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Release 2.0.0 RC3 #645

Merged
merged 108 commits into from
Dec 28, 2023
Merged

Release 2.0.0 RC3 #645

merged 108 commits into from
Dec 28, 2023

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ielis
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@ielis ielis commented Dec 28, 2023

Release candidate 3 where all APIs planned for removal are deprecated.

ielis and others added 30 commits April 7, 2023 14:43
@ielis
Next development iteration v2.0.0-RC3-SNAPSHOT.
7fb7225 
Signed-off-by: Daniel Danis <[email protected]>
@ielis
Update the pages.yml workflow and top-level POM Javadoc config.
886cf7d 
Signed-off-by: Daniel Danis <[email protected]>
@ielis
Update the workflow name, remove the other workflow.
1116de9 
Signed-off-by: Daniel Danis <[email protected]>
@ielis
Remove unnecessary parentheses.
ae2be92 
Signed-off-by: Daniel Danis <[email protected]>
@ielis
Merge pull request #608 from TheJacksonLaboratory/fix_docs_deployment
8318dfc 
Update the `pages.yml` workflow and top-level POM Javadoc config.
@ielis
We don't need to build the code to generate docs.
faf1036 
Signed-off-by: Daniel Danis <[email protected]>
@ielis
Update the repo after checking.
fa004f0 
Signed-off-by: Daniel Danis <[email protected]>
@ielis
Add javadoc options to CLI.
fe2d2fe 
Signed-off-by: Daniel Danis <[email protected]>
@ielis
Final touch to pages.yml workflow.
74db6ac 
Signed-off-by: Daniel Danis <[email protected]>
@iimpulse
fixing n/a on html templates
a92bc35
@ielis
Set the explanation to null to avoid showing genotype-related state…
ecba70d 
…ment when run in phenotype-only mode.

Signed-off-by: Daniel Danis <[email protected]>
@ielis
Merge pull request #612 from TheJacksonLaboratory/bug-610
4965889 
Fixing n/a on html templates
@ielis
Ignore results folder.
f793f4e 
Signed-off-by: Daniel Danis <[email protected]>
@ielis
Fix bugs in code for genotype-aware analysis starting from a YAML file.
30dbcff 
Signed-off-by: Daniel Danis <[email protected]>
@ielis
Merge pull request #613 from TheJacksonLaboratory/fix_yaml_genotype_code
7476461 
Fix code for genotype-aware analysis starting from a YAML file
@ielis
Deprecate --ddndv CLI option in favor of --sdwndv which we can ac…
471380f 
…tually turn off.

Signed-off-by: Daniel Danis <[email protected]>
@ielis
Describe changes to --ddndv and --sdwndv in the docs.
41ef034 
Signed-off-by: Daniel Danis <[email protected]>
@ielis
Halt the analysis if --ddndv option is used.
4131b7d 
Signed-off-by: Daniel Danis <[email protected]>
@ielis
Merge pull request #615 from TheJacksonLaboratory/fix_cli_bug
56e4532 
Fix `--ddndv` CLI bug
@ielis
We do not use apiguardian nor logback-classic in the test scope.
30aed4e 
Signed-off-by: Daniel Danis <[email protected]>
@ielis
Merge pull request #618 from TheJacksonLaboratory/clean_up_dependencies
0ce1a49 
Clean up dependencies
@ielis
Merge branch 'update_docs' into develop
c151171
@ielis
Fix NPE due to missing age occurring while writing the JSON output.
68436af 
Signed-off-by: Daniel Danis <[email protected]>
@ielis
Make Maven less verbose
9237e4d 
Signed-off-by: Daniel Danis <[email protected]>
@ielis
Simplify building aggregated docs.
66b60f2 
Signed-off-by: Daniel Danis <[email protected]>
@ielis
Merge pull request #621 from TheJacksonLaboratory/fix_age_npe
838a484 
Fix NPE due to missing age occurring while writing the JSON output.

Fixes #620
@ielis
Simplify TranscriptAnnotation implementation, use binary search to …
c2188b9 
…find gene ID.

Signed-off-by: Daniel Danis <[email protected]>
@ielis
Use lists and arrays instead of a map in GenotypedVariant implementat…
4746717 
…ion.

Signed-off-by: Daniel Danis <[email protected]>
@ielis
Merge pull request #622 from TheJacksonLaboratory/update_functional_a…
20114b1 
…nnotation

Simplify memory layout
@ielis
Add experimental phenopackets commands for running LIRICAL on a col…
dfb6dc1 
…lection of phenopackets.

Signed-off-by: Daniel Danis <[email protected]>
ielis added 28 commits December 22, 2023 10:02
@ielis
Tweak sanitation workflow.
77b4817
@ielis
Work out the workflow of the sample ID.
b9894d4
@ielis
Tweak benchmarking code.
aa9e425
@ielis
Polish validation policy.
fa25d39
@ielis
Simplify input validation in benchmark.
8555274
@ielis
The default validation policy is NONE to mimic the previous behavior.
82df799
@ielis
Update CLI options, remove unused function.
ade86cd
@ielis
MINIMAL is the most permissive validation policy where we check for >…
7f40583 
…0 terms, update the obsolete terms if necessary, and check VCF if present.
@ielis
Add docs section about input sanitation.
e28d3d4
@ielis
Log validation policy.
7012563
@ielis
Always report input sanitation results.
ad56661
@ielis
Improve the docs.
cdcc095
@ielis
Clarify the docs.
97e2f01
@ielis
Require phenol 2.0.5 or better.
a6f0adc
@ielis
Leverage phenol 2.0.5 to simplify JSON output analysis writer.
14173e0
@ielis
Merge pull request #641 from TheJacksonLaboratory/input-sanitation
f8ee662 
Input sanitation
@ielis
Fix permissive error catching, tweak logging filter, reword log messa…
01ce892 
…ges.
@ielis
Update README.
6febb4f
@ielis
Merge pull request #642 from TheJacksonLaboratory/update-readme
d4f4825 
Update README
@ielis
Wrap age in optional and disallow creating unknown age. Add javadocs.
28444a3
@ielis
Update Age docs.
3f68874
@ielis
Relax null criteria in the deprecated class.
5ea3709
@ielis
Add missing Jackson annotations to AnalysisData.
c3484e5
@ielis
Merge pull request #643 from TheJacksonLaboratory/streamline-age
30752c4 
Simplify handling of subject's age
@ielis
Move the phenopacket IO back to lirical-io.
20fb087
@ielis
Merge pull request #644 from TheJacksonLaboratory/move-phenopacket-io
7a5ceb2 
Return phenopacket IO code to `lirical-io`
@ielis
Make release 2.0.0-RC3.
07d410c
@ielis
Use latest logback.
3f27958
@ielis ielis merged commit d871901 into master Dec 28, 2023
3 checks passed
@ielis ielis deleted the release-2.0.0-RC3 branch December 28, 2023 20:31
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3 participants
@ielis @iimpulse @mabeckwith