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fix: require toposort >= 1.10 #2145

Merged
merged 3 commits into from
Feb 28, 2023
Merged

fix: require toposort >= 1.10 #2145

merged 3 commits into from
Feb 28, 2023

Commits on Feb 28, 2023

  1. fix: require toposort >= 1.10 

    closes #2134, speeds up DAG resolution
    @dlaehnemann
    dlaehnemann committed Feb 28, 2023
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  2. also require toposort >=1.10 in test-environment.yml

    @dlaehnemann
    dlaehnemann committed Feb 28, 2023
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  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:
actions/runner-images#675 (comment)

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.
```
    @dlaehnemann
    dlaehnemann committed Feb 28, 2023
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