HALFpipe · mathdugre · Jun 13, 2026 · Jun 1, 2026 · Jun 1, 2026 · Jun 1, 2026
diff --git a/.codespell-ignore-words b/.codespell-ignore-words
@@ -0,0 +1,2 @@
+# Citations
+Sepulcre
diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
@@ -58,9 +58,9 @@ jobs:
         with:
           path: ~/.cache/templateflow
           key: templateflow
-      - uses: prefix-dev/setup-pixi@1b2de7f3351f171c8b4dfeb558c639cb58ed4ec0
+      - uses: prefix-dev/setup-pixi@5185adfbffb4bd703da3010310260805d89ebb11
         with:
-          pixi-version: v0.53.0
+          pixi-version: v0.70.2
           cache: true
           environments: test
           frozen: true
@@ -88,9 +88,9 @@ jobs:
         with:
           path: ~/.cache/templateflow
           key: templateflow
-      - uses: prefix-dev/setup-pixi@1b2de7f3351f171c8b4dfeb558c639cb58ed4ec0
+      - uses: prefix-dev/setup-pixi@5185adfbffb4bd703da3010310260805d89ebb11
         with:
-          pixi-version: v0.53.0
+          pixi-version: v0.70.2
           cache: true
           environments: test
           frozen: true

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -28,7 +28,7 @@ repos:
     -   id: codespell
         additional_dependencies:
         - tomli
-        args: ["--skip=*.svg"]
+        args: ["--skip=*.svg", "-I .codespell-ignore-words"]
         exclude: 'paper/.*'
 -   repo: https://github.com/hadolint/hadolint
     rev: v2.14.0

diff --git 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/wonkyconn"
+repository-code: "https://github.com/HALFpipe/wonkyconn"
 
 contact:
   - email: htwangtw@gmail.com

diff --git a/Dockerfile b/Dockerfile
@@ -1,4 +1,4 @@
-FROM ghcr.io/prefix-dev/pixi:0.53.0 AS build
+FROM ghcr.io/prefix-dev/pixi:0.70.2 AS build
 
 SHELL ["/bin/bash", "-o", "pipefail", "-c"]
 

diff --git a/README.md b/README.md
@@ -1,19 +1,33 @@
 [![pre-commit.ci status](https://results.pre-commit.ci/badge/github/HALFpipe/wonkyconn/main.svg)](https://results.pre-commit.ci/latest/github/HALFpipe/wonkyconn/main)
 [![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/licenses/MIT)
-![https://github.com/psf/black](https://img.shields.io/badge/code%20style-black-000000.svg)
+[![Ruff](https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/astral-sh/ruff/main/assets/badge/v2.json)](https://github.com/astral-sh/ruff)
 [![Documentation Status](https://readthedocs.org/projects/wonkyconn/badge/?version=latest)](https://wonkyconn.readthedocs.io/en/latest/?badge=latest)
 
 # wonkyconn
 
-Evaluating the residual motion and analytic insights on fMRI connectome and visualise reports.
+Wonkyconn evaluates residual motion and analytic quality in group-level fMRI connectomes and creates visualization reports to compare the generated metrics.
 
 The project is based on the code of [`SIMEXP/fmriprep-denoise-benchmark`](https://github.com/SIMEXP/fmriprep-denoise-benchmark) and the publication by [Wang et al. 2024](http://dx.doi.org/10.1371/journal.pcbi.1011942).
 
 **This project is in alpha stage! This is not a stable project yet.**
 
+## Quick start
+
+Recommended container:
+
+```bash
+apptainer build wonkyconn-edge.sif docker://halfpipe/wonkyconn:edge
+```
+
+See the [documentation](https://wonkyconn.readthedocs.io/en/latest/) for usage, methods, and outputs.
+
 ## Textual GUI (optional)
 
-- Install the optional dependency: `pip install "wonkyconn[textual]"`.
-- Launch the GUI instead of running headless: `wonkyconn --textual`.
-- The GUI requires an interactive terminal (TTY). If you are running inside a non-interactive job (for example, on an HPC batch node), run the CLI without `--textual` instead.
-- All required inputs are collected in the GUI; existing CLI defaults and behaviour are preserved once you click **Run**.
+- Install: `pip install "wonkyconn[textual]`
+- Launch: `wonkyconn --textual`
+- The CLI is required for headless batch jobs or multi-atlas runs.
+
+> [!WARNING]
+>
+> - The textual UI requires an interactive terminal (TTY) if you are running Wonkyconn inside a non-interactive terminal (e.g., HPC batch job), use the CLI with `--textual`.
+> - Current GUI supports one atlas entry. Use the CLI for multi-atlas runs.
diff --git a/docs/source/changes.md b/docs/source/changes.md
@@ -53,7 +53,7 @@
 
 ## 25.12.0-alpha
 
-**Released December 2026**
+**Released December 2025**
 
 ### New
 

diff --git a/docs/source/conf.py b/docs/source/conf.py
@@ -5,9 +5,10 @@
 import os
 import sys
 
+sys.path.insert(0, os.path.abspath("../.."))
+
 from wonkyconn import __copyright__, __packagename__, __version__
 
-sys.path.insert(0, os.path.abspath(".."))
 # -- Project information -----------------------------------------------------
 # https://www.sphinx-doc.org/en/master/usage/configuration.html#project-information
 
@@ -29,7 +30,7 @@
 ]
 
 templates_path = ["_templates"]
-exclude_patterns = []
+exclude_patterns = ["seann_workflow_notes.md"]
 
 
 # -- Options for HTML output -------------------------------------------------
@@ -38,4 +39,4 @@
 html_theme = "sphinx_rtd_theme"
 
 # -- Options for myst_parser -------------------------------------------------
-myst_enable_extensions = ["colon_fence"]
+myst_enable_extensions = ["colon_fence", "alert"]
-Original file line number
+Diff line change
@@ Expand Up / @@ -53,7 +53,7 @@ @@
     ## 25.12.0-alpha
-    **Released December 2026**
+    **Released December 2025**
     ### New
@@ Expand Down @@