Merge pull request #408 from nipreps/enh/improve-standalone-cli

ENH: Standalone CLI now estimates fieldmaps

.circleci/config.yml

@@ -377,7 +377,7 @@ jobs:
             python -m venv /tmp/venv
             source /tmp/venv/bin/activate
             python -m pip install -U build hatch hatchling pip twine docutils
-            python -m pip install --no-cache-dir -r docs/requirements.txt
+            python -m pip install .[docs]
       - run:
           name: Build only this commit
           command: |

.github/workflows/pythonpackage.yml

@@ -63,7 +63,7 @@ jobs:
         python-version: 3
     - name: Display Python version
       run: python -c "import sys; print(sys.version)"
-    - name: Build niworkflows
+    - name: Build sdcflows
       run: pipx run build
     - name: Check distributions
       run: pipx run twine check dist/*
@@ -78,7 +78,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ["3.10", "3.12"]
+        python-version: ["3.9", "3.12"]
         install: [repo, sdist, wheel, editable]
 
     env:

.github/workflows/unittests.yml

@@ -34,7 +34,7 @@ jobs:
     strategy:
       max-parallel: 5
       matrix:
-        python-version: ["3.10", "3.11", "3.12"]
+        python-version: ["3.9", "3.10", "3.11", "3.12"]
 
     steps:
     - uses: actions/cache@v3

docs/Makefile

@@ -4,6 +4,7 @@
 # You can set these variables from the command line.
 SPHINXOPTS    =
 SPHINXBUILD   = sphinx-build
+SPHINX_APIDOC_OPTIONS = members,show-inheritance
 PAPER         =
 BUILDDIR      = _build
 OUTDIR        = html
@@ -57,7 +58,7 @@ docs-coverage:
 	PYTHONPATH=$(PYTHONPATH) $(SPHINXBUILD) -b coverage $(ALLSPHINXOPTS) $(BUILDDIR)/coverage
 
 html:
-	PYTHONPATH=$(PYTHONPATH) $(SPHINXBUILD) -b html $(ALLSPHINXOPTS) $(BUILDDIR)/$(OUTDIR)
+	PYTHONPATH=$(PYTHONPATH) SPHINX_APIDOC_OPTIONS=$(SPHINX_APIDOC_OPTIONS) $(SPHINXBUILD) -b html $(ALLSPHINXOPTS) $(BUILDDIR)/$(OUTDIR)
 	@echo
 	@echo "Build finished. The HTML pages are in $(BUILDDIR)/$(OUTDIR)."
 

docs/_static/config-example.toml

@@ -0,0 +1,53 @@
+[environment]
+cpu_count = 36
+exec_env = "posix"
+free_mem = 13.7
+overcommit_policy = "heuristic"
+overcommit_limit = "50%"
+nipype_version = "1.8.7.dev0"
+templateflow_version = "23.0.0"
+total_memory = 62.51573181152344
+version = "2.6.1.dev5+gaa86b0b08f.d20231128"
+
+[execution]
+ants_float = false
+bids_dir = "/data/datasets/hcph"
+bids_database_dir = "/data/datasets/hcph/.bids-index"
+bids_database_wipe = false
+cwd = "/home/oesteban/tmp/sdcflows-hcph"
+debug = false
+dry_run = false
+layout = "BIDS Layout: .../data/datasets/hcph | Subjects: 1 | Sessions: 59 | Runs: 4"
+log_dir = "/home/oesteban/tmp/sdcflows-hcph/out/logs"
+log_level = 15
+notrack = false
+output_dir = "/home/oesteban/tmp/sdcflows-hcph/out"
+participant_label = [ "001",]
+pdb = false
+run_uuid = "20231129-112254_e9d6d38e-35ff-463e-9f7e-1ff15ecd54ac"
+templateflow_home = "/data/templateflow"
+work_dir = "/home/oesteban/tmp/sdcflows-hcph/work"
+write_graph = false
+
+[workflow]
+analysis_level = [ "participant",]
+fmapless = false
+species = "human"
+template_id = "MNI152NLin2009cAsym"
+
+[nipype]
+crashfile_format = "txt"
+get_linked_libs = false
+local_hash_check = true
+nprocs = 8
+omp_nthreads = 16
+plugin = "MultiProc"
+remove_node_directories = false
+resource_monitor = false
+stop_on_first_crash = true
+
+[execution.bids_filters]
+
+[nipype.plugin_args]
+maxtasksperchild = 1
+raise_insufficient = false

docs/api.rst

@@ -7,6 +7,7 @@ Information on specific functions, classes, and methods.
    :glob:
 
    api/sdcflows.cli
+   api/sdcflows.config
    api/sdcflows.data
    api/sdcflows.fieldmaps
    api/sdcflows.interfaces

docs/cli.rst

@@ -0,0 +1,8 @@
+Standalone command line usage
+=============================
+*SDCFlows* can execute fieldmap estimation from a BIDS-compliant dataset by using the *standalone command line interface*:
+
+.. argparse::
+   :module: sdcflows.cli.parser
+   :func: _parser
+   :prog: sdcflows

docs/conf.py

@@ -35,6 +35,7 @@
     "sphinx.ext.intersphinx",
     "sphinx.ext.mathjax",
     "sphinx.ext.viewcode",
+    "sphinxarg.ext",
     "sphinxcontrib.apidoc",
     "nbsphinx",
     "nipype.sphinxext.apidoc",

docs/index.rst

@@ -9,5 +9,6 @@ Contents
     installation
     examples
     methods
+    cli
     api
     changes

docs/requirements.txt

@@ -7,14 +7,15 @@ matplotlib >= 2.2.0
 nbsphinx
 nibabel
 nipype >= 1.5.1
-niworkflows ~= 1.6.3
+niworkflows >= 1.7.0
 numpy
 packaging
 pandoc
 pydot >= 1.2.3
 pydotplus
 scipy
 sphinx >= 7.2.2
+sphinx-argparse
 sphinxcontrib-apidoc
 templateflow
-traits < 6.4
+traits < 6.4

pyproject.toml

@@ -13,24 +13,27 @@ classifiers = [
     "Topic :: Scientific/Engineering :: Image Recognition",
     "Topic :: Scientific/Engineering :: Bio-Informatics",
     "License :: OSI Approved :: Apache Software License",
+    "Programming Language :: Python :: 3.9",
     "Programming Language :: Python :: 3.10",
     "Programming Language :: Python :: 3.11",
     "Programming Language :: Python :: 3.12",
 ]
 license = "Apache-2.0"
-requires-python = ">=3.10"
+requires-python = ">=3.9"
 dependencies = [
     "attrs >= 20.1.0",
     "nibabel >=3.1.0",
     "nipype >=1.8.5,<2.0",
     "traits <6.4",
+    "migas >= 0.4.0",
     "niworkflows >= 1.7.0",
     "nitransforms >= 23.0.1",
     "numpy >= 1.21.0",
-    "pybids >= 0.15.1",
+    "pybids >= 0.16.4",
     "scikit-image >= 0.18",
     "scipy >= 1.8.1",
     "templateflow",
+    "toml",
 ]
 dynamic = ["version"]
 
@@ -44,18 +47,24 @@ doc = [
     "attrs >= 20.1.0",
     "furo",
     "importlib_resources",
+    "ipykernel",
+    "ipython",
     "matplotlib >= 2.2.0",
+    "nbsphinx",
     "nibabel",
     "nipype >= 1.5.1",
-    "traits < 6.4",
-    "niworkflows >= 1.7.0",
+    "niworkflows @ git+https://github.com/nipreps/niworkflows.git@master",
     "numpy",
     "packaging",
+    "pandoc",
     "pydot >= 1.2.3",
     "pydotplus",
+    "scipy",
     "sphinx >= 7.2.2",
+    "sphinx-argparse",
     "sphinxcontrib-apidoc",
-    "templateflow"
+    "templateflow",
+    "traits < 6.4"
 ]
 
 mem = [
@@ -83,7 +92,7 @@ tests = ["sdcflows[test]"]
 all = ["sdcflows[doc,test,mem,dev,test]"]
 
 [project.scripts]
-sdcflows-find-estimators = "sdcflows.cli.find_estimators:main"
+sdcflows = "sdcflows.cli.main:main"
 
 #
 # Hatch configurations

sdcflows/_warnings.py

@@ -0,0 +1,49 @@
+# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
+# vi: set ft=python sts=4 ts=4 sw=4 et:
+#
+# Copyright 2023 The NiPreps Developers <[email protected]>
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+#
+# We support and encourage derived works from this project, please read
+# about our expectations at
+#
+#     https://www.nipreps.org/community/licensing/
+#
+# STATEMENT OF CHANGES: This file is derived from sources licensed under the Apache-2.0 terms,
+# and this file has been changed.
+# The original file this work derives from is found at:
+# https://github.com/nipreps/mriqc/blob/8ceadba8669cc2a86119a97b9311ab968f11c6eb/mriqc/_warnings.py
+"""Manipulate Python warnings."""
+import logging
+import warnings
+
+_wlog = logging.getLogger("py.warnings")
+_wlog.addHandler(logging.NullHandler())
+
+
+def _warn(message, category=None, stacklevel=1, source=None):
+    """Redefine the warning function."""
+    if category is not None:
+        category = type(category).__name__
+        category = category.replace("type", "WARNING")
+
+    logging.getLogger("py.warnings").warning(f"{category or 'WARNING'}: {message}")
+
+
+def _showwarning(message, category, filename, lineno, file=None, line=None):
+    _warn(message, category=category)
+
+
+warnings.warn = _warn
+warnings.showwarning = _showwarning