enh: rename all instances of "eddymotion"

```
git ls-files -z | xargs -0 sed -i 's/eddymotion/nifreeze/g'
git mv src/eddymotion src/nifreeze
```

.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
 

.github/workflows/pythonpackage.yml

@@ -41,7 +41,7 @@ jobs:
         pip install -U build hatch pip twine
 
         python -m build -s -w
-        python -m twine check dist/eddymotion-*
+        python -m twine check dist/nifreeze-*
 
         mv dist /tmp/package
 
@@ -60,7 +60,7 @@ jobs:
         source /tmp/pip/bin/activate
         pip install -U pip
         python -m pip install .
-        INSTALLED_VERSION=$(python -c 'import eddymotion as em; print(em.__version__, end="")')
+        INSTALLED_VERSION=$(python -c 'import nifreeze as em; print(em.__version__, end="")')
         echo "VERSION: \"${THISVERSION}\""
         echo "INSTALLED: \"${INSTALLED_VERSION}\""
         test "${INSTALLED_VERSION}" = "${THISVERSION}"
@@ -70,8 +70,8 @@ jobs:
         python -m venv /tmp/install_sdist
         source /tmp/install_sdist/bin/activate
         pip install -U pip
-        python -m pip install /tmp/package/eddymotion*.tar.gz
-        INSTALLED_VERSION=$(python -c 'import eddymotion as em; print(em.__version__, end="")')
+        python -m pip install /tmp/package/nifreeze*.tar.gz
+        INSTALLED_VERSION=$(python -c 'import nifreeze as em; print(em.__version__, end="")')
         echo "VERSION: \"${THISVERSION}\""
         echo "INSTALLED: \"${INSTALLED_VERSION}\""
         test "${INSTALLED_VERSION}" = "${THISVERSION}"
@@ -81,7 +81,7 @@ jobs:
         python -m venv /tmp/install_wheel
         source /tmp/install_wheel/bin/activate
         pip install -U pip
-        python -m pip install /tmp/package/eddymotion*.whl
-        INSTALLED_VERSION=$(python -c 'import eddymotion as em; print(em.__version__, end="")')
+        python -m pip install /tmp/package/nifreeze*.whl
+        INSTALLED_VERSION=$(python -c 'import nifreeze as em; print(em.__version__, end="")')
         echo "INSTALLED: \"${INSTALLED_VERSION}\""
         test "${INSTALLED_VERSION}" = "${THISVERSION}"

.github/workflows/test.yml

@@ -19,7 +19,7 @@ defaults:
 # Force tox and pytest to use color
 env:
   FORCE_COLOR: true
-  TEST_DATA_HOME: /home/runner/eddymotion-tests/
+  TEST_DATA_HOME: /home/runner/nifreeze-tests/
   ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS: 4
   ANTSPATH: /usr/share/miniconda/bin/
 
@@ -54,20 +54,20 @@ jobs:
           datalad wtf
       - uses: actions/cache/restore@v4
         with:
-          path: /home/runner/eddymotion-tests/
+          path: /home/runner/nifreeze-tests/
           key: data-v0
       - name: Get test data with DataLad
         run: |
           if [[ ! -d "${TEST_DATA_HOME}" ]]; then
-            datalad install -rg --source=https://gin.g-node.org/nipreps-data/tests-eddymotion.git ${TEST_DATA_HOME}
+            datalad install -rg --source=https://gin.g-node.org/nipreps-data/tests-nifreeze.git ${TEST_DATA_HOME}
           else
             cd ${TEST_DATA_HOME}
             datalad update --merge -r .
             datalad get -r -J4 *
           fi
       - uses: actions/cache/save@v4
         with:
-          path: /home/runner/eddymotion-tests/
+          path: /home/runner/nifreeze-tests/
           key: data-v0
       - name: Install tox
         run: |

.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

.zenodo.json

@@ -20,7 +20,7 @@
       "scheme": "doi"
     }
   ],
-  "title": "eddymotion: model-based estimation of head-motion and eddy-current distortions",
+  "title": "nifreeze: model-based estimation of head-motion and eddy-current distortions",
   "upload_type": "software",
   "creators": [
     {

CHANGES.rst

@@ -23,7 +23,7 @@ A new minor release with fixes such as setting random seeds and enhancing parall
   * ENH: Drop support for Python 3.8 and 3.9 (#158)
   * ENH: Remove unused `tmp_path` parameter from test (#162)
   * ENH: Outsource leave-one-out splitter so it can be used across data types (#98)
-  * ENH: Simplify `eddymotion.estimator.EddyMotionEstimator.fit` (#149)
+  * ENH: Simplify `nifreeze.estimator.EddyMotionEstimator.fit` (#149)
   * ENH: Refactor code linter and formatter dependencies (#144)
   * ENH: Use NumPy's `Generator` class as a replacement for `RandomState` (#141)
   * ENH: Define instance attributes in ``__init__`` method (#133)

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/).

NOTICE

@@ -1,4 +1,4 @@
-eddymotion
+nifreeze
 Copyright 2021 The NiPreps Developers.
 
 This product includes software developed by

README.rst

@@ -7,23 +7,23 @@ Estimating head-motion and deformations derived from eddy-currents in diffusion
    :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
@@ -49,8 +49,8 @@ the work of ``eddy`` and *SHORELine*, while generalizing these methods to multip
 
 .. BEGIN FLOWCHART
 
-.. image:: https://raw.githubusercontent.com/nipreps/eddymotion/507fc9bab86696d5330fd6a86c3870968243aea8/docs/_static/eddymotion-flowchart.svg
-   :alt: The eddymotion flowchart
+.. image:: https://raw.githubusercontent.com/nipreps/nifreeze/507fc9bab86696d5330fd6a86c3870968243aea8/docs/_static/nifreeze-flowchart.svg
+   :alt: The nifreeze flowchart
 
 .. END FLOWCHART
 

docs/Makefile

@@ -97,17 +97,17 @@ qthelp:
 	@echo
 	@echo "Build finished; now you can run "qcollectiongenerator" with the" \
 	      ".qhcp project file in $(BUILDDIR)/qthelp, like this:"
-	@echo "# qcollectiongenerator $(BUILDDIR)/qthelp/eddymotion.qhcp"
+	@echo "# qcollectiongenerator $(BUILDDIR)/qthelp/nifreeze.qhcp"
 	@echo "To view the help file:"
-	@echo "# assistant -collectionFile $(BUILDDIR)/qthelp/eddymotion.qhc"
+	@echo "# assistant -collectionFile $(BUILDDIR)/qthelp/nifreeze.qhc"
 
 devhelp:
 	$(SPHINXBUILD) -b devhelp $(ALLSPHINXOPTS) $(BUILDDIR)/devhelp
 	@echo
 	@echo "Build finished."
 	@echo "To view the help file:"
-	@echo "# mkdir -p $$HOME/.local/share/devhelp/eddymotion"
-	@echo "# ln -s $(BUILDDIR)/devhelp $$HOME/.local/share/devhelp/eddymotion"
+	@echo "# mkdir -p $$HOME/.local/share/devhelp/nifreeze"
+	@echo "# ln -s $(BUILDDIR)/devhelp $$HOME/.local/share/devhelp/nifreeze"
 	@echo "# devhelp"
 
 epub:

docs/conf.py

@@ -9,7 +9,7 @@
 
 from packaging.version import Version
 
-from eddymotion import __copyright__, __packagename__, __version__
+from nifreeze import __copyright__, __packagename__, __version__
 
 # -- Path setup --------------------------------------------------------------
 # If extensions (or modules to document with autodoc) are in another directory,
@@ -104,7 +104,7 @@
     "_build",
     "Thumbs.db",
     ".DS_Store",
-    "api/eddymotion.rst",
+    "api/nifreeze.rst",
 ]
 
 # The name of the Pygments (syntax highlighting) style to use.
@@ -149,7 +149,7 @@
 # -- Options for HTMLHelp output ---------------------------------------------
 
 # Output file base name for HTML help builder.
-htmlhelp_basename = "eddymotiondoc"
+htmlhelp_basename = "nifreezedoc"
 
 
 # -- Options for LaTeX output ------------------------------------------------
@@ -228,7 +228,7 @@
 
 # -- Extension configuration -------------------------------------------------
 
-apidoc_module_dir = "../src/eddymotion"
+apidoc_module_dir = "../src/nifreeze"
 apidoc_output_dir = "api"
 apidoc_excluded_paths = ["conftest.py", "*/tests/*", "tests/*", "config/*"]
 apidoc_separate_modules = True

docs/developers.rst

@@ -7,18 +7,18 @@ Before delving into the code, please make sure you have read all the guidelines
 
 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/index.rst

@@ -4,8 +4,8 @@
 .. include:: ../README.rst
    :start-after: END FLOWCHART
 
-.. image:: _static/eddymotion-flowchart.svg
-   :alt: The eddymotion flowchart
+.. image:: _static/nifreeze-flowchart.svg
+   :alt: The nifreeze flowchart
 
 Contents
 --------

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 3.10 (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_.