Add a script that generates the list of clades to model (#27)

* Add a script that generates the list of clades to model

The list of clades will be saved as a file in
auxiliary-data/modeled-clades/YYYY-MM-DD.txt
where YYYY-MM-DD is the id of the upcoming modeling round.

* Add scheduled GitHub workflow to prep for round opening

* Add a stub R script for adding a new modeling round to the hub

This iteration of the script is a placeholder to get R code
hooked up to the GitHub workflowD

.github/workflows/create-modeling-round.yaml

@@ -0,0 +1,65 @@
+name: Create new modeling round
+
+on:
+  schedule:
+    - cron: "0 03 * * 1" # every Monday at 3 AM UTC
+  workflow_dispatch:
+
+permissions:
+    contents: write
+    pull-requests: write
+
+jobs:
+  create-modeling-round:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout 🛎️
+        uses: actions/checkout@v4
+        with:
+            # don't check out repo folders with large amounts of data
+            # (e.g., model-output, target-data)
+            sparse-checkout: |
+              auxiliary-data/
+              hub-config/
+              src/
+
+      - name: Install uv 🌈
+        uses: astral-sh/setup-uv@v2
+        with:
+          version: "0.4.9"
+
+      - name: Set up Python 🐍
+        uses: actions/setup-python@v5
+        with:
+            python-version-file: "src/.python-version"
+
+      - name: Create clade list 🦠
+        run: |
+          uv run src/get_clades_to_model.py
+
+      - name: Set up R 📊
+        uses: r-lib/actions/setup-r@v2
+
+      - name: Generate new round config 📝
+        run: |
+          Rscript src/make_round_config.R
+
+      - name: Get current date and time 🕰️
+        run: |
+          PR_DATETIME=$(date +'%Y-%m-%d_%H-%M-%S')
+          echo "PR_DATETIME=$PR_DATETIME" >> $GITHUB_ENV
+
+      - name: Create PR for new modeling round 🚀
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        run: |
+          git config user.name "github-actions[bot]"
+          git config user.email "41898282+github-actions[bot]@users.noreply.github.com"
+          git checkout -b new_round_"$PR_DATETIME"
+          git add auxiliary-data/modeled-clades/
+          git commit -m "Add new round $PR_DATETIME"
+          git push -u origin new_round_"$PR_DATETIME"
+          gh pr create \
+            --base main \
+            --title "Add new round $PR_DATETIME" \
+            --body "This PR was created via GitHub Actions: generate clade list and new round config."

.gitignore

@@ -2,3 +2,7 @@
 .Rhistory
 .RData
 .Ruserdata
+
+**/uv.lock
+
+.pre-commit-config.yaml

auxiliary-data/modeled-clades/2024-09-11.txt

@@ -0,0 +1,5 @@
+24A
+recombinant
+24B
+24C
+other

src/.python-version

@@ -0,0 +1 @@
+3.12

src/get_clades_to_model.py

@@ -0,0 +1,75 @@
+"""
+Create a list of Sars-CoV-2 clades to model and saves it to the hub's auxiliary-data folder.
+
+This script wraps the virus-clade-utils package, which generates the clade list using the
+latest GenBank-based Sars-CoV-2 sequence metadata from Nextstrain.
+https://github.com/reichlab/virus-clade-utils
+
+Current parameters for the clade list:
+    threshold = .01,
+    threshold_weeks = 3 week
+    max_clades = 9
+
+The script is scheduled to run every Monday, for use in the modeling round that will open
+on the following Wednesday.
+
+To run the script manually:
+1. Install uv on your machine: https://docs.astral.sh/uv/getting-started/installation/
+2. From the root of this repo: uv run src/get_clades_to_model.py
+"""
+
+# /// script
+# dependencies = [
+#   "virus_clade_utils@git+https://github.com/reichlab/virus-clade-utils/",
+# ]
+# ///
+
+import logging
+from datetime import datetime, timedelta
+from pathlib import Path
+
+from virus_clade_utils import get_clade_list  # type: ignore
+
+# Log to stdout
+logger = logging.getLogger(__name__)
+handler = logging.StreamHandler()
+formatter = logging.Formatter(
+    "%(asctime)s -  %(levelname)s - %(message)s", datefmt="%m/%d/%Y %I:%M:%S %p"
+)
+handler.setFormatter(formatter)
+logger.addHandler(handler)
+logger.setLevel(logging.INFO)
+
+
+def get_next_wednesday(starting_date: datetime) -> str:
+    """Return the date of the next Wednesday in YYYY-MM-DD format."""
+
+    current_day_of_week = starting_date.weekday()
+    days_until_wednesday = (2 - current_day_of_week + 7) % 7
+    if days_until_wednesday == 0:
+        days_until_wednesday = 7
+
+    next_wednesday = starting_date + timedelta(days=days_until_wednesday)
+    return next_wednesday.strftime("%Y-%m-%d")
+
+
+def main(round_id: str, clade_output_path: Path):
+    """Get a list of clades to model and save to the hub's auxiliary-data folder."""
+
+    clade_list = get_clade_list.main()
+    logger.info(f"Clade list: {clade_list}")
+
+    clade_file = clade_output_path / f"{round_id}.txt"
+    with open(clade_file, "w") as f:
+        for clade in clade_list:
+            f.write(f"{clade}\n")
+        f.write("other\n")
+
+    logger.info(f"Clade list saved: {clade_file}")
+
+
+if __name__ == "__main__":
+    # round_id will be the Wednesday following the creation of the clade list
+    round_id = get_next_wednesday(datetime.today())
+    clade_output_path = Path(__file__).parents[1] / "auxiliary-data" / "modeled-clades"
+    main(round_id, clade_output_path)

src/make_round_config.R

@@ -0,0 +1 @@
+print("Once implemented, script will update hub-config/tasks.config based on latest list of clades to model.")