From fefe1a7c5bcabe2cb62577f2d2e64353623c954e Mon Sep 17 00:00:00 2001 From: Jover Lee Date: Tue, 16 Jul 2024 14:24:15 -0700 Subject: [PATCH 1/3] phylogenetic: Rename CI config file MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Preparation for changing over the CI to the latest version of the `pathogen-repo-ci` workflow, which requires the CI config to be at `phylogenetic/build-configs/ci/config.yaml`¹ ¹ --- phylogenetic/build-configs/ci/config.yaml | 2 ++ .../{profiles => build-configs}/ci/copy_example_data.smk | 0 phylogenetic/profiles/ci/profiles_config.yaml | 2 -- 3 files changed, 2 insertions(+), 2 deletions(-) create mode 100644 phylogenetic/build-configs/ci/config.yaml rename phylogenetic/{profiles => build-configs}/ci/copy_example_data.smk (100%) delete mode 100644 phylogenetic/profiles/ci/profiles_config.yaml diff --git a/phylogenetic/build-configs/ci/config.yaml b/phylogenetic/build-configs/ci/config.yaml new file mode 100644 index 00000000..ab6a2cb5 --- /dev/null +++ b/phylogenetic/build-configs/ci/config.yaml @@ -0,0 +1,2 @@ +custom_rules: + - build-configs/ci/copy_example_data.smk diff --git a/phylogenetic/profiles/ci/copy_example_data.smk b/phylogenetic/build-configs/ci/copy_example_data.smk similarity index 100% rename from phylogenetic/profiles/ci/copy_example_data.smk rename to phylogenetic/build-configs/ci/copy_example_data.smk diff --git a/phylogenetic/profiles/ci/profiles_config.yaml b/phylogenetic/profiles/ci/profiles_config.yaml deleted file mode 100644 index 17bad213..00000000 --- a/phylogenetic/profiles/ci/profiles_config.yaml +++ /dev/null @@ -1,2 +0,0 @@ -custom_rules: - - profiles/ci/copy_example_data.smk From 5c539beda1aaf49f80369a683485df11c68e004e Mon Sep 17 00:00:00 2001 From: Jover Lee Date: Tue, 16 Jul 2024 14:34:22 -0700 Subject: [PATCH 2/3] phylogenetic/example_data: Remove outdated README --- phylogenetic/example_data/README.md | 17 ----------------- 1 file changed, 17 deletions(-) delete mode 100644 phylogenetic/example_data/README.md diff --git a/phylogenetic/example_data/README.md b/phylogenetic/example_data/README.md deleted file mode 100644 index 73d642dc..00000000 --- a/phylogenetic/example_data/README.md +++ /dev/null @@ -1,17 +0,0 @@ -FASTA fields follow: - -1. `strain` -2. `virus` -3. `accession` -4. `collection_date` -5. `region` -6. `country` -7. `division` -8. `location` -9. `source` -10. `locus` -11. `authors` -12. `url` -13. `title` -14. `journal` -15. `puburl` From 146c17ac5d205e22ccf52d42ba0362316a36ea1e Mon Sep 17 00:00:00 2001 From: Jover Lee Date: Tue, 16 Jul 2024 14:35:38 -0700 Subject: [PATCH 3/3] Switch CI to `pathogen-repo-ci` workflow See https://github.com/nextstrain/.github/issues/94 for context --- .github/workflows/ci.yaml | 30 +++++++----------------------- 1 file changed, 7 insertions(+), 23 deletions(-) diff --git a/.github/workflows/ci.yaml b/.github/workflows/ci.yaml index 12ce7187..520a4ae0 100644 --- a/.github/workflows/ci.yaml +++ b/.github/workflows/ci.yaml @@ -1,28 +1,12 @@ name: CI on: - - push - - pull_request + push: + branches: + - main + pull_request: + workflow_dispatch: jobs: - pathogen-ci: - strategy: - matrix: - runtime: [docker, conda] - permissions: - id-token: write - uses: nextstrain/.github/.github/workflows/pathogen-repo-build.yaml@master - secrets: inherit - with: - runtime: ${{ matrix.runtime }} - run: | - nextstrain build \ - phylogenetic \ - --configfile profiles/ci/profiles_config.yaml - artifact-name: output-${{ matrix.runtime }} - artifact-paths: | - phylogenetic/auspice/ - phylogenetic/results/ - phylogenetic/benchmarks/ - phylogenetic/logs/ - phylogenetic/.snakemake/log/ \ No newline at end of file + ci: + uses: nextstrain/.github/.github/workflows/pathogen-repo-ci.yaml@master