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

Validation of email address and app_name. Make app_name and version
mandatory fields

.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 +114,40 @@ jobs:
     - name: Install dependencies
       if: steps.cached-poetry-dependencies.outputs.cache-hit != 'true'
       run: poetry install --no-interaction --no-root --no-ansi
+
+
+    #---------------------------------------------
+    # Build docker container needed for test
+    #---------------------------------------------
+
+    - name: Set up QEMU
+      uses: docker/setup-qemu-action@v3
+
+    - name: Set up Docker Buildx
+      uses: docker/setup-buildx-action@v3
+
+    - name: Cache Template Testing Containers
+      uses: actions/cache@v3
+      with:
+        path: container-test-template-cache
+        key: ${{ runner.os }}-test-template-cache-${{ hashFiles('containers/test-template/**') }}-${{ matrix.python-version }}
+
+    - name: Inject container-test-template-cache into docker
+      uses: reproducible-containers/[email protected]
+      with:
+        cache-source: container-test-template-cache
+    - name: Build and push
+      uses: docker/build-push-action@v5
+      with:
+        context: containers/test-template
+        cache-from: type=gha
+        cache-to: type=gha,mode=max
+        push: false
+        load: true
+        tags: snakebids/test-template:${{ matrix.python-version }}
+        platforms: linux/amd64
+        build-args: |
+          PYTHON_VERSION=${{ matrix.python-version }}
     #----------------------------------------------
     # install your root project, if required
     #----------------------------------------------

containers/test-template/Dockerfile

@@ -0,0 +1,21 @@
+ARG PYTHON_VERSION=3.11
+FROM python:${PYTHON_VERSION}-slim
+
+# Install and uninstall snakebids to cache it and it's dependences
+RUN apt-get update && apt-get install -y gcc && \
+    rm -rf /var/lib/apt/lists/* && \
+    python -m pip install pipx && \
+    pipx install poetry && \
+    pipx install hatch && \
+    pipx install pdm && \
+    mkdir prebuild && \
+    cd prebuild && \
+    pip wheel snakebids && \
+    cd .. && \
+    rm -rf prebuild
+
+COPY ./test-template.sh /run/test-template.sh
+ENV PATH="/root/.local/bin:$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

@@ -64,6 +64,8 @@ scipy = [
     { version = ">=1.10.0,<=1.10.1", python = "<3.9" },
     { version = ">=1.10.0", python = ">=3.9" }
 ]
+copier = ">=8.2.0"
+jinja2-time = ">=0.2.0"
 
 [tool.poetry.group.dev.dependencies]
 black = "^23.1.0"
@@ -80,8 +82,10 @@ pyparsing = "^3.0.9"
 # Version 1.1.312-1.1.315 have a false positive handling some nested function
 # calls
 pathvalidate = "^3.0.0"
-pyright = ">=1.1.324"
+# As of pyright==1.1.327 only 1.1.324 is bug free
+pyright = "==1.1.324"
 ruff = "^0.0.285"
+tomli = "^2.0.1"
 
 [tool.poetry.scripts]
 snakebids = "snakebids.admin:main"
@@ -92,15 +96,28 @@ 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 snakebids"
+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._get_version]
+imports = ["platform"]
+expr = "platform.python_version()"
+
+[tool.poe.tasks.build-container]
+args = [{ name = "container_id", positional = true, required = true }]
+uses = { VERSION = "_get_version"}
+cmd = """
+    docker build 'containers/${container_id}' \
+        --tag 'snakebids/${container_id}:${VERSION}' \
+        --build-arg="PYTHON_VERSION=${VERSION}"
+"""
+
 [tool.isort]
 profile = "black"
 multi_line_output = 3

snakebids/admin.py

@@ -1,25 +1,52 @@
 """Script to generate a Snakebids project."""
 
 import argparse
+import re
+import sys
 from pathlib import Path
 
+import copier
 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)
+    if not re.match(r"^[a-zA-Z_][a-zA-Z_0-9]*$", output.name):
+        print(
+            f"{Fore.RED}Output directory name {Style.BRIGHT}{output.name}"
+            f"{Style.RESET_ALL}{Fore.RED} is not a valid python module name",
+            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(
+            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:
-    # pylint: disable=unsubscriptable-object
     app = SnakeBidsApp(args.app_dir.resolve())
     add_dynamic_args(app.parser, app.config["parse_args"], app.config["pybids_inputs"])
     app.create_descriptor(args.out_path)
@@ -57,7 +84,7 @@ def gen_parser() -> argparse.ArgumentParser:
 
 
 def main() -> None:
-    """Invoke Cookiecutter on the Snakebids project template."""
+    """Invoke snakebids cli."""
 
     parser = gen_parser()
     args = parser.parse_args()

snakebids/core/datasets.py

@@ -69,7 +69,7 @@ def __repr__(self) -> str:
         return f'{self.__class__.__name__}({list(self._data)}, entity="{self.entity}")'
 
     @property
-    def entities(self) -> tuple[str]:
+    def entities(self) -> tuple[str, ...]:
         """The unique values associated with the component"""
         return tuple(set(self._data))
 

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/toml_encode.py

@@ -0,0 +1,13 @@
+import json
+
+import jinja2
+from jinja2.ext import Extension
+
+
+def toml_string(item: str):
+    return json.dumps(item, ensure_ascii=False).replace("\x7F", "\\u007f")
+
+
+class TomlEncodeExtension(Extension):
+    def __init__(self, env: jinja2.Environment):
+        env.filters["toml_string"] = toml_string  # 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/README.md.jinja

@@ -0,0 +1,3 @@
+# {{app_full_name}}
+
+{{ app_description }}