Allow custom snakebids version in app template

containers/test-template/test-template.sh

@@ -11,9 +11,9 @@ case "$method" in
     "setuptools" )
         python -m venv .venv
         .venv/bin/python -m pip install .
-        if [ -d /src ]; then
-            .venv/bin/python -m pip install /src
-        fi
+        # if [ -d /src ]; then
+        #     .venv/bin/python -m pip install /src
+        # fi
         PATH=".venv/bin:$PATH" eval "$script"
         ;;
     "poetry" )

snakebids/admin.py

@@ -12,6 +12,7 @@
 import snakebids
 from snakebids.app import SnakeBidsApp
 from snakebids.cli import add_dynamic_args
+from snakebids.utils.utils import text_fold
 
 
 def create_app(args: argparse.Namespace) -> None:
@@ -31,6 +32,39 @@
             file=sys.stderr,
         )
         sys.exit(1)
+
+    data = {"app_full_name": output.name}
+
+    if args.snakebids_version is not None:
+        version = args.snakebids_version
+        if ("@" not in version and ";" in version) or (
+            "@" in version and " ;" in version
+        ):
+            print(
+                f"{Fore.RED}Snakebids version may not specify markers{Style.RESET_ALL}",
+                file=sys.stderr,
+            )
+            sys.exit(1)
+        if (
+            "@" in version
+            and version[1:].lstrip().startswith("git+")
+            and "@" in version[1:]
+        ):
+            print(
+                f"{Fore.RED}Credentials and rev specifiers in git requirement "
+                f"specifications are not supported{Style.RESET_ALL}",
+                file=sys.stderr,
+            )
+            sys.exit(1)
+        if version.strip().startswith("["):
+            print(
+                f"{Fore.RED}Snakebids version may not specify extras{Style.RESET_ALL}",
+                file=sys.stderr,
+            )
+            sys.exit(1)
+
+        data["snakebids_version"] = args.snakebids_version
+
     print(
         f"Creating Snakebids app at {Fore.GREEN}{output}{Fore.RESET}", file=sys.stderr
     )
@@ -39,7 +73,7 @@
         copier.run_copy(
             str(Path(itx.first(snakebids.__path__), "project_template")),
             output,
-            data={"app_full_name": output.name},
+            data=data,
             unsafe=True,
         )
     except KeyboardInterrupt:
@@ -64,6 +98,19 @@
 
     parser_create = subparsers.add_parser("create", help="Create a new Snakebids app.")
     parser_create.add_argument("output_dir", nargs="?", default=".")
+    parser_create.add_argument(
+        "--snakebids-version",
+        default=None,
+        metavar="VERSION_SPECIFIER",
+        help=text_fold(
+            """
+            Specify snakebids version requirement. Supports either a valid version
+            specifier (e.g. `>=x.x.x`, `==a.b.c`) or a url prepended with `@` (e.g. `@
+            https://...`). Paths can be specified with `@ file:///absolute/path/...`.
+            Markers and extras may not be specified.
+            """
+        ),
+    )
     parser_create.set_defaults(func=create_app)
 
     parser_boutiques = subparsers.add_parser(

snakebids/jinja2_ext/__init__.py

@@ -1,16 +1,10 @@
 # type: ignore
+__submodules__ = []
 
 # <AUTOGEN_INIT>
 import lazy_loader
 
 __getattr__, __dir__, __all__ = lazy_loader.attach_stub(__name__, __file__)
 
-__all__ = [
-    "ColoramaExtension",
-    "GitConfigExtension",
-    "SnakebidsVersionExtension",
-    "TomlEncodeExtension",
-    "executable",
-    "toml_string",
-]
+__all__ = []
 # </AUTOGEN_INIT>

snakebids/jinja2_ext/__init__.pyi

@@ -1,23 +1 @@
-from .colorama import (
-    ColoramaExtension,
-)
-from .snakebids_version import (
-    SnakebidsVersionExtension,
-)
-from .toml_encode import (
-    TomlEncodeExtension,
-    toml_string,
-)
-from .vcs import (
-    GitConfigExtension,
-    executable,
-)
-
-__all__ = [
-    "ColoramaExtension",
-    "GitConfigExtension",
-    "SnakebidsVersionExtension",
-    "TomlEncodeExtension",
-    "executable",
-    "toml_string",
-]
+__all__ = []

snakebids/jinja2_ext/format_dep_spec.py

@@ -0,0 +1,27 @@
+import jinja2
+from jinja2.ext import Extension
+
+from snakebids.jinja2_ext.toml_encode import toml_string
+
+
+def format_poetry(item: str):
+    """Format a pip style dependency specification for a poetry pyproject.toml.
+
+    Only supports urls (prefixed with @) and version specifiers. No markers or extras.
+    The package name should already be stripped.
+    """
+    if item.strip().startswith("@"):
+        url = item[1:].strip()
+        if url.startswith("git+"):
+            return f"{{ git = {toml_string(url[4:])} }}"
+        if url.startswith("file://"):
+            return f"{{ path = {toml_string(url[7:])} }}"
+        return f"{{ url = {toml_string(url)} }}"
+    return toml_string(item)
+
+
+class FormatDepSpec(Extension):
+    """Enable the toml_string filter, which encodes provided value as toml."""
+
+    def __init__(self, env: jinja2.Environment):
+        env.filters["format_poetry"] = format_poetry  # type: ignore

snakebids/jinja2_ext/snakebids_version.py

@@ -15,7 +15,7 @@ class SnakebidsVersionExtension(Extension):
     """
 
     def __init__(self, env: jinja2.Environment):
-        env.globals["snakebids_version"] = self._lookup_version()  # type: ignore
+        env.globals["curr_snakebids_version"] = self._lookup_version()  # type: ignore
         super().__init__(env)
 
     def _lookup_version(self):

snakebids/jinja2_ext/toml_encode.py

@@ -13,8 +13,18 @@ def toml_string(item: str):
     return json.dumps(item, ensure_ascii=False).replace("\x7F", "\\u007f")
 
 
+def toml_encode(item: str):
+    """Encode string for inclusion in toml without wrapping in quotes.
+
+    Technically encodes as json, a (mostly) strict subset of toml, with some encoding
+    fixes
+    """
+    return toml_string(item)[1:-1]
+
+
 class TomlEncodeExtension(Extension):
     """Enable the toml_string filter, which encodes provided value as toml."""
 
     def __init__(self, env: jinja2.Environment):
         env.filters["toml_string"] = toml_string  # type: ignore
+        env.filters["toml_encode"] = toml_encode  # type: ignore

snakebids/project_template/copier.yaml

@@ -69,7 +69,11 @@ python_version:
   when: false
 
 snakebids_version:
-  default: "{{ snakebids_version or '0.9.3' }}"
+  default: ">={{ curr_snakebids_version or '0.9.3' }}"
+  when: false
+
+snakebids_is_direct_reference:
+  default: "{{ snakebids_version.strip().startswith('@') }}"
   when: false
 
 snakemake_version:
@@ -128,3 +132,4 @@ _jinja_extensions:
   - snakebids.jinja2_ext.colorama.ColoramaExtension
   - snakebids.jinja2_ext.toml_encode.TomlEncodeExtension
   - snakebids.jinja2_ext.snakebids_version.SnakebidsVersionExtension
+  - snakebids.jinja2_ext.format_dep_spec.FormatDepSpec

snakebids/project_template/{% if build_system != 'poetry' %}pyproject.toml{% endif %}.jinja

@@ -29,7 +29,7 @@ classifiers = [
 requires-python = "{{ python_version }}"
 dependencies = [
     "snakemake >= {{ snakemake_version }},<8",
-    "snakebids >= {{ snakebids_version }}",
+    "snakebids {{ snakebids_version | toml_encode }}",
     {#- newer pulps are incompatible with old snakemakes, and we need to support
     old snakemakes for python versions <3.11. So cap pulp to the last working
     version
@@ -51,3 +51,9 @@ build-backend = "hatchling.build"
 requires = ["setuptools"]
 build-backend = "setuptools.build_meta"
 {%- endif %}
+
+{%- if snakebids_is_direct_reference == "True" and build_system == "hatch" %}
+
+[tool.hatch.metadata]
+allow-direct-references = true
+{%- endif %}

snakebids/project_template/{% if build_system == 'poetry' %}pyproject.toml{% endif %}.jinja

@@ -23,7 +23,7 @@ classifiers = [
 [tool.poetry.dependencies]
 python = "{{ python_version }}"
 snakemake = ">={{ snakemake_version }},<8"
-snakebids = ">={{ snakebids_version }}"
+snakebids = {{ snakebids_version | format_poetry }}
 {#- newer pulps are incompatible with old snakemakes, and we need to support
 old snakemakes for python versions <3.11. So cap pulp to the last working
 version

snakebids/tests/test_admin.py

@@ -1,8 +1,11 @@
+from __future__ import annotations
+
 import re
 import sys
 from argparse import ArgumentParser, Namespace
 from pathlib import Path
 
+import more_itertools as itx
 import pytest
 from hypothesis import given
 from hypothesis import strategies as st
@@ -18,21 +21,19 @@ def parser():
     return gen_parser()
 
 
-class TestAdminCli:
-    def test_fails_if_no_subcommand(
-        self, parser: ArgumentParser, mocker: MockerFixture
-    ):
-        mocker.patch.object(sys, "argv", ["snakebids"])
-        with pytest.raises(SystemExit):
-            parser.parse_args()
+def test_fails_if_no_subcommand(parser: ArgumentParser, mocker: MockerFixture):
+    mocker.patch.object(sys, "argv", ["snakebids"])
+    with pytest.raises(SystemExit):
+        parser.parse_args()
+
+
+def test_fails_if_invalid_subcommand(parser: ArgumentParser, mocker: MockerFixture):
+    mocker.patch.object(sys, "argv", ["snakebids", "dummy"])
+    with pytest.raises(SystemExit):
+        parser.parse_args()
 
-    def test_fails_if_invalid_subcommand(
-        self, parser: ArgumentParser, mocker: MockerFixture
-    ):
-        mocker.patch.object(sys, "argv", ["snakebids", "dummy"])
-        with pytest.raises(SystemExit):
-            parser.parse_args()
 
+class TestCreateCommand:
     @given(
         name=st.text()
         .filter(lambda s: not re.match(r"^[a-zA-Z_][a-zA-Z_0-9]*$", s))
@@ -79,6 +80,95 @@ def test_create_fails_missing_parent_dir(
         assert "does not exist" in capture.err
         assert str(path.parent) in capture.err
 
+    def test_create_fails_when_markers_in_snakebids_version(
+        self,
+        parser: ArgumentParser,
+        mocker: MockerFixture,
+        capsys: pytest.CaptureFixture[str],
+    ):
+        mocker.patch.object(
+            sys,
+            "argv",
+            ["snakebids", "create", "name", "--snakebids-version", "... ; markers"],
+        )
+        args = parser.parse_args()
+        with pytest.raises(SystemExit):
+            args.func(args)
+        capture = capsys.readouterr()
+        assert "may not specify markers" in capture.err
+
+    def test_create_fails_when_get_spec_has_at_sign(
+        self,
+        parser: ArgumentParser,
+        mocker: MockerFixture,
+        capsys: pytest.CaptureFixture[str],
+    ):
+        mocker.patch.object(
+            sys,
+            "argv",
+            ["snakebids", "create", "name", "--snakebids-version", "@ git+...@...@..."],
+        )
+        args = parser.parse_args()
+        with pytest.raises(SystemExit):
+            args.func(args)
+        capture = capsys.readouterr()
+        assert "in git requirement" in capture.err
+
+    def test_create_fails_when_snakebids_version_specifies_extras(
+        self,
+        parser: ArgumentParser,
+        mocker: MockerFixture,
+        capsys: pytest.CaptureFixture[str],
+    ):
+        mocker.patch.object(
+            sys,
+            "argv",
+            ["snakebids", "create", "name", "--snakebids-version", "[...] ..."],
+        )
+        args = parser.parse_args()
+        with pytest.raises(SystemExit):
+            args.func(args)
+        capture = capsys.readouterr()
+        assert "may not specify extras" in capture.err
+
+    @given(
+        name=st.from_regex(r"^[a-zA-Z_][a-zA-Z_0-9]*$"),
+        version=st.text(st.characters(blacklist_characters=["@", ";", "["]))
+        | st.none(),
+    )
+    @allow_function_scoped
+    def test_create_calls_copier_correctly(
+        self,
+        parser: ArgumentParser,
+        mocker: MockerFixture,
+        name: str,
+        version: str | None,
+        tmp_path: Path,
+        capsys: pytest.CaptureFixture[str],
+    ):
+        import snakebids
+        from snakebids.admin import copier
+
+        run_copy = mocker.patch.object(copier, "run_copy")
+        path = tmp_path / name
+        args = ["snakebids", "create", str(path)]
+        if version is not None:
+            args.extend(["--snakebids-version", version])
+        mocker.patch.object(sys, "argv", args)
+        args = parser.parse_args()
+        args.func(args)
+        capture = capsys.readouterr()
+        assert "Creating Snakebids app at" in capture.err
+        run_copy.assert_called_once_with(
+            str(Path(itx.first(snakebids.__path__), "project_template")),
+            path,
+            data={
+                "app_full_name": name,
+                **({"snakebids_version": version} if version is not None else {}),
+            },
+            unsafe=True,
+        )
+
     def test_create_succeeds(self, parser: ArgumentParser, mocker: MockerFixture):
         mocker.patch.object(sys, "argv", ["snakebids", "create"])
         assert isinstance(parser.parse_args(), Namespace)