From 4f8530ee0ae44830477d49ad1fd4c82431ee7333 Mon Sep 17 00:00:00 2001 From: Daniel Danis Date: Mon, 12 Jul 2021 17:15:23 -0400 Subject: [PATCH] Release v1.0.0-RC2 --- CHANGELOG.rst | 15 ++++++++++++++- docs/conf.py | 2 +- pom.xml | 2 +- svanna-benchmark/pom.xml | 2 +- .../main/java/org/jax/svanna/benchmark/Main.java | 4 ++-- svanna-cli/pom.xml | 2 +- .../src/main/java/org/jax/svanna/cli/Main.java | 4 ++-- svanna-core/pom.xml | 2 +- svanna-db/pom.xml | 2 +- svanna-ingest/pom.xml | 2 +- svanna-io/pom.xml | 2 +- svanna-spring-boot-autoconfigure/pom.xml | 2 +- svanna-spring-boot-starter/pom.xml | 2 +- svanna-test/pom.xml | 2 +- 14 files changed, 29 insertions(+), 16 deletions(-) diff --git a/CHANGELOG.rst b/CHANGELOG.rst index 24ac6908..e1387dec 100644 --- a/CHANGELOG.rst +++ b/CHANGELOG.rst @@ -2,11 +2,24 @@ Changelog ========= + +---------- +v1.0.0-RC2 +---------- + +- Implement VCF output format +- Clean up the repo from the obsolete code +- Improve documentation & test coverage +- Bug fixes + - remove null pointer in ``GeneService`` + - do not run coverage filter if the coverage data is missing for a variant + + ---------- v1.0.0-RC1 ---------- -- Rename `annotate` CLI command to `prioritize` +- Rename ``annotate`` CLI command to ``prioritize`` - Multiple minor adjustments diff --git a/docs/conf.py b/docs/conf.py index e343cbf4..9ca51355 100644 --- a/docs/conf.py +++ b/docs/conf.py @@ -56,7 +56,7 @@ # The short X.Y version. version = u'1.0' # The full version, including alpha/beta/rc tags. -release = u'1.0.0-RC1' +release = u'1.0.0-RC2' # The language for content autogenerated by Sphinx. Refer to documentation # for a list of supported languages. diff --git a/pom.xml b/pom.xml index 69fd4390..5381934f 100644 --- a/pom.xml +++ b/pom.xml @@ -18,7 +18,7 @@ svanna-benchmark org.jax.svanna - 1.0.0-RC2-SNAPSHOT + 1.0.0-RC2 SvAnna diff --git a/svanna-benchmark/pom.xml b/svanna-benchmark/pom.xml index 51419de3..d9b3ddbe 100644 --- a/svanna-benchmark/pom.xml +++ b/svanna-benchmark/pom.xml @@ -5,7 +5,7 @@ SvAnna org.jax.svanna - 1.0.0-RC2-SNAPSHOT + 1.0.0-RC2 4.0.0 diff --git a/svanna-benchmark/src/main/java/org/jax/svanna/benchmark/Main.java b/svanna-benchmark/src/main/java/org/jax/svanna/benchmark/Main.java index 2bd0abd4..d96b6eaf 100644 --- a/svanna-benchmark/src/main/java/org/jax/svanna/benchmark/Main.java +++ b/svanna-benchmark/src/main/java/org/jax/svanna/benchmark/Main.java @@ -15,11 +15,11 @@ footer = Main.FOOTER) public class Main implements Callable { - public static final String VERSION = "svanna-benchmark v1.0.0-RC1-SNAPSHOT"; + public static final String VERSION = "svanna-benchmark v1.0.0-RC2"; public static final int WIDTH = 120; - public static final String FOOTER = "See the full documentation at `https://github.com/TheJacksonLaboratory/SvAnna`"; + public static final String FOOTER = "See the full documentation at `https://svanna.readthedocs.io/en/v1.0.0-rc2`"; private static final CommandLine.Help.ColorScheme COLOR_SCHEME = new CommandLine.Help.ColorScheme.Builder() .commands(bold, fg_blue, underline) diff --git a/svanna-cli/pom.xml b/svanna-cli/pom.xml index eabf316d..615b91bc 100644 --- a/svanna-cli/pom.xml +++ b/svanna-cli/pom.xml @@ -5,7 +5,7 @@ SvAnna org.jax.svanna - 1.0.0-RC2-SNAPSHOT + 1.0.0-RC2 4.0.0 svanna-cli diff --git a/svanna-cli/src/main/java/org/jax/svanna/cli/Main.java b/svanna-cli/src/main/java/org/jax/svanna/cli/Main.java index df7ed673..7943303b 100644 --- a/svanna-cli/src/main/java/org/jax/svanna/cli/Main.java +++ b/svanna-cli/src/main/java/org/jax/svanna/cli/Main.java @@ -18,11 +18,11 @@ footer = Main.FOOTER) public class Main implements Callable { - public static final String VERSION = "svanna-cli v1.0.0-RC1"; + public static final String VERSION = "svanna-cli v1.0.0-RC2"; public static final int WIDTH = 120; - public static final String FOOTER = "See the full documentation at `https://github.com/TheJacksonLaboratory/SvAnna`"; + public static final String FOOTER = "See the full documentation at `https://svanna.readthedocs.io/en/v1.0.0-rc2`"; private static final CommandLine.Help.ColorScheme COLOR_SCHEME = new CommandLine.Help.ColorScheme.Builder() .commands(bold, fg_blue, underline) diff --git a/svanna-core/pom.xml b/svanna-core/pom.xml index 008fa04d..02123ebd 100644 --- a/svanna-core/pom.xml +++ b/svanna-core/pom.xml @@ -5,7 +5,7 @@ SvAnna org.jax.svanna - 1.0.0-RC2-SNAPSHOT + 1.0.0-RC2 4.0.0 diff --git a/svanna-db/pom.xml b/svanna-db/pom.xml index 5be9aaaf..7bfe13d7 100644 --- a/svanna-db/pom.xml +++ b/svanna-db/pom.xml @@ -5,7 +5,7 @@ SvAnna org.jax.svanna - 1.0.0-RC2-SNAPSHOT + 1.0.0-RC2 4.0.0 diff --git a/svanna-ingest/pom.xml b/svanna-ingest/pom.xml index b56d28e3..4081c9c6 100644 --- a/svanna-ingest/pom.xml +++ b/svanna-ingest/pom.xml @@ -5,7 +5,7 @@ SvAnna org.jax.svanna - 1.0.0-RC2-SNAPSHOT + 1.0.0-RC2 4.0.0 svanna-ingest diff --git a/svanna-io/pom.xml b/svanna-io/pom.xml index 30f15de0..697a560c 100644 --- a/svanna-io/pom.xml +++ b/svanna-io/pom.xml @@ -5,7 +5,7 @@ SvAnna org.jax.svanna - 1.0.0-RC2-SNAPSHOT + 1.0.0-RC2 4.0.0 diff --git a/svanna-spring-boot-autoconfigure/pom.xml b/svanna-spring-boot-autoconfigure/pom.xml index 8d9a0394..4d3ef14f 100644 --- a/svanna-spring-boot-autoconfigure/pom.xml +++ b/svanna-spring-boot-autoconfigure/pom.xml @@ -5,7 +5,7 @@ SvAnna org.jax.svanna - 1.0.0-RC2-SNAPSHOT + 1.0.0-RC2 4.0.0 diff --git a/svanna-spring-boot-starter/pom.xml b/svanna-spring-boot-starter/pom.xml index f2164368..bfe23007 100644 --- a/svanna-spring-boot-starter/pom.xml +++ b/svanna-spring-boot-starter/pom.xml @@ -5,7 +5,7 @@ SvAnna org.jax.svanna - 1.0.0-RC2-SNAPSHOT + 1.0.0-RC2 4.0.0 diff --git a/svanna-test/pom.xml b/svanna-test/pom.xml index bfc02896..d250b688 100644 --- a/svanna-test/pom.xml +++ b/svanna-test/pom.xml @@ -5,7 +5,7 @@ SvAnna org.jax.svanna - 1.0.0-RC2-SNAPSHOT + 1.0.0-RC2 4.0.0