Do not use pre-release PyInquirer

.github/CONTRIBUTING.md

@@ -18,15 +18,29 @@ is as follows:
 
 If you're not used to this workflow with git, you can start with some [basic docs from GitHub](https://help.github.com/articles/fork-a-repo/).
 
+## Installing dev requirements
+
+If you want to work with developing the nf-core/tools code, you'll need a couple of extra Python packages.
+These are listed in `requirements-dev.txt` and can be installed as follows:
+
+```bash
+pip install --upgrade -r requirements-dev.txt
+```
+
+Then install your local fork of nf-core/tools:
+
+```bash
+pip install -e .
+```
+
 ## Code formatting with Black
 
 All Python code in nf-core/tools must be passed through the [Black Python code formatter](https://black.readthedocs.io/en/stable/).
 This ensures a harmonised code formatting style throughout the package, from all contributors.
 
-You can run Black on the command line - first install using `pip` and then run recursively on the whole repository:
+You can run Black on the command line (it's included in `requirements-dev.txt`) - eg. to run recursively on the whole repository:
 
 ```bash
-pip install black
 black .
 ```
 
@@ -61,7 +75,6 @@ New features should also come with new tests, to keep the test-coverage high (we
 You can try running the tests locally before pushing code using the following command:
 
 ```bash
-pip install --upgrade pip pytest pytest-datafiles pytest-cov mock
 pytest --color=yes tests/
 ```
 

.github/workflows/pytest.yml

@@ -28,8 +28,8 @@ jobs:
 
     - name: Install python dependencies
       run: |
-        python -m pip install --upgrade pip pytest pytest-datafiles pytest-cov mock jsonschema
-        pip install .
+        python -m pip install --upgrade pip -r requirements-dev.txt
+        pip install -e .
 
     - name: Install Nextflow
       run: |

README.md

@@ -67,10 +67,10 @@ pip install --upgrade --force-reinstall git+https://github.com/nf-core/tools.git
 ```
 
 If you intend to make edits to the code, first make a fork of the repository and then clone it locally.
-Go to the cloned directory and either install with pip:
+Go to the cloned directory and install with pip (also installs development requirements):
 
 ```bash
-pip install -e .
+pip install --upgrade -r requirements-dev.txt -e .
 ```
 
 ### Using a specific Python interpreter

nf_core/launch.py

@@ -4,13 +4,13 @@
 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
 import os
-from PyInquirer import prompt, Separator
+import PyInquirer
 import re
 import subprocess
 import textwrap
@@ -21,16 +21,14 @@
 log = logging.getLogger(__name__)
 
 #
-# NOTE: WE ARE USING A PRE-RELEASE VERSION OF PYINQUIRER
-#
-# This is so that we can capture keyboard interruptions in a nicer way
-# with the raise_keyboard_interrupt=True argument in the prompt.prompt() calls
+# NOTE: When PyInquirer 1.0.3 is released we can capture keyboard interruptions
+# in a nicer way # with the raise_keyboard_interrupt=True argument in the PyInquirer.prompt() calls
 # It also allows list selections to have a default set.
 #
-# Waiting for a release of version of >1.0.3 of PyInquirer.
-# See https://github.com/CITGuru/PyInquirer/issues/90
+# Until then we have workarounds:
+# * Default list item is moved to the top of the list
+# * We manually raise a KeyboardInterrupt if we get None back from a question
 #
-# When available, update setup.py to use regular pip version
 
 
 class Launch(object):
@@ -114,11 +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:
@@ -250,17 +244,20 @@ 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",
             "name": "use_web_gui",
             "message": "Choose launch method",
             "choices": ["Web based", "Command line"],
         }
-        answer = prompt.prompt([question], raise_keyboard_interrupt=True)
+        answer = PyInquirer.prompt([question])
+        # TODO: use raise_keyboard_interrupt=True when PyInquirer 1.0.3 is released
+        if answer == {}:
+            raise KeyboardInterrupt
         return answer["use_web_gui"] == "Web based"
 
     def launch_web_gui(self):
@@ -399,12 +396,18 @@ def prompt_param(self, param_id, param_obj, is_required, answers):
 
         # Print the question
         question = self.single_param_to_pyinquirer(param_id, param_obj, answers)
-        answer = prompt.prompt([question], raise_keyboard_interrupt=True)
+        answer = PyInquirer.prompt([question])
+        # TODO: use raise_keyboard_interrupt=True when PyInquirer 1.0.3 is released
+        if answer == {}:
+            raise KeyboardInterrupt
 
         # 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)
-            answer = prompt.prompt([question], raise_keyboard_interrupt=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 == {}:
+                raise KeyboardInterrupt
 
         # Don't return empty answers
         if answer[param_id] == "":
@@ -426,7 +429,7 @@ def prompt_group(self, param_id, param_obj):
             "type": "list",
             "name": param_id,
             "message": param_id,
-            "choices": ["Continue >>", Separator()],
+            "choices": ["Continue >>", PyInquirer.Separator()],
         }
 
         for child_param, child_param_obj in param_obj["properties"].items():
@@ -445,7 +448,10 @@ def prompt_group(self, param_id, param_obj):
         answers = {}
         while not while_break:
             self.print_param_header(param_id, param_obj)
-            answer = prompt.prompt([question], raise_keyboard_interrupt=True)
+            answer = PyInquirer.prompt([question])
+            # TODO: use raise_keyboard_interrupt=True when PyInquirer 1.0.3 is released
+            if answer == {}:
+                raise KeyboardInterrupt
             if answer[param_id] == "Continue >>":
                 while_break = True
                 # Check if there are any required parameters that don't have answers
@@ -454,7 +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("'{}' is required.".format(p_required))
                             while_break = False
             else:
                 child_param = answer[param_id]
@@ -620,6 +626,21 @@ def validate_pattern(val):
 
             question["validate"] = validate_pattern
 
+        # WORKAROUND - PyInquirer <1.0.3 cannot have a default position in a list
+        # For now, move the default option to the top.
+        # TODO: Delete this code when PyInquirer <1.0.3 is released.
+        if question["type"] == "list" and "default" in question:
+            try:
+                question["choices"].remove(question["default"])
+                question["choices"].insert(0, question["default"])
+            except ValueError:
+                log.warning(
+                    "Default value `{}` not found in list of choices: {}".format(
+                        question["default"], ", ".join(question["choices"])
+                    )
+                )
+        ### End of workaround code
+
         return question
 
     def print_param_header(self, param_id, param_obj):
@@ -683,14 +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
 

requirements-dev.txt

@@ -0,0 +1,5 @@
+pytest
+pytest-datafiles
+pytest-cov
+mock
+black

setup.py

@@ -36,13 +36,11 @@
         "GitPython",
         "jinja2",
         "jsonschema",
-        # 'PyInquirer>1.0.3',
-        # Need the new release of PyInquirer, see nf_core/launch.py for details
-        "PyInquirer @ https://github.com/CITGuru/PyInquirer/archive/master.zip",
+        "PyInquirer==1.0.2",
         "pyyaml",
         "requests",
         "requests_cache",
-        "rich",
+        "rich>=3.4.0",
         "tabulate",
     ],
     setup_requires=["twine>=1.11.0", "setuptools>=38.6."],

tests/test_launch.py

@@ -29,8 +29,8 @@ def test_launch_pipeline(self, mock_webbrowser, mock_lauch_web_gui):
         """ Test the main launch function """
         self.launcher.launch_pipeline()
 
-    @mock.patch("click.confirm", side_effect=[False])
-    def test_launch_file_exists(self, mock_click_confirm):
+    @mock.patch.object(nf_core.launch.Confirm, "ask", side_effect=[False])
+    def test_launch_file_exists(self, mock_confirm):
         """ Test that we detect an existing params file and return """
         # Make an empty params file to be overwritten
         open(self.nf_params_fn, "a").close()
@@ -39,8 +39,8 @@ def test_launch_file_exists(self, mock_click_confirm):
 
     @mock.patch.object(nf_core.launch.Launch, "prompt_web_gui", side_effect=[True])
     @mock.patch.object(nf_core.launch.Launch, "launch_web_gui")
-    @mock.patch("click.confirm", side_effect=[True])
-    def test_launch_file_exists_overwrite(self, mock_webbrowser, mock_lauch_web_gui, mock_click_confirm):
+    @mock.patch.object(nf_core.launch.Confirm, "ask", side_effect=[False])
+    def test_launch_file_exists_overwrite(self, mock_webbrowser, mock_lauch_web_gui, mock_confirm):
         """ Test that we detect an existing params file and we overwrite it """
         # Make an empty params file to be overwritten
         open(self.nf_params_fn, "a").close()
@@ -104,12 +104,12 @@ def test_ob_to_pyinquirer_string(self):
         result = self.launcher.single_param_to_pyinquirer("input", sc_obj)
         assert result == {"type": "input", "name": "input", "message": "input", "default": "data/*{1,2}.fastq.gz"}
 
-    @mock.patch("PyInquirer.prompt.prompt", side_effect=[{"use_web_gui": "Web based"}])
+    @mock.patch("PyInquirer.prompt", side_effect=[{"use_web_gui": "Web based"}])
     def test_prompt_web_gui_true(self, mock_prompt):
         """ Check the prompt to launch the web schema or use the cli """
         assert self.launcher.prompt_web_gui() == True
 
-    @mock.patch("PyInquirer.prompt.prompt", side_effect=[{"use_web_gui": "Command line"}])
+    @mock.patch("PyInquirer.prompt", side_effect=[{"use_web_gui": "Command line"}])
     def test_prompt_web_gui_false(self, mock_prompt):
         """ Check the prompt to launch the web schema or use the cli """
         assert self.launcher.prompt_web_gui() == False