feat: updated Nextflow workflows with profiles, auto-assess, rehoming

.github/workflows/python-app.yml

@@ -19,22 +19,19 @@ jobs:
 
     steps:
     - uses: actions/checkout@v4
+    - name: Install uv
+      uses: astral-sh/setup-uv@v5
     - name: Set up Python 3.12
-      uses: actions/setup-python@v3
-      with:
-        python-version: "3.12"
+      run: uv python install 3.12
     - name: Install dependencies
+      run: uv sync
+    - name: Lint with ruff
       run: |
-        python -m pip install --upgrade pip
-        pip install flake8 pytest
-        pip install .
-        pip install -r requirements-pytest.txt
-    - name: Lint with flake8
-      run: |
-        # stop the build if there are Python syntax errors or undefined names
-        flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
-        # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
-        flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
+        uv run ruff check .
+        uv run ruff format --check .
+    - name: Type check with ty
+      continue-on-error: true
+      run: uv run ty check
     - name: Test with pytest
       run: |
-        pytest
+        uv run pytest

.gitignore

@@ -143,6 +143,9 @@ venv.bak/
 .dmypy.json
 dmypy.json
 
+# ruff
+.ruff_cache/
+
 # Pyre type checker
 .pyre/
 
@@ -184,3 +187,8 @@ workflows/work/
 
 # Temp code file
 draft.py
+
+# Exculde subject data folders (symlinks)
+sub-*
+
+.python-version

.pre-commit-config.yaml

@@ -0,0 +1,19 @@
+repos:
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.15.8
+    hooks:
+      - id: ruff-format
+      - id: ruff
+        args: [--fix]
+  - repo: local
+    hooks:
+      - id: ty
+        name: ty (type check)
+        entry: bash -c 'uv run ty check || true'
+        language: system
+        types: [python]
+        files: ^linumpy/
+        pass_filenames: false
+        # Non-blocking (advisory) until the existing error baseline is resolved.
+        # Switch entry to just "uv run ty check" once errors reach zero.
+        verbose: true

Dockerfile

@@ -1,5 +1,7 @@
 FROM python:3.12
 
+COPY --from=ghcr.io/astral-sh/uv:latest /uv /uvx /bin/
+
 WORKDIR /linumpy/
 
 ENV PYTHONDONTWRITEBYTECODE=1
@@ -14,11 +16,8 @@ RUN apt-get update && apt-get install -y \
     zip \
     && rm -rf /var/lib/apt/lists/*
 
-# Upgrade pip, setuptools and wheel
-RUN pip install --upgrade pip setuptools wheel build
-
-# Install with verbose output
+# Install with uv
 COPY linumpy ./linumpy
 COPY scripts ./scripts
-COPY pyproject.toml requirements.txt README.md setup.py ./
-RUN pip install --no-cache-dir -v -e .
+COPY pyproject.toml uv.lock README.md ./
+RUN uv sync --frozen --no-dev

linumpy/__init__.py

@@ -1,23 +1,30 @@
 # Configure thread limits FIRST, before any numerical libraries are imported
-import os as _os
-
 from linumpy._thread_config import (
-    configure_thread_limits,
-    apply_threadpool_limits,
-    configure_all_libraries,
-    configure_sitk,
+    apply_threadpool_limits as apply_threadpool_limits,
+)
+from linumpy._thread_config import (
+    configure_all_libraries as configure_all_libraries,
+)
+from linumpy._thread_config import (
+    configure_sitk as configure_sitk,
+)
+from linumpy._thread_config import (
+    configure_thread_limits as configure_thread_limits,
 )
 
+import os as _os
+from pathlib import Path as _Path
+
 
 def get_home():
-    """ Set a user-writeable file-system location to put files. """
-    if 'LINUMPY_HOME' in _os.environ:
-        return _os.environ['LINUMPY_HOME']
-    return _os.path.join(_os.path.expanduser('~'), '.linumpy')
+    """Set a user-writeable file-system location to put files."""
+    if "LINUMPY_HOME" in _os.environ:
+        return _os.environ["LINUMPY_HOME"]
+    return str(_Path.home() / ".linumpy")
 
 
 def get_root():
-    return _os.path.realpath(f"{_os.path.dirname(_os.path.abspath(__file__))}/..")
+    return str(_Path(__file__).resolve().parent.parent)
 
 
 LINUMPY_HOME = get_home()

linumpy/_thread_config.py

@@ -1,4 +1,3 @@
-# -*- coding: utf-8 -*-
 """
 Thread configuration module for linumpy.
 
@@ -30,6 +29,7 @@
 To ensure proper limiting, scripts should call configure_all_libraries() after imports.
 """
 
+import contextlib
 import multiprocessing
 import os
 import sys
@@ -47,18 +47,21 @@ def get_max_threads():
     """
     total_cpus = multiprocessing.cpu_count()
 
-    try:
-        # Check for explicit max CPUs limit
-        max_cpus = os.environ.get('LINUMPY_MAX_CPUS')
-        if max_cpus is not None:
+    # Check for explicit max CPUs limit
+    max_cpus = os.environ.get("LINUMPY_MAX_CPUS")
+    if max_cpus is not None:
+        try:
             return max(1, min(int(max_cpus), total_cpus))
+        except ValueError:
+            pass
 
-        # Check for reserved CPUs
-        reserved = os.environ.get('LINUMPY_RESERVED_CPUS')
-        if reserved is not None:
+    # Check for reserved CPUs
+    reserved = os.environ.get("LINUMPY_RESERVED_CPUS")
+    if reserved is not None:
+        try:
             return max(1, total_cpus - int(reserved))
-    except ValueError:
-        pass
+        except ValueError:
+            pass
 
     # Default: use all CPUs
     return total_cpus
@@ -79,42 +82,42 @@ def configure_thread_limits():
     max_threads = get_max_threads()
 
     # If OMP_NUM_THREADS is already set, use that value instead
-    if 'OMP_NUM_THREADS' in os.environ:
-        try:
-            max_threads = int(os.environ['OMP_NUM_THREADS'])
-        except ValueError:
-            pass
+    if "OMP_NUM_THREADS" in os.environ:
+        with contextlib.suppress(ValueError):
+            max_threads = int(os.environ["OMP_NUM_THREADS"])
 
     # Set environment variables for all common threading libraries
     # Set ALL of them unconditionally to ensure consistency
     thread_vars = [
-        'OMP_NUM_THREADS',  # OpenMP (used by numpy, scipy, etc.)
-        'MKL_NUM_THREADS',  # Intel MKL
-        'OPENBLAS_NUM_THREADS',  # OpenBLAS
-        'VECLIB_MAXIMUM_THREADS',  # macOS Accelerate
-        'NUMEXPR_NUM_THREADS',  # NumExpr
-        'NUMBA_NUM_THREADS',  # Numba
-        'GOTO_NUM_THREADS',  # GotoBLAS
-        'BLIS_NUM_THREADS',  # BLIS
-        'ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS',  # SimpleITK/ITK
-        'XLA_FLAGS',  # JAX/XLA thread pool (set below with special format)
+        "OMP_NUM_THREADS",  # OpenMP (used by numpy, scipy, etc.)
+        "MKL_NUM_THREADS",  # Intel MKL
+        "OPENBLAS_NUM_THREADS",  # OpenBLAS
+        "VECLIB_MAXIMUM_THREADS",  # macOS Accelerate
+        "NUMEXPR_NUM_THREADS",  # NumExpr
+        "NUMBA_NUM_THREADS",  # Numba
+        "GOTO_NUM_THREADS",  # GotoBLAS
+        "BLIS_NUM_THREADS",  # BLIS
+        "ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS",  # SimpleITK/ITK
+        "XLA_FLAGS",  # JAX/XLA thread pool (set below with special format)
     ]
 
     for var in thread_vars:
-        if var == 'XLA_FLAGS':
+        if var == "XLA_FLAGS":
             # XLA flags use a special format
             # This limits JAX's XLA thread pool (used by BaSiCPy)
-            xla_flags = os.environ.get('XLA_FLAGS', '')
-            if f'--xla_cpu_multi_thread_eigen=false' not in xla_flags:
+            xla_flags = os.environ.get("XLA_FLAGS", "")
+            if "--xla_cpu_multi_thread_eigen=false" not in xla_flags:
                 # Disable multi-threading in XLA's Eigen backend for better control
-                new_flags = f'{xla_flags} --xla_cpu_multi_thread_eigen=false intra_op_parallelism_threads={max_threads}'.strip()
-                os.environ['XLA_FLAGS'] = new_flags
+                new_flags = (
+                    f"{xla_flags} --xla_cpu_multi_thread_eigen=false intra_op_parallelism_threads={max_threads}".strip()
+                )
+                os.environ["XLA_FLAGS"] = new_flags
         else:
             os.environ[var] = str(max_threads)
 
     # Also set dask configuration via environment variable
     # This limits dask's thread pool before dask is imported
-    os.environ['DASK_NUM_WORKERS'] = str(max_threads)
+    os.environ["DASK_NUM_WORKERS"] = str(max_threads)
 
     return max_threads
 
@@ -126,10 +129,11 @@ def configure_dask():
     """
     try:
         import dask
-        max_threads = int(os.environ.get('OMP_NUM_THREADS', multiprocessing.cpu_count()))
+
+        max_threads = int(os.environ.get("OMP_NUM_THREADS", multiprocessing.cpu_count()))
         dask.config.set(num_workers=max_threads)
-        dask.config.set(scheduler='threads')  # Use thread scheduler, not process
-        dask.config.set({'array.slicing.split_large_chunks': False})
+        dask.config.set(scheduler="threads")  # Use thread scheduler, not process
+        dask.config.set({"array.slicing.split_large_chunks": False})
     except ImportError:
         pass
 
@@ -145,7 +149,8 @@ def configure_sitk():
     """
     try:
         import SimpleITK as sitk
-        max_threads = int(os.environ.get('OMP_NUM_THREADS', multiprocessing.cpu_count()))
+
+        max_threads = int(os.environ.get("OMP_NUM_THREADS", multiprocessing.cpu_count()))
         sitk.ProcessObject.SetGlobalDefaultNumberOfThreads(max_threads)
     except ImportError:
         pass
@@ -165,7 +170,7 @@ def apply_threadpool_limits():
         from threadpoolctl import threadpool_limits
 
         # Get the configured thread limit
-        max_threads = int(os.environ.get('OMP_NUM_THREADS', multiprocessing.cpu_count()))
+        max_threads = int(os.environ.get("OMP_NUM_THREADS", multiprocessing.cpu_count()))
 
         # Apply limits globally - this returns a context manager but also applies immediately
         limiter = threadpool_limits(limits=max_threads)
@@ -192,20 +197,21 @@ def configure_all_libraries():
     """
     global _thread_config_applied
 
-    max_threads = int(os.environ.get('OMP_NUM_THREADS', multiprocessing.cpu_count()))
+    max_threads = int(os.environ.get("OMP_NUM_THREADS", multiprocessing.cpu_count()))
 
     # Configure SimpleITK if imported (CRITICAL - major source of CPU spikes)
-    if 'SimpleITK' in sys.modules:
+    if "SimpleITK" in sys.modules:
         configure_sitk()
 
     # Configure dask if imported
-    if 'dask' in sys.modules:
+    if "dask" in sys.modules:
         configure_dask()
 
     # Configure numba if imported
-    if 'numba' in sys.modules:
+    if "numba" in sys.modules:
         try:
             from numba import set_num_threads
+
             set_num_threads(max_threads)
         except (ImportError, Exception):
             pass
@@ -226,31 +232,32 @@ def get_thread_info():
         dict: Thread configuration information
     """
     info = {
-        'total_cpus': multiprocessing.cpu_count(),
-        'configured_threads': int(os.environ.get('OMP_NUM_THREADS', multiprocessing.cpu_count())),
-        'env_vars': {},
-        'libraries': {},
+        "total_cpus": multiprocessing.cpu_count(),
+        "configured_threads": int(os.environ.get("OMP_NUM_THREADS", multiprocessing.cpu_count())),
+        "env_vars": {},
+        "libraries": {},
     }
 
     # Check environment variables
-    for var in ['OMP_NUM_THREADS', 'MKL_NUM_THREADS', 'OPENBLAS_NUM_THREADS',
-                'LINUMPY_MAX_CPUS', 'LINUMPY_RESERVED_CPUS']:
-        info['env_vars'][var] = os.environ.get(var, 'NOT SET')
+    for var in ["OMP_NUM_THREADS", "MKL_NUM_THREADS", "OPENBLAS_NUM_THREADS", "LINUMPY_MAX_CPUS", "LINUMPY_RESERVED_CPUS"]:
+        info["env_vars"][var] = os.environ.get(var, "NOT SET")
 
     # Check SimpleITK
-    if 'SimpleITK' in sys.modules:
+    if "SimpleITK" in sys.modules:
         try:
             import SimpleITK as sitk
-            info['libraries']['SimpleITK'] = sitk.ProcessObject.GetGlobalDefaultNumberOfThreads()
+
+            info["libraries"]["SimpleITK"] = sitk.ProcessObject.GetGlobalDefaultNumberOfThreads()
         except Exception:
-            info['libraries']['SimpleITK'] = 'ERROR'
+            info["libraries"]["SimpleITK"] = "ERROR"
 
     # Check threadpoolctl
     try:
         from threadpoolctl import threadpool_info
-        info['libraries']['threadpoolctl'] = threadpool_info()
+
+        info["libraries"]["threadpoolctl"] = threadpool_info()
     except ImportError:
-        info['libraries']['threadpoolctl'] = 'NOT INSTALLED'
+        info["libraries"]["threadpoolctl"] = "NOT INSTALLED"
 
     return info
 
@@ -261,10 +268,10 @@ def print_thread_info():
     print(f"CPU cores: {info['total_cpus']}")
     print(f"Configured threads: {info['configured_threads']}")
     print("Environment variables:")
-    for var, val in info['env_vars'].items():
+    for var, val in info["env_vars"].items():
         print(f"  {var}: {val}")
     print("Library configurations:")
-    for lib, val in info['libraries'].items():
+    for lib, val in info["libraries"].items():
         print(f"  {lib}: {val}")
 
 

linumpy/io/__init__.py

@@ -1,4 +1,15 @@
-from .allen import *
-from .data_io import *
-from .zarr import *
-from .npz import write_numpy, read_numpy, read_numpy_data, read_numpy_metadata
+from .allen import *  # noqa: F403
+from .data_io import *  # noqa: F403
+from .npz import (
+    read_numpy as read_numpy,
+)
+from .npz import (
+    read_numpy_data as read_numpy_data,
+)
+from .npz import (
+    read_numpy_metadata as read_numpy_metadata,
+)
+from .npz import (
+    write_numpy as write_numpy,
+)
+from .zarr import *  # noqa: F403