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Fix broken documentation links#202

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ielis wants to merge 54 commits intomainfrom
fix-broken-doc-links
Closed

Fix broken documentation links#202
ielis wants to merge 54 commits intomainfrom
fix-broken-doc-links

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@ielis ielis commented Feb 17, 2026

Fix the broken links and deploy the documentation to Github Pages.

ielis added 30 commits April 25, 2023 11:50
@ielis
Next development iteration v1.0.0-RC4-SNAPSHOT.
3124feb 
Signed-off-by: Daniel Danis <daniel.gordon.danis@protonmail.com>
@ielis
Merge pull request #183 from ielis/develop
71c6a2e 
Next development iteration
@ielis
Add molecule context to the variation descriptor during conversion fr…
03de2a9 
…om v1.

Signed-off-by: Daniel Danis <daniel.gordon.danis@protonmail.com>
@ielis
Improve handling of the VcfRecord filter field.
3cc54e1 
Signed-off-by: Daniel Danis <daniel.gordon.danis@protonmail.com>
@ielis
Add missing VCF info field.
6cf109f 
Signed-off-by: Daniel Danis <daniel.gordon.danis@protonmail.com>
@ielis
Fix conversion test.
b477d3f 
Signed-off-by: Daniel Danis <daniel.gordon.danis@protonmail.com>
@ielis
Merge pull request #185 from ielis/fix_variant_conversion
4869dc3 
Include VCF info field in v1 -> v2 conversion, improve handling of VCF filter fields in phenopacket builder
@ielis
The conversion code should not set default instances to a field in ca…
f9a0219 
…se the field is missing in the v1 message.

Signed-off-by: Daniel Danis <daniel.gordon.danis@protonmail.com>
@ielis
Fix bug in PhenotypicFeatureConverter.
10e6420 
Signed-off-by: Daniel Danis <daniel.gordon.danis@protonmail.com>
@ielis
Merge pull request #187 from ielis/conversion_subtleties
930c3c3 
Fix conversion subtleties
@ielis
Add instructions for validation results serialization.
70c79bd 
Signed-off-by: Daniel Danis <daniel.gordon.danis@protonmail.com>
@ielis
phenopacket-tools-validator-jsonschema requires `phenopacket.schema…
eb2f991 
…` in a transitive fashion.

Signed-off-by: Daniel Danis <daniel.gordon.danis@protonmail.com>
@ielis
Try to be portable with Windows.
f3dbf59 
Signed-off-by: Daniel Danis <daniel.gordon.danis@protonmail.com>
@ielis
Merge pull request #188 from ielis/add_json_annotations
ac1fc24 
Enable JSON serialization for validation results
@ielis
Add message utils package into phenopacket-tools-util.
56f605c 
Signed-off-by: Daniel Danis <daniel.gordon.danis@protonmail.com>
@ielis
Merge pull request #189 from ielis/message_utils
41c3734 
Add package with utility functions for working with protobuf messages
@ielis
Use phenol 2.0.2. Use MinimalOntology and the new graph API inste…
5516c33 
…ad of `Ontology` and `OntologyAlgorithm`.

Signed-off-by: Daniel Danis <daniel.gordon.danis@protonmail.com>
@ielis
Run CI using mvnw.
b770324 
Signed-off-by: Daniel Danis <daniel.gordon.danis@protonmail.com>
@ielis
Merge pull request #190 from ielis/update-phenol
e6fb479 
Use phenol `2.0.2`
@ielis
Check that phenotypic features are present at most once.
7a431fc 
Signed-off-by: Daniel Danis <daniel.gordon.danis@protonmail.com>
@ielis
Remove unused conf.py parts.
848e357 
Signed-off-by: Daniel Danis <daniel.gordon.danis@protonmail.com>
@ielis
Add unique validator into the standard validation pipeline.
11a452a 
Signed-off-by: Daniel Danis <daniel.gordon.danis@protonmail.com>
@ielis
Update changelog.
539ce11 
Signed-off-by: Daniel Danis <daniel.gordon.danis@protonmail.com>
@ielis
Merge pull request #191 from ielis/check-phenotypic-features-are-unique
3db71e5 
Check phenotypic features are unique
@ielis
Check Age is a valid ISO8601 period string.
53c9733 
Signed-off-by: Daniel Danis <daniel.gordon.danis@protonmail.com>
@ielis
Merge pull request #193 from ielis/validate-iso8601
b911773 
Validate ISO8601 period strings
@ielis
Ignore venv.
1ba1d94
@ielis
Update action step versions.
e469eb0
@ielis
Update the documentation links.
8c809c7
@ielis
Update Maven and several plugins.
5551bd7
@ielis ielis changed the base branch from develop to main February 17, 2026 15:54
ielis added 23 commits February 17, 2026 16:56
@ielis
Add molecule context to the variation descriptor during conversion fr…
436c876 
…om v1.

Signed-off-by: Daniel Danis <daniel.gordon.danis@protonmail.com>
@ielis
Improve handling of the VcfRecord filter field.
3ebfe57 
Signed-off-by: Daniel Danis <daniel.gordon.danis@protonmail.com>
@ielis
Add missing VCF info field.
2dfd635 
Signed-off-by: Daniel Danis <daniel.gordon.danis@protonmail.com>
@ielis
Fix conversion test.
b85416d 
Signed-off-by: Daniel Danis <daniel.gordon.danis@protonmail.com>
@ielis
The conversion code should not set default instances to a field in ca…
bc12ca7 
…se the field is missing in the v1 message.

Signed-off-by: Daniel Danis <daniel.gordon.danis@protonmail.com>
@ielis
Fix bug in PhenotypicFeatureConverter.
b979e3e 
Signed-off-by: Daniel Danis <daniel.gordon.danis@protonmail.com>
@ielis
Add instructions for validation results serialization.
44debbf 
Signed-off-by: Daniel Danis <daniel.gordon.danis@protonmail.com>
@ielis
phenopacket-tools-validator-jsonschema requires `phenopacket.schema…
6a75ba3 
…` in a transitive fashion.

Signed-off-by: Daniel Danis <daniel.gordon.danis@protonmail.com>
@ielis
Try to be portable with Windows.
d9dabb6 
Signed-off-by: Daniel Danis <daniel.gordon.danis@protonmail.com>
@ielis
Add message utils package into phenopacket-tools-util.
e7e9991 
Signed-off-by: Daniel Danis <daniel.gordon.danis@protonmail.com>
@ielis
Use phenol 2.0.2. Use MinimalOntology and the new graph API inste…
50f93ae 
…ad of `Ontology` and `OntologyAlgorithm`.

Signed-off-by: Daniel Danis <daniel.gordon.danis@protonmail.com>
@ielis
Run CI using mvnw.
c5a9b81 
Signed-off-by: Daniel Danis <daniel.gordon.danis@protonmail.com>
@ielis
Check that phenotypic features are present at most once.
f6ca2f9 
Signed-off-by: Daniel Danis <daniel.gordon.danis@protonmail.com>
@ielis
Remove unused conf.py parts.
59c49e1 
Signed-off-by: Daniel Danis <daniel.gordon.danis@protonmail.com>
@ielis
Add unique validator into the standard validation pipeline.
7952210 
Signed-off-by: Daniel Danis <daniel.gordon.danis@protonmail.com>
@ielis
Update changelog.
155bca4 
Signed-off-by: Daniel Danis <daniel.gordon.danis@protonmail.com>
@ielis
Check Age is a valid ISO8601 period string.
d88585d 
Signed-off-by: Daniel Danis <daniel.gordon.danis@protonmail.com>
@ielis
Ignore venv.
42c878b
@ielis
Update action step versions.
5219119
@ielis
Update the documentation links.
bf4ea5c
@ielis
Update Maven and several plugins.
2448374
@ielis
Update HPO test resource.
ba1a4ba
@ielis
Merge remote-tracking branch 'origin/fix-broken-doc-links' into fix-b…
4ae3a89 
…roken-doc-links
@ielis ielis closed this Feb 17, 2026
@ielis ielis deleted the fix-broken-doc-links branch February 17, 2026 15:57
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