submitted.

Closes #417.
---
 src/gwf/plugins/run.py |  6 +++++-
 src/gwf/scheduling.py  | 39 +++++++++++++++++++++++++++++++++------
 2 files changed, 38 insertions(+), 7 deletions(-)

diff --git a/src/gwf/plugins/run.py b/src/gwf/plugins/run.py
index f72522ec..45586e91 100644
--- a/src/gwf/plugins/run.py
+++ b/src/gwf/plugins/run.py
@@ -31,8 +31,10 @@ def clean_logs(working_dir, graph):
 @click.command()
 @click.argument("targets", nargs=-1)
 @click.option("-d", "--dry-run", is_flag=True, default=False)
+@click.option("-f", "--force", is_flag=True, default=False)
+@click.option("-n", "--no-deps", is_flag=True, default=False)
 @pass_context
-def run(ctx, targets, dry_run):
+def run(ctx, targets, dry_run, force, no_deps):
     """Run the specified workflow."""
     workflow = Workflow.from_context(ctx)
 
@@ -56,4 +58,6 @@ def run(ctx, targets, dry_run):
             spec_hashes,
             backend,
             dry_run=dry_run,
+            force=force,
+            no_deps=no_deps,
         )
diff --git a/src/gwf/scheduling.py b/src/gwf/scheduling.py
index 5dffe0d0..fcd05951 100644
--- a/src/gwf/scheduling.py
+++ b/src/gwf/scheduling.py
@@ -52,13 +52,29 @@ def should_run(target, fs, spec_hashes):
     return False
 
 
-def schedule(endpoints, graph, fs, spec_hashes, status_func, submit_func):
+def schedule(
+    endpoints,
+    graph,
+    fs,
+    spec_hashes,
+    status_func,
+    submit_func,
+    force=False,
+    no_deps=False,
+):
     def _schedule(target):
         submitted_deps = []
-        for dep in sorted(graph.dependencies[target], key=lambda t: t.name):
-            status = _cached_schedule(dep)
-            if status in SUBMITTED_STATES:
-                submitted_deps.append(dep)
+
+        if not no_deps:
+            for dep in sorted(graph.dependencies[target], key=lambda t: t.name):
+                status = _cached_schedule(dep)
+                if status in SUBMITTED_STATES:
+                    submitted_deps.append(dep)
+
+        if force:
+            logger.debug("Target %s is being forcibly submitted", target)
+            submit_func(target, dependencies=submitted_deps)
+            return Status.SHOULDRUN
 
         if status_func(target) == BackendStatus.SUBMITTED:
             logger.debug("Target %s is already submitted", target)
@@ -147,7 +163,16 @@ def submit_backend(target, dependencies, backend, spec_hashes):
     spec_hashes.update(target)
 
 
-def submit_workflow(endpoints, graph, fs, spec_hashes, backend, dry_run=False):
+def submit_workflow(
+    endpoints,
+    graph,
+    fs,
+    spec_hashes,
+    backend,
+    dry_run=False,
+    force=False,
+    no_deps=False,
+):
     """Submit a workflow to a backend."""
     submit_func = partial(
         _submit_dryrun if dry_run else submit_backend,
@@ -161,6 +186,8 @@ def submit_workflow(endpoints, graph, fs, spec_hashes, backend, dry_run=False):
         spec_hashes,
         status_func=backend.status,
         submit_func=submit_func,
+        force=force,
+        no_deps=no_deps,
     )