From 099da34051cc19d2980bc417c30341f9d643e812 Mon Sep 17 00:00:00 2001 From: David Laehnemann Date: Tue, 28 Feb 2023 09:57:41 +0100 Subject: [PATCH 1/3] fix: require toposort >= 1.10 closes #2134, speeds up DAG resolution --- setup.cfg | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.cfg b/setup.cfg index 704828ba9..9340b3e1d 100644 --- a/setup.cfg +++ b/setup.cfg @@ -54,7 +54,7 @@ install_requires = stopit tabulate throttler - toposort + toposort >=1.10 wrapt yte >=1.0,<2.0 From 511daf9efce295ff9089956a9d75a1409153d042 Mon Sep 17 00:00:00 2001 From: David Laehnemann Date: Tue, 28 Feb 2023 10:00:30 +0100 Subject: [PATCH 2/3] also require toposort >=1.10 in test-environment.yml --- test-environment.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/test-environment.yml b/test-environment.yml index 865283fae..1019bfc9d 100644 --- a/test-environment.yml +++ b/test-environment.yml @@ -49,7 +49,7 @@ dependencies: - tibanna - environment-modules - nbformat - - toposort + - toposort >=1.10 - mamba - crc32c - pip From b16b5a1c1cce89bca6090083a28ac3ac40f3783d Mon Sep 17 00:00:00 2001 From: David Laehnemann Date: Tue, 28 Feb 2023 14:13:51 +0100 Subject: [PATCH 3/3] make sudo apt install stably choose the best mirror This should make this step stable against otherwise randomly recurring trouble with the azure mirror. The solution is given and explained here: https://github.com/actions/runner-images/issues/675#issuecomment-1419388451 Basically, this looks for the best mirror in US, where GitHub Actions seems to be hosted, and then updates to get the latest index from there. Hopefully, this consistently avoids failures like this one in the future: https://github.com/snakemake/snakemake/actions/runs/4291216092/jobs/7478626266#step:13:112 ``` sudo apt install -y stress git wget openmpi-bin libopenmpi-dev mariadb-server [...] Err:1 http://azure.archive.ubuntu.com/ubuntu jammy-updates/universe amd64 mariadb-common all 1:10.6.11-0ubuntu0.22.04.1 404 Not Found [IP: 40.81.13.82 80] Err:5 http://azure.archive.ubuntu.com/ubuntu jammy-updates/universe amd64 libmariadb3 amd64 1:10.6.11-0ubuntu0.22.04.1 404 Not Found [IP: 40.81.13.82 80] Err:6 http://azure.archive.ubuntu.com/ubuntu jammy-updates/universe amd64 mariadb-client-core-10.6 amd64 1:10.6.11-0ubuntu0.22.04.1 404 Not Found [IP: 40.81.13.82 80] Err:7 http://azure.archive.ubuntu.com/ubuntu jammy-updates/universe amd64 mariadb-client-10.6 amd64 1:10.6.11-0ubuntu0.22.04.1 404 Not Found [IP: 40.81.13.82 80] Err:12 http://azure.archive.ubuntu.com/ubuntu jammy-updates/universe amd64 mariadb-server-core-10.6 amd64 1:10.6.11-0ubuntu0.22.04.1 404 Not Found [IP: 40.81.13.82 80] Err:14 http://azure.archive.ubuntu.com/ubuntu jammy-updates/universe amd64 mariadb-server-10.6 amd64 1:10.6.11-0ubuntu0.22.04.1 404 Not Found [IP: 40.81.13.82 80] Err:41 http://azure.archive.ubuntu.com/ubuntu jammy-updates/universe amd64 mariadb-server all 1:10.6.11-0ubuntu0.22.04.1 404 Not Found [IP: 40.81.13.82 80] Fetched 12.2 MB in 12s (985 kB/s) E: Failed to fetch http://azure.archive.ubuntu.com/ubuntu/pool/universe/m/mariadb-10.6/mariadb-common_10.6.11-0ubuntu0.22.04.1_all.deb 404 Not Found [IP: 40.81.13.82 80] E: Failed to fetch http://azure.archive.ubuntu.com/ubuntu/pool/universe/m/mariadb-10.6/libmariadb3_10.6.11-0ubuntu0.22.04.1_amd64.deb 404 Not Found [IP: 40.81.13.82 80] E: Failed to fetch http://azure.archive.ubuntu.com/ubuntu/pool/universe/m/mariadb-10.6/mariadb-client-core-10.6_10.6.11-0ubuntu0.22.04.1_amd64.deb 404 Not Found [IP: 40.81.13.82 80] E: Failed to fetch http://azure.archive.ubuntu.com/ubuntu/pool/universe/m/mariadb-10.6/mariadb-client-10.6_10.6.11-0ubuntu0.22.04.1_amd64.deb 404 Not Found [IP: 40.81.13.82 80] E: Failed to fetch http://azure.archive.ubuntu.com/ubuntu/pool/universe/m/mariadb-10.6/mariadb-server-core-10.6_10.6.11-0ubuntu0.22.04.1_amd64.deb 404 Not Found [IP: 40.81.13.82 80] E: Failed to fetch http://azure.archive.ubuntu.com/ubuntu/pool/universe/m/mariadb-10.6/mariadb-server-10.6_10.6.11-0ubuntu0.22.04.1_amd64.deb 404 Not Found [IP: 40.81.13.82 80] E: Failed to fetch http://azure.archive.ubuntu.com/ubuntu/pool/universe/m/mariadb-10.6/mariadb-server_10.6.11-0ubuntu0.22.04.1_all.deb 404 Not Found [IP: 40.81.13.82 80] E: Unable to fetch some archives, maybe run apt-get update or try with --fix-missing? Error: Process completed with exit code 100. ``` --- .github/workflows/main.yml | 3 +++ 1 file changed, 3 insertions(+) diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml index 25aba9a96..11d8f5bc1 100644 --- a/.github/workflows/main.yml +++ b/.github/workflows/main.yml @@ -169,6 +169,9 @@ jobs: mamba install -n snakemake "singularity<=3.8.6" - name: Setup apt dependencies run: | + sudo gem install apt-spy2 + sudo apt-spy2 fix --commit --launchpad --country=US + sudo apt-get update sudo apt install -y stress git wget openmpi-bin libopenmpi-dev mariadb-server - name: Setup iRODS run: |