fix: require toposort >= 1.10 #2145
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closes #2134, speeds up DAG resolution
johanneskoester
approved these changes
Feb 28, 2023
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. ```
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johanneskoester
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Mar 1, 2023
🤖 I have created a release *beep* *boop* --- ## [7.24.0](v7.23.1...v7.24.0) (2023-03-01) ### Features * limit the number of input/output files in job properties ([#2149](#2149)) ([d93f091](d93f091)) ### Bug Fixes * [#2130](#2130) by patching the protect() method so the path of files in subdirectories is properly resolved during write-protection ([#2131](#2131)) ([1a754fd](1a754fd)) * `sre_constants` import because of deprecation ([#2139](#2139)) ([3b326db](3b326db)) * ensure user and group rw permissions for metadata files and source cache ([#2132](#2132)) ([cc51faa](cc51faa)) * is_run error with local, group jobs ([#2133](#2133)) ([31bfcd5](31bfcd5)) * require toposort >= 1.10 ([#2145](#2145)) ([3cb54b8](3cb54b8)) ### Documentation * Update modularization.rst ([#2137](#2137)) ([16954c7](16954c7)) --- This PR was generated with [Release Please](https://github.com/googleapis/release-please). See [documentation](https://github.com/googleapis/release-please#release-please). Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
dlaehnemann
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Mar 3, 2023
…of dag sorting Follow-up to [snakemake pull request 2145](snakemake/snakemake#2145), which addresses [snakemake issue 2134](snakemake/snakemake#2134), via the [toposort merge request 4 that gives a 200x speedup in DAG sorting](https://gitlab.com/ericvsmith/toposort/-/merge_requests/4).
BiocondaBot
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Mar 3, 2023
Merge PR #39729, commits were: * Merge branch 'master' into snakemake-require-latest-toposort * Merge branch 'master' into snakemake-require-latest-toposort * snakemake-minimal: require latest toposort `>=1.10` for 200x speedup of dag sorting Follow-up to [snakemake pull request 2145](snakemake/snakemake#2145), which addresses [snakemake issue 2134](snakemake/snakemake#2134), via the [toposort merge request 4 that gives a 200x speedup in DAG sorting](https://gitlab.com/ericvsmith/toposort/-/merge_requests/4).
cokelaer
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Apr 28, 2023
Merge PR bioconda#39729, commits were: * Merge branch 'master' into snakemake-require-latest-toposort * Merge branch 'master' into snakemake-require-latest-toposort * snakemake-minimal: require latest toposort `>=1.10` for 200x speedup of dag sorting Follow-up to [snakemake pull request 2145](snakemake/snakemake#2145), which addresses [snakemake issue 2134](snakemake/snakemake#2134), via the [toposort merge request 4 that gives a 200x speedup in DAG sorting](https://gitlab.com/ericvsmith/toposort/-/merge_requests/4).
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Closes #2134, speeds up DAG resolution through pulling in the latest
toposortthat leads to a 200x speedup of thetoposort()function for larger DAGs, see:https://gitlab.com/ericvsmith/toposort/-/merge_requests/4
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QC
docs/) is updated to reflect the changes or this is not necessary (e.g. if the change does neither modify the language nor the behavior or functionalities of Snakemake).