STYLE: Rename tool to NiFreeze

Rename the tool to `NiFreeze` following the voting and the discussion.

.dockerignore

@@ -8,8 +8,8 @@ build/**/*
 build
 dist/**/*
 dist
-src/eddymotion.egg-info/**/*
-src/eddymotion.egg-info
+src/nifreeze.egg-info/**/*
+src/nifreeze.egg-info
 .eggs/**/*
 .eggs
 

.gitignore

@@ -1,5 +1,5 @@
 # setuptools-scm
-eddymotion/_version.py
+nifreeze/_version.py
 
 # Byte-compiled / optimized / DLL files
 __pycache__/
@@ -115,4 +115,4 @@ ENV/
 kubernetes/jobs/
 
 # Version files
-src/eddymotion/_version.py
+src/nifreeze/_version.py

CONTRIBUTING.md

@@ -1,3 +1,3 @@
-# Contributing to *eddymotion*
+# Contributing to *NiFreeze*
 
-*eddymotion* is a project of the [*NiPreps* Community, which specifies the contributing guidelines](https://www.nipreps.org/community/).
+*NiFreeze* is a project of the [*NiPreps* Community, which specifies the contributing guidelines](https://www.nipreps.org/community/).

README.rst

@@ -1,29 +1,29 @@
-*Eddymotion*
-============
+*NiFreeze*
+==========
 Estimating head-motion and deformations derived from eddy-currents in diffusion MRI data.
 
 .. image:: https://zenodo.org/badge/DOI/10.5281/zenodo.4680599.svg
    :target: https://doi.org/10.5281/zenodo.4680599
    :alt: DOI
 
 .. image:: https://img.shields.io/badge/License-Apache_2.0-blue.svg
-   :target: https://github.com/nipreps/eddymotion/blob/main/LICENSE
+   :target: https://github.com/nipreps/nifreeze/blob/main/LICENSE
    :alt: License
 
-.. image:: https://img.shields.io/pypi/v/eddymotion.svg
-   :target: https://pypi.python.org/pypi/eddymotion/
+.. image:: https://img.shields.io/pypi/v/nifreeze.svg
+   :target: https://pypi.python.org/pypi/nifreeze/
    :alt: Latest Version
 
-.. image:: https://github.com/nipreps/eddymotion/actions/workflows/test.yml/badge.svg
-   :target: https://github.com/nipreps/eddymotion/actions/workflows/test.yml
+.. image:: https://github.com/nipreps/nifreeze/actions/workflows/test.yml/badge.svg
+   :target: https://github.com/nipreps/nifreeze/actions/workflows/test.yml
    :alt: Testing
 
-.. image:: https://github.com/nipreps/eddymotion/actions/workflows/pages/pages-build-deployment/badge.svg
-   :target: https://www.nipreps.org/eddymotion/main/index.html
+.. image:: https://github.com/nipreps/nifreeze/actions/workflows/pages/pages-build-deployment/badge.svg
+   :target: https://www.nipreps.org/nifreeze/main/index.html
    :alt: Documentation
 
-.. image:: https://github.com/nipreps/eddymotion/actions/workflows/pythonpackage.yml/badge.svg
-   :target: https://github.com/nipreps/eddymotion/actions/workflows/pythonpackage.yml
+.. image:: https://github.com/nipreps/nifreeze/actions/workflows/pythonpackage.yml/badge.svg
+   :target: https://github.com/nipreps/nifreeze/actions/workflows/pythonpackage.yml
    :alt: Python package
 
 Retrospective estimation of head-motion between diffusion-weighted images (DWI) acquired within
@@ -43,7 +43,7 @@ More recently, Cieslak et al. [#r3]_ integrated both approaches in *SHORELine*,
 (i) setting up a leave-one-out prediction framework as in eddy; and
 (ii) replacing eddy’s general-purpose Gaussian process prediction with the SHORE [#r4]_ diffusion model.
 
-*Eddymotion* is an open implementation of eddy-current and head-motion correction that builds upon
+*NiFreeze* is an open implementation of eddy-current and head-motion correction that builds upon
 the work of ``eddy`` and *SHORELine*, while generalizing these methods to multiple acquisition schemes
 (single-shell, multi-shell, and diffusion spectrum imaging) using diffusion models available with DIPY [#r5]_.
 

docs/developers.rst

@@ -2,23 +2,23 @@ For developers
 ==============
 Contributing
 ------------
-*Eddymotion* is a project of the *NiPreps Community*, `which specifies the contributing guidelines <https://www.nipreps.org/community/>`__.
+*NiFreeze* is a project of the *NiPreps Community*, `which specifies the contributing guidelines <https://www.nipreps.org/community/>`__.
 Before delving into the code, please make sure you have read all the guidelines offered online.
 
 Documentation
 -------------
-Documentation sources are found under the ``docs/`` folder, and builds are archived in the `gh-pages <https://github.com/nipreps/eddymotion/tree/gh-pages>`__ branch of the repository.
-With GitHub Pages, the documentation is posted under https://www.nipreps.org/eddymotion.
+Documentation sources are found under the ``docs/`` folder, and builds are archived in the `gh-pages <https://github.com/nipreps/nifreeze/tree/gh-pages>`__ branch of the repository.
+With GitHub Pages, the documentation is posted under https://www.nipreps.org/nifreeze.
 We maintain versioned documentation, by storing git tags under ``<major>.<minor>/`` folders, i.e., we do not archive every patch release, but only every minor release.
 In other words, folder ``0.1/`` of the documentation tree contains the documents for the latest release within the *0.1.x* series.
 With every commit (or merge commit) to ``main``, the *development* version of the documentation under the folder ``main/`` is updated too.
-The ``gh-pages`` branch is automatically maintained with `a GitHub Action <https://github.com/nipreps/eddymotion/blob/main/.github/workflows/docs-build-update.yml>`__.
+The ``gh-pages`` branch is automatically maintained with `a GitHub Action <https://github.com/nipreps/nifreeze/blob/main/.github/workflows/docs-build-update.yml>`__.
 Please, do not commit manually to ``gh-pages``.
 
 To build the documentation locally, you first need to make sure that ``setuptools_scm[toml] >= 6.2`` is installed in your environment and then::
 
-  $ cd <eddymotion-repository>/
-  $ python -m setuptools_scm  # This will generate ``src/eddymotion/_version.py``
+  $ cd <nifreeze-repository>/
+  $ python -m setuptools_scm  # This will generate ``src/nifreeze/_version.py``
   $ make -C docs/ html
 
 Library API (application program interface)
@@ -28,14 +28,14 @@ Information on specific functions, classes, and methods.
 .. toctree::
    :glob:
 
-   api/eddymotion.cli
-   api/eddymotion.data
-   api/eddymotion.data.dmri
-   api/eddymotion.estimator
-   api/eddymotion.exceptions
-   api/eddymotion.math
-   api/eddymotion.model
-   api/eddymotion.registration
-   api/eddymotion.testing
-   api/eddymotion.utils
-   api/eddymotion.viz
+   api/nifreeze.cli
+   api/nifreeze.data
+   api/nifreeze.data.dmri
+   api/nifreeze.estimator
+   api/nifreeze.exceptions
+   api/nifreeze.math
+   api/nifreeze.model
+   api/nifreeze.registration
+   api/nifreeze.testing
+   api/nifreeze.utils
+   api/nifreeze.viz

docs/installation.rst

@@ -3,18 +3,18 @@
 
 Installation
 ============
-Make sure all of *eddymotion*' `External Dependencies`_ are installed.
+Make sure all of *NiFreeze*' `External Dependencies`_ are installed.
 
 On a functional Python 3.7 (or above) environment with ``pip`` installed,
-*eddymotion* can be installed using the habitual command ::
+*NiFreeze* can be installed using the habitual command ::
 
-    $ python -m pip install eddymotion
+    $ python -m pip install nifreeze
 
 Check your installation with the following command line ::
 
-    $ python -c "from eddymotion import __version__; print(__version__)"
+    $ python -c "from nifreeze import __version__; print(__version__)"
 
 
 External Dependencies
 ---------------------
-*eddymotion* requires DIPY_, and ANTs_.
+*NiFreeze* requires DIPY_, and ANTs_.

docs/notebooks/dmri_covariance.ipynb

@@ -24,7 +24,7 @@
     "import matplotlib.pyplot as plt\n",
     "import numpy as np\n",
     "\n",
-    "from eddymotion.model.gpr import (\n",
+    "from nifreeze.model.gpr import (\n",
     "    compute_pairwise_angles,\n",
     "    exponential_covariance,\n",
     "    spherical_covariance,\n",
@@ -229,7 +229,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "from eddymotion.testing.simulations import simulate_voxels\n",
+    "from nifreeze.testing.simulations import simulate_voxels\n",
     "\n",
     "NUM_VOXELS = 3000\n",
     "BVAL_SHELL = 3000\n",
@@ -345,7 +345,7 @@
     }
    ],
    "source": [
-    "from eddymotion.model.gpr import EddyMotionGPR, SphericalKriging\n",
+    "from nifreeze.model.gpr import EddyMotionGPR, SphericalKriging\n",
     "\n",
     "K = SphericalKriging(beta_a=PARAMETER_SPHERICAL_a, beta_l=PARAMETER_lambda)(X_real)\n",
     "K -= K.min()\n",

docs/notebooks/dwi_gp_estimation.ipynb

@@ -4,9 +4,7 @@
    "cell_type": "markdown",
    "id": "d11e5969ed6af8a5",
    "metadata": {},
-   "source": [
-    "Estimate a DWI signal using the eddymotion Gaussian Process (GP) regressor estimator."
-   ]
+   "source": "Estimate a DWI signal using the nifreeze Gaussian Process (GP) regressor estimator."
   },
   {
    "cell_type": "markdown",
@@ -143,7 +141,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "from eddymotion.model.gpr import EddyMotionGPR, SphericalKriging\n",
+    "from nifreeze.model.gpr import EddyMotionGPR, SphericalKriging\n",
     "\n",
     "beta_a = 1.38\n",
     "beta_l = 1 / 2.1\n",

docs/usage.rst

@@ -2,17 +2,17 @@
 
 How to Use
 ==========
-Incorporating Eddymotion into a Python module or script
--------------------------------------------------------
-To utilize Eddymotion functionalities within your Python module or script, follow these steps:
+Incorporating NiFreeze into a Python module or script
+-----------------------------------------------------
+To utilize NiFreeze functionalities within your Python module or script, follow these steps:
 
-1. **Import Eddymotion Components**: Start by importing necessary components from the Eddymotion package:
+1. **Import NiFreeze Components**: Start by importing necessary components from the NiFreeze package:
 
    .. code-block:: python
 
-      # Import required components from the Eddymotion package
-      from eddymotion.data import dmri
-      from eddymotion.estimator import EddyMotionEstimator
+      # Import required components from the NiFreeze package
+      from nifreeze.data import dmri
+      from nifreeze.estimator import EddyMotionEstimator
 
 2. **Load DWI Data**: Load diffusion MRI (dMRI) data into a `DWI` object using the `load` function. Ensure the gradient table is provided. It should have one row per diffusion-weighted image. The first three columns represent the gradient directions, and the last column indicates the timing and strength of the gradients in units of s/mm² [ R A S+ b ]. If your data are in NIfTI file format, include a file containing the gradient information with the argument "gradients_file":
 
@@ -32,7 +32,7 @@ To utilize Eddymotion functionalities within your Python module or script, follo
          dwi_data = dmri.DWI.from_filename('/path/to/downloaded/dwi_full.h5')
 
 
-3. **Instantiate an Eddymotion Estimator Object**: Create an instance of the `EddyMotionEstimator` class, which encapsulates tools for estimating rigid-body head motion and distortions due to eddy currents.
+3. **Instantiate an NiFreeze Estimator Object**: Create an instance of the `EddyMotionEstimator` class, which encapsulates tools for estimating rigid-body head motion and distortions due to eddy currents.
 
    .. code-block:: python
 
@@ -59,7 +59,7 @@ To utilize Eddymotion functionalities within your Python module or script, follo
 
    - `dwi_data`: The target DWI dataset, represented by this tool's internal type.
    - `align_kwargs`: Parameters to configure the image registration process.
-   - `models`: list of diffusion models used to generate the registration target for each gradient map. For a list of available models, see :doc:`api/eddymotion.model`.
+   - `models`: list of diffusion models used to generate the registration target for each gradient map. For a list of available models, see :doc:`api/nifreeze.model`.
    - `omp_nthreads`: Maximum number of threads an individual process may use.
    - `n_jobs`: Number of parallel jobs.
    - `seed`: Seed for the random number generator (necessary for deterministic estimation).

pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "hatchling.build"
 
 
 [project]
-name = "eddymotion"
+name = "nifreeze"
 description = "Pure python eddy-current and head-motion correction for dMRI, an extension of QSIprep's SHOREline algorithm (Cieslak, 2020) to multiple diffusion models."
 readme = "README.rst"
 authors = [{name = "The NiPreps Developers", email = "[email protected]"}]
@@ -34,8 +34,8 @@ dependencies = [
 dynamic = ["version"]
 
 [project.urls]
-Documentation = "https://www.nipreps.org/eddymotion"
-Home = "https://github.com/nipreps/eddymotion"
+Documentation = "https://www.nipreps.org/nifreeze"
+Home = "https://github.com/nipreps/nifreeze"
 NiPreps = "https://www.nipreps.org/"
 
 [project.optional-dependencies]
@@ -80,12 +80,12 @@ antsopt = [
 ]
 
 # Aliases
-docs = ["eddymotion[doc]"]
-tests = ["eddymotion[test]"]
-all = ["eddymotion[doc,test,dev,plotting,resmon,antsopt]"]
+docs = ["nifreeze[doc]"]
+tests = ["nifreeze[test]"]
+all = ["nifreeze[doc,test,dev,plotting,resmon,antsopt]"]
 
 [project.scripts]
-eddymotion = "eddymotion.cli.run:main"
+nifreeze = "nifreeze.cli.run:main"
 
 #
 # Hatch configurations
@@ -98,9 +98,9 @@ allow-direct-references = true
 exclude = [".git_archival.txt"]  # No longer needed in sdist
 
 [tool.hatch.build.targets.wheel]
-packages = ["src/eddymotion"]
+packages = ["src/nifreeze"]
 # exclude = [
-#     "eddymotion/tests/data",  # Large test data directory
+#     "nifreeze/tests/data",  # Large test data directory
 # ]
 
 
@@ -114,7 +114,7 @@ local_scheme = "no-local-version"
 
 
 [tool.hatch.build.hooks.vcs]
-version-file = "src/eddymotion/_version.py"
+version-file = "src/nifreeze/_version.py"
 
 #
 # Developer tool configurations
@@ -161,7 +161,7 @@ inline-quotes = "double"
 quote-style = "double"
 
 [tool.ruff.lint.isort]
-known-first-party=["eddymotion"]
+known-first-party=["nifreeze"]
 
 [tool.pytest.ini_options]
 pythonpath = "src/ test/"
@@ -181,7 +181,7 @@ omit = [
     '*/viz/*',
     '*/__init__.py',
     '*/conftest.py',
-    'src/eddymotion/_version.py'
+    'src/nifreeze/_version.py'
 ]
 
 [tool.coverage.report]

src/eddymotion/__init__.py

@@ -20,12 +20,12 @@
 #
 #     https://www.nipreps.org/community/licensing/
 #
-"""Top-level package for eddymotion."""
+"""Top-level package for NiFreeze."""
 
-from eddymotion._version import __version__
+from nifreeze._version import __version__
 
-__packagename__ = "eddymotion"
-__copyright__ = "Copyright 2021, The eddymotion developers"
-__url__ = "https://github.com/nipreps/EddyMotionCorrection"
+__packagename__ = "nifreeze"
+__copyright__ = "Copyright 2021, The NiPreps developers"
+__url__ = "https://github.com/nipreps/nifreeze"
 
 DOWNLOAD_URL = f"https://github.com/nipreps/{__packagename__}/archive/{__version__}.tar.gz"

src/eddymotion/__main__.py

@@ -20,7 +20,7 @@
 #
 #     https://www.nipreps.org/community/licensing/
 #
-"""Entry point for Eddymotion."""
+"""Entry point for NiFreeze."""
 
 import sys
 

src/eddymotion/cli/run.py

@@ -20,13 +20,13 @@
 #
 #     https://www.nipreps.org/community/licensing/
 #
-"""Eddymotion runner."""
+"""NiFreeze runner."""
 
 from pathlib import Path
 
-from eddymotion.cli.parser import parse_args
-from eddymotion.data.dmri import DWI
-from eddymotion.estimator import EddyMotionEstimator
+from nifreeze.cli.parser import parse_args
+from nifreeze.data.dmri import DWI
+from nifreeze.estimator import EddyMotionEstimator
 
 
 def main(argv=None) -> None:

src/eddymotion/conftest.py

@@ -29,7 +29,7 @@
 import numpy
 import pytest
 
-test_data_env = os.getenv("TEST_DATA_HOME", str(Path.home() / "eddymotion-tests"))
+test_data_env = os.getenv("TEST_DATA_HOME", str(Path.home() / "nifreeze-tests"))
 test_output_dir = os.getenv("TEST_OUTPUT_DIR")
 test_workdir = os.getenv("TEST_WORK_DIR")
 

src/eddymotion/data/splitting.py

@@ -34,7 +34,7 @@ def lovo_split(dataset, index, with_b0=False):
 
     Parameters
     ----------
-    dataset : :obj:`eddymotion.data.dmri.DWI`
+    dataset : :obj:`nifreeze.data.dmri.DWI`
         DWI object
     index : :obj:`int`
         Index of the DWI orientation to be left out in this fold.