Add testing for Python 3.12

.github/workflows/nightly.yml

@@ -9,7 +9,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ["3.8", "3.9", "3.10", "3.11"]
+        python-version: ["3.8", "3.9", "3.10", "3.11", "3.12"]
     steps:
       - uses: khanlab/actions/.github/actions/[email protected]
         id: setup

.github/workflows/test.yml

@@ -39,7 +39,7 @@ jobs:
     needs: [ 'quality'  ]
     strategy:
       matrix:
-        python-version: ['3.8', '3.9', '3.10', '3.11']
+        python-version: ['3.8', '3.9', '3.10', '3.11', '3.12']
     steps:
     - uses: khanlab/actions/.github/actions/[email protected]
       id: setup
@@ -55,7 +55,7 @@ jobs:
     needs: [ 'build-cache-env'  ]
     strategy:
       matrix:
-        python-version: ['3.8', '3.9', '3.10', '3.11']
+        python-version: ['3.8', '3.9', '3.10', '3.11', '3.12']
         split: ['1', '2', '3', '4', '5']
       fail-fast: false
     steps:

pyproject.toml

@@ -23,23 +23,21 @@ style = "pep440"
 bump = true
 
 [tool.poetry-dynamic-versioning.substitution]
-files = [
-    'snakebids/__init__.py',
-]
+files = ['snakebids/__init__.py']
 patterns = [
     "(^\\s+\"snakebids_version\":\\s*\")[^'\"]*(\")",
     "(^__version__\\s*(?::.*?)?=\\s*['\"])[^'\"]*(['\"])",
 ]
 
 [tool.poetry.dependencies]
-# upper cap imposed by scipy
-python = ">=3.8,<3.13"
+# upper cap imposed by pytest-split
+python = ">=3.8,<4.0"
 # core dep with high breakage potential given plans for redesign, so
 # keep upper limit
 pybids = ">=0.16.0,<0.17"
 snakemake = [
-    { version = ">=5.28.0", python = ">=3.8" },
-    { version = ">=7.18.2", python = ">=3.11" },
+    { version = ">=5.28.0,<8", python = ">=3.8" },
+    { version = ">=7.18.2,<8", python = ">=3.11" },
 ]
 PyYAML = ">=6"
 typing-extensions = ">=3.10.0"
@@ -63,6 +61,10 @@ scipy = [
     { version = ">=1.10.0,<=1.10.1", python = "<3.9" },
     { version = ">=1.10.0", python = ">=3.9" },
 ]
+pandas = [
+    { version = "<=2.0.3", python = "<3.9" },
+    { version = ">=2.1.1", python = ">=3.12" },
+]
 # minimum 8.2.0 to use post-copy mesages
 copier = ">=8.2.0"
 jinja2-time = ">=0.2.0"
@@ -127,8 +129,8 @@ expr = "platform.python_version()"
 args = [{ name = "container_id", positional = true, required = true }]
 uses = { VERSION = "_get_version" }
 cmd = """
-    docker build 'containers/${container_id}' \
-        --tag 'snakebids/${container_id}:${VERSION}' \
+    docker build "containers/${container_id}" \
+        --tag "snakebids/${container_id}:${VERSION}" \
         --build-arg="PYTHON_VERSION=${VERSION}"
 """
 
@@ -138,18 +140,15 @@ markers = [
 ]
 
 [tool.coverage.run]
-omit = [
-    "snakebids/project_template/**",
-    "snakebids/tests/**",
-]
+omit = ["snakebids/project_template/**", "snakebids/tests/**"]
 
 [tool.coverage.report]
 exclude_lines = [
     "pragma: not covered",
     "@overload",
     'class [a-zA-Z0-9_]+\([^)]*Protocol.*\)',
     'if TYPE_CHECKING',
-    "def __dir__"
+    "def __dir__",
 ]
 
 [tool.isort]
@@ -165,31 +164,31 @@ reportImportCycles = false
 
 [tool.ruff]
 select = [
-    "E",    # pycodestyle error
-    "W",    # pycodestyle warning
-    "F",    # pyflakes
-    "N",    # pep8-naming
-    "UP",   # pyupgrade
-    "YTT",  # flake8-2020
-    "S",    # flake8-bandit
-    "BLE",  # flake8-blind-except
-    "B",    # flake8-bugbear
-    "A",    # flake8-builtins
-    "COM",  # flake8-commas
-    "C4",   # flake8-comprehensions
-    "T10",  # flake8-debugger
-    "EM",   # flake8-errmsg
-    "FA",   # flake8-future-annotations
-    "ISC",  # flake8-implicit-str-concat
-    "ICN",  # flake8-import-conventions
-    "G",    # flake8-logging-format
-    "INP",  # flake8-no-pep420
-    "PIE",  # flake8-pie
-    "PT",   # flake8-pytest-style
-    "RSE",  # flake8-raise
-    "RET",  # flake8-return
-    "SLF",  # flake8-self
-    "SIM",  # flake8-simplify
+    "E",   # pycodestyle error
+    "W",   # pycodestyle warning
+    "F",   # pyflakes
+    "N",   # pep8-naming
+    "UP",  # pyupgrade
+    "YTT", # flake8-2020
+    "S",   # flake8-bandit
+    "BLE", # flake8-blind-except
+    "B",   # flake8-bugbear
+    "A",   # flake8-builtins
+    "COM", # flake8-commas
+    "C4",  # flake8-comprehensions
+    "T10", # flake8-debugger
+    "EM",  # flake8-errmsg
+    "FA",  # flake8-future-annotations
+    "ISC", # flake8-implicit-str-concat
+    "ICN", # flake8-import-conventions
+    "G",   # flake8-logging-format
+    "INP", # flake8-no-pep420
+    "PIE", # flake8-pie
+    "PT",  # flake8-pytest-style
+    "RSE", # flake8-raise
+    "RET", # flake8-return
+    "SLF", # flake8-self
+    "SIM", # flake8-simplify
     # We use os.path a lot in "legitimate" ways, so this ruleset has too many
     # false positives
     # "PTH",  # flake8-use-pathlib
@@ -205,11 +204,11 @@ select = [
 ]
 ignore = [
     "PLR0913",
-    "D105",     # missing docstring in magic method
-    "D100",     # Require docstring in public modules
-    "D104",     # Require docstring in public packages
-    "S603",     # Subprocess without shell equals true
-    "S607",     # start-process-with-partial-path
+    "D105",    # missing docstring in magic method
+    "D100",    # Require docstring in public modules
+    "D104",    # Require docstring in public packages
+    "S603",    # Subprocess without shell equals true
+    "S607",    # start-process-with-partial-path
     # recommended ignores for ruff format
     "W191",
     "E111",
@@ -236,8 +235,8 @@ namespace-packages = ["snakebids/plugins"]
 "snakebids/project_template/**" = ["N999"]
 "snakebids/tests/**" = [
     "D",
-    "S101",     # assert
-    "S307",     # Use of eval
+    "S101", # assert
+    "S307", # Use of eval
     "SLF",
 ]
 

snakebids/project_template/copier.yaml

@@ -65,7 +65,7 @@ bids_version:
   when: false
 
 python_version:
-  default: ">=3.8,<3.12"
+  default: ">=3.8,<3.13"
   when: false
 
 snakebids_version:
@@ -96,27 +96,16 @@ _message_after_copy: >
 
     $ cd {{ _copier_conf.dst_path }}
 
-  {% if build_system == "poetry" -%}
   {{ Fore.BLUE }}2.{{ Fore.RESET }} Install dependencies.
 
+  {% if build_system == "poetry" %}
     $ 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
+  {%- elif build_system == "hatch" %}
+    $ hatch env create
+  {%- else %}
+    $ python -m venv .venv
+    $ source .venv/bin/activate
+    $ pip install .
   {%- endif %}
 
 
@@ -125,15 +114,12 @@ _message_after_copy: >
   {% if build_system == "poetry" %}
     $ poetry run {{ test_run_cmd }}
 
-  {%- else %}
-    * {{Fore.YELLOW}}Virtual Environment and setuptools:{{Fore.RESET}}
-      $ {{ test_run_cmd }}
+  {%- elif build_system == "hatch" %}
+    $ hatch env run -- {{ test_run_cmd }}
 
-    * {{Fore.YELLOW}}Hatch:{{Fore.RESET}}
-      $ hatch env run -- {{ test_run_cmd }}
+  {%- else %}
+    $ {{ test_run_cmd }}
 
-    * {{Fore.YELLOW}}PDM:{{Fore.RESET}}
-      $ pdm run {{ test_run_cmd }}
   {%- endif %}
 
 _jinja_extensions:

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

@@ -28,12 +28,8 @@ classifiers = [
 
 requires-python = "{{ python_version }}"
 dependencies = [
-    "snakemake >= {{ snakemake_version }}",
+    "snakemake >= {{ snakemake_version }},<8",
     "snakebids >= {{ snakebids_version }}",
-    {# Explicitly specify numpy version for py38 until snakebids 0.10.x to
-       work around specification bug causing numpys too high for py38 to be
-       locked by pdm -#}
-    "numpy <=1.24.4; python_version < \"3.9\"",
 ]
 
 [project.scripts]

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

@@ -22,8 +22,12 @@ classifiers = [
 
 [tool.poetry.dependencies]
 python = "{{ python_version }}"
-snakemake = ">={{ snakemake_version }}"
+snakemake = ">={{ snakemake_version }},<8"
 snakebids = ">={{ snakebids_version }}"
+pandas = [
+    { version = "<=2.0.3", python = "<3.9" },
+    { version = ">=2.1.1", python = ">=3.12" },
+]
 
 [tool.poetry.scripts]
 {{ name_slug }} = "{{ name_slug }}.run:main"

snakebids/tests/test_template.py

@@ -270,7 +270,7 @@ def test_pyproject_correctly_formatted(
         ("setuptools", "setuptools"),
         ("poetry", "poetry"),
         ("hatch", "hatch"),
-        ("flit", "pdm"),
+        ("flit", "setuptools"),
     ],
 )
 def test_template_dry_runs_successfully(tmp_path: Path, build: BuildBackend, venv: str):

snakebids/utils/utils.py

@@ -474,32 +474,24 @@ def __getitem__(self, index: int | slice) -> _T_co | Self:
         return self._data[index]
 
     def __lt__(self, value: tuple[_T_co, ...] | Self, /) -> bool:
-        if isinstance(value, tuple):
-            return self._data < value
         if isinstance(value, ImmutableList):
             return self._data < value._data
-        return False
+        return self._data < value
 
     def __le__(self, value: tuple[_T_co, ...] | Self, /) -> bool:
-        if isinstance(value, tuple):
-            return self._data <= value
         if isinstance(value, ImmutableList):
             return self._data <= value._data
-        return False
+        return self._data <= value
 
     def __gt__(self, value: tuple[_T_co, ...] | Self, /) -> bool:
-        if isinstance(value, tuple):
-            return self._data > value
         if isinstance(value, ImmutableList):
             return self._data > value._data
-        return False
+        return self._data > value
 
     def __ge__(self, value: tuple[_T_co, ...] | Self, /) -> bool:
-        if isinstance(value, tuple):
-            return self._data >= value
         if isinstance(value, ImmutableList):
             return self._data >= value._data
-        return False
+        return self._data >= value
 
     @override
     def __eq__(self, value: object, /) -> bool: