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Merge pull request #3036 from mirpedrol/deprecation-message
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Add warning deprecation message to top-level commands
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@mirpedrol
mirpedrol authored Jun 25, 2024
2 parents b8c5533 + 31b3663 commit 020e9e3
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1 change: 1 addition & 0 deletions CHANGELOG.md
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Original file line number Diff line number Diff line change
Expand Up @@ -34,6 +34,7 @@
- Update python:3.12-slim Docker digest to e3ae8cf ([#3020](https://github.com/nf-core/tools/pull/3020))
- Update python:3.12-slim Docker digest to 2fba8e7 ([#3023](https://github.com/nf-core/tools/pull/3023))
- Update pre-commit hook astral-sh/ruff-pre-commit to v0.4.10 ([#3031](https://github.com/nf-core/tools/pull/3031))
- Add warning deprecation message to top-level commands ([#3036](https://github.com/nf-core/tools/pull/3036))

## [v2.14.1 - Tantalum Toad - Patch](https://github.com/nf-core/tools/releases/tag/2.14.1) - [2024-05-09]

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261 changes: 233 additions & 28 deletions nf_core/__main__.py
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Original file line number Diff line number Diff line change
Expand Up @@ -641,7 +641,7 @@ def launch_pipeline(
sys.exit(1)


# nf-core pipelnies list
# nf-core pipelines list
@pipelines.command("list")
@click.argument("keywords", required=False, nargs=-1, metavar="<filter keywords>")
@click.option(
Expand Down Expand Up @@ -2248,10 +2248,24 @@ def validate(pipeline, params):
This command takes such a file and validates it against the pipeline
schema, checking whether all schema rules are satisfied.
"""
log.error(
log.warning(
"The `[magenta]nf-core schema validate[/]` command is deprecated. Use `[magenta]nf-core pipelines schema validate[/]` instead."
)
sys.exit(0)
from nf_core.pipelines.schema import PipelineSchema

schema_obj = PipelineSchema()
try:
schema_obj.get_schema_path(pipeline)
# Load and check schema
schema_obj.load_lint_schema()
except AssertionError as e:
log.error(e)
sys.exit(1)
schema_obj.load_input_params(params)
try:
schema_obj.validate_params()
except AssertionError:
sys.exit(1)


# nf-core schema build (deprecated)
Expand Down Expand Up @@ -2292,10 +2306,18 @@ def build(dir, no_prompts, web_only, url):
https://nf-co.re website where you can annotate and organise parameters.
Listens for this to be completed and saves the updated schema.
"""
log.error(
log.warning(
"The `[magenta]nf-core schema build[/]` command is deprecated. Use `[magenta]nf-core pipelines schema build[/]` instead."
)
sys.exit(0)
from nf_core.pipelines.schema import PipelineSchema

try:
schema_obj = PipelineSchema()
if schema_obj.build_schema(dir, no_prompts, web_only, url) is False:
sys.exit(1)
except (UserWarning, AssertionError) as e:
log.error(e)
sys.exit(1)


# nf-core schema lint (deprecated)
Expand All @@ -2319,10 +2341,22 @@ def schema_lint(schema_path):
If no schema path is provided, "nextflow_schema.json" will be used (if it exists).
"""
log.error(
log.warning(
"The `[magenta]nf-core schema lint[/]` command is deprecated. Use `[magenta]nf-core pipelines schema lint[/]` instead."
)
sys.exit(0)
from nf_core.pipelines.schema import PipelineSchema

schema_obj = PipelineSchema()
try:
schema_obj.get_schema_path(schema_path)
schema_obj.load_lint_schema()
# Validate title and description - just warnings as schema should still work fine
try:
schema_obj.validate_schema_title_description()
except AssertionError as e:
log.warning(e)
except AssertionError:
sys.exit(1)


# nf-core schema docs (deprecated)
Expand Down Expand Up @@ -2362,10 +2396,20 @@ def docs(schema_path, output, format, force, columns):
DEPRECATED
Outputs parameter documentation for a pipeline schema.
"""
log.error(
log.warning(
"The `[magenta]nf-core schema docs[/]` command is deprecated. Use `[magenta]nf-core pipelines schema docs[/]` instead."
)
sys.exit(0)
if not os.path.exists(schema_path):
log.error("Could not find 'nextflow_schema.json' in current directory. Please specify a path.")
sys.exit(1)

from nf_core.pipelines.schema import PipelineSchema

schema_obj = PipelineSchema()
# Assume we're in a pipeline dir root if schema path not set
schema_obj.get_schema_path(schema_path)
schema_obj.load_schema()
schema_obj.print_documentation(output, format, force, columns.split(","))


# nf-core create-logo (deprecated)
Expand Down Expand Up @@ -2413,10 +2457,24 @@ def logo(logo_text, dir, name, theme, width, format, force):
This command generates an nf-core pipeline logo, using the supplied <logo_text>
"""
log.error(
log.warning(
"The `[magenta]nf-core create-logo[/]` command is deprecated. Use `[magenta]nf-core pipelines screate-logo[/]` instead."
)
sys.exit(0)
from nf_core.pipelines.create_logo import create_logo

try:
if dir == ".":
dir = Path.cwd()
logo_path = create_logo(logo_text, dir, name, theme, width, format, force)
# Print path to logo relative to current working directory
try:
logo_path = Path(logo_path).relative_to(Path.cwd())
except ValueError:
logo_path = Path(logo_path)
log.info(f"Created logo: [magenta]{logo_path}[/]")
except UserWarning as e:
log.error(e)
sys.exit(1)


# nf-core sync (deprecated)
Expand Down Expand Up @@ -2464,8 +2522,22 @@ def sync(dir, from_branch, pull_request, github_repository, username, template_y
the pipeline. It is run automatically for all pipelines when ever a
new release of [link=https://github.com/nf-core/tools]nf-core/tools[/link] (and the included template) is made.
"""
log.error("The `[magenta]nf-core sync[/]` command is deprecated. Use `[magenta]nf-core pipelines sync[/]` instead.")
sys.exit(0)
log.warning(
"The `[magenta]nf-core sync[/]` command is deprecated. Use `[magenta]nf-core pipelines sync[/]` instead."
)
from nf_core.pipelines.sync import PipelineSync, PullRequestExceptionError, SyncExceptionError
from nf_core.utils import is_pipeline_directory

# Check if pipeline directory contains necessary files
is_pipeline_directory(dir)

# Sync the given pipeline dir
sync_obj = PipelineSync(dir, from_branch, pull_request, github_repository, username, template_yaml, force_pr)
try:
sync_obj.sync()
except (SyncExceptionError, PullRequestExceptionError) as e:
log.error(e)
sys.exit(1)


# nf-core bump-version (deprecated)
Expand Down Expand Up @@ -2499,10 +2571,28 @@ def bump_version(new_version, dir, nextflow):
As well as the pipeline version, you can also change the required version of Nextflow.
"""
log.error(
log.warning(
"The `[magenta]nf-core bump-version[/]` command is deprecated. Use `[magenta]nf-core pipelines bump-version[/]` instead."
)
sys.exit(0)
from nf_core.pipelines.bump_version import bump_nextflow_version, bump_pipeline_version
from nf_core.utils import Pipeline, is_pipeline_directory

try:
# Check if pipeline directory contains necessary files
is_pipeline_directory(dir)

# Make a pipeline object and load config etc
pipeline_obj = Pipeline(dir)
pipeline_obj._load()

# Bump the pipeline version number
if not nextflow:
bump_pipeline_version(pipeline_obj, new_version)
else:
bump_nextflow_version(pipeline_obj, new_version)
except UserWarning as e:
log.error(e)
sys.exit(1)


# nf-core list (deprecated)
Expand All @@ -2525,8 +2615,12 @@ def list(keywords, sort, json, show_archived):
Checks the web for a list of nf-core pipelines with their latest releases.
Shows which nf-core pipelines you have pulled locally and whether they are up to date.
"""
log.error("The `[magenta]nf-core list[/]` command is deprecated. Use `[magenta]nf-core pipelines list[/]` instead.")
sys.exit(0)
log.warning(
"The `[magenta]nf-core list[/]` command is deprecated. Use `[magenta]nf-core pipelines list[/]` instead."
)
from nf_core.pipelines.list import list_workflows

stdout.print(list_workflows(keywords, sort, json, show_archived))


# nf-core launch (deprecated)
Expand Down Expand Up @@ -2600,10 +2694,24 @@ def launch(
Run using a remote pipeline name (such as GitHub `user/repo` or a URL),
a local pipeline directory or an ID from the nf-core web launch tool.
"""
log.error(
log.warning(
"The `[magenta]nf-core launch[/]` command is deprecated. Use `[magenta]nf-core pipelines launch[/]` instead."
)
sys.exit(0)
from nf_core.pipelines.launch import Launch

launcher = Launch(
pipeline,
revision,
command_only,
params_in,
params_out,
save_all,
show_hidden,
url,
id,
)
if not launcher.launch_pipeline():
sys.exit(1)


# nf-core create-params-file (deprecated)
Expand Down Expand Up @@ -2639,10 +2747,13 @@ def create_params_file(pipeline, revision, output, force, show_hidden):
Run using a remote pipeline name (such as GitHub `user/repo` or a URL),
a local pipeline directory.
"""
log.error(
log.warning(
"The `[magenta]nf-core create-params-file[/]` command is deprecated. Use `[magenta]nf-core pipelines create-params-file[/]` instead."
)
sys.exit(0)
builder = ParamsFileBuilder(pipeline, revision)

if not builder.write_params_file(output, show_hidden=show_hidden, force=force):
sys.exit(1)


# nf-core download (deprecated)
Expand Down Expand Up @@ -2742,10 +2853,30 @@ def download(
Collects all files in a single archive and configures the downloaded
workflow to use relative paths to the configs and singularity images.
"""
log.error(
log.warning(
"The `[magenta]nf-core download[/]` command is deprecated. Use `[magenta]nf-core pipelines download[/]` instead."
)
sys.exit(0)
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
download_configuration,
tag,
container_system,
container_library,
container_cache_utilisation,
container_cache_index,
parallel_downloads,
)
dl.download_workflow()


# nf-core lint (deprecated)
Expand Down Expand Up @@ -2828,8 +2959,45 @@ def lint(
You can ignore tests using a file called [blue].nf-core.yml[/] [i](if you have a good reason!)[/].
See the documentation for details.
"""
log.error("The `[magenta]nf-core lint[/]` command is deprecated. Use `[magenta]nf-core pipelines lint[/]` instead.")
sys.exit(0)
log.warning(
"The `[magenta]nf-core lint[/]` command is deprecated. Use `[magenta]nf-core pipelines lint[/]` instead."
)
from nf_core.pipelines.lint import run_linting
from nf_core.utils import is_pipeline_directory

# Check if pipeline directory is a pipeline
try:
is_pipeline_directory(dir)
except UserWarning as e:
log.error(e)
sys.exit(1)

# Run the lint tests!
try:
lint_obj, module_lint_obj, subworkflow_lint_obj = run_linting(
dir,
release,
fix,
key,
show_passed,
fail_ignored,
fail_warned,
sort_by,
markdown,
json,
ctx.obj["hide_progress"],
)
swf_failed = 0
if subworkflow_lint_obj is not None:
swf_failed = len(subworkflow_lint_obj.failed)
if len(lint_obj.failed) + len(module_lint_obj.failed) + swf_failed > 0:
sys.exit(1)
except AssertionError as e:
log.critical(e)
sys.exit(1)
except UserWarning as e:
log.error(e)
sys.exit(1)


# nf-core create (deprecated)
Expand All @@ -2847,18 +3015,55 @@ def lint(
@click.option("-o", "--outdir", help="Output directory for new pipeline (default: pipeline name)")
@click.option("-t", "--template-yaml", help="Pass a YAML file to customize the template")
@click.option("--plain", is_flag=True, help="Use the standard nf-core template")
def create(name, description, author, version, force, outdir, template_yaml, plain):
@click.option(
"--organisation",
type=str,
default="nf-core",
help="The name of the GitHub organisation where the pipeline will be hosted (default: nf-core)",
)
def create(name, description, author, version, force, outdir, template_yaml, plain, organisation):
"""
DEPRECATED
Create a new pipeline using the nf-core template.
Uses the nf-core template to make a skeleton Nextflow pipeline with all required
files, boilerplate code and best-practices.
"""
log.error(
log.warning(
"The `[magenta]nf-core create[/]` command is deprecated. Use `[magenta]nf-core pipelines create[/]` instead."
)
sys.exit(0)
from nf_core.pipelines.create import PipelineCreateApp
from nf_core.pipelines.create.create import PipelineCreate

if (name and description and author) or (template_yaml):
# If all command arguments are used, run without the interactive interface
try:
create_obj = PipelineCreate(
name,
description,
author,
version=version,
force=force,
outdir=outdir,
template_config=template_yaml,
organisation=organisation,
)
create_obj.init_pipeline()
except UserWarning as e:
log.error(e)
sys.exit(1)
elif name or description or author or version != "1.0.0dev" or force or outdir or organisation != "nf-core":
log.error(
"[red]Partial arguments supplied.[/] "
"Run without [i]any[/] arguments for an interactive interface, "
"or with at least name + description + author to use non-interactively."
)
sys.exit(1)
else:
log.info("Launching interactive nf-core pipeline creation tool.")
app = PipelineCreateApp()
app.run()
sys.exit(app.return_code or 0)


# Main script is being run - launch the CLI
Expand Down

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