⬆️ pre-commit.ci autoupdate (#130)

.github/workflows/test_cpac.yaml

@@ -68,14 +68,14 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        apptainer: [1.0.0, 1.3.0]
+        apptainer: [1.3.6]
         go: [1.14]
         platform: [apptainer, docker]
         python: ['3.10', 3.11, 3.12]
         tag: [latest, nightly]
         exclude:
         - platform: apptainer
-          python: 3.11
+          python: '3.10'
         - platform: apptainer
           python: 3.12
     steps:
@@ -102,6 +102,11 @@ jobs:
       uses: eWaterCycle/setup-apptainer@v2
       with:
         apptainer-version: ${{ matrix.apptainer }}
+    - name: Allow unprivileged user namespaces
+      if: ${{ matrix.platform == 'applainer' }}
+      run: |
+        sudo sh -c 'echo kernel.apparmor_restrict_unprivileged_userns=0 >/etc/sysctl.d/90-disable-userns-restrictions.conf'
+        sudo sysctl -p /etc/sysctl.d/90-disable-userns-restrictions.conf
     - name: Install cpac
       run: cd $GITHUB_WORKSPACE && pip install -e ".[dev,testing,tsconcat]"
     - name: Pull images

.pre-commit-config.yaml

@@ -9,14 +9,14 @@ fail_fast: false
 
 repos:
 - repo: https://github.com/astral-sh/ruff-pre-commit
-  rev: v0.8.1
+  rev: v0.8.6
   hooks:
   - id: ruff
     args: [--fix]
   - id: ruff-format
 
 - repo: https://github.com/pre-commit/mirrors-mypy
-  rev: v1.13.0
+  rev: v1.14.1
   hooks:
   - id: mypy
     additional_dependencies:
@@ -39,14 +39,19 @@ repos:
     - --no-sort
 
 - repo: https://github.com/python-poetry/poetry
-  rev: 1.8.3
+  rev: 2.0.0
   hooks:
   - id: poetry-check
   - id: poetry-lock
-    args: [--no-update]
 
 - repo: local
   hooks:
+  - id: store-optional-dependencies
+    name: Store optional dependencies
+    entry: ./src/cpac/helpers/store_optional_dependencies.py
+    language: python
+    additional_dependencies: [packaging]
+    always_run: true
   - id: update-README
     name: Update README from usage string
     entry: ./.pre-commit-hooks/update_README.py

pyproject.toml

@@ -1,5 +1,60 @@
+[project]
+name = "cpac"
+description = "C-PAC Python Package"
+authors = [{name = "C-PAC developers", email = "cpac@cnl.childmind.org"}]
+license = "MIT"
+classifiers = [
+  "Development Status :: 3 - Alpha",
+  "Intended Audience :: Science/Research",
+  "License :: OSI Approved :: MIT License",
+  "Natural Language :: English",
+  "Operating System :: OS Independent",
+  "Programming Language :: Python :: 3",
+  "Topic :: Scientific/Engineering :: Bio-Informatics"
+]
+requires-python = ">=3.10,<4.0"
+dependencies = [
+  "docker>=7.1.0",
+  "dockerpty",
+  "docker-pycreds",
+  "pandas>=0.23.4",
+  "poetry>=2.0.0",
+  "pyyaml",
+  "rich",
+  "semver",
+  "spython>=0.3.0",
+  "tabulate>=0.8.6",
+  "tomli; python_version < '3.11'",
+  "tornado",
+  "websocket-client"
+]
+readme = "README.rst"
+version = "1.8.8.dev1"
+
+[project.optional-dependencies]
+dev = ["coveralls", "pytest", "pytest-remotedata>=0.3.2", "pytest-runner", "sphinx"]
+gradients = []
+testing = ["alabaster", "imagesize", "pytest", "pytest-cov", "pytest-runner", "sphinx"]
+tsconcat = [
+  "ba-tsconcat>=0.1.2,<0.2.0; python_version >= '3.11' and python_version < '4.0'",
+  "bids2table==0.1.0",
+  "elbow==0.1.1",
+  "imagesize",
+  "nibabel==5.3.2",
+  "numpy>=1.26.3,<2.0.0",
+  "pandas==2.2.2",
+  "pyarrow==18.1.0"
+]
+
+[project.scripts]
+cpac = "cpac.__main__:run"
+
+[project.urls]
+documentation = "https://fcp-indi.github.io/docs/latest/user/cpac"
+repository = "https://github.com/FCP-INDI/cpac"
+
 [build-system]
-requires = ["poetry-core>=1.0.0"]
+requires = ["poetry-core>=2.0.0"]
 build-backend = "poetry.core.masonry.api"
 
 [tool.aliases]
@@ -42,63 +97,7 @@ no-vcs = "1"
 formats = "bdist_wheel"
 
 [tool.poetry]
-name = "cpac"
-description = "C-PAC Python Package"
-authors = ["C-PAC developers <cpac@cnl.childmind.org>"]
-license = "MIT"
-classifiers = [
-  "Development Status :: 3 - Alpha",
-  "Intended Audience :: Science/Research",
-  "License :: OSI Approved :: MIT License",
-  "Natural Language :: English",
-  "Operating System :: OS Independent",
-  "Programming Language :: Python :: 3",
-  "Topic :: Scientific/Engineering :: Bio-Informatics"
-]
-documentation = "https://fcp-indi.github.io/docs/latest/user/cpac"
-readme = "README.rst"
-repository = "https://github.com/FCP-INDI/cpac"
-version = "1.8.8.dev1"
-
-[tool.poetry.dependencies]
-python = ">=3.10,<4.0"
-docker = ">=7.1.0"
-dockerpty = "*"
-docker-pycreds = "*"
-pandas = [
-  {version = ">=0.23.4"},
-  {version = "2.2.2", markers = "python_version >= '3.11' and python_version < '4.0' and extra == 'tsconcat'"}
-]
-poetry = ">=1.8.2"
-pyyaml = "*"
-rich = "*"
-semver = "*"
-spython = ">=0.3.0"
-tabulate = ">=0.8.6"
-tornado = "*"
-websocket-client = "*"
-alabaster = {version = "*", optional = true}
-ba-tsconcat = {version = ">=0.1.2,<0.2.0", optional = true, markers = "python_version >= '3.11' and python_version < '4.0'"}
-bids2table = {version = "0.1.0", markers = "extra == 'tsconcat'"}
-coveralls = {version = "*", optional = true}
-elbow = {version = "0.1.1", markers = "extra == 'tsconcat'"}
-imagesize = {version = "*", optional = true}
-nibabel = {version = "5.3.2", markers = "extra == 'tsconcat'"}
-pyarrow = {version = "18.1.0", markers = "extra == 'tsconcat'"}
-pytest = {version = "*", optional = true}
-pytest-cov = {version = "*", optional = true}
-pytest-remotedata = {version = ">=0.3.2", optional = true}
-pytest-runner = {version = "*", optional = true}
-sphinx = {version = "*", optional = true}
-
-[tool.poetry.extras]
-dev = ["coveralls", "pytest", "pytest-remotedata", "pytest-runner", "sphinx"]
-gradients = []
-testing = ["alabaster", "imagesize", "pytest", "pytest-cov", "pytest-runner", "sphinx"]
-tsconcat = ["ba-tsconcat"]
-
-[tool.poetry.scripts]
-cpac = "cpac.__main__:run"
+requires-poetry = ">=2.0"
 
 [tool.pytest.ini_options]
 addopts = "-s"
@@ -121,6 +120,7 @@ extend-select = ["A", "C4", "D", "G", "I", "ICN", "NPY", "PL", "RET", "RSE", "RU
 
 [tool.ruff.lint.isort]
 combine-as-imports = true
+extra-standard-library = ["tomllib"]
 force-sort-within-sections = true
 known-first-party = ["cpac"]
 no-lines-before = ["collab", "other-first-party", "local-folder"]

src/cpac/helpers/store_optional_dependencies.py

@@ -0,0 +1,46 @@
+#!/usr/bin/env python3
+"""Store optional dependencies for dynamic metadata access."""
+
+from itertools import chain
+from pathlib import Path
+from pickle import dump, load
+from typing import cast
+
+from packaging.requirements import Requirement
+
+try:
+    import tomllib
+except ImportError:
+    # Python < 3.11
+    import tomli as tomllib
+
+PICKLE_PATH = Path(__file__).parents[1] / "optional_dependencies.pkl"
+
+
+def store_optional_dependencies(output_path: str) -> None:
+    """Store optional dependencies."""
+    # Extract optional dependencies
+    with open("pyproject.toml", "rb") as f:
+        toml_data = tomllib.load(f)
+    optional_deps: dict[str, Requirement] = {}
+    reqs = [
+        Requirement(req)
+        for req in chain.from_iterable(
+            toml_data.get("project", {}).get("optional-dependencies", {}).values()
+        )
+    ]
+    for req in reqs:
+        if req.name in optional_deps:
+            optional_deps[req.name].specifier &= req.specifier
+        else:
+            optional_deps[req.name] = req
+
+    with open(output_path, "rb") as f:
+        existing_optional_deps = cast(dict[str, Requirement], load(f))
+    if not optional_deps == existing_optional_deps:
+        with open(output_path, "wb") as f:
+            dump(optional_deps, f)
+
+
+if __name__ == "__main__":
+    store_optional_dependencies(str(PICKLE_PATH))

src/cpac/utils/bare_wrap.py

@@ -5,7 +5,10 @@
 from argparse import _SubParsersAction, ArgumentParser, HelpFormatter, REMAINDER
 from dataclasses import dataclass
 from importlib.metadata import requires
+from importlib.resources import files
 from logging import ERROR, log
+from pathlib import Path
+import pickle
 from shutil import which
 from subprocess import call as sub_call, CalledProcessError
 from sys import exit as sys_exit, version_info
@@ -132,7 +135,15 @@ def helpstring(self):
     @property
     def package_info(self) -> Optional[Requirement]:
         """Return metadata about how a package is required for this version of cpac."""
-        return self.requirements().get(self.package)
+        pkg_info = self.requirements().get(self.package)
+        if not pkg_info:
+            optional_deps = Path(
+                str(files("cpac").joinpath("optional_dependencies.pkl"))
+            )
+            if optional_deps.exists():
+                with optional_deps.open("rb") as _pickle:
+                    pkg_info = pickle.load(_pickle).get(self.package)
+        return pkg_info
 
     @classmethod
     def requirements(cls) -> dict[str, Requirement]:
@@ -172,7 +183,7 @@ def version(self) -> str:
         """Return the supported version(s) of the wrapped package."""
         if self.package_info:
             if self.package_info.specifier:
-                return self.package_info.specifier
+                return str(self.package_info.specifier)
             return getattr(self.package_info, "url", "*")
         return "*"