chore(sync): 🔨 synced file(s) with seedcase-project/template-data-package

.github/pull_request_template.md

@@ -4,11 +4,9 @@ This PR will [DESCRIBE CHANGES].
 
 Closes #
 
-<!-- Select quick/in-depth as necessary -->
 This PR needs a quick/an in-depth review.
 
 ## Checklist
 
-- [ ] Read through for typos, added new words to the dictionary
 - [ ] Checked that the README is up to date
-- [ ] Resolved any Ruff errors / formatted in Markdown
+- [ ] Run `just run-all`

.pre-commit-config.yaml

@@ -12,6 +12,14 @@ repos:
       - id: end-of-file-fixer
 
   - repo: https://github.com/commitizen-tools/commitizen
-    rev: v4.7.0
+    rev: v4.7.2
     hooks:
       - id: commitizen
+
+  # Use the mirror since the main `typos` repo has tags for different
+  # sub-packages, which confuses pre-commit when it tries to find the latest
+  # version
+  - repo: https://github.com/adhtruong/mirrors-typos
+    rev: v1.32.0
+    hooks:
+      - id: typos

.vscode/extensions.json

@@ -1,22 +1,21 @@
 {
-  // See https://go.microsoft.com/fwlink/?LinkId=827846 to learn about workspace recommendations.
-  // Extension identifier format: ${publisher}.${name}. Example: vscode.csharp
-  // List of extensions which should be recommended for users of this workspace.
   "recommendations": [
+    "eamodio.gitlens",
+    "github.vscode-github-actions",
+    "redhat.vscode-yaml",
     "donjayamanne.githistory",
     "felipecaputo.git-project-manager",
     "GitHub.vscode-pull-request-github",
-    "ms-azuretools.vscode-docker",
     "ms-python.python",
     "ms-python.vscode-pylance",
     "njpwerner.autodocstring",
     "quarto.quarto",
     "ms-toolsai.jupyter",
-    "streetsidesoftware.code-spell-checker",
     "vivaxy.vscode-conventional-commits",
     "charliermarsh.ruff",
     "pshaddel.conventional-branch",
-    "yy0931.vscode-sqlite3-editor"
+    "tekumara.typos-vscode",
+    "EditorConfig.EditorConfig"
   ],
   // List of extensions recommended by VS Code that should not be recommended for users of this workspace.
   "unwantedRecommendations": []

.vscode/settings.json

@@ -31,9 +31,5 @@
   },
   "python.defaultInterpreterPath": "${workspaceFolder}/.venv",
   "python.languageServer": "Pylance",
-  "files.insertFinalNewline": true,
-  "cSpell.enabledFileTypes": {
-    "quarto": true
-  },
-  "cSpell.language": "en,en-GB",
+  "files.insertFinalNewline": true
 }

datapackage.json

@@ -69,4 +69,4 @@
       "path": "https://zenodo.org/records/7055715"
     }
   ]
-}
+}

justfile

@@ -2,11 +2,20 @@
     just --list --unsorted
 
 # Run all build-related recipes in the justfile
-run-all: install-deps format-python check-python check-commits
+run-all: install-deps format-python check-python check-spelling check-commits
+
+# Install the pre-commit hooks
+install-precommit:
+  # Install pre-commit hooks
+  uvx pre-commit install
+  # Run pre-commit hooks on all files
+  uvx pre-commit run --all-files
+  # Update versions of pre-commit hooks
+  uvx pre-commit autoupdate
 
 # Install Python package dependencies
 install-deps:
-  uv sync --upgrade --dev
+  uv sync --upgrade --dev --all-extras
 
 # Check Python code with the linter for any errors that need manual attention
 check-python:
@@ -28,3 +37,7 @@ check-commits:
   else
     echo "Not on main or haven't committed yet."
   fi
+
+# Check for spelling errors in files
+check-spelling:
+  uv run typos

scripts/convert-meta.py

@@ -171,18 +171,18 @@
 # More than one measure in metadata_maternal_bl?
 """
 11 - Metadata_Maternal_placenta.csv
-* Variables 
+* Variables
 o Exp: Samples IDs. The same “Exp” represent the same sample in Concentration_Maternal.placenta.csv file.
-o Mother_ID: IDs of mothers. 
+o Mother_ID: IDs of mothers.
 o Batch: The experiment was conducted over two batches (Batch1 or Batch2)
 o Group: Lean or Obese.
 o GD: Exact gestational day (GD) when samples were collected.
-o Target_GD: Target GD for sample collection. 
-o Dilution_factor: Dilution factor used to prepare NMR samples. 
-o BCS: Body Condition Score (BCS) 
-o Tissue_weight: Weight of placental tissue sample. 
+o Target_GD: Target GD for sample collection.
+o Dilution_factor: Dilution factor used to prepare NMR samples.
+o BCS: Body Condition Score (BCS)
+o Tissue_weight: Weight of placental tissue sample.
 o V1: Volume of solvent used to extract (uL). Used to correct the metabolite concentration.
 o V2: Volume of polar layer (methanol + water) collected (uL). Used to correct the metabolite concentration.
-o V3: Buffer added to reconstitute the sample after freeze drying (uL). Used to correct the metabolite concentration. 
+o V3: Buffer added to reconstitute the sample after freeze drying (uL). Used to correct the metabolite concentration.
 * Missing data codes: Indicated by NAs.
 """