From 4366771cea2482d31395ad9b5d351b950daa798d Mon Sep 17 00:00:00 2001 From: Victor Lin <13424970+victorlin@users.noreply.github.com> Date: Mon, 25 Sep 2023 13:58:57 -0700 Subject: [PATCH 1/2] Run nextstrain update on conda runtime only This was added as a workaround for the conda runtime only, though that reasoning is not clear without digging into commit messages and GitHub comments. This makes that more clear, and also removes the need to continue-on-error for runtimes unsupported by nextstrain update. --- actions/setup-nextstrain-cli/action.yaml | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/actions/setup-nextstrain-cli/action.yaml b/actions/setup-nextstrain-cli/action.yaml index facfa42..def4f03 100644 --- a/actions/setup-nextstrain-cli/action.yaml +++ b/actions/setup-nextstrain-cli/action.yaml @@ -65,9 +65,10 @@ runs: env: runtime: ${{ inputs.runtime }} - - run: nextstrain update + # TODO: Remove this once https://github.com/nextstrain/cli/issues/318 is resolved. + - if: inputs.runtime == 'conda' + run: nextstrain update shell: bash - continue-on-error: true - run: nextstrain version --verbose shell: bash From 6fc4427232c4be3bcc2a1e233e8c8dc3fb02e2b7 Mon Sep 17 00:00:00 2001 From: Victor Lin <13424970+victorlin@users.noreply.github.com> Date: Mon, 25 Sep 2023 14:26:19 -0700 Subject: [PATCH 2/2] pathogen-repo-ci: Update ref for setup-nextstrain-cli --- .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 60fd2ab..e9ffe4f 100644 --- a/.github/workflows/pathogen-repo-ci.yaml +++ b/.github/workflows/pathogen-repo-ci.yaml @@ -229,7 +229,7 @@ jobs: # future changes to setup-nextstrain-cli. # # -trs, 28 April 2022 - - uses: nextstrain/.github/actions/setup-nextstrain-cli@1fbb3f2e3bf29374d2706f720f65d4025853a89a + - uses: nextstrain/.github/actions/setup-nextstrain-cli@4366771cea2482d31395ad9b5d351b950daa798d with: runtime: ${{ matrix.runtime }} # Consider parameterizing the Python version. -trs, 1 April 2022