Release 2.1.0

.github/workflows/codespell.yml

@@ -32,11 +32,11 @@ jobs:
 
     steps:
     - name: Checkout repository
-      uses: actions/checkout@v4
+      uses: actions/checkout@v7
       with:
         fetch-depth: 0
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v5
+      uses: actions/setup-python@v7
       with:
         python-version: ${{ matrix.python-version }}
     - name: Codespell

.github/workflows/documentation.yml

@@ -55,11 +55,11 @@ jobs:
           echo "DEPLOY_TYPE=pr" >> $GITHUB_OUTPUT
         fi
     - name: Checkout repository
-      uses: actions/checkout@v5
+      uses: actions/checkout@v7
       with:
         fetch-depth: 0
     - name: Set up Python
-      uses: actions/setup-python@v6
+      uses: actions/setup-python@v7
       with:
         python-version: ${{ env.MIN_PYTHON_VERSION }}
         cache: "pip"

.github/workflows/pycodestyle.yml

@@ -32,11 +32,11 @@ jobs:
 
     steps:
     - name: Checkout repository
-      uses: actions/checkout@v4
+      uses: actions/checkout@v7
       with:
         fetch-depth: 0
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v5
+      uses: actions/setup-python@v7
       with:
         python-version: ${{ matrix.python-version }}
     - name: Install dependencies

.github/workflows/pydoclint.yml

@@ -34,11 +34,11 @@ jobs:
 
     steps:
     - name: Checkout repository
-      uses: actions/checkout@v4
+      uses: actions/checkout@v7
       with:
         fetch-depth: 0
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v5
+      uses: actions/setup-python@v7
       with:
         python-version: ${{ matrix.python-version }}
     - name: Install dependencies

.github/workflows/release-documentation.yml

@@ -33,11 +33,11 @@ jobs:
       shell: bash
       run: echo "BRANCH=${GITHUB_HEAD_REF:-${GITHUB_REF#refs/heads/}}" >> $GITHUB_OUTPUT
     - name: Checkout repository
-      uses: actions/checkout@v5
+      uses: actions/checkout@v7
       with:
         fetch-depth: 0
     - name: Set up Python
-      uses: actions/setup-python@v6
+      uses: actions/setup-python@v7
       with:
         python-version: ${{ env.MIN_PYTHON_VERSION }}
         cache: "pip"

.github/workflows/ruff.yml

@@ -32,11 +32,11 @@ jobs:
 
     steps:
     - name: Checkout repository
-      uses: actions/checkout@v4
+      uses: actions/checkout@v7
       with:
         fetch-depth: 0
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v5
+      uses: actions/setup-python@v7
       with:
         python-version: ${{ matrix.python-version }}
     - name: Install dependencies

.github/workflows/testing.yml

@@ -5,7 +5,6 @@
 # .. code-block:: bash
 #
 #   $ nosetests --with-coverage --cover-package=brainprep --verbosity=2
-#     --with-doctest --doctest-options='+ELLIPSIS,+NORMALIZE_WHITESPACE'
 ###
 name: "testing[nosetests]"
 
@@ -34,11 +33,11 @@ jobs:
 
     steps:
     - name: Checkout repository
-      uses: actions/checkout@v5
+      uses: actions/checkout@v7
       with:
         fetch-depth: 0
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v5
+      uses: actions/setup-python@v7
       with:
         python-version: ${{ matrix.python-version }}
         cache: "pip"
@@ -48,7 +47,7 @@ jobs:
         python -m pip install --progress-bar off ".[ci]"
     - name: Run unit tests
       run: |
-        nosetests --with-coverage --cover-package=brainprep --verbosity=2 --with-doctest --doctest-options='+ELLIPSIS,+NORMALIZE_WHITESPACE'
+        nosetests --with-coverage --cover-package=brainprep --verbosity=2
     - name: Coveralls
       if: matrix.python-version == 3.12
       env:

CHANGELOG.rst

@@ -1,6 +1,7 @@
 .. -*- mode: rst -*-
 
-2.1.0.dev
+
+2.2.0.dev
 =========
 
 HIGHLIGHTS
@@ -9,36 +10,69 @@ HIGHLIGHTS
 NEW
 ---
 
+Fixes
+-----
+
+Enhancements
+------------
+
+Changes
+-------
+
+
+2.1.0
+=====
+
+HIGHLIGHTS
+----------
+
+This release optimizes existing or introduces new workflows. Please review
+the modifications below.
+
+NEW
+---
+
 - :bdg-success:`Enhancement` Add the dmriprep workflow.
-- :bdg-success:`Enhancement` Add the tbss workflow.
-- :bdg-success:`Enhancement` Add the mrophologist workflow.
+- :bdg-success:`Enhancement` Add the morphologist workflow.
 
 Fixes
 -----
 
+- :bdg-danger:`Deprecation` Fix the containers that are using `mri_synthstrip`.
+- :bdg-danger:`Deprecation` The run mapping file has been moved to avoid
+  conflicts with FreeSurfer.
+
 Enhancements
 ------------
 
+- :bdg-success:`Enhancement` Add signature hook.
+- :bdg-success:`Enhancement` Add live comand line monitoring support.
+- :bdg-success:`Enhancement` Support multi-modality in Quasi-Raw workflow.
+- :bdg-success:`Enhancement` Add `quick` mode in Quasi-Raw workflow.
+- :bdg-success:`Enhancement` Support multi-modality in Deface workflow.
+
 Changes
 -------
 
+- :bdg-danger:`Deprecation` Optimize the Quasi-Raw workflow steps.
+
 
 2.0.0
 =====
 
 HIGHLIGHTS
 ----------
 
-his is a major release featuring significant changes to both the API and
+This is a major release featuring significant changes to both the API and
 CLI. Please review the modifications below.
 
 NEW
 ---
 
 - :bdg-success:`Doc` Create doc with `furo <https://github.com/pradyunsg/furo>`_.
-- :bdg-success:`Enhancement` Worflows generate a report file.
+- :bdg-success:`Enhancement` Workflows generate a report file.
 - :bdg-success:`Enhancement` Anonymize workflow outputs.
-- :bdg-success:`Enhancement` Worflows generate BIDS-compliant organization.
+- :bdg-success:`Enhancement` workflows generate BIDS-compliant organization.
 - :bdg-success:`Enhancement` New workflows can generate HTML reporting.
 - :bdg-success:`Datasets` Toy datasets have been added to test the module.
 - :bdg-success:`Enhancement` Quasi-RAW preprocessing compute the brain mask
@@ -82,19 +116,18 @@ Changes
 0.0.2
 =====
 
-**Released September 2022**
-
 HIGHLIGHTS
 ----------
 
-- :bdg-success:`API` This release includes different workflows to process
-  antomical, functional and diffusion MR images.
-- :bdg-success:`API` All workflows are integrated in a dedicated container
-  to enforce reproducible research.
+This is the legacy release of brainprep.
 
 NEW
 ---
 
+- :bdg-success:`API` This release includes different workflows to process
+  antomical, functional and diffusion MR images.
+- :bdg-success:`API` All workflows are integrated in a dedicated container
+  to enforce reproducible research.
 - :bdg-success:`API` The following workflows are released:
 
 * fsreconall
@@ -114,13 +147,3 @@ NEW
 * tbss-preproc
 * tbss
 * dmriprep
-
-Fixes
------
-
-Enhancements
-------------
-
-Changes
--------
-

README.rst

@@ -14,27 +14,27 @@
 
 **Development**
 
-.. image:: https://coveralls.io/repos/brainprepdesk/brainprep/badge.svg?branch=dev&service=github
+.. image:: https://coveralls.io/repos/brainprepdesk/brainprep/badge.svg?service=github
     :target: https://coveralls.io/github/brainprepdesk/brainprep
     :alt: Coveralls
 
-.. image:: https://github.com/brainprepdesk/brainprep/actions/workflows/testing.yml/badge.svg?branch=dev
+.. image:: https://github.com/brainprepdesk/brainprep/actions/workflows/testing.yml/badge.svg
     :target: https://github.com/brainprepdesk/brainprep/actions
     :alt: Testing Status
 
-.. image:: https://github.com/brainprepdesk/brainprep/actions/workflows/pycodestyle.yml/badge.svg?branch=dev
+.. image:: https://github.com/brainprepdesk/brainprep/actions/workflows/pycodestyle.yml/badge.svg
     :target: https://github.com/brainprepdesk/brainprep/actions
     :alt: PyCodeStyle
 
-.. image:: https://github.com/brainprepdesk/brainprep/actions/workflows/ruff.yml/badge.svg?branch=dev
+.. image:: https://github.com/brainprepdesk/brainprep/actions/workflows/ruff.yml/badge.svg
     :target: https://github.com/brainprepdesk/brainprep/actions
     :alt: Ruff Linter
 
-.. image:: https://github.com/brainprepdesk/brainprep/actions/workflows/pydoclint.yml/badge.svg?branch=dev
+.. image:: https://github.com/brainprepdesk/brainprep/actions/workflows/pydoclint.yml/badge.svg
     :target: https://github.com/brainprepdesk/brainprep/actions
     :alt: PyDocLint
 
-.. image:: https://github.com/brainprepdesk/brainprep/actions/workflows/documentation.yml/badge.svg?branch=dev
+.. image:: https://github.com/brainprepdesk/brainprep/actions/workflows/documentation.yml/badge.svg
     :target: https://brainprepdesk.github.io/brainprep
     :alt: Documentation Status
 

brainprep/_version.py

@@ -1 +1 @@
-__version__ = "2.0.0"
+__version__ = "2.1.0"

brainprep/cli.py

@@ -22,13 +22,17 @@
 
 import fire
 
+import brainprep.interfaces as interfaces
 import brainprep.workflow as wf
 from brainprep.config import DEFAULT_OPTIONS
+from brainprep.utils import coerce_to_list
 
 
 def make_wrapped(
         fn: Callable,
-        is_vbm: bool = False) -> Callable:
+        is_vbm: bool = False,
+        is_dmriprep: bool = False,
+        is_interface: bool = False) -> Callable:
     """
     Wrap a workflow function and extend its signature with global
     configuration parameters.
@@ -54,8 +58,18 @@ def make_wrapped(
        If ``False`` (default), VBM-specific configuration parameters
        such as ``cat12_file``, ``spm12_dir``, ``matlab_dir``,
        ``tpm_file``, and ``darteltpm_file`` are excluded from the
-       generated signature. If ``True``, all configuration parameters
+       generated signature. If ``True``, all these configuration parameters
        are included. Default False.
+    is_dmriprep : bool
+       Whether the wrapped function corresponds to a dMRIprep workflow.
+       If ``False`` (default), dMRIprep-specific configuration parameters
+       such as ``mni_2iso_file``, and ``geolab_atlas_dir`` are excluded from
+       the generated signature. If ``True``, all these configuration parameters
+       are included. Default False.
+    is_interface : bool
+       Whether the wrapped function corresponds to a brainprep interface.
+       If ``True``, the ``dryrun`` configuration parameters is excluded from
+       the generated signature. Default False.
 
     Returns
     -------
@@ -83,17 +97,54 @@ def wrapped_fn(*args, **kwargs):
             for key in DEFAULT_OPTIONS
             if key in kwargs
         }
+
+        sig = inspect.signature(fn)
+        args = list(args)
+        for idx, param in enumerate(sig.parameters.values()):
+            if param.name == "entities":
+                if param.kind in (
+                        param.POSITIONAL_ONLY,
+                        param.POSITIONAL_OR_KEYWORD):
+                    val = coerce_to_list(args[idx], list[str])
+                    if len(val) == 1:
+                        val = val[0]
+                    args[idx] = (
+                        [
+                            dict(
+                                item_text.split("-")
+                                for item_text in dict_text.split("_")
+                            )
+                            for dict_text in val
+                        ]
+                        if isinstance(val, list)
+                        else dict(
+                            item_text.split("-")
+                            for item_text in val.split("_")
+                        )
+                    )
+                break
+        args = tuple(args)
+
         with Config(**config_params):
             return fn(*args, **kwargs)
 
     sig = inspect.signature(fn)
     kwargs_in_keys = "kwargs" in sig.parameters
     params = list(sig.parameters.values())
+    if is_interface:
+        params = [
+            param
+            for param in params
+            if param.name != "dryrun"
+        ]
     for key, val in DEFAULT_OPTIONS.items():
-        if not is_vbm and key in (
+        if not is_interface and not is_vbm and key in (
                 "cat12_file", "spm12_dir", "matlab_dir", "tpm_file",
                 "darteltpm_file"):
             continue
+        if not is_interface and not is_dmriprep and key in (
+                "mni_2iso_file", "geolab_atlas_dir"):
+            continue
         param = inspect.Parameter(
             key,
             inspect.Parameter.KEYWORD_ONLY,
@@ -149,7 +200,21 @@ def main():
         "group-level-vbm": wf.brainprep_group_vbm,
         "subject-level-fmriprep": wf.brainprep_fmriprep,
         "group-level-fmriprep": wf.brainprep_group_fmriprep,
+        "subject-level-sulcirec": wf.brainprep_sulcirec,
+        "group-level-sulcirec": wf.brainprep_group_sulcirec,
+        "subject-level-dmriprep": wf.brainprep_dmriprep,
+        "group-level-reporting": wf.brainprep_group_reporting,
     }
     for key, fn in commands.items():
-        commands[key] = make_wrapped(fn, is_vbm=key.endswith("vbm"))
+        commands[key] = make_wrapped(
+            fn,
+            is_vbm=key.endswith("vbm"),
+            is_dmriprep=key.endswith("dmriprep"),
+        )
+    for key, fn in inspect.getmembers(interfaces, inspect.isfunction):
+        key = key.replace("_", "-")
+        commands.setdefault("interface", {})[key] = make_wrapped(
+            fn,
+            is_interface=True,
+        )
     fire.Fire(commands)