Closed daemontus closed 3 years ago
Merging #9 (e47f246) into master (f11a06f) will decrease coverage by
0.29%
. The diff coverage is73.91%
.
@@ Coverage Diff @@
## master #9 +/- ##
==========================================
- Coverage 84.93% 84.63% -0.30%
==========================================
Files 29 29
Lines 1859 1901 +42
==========================================
+ Hits 1579 1609 +30
- Misses 280 292 +12
Impacted Files | Coverage Δ | |
---|---|---|
src/sbml/mod.rs | 73.09% <73.91%> (-0.16%) |
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Good point, since this will close #1, I have created #10 as a reminder to refactor this. However, we should also seriously think about extending aeon model format with stuff like input/output/constant, better handling of explicit parameters, variable annotations, etc. because there are things we can't really import at the moment...
This PR extends #7 and resolves several new problems discovered when using the SBML parser.
and/or
tags with only one argument. This previously caused an error, but now these useless tags are simply ignored.xml-rs
contains a bug that considers strings with value/>
to be invalid. Such strings appear in SBML models when HTML formatting is included in annotations/notes. Thankfully, a pull request for this issue exists, but is not released yet. So for the time being, we switch to the fork where the bug is already fixed. Once the issue is resolved, we can move back to depending onxml-rs
.Overall, this pull request closes all major issues with SBML parsing that I am aware of (So far, I haven't found any problematic SBML model in ginsim/cellcollective databases). It is therefore related to #1, however, I still don't believe the issue should be closed because: a) I am expecting further problems as more models are tested, the issue will track those. b) The SBML parser is still a poorly designed and poorly tested heap of garbage. We really need a better way to handle it. However, it will probably also require minor changes to the
.aeon
text format.