Merge branch 'main' into develop

Author: ielis

README.md

@@ -33,15 +33,15 @@ a *Library user guide*, and the *Javadoc API documentation*.
 
 The documentation is published in two documentation branches:
 - **stable**: corresponds to the latest published release, and generally also to the last commit of the `main` Git branch
-  - [Tutorial](http://phenopackets.org/phenopacket-tools/stable/tutorial.html)
-  - [CLI user guide](http://phenopackets.org/phenopacket-tools/stable/cli.html)
-  - [Library user guide](http://phenopackets.org/phenopacket-tools/stable)
-  - [Javadoc API documentation](http://phenopackets.org/phenopacket-tools/stable/apidocs)
+  - [Tutorial](https://phenopackets.github.io/phenopacket-tools/stable/tutorial.html)
+  - [CLI user guide](https://phenopackets.github.io/phenopacket-tools/stable/cli.html)
+  - [Library user guide](https://phenopackets.github.io/phenopacket-tools/stable)
+  - [Javadoc API documentation](https://phenopackets.github.io/phenopacket-tools/stable/apidocs)
 - **latest**: corresponds to the bleeding edge code that is on the `develop` Git branch
-  - [Tutorial](http://phenopackets.org/phenopacket-tools/latest/tutorial.html)
-  - [CLI user guide](http://phenopackets.org/phenopacket-tools/latest/cli.html)
-  - [Library user guide](http://phenopackets.org/phenopacket-tools/latest)
-  - [Javadoc API documentation](http://phenopackets.org/phenopacket-tools/latest/apidocs)  
+  - [Tutorial](https://phenopackets.github.io/phenopacket-tools/latest/tutorial.html)
+  - [CLI user guide](https://phenopackets.github.io/phenopacket-tools/latest/cli.html)
+  - [Library user guide](https://phenopackets.github.io/phenopacket-tools/latest)
+  - [Javadoc API documentation](https://phenopackets.github.io/phenopacket-tools/latest/apidocs)  
 
 ## Issues
 

docs/converting.rst

@@ -44,5 +44,5 @@ See also
 ^^^^^^^^
 
 The API documentation of the conversion functionality is located in the
-`org.phenopackets.phenopackettools.converter <http://phenopackets.org/phenopacket-tools/apidocs/org.phenopackets.phenopackettools.converter/module-summary.html>`_
+`org.phenopackets.phenopackettools.converter <https://phenopackets.github.io/phenopacket-tools/apidocs/org.phenopackets.phenopackettools.converter/module-summary.html>`_
 module.

docs/creating.rst

@@ -12,7 +12,7 @@ of the phenopacket framework will want to use a recommended set of ontology term
 the equivalent message.
 
 This section exemplifies usage of `PhenotypicFeatureBuilder`, one of many builders provided by the
-`org.phenopackets.phenopackettools.builder <http://phenopackets.org/phenopacket-tools/apidocs/org.phenopackets.phenopackettools.builder/module-summary.html>`_
+`org.phenopackets.phenopackettools.builder <https://phenopackets.github.io/phenopacket-tools/apidocs/org.phenopackets.phenopackettools.builder/module-summary.html>`_
 module.
 
 
@@ -89,7 +89,7 @@ See also
 ========
 
 See the API documentation of the
-`org.phenopackets.phenopackettools.builder <http://phenopackets.org/phenopacket-tools/apidocs/org.phenopackets.phenopackettools.builder/module-summary.html>`_
+`org.phenopackets.phenopackettools.builder <https://phenopackets.github.io/phenopacket-tools/apidocs/org.phenopackets.phenopackettools.builder/module-summary.html>`_
 module for a comprehensive list of ontology constants, convenience methods, and builders provided
 by the *phenopacket-tools* library.
 

docs/validation.rst

@@ -185,7 +185,7 @@ and the discovered issues (if any):
 
 
 The API documentation of the core validation API can be found in the
-`org.phenopackets.phenopackettools.validator.core <http://phenopackets.org/phenopacket-tools/apidocs/org.phenopackets.phenopackettools.validator.core/module-summary.html>`_
+`org.phenopackets.phenopackettools.validator.core <https://phenopackets.github.io/phenopacket-tools/apidocs/org.phenopackets.phenopackettools.validator.core/module-summary.html>`_
 module.
 
 
@@ -327,7 +327,7 @@ because an annotation with a specific HPO term (e.g., a patient with perimembran
 
 In this section, we describe validators that use HPO file to perform several checks that can be useful in many contexts.
 The API documentation and the corresponding Java classes can be found in
-`org.phenopackets.phenopackettools.validator.core.phenotype <http://phenopackets.org/phenopacket-tools/apidocs/org.phenopackets.phenopackettools.validator.core/org/phenopackets/phenopackettools/validator/core/phenotype/package-summary.html>`_
+`org.phenopackets.phenopackettools.validator.core.phenotype <https://phenopackets.github.io/phenopacket-tools/apidocs/org.phenopackets.phenopackettools.validator.core/org/phenopackets/phenopackettools/validator/core/phenotype/package-summary.html>`_
 package.
 
 
@@ -446,7 +446,7 @@ See also
 ^^^^^^^^
 
 Check out the
-`org.phenopackets.phenopackettools.validator.core <http://phenopackets.org/phenopacket-tools/apidocs/org.phenopackets.phenopackettools.validator.core/module-summary.html>`_
+`org.phenopackets.phenopackettools.validator.core <https://phenopackets.github.io/phenopacket-tools/apidocs/org.phenopackets.phenopackettools.validator.core/module-summary.html>`_
 and
-`org.phenopackets.phenopackettools.validator.jsonschema <http://phenopackets.org/phenopacket-tools/apidocs/org.phenopackets.phenopackettools.validator.jsonschema/module-summary.html>`_
+`org.phenopackets.phenopackettools.validator.jsonschema <https://phenopackets.github.io/phenopacket-tools/apidocs/org.phenopackets.phenopackettools.validator.jsonschema/module-summary.html>`_
 modules for more information regarding the public validation API.

phenopacket-tools-cli/src/main/java/org/phenopackets/phenopackettools/cli/Main.java

@@ -38,7 +38,7 @@ public class Main {
             .optionParams(italic)
             .build();
 
-    public static final String FOOTER = "\nSee the full documentation at http://phenopackets.org/phenopacket-tools/stable\n";
+    public static final String FOOTER = "\nSee the full documentation at https://phenopackets.github.io/phenopacket-tools/stable\n";
 
     private Main() {
         // private no-op