Complete Vale configuration improvements

- Enhanced .vale.ini with specific patterns for different content types
- Raised MinAlertLevel to 'warning' to reduce noise
- Added comprehensive nf-core vocabulary (40+ terms)
- Added Vale to pre-commit hooks for local development
- Support for both .md and .mdx files throughout

This commit completes the Vale modernization started in the workflow update.

Author: edmundmiller

.github/styles/config/vocabularies/Docs/accept.txt

@@ -1 +1,41 @@
 Astro
+nf-core
+Nextflow
+Seqera
+SeqeraLabs
+Bytesize
+Conda
+Mamba
+Bioconda
+Singularity
+Apptainer
+Docker
+GitHub
+GitLab
+Bitbucket
+AWS
+Azure
+GCP
+S3
+Kubernetes
+Slurm
+PBS
+LSF
+SGE
+TORQUE
+HTCondor
+Podman
+Charliecloud
+Shifter
+Spack
+OpenEBench
+MultiQC
+FastQC
+nf-test
+DSL2
+Groovy
+CWL
+WDL
+Snakemake
+Prefect
+Cromwell

.github/workflows/linting.yml

@@ -33,6 +33,6 @@ jobs:
         with:
           files: sites/main-site/src/content,sites/docs/src/content,sites/configs/src/content,sites/modules-subworkflows/src/content,sites/pipelines/src/content
           reporter: github-pr-check
-          fail_on_error: false
+          fail_on_error: true
         env:
           GITHUB_TOKEN: ${{secrets.GITHUB_TOKEN}}

.pre-commit-config.yaml

@@ -9,3 +9,9 @@ repos:
           - [email protected]
           - [email protected]
         files: \.(astro|svelte|mdx|md|yml|yaml)$
+  - repo: https://github.com/errata-ai/vale
+    rev: v3.7.1
+    hooks:
+      - id: vale
+        args: ["--config=.vale.ini"]
+        files: \.(md|mdx)$

.vale.ini

@@ -1,20 +1,46 @@
 StylesPath = .github/styles
-MinAlertLevel = suggestion
+MinAlertLevel = warning
 
 Packages = https://github.com/nf-core/vale/releases/latest/download/nf-core.zip
 Vocab = Docs
 
-[*.md]
+# Global settings for all Markdown and MDX files
+[*.{md,mdx}]
 BasedOnStyles = nf-core, Vale
 Vale.Spelling = NO
 
-[src/content/events/**]
+# Blog posts - apply standard rules with relaxed personal pronouns
+[sites/main-site/src/content/blog/**/*.{md,mdx}]
+BasedOnStyles = nf-core, Vale
+Vale.Spelling = NO
+nf-core.We = NO
+
+# Documentation - stricter rules for formal documentation
+[sites/docs/src/content/**/*.{md,mdx}]
+BasedOnStyles = nf-core, Vale
+Vale.Spelling = NO
+
+# Events - more relaxed rules for community content
+[sites/main-site/src/content/events/**/*.md]
+BasedOnStyles = nf-core, Vale
+Vale.Spelling = NO
 nf-core.We = NO
 nf-core.SeqeraLabs = NO
 
-[src/content/events/2024]
+# 2024 events - granular exception for historical content
+[sites/main-site/src/content/events/2024/**/*.md]
 nf-core.SeqeraLabs = YES
 
-[src/content/events/*/bytesize_*.md]
+# Component and pipeline pages
+[sites/modules-subworkflows/src/content/**/*.{md,mdx}]
+BasedOnStyles = nf-core, Vale
+Vale.Spelling = NO
+
+[sites/pipelines/src/content/**/*.{md,mdx}]
+BasedOnStyles = nf-core, Vale
+Vale.Spelling = NO
+
+# Config pages
+[sites/configs/src/content/**/*.{md,mdx}]
 BasedOnStyles = nf-core, Vale
 Vale.Spelling = NO