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Bsweger/hotfix cladetime #12

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merged 2 commits into from
Dec 2, 2024
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Bsweger/hotfix cladetime #12

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07aa288
Use last week's cladetime hotfix (temporarily)
bsweger Dec 2, 2024
27ba18f
Add parameter to manual run
bsweger Dec 2, 2024
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18 changes: 17 additions & 1 deletion .github/workflows/get-covid-clade-counts.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -4,6 +4,11 @@ on:
schedule:
- cron: "37 04 * * 1" # 4:37 AM UTC every Mon
workflow_dispatch:
inputs:
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@bsweger bsweger Dec 2, 2024 •
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Allowing someone to pass in YYYY-MM-DD when running this workflow manually makes it easier to recover in the event of an error.

In this case, I think we can pass in the dates of the failed runs:

as_of:
description: "Get clade counts as of 11:59 UTC on this date (YYYY-MM-DD)"
required: true
default: $(date +'%Y-%m-%d')

env:
# Hubverse AWS account number
Expand All @@ -19,6 +24,17 @@ jobs:
runs-on: ubuntu-latest

steps:

- name: Get --as-of date 🕰️
run: |
if [[ ${{ github.event_name == 'workflow_dispatch' }} == true ]]; then
AS_OF=${{ inputs.as_of }}
else
AS_OF=$(date +'%Y-%m-%d')
fi
echo "as_of date is set to $AS_OF"
echo "AS_OF=$AS_OF" >> $GITHUB_ENV

- name: Checkout
uses: actions/checkout@v4

Expand All @@ -37,7 +53,7 @@ jobs:

- name: Get covid clade counts
run: |
uv run get_covid_clade_counts.py --as-of=$(date +'%Y-%m-%d')
uv run get_covid_clade_counts.py --as-of="$AS_OF"

- name: Install rclone
run: |
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2 changes: 1 addition & 1 deletion get_covid_clade_counts.py
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Expand Up @@ -17,7 +17,7 @@
# requires-python = "==3.12"
# dependencies = [
# "click",
# "cladetime@git+https://github.com/reichlab/cladetime"
# "cladetime@git+https://github.com/reichlab/cladetime@elr/use_metadata_url"
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Copied this from https://github.com/reichlab/variant-nowcast-hub/pull/176/files

# ]
# ///

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