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Change default representation of edge attributes from vectors to lists & other miscellaneous adjustments #274

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Change default representation of edge attributes from vectors to lists & other miscellaneous adjustments #274

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e3617b8
Replace deprecated igraph functions
maxloeffler Nov 8, 2024
f591528
Fix read.commit.interactions()
hechtlC Oct 24, 2024
4b0d522
Adjust `metrics.scale.freeness` to igraph changes
bockthom Oct 30, 2024
87911ad
Add range information to splits in 'split.network.time.based.by.ranges'
maxloeffler Nov 12, 2024
1c35d1f
Convert edge attributes to list
maxloeffler Dec 3, 2024
eda30b8
Adjust tests to expect edge attributes as lists
maxloeffler Dec 3, 2024
0c6b2eb
!TEMPORARY! replace NULLs in edge attributes with NA
maxloeffler Dec 3, 2024
44c7b72
Ensure missing edge attributes are filled with NA instead of NULL
maxloeffler Dec 3, 2024
7303eab
Add test for 'convert.edge.attributes.to.list'
maxloeffler Dec 4, 2024
260af89
Update 'NEWS.md'
maxloeffler Dec 16, 2024
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5 changes: 4 additions & 1 deletion NEWS.md
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Original file line number Diff line number Diff line change
Expand Up @@ -15,19 +15,22 @@
- Add commit network as a new type of network. It uses commits as vertices and connects them either via cochange or commit interactions. This includes adding new config parameters and the function `add.vertex.attribute.commit.network` for adding vertex attributes to a commit network (PR #263, ab73271781e8e9a0715f784936df4b371d64c338, ab73271781e8e9a0715f784936df4b371d64c338, cd9a930fcb54ff465c2a5a7c43cfe82ac15c134d)
- Add `remove.duplicate.edges` function that takes a network as input and conflates identical edges (PR #268, d9a4be417b340812b744f59398ba6460ba527e1c, 0c2f47c4fea6f5f2f582c0259f8cf23af985058a, c6e90dd9cb462232563f753f414da14a24b392a3)
- Add `cumulative` as an argument to `construct.ranges` which enables the creation of cumulative ranges from given revisions (PR #268, a135f6bb6f83ccb03ae27c735c2700fccc1ee0c8, 8ec207f1e306ef6a641fb0205a9982fa89c7e0d9)
- Add range information to network-splits when splitting a network using `split.network.time.based.by.ranges` (PR #274, 87911ade231c44b93be194a1d6734f7de043a4af)
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Please move this to the ## Fixed section, as this is actually a bug fix. And please also mention that this change also affects the function split.networks.time.based.


### Changed/Improved

- Change the default value for the `issues.from.source` configuration parameter. Instead of reading JIRA and GitHub issues together, which was the previous default, the new default value causes only GitHub issue data to be read. To restore the previous default behavior and read data from both issue sources, this now needs to be manually configured when needed. (PR #264, 5ff83c364f6bfc1e6ff95e9c5f1087e031c48a5d, 8c8080cb9caf115f19d9f145ad6e6c108b131a67, 8bcbc81db521877908d2e5c2989082ed672f2a3b)
- Replace deprecated `igraph` functions by their preferred alternatives (PR #264, PR #268, 0df9d5bf6bafbb5d440f4c47db4ec901cf11f037, 7ac840d287a862eff61b1a84e194a4cba399f9e5)
- Replace deprecated `igraph` functions by their preferred alternatives (PR #264, PR #268, PR #274 0df9d5bf6bafbb5d440f4c47db4ec901cf11f037, 7ac840d287a862eff61b1a84e194a4cba399f9e5, e3617b8c6b21fb4242c1d392124813501069ca84, 4b0d5221dd56bb3c9ddf196f67719d4f503d9b61)
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Missing comma after the inserted PR number.

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@bockthom bockthom Dec 16, 2024 •
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And: Please also add commit 4b0d5221dd56bb3c9ddf196f67719d4f503d9b61 (in addition to the current mention) to the fixes section to state that the functions metrics.scale.freeness and metrics.is.scale.free now are compatible with old and new igraph versions again (see the commit message as well as the "Announcement" regarding our previous release in our NEWS.md; due to this announcement, we also need to state that this fixed now).

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Is that still the case if we deprecate support for igraph versions below 2.1? I should probably add that somewhere in the NEWS.md I just haven't found a good place for it.

- Deprecate support for R version 3.6 (PR #264, c8e6f45111e487fadbe7f0a13c7595eb23f3af6e, fb3f5474259d4a88f4ff545691cca9d1ccde90e3)
- Explicitly add R version 4.4 to the CI test pipeline (c8e6f45111e487fadbe7f0a13c7595eb23f3af6e)
- Refactor function `construct.edge.list.from.key.value.list` to be more readable (PR #263, 05c3bc09cb1d396fd59c34a88030cdca58fd04dd)
- Change the default representation of edge attributes from vectors to lists. This change is necessary for the interplay of coronet networks with certain igraph functionality since igraph version 2.1. (PR #274, 1c35d1fa2548deb297dbfa5e2b07fce31962c5b7, eda30b838369ec46376812298a3ea8159eec5789, 44c7b72e3234cb332bb2713fb408c124e67255d9, 7303eabef6a78198575fe5bdfc02813fde3d3974)
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We might think about marking this as a **Breaking Change**:, as we also did for other changes in earlier releases.
What do you think, is this a breaking change or not? So, is there a possibility that "old code" that relies on coronet breaks or that reading networks generated with an old version of igraph now breaks, that is, old networks are not any more compatible with how we treat networks now? Actually, I am not sure about that.

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How I see it is that coronet in itself is consistent. So every action you can perform with it should work just as it did before. While networks created with older coronet versions may not necessarily be compatible with networks created with this version, I don't know how this should ever happen, if not through serializing an old network and now deserializing it. Apart from that, there should be no incompatibilities.


### Fixed

- Fix the creation of edgelists for issue-based artifact-networks by correctly iterating over the issue data (PR #264, 321d85043112971c04998249c14a0677a32c9004)
- Fix a bug in `extract.timestamps` that occurs when the first `data.source` contains empty data and that leads to a return value of type numeric which should be POSIXct (PR #270, 10696e4cf4ae92371917ed8ccaec2b0183da145c, 646c01a42ad8decfbc9040030e790e51cb65cffd)
- Fix `read.commit.interactions` by explicitly considering empty commit interaction data (PR #274, f591528a0f1f11b1a4390949ab770f3f74a766f9)
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empty commit interaction data ➡️ non-existent commit interactions

(for explanation: the commit-interaction data per se are present, but specific interactions between specific commits are empty, that is, non-existent)


## 4.4

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