From e8e1f3213711d8c4b5022f7c29d3eb8ee3f46b4b Mon Sep 17 00:00:00 2001 From: Jover Date: Fri, 1 Sep 2023 10:44:36 -0700 Subject: [PATCH 1/2] setup-nextstrain-cli: Run nextstrain update after runtime setup MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit There's a weird issue with the Conda runtime where the inital setup uses an older version.¹ Do an update of the default runtime after setup to ensure we are using the latest version. We could remove this extra step after we rework `nextstrain setup` to use the same logic as `nextstrain update`. ¹ https://github.com/nextstrain/monkeypox/issues/177 --- actions/setup-nextstrain-cli/action.yaml | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/actions/setup-nextstrain-cli/action.yaml b/actions/setup-nextstrain-cli/action.yaml index 90815a8..9bfbff3 100644 --- a/actions/setup-nextstrain-cli/action.yaml +++ b/actions/setup-nextstrain-cli/action.yaml @@ -8,7 +8,7 @@ description: >- repos when they need a working copy of the Nextstrain CLI (the `nextstrain` program) installed and don't particularly care about the exact Python environment in which its installed. - + For example, this is typically the case when the workflow's primary step invokes `nextstrain build` to run a build in a container runtime (locally via Docker or remotely via AWS Batch). Workflows that are more complex (e.g. @@ -65,5 +65,8 @@ runs: env: runtime: ${{ inputs.runtime }} + - run: nextstrain update + shell: bash + - run: nextstrain version --verbose shell: bash From 2235407271da7cf7c0e8dc52ac448429e2a716c5 Mon Sep 17 00:00:00 2001 From: Jover Date: Fri, 1 Sep 2023 10:58:07 -0700 Subject: [PATCH 2/2] pathogen-repo-ci: Update ref for setup-nextstrain-cli We could start using the workflow-context action like the pathogen-repo-build workflow, but that will require all uses of the pathogen-repo-ci to be updated to give id-token write permissions. That's a bigger change that I think can be done separately. --- .github/workflows/pathogen-repo-ci.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/pathogen-repo-ci.yaml b/.github/workflows/pathogen-repo-ci.yaml index 90bcd7f..76d1484 100644 --- a/.github/workflows/pathogen-repo-ci.yaml +++ b/.github/workflows/pathogen-repo-ci.yaml @@ -221,7 +221,7 @@ jobs: # future changes to setup-nextstrain-cli. # # -trs, 28 April 2022 - - uses: nextstrain/.github/actions/setup-nextstrain-cli@29b00885dff495824a12d95d709c03d3891cc12d + - uses: nextstrain/.github/actions/setup-nextstrain-cli@e8e1f3213711d8c4b5022f7c29d3eb8ee3f46b4b with: runtime: ${{ matrix.runtime }} # Consider parameterizing the Python version. -trs, 1 April 2022