From ad487a13cc553461e7418f02ea01132d39b96dbe Mon Sep 17 00:00:00 2001
From: Oscar Esteban <code@oscaresteban.es>
Date: Tue, 19 Apr 2022 15:34:16 +0200
Subject: [PATCH] maint: conclude migration poldracklab -> nipy

---
 .github/workflows/travis.yml  |  2 +-
 CONTRIBUTING.rst              |  2 +-
 Dockerfile                    |  2 +-
 README.md                     |  8 ++++----
 docs/conf.py                  |  2 +-
 docs/index.rst                | 14 +++++++-------
 docs/installation.rst         |  4 ++--
 docs/notebooks/isbi2020.ipynb |  4 ++--
 joss/paper.md                 |  2 +-
 setup.cfg                     |  2 +-
 10 files changed, 21 insertions(+), 21 deletions(-)

diff --git a/.github/workflows/travis.yml b/.github/workflows/travis.yml
index 9f97a4db..19c6a2a1 100644
--- a/.github/workflows/travis.yml
+++ b/.github/workflows/travis.yml
@@ -4,7 +4,7 @@ on: [push]
 
 jobs:
   build-linux:
-    if: "!contains(github.event.head_commit.message, '[skip ci]' && (github.event_name == 'push' || github.event.pull_request.head.repo.full_name != 'poldracklab/nitransforms'))"
+    if: "!contains(github.event.head_commit.message, '[skip ci]' && (github.event_name == 'push' || github.event.pull_request.head.repo.full_name != 'nipy/nitransforms'))"
     runs-on: ubuntu-latest
     env:
       TEST_DATA_HOME: /home/runner/testdata/nitransforms-tests
diff --git a/CONTRIBUTING.rst b/CONTRIBUTING.rst
index e94342a8..fdf1650c 100644
--- a/CONTRIBUTING.rst
+++ b/CONTRIBUTING.rst
@@ -11,4 +11,4 @@ These guidelines are designed to make it as easy as possible to get
 involved. If you have any questions that aren’t discussed in our
 documentation, or it’s difficult to find what you’re looking for, please
 let us know by opening an
-`issue <https://github.com/poldracklab/fmriprep/issues>`__!
+`issue <https://github.com/nipy/nitransforms/issues>`__!
diff --git a/Dockerfile b/Dockerfile
index 16f122c6..ae270b45 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -154,6 +154,6 @@ ARG VCS_REF
 ARG VERSION
 LABEL org.label-schema.build-date=$BUILD_DATE \
       org.label-schema.name="nitransforms" \
-      org.label-schema.vcs-url="https://github.com/poldracklab/nitransforms" \
+      org.label-schema.vcs-url="https://github.com/nipy/nitransforms" \
       org.label-schema.version=$VERSION \
       org.label-schema.schema-version="1.0"
diff --git a/README.md b/README.md
index 3f655a5d..b5a45349 100644
--- a/README.md
+++ b/README.md
@@ -1,10 +1,10 @@
 # NiTransforms
 [![DOI](https://joss.theoj.org/papers/10.21105/joss.03459/status.svg)](https://doi.org/10.21105/joss.03459)
 [![ISBI2020](https://img.shields.io/badge/doi-10.31219%2Fosf.io%2F8aq7b-blue.svg)](https://doi.org/10.31219/osf.io/8aq7b)
-[![Deps & CI](https://github.com/poldracklab/nitransforms/actions/workflows/travis.yml/badge.svg)](https://github.com/poldracklab/nitransforms/actions/workflows/travis.yml)
-[![CircleCI](https://circleci.com/gh/poldracklab/nitransforms.svg?style=svg)](https://circleci.com/gh/poldracklab/nitransforms)
-[![codecov](https://codecov.io/gh/poldracklab/nitransforms/branch/master/graph/badge.svg)](https://codecov.io/gh/poldracklab/nitransforms)
-[![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/poldracklab/nitransforms/master?filepath=docs%2Fnotebooks%2F)
+[![Deps & CI](https://github.com/nipy/nitransforms/actions/workflows/travis.yml/badge.svg)](https://github.com/nipy/nitransforms/actions/workflows/travis.yml)
+[![CircleCI](https://circleci.com/gh/nipy/nitransforms.svg?style=svg)](https://circleci.com/gh/nipy/nitransforms)
+[![codecov](https://codecov.io/gh/nipy/nitransforms/branch/master/graph/badge.svg)](https://codecov.io/gh/nipy/nitransforms)
+[![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/nipy/nitransforms/master?filepath=docs%2Fnotebooks%2F)
 [![Docs](https://readthedocs.org/projects/nitransforms/badge/?version=latest)](http://nitransforms.readthedocs.io/en/latest/?badge=latest)
 
 A development repo for [nipy/nibabel#656](https://github.com/nipy/nibabel/pull/656)
diff --git a/docs/conf.py b/docs/conf.py
index 02d270ad..18e532a1 100644
--- a/docs/conf.py
+++ b/docs/conf.py
@@ -231,7 +231,7 @@
 
     <div class="admonition note">
       This page was generated from
-      <a class="reference external" href="https://github.com/poldracklab/nitransforms/blob/master\
+      <a class="reference external" href="https://github.com/nipy/nitransforms/blob/master\
 /{{ docname|e }}">{{ docname|e }}</a>.
       <script>
         if (document.location.host) {
diff --git a/docs/index.rst b/docs/index.rst
index 8aba91cc..4edf3198 100644
--- a/docs/index.rst
+++ b/docs/index.rst
@@ -8,20 +8,20 @@ A development repo for `nipy/nibabel#656 <https://github.com/nipy/nibabel/pull/6
   :target: https://pypi.python.org/pypi/nitransforms/
   :alt: Latest Version
 
-.. image:: https://codecov.io/gh/poldracklab/nitransforms/branch/master/graph/badge.svg
-  :target: https://codecov.io/gh/poldracklab/nitransforms
+.. image:: https://codecov.io/gh/nipy/nitransforms/branch/master/graph/badge.svg
+  :target: https://codecov.io/gh/nipy/nitransforms
 
-.. image:: https://circleci.com/gh/poldracklab/nitransforms.svg?style=svg
-    :target: https://circleci.com/gh/poldracklab/nitransforms
+.. image:: https://circleci.com/gh/nipy/nitransforms.svg?style=svg
+    :target: https://circleci.com/gh/nipy/nitransforms
 
-.. image:: https://github.com/poldracklab/nitransforms/actions/workflows/travis.yml/badge.svg
-    :target: https://github.com/poldracklab/nitransforms/actions
+.. image:: https://github.com/nipy/nitransforms/actions/workflows/travis.yml/badge.svg
+    :target: https://github.com/nipy/nitransforms/actions
 
 .. image:: https://img.shields.io/badge/doi-10.31219%2Fosf.io%2F8aq7b-blue.svg
     :target: https://doi.org/10.31219/osf.io/8aq7b
 
 .. image:: https://mybinder.org/badge_logo.svg
-    :target: https://mybinder.org/v2/gh/poldracklab/nitransforms/master?filepath=docs%2Fnotebooks%2F
+    :target: https://mybinder.org/v2/gh/nipy/nitransforms/master?filepath=docs%2Fnotebooks%2F
 
 About
 -----
diff --git a/docs/installation.rst b/docs/installation.rst
index b5fa97ca..9b17826d 100644
--- a/docs/installation.rst
+++ b/docs/installation.rst
@@ -8,7 +8,7 @@ within your Python distribution with::
 Alternatively, you can install the bleeding-edge version of the software
 directly from the GitHub repo with::
 
-  python -m pip install git+https://github.com/poldracklab/nitransforms.git@master
+  python -m pip install git+https://github.com/nipy/nitransforms.git@master
 
 To verify the installation, you can run the following command::
 
@@ -21,7 +21,7 @@ Developers
 Advanced users and developers who plan to contribute with bugfixes, documentation,
 etc. can first clone our Git repository::
 
-  git clone https://github.com/poldracklab/nitransforms.git
+  git clone https://github.com/nipy/nitransforms.git
 
 
 and install the tool in *editable* mode::
diff --git a/docs/notebooks/isbi2020.ipynb b/docs/notebooks/isbi2020.ipynb
index 10cdbd8f..80442dbe 100644
--- a/docs/notebooks/isbi2020.ipynb
+++ b/docs/notebooks/isbi2020.ipynb
@@ -13,7 +13,7 @@
    "source": [
     "### Introduction\n",
     "#### Submission (654) Software tool to read, represent, manipulate and apply $n$-dimensional spatial transforms\n",
-    "Spatial transforms formalize mappings between coordinates of objects in biomedical images. Transforms typically are the outcome of image registration methodologies, which estimate the alignment between two images. Image registration is a prominent task present in nearly all standard image processing and analysis pipelines. The proliferation of software implementations of image registration methodologies has resulted in a spread of data structures and file formats used to preserve and communicate transforms. This segregation of formats hinders the compatibility between tools and endangers the reproducibility of results. We propose a software tool capable of converting between formats and resampling images to apply transforms generated by the most popular neuroimaging packages and libraries (AFNI, FSL, FreeSurfer, ITK, and SPM). The proposed software is subject to continuous integration tests to check the compatibility with each supported tool after every change to the [code base](https://github.com/poldracklab/nitransforms). Compatibility between software tools and imaging formats is a necessary bridge to ensure the reproducibility of results and enable the optimization and evaluation of current image processing and analysis workflows.\n",
+    "Spatial transforms formalize mappings between coordinates of objects in biomedical images. Transforms typically are the outcome of image registration methodologies, which estimate the alignment between two images. Image registration is a prominent task present in nearly all standard image processing and analysis pipelines. The proliferation of software implementations of image registration methodologies has resulted in a spread of data structures and file formats used to preserve and communicate transforms. This segregation of formats hinders the compatibility between tools and endangers the reproducibility of results. We propose a software tool capable of converting between formats and resampling images to apply transforms generated by the most popular neuroimaging packages and libraries (AFNI, FSL, FreeSurfer, ITK, and SPM). The proposed software is subject to continuous integration tests to check the compatibility with each supported tool after every change to the [code base](https://github.com/nipy/nitransforms). Compatibility between software tools and imaging formats is a necessary bridge to ensure the reproducibility of results and enable the optimization and evaluation of current image processing and analysis workflows.\n",
     "\n",
     "The process is summarized in the following figure:\n",
     "![alt text](../_static/figure1-joss.png \"Figure 1\")"
@@ -302,7 +302,7 @@
     "```Python\n",
     "pip install nitransforms\n",
     "```\n",
-    "See also: https://github.com/poldracklab/nitransforms"
+    "See also: https://github.com/nipy/nitransforms"
    ]
   },
   {
diff --git a/joss/paper.md b/joss/paper.md
index 8b89c29e..66d138df 100644
--- a/joss/paper.md
+++ b/joss/paper.md
@@ -75,7 +75,7 @@ An example of image fusion application would be the alignment of functional data
 Therefore, "applying a transform" entails two operations (\autoref{fig:resampling}): first, transforming the coordinates of the samples in the reference image $R$ to find their mapping $\vec{x}'$ on $M$ via $T\{\cdot\}$, and second an interpolation step, as $\vec{x}'$ will likely fall off-the-grid of the moving image $M$.
 These two operations are confusing because, while the spatial transformation projects from $R$ to $M$, the data flows in reversed way after the interpolation of the values of $M$ at the mapped coordinates $\vec{x}'$.
 
-![Resampling a 3D image via a spatial transform to fuse the information of one into another image. \label{fig:resampling}](https://github.com/poldracklab/nitransforms/raw/master/docs/_static/figure1-joss.png)
+![Resampling a 3D image via a spatial transform to fuse the information of one into another image. \label{fig:resampling}](https://github.com/nipy/nitransforms/raw/master/docs/_static/figure1-joss.png)
 
 ## Software Architecture
 
diff --git a/setup.cfg b/setup.cfg
index 0c798290..51fdd474 100644
--- a/setup.cfg
+++ b/setup.cfg
@@ -17,7 +17,7 @@ provides = nitransforms
 project_urls =
     Manuscript=https://doi.org/10.31219/osf.io/8aq7b
     NiBabel=https://github.com/nipy/nibabel/pull/656
-url = https://github.com/poldracklab/nitransforms
+url = https://github.com/nipy/nitransforms
 
 [options]
 python_requires = >= 3.7