Add nf-core configs create sub command (attempt 2)

CHANGELOG.md

@@ -426,6 +426,10 @@ We also enabled to install subworkflows with modules from different remotes.
 | `-p` / `--parallel-downloads`     | `-d` / `--parallel-downloads`     |
 | new parameter                     | `-p` / (`--platform`)             |
 
+### Configs
+
+- New command: `nf-core configs create wizard` for generating configs for nf-core pipelines ([#3001](https://github.com/nf-core/tools/pull/3001))
+
 ### General
 
 - Change default branch to `main` for the nf-core/tools repository

MANIFEST.in

@@ -9,5 +9,5 @@ include nf_core/assets/logo/nf-core-repo-logo-base-lightbg.png
 include nf_core/assets/logo/nf-core-repo-logo-base-darkbg.png
 include nf_core/assets/logo/placeholder_logo.svg
 include nf_core/assets/logo/MavenPro-Bold.ttf
-include nf_core/pipelines/create/create.tcss
+include nf_core/textual.tcss
 include nf_core/pipelines/create/template_features.yml

nf_core/__main__.py

@@ -63,7 +63,12 @@
 from nf_core.components.constants import NF_CORE_MODULES_REMOTE
 from nf_core.pipelines.download import DownloadError
 from nf_core.pipelines.list import autocomplete_pipelines
-from nf_core.utils import check_if_outdated, nfcore_logo, rich_force_colors, setup_nfcore_dir
+from nf_core.utils import (
+    check_if_outdated,
+    nfcore_logo,
+    rich_force_colors,
+    setup_nfcore_dir,
+)
 
 # Set up logging as the root logger
 # Submodules should all traverse back to this
@@ -79,7 +84,7 @@
     "nf-core": [
         {
             "name": "Commands",
-            "commands": ["pipelines", "modules", "subworkflows", "test-datasets", "interface"],
+            "commands": ["pipelines", "modules", "subworkflows", "configs", "test-datasets", "interface"],
         },
     ],
     "nf-core pipelines": [
@@ -89,7 +94,15 @@
         },
         {
             "name": "For developers",
-            "commands": ["create", "lint", "bump-version", "sync", "schema", "rocrate", "create-logo"],
+            "commands": [
+                "create",
+                "lint",
+                "bump-version",
+                "sync",
+                "schema",
+                "rocrate",
+                "create-logo",
+            ],
         },
     ],
     "nf-core modules": [
@@ -112,13 +125,18 @@
             "commands": ["create", "lint", "test"],
         },
     ],
+    "nf-core configs": [
+        {
+            "name": "Config commands",
+            "commands": ["create"],
+        },
+    ],
     "nf-core pipelines schema": [{"name": "Schema commands", "commands": ["validate", "build", "lint", "docs"]}],
     "nf-core test-datasets": [{"name": "For developers", "commands": ["search", "list", "list-branches"]}],
 }
 click.rich_click.OPTION_GROUPS = {
     "nf-core modules list local": [{"options": ["--dir", "--json", "--help"]}],
 }
-
 # Set up rich stderr console
 stderr = rich.console.Console(stderr=True, force_terminal=rich_force_colors())
 stdout = rich.console.Console(force_terminal=rich_force_colors())
@@ -262,7 +280,13 @@ def pipelines(ctx):
 @click.option("-d", "--description", type=str, help="A short description of your pipeline")
 @click.option("-a", "--author", type=str, help="Name of the main author(s)")
 @click.option("--version", type=str, default="1.0.0dev", help="The initial version number to use")
-@click.option("-f", "--force", is_flag=True, default=False, help="Overwrite output directory if it already exists")
+@click.option(
+    "-f",
+    "--force",
+    is_flag=True,
+    default=False,
+    help="Overwrite output directory if it already exists",
+)
 @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(
@@ -1877,6 +1901,18 @@ def command_subworkflows_update(
     )
 
 
+# nf-core configs subcommands
+@nf_core_cli.group()
+@click.pass_context
+def configs(ctx):
+    """
+    Commands to manage nf-core configs.
+    """
+    # ensure that ctx.obj exists and is a dict (in case `cli()` is called
+    # by means other than the `if` block below)
+    ctx.ensure_object(dict)
+
+
 # nf-core test-dataset subcommands
 @nf_core_cli.group()
 @click.pass_context
@@ -1889,6 +1925,25 @@ def test_datasets(ctx):
     ctx.ensure_object(dict)
 
 
+# nf-core configs create
+@configs.command("create")
+@click.pass_context
+def create_configs(ctx):
+    """
+    Command to interactively create a nextflow or nf-core config
+    """
+    from nf_core.configs.create import ConfigsCreateApp
+
+    try:
+        log.info("Launching interactive nf-core configs creation tool.")
+        app = ConfigsCreateApp()
+        app.run()
+        sys.exit(app.return_code or 0)
+    except UserWarning as e:
+        log.error(e)
+        sys.exit(1)
+
+
 # nf-core test-dataset search
 @test_datasets.command("search", short_help="Search files in the nf-core/test-datasets repository")
 @click.pass_context

nf_core/configs/__init__.py

@@ -0,0 +1 @@
+from .create import ConfigsCreateApp

nf_core/configs/create/__init__.py

@@ -0,0 +1,116 @@
+"""A Textual app to create a config."""
+
+import logging
+
+import click
+from rich.logging import RichHandler
+
+## Textual objects
+from textual.app import App
+from textual.widgets import Button
+
+from nf_core.configs.create import utils
+
+## nf-core question page (screen) imports
+from nf_core.configs.create.basicdetails import BasicDetails
+from nf_core.configs.create.configtype import ChooseConfigType
+from nf_core.configs.create.final import FinalScreen
+from nf_core.configs.create.finalinfradetails import FinalInfraDetails
+from nf_core.configs.create.hpccustomisation import HpcCustomisation
+from nf_core.configs.create.hpcquestion import ChooseHpc
+from nf_core.configs.create.nfcorequestion import ChooseNfcoreConfig
+from nf_core.configs.create.welcome import WelcomeScreen
+
+## General utilities
+from nf_core.utils import LoggingConsole
+
+## Logging
+logger = logging.getLogger(__name__)
+rich_log_handler = RichHandler(
+    console=LoggingConsole(classes="log_console"),
+    level=logging.INFO,
+    rich_tracebacks=True,
+    show_time=False,
+    show_path=False,
+    markup=True,
+    tracebacks_suppress=[click],
+)
+logger.addHandler(rich_log_handler)
+
+
+## Main workflow
+class ConfigsCreateApp(App[utils.ConfigsCreateConfig]):
+    """A Textual app to create nf-core configs."""
+
+    CSS_PATH = "../../textual.tcss"
+    TITLE = "nf-core configs create"
+    SUB_TITLE = "Create a new nextflow config with an interactive interface"
+    BINDINGS = [
+        ("d", "toggle_dark", "Toggle dark mode"),
+        ("q", "quit", "Quit"),
+    ]
+
+    ## New question screens (sections) loaded here
+    SCREENS = {
+        "welcome": WelcomeScreen,
+        "choose_type": ChooseConfigType,
+        "nfcore_question": ChooseNfcoreConfig,
+        "basic_details": BasicDetails,
+        "final": FinalScreen,
+        "hpc_question": ChooseHpc,
+        "hpc_customisation": HpcCustomisation,
+        "final_infra_details": FinalInfraDetails,
+    }
+
+    # Initialise config as empty
+    TEMPLATE_CONFIG = utils.ConfigsCreateConfig()
+
+    # Tracking variables
+    CONFIG_TYPE = None
+    NFCORE_CONFIG = True
+
+    # Log handler
+    LOG_HANDLER = rich_log_handler
+    # Logging state
+    LOGGING_STATE = None
+
+    ## Question dialogue order defined here
+    def on_mount(self) -> None:
+        self.push_screen("welcome")
+
+    def on_button_pressed(self, event: Button.Pressed) -> None:
+        """Handle all button pressed events."""
+        if event.button.id == "lets_go":
+            self.push_screen("choose_type")
+        elif event.button.id == "type_infrastructure":
+            self.CONFIG_TYPE = "infrastructure"
+            utils.CONFIG_ISINFRASTRUCTURE_GLOBAL = True
+            self.push_screen("nfcore_question")
+        elif event.button.id == "type_nfcore":
+            self.NFCORE_CONFIG = True
+            utils.NFCORE_CONFIG_GLOBAL = True
+            self.push_screen("basic_details")
+        elif event.button.id == "type_pipeline":
+            self.CONFIG_TYPE = "pipeline"
+            utils.CONFIG_ISINFRASTRUCTURE_GLOBAL = False
+            self.push_screen("nfcore_question")
+        elif event.button.id == "type_custom":
+            self.NFCORE_CONFIG = False
+            utils.NFCORE_CONFIG_GLOBAL = False
+            self.push_screen("basic_details")
+        elif event.button.id == "type_hpc":
+            self.push_screen("hpc_customisation")
+        elif event.button.id == "toconfiguration":
+            self.push_screen("final_infra_details")
+        elif event.button.id == "finish":
+            self.push_screen("final")
+        ## General options
+        if event.button.id == "close_app":
+            self.exit(return_code=0)
+        if event.button.id == "back":
+            self.pop_screen()
+
+    ## User theme options
+    def action_toggle_dark(self) -> None:
+        """An action to toggle dark mode."""
+        self.theme: str = "textual-dark" if self.theme == "textual-light" else "textual-light"

nf_core/configs/create/basicdetails.py

@@ -0,0 +1,130 @@
+"""Get basic contact information to set in params to help with debugging. By
+displaying such info in the pipeline run header on run execution"""
+
+from textwrap import dedent
+
+from textual import on
+from textual.app import ComposeResult
+from textual.containers import Center, Horizontal
+from textual.screen import Screen
+from textual.widgets import Button, Footer, Header, Input, Markdown
+
+from nf_core.configs.create.utils import (
+    ConfigsCreateConfig,
+    TextInput,
+)  ## TODO Move somewhere common?
+from nf_core.utils import add_hide_class, remove_hide_class
+
+config_exists_warn = """
+> ⚠️  **The config file you are trying to create already exists.**
+>
+> If you continue, you will **overwrite** the existing config.
+> Please change the config name to create a different config!.
+"""
+
+
+class BasicDetails(Screen):
+    """Name, description, author, etc."""
+
+    def compose(self) -> ComposeResult:
+        yield Header()
+        yield Footer()
+        yield Markdown(
+            dedent(
+                """
+                # Basic details
+                """
+            )
+        )
+        ## TODO Add validation, <config_name>.conf already exists?
+        yield TextInput(
+            "general_config_name",
+            "custom",
+            "Config Name. Used for naming resulting file.",
+            "",
+            classes="column",
+        )
+        with Horizontal():
+            yield TextInput(
+                "config_profile_contact",
+                "Boaty McBoatFace",
+                "Author full name.",
+                classes="column hide" if self.parent.CONFIG_TYPE == "pipeline" else "column",
+            )
+            yield TextInput(
+                "config_profile_handle",
+                "@BoatyMcBoatFace",
+                "Author Git(Hub) handle.",
+                classes="column hide" if self.parent.CONFIG_TYPE == "pipeline" else "column",
+            )
+        yield TextInput(
+            "config_pipeline_name",
+            "Pipeline name",
+            "The pipeline name you want to create the config for.",
+            classes="hide" if self.parent.CONFIG_TYPE == "infrastructure" or not self.parent.NFCORE_CONFIG else "",
+        )
+        yield TextInput(
+            "config_pipeline_path",
+            "Pipeline path",
+            "The path to the pipeline you want to create the config for.",
+            classes="hide" if self.parent.CONFIG_TYPE == "infrastructure" or self.parent.NFCORE_CONFIG else "",
+        )
+
+        yield TextInput(
+            "config_profile_description",
+            "Description",
+            "A short description of your config.",
+        )
+        yield TextInput(
+            "config_profile_url",
+            "https://nf-co.re",
+            "URL of infrastructure website or owning institution (infrastructure configs only).",
+            classes="hide" if self.parent.CONFIG_TYPE == "pipeline" else "",
+        )
+        yield Center(
+            Button("Back", id="back", variant="default"),
+            Button("Next", id="next", variant="success"),
+            classes="cta",
+        )
+
+    ## Updates the __init__ initialised TEMPLATE_CONFIG object (which is built from the ConfigsCreateConfig class) with the values from the text inputs
+    @on(Button.Pressed)
+    def on_button_pressed(self, event: Button.Pressed) -> None:
+        """Save fields to the config."""
+        config = {}
+        for text_input in self.query("TextInput"):
+            this_input = text_input.query_one(Input)
+            validation_result = this_input.validate(this_input.value)
+            config[text_input.field_id] = this_input.value
+            if not validation_result.is_valid:
+                text_input.query_one(".validation_msg").update("\n".join(validation_result.failure_descriptions))
+            else:
+                text_input.query_one(".validation_msg").update("")
+        try:
+            self.parent.TEMPLATE_CONFIG = ConfigsCreateConfig(**config)
+            if event.button.id == "next":
+                if self.parent.CONFIG_TYPE == "infrastructure":
+                    self.parent.push_screen("hpc_question")
+                elif self.parent.CONFIG_TYPE == "pipeline":
+                    self.parent.push_screen("final")
+        except ValueError:
+            pass
+
+    def on_screen_resume(self):
+        """Show or hide form fields on resume depending on config type."""
+        if self.parent.CONFIG_TYPE == "pipeline":
+            add_hide_class(self.parent, "config_profile_contact")
+            add_hide_class(self.parent, "config_profile_handle")
+            add_hide_class(self.parent, "config_profile_url")
+            if self.parent.NFCORE_CONFIG:
+                remove_hide_class(self.parent, "config_pipeline_name")
+                add_hide_class(self.parent, "config_pipeline_path")
+            else:
+                remove_hide_class(self.parent, "config_pipeline_path")
+                add_hide_class(self.parent, "config_pipeline_name")
+        if self.parent.CONFIG_TYPE == "infrastructure":
+            remove_hide_class(self.parent, "config_profile_contact")
+            remove_hide_class(self.parent, "config_profile_handle")
+            remove_hide_class(self.parent, "config_profile_url")
+            add_hide_class(self.parent, "config_pipeline_name")
+            add_hide_class(self.parent, "config_pipeline_path")