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

ENH: Standalone CLI now estimates fieldmaps

Author: oesteban

.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