Added '--dir' to 'bump-version' and 'sync'

nf_core/__main__.py

@@ -619,12 +619,12 @@ def lint(schema_path):
 
 
 @nf_core_cli.command("bump-version", help_priority=9)
-@click.argument("pipeline_dir", type=click.Path(exists=True), required=True, metavar="<pipeline directory>")
 @click.argument("new_version", required=True, metavar="<new version>")
+@click.option("-d", "--dir", type=click.Path(exists=True), default=".", help="Pipeline directory. Defaults to CWD")
 @click.option(
     "-n", "--nextflow", is_flag=True, default=False, help="Bump required nextflow version instead of pipeline version"
 )
-def bump_version(pipeline_dir, new_version, nextflow):
+def bump_version(new_version, dir, nextflow):
     """
     Update nf-core pipeline version number.
 
@@ -637,24 +637,28 @@ def bump_version(pipeline_dir, new_version, nextflow):
 
     As well as the pipeline version, you can also change the required version of Nextflow.
     """
-    # Make a pipeline object and load config etc
-    pipeline_obj = nf_core.utils.Pipeline(pipeline_dir)
-    pipeline_obj._load()
-
-    # Bump the pipeline version number
-    if not nextflow:
-        nf_core.bump_version.bump_pipeline_version(pipeline_obj, new_version)
-    else:
-        nf_core.bump_version.bump_nextflow_version(pipeline_obj, new_version)
+    try:
+        # Make a pipeline object and load config etc
+        pipeline_obj = nf_core.utils.Pipeline(dir)
+        pipeline_obj._load()
+
+        # Bump the pipeline version number
+        if not nextflow:
+            nf_core.bump_version.bump_pipeline_version(pipeline_obj, new_version)
+        else:
+            nf_core.bump_version.bump_nextflow_version(pipeline_obj, new_version)
+    except UserWarning as e:
+        log.error(e)
+        sys.exit(1)
 
 
 @nf_core_cli.command("sync", help_priority=10)
-@click.argument("pipeline_dir", required=True, type=click.Path(exists=True), metavar="<pipeline directory>")
+@click.option("-d", "--dir", type=click.Path(exists=True), default=".", help="Pipeline directory. Defaults to CWD")
 @click.option("-b", "--from-branch", type=str, help="The git branch to use to fetch workflow vars.")
 @click.option("-p", "--pull-request", is_flag=True, default=False, help="Make a GitHub pull-request with the changes.")
 @click.option("-r", "--repository", type=str, help="GitHub PR: target repository.")
 @click.option("-u", "--username", type=str, help="GitHub PR: auth username.")
-def sync(pipeline_dir, from_branch, pull_request, repository, username):
+def sync(dir, from_branch, pull_request, repository, username):
     """
     Sync a pipeline TEMPLATE branch with the nf-core template.
 
@@ -669,7 +673,7 @@ def sync(pipeline_dir, from_branch, pull_request, repository, username):
     """
 
     # Sync the given pipeline dir
-    sync_obj = nf_core.sync.PipelineSync(pipeline_dir, from_branch, pull_request, repository, username)
+    sync_obj = nf_core.sync.PipelineSync(dir, from_branch, pull_request, repository, username)
     try:
         sync_obj.sync()
     except (nf_core.sync.SyncException, nf_core.sync.PullRequestException) as e:

nf_core/bump_version.py

@@ -29,8 +29,8 @@ def bump_pipeline_version(pipeline_obj, new_version):
         log.warning("Stripping leading 'v' from new version number")
         new_version = new_version[1:]
     if not current_version:
-        log.error("Could not find config variable 'manifest.version'")
-        sys.exit(1)
+        raise UserWarning("Could not find config variable 'manifest.version'")
+
     log.info("Changing version number from '{}' to '{}'".format(current_version, new_version))
 
     # nextflow.config - workflow manifest version
@@ -60,8 +60,7 @@ def bump_nextflow_version(pipeline_obj, new_version):
     current_version = re.sub(r"^[^0-9\.]*", "", current_version)
     new_version = re.sub(r"^[^0-9\.]*", "", new_version)
     if not current_version:
-        log.error("Could not find config variable 'manifest.nextflowVersion'")
-        sys.exit(1)
+        raise UserWarning("Could not find config variable 'manifest.nextflowVersion'")
     log.info("Changing Nextlow version number from '{}' to '{}'".format(current_version, new_version))
 
     # nextflow.config - manifest minimum nextflowVersion

nf_core/sync.py

@@ -66,6 +66,12 @@ def __init__(
     ):
         """Initialise syncing object"""
 
+        # Check if 'pipeline_dir' is a pipeline directory
+        try:
+            nf_core.utils.is_pipeline_directory(pipeline_dir)
+        except UserWarning:
+            raise
+
         self.pipeline_dir = os.path.abspath(pipeline_dir)
         self.from_branch = from_branch
         self.original_branch = None

nf_core/utils.py

@@ -121,6 +121,12 @@ def __init__(self, wf_path):
         self.pipeline_name = None
         self.schema_obj = None
 
+        # Check if 'wf_path' is a pipeline directory
+        try:
+            is_pipeline_directory(self.wf_path)
+        except UserWarning:
+            raise
+
         try:
             repo = git.Repo(self.wf_path)
             self.git_sha = repo.head.object.hexsha
@@ -183,6 +189,23 @@ def _fp(self, fn):
         return os.path.join(self.wf_path, fn)
 
 
+def is_pipeline_directory(wf_path):
+    """
+    Checks if the specified directory have the minimum required files
+    ('main.nf', 'nextflow.config') for a pipeline directory
+
+    Args:
+        wf_path (str): The directory to be inspected
+
+    Raises:
+        UserWarning: If one of the files are missing
+    """
+    for fn in ["main.nf", "nextflow.config"]:
+        path = os.path.join(wf_path, fn)
+        if not os.path.isfile(path):
+            raise UserWarning(f"'{wf_path}' is not a pipeline - '{fn}' is missing")
+
+
 def fetch_wf_config(wf_path):
     """Uses Nextflow to retrieve the the configuration variables
     from a Nextflow workflow.