From 7fa8c2f3d6e93432f425fc2909be7555207c9b70 Mon Sep 17 00:00:00 2001 From: Remi Gau Date: Fri, 12 Apr 2024 08:48:38 +0200 Subject: [PATCH] add docker badge and update docs and links --- .github/workflows/update_precommit_hooks.yml | 2 +- CITATION.cff | 2 +- README.md | 26 ++++++++++++-------- docs/source/changes.md | 2 +- docs/source/contributing.md | 2 +- docs/source/installation.md | 6 ++--- docs/source/usage.md | 6 ++--- giga_connectome/utils.py | 6 ++--- pyproject.toml | 2 +- 9 files changed, 30 insertions(+), 24 deletions(-) diff --git a/.github/workflows/update_precommit_hooks.yml b/.github/workflows/update_precommit_hooks.yml index cdacc3c..cf55994 100644 --- a/.github/workflows/update_precommit_hooks.yml +++ b/.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: diff --git a/CITATION.cff b/CITATION.cff index cf6dda5..edf41fa 100644 --- a/CITATION.cff +++ b/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: htwangtw@gmail.com diff --git a/README.md b/README.md index 5649c1a..5563993 100644 --- a/README.md +++ b/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 git@github.com: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 diff --git a/docs/source/changes.md b/docs/source/changes.md index 527ada1..42c149a 100644 --- a/docs/source/changes.md +++ b/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 diff --git a/docs/source/contributing.md b/docs/source/contributing.md index 5b32379..6e270c2 100644 --- a/docs/source/contributing.md +++ b/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 diff --git a/docs/source/installation.md b/docs/source/installation.md index a5e85cd..298aa33 100644 --- a/docs/source/installation.md +++ b/docs/source/installation.md @@ -7,12 +7,12 @@ 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 @@ -20,7 +20,7 @@ docker pull haotingwang/giga_connectome:latest Install the project in a Python environment: ```bash -pip install git+https://github.com/SIMEXP/giga_connectome.git@0.4.0 +pip install git+https://github.com/bids-apps/giga_connectome.git@0.4.0 ``` This method is available for all versions. diff --git a/docs/source/usage.md b/docs/source/usage.md index 7672527..93843f1 100644 --- a/docs/source/usage.md +++ b/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. diff --git a/giga_connectome/utils.py b/giga_connectome/utils.py index e860eb9..908d5bf 100644 --- a/giga_connectome/utils.py +++ b/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) diff --git a/pyproject.toml b/pyproject.toml index 2f4d117..0d20183 100644 --- a/pyproject.toml +++ b/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]