Overhaul of snakebids create

Use copier instead of cookiecutter
- Better feature set
- Better documentation
- More polished (e.g. typed codebase)

Change starting workflow into a "welcome" workflow
- Pregenerated empty data file based on the tutorial
- workflow reads in the datafiles using generate_inputs and prints a
  welcome message

Allow choice of build systems. App will be immediately installable and
publishable

End-to-end testing of app creation, dependency installation, and initial
run

.github/workflows/test.yml

@@ -58,6 +58,7 @@ jobs:
       - name: Install library
         run: poetry install --no-interaction --no-ansi
 
+
       #----------------------------------------------
       #       run python style checks
       #----------------------------------------------
@@ -113,6 +114,27 @@ jobs:
     - name: Install dependencies
       if: steps.cached-poetry-dependencies.outputs.cache-hit != 'true'
       run: poetry install --no-interaction --no-root --no-ansi
+
+    - name: Cache Template Testing Containers
+      uses: actions/cache@v3
+      with:
+        path: container-test-template-cache
+        key: ${{ runner.os }}-go-build-cache-${{ hashFiles('containers/test-template/**') }}
+
+    - name: Inject container-test-template-cache into docker
+      uses: reproducible-containers/[email protected]
+      with:
+        cache-source: container-test-template-cache
+    - name: Build and push
+      uses: docker/build-push-action@v5
+      with:
+        context: containers/test-template
+        cache-from: type=gha
+        cache-to: type=gha,mode=max
+        push: false
+        load: true
+        tags: snakebids/test-template
+        platforms: linux/amd64
     #----------------------------------------------
     # install your root project, if required
     #----------------------------------------------

containers/test-template/Dockerfile

@@ -0,0 +1,18 @@
+FROM python:3.11.5
+
+# Install and uninstall snakebids to cache it and it's dependences
+RUN python -m pip install pipx && \
+    pipx install poetry && \
+    pipx install hatch && \
+    pipx install pdm && \
+    mkdir prebuild && \
+    cd prebuild && \
+    pip wheel snakebids && \
+    cd .. && \
+    rm -rf prebuild
+
+COPY ./test-template.sh /run/test-template.sh
+ENV PATH="/root/.local/bin:$PATH"
+
+WORKDIR /work
+ENTRYPOINT [ "/run/test-template.sh" ]

containers/test-template/test-template.sh

@@ -0,0 +1,32 @@
+#!/bin/sh
+
+set -eu
+
+method="$1"
+script_name="$2"
+
+cp -r /app/* /work
+script="'${script_name}' tests/data tests/result participant -c1 --skip-bids-validation"
+case "$method" in
+    "setuptools" )
+        python -m venv .venv
+        .venv/bin/python -m pip install .
+        PATH=".venv/bin:$PATH" eval "$script"
+        ;;
+    "poetry" )
+        poetry install
+        eval "poetry run $script"
+        ;;
+    "hatch" )
+        hatch env create
+        eval "hatch env run -- $script"
+        ;;
+    "pdm" )
+        pdm install
+        eval "pdm run $script"
+        ;;
+    * )
+        >&2 echo "Invalid method"
+        exit 1
+        ;;
+esac

pyproject.toml

@@ -64,7 +64,8 @@ scipy = [
     { version = ">=1.10.0,<=1.10.1", python = "<3.9" },
     { version = ">=1.10.0", python = ">=3.9" }
 ]
-copier = "^8.1.0"
+copier = ">=8.2.0"
+jinja2-time = "^0.2.0"
 
 [tool.poetry.group.dev.dependencies]
 black = "^23.1.0"
@@ -93,15 +94,22 @@ build-backend = "poetry_dynamic_versioning.backend"
 
 [tool.poe.tasks]
 setup = "pre-commit install"
-quality = { shell = "isort snakebids && black snakebids && ruff snakebids && pyright" }
-fix = { shell = "ruff --fix snakebids && isort snakebids && black snakebids"}
+quality.shell = "isort snakebids && black snakebids && ruff snakebids && pyright"
+fix.shell = "ruff --fix snakebids && isort snakebids && black snakebids"
 test = """
 pytest --doctest-modules --ignore=docs \
     --ignore=snakebids/project_template --benchmark-disable
 """
 mkinit = "mkinit --recursive --nomods --black -i snakebids"
 benchmark = "pytest --benchmark-only --benchmark-autosave"
 
+[tool.poe.tasks.build-container]
+args = [{ name = "container_id", positional = true, required = true }]
+cmd = """
+    docker build 'containers/${container_id}' \
+        --tag 'snakebids/${container_id}:dev'
+"""
+
 [tool.isort]
 profile = "black"
 multi_line_output = 3

snakebids/admin.py

@@ -1,21 +1,41 @@
 """Script to generate a Snakebids project."""
 
 import argparse
+import sys
 from pathlib import Path
 
+import copier  # type: ignore
 import more_itertools as itx
-from cookiecutter.main import cookiecutter  # type: ignore
+from colorama import Fore, Style
 
 import snakebids
 from snakebids.app import SnakeBidsApp
 from snakebids.cli import add_dynamic_args
 
 
 def create_app(args: argparse.Namespace) -> None:
-    cookiecutter(
-        str(Path(itx.first(snakebids.__path__)) / "project_template"),
-        output_dir=args.output_dir,
+    output = Path(args.output_dir).resolve()
+    if not output.parent.exists():
+        print(
+            f"{Fore.RED}{Style.BRIGHT}{output.parent}{Style.RESET_ALL}{Fore.RED} does "
+            f"not exist{Fore.RESET}",
+            file=sys.stderr,
+        )
+        sys.exit(1)
+    print(
+        f"Creating Snakebids app at {Fore.GREEN}{output}{Fore.RESET}", file=sys.stderr
     )
+    print(file=sys.stderr)
+    try:
+        copier.run_copy(  # type: ignore
+            str(Path(itx.first(snakebids.__path__), "project_template")),
+            output,
+            data={"app_full_name": output.name},
+            unsafe=True,
+        )
+    except KeyboardInterrupt:
+        print(f"{Fore.RED}Aborted!{Fore.RESET}", file=sys.stderr)
+        sys.exit(1)
 
 
 def create_descriptor(args: argparse.Namespace) -> None:

snakebids/jinja2_ext/colorama.py

@@ -0,0 +1,11 @@
+from __future__ import annotations
+
+import jinja2.parser
+from colorama import Fore
+from jinja2.ext import Extension
+
+
+class ColoramaExtension(Extension):
+    def __init__(self, env: jinja2.Environment):
+        super().__init__(env)
+        env.globals["Fore"] = Fore  # type: ignore

snakebids/jinja2_ext/vcs.py

@@ -0,0 +1,79 @@
+from __future__ import annotations
+
+import re
+import subprocess
+import sys
+from pathlib import Path
+
+import jinja2.parser
+from jinja2 import nodes
+from jinja2.ext import Extension
+
+
+class GitConfigExtension(Extension):
+    tags = {"gitconfig"}  # noqa: RUF012
+    _config: dict[str, str]
+
+    def __init__(self, env: jinja2.Environment) -> None:
+        self._config = {}
+
+        try:
+            config_list = subprocess.check_output(
+                [executable(), "config", "-l"], stderr=subprocess.STDOUT
+            ).decode()
+
+            m = re.findall("(?ms)^([^=]+)=(.*?)$", config_list)
+            if m:
+                for group in m:
+                    self._config[group[0]] = group[1]
+        except (subprocess.CalledProcessError, OSError):
+            pass
+
+    def get(self, key: str, default: str | None = None) -> str | None:
+        return self._config.get(key, default)
+
+    def __getitem__(self, item: str) -> str:
+        return self._config[item]
+
+    def parse(self, parser: jinja2.parser.Parser):
+        lineno = next(parser.stream).lineno
+
+        node = parser.parse_expression()
+
+        if not isinstance(node, nodes.Const):
+            raise ValueError("Argument to `gitconfig` must be a string")
+        call_method = self.call_method(
+            "get",
+            [node],
+            lineno=lineno,
+        )
+        return nodes.Output([call_method], lineno=lineno)
+
+
+def executable() -> str:
+    _executable = None
+
+    if sys.platform == "win32":
+        # Finding git via where.exe
+        where = "%WINDIR%\\System32\\where.exe"
+        paths = subprocess.check_output(
+            [where, "git"], shell=True, encoding="oem"
+        ).split("\n")
+        for path in paths:
+            if not path:
+                continue
+
+            _path = Path(path.strip())
+            try:
+                _path.relative_to(Path.cwd())
+            except ValueError:
+                _executable = str(_path)
+
+                break
+    else:
+        _executable = "git"
+
+    if _executable is None:  # type: ignore
+        raise RuntimeError("Unable to find a valid git executable")
+
+    return _executable

snakebids/plugins/validator.py

@@ -56,7 +56,7 @@ def __call__(self, app: SnakeBidsApp) -> None:
             temp.flush()
             try:
                 subprocess.check_call(
-                    ["bids-validator", app.config["bids_dirs"], "-c", temp.name]
+                    ["bids-validator", app.config["bids_dir"], "-c", temp.name]
                 )
 
                 # If successfully bids-validation performed

snakebids/project_template/copier.yaml

@@ -1,11 +1,12 @@
 full_name:
   type: str
   help: What is your name?
-  placeholder: " optional"
+  default: '{% gitconfig "user.name" %}'
 
 email:
   type: str
   help: What is your email?
+  default: '{% gitconfig "user.email" %}'
 
 github:
   type: str
@@ -14,7 +15,6 @@ github:
 app_full_name:
   type: str
   help: What is the name of your app?
-  default: "{{ dst_path }}"
   validator: '{% if not app_full_name %}Required{% endif %}'
 
 app_description:
@@ -24,6 +24,25 @@ app_description:
 app_version:
   default: "0.1.0"
   help: Starting version number for your app
+  validator: '{% if not app_version %}Required{% endif %}'
+
+build_system:
+  help: >
+    What build system would you like to use? If you don't know what this means,
+    choose setuptools
+  choices:
+    - setuptools
+    - poetry
+    - hatch
+    - flit
+
+# Flit and setuptools requires specifying license via Trove classifiers; too
+# complicated to get via interactive prompt
+license:
+  default: >-
+    {% if build_system != "flit" and build_system != "setuptools" %}MIT{% endif %}
+  help: Usage license for your app
+  when: "{{ build_system != 'flit' and build_system != 'setuptools' }}"
 
 create_doc_template:
   type: bool
@@ -34,12 +53,74 @@ bids_version:
   when: false
 
 snakebids_version:
-  default: "0.0.0"
+  default: "0.9.2"
+  when: false
+
+snakemake_version:
+  default: "7.20"
   when: false
 
 name_slug:
   default: "{{ app_full_name|lower|replace(' ', '_')|replace('-', '_') }}"
   when: false
 
+test_run_cmd:
+  default: "{{ name_slug }} tests/data tests/result participant -c1"
+  when: false
+
+_message_after_copy: >
+  Snakebids project successfully created in
+  {{ Fore.GREEN }}{{ _copier_conf.dst_path }}{{ Fore.RESET }}
+
+
+  Just a few steps before coding:
+
+
+  {{ Fore.BLUE }}1.{{ Fore.RESET }} Change into the project directory:
+
+    $ cd {{ _copier_conf.dst_path }}
+
+  {% if build_system == "poetry" -%}
+  {{ Fore.BLUE }}2.{{ Fore.RESET }} Install dependencies.
+
+    $ poetry install
+
+  {%- else -%}
+  {{ Fore.BLUE + "2." + Fore.RESET + """ Install dependencies. This may vary
+  depending on your tooling. The following are examples (the first example
+  should work on any python environment; the others require 3rd party tools):
+  """ | wordwrap(80)}}
+
+    * {{Fore.YELLOW}}Virtual Environment and setuptools:{{Fore.RESET}}
+      $ python -m venv .venv
+      $ source .venv/bin/activate
+      $ pip install .
+
+    * {{Fore.YELLOW}}Hatch:{{Fore.RESET}}
+      $ hatch env create
+
+    * {{Fore.YELLOW}}PDM:{{Fore.RESET}}
+      $ pdm install
+  {%- endif %}
+
+
+  {{ Fore.BLUE }}3.{{Fore.RESET }} Perform a test run.
+
+  {% if build_system == "poetry" %}
+    $ poetry run {{ test_run_cmd }}
+
+  {%- else %}
+    * {{Fore.YELLOW}}Virtual Environment and setuptools:{{Fore.RESET}}
+      $ {{ test_run_cmd }}
+
+    * {{Fore.YELLOW}}Hatch:{{Fore.RESET}}
+      $ hatch env run -- {{ test_run_cmd }}
+
+    * {{Fore.YELLOW}}PDM:{{Fore.RESET}}
+      $ pdm run {{ test_run_cmd }}
+  {%- endif %}
+
 _jinja_extensions:
   - jinja2_time.TimeExtension
+  - snakebids.jinja2_ext.vcs.GitConfigExtension
+  - snakebids.jinja2_ext.colorama.ColoramaExtension