rust-bio / rust-bio / 5410113412
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fix: include `doctests` in the test coverage of code that tarpaulin calculates (#533)

* fix: update deprecated alias `--all` to new argument `--workspace`

* fix: include `doctests` in test coverage calculation, see https://github.com/xd009642/tarpaulin/issues/538#issuecomment-675921588

* try fixing failing doctest compilation during coverage estimation by copying rust-htslib approach

* make coverage CI step identical to rust-htslib setup

* remove unused / inexistent tarpaulin option

* try updating rust-cache action to address save-state deprecation warning

* add `--verbose` and `--debug` to tarpaulin, to figure out doctest failures

* fix newick doctest

* remove caching for coverage calculation, as this uses nightly

for nightly, caching is not very useful, see:
https://github.com/marketplace/actions/rust-cache#cache-effectiveness

* revert installation of deps that was only added for identical syntax with rust-htslib

these are probably not needed...

* remove debugging output from tarpaulin CI step and put `--workspace` argument back in

* increase tarpaulin timeout for tests to 5 minutes (instead of 1 minute for default)

* increase `--timeout` back to the original 10 minutes

* allow tarpaulin multithreading and increase --timeout to 15 minutes

* make code coverage CI step run only after successful testing, increase --timeout for it to 30 minutes

* do not run bio::io::fastq doctests that read from stdin

* exclude all doctests that read from io::stdin() from being run (they are still compiled)

* reduce tarpaulin --timeout back to 5 minutes, put needs: back to Formatting

4318 of 5067 relevant lines covered (85.22%)

7.59 hits per line

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ID Job ID Ran Files Coverage
1 5410113412.1 65
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Source Files on build 5410113412