Merge pull request #3178 from MatthiasZepper/download_cli_refactor

Changes to nf-core pipelines download CLI

CHANGELOG.md

@@ -72,6 +72,17 @@
 - Components: allow spaces at the beginning of include statements ([#3115](https://github.com/nf-core/tools/pull/3115))
 - Add option `--fix` to update the `meta.yml` file of subworkflows ([#3077](https://github.com/nf-core/tools/pull/3077))
 
+### Download
+
+- Fully removed already deprecated `-t` / `--tower` flag.
+- Refactored the CLI for consistency (short flag is usually second word, e.g. also for `--container-library` etc.):
+
+| Old parameter                     | New parameter                     |
+| --------------------------------- | --------------------------------- |
+| `-d` / `--download-configuration` | `-c` / `--download-configuration` |
+| `-p` / `--parallel-downloads`     | `-d` / `--parallel-downloads`     |
+| new parameter                     | `-p` / (`--platform`)             |
+
 ### General
 
 - Update output of generation script for API docs to new structure ([#2988](https://github.com/nf-core/tools/pull/2988))

nf_core/__main__.py

@@ -366,26 +366,18 @@ def command_pipelines_lint(
     help="Archive compression type",
 )
 @click.option("-f", "--force", is_flag=True, default=False, help="Overwrite existing files")
-# TODO: Remove this in a future release. Deprecated in March 2024.
-@click.option(
-    "-t",
-    "--tower",
-    is_flag=True,
-    default=False,
-    hidden=True,
-    help="Download for Seqera Platform. DEPRECATED: Please use `--platform` instead.",
-)
 @click.option(
+    "-p",
     "--platform",
     is_flag=True,
     default=False,
     help="Download for Seqera Platform (formerly Nextflow Tower)",
 )
 @click.option(
-    "-d",
+    "-c",
     "--download-configuration",
-    is_flag=True,
-    default=False,
+    type=click.Choice(["yes", "no"]),
+    default="no",
     help="Include configuration profiles in download. Not available with `--platform`",
 )
 @click.option(
@@ -420,7 +412,7 @@ def command_pipelines_lint(
     help="List of images already available in a remote `singularity.cacheDir`.",
 )
 @click.option(
-    "-p",
+    "-d",
     "--parallel-downloads",
     type=int,
     default=4,
@@ -434,7 +426,6 @@ def command_pipelines_download(
     outdir,
     compress,
     force,
-    tower,
     platform,
     download_configuration,
     tag,
@@ -454,7 +445,6 @@ def command_pipelines_download(
         outdir,
         compress,
         force,
-        tower,
         platform,
         download_configuration,
         tag,
@@ -2120,8 +2110,7 @@ def command_download(
         outdir,
         compress,
         force,
-        tower,
-        platform,
+        platform or tower,
         download_configuration,
         tag,
         container_system,

nf_core/commands_pipelines.py

@@ -167,7 +167,6 @@ def pipelines_download(
     outdir,
     compress,
     force,
-    tower,
     platform,
     download_configuration,
     tag,
@@ -185,16 +184,13 @@ def pipelines_download(
     """
     from nf_core.pipelines.download import DownloadWorkflow
 
-    if tower:
-        log.warning("[red]The `-t` / `--tower` flag is deprecated. Please use `--platform` instead.[/]")
-
     dl = DownloadWorkflow(
         pipeline,
         revision,
         outdir,
         compress,
         force,
-        tower or platform,  # True if either specified
+        platform,
         download_configuration,
         tag,
         container_system,

nf_core/pipeline-template/.github/workflows/download_pipeline.yml

@@ -65,7 +65,7 @@ jobs:
           --container-system 'singularity' \
           --container-library "quay.io" -l "docker.io" -l "ghcr.io" \
           --container-cache-utilisation 'amend' \
-          --download-configuration
+          --download-configuration 'yes'
 
       - name: Inspect download
         run: tree ./${{ env.REPOTITLE_LOWERCASE }}{% endraw %}{% if test_config %}{% raw %}

nf_core/pipelines/download.py

@@ -133,10 +133,8 @@ def __init__(
         self.force = force
         self.platform = platform
         self.fullname: Optional[str] = None
-        # if flag is not specified, do not assume deliberate choice and prompt config inclusion interactively.
-        # this implies that non-interactive "no" choice is only possible implicitly (e.g. with --platform or if prompt is suppressed by !stderr.is_interactive).
-        # only alternative would have been to make it a parameter with argument, e.g. -d="yes" or -d="no".
-        self.include_configs = True if download_configuration else False if bool(platform) else None
+        # downloading configs is not supported for Seqera Platform downloads.
+        self.include_configs = True if download_configuration == "yes" and not bool(platform) else False
         # Additional tags to add to the downloaded pipeline. This enables to mark particular commits or revisions with
         # additional tags, e.g. "stable", "testing", "validated", "production" etc. Since this requires a git-repo, it is only
         # available for the bare / Seqera Platform download.

tests/test_cli.py

@@ -167,7 +167,7 @@ def test_cli_download(self, mock_dl):
             "compress": "tar.gz",
             "force": None,
             "platform": None,
-            "download-configuration": None,
+            "download-configuration": "yes",
             "tag": "3.12=testing",
             "container-system": "singularity",
             "container-library": "quay.io",
@@ -188,7 +188,7 @@ def test_cli_download(self, mock_dl):
             params["compress"],
             "force" in params,
             "platform" in params,
-            "download-configuration" in params,
+            params["download-configuration"],
             (params["tag"],),
             params["container-system"],
             (params["container-library"],),