Move psy-fer to scverse

CHANGELOG.md

@@ -4,7 +4,7 @@
 Release notes are extracted from this file by the release workflow.
 Each released version needs a heading of the form:
 
-    ## [Version X.Y.Z](https://github.com/Psy-Fer/rustar-aligner/releases/tag/vX.Y.Z) - YYYY-MM-DD
+    ## [Version X.Y.Z](https://github.com/scverse/rustar-aligner/releases/tag/vX.Y.Z) - YYYY-MM-DD
 
 Sections commonly used: Features, Bug fixes, Other changes.
 -->

Cargo.toml

@@ -6,7 +6,7 @@ rust-version = "1.88"
 authors = ["James Ferguson"]
 description = "A Rust reimplementation of STAR (Spliced Transcripts Alignment to a Reference), the RNA-seq aligner"
 license = "MIT"
-repository = "https://github.com/Psy-Fer/rustar-aligner"
+repository = "https://github.com/scverse/rustar-aligner"
 readme = "README.md"
 keywords = ["bioinformatics", "rna-seq", "aligner", "sequencing", "star"]
 categories = ["command-line-utilities", "science"]

docs/astro.config.mjs

@@ -3,7 +3,7 @@ import { defineConfig } from 'astro/config';
 import starlight from '@astrojs/starlight';
 
 export default defineConfig({
-  site: 'https://psy-fer.github.io',
+  site: 'https://scverse.org',
   base: '/rustar-aligner',
   integrations: [
     starlight({
@@ -31,11 +31,11 @@ export default defineConfig({
         {
           icon: 'github',
           label: 'GitHub',
-          href: 'https://github.com/Psy-Fer/rustar-aligner',
+          href: 'https://github.com/scverse/rustar-aligner',
         },
       ],
       editLink: {
-        baseUrl: 'https://github.com/Psy-Fer/rustar-aligner/edit/main/docs/',
+        baseUrl: 'https://github.com/scverse/rustar-aligner/edit/main/docs/',
       },
       sidebar: [
         {

docs/src/components/Header.astro

@@ -9,7 +9,7 @@ import ThemeToggle from './ThemeToggle.astro';
 const shouldRenderSearch =
   config.pagefind || config.components.Search !== '@astrojs/starlight/components/Search.astro';
 
-const REPO = 'Psy-Fer/rustar-aligner';
+const REPO = 'scverse/rustar-aligner';
 const BASE = import.meta.env.BASE_URL.replace(/\/?$/, '/');
 
 const navLinks = [

docs/src/content/docs/about/changelog.md

@@ -3,12 +3,12 @@ title: Changelog
 description: Release history for rustar-aligner.
 ---
 
-The authoritative changelog lives at [`CHANGELOG.md`](https://github.com/Psy-Fer/rustar-aligner/blob/main/CHANGELOG.md) in the repository root. This page is a snapshot.
+The authoritative changelog lives at [`CHANGELOG.md`](https://github.com/scverse/rustar-aligner/blob/main/CHANGELOG.md) in the repository root. This page is a snapshot.
 
 ## Unreleased
 
 Initial release of Rust rewrite of STAR.
 
 ---
 
-For the full commit-level history, see the [GitHub releases page](https://github.com/Psy-Fer/rustar-aligner/releases).
+For the full commit-level history, see the [GitHub releases page](https://github.com/scverse/rustar-aligner/releases).

docs/src/content/docs/about/contributing.md

@@ -3,7 +3,7 @@ title: Contributing
 description: How to build, test, and contribute to rustar-aligner.
 ---
 
-Contributions are welcome. The repository is on GitHub at [Psy-Fer/rustar-aligner](https://github.com/Psy-Fer/rustar-aligner).
+Contributions are welcome. The repository is on GitHub at [scverse/rustar-aligner](https://github.com/scverse/rustar-aligner).
 
 ## Building and testing
 

docs/src/content/docs/about/license.md

@@ -29,4 +29,4 @@ SOFTWARE.
 
 ## Vendored notices
 
-The repository's `LICENSES/` directory contains license notices for vendored or referenced third-party material. See [`LICENSES/`](https://github.com/Psy-Fer/rustar-aligner/tree/main/LICENSES) on GitHub.
+The repository's `LICENSES/` directory contains license notices for vendored or referenced third-party material. See [`LICENSES/`](https://github.com/scverse/rustar-aligner/tree/main/LICENSES) on GitHub.

docs/src/content/docs/getting-started/installation.md

@@ -27,11 +27,11 @@ To upgrade later, repeat the same command — `cargo install` overwrites in plac
 
 ## 2. Docker image from GHCR
 
-Pre-built multi-arch images are published to the [GitHub Container Registry](https://github.com/Psy-Fer/rustar-aligner/pkgs/container/rustar-aligner) for every release. Linux x86_64 and aarch64 are both supported.
+Pre-built multi-arch images are published to the [GitHub Container Registry](https://github.com/scverse/rustar-aligner/pkgs/container/rustar-aligner) for every release. Linux x86_64 and aarch64 are both supported.
 
 ```bash
-docker pull ghcr.io/psy-fer/rustar-aligner:latest
-docker run --rm ghcr.io/psy-fer/rustar-aligner:latest --version
+docker pull ghcr.io/scverse/rustar-aligner:latest
+docker run --rm ghcr.io/scverse/rustar-aligner:latest --version
 ```
 
 ### Available tags
@@ -52,7 +52,7 @@ docker run --rm \
   -v /local/genome_index:/genome \
   -v /local/reads:/reads \
   -v /local/output:/output \
-  ghcr.io/psy-fer/rustar-aligner:latest \
+  ghcr.io/scverse/rustar-aligner:latest \
     --genomeDir /genome \
     --readFilesIn /reads/sample_1.fq.gz /reads/sample_2.fq.gz \
     --readFilesCommand zcat \
@@ -73,7 +73,7 @@ For development work, or when you want a build tuned for your specific machine,
 ### Clone and build
 
 ```bash
-git clone https://github.com/Psy-Fer/rustar-aligner.git
+git clone https://github.com/scverse/rustar-aligner.git
 cd rustar-aligner
 cargo build --release
 ```

docs/src/content/docs/guides/migrating-from-star.md

@@ -98,7 +98,7 @@ Then compare with your favourite SAM/BAM diff tool. The repository's `test/compa
 
 ## Reporting incompatibilities
 
-If you find a divergence from STAR that isn't documented in [STAR compatibility](/rustar-aligner/reference/star-compatibility/), please [open an issue](https://github.com/Psy-Fer/rustar-aligner/issues) with:
+If you find a divergence from STAR that isn't documented in [STAR compatibility](/rustar-aligner/reference/star-compatibility/), please [open an issue](https://github.com/scverse/rustar-aligner/issues) with:
 
 - The STAR command line you ran
 - A small input dataset (or pointer to one) that reproduces the divergence

docs/src/content/docs/index.mdx

@@ -7,7 +7,7 @@ import { Image } from 'astro:assets';
 import rustarIcon from '../../assets/rustar-icon.svg';
 
 export const installCode = `<span class="comment"># Step 1 · install</span>
-<span class="prompt">$</span> cargo install <span class="flag">--git</span> https://github.com/Psy-Fer/rustar-aligner
+<span class="prompt">$</span> cargo install <span class="flag">--git</span> https://github.com/scverse/rustar-aligner
 
 <span class="comment"># Step 2 · align</span>
 <span class="prompt">$</span> rustar-aligner \\
@@ -26,7 +26,7 @@ export const installCode = `<span class="comment"># Step 1 · install</span>
     <p class="lead-2">Same <code>{'--camelCase'}</code> CLI. Same SAM/BAM output formats. 99.883% mate-pair faithfulness on a 10,000-pair yeast benchmark, with zero MAPQ inflations.</p>
     <div class="rustar-btns rustar-hero-btns">
       <a href="/rustar-aligner/getting-started/introduction/" class="primary">Documentation</a>
-      <a href="https://github.com/Psy-Fer/rustar-aligner">GitHub ↗</a>
+      <a href="https://github.com/scverse/rustar-aligner">GitHub ↗</a>
     </div>
   </div>
   <Image src={rustarIcon} alt="rustar-aligner mascot: a red crab cradling a golden starfish" class="rustar-mascot" loading="eager" />

docs/src/content/docs/reference/performance.md

@@ -46,4 +46,4 @@ The benchmark suite under construction will report:
 
 ## Reporting your own numbers
 
-If you've benchmarked rustar-aligner on a real dataset, we'd love to hear about it — please [open an issue](https://github.com/Psy-Fer/rustar-aligner/issues) with the genome, read count, hardware, parameters, and timing. Real-world data shapes the optimisation work.
+If you've benchmarked rustar-aligner on a real dataset, we'd love to hear about it — please [open an issue](https://github.com/scverse/rustar-aligner/issues) with the genome, read count, hardware, parameters, and timing. Real-world data shapes the optimisation work.

docs/src/content/docs/reference/star-compatibility.md

@@ -103,4 +103,4 @@ For the overwhelming majority of bioinformatics workflows — read counting, dif
 - Workflows that depend on the *specific copy* a multi-mapper landed on (rare; in those cases, you should be using the full alignment set anyway, not just the primary).
 - Reproducing exact byte-equality of SAM output across STAR and rustar-aligner runs (not achievable today; the RNG difference is the dominant source).
 
-If you find a divergence not described here, please [open an issue](https://github.com/Psy-Fer/rustar-aligner/issues) — the project goal is to keep this list as short as possible.
+If you find a divergence not described here, please [open an issue](https://github.com/scverse/rustar-aligner/issues) — the project goal is to keep this list as short as possible.

src/cpu.rs

@@ -127,12 +127,12 @@ pub fn check_cpu_compat() -> Result<()> {
         "x86-64-v4" if !is_x86_feature_detected!("avx512f") => bail!(
             "This rustar-aligner binary was compiled for x86-64-v4 (AVX-512) but your CPU \
              does not support AVX-512.\nPlease use the x86-64-v3 or baseline build instead.\n\
-             See: https://github.com/Psy-Fer/rustar-aligner#installation"
+             See: https://github.com/scverse/rustar-aligner#installation"
         ),
         "x86-64-v3" if !is_x86_feature_detected!("avx2") => bail!(
             "This rustar-aligner binary was compiled for x86-64-v3 (AVX2) but your CPU \
              does not support AVX2.\nPlease use the baseline build instead.\n\
-             See: https://github.com/Psy-Fer/rustar-aligner#installation"
+             See: https://github.com/scverse/rustar-aligner#installation"
         ),
         _ => {}
     }
@@ -142,7 +142,7 @@ pub fn check_cpu_compat() -> Result<()> {
         bail!(
             "This rustar-aligner binary was compiled for aarch64-neoverse-v1 (SVE) but your CPU \
              does not support SVE.\nPlease use the baseline aarch64 build instead.\n\
-             See: https://github.com/Psy-Fer/rustar-aligner#installation"
+             See: https://github.com/scverse/rustar-aligner#installation"
         );
     }