add docker badge and update docs and links

.github/workflows/update_precommit_hooks.yml

@@ -27,7 +27,7 @@ jobs:
     update_precommit_hooks:
 
     # only run on upstream repo
-        if: github.repository_owner == 'SIMEXP'
+        if: github.repository_owner == 'bids-apps'
 
         runs-on: ubuntu-latest
         steps:

CITATION.cff

@@ -9,7 +9,7 @@ abstract:
 
 message: "If you use this software, please cite it as below."
 
-repository-code: "https://github.com/SIMEXP/giga_connectome"
+repository-code: "https://github.com/bids-apps/giga_connectome"
 
 contact:
   - email: [email protected]

README.md

@@ -1,9 +1,10 @@
 [![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/licenses/MIT)
 [![codecov](https://codecov.io/gh/bids-apps/giga_connectome/branch/main/graph/badge.svg?token=P4EGV7NKZ8)](https://codecov.io/gh/bids-apps/giga_connectome)
-[![.github/workflows/test.yml](https://github.com/SIMEXP/giga_connectome/actions/workflows/test.yml/badge.svg)](https://github.com/SIMEXP/giga_connectome/actions/workflows/test.yml)
-[![pre-commit](https://github.com/SIMEXP/giga_connectome/actions/workflows/run_precommit.yml/badge.svg)](https://github.com/SIMEXP/giga_connectome/actions/workflows/run_precommit.yml)
+[![.github/workflows/test.yml](https://github.com/bids-apps/giga_connectome/actions/workflows/test.yml/badge.svg)](https://github.com/bids-apps/giga_connectome/actions/workflows/test.yml)
+[![pre-commit](https://github.com/bids-apps/giga_connectome/actions/workflows/run_precommit.yml/badge.svg)](https://github.com/bids-apps/giga_connectome/actions/workflows/run_precommit.yml)
 [![Documentation Status](https://readthedocs.org/projects/giga-connectome/badge/?version=stable)](https://giga-connectome.readthedocs.io/en/latest/?badge=stable)
 ![https://github.com/psf/black](https://img.shields.io/badge/code%20style-black-000000.svg)
+![](https://img.shields.io/docker/pulls/bids/giga_connectome)
 
 # giga_connectome
 
@@ -23,24 +24,29 @@ Users can customise their own strategies and atlases using the configuration jso
 
 ## Quick start
 
-Clone the project and build from `Dockerfile` (Recommended)
+Pull from `Dockerhub` (Recommended)
 
+```bash
+docker pull bids/giga_connectome:latest
+docker run -ti --rm --read-only bids/giga_connectome --help
 ```
-git clone [email protected]:SIMEXP/giga_connectome.git
-cd giga_connectome
-docker build . --file Dockerfile
-docker run -ti --rm --read-only giga_connectome --help
+
+If you want to get the bleeding-edge version of the app,
+pull the `unstable` version.
+
+```bash
+docker pull bids/giga_connectome:unstable
 ```
 
 ## How to report errors
 
-Please use the [GitHub issue](https://github.com/SIMEXP/giga_connectome/issues) to report errors.
+Please use the [GitHub issue](https://github.com/bids-apps/giga_connectome/issues) to report errors.
 Check out the open issues first to see if we're already working on it.
-If not, [open up a new issue](https://github.com/SIMEXP/giga_connectome/issues/new)!
+If not, [open up a new issue](https://github.com/bids-apps/giga_connectome/issues/new)!
 
 ## How to contribute
 
-You can review open [issues]((https://github.com/SIMEXP/giga_connectome/issues)) that we are looking for help with.
+You can review open [issues]((https://github.com/bids-apps/giga_connectome/issues)) that we are looking for help with.
 If you submit a new pull request please be as detailed as possible in your comments.
 
 ## Acknowledgements

docs/source/changes.md

@@ -11,7 +11,7 @@ Released MONTH YEAR
 
 ### Fixes
 
-- [FIX] Bump nilearn version to 0.10.2 to fix issues [#26](https://github.com/SIMEXP/giga_connectome/issues/26) and [#27](https://github.com/SIMEXP/giga_connectome/issues/27). (@Remi-Gau)
+- [FIX] Bump nilearn version to 0.10.2 to fix issues [#26](https://github.com/bids-apps/giga_connectome/issues/26) and [#27](https://github.com/bids-apps/giga_connectome/issues/27). (@Remi-Gau)
 
 ### Changes
 

docs/source/contributing.md

@@ -143,7 +143,7 @@ giga_connectome \
 
 Currently this project is not pushed to PyPi.
 We simply tag the version on the repository so users can reference the version of installation.
-You need to be a administrator of the upstream repository (`SIMEXP/giga_connectome`) to do this.
+You need to be a administrator of the upstream repository (`bids-apps/giga_connectome`) to do this.
 
 ```bash
 git checkout main

docs/source/installation.md

@@ -7,20 +7,20 @@ Pull the latest image from docker hub, available for version > `0.4.0`(Recommend
 Apptainer (formerly known as Singularity; recommended):
 
 ```bash
-apptainer build giga_connectome.simg docker://haotingwang/giga_connectome:latest
+apptainer build giga_connectome.simg docker://bids/giga_connectome:latest
 ```
 
 Docker:
 ```bash
-docker pull haotingwang/giga_connectome:latest
+docker pull bids/giga_connectome:latest
 ```
 
 ## Install as a python package
 
 Install the project in a Python environment:
 
 ```bash
-pip install git+https://github.com/SIMEXP/[email protected]
+pip install git+https://github.com/bids-apps/[email protected]
 ```
 
 This method is available for all versions.

docs/source/usage.md

@@ -16,7 +16,7 @@ We encourage the users to use the container version of the BIDS app, hence all d
 Users can use the preset template as examples for creating their own configuration files.
 This section will walk through the details of the configuration files and extra steps needed.
 
-All presets can be found in [`giga_connectome/data`](https://github.com/SIMEXP/giga_connectome/tree/main/giga_connectome/data).
+All presets can be found in [`giga_connectome/data`](https://github.com/bids-apps/giga_connectome/tree/main/giga_connectome/data).
 
 ### Denoising strategy
 
@@ -38,7 +38,7 @@ In a `json` file, define the customised strategy in the following format:
 }
 ```
 
-See examples in [`giga_connectome/data/denoise_strategy`](https://github.com/SIMEXP/giga_connectome/tree/main/giga_connectome/data/denoise_strategy).
+See examples in [`giga_connectome/data/denoise_strategy`](https://github.com/bids-apps/giga_connectome/tree/main/giga_connectome/data/denoise_strategy).
 
 2. Mount the path to the configuration file to the container and pass the **mounted path** to `--denoise-strategy`.
 
@@ -118,7 +118,7 @@ Example:
 }
 ```
 
-See examples in [`giga_connectome/data`](https://github.com/SIMEXP/giga_connectome/tree/main/giga_connectome/data).
+See examples in [`giga_connectome/data`](https://github.com/bids-apps/giga_connectome/tree/main/giga_connectome/data).
 
 4. Mount the path to the configuration file to the container and pass the **mounted path** to `--atlas`.
 The path in your configuration file under `templateflow_dir` should be exported as an environment variable of the container.

giga_connectome/utils.py

@@ -221,12 +221,12 @@ def create_ds_description(output_dir: Path) -> None:
             {
                 "Name": "giga_connectome",
                 "Version": __version__,
-                "CodeURL": "https://github.com/SIMEXP/giga_connectome.git",
+                "CodeURL": "https://github.com/bids-apps/giga_connectome.git",
             }
         ],
         "HowToAcknowledge": (
             "Please refer to our repository: "
-            "https://github.com/SIMEXP/giga_connectome.git."
+            "https://github.com/bids-apps/giga_connectome.git."
         ),
     }
     with open(output_dir / "dataset_description.json", "w") as f:
@@ -243,7 +243,7 @@ def create_sidecar(output_path: Path) -> None:
         "ValidDiagonal": True,
         "StorageFormat": "Full",
         "NonNegative": "",
-        "Code": "https://github.com/SIMEXP/giga_connectome.git",
+        "Code": "https://github.com/bids-apps/giga_connectome.git",
     }
     with open(output_path, "w") as f:
         json.dump(metadata, f, indent=4)

pyproject.toml

@@ -58,7 +58,7 @@ docs = [
 tests = ["giga_connectome[test]"]
 
 [project.urls]
-"Homepage" = "https://github.com/simexp/giga_connectome"
+"Homepage" = "https://github.com/bids-apps/giga_connectome"
 "Documentation" = "https://giga-connectome.readthedocs.io/en/latest/"
 
 [tool.hatch.version]