From d9d2e95079b3335da5d012a7738a0322fe3b5935 Mon Sep 17 00:00:00 2001
From: pdiakumis <peterdiakumis@gmail.com>
Date: Thu, 14 Dec 2023 12:45:44 +1100
Subject: [PATCH] =?UTF-8?q?Bump=20version:=201.4.1=20=E2=86=92=201.4.1.900?=
 =?UTF-8?q?0?=
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

---
 .bumpversion.cfg                           | 2 +-
 .github/workflows/build_conda_recipes.yaml | 2 +-
 conda/env/yml/pcgr.yml                     | 2 +-
 conda/env/yml/pcgrr.yml                    | 2 +-
 conda/env/yml/pkgdown.yml                  | 2 +-
 conda/recipe/pcgrr/meta.yaml               | 2 +-
 pcgr/_version.py                           | 2 +-
 pcgrr/DESCRIPTION                          | 2 +-
 pcgrr/vignettes/installation.Rmd           | 6 +++---
 setup.py                                   | 2 +-
 10 files changed, 12 insertions(+), 12 deletions(-)

diff --git a/.bumpversion.cfg b/.bumpversion.cfg
index 46b1ba81..ae726322 100644
--- a/.bumpversion.cfg
+++ b/.bumpversion.cfg
@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 1.4.1
+current_version = 1.4.1.9000
 commit = True
 tag = False
 parse = (?P<major>\d+)\.(?P<minor>\d+)\.(?P<patch>\d+)(\.(?P<dev>\d+))?
diff --git a/.github/workflows/build_conda_recipes.yaml b/.github/workflows/build_conda_recipes.yaml
index 5e5a3998..f9a40836 100644
--- a/.github/workflows/build_conda_recipes.yaml
+++ b/.github/workflows/build_conda_recipes.yaml
@@ -10,7 +10,7 @@ env:
   recipe_path: conda/recipe
   env_yml_path: conda/env/yml
   env_lock_path: conda/env/lock
-  VERSION: '1.4.1' # versioned by bump2version
+  VERSION: '1.4.1.9000' # versioned by bump2version
 jobs:
   build_pcgrr_conda_pkg:
     # When merging to one of the branches above and the commit message matches
diff --git a/conda/env/yml/pcgr.yml b/conda/env/yml/pcgr.yml
index 0274d39a..85cf1345 100644
--- a/conda/env/yml/pcgr.yml
+++ b/conda/env/yml/pcgr.yml
@@ -6,7 +6,7 @@ channels:
   - conda-forge
 
 dependencies:
-  - pcgr::pcgr ==1.4.1 # versioned by bump2version
+  - pcgr::pcgr ==1.4.1.9000 # versioned by bump2version
   - bedtools
   - bcftools
   - cyvcf2
diff --git a/conda/env/yml/pcgrr.yml b/conda/env/yml/pcgrr.yml
index c08fb4d2..9bbb69fb 100644
--- a/conda/env/yml/pcgrr.yml
+++ b/conda/env/yml/pcgrr.yml
@@ -7,7 +7,7 @@ channels:
 
 dependencies:
   - python
-  - pcgr::r-pcgrr ==1.4.1 # versioned by bump2version
+  - pcgr::r-pcgrr ==1.4.1.9000 # versioned by bump2version
   - pcgr::r-cpsr
   - r-argparse
   - bioconductor-bsgenome.hsapiens.ucsc.hg38
diff --git a/conda/env/yml/pkgdown.yml b/conda/env/yml/pkgdown.yml
index e1b6283a..7094f63a 100644
--- a/conda/env/yml/pkgdown.yml
+++ b/conda/env/yml/pkgdown.yml
@@ -4,7 +4,7 @@ channels:
   - bioconda
   - conda-forge
 dependencies:
-  - pcgr::r-pcgrr ==1.4.1 # versioned by bump2version
+  - pcgr::r-pcgrr ==1.4.1.9000 # versioned by bump2version
   - r-pkgdown
   - r-readr
   - pandoc
diff --git a/conda/recipe/pcgrr/meta.yaml b/conda/recipe/pcgrr/meta.yaml
index f2916417..7ce47b2d 100644
--- a/conda/recipe/pcgrr/meta.yaml
+++ b/conda/recipe/pcgrr/meta.yaml
@@ -1,6 +1,6 @@
 package:
   name: r-pcgrr
-  version: 1.4.1 # versioned by bump2version
+  version: 1.4.1.9000 # versioned by bump2version
 
 source:
   path: ../../../pcgrr
diff --git a/pcgr/_version.py b/pcgr/_version.py
index 4ec7a8de..5ba7a341 100644
--- a/pcgr/_version.py
+++ b/pcgr/_version.py
@@ -1,2 +1,2 @@
 # versioned by bump2version
-__version__ = '1.4.1'
+__version__ = '1.4.1.9000'
diff --git a/pcgrr/DESCRIPTION b/pcgrr/DESCRIPTION
index 8bf016b2..c6ceb068 100644
--- a/pcgrr/DESCRIPTION
+++ b/pcgrr/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: pcgrr
 Type: Package
 Title: Personal Cancer Genome ReporteR
-Version: 1.4.1
+Version: 1.4.1.9000
 Date: 2023-12-12
 Authors@R:
     c(person(given = "Sigve",
diff --git a/pcgrr/vignettes/installation.Rmd b/pcgrr/vignettes/installation.Rmd
index e76abd55..d5bd8927 100644
--- a/pcgrr/vignettes/installation.Rmd
+++ b/pcgrr/vignettes/installation.Rmd
@@ -12,7 +12,7 @@ output: rmarkdown::html_document
   software requirements:
 
 ```bash
-PCGR_VERSION="1.4.1"
+PCGR_VERSION="1.4.1.9000"
 PCGR_REPO="https://raw.githubusercontent.com/sigven/pcgr/v${PCGR_VERSION}/conda/env/lock/"
 PLATFORM="linux" # or "osx"
 
@@ -79,7 +79,7 @@ Download and unpack the latest software release from <https://github.com/sigven/
 Alternatively if you have `git` installed, you can do:
 
 ```bash
-PCGR_VERSION="1.4.1"
+PCGR_VERSION="1.4.1.9000"
 OUTPUT_DIRECTORY="PCGR"
 
 git clone \
@@ -235,7 +235,7 @@ docker container run -it --rm \
     -v /Users/you/dir1/data:/root/pcgr_data \
     -v /Users/you/dir2/pcgr_inputs:/root/pcgr_inputs \
     -v /Users/you/dir3/pcgr_outputs:/root/pcgr_outputs \
-    sigven/pcgr:1.4.1 \
+    sigven/pcgr:1.4.1.9000 \
     pcgr \
       --input_vcf "/root/pcgr_inputs/tumor_sample.BRCA.vcf.gz" \
       --pcgr_dir "/root/pcgr_data" \
diff --git a/setup.py b/setup.py
index 76762f0c..ec2066da 100644
--- a/setup.py
+++ b/setup.py
@@ -2,7 +2,7 @@
 
 setuptools.setup(
     name='pcgr',
-    version='1.4.1', # versioned by bump2version
+    version='1.4.1.9000', # versioned by bump2version
     license='MIT',
     author='Sigve Nakken',
     author_email='sigven@gmail.com',