From 9e3f30d00052bfd79057e538b10251e0e79ed173 Mon Sep 17 00:00:00 2001 From: Jover Lee Date: Thu, 25 Jul 2024 12:18:59 -0700 Subject: [PATCH 1/3] Add CI GH Action workflow --- .github/workflows/ci.yaml | 12 ++++++++++++ 1 file changed, 12 insertions(+) create mode 100644 .github/workflows/ci.yaml diff --git a/.github/workflows/ci.yaml b/.github/workflows/ci.yaml new file mode 100644 index 0000000..520a4ae --- /dev/null +++ b/.github/workflows/ci.yaml @@ -0,0 +1,12 @@ +name: CI + +on: + push: + branches: + - main + pull_request: + workflow_dispatch: + +jobs: + ci: + uses: nextstrain/.github/.github/workflows/pathogen-repo-ci.yaml@master From d04cd77ab11adee4c1ee520e4edd8dd74613a322 Mon Sep 17 00:00:00 2001 From: Jover Lee Date: Thu, 25 Jul 2024 12:22:11 -0700 Subject: [PATCH 2/3] ingest: Add build-configs for CI Uses a `bogus_ci_config` to satisfy Snakemakes requirement for config file having at least one top level key. Once the ingest is fully automated and runs daily, then we can add example data for just testing the workflow runs as expected. --- ingest/build-configs/ci/config.yaml | 6 ++++++ 1 file changed, 6 insertions(+) create mode 100644 ingest/build-configs/ci/config.yaml diff --git a/ingest/build-configs/ci/config.yaml b/ingest/build-configs/ci/config.yaml new file mode 100644 index 0000000..4b15515 --- /dev/null +++ b/ingest/build-configs/ci/config.yaml @@ -0,0 +1,6 @@ +# TODO: If the ingest workflow ever runs too long, we should figure out a way +# to subset the ingest data. Currently, the CI just runs the default ingest workflow. + +# Snakemake requires at least one top level key in a config file, so including +# a bogus key here that should not be used anywhere in the Snakemake workflow +bogus_ci_config: "bogus_ci_config" From a3e4a57518926c6d1553aad4b4b109394ee9626a Mon Sep 17 00:00:00 2001 From: Jover Lee Date: Thu, 25 Jul 2024 12:24:12 -0700 Subject: [PATCH 3/3] phylogenetic: Remove CI config.yaml The phylogenetic workflow is WIP and does not fully run yet. Rather than let CI error, just remove the config.yaml for now. --- phylogenetic/build-configs/ci/config.yaml | 7 ------- 1 file changed, 7 deletions(-) delete mode 100644 phylogenetic/build-configs/ci/config.yaml diff --git a/phylogenetic/build-configs/ci/config.yaml b/phylogenetic/build-configs/ci/config.yaml deleted file mode 100644 index de89c67..0000000 --- a/phylogenetic/build-configs/ci/config.yaml +++ /dev/null @@ -1,7 +0,0 @@ -# This configuration file contains the custom configurations parameters -# for the CI workflow to run with the example data. - -# Custom rules to run as part of the CI automated workflow -# The paths should be relative to the phylogenetic directory. -custom_rules: - - build-configs/ci/copy_example_data.smk