Use Rich.prompt Confirm.ask instead of click.confirm

See nf-core#682 (comment)

nf_core/launch.py

@@ -4,8 +4,8 @@
 from __future__ import print_function
 from rich.console import Console
 from rich.markdown import Markdown
+from rich.prompt import Confirm
 
-import click
 import copy
 import json
 import logging
@@ -112,11 +112,7 @@ def launch_pipeline(self):
         # Check if the output file exists already
         if os.path.exists(self.params_out):
             log.warning("Parameter output file already exists! {}".format(os.path.relpath(self.params_out)))
-            if click.confirm(
-                click.style("Do you want to overwrite this file? ", fg="yellow") + click.style("[y/N]", fg="red"),
-                default=False,
-                show_default=False,
-            ):
+            if Confirm.ask("[yellow]Do you want to overwrite this file?"):
                 os.remove(self.params_out)
                 log.info("Deleted {}\n".format(self.params_out))
             else:
@@ -248,9 +244,9 @@ def merge_nxf_flag_schema(self):
 
     def prompt_web_gui(self):
         """ Ask whether to use the web-based or cli wizard to collect params """
-        click.secho(
-            "\nWould you like to enter pipeline parameters using a web-based interface or a command-line wizard?\n",
-            fg="magenta",
+        log.info(
+            "[magenta]Would you like to enter pipeline parameters using a web-based interface or a command-line wizard?",
+            extra={"markup": True},
         )
         question = {
             "type": "list",
@@ -407,7 +403,7 @@ def prompt_param(self, param_id, param_obj, is_required, answers):
 
         # If required and got an empty reponse, ask again
         while type(answer[param_id]) is str and answer[param_id].strip() == "" and is_required:
-            click.secho("Error - this property is required.", fg="red", err=True)
+            log.error("This property is required.")
             answer = PyInquirer.prompt([question])
             # TODO: use raise_keyboard_interrupt=True when PyInquirer 1.0.3 is released
             if answer == {}:
@@ -464,7 +460,7 @@ def prompt_group(self, param_id, param_obj):
                         req_default = self.schema_obj.input_params.get(p_required, "")
                         req_answer = answers.get(p_required, "")
                         if req_default == "" and req_answer == "":
-                            click.secho("Error - '{}' is required.".format(p_required), fg="red", err=True)
+                            log.error("Error - [bold]'{}'[/] is required.".format(p_required), extra={"markup": True})
                             while_break = False
             else:
                 child_param = answer[param_id]
@@ -708,14 +704,9 @@ def build_command(self):
     def launch_workflow(self):
         """ Launch nextflow if required  """
         log.info(
-            "[bold underline]Nextflow command:{}[/]\n  [magenta]{}\n\n".format(self.nextflow_cmd),
-            extra={"markup": True},
+            "[bold underline]Nextflow command:[/]\n[magenta]{}\n\n".format(self.nextflow_cmd), extra={"markup": True},
         )
 
-        if click.confirm(
-            "Do you want to run this command now? " + click.style("[y/N]", fg="green"),
-            default=False,
-            show_default=False,
-        ):
-            log.info("Launching workflow!")
+        if Confirm.ask("Do you want to run this command now? "):
+            log.info("Launching workflow! :rocket:", extra={"markup": True})
             subprocess.call(self.nextflow_cmd, shell=True)

nf_core/schema.py

@@ -2,8 +2,8 @@
 """ Code to deal with pipeline JSON Schema """
 
 from __future__ import print_function
+from rich.prompt import Confirm
 
-import click
 import copy
 import jinja2
 import json
@@ -244,7 +244,7 @@ def build_schema(self, pipeline_dir, no_prompts, web_only, url):
 
         # If running interactively, send to the web for customisation
         if not self.no_prompts:
-            if click.confirm(click.style("\nLaunch web builder for customisation and editing?", fg="magenta"), True):
+            if Confirm.ask(":rocket: Launch web builder for customisation and editing?"):
                 try:
                     self.launch_web_builder()
                 except AssertionError as e:
@@ -334,13 +334,6 @@ def remove_schema_notfound_configs(self):
                     log.debug("Removing '{}' from JSON Schema".format(p_key))
                     params_removed.append(p_key)
 
-        if len(params_removed) > 0:
-            log.info(
-                "Removed {} params from existing JSON Schema that were not found with `nextflow config`:\n {}\n".format(
-                    len(params_removed), ", ".join(params_removed)
-                )
-            )
-
         return params_removed
 
     def prompt_remove_schema_notfound_config(self, p_key):
@@ -350,13 +343,11 @@ def prompt_remove_schema_notfound_config(self, p_key):
         Returns True if it should be removed, False if not.
         """
         if p_key not in self.pipeline_params.keys():
-            p_key_nice = click.style("params.{}".format(p_key), fg="white", bold=True)
-            remove_it_nice = click.style("Remove it?", fg="yellow")
-            if (
-                self.no_prompts
-                or self.schema_from_scratch
-                or click.confirm(
-                    "Unrecognised '{}' found in schema but not pipeline. {}".format(p_key_nice, remove_it_nice), True
+            if self.no_prompts or self.schema_from_scratch:
+                return True
+            if Confirm.ask(
+                ":question: Unrecognised [white bold]'params.{}'[/] found in schema but not pipeline! [yellow]Remove it?".format(
+                    p_key
                 )
             ):
                 return True
@@ -372,24 +363,18 @@ def add_schema_found_configs(self):
             if not p_key in self.schema["properties"].keys():
                 # Check if key is in group-level params
                 if not any([p_key in param.get("properties", {}) for k, param in self.schema["properties"].items()]):
-                    p_key_nice = click.style("params.{}".format(p_key), fg="white", bold=True)
-                    add_it_nice = click.style("Add to JSON Schema?", fg="cyan")
                     if (
                         self.no_prompts
                         or self.schema_from_scratch
-                        or click.confirm(
-                            "Found '{}' in pipeline but not in schema. {}".format(p_key_nice, add_it_nice), True
+                        or Confirm.ask(
+                            ":sparkles: Found [white bold]'params.{}'[/] in pipeline but not in schema! [blue]Add to JSON Schema?".format(
+                                p_key
+                            )
                         )
                     ):
                         self.schema["properties"][p_key] = self.build_schema_param(p_val)
                         log.debug("Adding '{}' to JSON Schema".format(p_key))
                         params_added.append(p_key)
-        if len(params_added) > 0:
-            log.info(
-                "Added {} params to JSON Schema that were found with `nextflow config`:\n {}".format(
-                    len(params_added), ", ".join(params_added)
-                )
-            )
 
         return params_added
 

setup.py

@@ -40,7 +40,7 @@
         "pyyaml",
         "requests",
         "requests_cache",
-        "rich",
+        "rich>=3.4.0",
         "tabulate",
     ],
     setup_requires=["twine>=1.11.0", "setuptools>=38.6."],