Release v1.0.0-RC3.

Signed-off-by: Daniel Danis <daniel.gordon.danis@protonmail.com>

Author: ielis

CHANGELOG.rst

@@ -6,8 +6,11 @@ Changelog
 -----
 
 * Update predefined constants, convenience functions and builders
-* Improve user guide, tutorial, and documentation
+* Improve user guide, tutorial, and documentation.
+  * Introduce *latest* and *stable* documentation branches
+  * Add showcase of apps that use phenopacket-tools to add more code examples
 * Run `MetaDataValidator` during base validation
+* Finalize JSON and YAML format sniffing
 * Fix example phenopackets
 
 0.4.7

README.md

@@ -15,27 +15,33 @@ as the adherence to additional user-defined requirements.
 
 ## Availability
 
-Most users should download the latest distribution archive from the [Releases page](https://github.com/phenopackets/phenopacket-tools/releases).
-Alternatively, *phenopacket-tools* can be built from source, as described in the user guide.
+### CLI application
 
-## Documentation
+A ZIP file with prebuilt CLI application is available for download from the [Releases page](https://github.com/phenopackets/phenopacket-tools/releases).
+Alternatively, the application can be built from source, as described in the library user guide (see the links below).
+
+### Library
 
-We provide the documentation for the latest release (`stable`) as well as the development version (`latest`).  
+We provide *phenopacket-tools* library for use in JVM-based applications. 
+We publish the JAR artifacts to public [Maven central](https://mvnrepository.com/artifact/org.phenopackets.phenopackettools) 
+repository, and we make the Javadoc API documentation available for the *latest.
+
+## Documentation
 
-The documentation includes a *Tutorial* showing how to use the CLI, a comprehensive *CLI user guide*, 
+We provide documentation with a *Tutorial* showing how to use the CLI, a comprehensive *CLI user guide*,
 a *Library user guide*, and the *Javadoc API documentation*.
 
-**Stable**
-- [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)
-
-**Latest**
-- [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)
+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)
+- **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)  
 
 ## Issues
 

docs/conf.py

@@ -33,7 +33,7 @@
 # The short X.Y version.
 version = '1.0'
 # The full version, including alpha/beta/rc tags.
-release = '1.0.0-RC3-SNAPSHOT'
+release = '1.0.0-RC3'
 
 # -- General configuration ---------------------------------------------------
 # https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration

phenopacket-tools-builder/pom.xml

@@ -7,7 +7,7 @@
     <parent>
         <groupId>org.phenopackets.phenopackettools</groupId>
         <artifactId>phenopacket-tools</artifactId>
-        <version>1.0.0-RC3-SNAPSHOT</version>
+        <version>1.0.0-RC3</version>
     </parent>
 
     <artifactId>phenopacket-tools-builder</artifactId>

phenopacket-tools-cli/pom.xml

@@ -7,7 +7,7 @@
     <parent>
         <groupId>org.phenopackets.phenopackettools</groupId>
         <artifactId>phenopacket-tools</artifactId>
-        <version>1.0.0-RC3-SNAPSHOT</version>
+        <version>1.0.0-RC3</version>
     </parent>
 
     <artifactId>phenopacket-tools-cli</artifactId>

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

@@ -15,7 +15,7 @@
                 "phenopacket-tools (pxf)",
                 "An application and library for building, conversion, and validation of GA4GH Phenopackets.\n"
         },
-        version = "v1.0.0-RC3-SNAPSHOT",
+        version = "v1.0.0-RC3",
         mixinStandardHelpOptions = true,
         subcommands = {
                 // see https://picocli.info/autocomplete.html
@@ -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\n";
+    public static final String FOOTER = "\nSee the full documentation at http://phenopackets.org/phenopacket-tools/stable\n";
 
     private Main() {
         // private no-op

phenopacket-tools-converter/pom.xml

@@ -7,7 +7,7 @@
     <parent>
         <groupId>org.phenopackets.phenopackettools</groupId>
         <artifactId>phenopacket-tools</artifactId>
-        <version>1.0.0-RC3-SNAPSHOT</version>
+        <version>1.0.0-RC3</version>
     </parent>
 
     <artifactId>phenopacket-tools-converter</artifactId>

phenopacket-tools-core/pom.xml

@@ -6,7 +6,7 @@
     <parent>
         <artifactId>phenopacket-tools</artifactId>
         <groupId>org.phenopackets.phenopackettools</groupId>
-        <version>1.0.0-RC3-SNAPSHOT</version>
+        <version>1.0.0-RC3</version>
     </parent>
 
     <artifactId>phenopacket-tools-core</artifactId>

phenopacket-tools-io/pom.xml

@@ -6,7 +6,7 @@
     <parent>
         <artifactId>phenopacket-tools</artifactId>
         <groupId>org.phenopackets.phenopackettools</groupId>
-        <version>1.0.0-RC3-SNAPSHOT</version>
+        <version>1.0.0-RC3</version>
     </parent>
 
     <artifactId>phenopacket-tools-io</artifactId>

phenopacket-tools-test/pom.xml

@@ -5,7 +5,7 @@
     <parent>
         <artifactId>phenopacket-tools</artifactId>
         <groupId>org.phenopackets.phenopackettools</groupId>
-        <version>1.0.0-RC3-SNAPSHOT</version>
+        <version>1.0.0-RC3</version>
     </parent>
     <modelVersion>4.0.0</modelVersion>