Merge pull request #140 from nextstrain/auto-deploy-dated-private-builds

Automatically deploy dated builds to nextflu-private group

.github/workflows/run-nextflu-private-builds.yaml

@@ -25,8 +25,10 @@ jobs:
           --memory 72gib \
           --env AWS_ACCESS_KEY_ID \
           --env AWS_SECRET_ACCESS_KEY \
+          --env NEXTSTRAIN_USERNAME \
+          --env NEXTSTRAIN_PASSWORD \
           . \
-          all \
+          deploy_all \
           all_counts_of_recent_tips_by_clade \
           -p \
           --configfile profiles/nextflu-private.yaml

Snakefile

@@ -37,10 +37,6 @@ include:  "workflow/snakemake_rules/fitness.smk"
 
 include:  "workflow/snakemake_rules/report.smk"
 
-if "custom_rules" in config:
-    for rule_file in config["custom_rules"]:
-        include: rule_file
-
 def _get_build_outputs():
     outputs = []
     for build_name, build_params in config["builds"].items():
@@ -60,6 +56,10 @@ def _get_build_outputs():
 
     return outputs
 
+if "custom_rules" in config:
+    for rule_file in config["custom_rules"]:
+        include: rule_file
+
 rule all:
     input:
         _get_build_outputs()

profiles/nextflu-private.yaml

@@ -2,6 +2,10 @@ custom_rules:
   - workflow/snakemake_rules/download_from_s3.smk
   - profiles/nextflu-private/antigenic_distances.smk
   - profiles/nextflu-private/report.smk
+  - profiles/nextflu-private/deploy.smk
+
+# URL for auto-deploying builds
+deploy_url: https://nextstrain.org/groups/nextflu-private/
 
 fasta_fields:
   - strain

profiles/nextflu-private/README.md

@@ -1,28 +1,10 @@
 # Monthly reports on seasonal influenza evolution
 
-## Build trees
+## Build and deploy trees
 
-[Run the nextflu-private build with the GitHub Action](https://github.com/nextstrain/seasonal-flu/actions/workflows/run-nextflu-private-builds.yaml).
-Use the build summary for the job to track the progress of the builds on AWS Batch and download the final builds.
-If trees look reasonable, rename them to match the current date (or the date corresponding to when the data were updated).
-
-``` bash
-export DATE=2022-10-03
-cd auspice/
-
-for file in {h1n1pdm,h3n2,vic}*
-do
-  mv ${file} "flu_seasonal_${DATE}_${file}"
-done
-```
-
-Upload the files to the Nextstrain group.
-
-``` bash
-nextstrain remote upload \
-  https://nextstrain.org/groups/nextflu-private/ \
-  *.json
-```
+[Run the nextflu-private builds with the GitHub Action](https://github.com/nextstrain/seasonal-flu/actions/workflows/run-nextflu-private-builds.yaml).
+The workflow automatically deploys dated Auspice JSONs to [the nextflu-private group](https://nextstrain.org/groups/nextflu-private/) (e.g., https://nextstrain.org/groups/nextflu-private/flu/seasonal/2024-01-08/h3n2/2y/ha).
+View the GitHub Action summary for details about how to download the build artifacts from AWS Batch.
 
 ## Prepare a report
 

profiles/nextflu-private/deploy.smk

@@ -0,0 +1,30 @@
+"""
+This part of the workflow handles automatic deployments of nextflu-private builds.
+"""
+
+rule all_private:
+    input:
+        jsons=_get_build_outputs(),
+    output:
+        json_dir=directory("auspice_renamed"),
+    params:
+        build_date=datetime.date.today().strftime("%Y-%m-%d"),
+    shell:
+        """
+        mkdir -p {output.json_dir};
+        for file in {input.jsons}
+        do
+            ln ${{file}} {output.json_dir}/"flu_seasonal_{params.build_date}_`basename ${{file}}`"
+        done
+        """
+
+rule deploy_all:
+    input:
+        json_dir=directory("auspice_renamed"),
+    params:
+        deploy_url = config["deploy_url"]
+    shell:
+        """
+        nextstrain login --no-prompt;
+        nextstrain remote upload {params.deploy_url} {input.json_dir}/*.json
+        """