Add support for snakemake > 8.0

docs/bids_app/config.md

@@ -40,7 +40,7 @@ The value of `filters` should be a dictionary where each key corresponds to a BI
   ```
   The above example selects all paths in the `func/` datatype folder that have a `_desc-` entity but do not have the `_acq-` entity.
 
-* [`list`](#list): Specify multiple string or boolean filters. Any path matching any one of the filters will be selected. Using `False` as one of the filters allows the entity to optionally be absent in addition to matching one of the string filters. Using `True` along with text is redundant, as `True` will cause any value to be selected. Using `True` with `False` is equivalent to not providing the filter at all.
+* [`list`](inv:*:py#list): Specify multiple string or boolean filters. Any path matching any one of the filters will be selected. Using `False` as one of the filters allows the entity to optionally be absent in addition to matching one of the string filters. Using `True` along with text is redundant, as `True` will cause any value to be selected. Using `True` with `False` is equivalent to not providing the filter at all.
 
   These filters:
 

pyproject.toml

@@ -36,8 +36,8 @@ python = ">=3.8,<4.0"
 # keep upper limit
 pybids = ">=0.16.0,<0.17"
 snakemake = [
-    { version = ">=5.28.0,<8", python = ">=3.8" },
-    { version = ">=7.18.2,<8", python = ">=3.11" },
+    { version = ">=5.28.0,<8", python = "<3.11" },
+    { version = ">=7.18.2", python = ">=3.11" },
 ]
 typing-extensions = ">=3.10.0"
 # minimum 22.2 to get "alias" parameter on attrs.field

snakebids/core/datasets.py

@@ -13,14 +13,14 @@
 import more_itertools as itx
 from bids import BIDSLayout
 from pvandyken.deprecated import deprecated
-from snakemake.io import expand as sn_expand
 from typing_extensions import Self, TypedDict
 
 import snakebids.utils.sb_itertools as sb_it
 from snakebids.core.filtering import filter_list
 from snakebids.exceptions import DuplicateComponentError
 from snakebids.io.console import get_console_size
 from snakebids.io.printing import format_zip_lists, quote_wrap
+from snakebids.snakemake_compat import expand as sn_expand
 from snakebids.types import ZipList
 from snakebids.utils.containers import ImmutableList, MultiSelectDict, UserDictPy38
 from snakebids.utils.utils import get_wildcard_dict, property_alias, zip_list_eq

snakebids/core/input_generation.py

@@ -17,7 +17,6 @@
 
 import more_itertools as itx
 from bids import BIDSLayout, BIDSLayoutIndexer
-from snakemake.script import Snakemake
 
 from snakebids.core._querying import (
     FilterSpecError,
@@ -32,6 +31,7 @@
     DuplicateComponentError,
     RunError,
 )
+from snakebids.snakemake_compat import Snakemake
 from snakebids.types import InputConfig, InputsConfig, ZipList
 from snakebids.utils.snakemake_io import glob_wildcards
 from snakebids.utils.utils import (

snakebids/plugins/snakemake.py

@@ -9,8 +9,6 @@
 
 import attrs
 import more_itertools as itx
-import snakemake
-from snakemake.io import load_configfile
 from typing_extensions import overload, override
 
 from snakebids import bidsapp
@@ -20,6 +18,8 @@
 from snakebids.plugins.cli_config import CliConfig
 from snakebids.plugins.component_edit import ComponentEdit
 from snakebids.plugins.pybidsdb import Pybidsdb
+from snakebids.snakemake_compat import load_configfile
+from snakebids.snakemake_compat import main as snakemake_main
 from snakebids.utils.output import (
     prepare_bidsapp_output,
     write_output_mode,
@@ -66,7 +66,7 @@ def __call__(
         values: str | Sequence[Any] | None,
         option_string: str | None = None,
     ):
-        snakemake.main(["-h"])  # type: ignore
+        snakemake_main(["-h"])  # type: ignore
 
 
 def _get_file_paths(
@@ -330,7 +330,7 @@ def finalize_config(self, config: dict[str, Any]):
     @bidsapp.hookimpl
     def run(self, config: dict[str, Any]):
         """Run snakemake with the given config, after applying plugins."""
-        snakemake.main(  # type: ignore
+        snakemake_main(  # type: ignore
             [
                 *filter(
                     None,

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

@@ -28,13 +28,14 @@ classifiers = [
 
 requires-python = "{{ python_version }}"
 dependencies = [
-    "snakemake >= {{ snakemake_version }},<8",
     "snakebids {{ snakebids_version | toml_encode }}",
+    "snakemake>={{ snakemake_version }},<8; python_version < \"3.11\"",
+    "snakemake>=8.1.2; python_version >= \"3.11\"",
     {#- 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
     #}
-    "pulp < 2.8.0",
+    "pulp < 2.8.0; python_version < \"3.11\"",
 ]
 
 [project.scripts]

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

@@ -22,13 +22,16 @@ classifiers = [
 
 [tool.poetry.dependencies]
 python = "{{ python_version }}"
-snakemake = ">={{ snakemake_version }},<8"
+snakemake = [
+    { version=">={{ snakemake_version }},<8", python = "<3.11" },
+    { version=">=8.1.2", python = ">=3.11" },
+]
 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
 #}
-pulp = "<2.8.0"
+pulp = { version="<2.8.0", python = "<3.11" }
 pandas = [
     { version = "<=2.0.3", python = "<3.9" },
     { version = ">=2.1.1", python = ">=3.12" },

snakebids/project_template/{% if create_doc_template %}docs{% endif %}/usage/snakemake_cli.md

@@ -1,7 +1,7 @@
 # Snakemake Command line interface
 
 ```{argparse}
-:module: snakemake
+:module: snakebids.snakemake_compat
 :func: get_argument_parser
 :prog: snakemake
 ```

snakebids/snakemake_compat.py

@@ -0,0 +1,24 @@
+# type: ignore
+
+try:
+    from snakemake.cli import get_argument_parser, main
+    from snakemake.common import configfile
+    from snakemake.common.configfile import load_configfile
+except ImportError:
+    import snakemake.io as configfile
+    from snakemake import get_argument_parser, main
+    from snakemake.io import load_configfile
+
+from snakemake.exceptions import WildcardError
+from snakemake.io import expand
+from snakemake.script import Snakemake
+
+__all__ = [
+    "load_configfile",
+    "main",
+    "expand",
+    "Snakemake",
+    "WildcardError",
+    "configfile",
+    "get_argument_parser",
+]