dynverse / dyngen

Simulating single-cell data using gene regulatory networks 📠
https://dyngen.dynverse.org
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Require igraph version >=1.3.0 #48

Closed george-hall-ucl closed 2 years ago

george-hall-ucl commented 2 years ago

Hi,

Thank you for developing this nice set of packages! I recently hit up against a bug when using generate_dataset (more specifically, generate_feature_network), seeing the error message:

Error in igraph::bfs(., sample.int(ncol(realnet), 1), mode = "all") : 
  unused argument (mode = "all")

I was running igraph v1.2.9. Updating igraph to v1.3.0 fixed this bug. My patch makes the package require at least this version of igraph.

I'm afraid I've not been able to test properly since the process then crashes at a later stage, but I believe that this patch should at least fix the first problem!

Thanks, George

codecov[bot] commented 2 years ago

Codecov Report

Base: 66.22% // Head: 67.51% // Increases project coverage by +1.28% :tada:

Coverage data is based on head (8925de4) compared to base (d8acb23). Patch coverage: 66.66% of modified lines in pull request are covered.

:exclamation: Current head 8925de4 differs from pull request most recent head b47e84a. Consider uploading reports for the commit b47e84a to get more accurate results

Additional details and impacted files ```diff @@ Coverage Diff @@ ## master #48 +/- ## ========================================== + Coverage 66.22% 67.51% +1.28% ========================================== Files 23 23 Lines 2688 2687 -1 ========================================== + Hits 1780 1814 +34 + Misses 908 873 -35 ``` | [Impacted Files](https://codecov.io/gh/dynverse/dyngen/pull/48?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=dynverse) | Coverage Δ | | |---|---|---| | [R/7\_experiment.R](https://codecov.io/gh/dynverse/dyngen/pull/48/diff?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=dynverse#diff-Ui83X2V4cGVyaW1lbnQuUg==) | `74.28% <ø> (ø)` | | | [R/timings.R](https://codecov.io/gh/dynverse/dyngen/pull/48/diff?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=dynverse#diff-Ui90aW1pbmdzLlI=) | `25.00% <ø> (ø)` | | | [R/6\_simulation.R](https://codecov.io/gh/dynverse/dyngen/pull/48/diff?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=dynverse#diff-Ui82X3NpbXVsYXRpb24uUg==) | `79.11% <50.00%> (ø)` | | | [R/dimred.R](https://codecov.io/gh/dynverse/dyngen/pull/48/diff?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=dynverse#diff-Ui9kaW1yZWQuUg==) | `90.74% <100.00%> (-0.17%)` | :arrow_down: | | [R/0c\_backbone\_lego.R](https://codecov.io/gh/dynverse/dyngen/pull/48/diff?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=dynverse#diff-Ui8wY19iYWNrYm9uZV9sZWdvLlI=) | `53.21% <0.00%> (+20.46%)` | :arrow_up: | Help us with your feedback. Take ten seconds to tell us [how you rate us](https://about.codecov.io/nps?utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=dynverse). Have a feature suggestion? [Share it here.](https://app.codecov.io/gh/feedback/?utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=dynverse)

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rcannood commented 2 years ago

Thanks George!