fix: Fix profile's mechanism and update OSL profile (#189)

.makim.yaml

@@ -1,22 +1,23 @@
 version: 1.0
 groups:
-  default:
+  clean:
     targets:
-      clean:
+      tmp:
         help: Clean unnecessary temporary files
+        shell: bash
         run: |
           rm -fr build/
           rm -fr dist/
           rm -fr .eggs/
-          find . -name '*.egg-info' -exec rm -fr {} +
-          find . -name '*.egg' -exec rm -f {} +
-          find . -name '*.pyc' -exec rm -f {} +
-          find . -name
-          find . -name '__pycache__' -exec rm -fr '*.pyo' -exec rm -f {} +
-          find . -name '*~' -exec rm -f {} +{} +
           rm -f .coverage
           rm -fr htmlcov/
           rm -fr .pytest_cache
+          find . -name '*.egg-info' -exec rm -fr {} +
+          find . -name '*.egg' -exec rm -f {} +
+          find . -name '*.pyc' -exec rm -f {} +
+          find . -name '*.pyo' -exec rm -f {} +
+          find . -name '__pycache__' -exec rm -fr {} +
+          find . -name '*~' -exec rm -f {} +
 
   docs:
     targets:

.pre-commit-config.yaml

@@ -10,14 +10,6 @@ repos:
 
   - repo: local
     hooks:
-    - id: black
-      entry: black
-      name: black
-      language: system
-      pass_filenames: true
-      types:
-        - python
-
     - id: mypy
       name: mypy
       entry: mypy
@@ -33,9 +25,24 @@ repos:
       types:
         - python
 
-    - id: ruff
-      name: ruff
-      entry: ruff --no-cache --fix
+    - id: ruff format
+      name: ruff format
+      entry: ruff format
+      language: system
+      pass_filenames: true
+      files: "./"
+      # pre-commit + ruff doesn't honor the exclusion defined in the config
+      exclude: |
+        (?x)(
+            src/scicookie/{{cookiecutter.project_slug}}
+          | src/scicookie/hooks
+        )
+      types:
+        - python
+
+    - id: ruff check
+      name: ruff check
+      entry: ruff check
       language: system
       pass_filenames: true
       files: "./"

conda/dev.yaml

@@ -4,10 +4,10 @@ channels:
   - conda-forge
 dependencies:
   - git
-  - python <3.11
-  - poetry
+  - python >=3.8.1,<3.12
+  - poetry >=1.5
   - nodejs
   - compilers
   - pip
   - pip:
-    - makim==1.8.2
+    - makim==1.8.3

pyproject.toml

@@ -3,18 +3,19 @@ name = "scicookie"
 version = "0.6.2"  # semantic-release
 description = "Cookiecutter template for a Python package"
 authors = ["Ivan Ogasawara <[email protected]>"]
-license = "BSD"
+license = "BSD-3-Clause"
 include = [
     {path = "src/scicookie/cookiecutter.json"},
     {path = "src/scicookie/{{cookiecutter.project_slug}}"},
     {path = "src/scicookie/hooks"},
+    {path = "src/scicookie/profiles"},
 ]
 
 [tool.poetry.scripts]
 "scicookie" = "scicookie.__main__:app"
 
 [tool.poetry.dependencies]
-python = ">=3.8.1,<4"
+python = ">=3.8.1,<3.12"
 cookieninja = "1.0.0"
 sh = "^2.0.4"
 colorama = "^0.4.6"
@@ -23,35 +24,21 @@ pyyaml = ">=6.0.1"
 
 [tool.poetry.group.dev.dependencies]
 pytest = ">=7"
-black = ">=22"
-isort = ">=5"
 pre-commit = ">=3"
-ruff = ">=0.0.278"
-mypy = ">=1"
+ruff = ">=0.1.5"
+mypy = ">=1.5"
 pytest-cov = ">=3"
 pytest-cookies = ">=0.6.1"
 Sphinx = ">=4.4"
 jupyterlab = ">=3.5.1"
 jupyter-book = ">=0.12.3"
 myst-parser = ">=0.15"
-makim = "1.8.2"
+makim = "1.8.3"
 
 [build-system]
 requires = ["poetry-core>=1.0.0"]
 build-backend = "poetry.core.masonry.api"
 
-[tool.black]
-line-length = 79
-# note: for support "py39", we need to update black using poetry
-#       currently, it has conflicts with typing-extensions.
-target-version = ["py38"]
-force-exclude = '''(?x)(
-    docs/*
-  | src/scicookie/{{cookiecutter.project_slug}}/*
-  | src/scicookie/hooks/*
-  |.*\\.egg-info
-)'''  # TOML's single-quoted strings do not require escaping backslashes
-
 [tool.mypy]
 no_strict_optional = false
 exclude = '''(?x)(
@@ -76,6 +63,8 @@ exclude = [
    'src/scicookie/\{\{cookiecutter.project_slug\}\}',
    'src/scicookie/hooks',
 ]
+
+[tool.ruff.lint]
 select = [
   "E",   # pycodestyle
   "F",   # pyflakes
@@ -85,11 +74,17 @@ select = [
   "RUF", # Ruff-specific rules
   "I001", # isort
 ]
-fixable = ["I001"]
 
 [tool.ruff.pydocstyle]
 convention = "numpy"
 
+[tool.ruff.isort]
+# Use a single line between direct and from import
+lines-between-types = 1
+
+[tool.ruff.format]
+quote-style = "double"
+
 [tool.pytest.ini_options]
 testpaths = [
     "tests",

src/scicookie/__init__.py

@@ -1 +1 @@
-"""SciCookie is a wrap around cookiecutter/cookieninja with a better TUI."""
+"""SciCookie is a wrap around cookiecutter/cookieninja with an improved TUI."""

src/scicookie/cli.py

@@ -1,7 +1,9 @@
 """Module with CLI functions."""
+import argparse
 import json
 import os
 import sys
+
 from pathlib import Path
 from typing import Union
 
@@ -15,6 +17,31 @@
 COOKIECUTTER_FILE_PATH = PACKAGE_PATH / "cookiecutter.json"
 
 
+class CustomHelpFormatter(argparse.RawTextHelpFormatter):
+    """Formatter for generating usage messages and argument help strings.
+
+    Only the name of this class is considered a public API. All the methods
+    provided by the class are considered an implementation detail.
+    """
+
+    def __init__(
+        self,
+        prog,
+        indent_increment=2,
+        max_help_position=4,
+        width=None,
+        **kwargs,
+    ):
+        """Define the parameters for the argparse help text."""
+        super().__init__(
+            prog,
+            indent_increment=indent_increment,
+            max_help_position=max_help_position,
+            width=width,
+            **kwargs,
+        )
+
+
 def _get_cookiecutter_default_answer(
     answer_definition: Union[str, list]
 ) -> str:
@@ -30,7 +57,7 @@ def _get_cookiecutter_default_answer(
     return answer_definition[0]
 
 
-def call_cookiecutter(profile: Profile, answers: dict):
+def call_cookiecutter(profile: Profile, answers: dict):  # noqa: PLR0912
     """Call cookiecutter/cookieninja with the parameters from the TUI."""
     answers_profile = {}
     cookie_args = []
@@ -41,7 +68,13 @@ def call_cookiecutter(profile: Profile, answers: dict):
 
     # fill the answers with default value
     for question_id, question in questions.items():
-        if not question.get("enabled", False) or question.get("control_flow"):
+        if question.get("control_flow", False):
+            # "control_flow" is not defined in cookiecutter config
+            continue
+
+        if not question.get("visible", False):
+            # get the default for non visible questions
+            answers_profile[question_id] = question.get("default")
             continue
 
         if question.get("type") == "multiple-choices":
@@ -98,7 +131,35 @@ def call_cookiecutter(profile: Profile, answers: dict):
 def app():
     """Run SciCookie."""
     # note: this parameter should be provided by a CLI argument
-    profile = Profile("osl")
+
+    parser = argparse.ArgumentParser(
+        prog="SciCookie",
+        description=(
+            "SciCookie is a template developed by Open Science Labs that "
+            "creates projects through different options of profile. "
+            "It serves as a boilerplate which can be used by beginners as "
+            "well as full fledged developers to simplify the project creation "
+            "process and save considerable amount of time. It creates  "
+            "projects with an initial layout that includes recommended  "
+            "tools, workflows, and project structure."
+        ),
+        epilog=(
+            "If you have any problem, open an issue at: "
+            "https://github.com/osl-incubator/scicookie"
+        ),
+        add_help=True,
+        formatter_class=CustomHelpFormatter,
+    )
+    parser.add_argument(
+        "--profile",
+        type=str,
+        default="base",
+        help="Select the profile to be used",
+    )
+
+    args = parser.parse_args()
+
+    profile = Profile(args.profile)
 
     answers = make_questions(profile.config)
 

src/scicookie/cookiecutter.json

@@ -20,7 +20,7 @@
     "flat"
   ],
   "command_line_interface": [
-    "No command-line interface",
+    "None",
     "Click",
     "Argparse"
   ],

src/scicookie/hooks/post_gen_project.py

@@ -31,7 +31,7 @@
 USE_BLUE = {{ cookiecutter.use_blue == "yes" }}
 USE_BANDIT = {{ cookiecutter.use_bandit == "yes" }}
 USE_CONTAINERS = {{ cookiecutter.use_containers in ['Docker', 'Podman'] }}
-USE_CLI = {{ cookiecutter.command_line_interface != "No command-line interface" }}
+USE_CLI = {{ cookiecutter.command_line_interface != "None" }}
 USE_CONDA = {{ cookiecutter.use_conda == "yes" }}
 USE_MAKE = {{ cookiecutter.use_make == "yes" }}
 USE_MAKIM = {{ cookiecutter.use_makim == "yes" }}
@@ -266,48 +266,70 @@ def validation():
         )
 
 
-def prepare_git():
-    subprocess.call(["git", "init"])
-
+def prepare_git() -> None:
     git_https_origin = http2ssh("{{cookiecutter.git_https_origin}}")
     git_https_upstream = http2ssh("{{cookiecutter.git_https_upstream}}")
     git_main_branch = http2ssh("{{cookiecutter.git_main_branch}}")
     unique_id = datetime.datetime.now().strftime("%Y%m%d%H%M%S")
-    git_new_branch = f"add-initial-structure-{unique_id}"
+    git_new_branch = f"initial-from-scicookie-{unique_id}"
+    git_stash_branch = f"stash-from-scicookie-{unique_id}"
 
     git_author_name = "{{cookiecutter.author_full_name}}"
     git_author_email = "{{cookiecutter.author_email}}"
 
-    empty_repo = not (git_https_origin or git_https_upstream)
-
-    if not empty_repo:
-        subprocess.call(["git", "stash"])
-
-    if git_https_origin != "":
-        subprocess.call(["git", "remote", "add", "origin", git_https_origin])
-        subprocess.call(["git", "fetch", "--all"])
-        subprocess.call(["git", "checkout", f"origin/{git_main_branch}"])
+    use_remote = git_https_origin != '' or git_https_upstream != ''
 
-    if git_https_upstream != "":
+    if not use_remote:
+        subprocess.call(["git", "init", "-b", git_main_branch])
         subprocess.call(
-            ["git", "remote", "add", "upstream", git_https_upstream]
+            ["git", "config", "user.name", git_author_name]
         )
-        subprocess.call(["git", "fetch", "--all"])
+        subprocess.call(
+            ["git", "config", "user.email", git_author_email]
+        )
+        subprocess.call(["git", "add", "."])
+        subprocess.call([
+            "git", "commit", "-m", "Initial commit from SciCookie", "--no-verify"
+        ])
+        return
+
+    subprocess.call(["git", "init", "-b", git_stash_branch])
 
+    # config
     subprocess.call(
         ["git", "config", "user.name", git_author_name]
     )
     subprocess.call(
         ["git", "config", "user.email", git_author_email]
     )
+    if git_https_origin != "":
+        subprocess.call(["git", "remote", "add", "origin", git_https_origin])
 
-    subprocess.call(["git", "checkout", "-b", git_new_branch])
+    if git_https_upstream != "":
+        subprocess.call(
+            ["git", "remote", "add", "upstream", git_https_upstream]
+        )
 
-    if not empty_repo:
-        subprocess.call(["git", "stash", "pop"])
+    subprocess.call(["git", "fetch", "--all"])
 
+    # prepare the first commit
+    subprocess.call(["git", "add", "."])
+    subprocess.call([
+        "git",
+        "commit",
+        "-m",
+        "A temporary from SciCookie",
+        "--no-verify"
+    ])
+
+    subprocess.call(["git", "checkout", f"origin/{git_main_branch}"])
+    subprocess.call(["git", "checkout", "-b", git_new_branch])
+    subprocess.call(["git", "checkout", git_stash_branch, "--", "."])
     subprocess.call(["git", "add", "."])
-    subprocess.call(["git", "commit", "-m", "Initial commit", "--no-verify"])
+    subprocess.call([
+        "git", "commit", "-m", "Initial commit from SciCookie", "--no-verify"
+    ])
+    subprocess.call(["git", "branch", "-D", git_stash_branch])
 
 
 def add_binding_source_files():

src/scicookie/logs.py

@@ -1,5 +1,6 @@
 """Module for functions and classes for systen logs."""
 import os
+
 from enum import Enum
 
 from colorama import Fore