diff --git a/README.md b/README.md index 09325c1..7f74b40 100644 --- 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 index 5129efe..b5d2bac 100644 --- 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 index d0cd262..bdd1d50 100644 --- 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 index 13503af..d1af18e 100644 --- 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 index 94a48b8..51e6a1a 100644 --- 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 index d280623..7b12b10 100644 --- 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 index 862f275..d38b3bb 100644 --- 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 index 05c15ea..85b5aad 100644 --- 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 index 927cebe..9d65b38 100644 --- 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"