From 70be4cf740d8de59e6b53cd864508f0a49672643 Mon Sep 17 00:00:00 2001 From: james hadfield Date: Tue, 5 Mar 2024 12:52:50 +1300 Subject: [PATCH] git subrepo pull (merge) ingest/vendored subrepo: subdir: "ingest/vendored" merged: "c0b4c6b" upstream: origin: "https://github.com/nextstrain/ingest" branch: "main" commit: "c0b4c6b" git-subrepo: version: "0.4.6" origin: "https://github.com/ingydotnet/git-subrepo" commit: "73a0129" --- ingest/vendored/.github/dependabot.yml | 17 +++++++++++++++++ ingest/vendored/.github/workflows/ci.yaml | 6 +++--- ingest/vendored/.gitrepo | 4 ++-- ingest/vendored/README.md | 15 +++++++++------ 4 files changed, 31 insertions(+), 11 deletions(-) create mode 100644 ingest/vendored/.github/dependabot.yml diff --git a/ingest/vendored/.github/dependabot.yml b/ingest/vendored/.github/dependabot.yml new file mode 100644 index 0000000..89bd084 --- /dev/null +++ b/ingest/vendored/.github/dependabot.yml @@ -0,0 +1,17 @@ +# Dependabot configuration file +# +# +# Each ecosystem is checked on a scheduled interval defined below. To trigger +# a check manually, go to +# +# https://github.com/nextstrain/ingest/network/updates +# +# and look for a "Check for updates" button. You may need to click around a +# bit first. +--- +version: 2 +updates: + - package-ecosystem: "github-actions" + directory: "/" + schedule: + interval: "weekly" diff --git a/ingest/vendored/.github/workflows/ci.yaml b/ingest/vendored/.github/workflows/ci.yaml index c6a218a..e75d828 100644 --- a/ingest/vendored/.github/workflows/ci.yaml +++ b/ingest/vendored/.github/workflows/ci.yaml @@ -11,13 +11,13 @@ jobs: shellcheck: runs-on: ubuntu-latest steps: - - uses: actions/checkout@v3 + - uses: actions/checkout@v4 - uses: nextstrain/.github/actions/shellcheck@master cram: runs-on: ubuntu-latest steps: - - uses: actions/checkout@v3 - - uses: actions/setup-python@v4 + - uses: actions/checkout@v4 + - uses: actions/setup-python@v5 - run: pip install cram - run: cram tests/ \ No newline at end of file diff --git a/ingest/vendored/.gitrepo b/ingest/vendored/.gitrepo index de1413c..25ea828 100644 --- a/ingest/vendored/.gitrepo +++ b/ingest/vendored/.gitrepo @@ -6,7 +6,7 @@ [subrepo] remote = https://github.com/nextstrain/ingest branch = main - commit = 7617c39fae05e5882c5e6c065c5b47d500c998af - parent = b0ee1497a4d1f471ec87529fd7913fb96fbdf032 + commit = c0b4c6bb5e6ccbba86374d2c09b42077768aac23 + parent = 28e9bc3cca47ecc42f032b7252672b2c7e74b8f4 method = merge cmdver = 0.4.6 diff --git a/ingest/vendored/README.md b/ingest/vendored/README.md index fa91891..2c14573 100644 --- a/ingest/vendored/README.md +++ b/ingest/vendored/README.md @@ -2,7 +2,7 @@ Shared internal tooling for pathogen data ingest. Used by our individual pathogen repos which produce Nextstrain builds. Expected to be vendored by -each pathogen repo using `git subtree`. +each pathogen repo using `git subrepo`. Some tools may only live here temporarily before finding a permanent home in `augur curate` or Nextstrain CLI. Others may happily live out their days here. @@ -12,6 +12,9 @@ Some tools may only live here temporarily before finding a permanent home in Nextstrain maintained pathogen repos will use [`git subrepo`](https://github.com/ingydotnet/git-subrepo) to vendor ingest scripts. (See discussion on this decision in https://github.com/nextstrain/ingest/issues/3) +For a list of Nextstrain repos that are currently using this method, use [this +GitHub code search](https://github.com/search?type=code&q=org%3Anextstrain+subrepo+%22remote+%3D+https%3A%2F%2Fgithub.com%2Fnextstrain%2Fingest%22). + If you don't already have `git subrepo` installed, follow the [git subrepo installation instructions](https://github.com/ingydotnet/git-subrepo#installation). Then add the latest ingest scripts to the pathogen repo by running: @@ -54,14 +57,14 @@ commit hash if needed. Much of this tooling originated in [ncov-ingest](https://github.com/nextstrain/ncov-ingest) and was passaged thru -[monkeypox's ingest/](https://github.com/nextstrain/monkeypox/tree/@/ingest/). -It subsequently proliferated from [monkeypox][] to other pathogen repos -([rsv][], [zika][], [dengue][], [hepatitisB][], [forecasts-ncov][]) primarily -thru copying. To [counter that +[mpox's ingest/](https://github.com/nextstrain/mpox/tree/@/ingest/). It +subsequently proliferated from [mpox][] to other pathogen repos ([rsv][], +[zika][], [dengue][], [hepatitisB][], [forecasts-ncov][]) primarily thru +copying. To [counter that proliferation](https://bedfordlab.slack.com/archives/C7SDVPBLZ/p1688577879947079), this repo was made. -[monkeypox]: https://github.com/nextstrain/monkeypox +[mpox]: https://github.com/nextstrain/mpox [rsv]: https://github.com/nextstrain/rsv [zika]: https://github.com/nextstrain/zika/pull/24 [dengue]: https://github.com/nextstrain/dengue/pull/10