Update template (#24)

childmindresearch · Feb 23, 2024 · 2d1f0e8 · 2d1f0e8
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diff --git a/README.md b/README.md
@@ -1,7 +1,7 @@
 # bids2table
-[![Build](https://github.com/cmi-dair/bids2table/actions/workflows/ci.yaml/badge.svg?branch=main)](https://github.com/cmi-dair/bids2table/actions/workflows/ci.yaml?query=branch%3Amain)
-[![Docs](https://github.com/cmi-dair/bids2table/actions/workflows/docs.yaml/badge.svg?branch=main)](https://cmi-dair.github.io/bids2table/bids2table)
-[![codecov](https://codecov.io/gh/cmi-dair/bids2table/branch/main/graph/badge.svg?token=22HWWFWPW5)](https://codecov.io/gh/cmi-dair/bids2table)
+[![Build](https://github.com/childmindresearch/bids2table/actions/workflows/ci.yaml/badge.svg?branch=main)](https://github.com/childmindresearch/bids2table/actions/workflows/ci.yaml?query=branch%3Amain)
+[![Docs](https://github.com/childmindresearch/bids2table/actions/workflows/docs.yaml/badge.svg?branch=main)](https://childmindresearch.github.io/bids2table/bids2table)
+[![codecov](https://codecov.io/gh/childmindresearch/bids2table/branch/main/graph/badge.svg?token=22HWWFWPW5)](https://codecov.io/gh/childmindresearch/bids2table)
 [![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black)
 [![MIT License](https://img.shields.io/badge/license-MIT-blue.svg)](LICENSE)
 
@@ -20,12 +20,12 @@ pip install bids2table
 The latest development version can be installed with
 
 ```sh
-pip install git+https://github.com/cmi-dair/bids2table.git
+pip install git+https://github.com/childmindresearch/bids2table.git
 ```
 
 ## Documentation
 
-Our documentation is [here](https://cmi-dair.github.io/bids2table/).
+Our documentation is [here](https://childmindresearch.github.io/bids2table/).
 
 ## Example
 

diff --git a/benchmark/indexing/README.md b/benchmark/indexing/README.md
@@ -1,6 +1,6 @@
 # Indexing benchmark
 
-In this benchmark we compare the indexing performance for [PyBIDS](https://github.com/bids-standard/pybids), [ancpBIDS](https://github.com/ANCPLabOldenburg/ancp-bids), and [bids2table](https://github.com/cmi-dair/bids2table) using the raw data from the [NKI Rockland Sample](https://fcon_1000.projects.nitrc.org/indi/pro/nki.html) (1334 subjects, 1.5TB).
+In this benchmark we compare the indexing performance for [PyBIDS](https://github.com/bids-standard/pybids), [ancpBIDS](https://github.com/ANCPLabOldenburg/ancp-bids), and [bids2table](https://github.com/childmindresearch/bids2table) using the raw data from the [NKI Rockland Sample](https://fcon_1000.projects.nitrc.org/indi/pro/nki.html) (1334 subjects, 1.5TB).
 
 ## Setup environment
 

diff --git a/benchmark/indexing/setup_environments.sh b/benchmark/indexing/setup_environments.sh
@@ -21,6 +21,6 @@ python3.10 -m venv envs/ancpbids && \
 python3.10 -m venv envs/bids2table && \
     source envs/bids2table/bin/activate && \
     pip install -U pip && \
-    pip install -U git+https://github.com/cmi-dair/elbow.git@3117427 && \
-    pip install -U git+https://github.com/cmi-dair/bids2table.git@b7b1658 && \
+    pip install -U git+https://github.com/childmindresearch/elbow.git@3117427 && \
+    pip install -U git+https://github.com/childmindresearch/bids2table.git@b7b1658 && \
     deactivate
diff --git a/benchmark/query/README.md b/benchmark/query/README.md
@@ -1,6 +1,6 @@
 # Query benchmark
 
-In this benchmark we compare the query performance for [PyBIDS](https://github.com/bids-standard/pybids), [ancpBIDS](https://github.com/ANCPLabOldenburg/ancp-bids), and [bids2table](https://github.com/cmi-dair/bids2table). The queries are modeled after the [PyBIDS `BIDSLayout` tutorial](https://bids-standard.github.io/pybids/examples/pybids_tutorial.html#querying-the-bidslayout).
+In this benchmark we compare the query performance for [PyBIDS](https://github.com/bids-standard/pybids), [ancpBIDS](https://github.com/ANCPLabOldenburg/ancp-bids), and [bids2table](https://github.com/childmindresearch/bids2table). The queries are modeled after the [PyBIDS `BIDSLayout` tutorial](https://bids-standard.github.io/pybids/examples/pybids_tutorial.html#querying-the-bidslayout).
 
 For this benchmark, we use raw data from the [Chinese Color Nest Project](http://deepneuro.bnu.edu.cn/?p=163) (195 subjects, 2 resting state sessions per subject).
 

diff --git a/benchmark/query/query_benchmark.ipynb b/benchmark/query/query_benchmark.ipynb
@@ -6,7 +6,7 @@
    "source": [
     "# Query benchmark\n",
     "\n",
-    "In this benchmark we compare the query performance for [PyBIDS](https://github.com/bids-standard/pybids), [ancpBIDS](https://github.com/ANCPLabOldenburg/ancp-bids), and [bids2table](https://github.com/cmi-dair/bids2table). The queries are modeled after the [PyBIDS `BIDSLayout` tutorial](https://bids-standard.github.io/pybids/examples/pybids_tutorial.html#querying-the-bidslayout).\n",
+    "In this benchmark we compare the query performance for [PyBIDS](https://github.com/bids-standard/pybids), [ancpBIDS](https://github.com/ANCPLabOldenburg/ancp-bids), and [bids2table](https://github.com/childmindresearch/bids2table). The queries are modeled after the [PyBIDS `BIDSLayout` tutorial](https://bids-standard.github.io/pybids/examples/pybids_tutorial.html#querying-the-bidslayout).\n",
     "\n",
     "For this benchmark, we use raw data from the [Chinese Color Nest Project](http://deepneuro.bnu.edu.cn/?p=163) (195 subjects, 2 resting state sessions per subject)."
    ]

diff --git a/benchmark/query/requirements.txt b/benchmark/query/requirements.txt
@@ -1,4 +1,4 @@
 pybids==0.16.0
 ancpbids==0.2.2
-elbow @ git+https://github.com/cmi-dair/elbow.git@3117427
-bids2table @ git+https://github.com/cmi-dair/bids2table.git@b7b1658
+elbow @ git+https://github.com/childmindresearch/elbow.git@3117427
+bids2table @ git+https://github.com/childmindresearch/bids2table.git@b7b1658
diff --git a/bids2table/__init__.py b/bids2table/__init__.py
@@ -1,5 +1,5 @@
 r"""
-[bids2table](https://github.com/cmi-dair/bids2table) is a library for efficiently
+[bids2table](https://github.com/childmindresearch/bids2table) is a library for efficiently
 indexing and querying large-scale BIDS neuroimaging datasets and derivatives. It aims to
 improve upon the efficiency of [PyBIDS](https://github.com/bids-standard/pybids) by
 leveraging modern data science tools.
@@ -20,7 +20,7 @@
 The latest development version can be installed with
 
 ```sh
-pip install git+https://github.com/cmi-dair/bids2table.git
+pip install git+https://github.com/childmindresearch/bids2table.git
 ```
 
 ## Quickstart

diff --git a/bids2table/extractors/__init__.py b/bids2table/extractors/__init__.py
@@ -1,3 +1,3 @@
 """
-[Elbow](https://github.com/cmi-dair/elbow) extract functions for BIDS datasets.
+[Elbow](https://github.com/childmindresearch/elbow) extract functions for BIDS datasets.
 """
diff --git a/pyproject.toml b/pyproject.toml
@@ -47,7 +47,7 @@ dev = [
 ]
 
 [project.urls]
-"Homepage" = "https://github.com/cmi-dair/bids2table"
+"Homepage" = "https://github.com/childmindresearch/bids2table"
 
 [project.scripts]
 bids2table = "bids2table.__main__:main"