From 1195b2a0e5cdfadd601e91ff3df2b45bb5b61aae Mon Sep 17 00:00:00 2001 From: Angie Hinrichs Date: Tue, 2 Jul 2024 11:07:10 -0700 Subject: [PATCH 1/6] Add entries for pangolin-data/-assignment 1.28.1 --- pangolin/data/data_compatibility.csv | 4 ---- 1 file changed, 4 deletions(-) diff --git a/pangolin/data/data_compatibility.csv b/pangolin/data/data_compatibility.csv index 0d77819..a871faa 100644 --- a/pangolin/data/data_compatibility.csv +++ b/pangolin/data/data_compatibility.csv @@ -1,6 +1,4 @@ data_source,version,min_pangolin_version,min_scorpio_version -pangolin-data,1.30,4.3, -pangolin-data,1.29,4.3, pangolin-data,1.28.1,4.3, pangolin-data,1.28,4.3, pangolin-data,1.27,4.3, @@ -29,8 +27,6 @@ pangolin-data,1.6,4, pangolin-data,1.3,4, pangolin-data,1.2.133,4, pangolin-data,1.2.127,4, -pangolin-assignment,1.30,4.3, -pangolin-assignment,1.29,4.3, pangolin-assignment,1.28.1,4.3, pangolin-assignment,1.28,4.3, pangolin-assignment,1.27,4.3, From fde1a27da0e633e53470d117e207ab87a6f1a36e Mon Sep 17 00:00:00 2001 From: Angie Hinrichs Date: Fri, 9 Aug 2024 10:44:43 -0700 Subject: [PATCH 2/6] Add entries for pangolin-data/-assignment 1.28.1 (#547) From 4265113519854f36f6d7f4ed04d67f344b9e9776 Mon Sep 17 00:00:00 2001 From: Angie Hinrichs Date: Mon, 29 Jul 2024 18:52:59 -0700 Subject: [PATCH 3/6] Add entries for pangolin-data/-assignment 1.29 --- pangolin/data/data_compatibility.csv | 2 ++ 1 file changed, 2 insertions(+) diff --git a/pangolin/data/data_compatibility.csv b/pangolin/data/data_compatibility.csv index a871faa..669f26b 100644 --- a/pangolin/data/data_compatibility.csv +++ b/pangolin/data/data_compatibility.csv @@ -1,4 +1,5 @@ data_source,version,min_pangolin_version,min_scorpio_version +pangolin-data,1.29,4.3, pangolin-data,1.28.1,4.3, pangolin-data,1.28,4.3, pangolin-data,1.27,4.3, @@ -27,6 +28,7 @@ pangolin-data,1.6,4, pangolin-data,1.3,4, pangolin-data,1.2.133,4, pangolin-data,1.2.127,4, +pangolin-assignment,1.29,4.3, pangolin-assignment,1.28.1,4.3, pangolin-assignment,1.28,4.3, pangolin-assignment,1.27,4.3, From cf955584251d1f3e776a68252c89bc20a96f2e5f Mon Sep 17 00:00:00 2001 From: Angie Hinrichs Date: Sun, 22 Sep 2024 15:24:47 -0700 Subject: [PATCH 4/6] Add entries for pangolin-data/-assignment 1.30 --- pangolin/data/data_compatibility.csv | 2 ++ 1 file changed, 2 insertions(+) diff --git a/pangolin/data/data_compatibility.csv b/pangolin/data/data_compatibility.csv index 669f26b..0d77819 100644 --- a/pangolin/data/data_compatibility.csv +++ b/pangolin/data/data_compatibility.csv @@ -1,4 +1,5 @@ data_source,version,min_pangolin_version,min_scorpio_version +pangolin-data,1.30,4.3, pangolin-data,1.29,4.3, pangolin-data,1.28.1,4.3, pangolin-data,1.28,4.3, @@ -28,6 +29,7 @@ pangolin-data,1.6,4, pangolin-data,1.3,4, pangolin-data,1.2.133,4, pangolin-data,1.2.127,4, +pangolin-assignment,1.30,4.3, pangolin-assignment,1.29,4.3, pangolin-assignment,1.28.1,4.3, pangolin-assignment,1.28,4.3, From b49546ec2cc5b00fbb6a492dbde32311f86c71e5 Mon Sep 17 00:00:00 2001 From: Angie Hinrichs Date: Thu, 21 Nov 2024 13:10:59 -0800 Subject: [PATCH 5/6] Add entries for pangolin-data/-assignment 1.31 --- pangolin/data/data_compatibility.csv | 2 ++ 1 file changed, 2 insertions(+) diff --git a/pangolin/data/data_compatibility.csv b/pangolin/data/data_compatibility.csv index 0d77819..23c181e 100644 --- a/pangolin/data/data_compatibility.csv +++ b/pangolin/data/data_compatibility.csv @@ -1,4 +1,5 @@ data_source,version,min_pangolin_version,min_scorpio_version +pangolin-data,1.31,4.3, pangolin-data,1.30,4.3, pangolin-data,1.29,4.3, pangolin-data,1.28.1,4.3, @@ -29,6 +30,7 @@ pangolin-data,1.6,4, pangolin-data,1.3,4, pangolin-data,1.2.133,4, pangolin-data,1.2.127,4, +pangolin-assignment,1.31,4.3, pangolin-assignment,1.30,4.3, pangolin-assignment,1.29,4.3, pangolin-assignment,1.28.1,4.3, From d6b132359eecd84c3763b57b0f77a3621d5592e7 Mon Sep 17 00:00:00 2001 From: Angie Hinrichs Date: Thu, 21 Nov 2024 13:19:18 -0800 Subject: [PATCH 6/6] Get workflows running again * Remove conda-version setting because it constrained python to 3.10 or 3.11 but that caused a conflict with a pinned python 3.12. * pangolin_macos.yml needs setup-miniconda@v2 for now because it sets architecture to x86_64, and setup-miniconda@v3 uses arm64 which is not working for usher yet. pangolin_macos.yml also needs to set miniconda-version to latest so conda installation doesn't fail. --- .github/workflows/pangolin.yml | 6 ++---- .github/workflows/pangolin_macos.yml | 5 ++--- 2 files changed, 4 insertions(+), 7 deletions(-) diff --git a/.github/workflows/pangolin.yml b/.github/workflows/pangolin.yml index 8d297d8..3dc2aea 100644 --- a/.github/workflows/pangolin.yml +++ b/.github/workflows/pangolin.yml @@ -12,14 +12,12 @@ jobs: matrix: os: ["ubuntu-latest"] steps: - - uses: actions/checkout@v2 - - uses: conda-incubator/setup-miniconda@v2 + - uses: actions/checkout@v4 + - uses: conda-incubator/setup-miniconda@v3 with: environment-file: environment.yml activate-environment: pangolin channels: conda-forge,bioconda,defaults - conda-version: "23.5.0" - mamba-version: "*" - name: Install pangolin run: pip install -e . - name: Check pangolin version diff --git a/.github/workflows/pangolin_macos.yml b/.github/workflows/pangolin_macos.yml index d5a1aaf..c719c2c 100644 --- a/.github/workflows/pangolin_macos.yml +++ b/.github/workflows/pangolin_macos.yml @@ -12,14 +12,13 @@ jobs: matrix: os: ["macos-latest"] steps: - - uses: actions/checkout@v2 + - uses: actions/checkout@v4 - uses: conda-incubator/setup-miniconda@v2 with: environment-file: environment.yml activate-environment: pangolin channels: conda-forge,bioconda,defaults - conda-version: "23.5.0" - mamba-version: "*" + miniconda-version: "latest" - name: Install pangolin run: pip install -e . - name: Check pangolin version