modules create-test-yml - prompt to set profile to docker, singularit…

…y or conda
nf-core · drpatelh · Mar 15, 2021 · Mar 15, 2021 · Mar 15, 2021 · Mar 15, 2021
commit 5e82962d5e34cdb4486f49e820af5e7046bcadab
diff --git a/nf_core/launch.py b/nf_core/launch.py
@@ -10,36 +10,15 @@
 import json
 import logging
 import os
-import prompt_toolkit
 import questionary
 import re
 import subprocess
-import textwrap
 import webbrowser
 
 import nf_core.schema, nf_core.utils
 
 log = logging.getLogger(__name__)
 
-# Custom style for questionary
-nfcore_question_style = prompt_toolkit.styles.Style(
-    [
-        ("qmark", "fg:ansiblue bold"),  # token in front of the question
-        ("question", "bold"),  # question text
-        ("answer", "fg:ansigreen nobold"),  # submitted answer text behind the question
-        ("pointer", "fg:ansiyellow bold"),  # pointer used in select and checkbox prompts
-        ("highlighted", "fg:ansiblue bold"),  # pointed-at choice in select and checkbox prompts
-        ("selected", "fg:ansigreen noreverse"),  # style for a selected item of a checkbox
-        ("separator", "fg:ansiblack"),  # separator in lists
-        ("instruction", ""),  # user instructions for select, rawselect, checkbox
-        ("text", ""),  # plain text
-        ("disabled", "fg:gray italic"),  # disabled choices for select and checkbox prompts
-        ("choice-default", "fg:ansiblack"),
-        ("choice-default-changed", "fg:ansiyellow"),
-        ("choice-required", "fg:ansired"),
-    ]
-)
-
 
 class Launch(object):
     """ Class to hold config option to launch a pipeline """
@@ -268,7 +247,7 @@ def prompt_web_gui(self):
             "choices": ["Web based", "Command line"],
             "default": "Web based",
         }
-        answer = questionary.unsafe_prompt([question], style=nfcore_question_style)
+        answer = questionary.unsafe_prompt([question], style=nf_core.utils.nfcore_question_style)
         return answer["use_web_gui"] == "Web based"
 
     def launch_web_gui(self):
@@ -405,12 +384,12 @@ def prompt_param(self, param_id, param_obj, is_required, answers):
 
         # Print the question
         question = self.single_param_to_questionary(param_id, param_obj, answers)
-        answer = questionary.unsafe_prompt([question], style=nfcore_question_style)
+        answer = questionary.unsafe_prompt([question], style=nf_core.utils.nfcore_question_style)
 
         # If required and got an empty reponse, ask again
         while type(answer[param_id]) is str and answer[param_id].strip() == "" and is_required:
             log.error("'–-{}' is required".format(param_id))
-            answer = questionary.unsafe_prompt([question], style=nfcore_question_style)
+            answer = questionary.unsafe_prompt([question], style=nf_core.utils.nfcore_question_style)
 
         # Ignore if empty
         if answer[param_id] == "":
@@ -480,7 +459,7 @@ def prompt_group(self, group_id, group_obj):
             if len(question["choices"]) == 2:
                 return {}
 
-            answer = questionary.unsafe_prompt([question], style=nfcore_question_style)
+            answer = questionary.unsafe_prompt([question], style=nf_core.utils.nfcore_question_style)
             if answer[group_id] == "Continue >>":
                 while_break = True
                 # Check if there are any required parameters that don't have answers

diff --git a/nf_core/modules/pipeline_modules.py b/nf_core/modules/pipeline_modules.py
@@ -17,13 +17,14 @@
 import json
 import logging
 import os
-import prompt_toolkit
 import questionary
 import requests
 import rich
 import shutil
 import sys
 
+import nf_core.utils
+
 log = logging.getLogger(__name__)
 
 
@@ -95,9 +96,8 @@ def install(self, module=None):
         self.get_modules_file_tree()
 
         if module is None:
-            nfcore_question_style = prompt_toolkit.styles.Style([("answer", "fg:ansigreen nobold bg:")])
             module = questionary.autocomplete(
-                "Choose module", choices=self.modules_avail_module_names, style=nfcore_question_style
+                "Choose module", choices=self.modules_avail_module_names, style=nf_core.utils.nfcore_question_style
             ).ask()
 
         log.info("Installing {}".format(module))

diff --git a/nf_core/modules/test_yml_builder.py b/nf_core/modules/test_yml_builder.py
@@ -5,21 +5,22 @@
 """
 
 from __future__ import print_function
-from rich.console import Console
-from rich.syntax import Syntax
 
 import errno
 import hashlib
 import logging
 import os
 import re
-import rich
 import shlex
 import subprocess
 import tempfile
-import yaml
 
 import nf_core.utils
+import questionary
+import rich
+import yaml
+from rich.console import Console
+from rich.syntax import Syntax
 
 log = logging.getLogger(__name__)
 
@@ -222,12 +223,25 @@ def run_tests_workflow(self, command):
 
         # The config expects $PROFILE and Nextflow fails if it's not set
         if os.environ.get("PROFILE") is None:
-            log.info(
-                "Setting env var '$PROFILE' to an empty string as not set.\n"
-                "Tests will run with Docker by default. "
-                "To use Singularity set 'export PROFILE=singularity' in your shell before running this command."
-            )
             os.environ["PROFILE"] = ""
+            if self.no_prompts:
+                log.info(
+                    "Setting env var '$PROFILE' to an empty string as not set.\n"
+                    "Tests will run with Docker by default. "
+                    "To use Singularity set 'export PROFILE=singularity' in your shell before running this command."
+                )
+            else:
+                question = {
+                    "type": "list",
+                    "name": "profile",
+                    "message": "Choose software profile",
+                    "choices": ["Docker", "Singularity", "Conda"],
+                }
+                answer = questionary.unsafe_prompt([question], style=nf_core.utils.nfcore_question_style)
+                profile = answer["profile"].lower()
+                if profile in ["singularity", "conda"]:
+                    os.environ["PROFILE"] = profile
+                    log.info(f"Setting env var '$PROFILE' to '{profile}'")
 
         tmp_dir = tempfile.mkdtemp()
         command += f" --outdir {tmp_dir}"

diff --git a/nf_core/utils.py b/nf_core/utils.py
@@ -12,6 +12,7 @@
 import json
 import logging
 import os
+import prompt_toolkit
 import re
 import requests
 import requests_cache
@@ -25,6 +26,24 @@
 
 log = logging.getLogger(__name__)
 
+# Custom style for questionary
+nfcore_question_style = prompt_toolkit.styles.Style(
+    [
+        ("qmark", "fg:ansiblue bold"),  # token in front of the question
+        ("question", "bold"),  # question text
+        ("answer", "fg:ansigreen nobold"),  # submitted answer text behind the question
+        ("pointer", "fg:ansiyellow bold"),  # pointer used in select and checkbox prompts
+        ("highlighted", "fg:ansiblue bold"),  # pointed-at choice in select and checkbox prompts
+        ("selected", "fg:ansigreen noreverse"),  # style for a selected item of a checkbox
+        ("separator", "fg:ansiblack"),  # separator in lists
+        ("instruction", ""),  # user instructions for select, rawselect, checkbox
+        ("text", ""),  # plain text
+        ("disabled", "fg:gray italic"),  # disabled choices for select and checkbox prompts
+        ("choice-default", "fg:ansiblack"),
+        ("choice-default-changed", "fg:ansiyellow"),
+        ("choice-required", "fg:ansired"),
+    ]
+)
 
 def check_if_outdated(current_version=None, remote_version=None, source_url="https://nf-co.re/tools_version"):
     """