microbiomedata · eecavanna · Feb 5, 2025 · Feb 20, 2025 · Feb 20, 2025 · Feb 20, 2025
diff --git a/.github/workflows/assemble-website.yml b/.github/workflows/assemble-website.yml
@@ -67,9 +67,14 @@ jobs:
           #       artifact; e.g., spell checkers and link checkers.
           name: github-pages
 
-  # Use existing workflow(s) to check the file tree for broken links.
+  # Use existing workflows to check the file tree for broken links and spelling errors.
   check-links:
     name: Check links
     uses: ./.github/workflows/check-links.yml
     needs:
       - assemble
+  check-spelling:
+    name: Check spelling
+    uses: ./.github/workflows/check-spelling.yml
+    needs:
+      - assemble
diff --git a/.github/workflows/check-spelling.yml b/.github/workflows/check-spelling.yml
@@ -0,0 +1,37 @@
+# This GitHub Actions workflow checks spelling in HTML files and creates a GitHub Issue if it finds misspelled words.
+# Reference: https://docs.github.com/en/actions/writing-workflows/workflow-syntax-for-github-actions
+name: Check spelling
+
+on:
+  # Allow this workflow to be called by other workflows.
+  # Reference: https://docs.github.com/en/actions/using-workflows/reusing-workflows
+  workflow_call: { }
+
+jobs:
+  check-spelling:
+    name: Check spelling
+    runs-on: ubuntu-latest
+    steps:
+      # Check out the commit so that we have access to the spellcheck configuration file residing in the repository.
+      - name: Check out commit
+        uses: actions/checkout@v4
+      - name: Get website file tree
+        uses: actions/download-artifact@v4  # docs: https://github.com/actions/download-artifact
+        with:
+          name: github-pages
+          path: _downloads
+      - name: Un-tar the archive
+        run: |
+          pwd
+          mkdir -p _build/html
+          tar -xvf _downloads/artifact.tar -C _build/html
+          ls -lR _build/html
+      # Use `GitHub Spellcheck Action`, from the GHA Marketplace, to check spelling.
+      # Reference: https://github.com/marketplace/actions/github-spellcheck-action
+      - name: Dump Spellcheck configuration file
+        run: cat .github/workflows/supporting_files/spellcheck.yml
+      - name: Run Spellcheck
+        uses: rojopolis/spellcheck-github-actions@0.47.0
+        with:
+          config_path: .github/workflows/supporting_files/spellcheck.yml
+          task_name: HTML
diff --git a/.github/workflows/supporting_files/spellcheck.yml b/.github/workflows/supporting_files/spellcheck.yml
@@ -0,0 +1,22 @@
+matrix:
+- name: HTML
+  sources:
+  - _build/html/**/*.html
+  dictionary:
+    wordlists:
+    - .github/workflows/supporting_files/spellcheck_allow_list.txt
+    encoding: utf-8
+  aspell: { lang: en }
+  pipeline:
+  # Docs: https://facelessuser.github.io/pyspelling/filters/html/
+  - pyspelling.filters.html:
+      comments: false
+      # CSS selectors supported: https://facelessuser.github.io/soupsieve/
+      ignores:
+      - code
+      - pre
+      # Ignore code cells in Jupyter notebooks; i.e., `.jp-CodeCell` elements within `.jupyter-wrapper` elements.
+      - .jupyter-wrapper .jp-CodeCell
  # Docs: https://facelessuser.github.io/pyspelling/filters/url/
+  - pyspelling.filters.url: {}
+  default_encoding: utf-8
diff --git a/.github/workflows/supporting_files/spellcheck_allow_list.txt b/.github/workflows/supporting_files/spellcheck_allow_list.txt
@@ -0,0 +1,138 @@
+acyclic
+ADR
+APK
+APIs
+API's
+Archaeal
+archaeal
+AST
+BBTools
+Bioinformatics
+bioinformatics
+Biomes
+biomes
+Biosample
+biosample
+Biosamples
+biosamples
+Changesheets
+changesheets
+Community-centric
+community-centric
+Contig
+contig
+Contigs
+contigs
+CSV
+Dagit
+Dagster
+Dagster's
+DataHarmonizer
+DataObject
+DataObjects
+Diátaxis
+DOI
+EMSL
+EMSL's
+ENVO
+EnvO
+ESS
+ETL
+FastAPI
+FASTA
+FASTQ
+funder
+Globus
+GOTTCHA
+GPL
+GSC
+GSC's
+Heatmap
+heatmap
+Heatmaps
+heatmaps
+IMG
+JGI
+JSON
+Jupyter
+KBase
+KEGG
+Kubernetes
+LANL
+LANL's
+LBNL
+LBNL's
+LinkML
+Lipidomics
+lipidomics
+Metabolomics
+metabolomics
+MetaG
+Metagenome
+metagenome
+Metagenomes
+metagenomes
+Metagenomic
+metagenomic
+Metagenomics
+metagenomics
+Metaproteomic
+Metaproteomics
+MetaT
+Metatranscriptome
+metatranscriptome
+Metatranscriptomic
+metatranscriptomic
+Metatranscriptomics
+metatranscriptomics
+Microbiome
+microbiome
+Microbiomes
+microbiomes
+MIxS
+Mgt
+MkDocs
+multi-omics
+namespace
+NCBI
+NERSC
+NMDC
+NMDC's
+NOM
+nmdc-runtime
+nmdc-schema
+nmdc-server
+Omics
+omics
+OmicsProcessing
+Ontologies
+ontologies
+Ontologists
+ontologists
+PNNL
+PNNL's
+programmatically
+Proteomics
+proteomics
+PyPI
+repo
+RESTful
+Runtime
+Runtime's
+Sankey
+SQLAlchemy
+Spectrometry
+spectrometry
+Submitter
+submitter
+submitter's
+TestFlight
+TODO
+TOML
+TSV
+Vue
+Vuetify
+WDL
+XLS
+XLSX
+YAML