Bump version: 1.4.1.9003 → 1.4.1.9004

sigven · May 29, 2024 · e9bf9b6 · e9bf9b6
1 parent 45bf26d
commit e9bf9b6
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Showing 10 changed files with 14 additions and 13 deletions.
diff --git a/.bumpversion.cfg b/.bumpversion.cfg
@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 1.4.1.9003
+current_version = 1.4.1.9004
 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
@@ -11,7 +11,7 @@ env:
   recipe_path: conda/recipe
   env_yml_path: conda/env/yml
   env_lock_path: conda/env/lock
-  VERSION: '1.4.1.9003' # versioned by bump2version
+  VERSION: '1.4.1.9004' # versioned by bump2version
 jobs:
   build_pcgrr_conda_pkg:
     # When merging to one of the branches above and the commit message matches
@@ -31,6 +31,7 @@ jobs:
       - name: 🐍 Conda pkg build and upload
         run: |
           conda mambabuild ${recipe_path}/pcgrr -c conda-forge -c bioconda --token ${atoken}
+
   build_pcgr_conda_pkg:
     # When merging to one of the branches above and the commit message matches
     if: "startsWith(github.event.head_commit.message, 'Bump version:')"
@@ -91,7 +92,7 @@ jobs:
           cp pcgrr/DESCRIPTION . # hack for pkgdown to work
           printf "pcgrr version:\n"
           Rscript -e "packageVersion('pcgrr')"
-          Rscript -e "pkgdown::deploy_to_branch(pkg = 'pcgrr', commit_message = 'Built PCGR website - see https://sigven.github.io/pcgr/', branch = 'gh-pages', new_process = FALSE)"
+          Rscript -e "pkgdown::deploy_to_branch(pkg = 'pcgrr', commit_message = 'Built PCGR website: https://sigven.github.io/pcgr/', branch = 'gh-pages', new_process = FALSE)"
 
   docker_deploy:
     name: Build and deploy Docker

diff --git a/conda/env/yml/pcgr.yml b/conda/env/yml/pcgr.yml
@@ -6,7 +6,7 @@ channels:
   - conda-forge
 
 dependencies:
-  - pcgr::pcgr ==1.4.1.9003 # versioned by bump2version
+  - pcgr::pcgr ==1.4.1.9004 # versioned by bump2version
   - bedtools
   - bcftools
   - cyvcf2

diff --git a/conda/env/yml/pcgrr.yml b/conda/env/yml/pcgrr.yml
@@ -7,7 +7,7 @@ channels:
 
 dependencies:
   - python
-  - pcgr::r-pcgrr ==1.4.1.9003 # versioned by bump2version
+  - pcgr::r-pcgrr ==1.4.1.9004 # 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
@@ -4,7 +4,7 @@ channels:
   - bioconda
   - conda-forge
 dependencies:
-  - pcgr::r-pcgrr ==1.4.1.9003 # versioned by bump2version
+  - pcgr::r-pcgrr ==1.4.1.9004 # versioned by bump2version
   - r-pkgdown
   - r-readr
   - pandoc
diff --git a/conda/recipe/pcgrr/meta.yaml b/conda/recipe/pcgrr/meta.yaml
@@ -1,6 +1,6 @@
 package:
   name: r-pcgrr
-  version: 1.4.1.9003 # versioned by bump2version
+  version: 1.4.1.9004 # versioned by bump2version
 
 source:
   path: ../../../pcgrr

diff --git a/pcgr/_version.py b/pcgr/_version.py
@@ -1,2 +1,2 @@
 # versioned by bump2version
-__version__ = '1.4.1.9003'
+__version__ = '1.4.1.9004'
diff --git a/pcgrr/DESCRIPTION b/pcgrr/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: pcgrr
 Type: Package
 Title: Personal Cancer Genome ReporteR
-Version: 1.4.1.9003
+Version: 1.4.1.9004
 Date: 2024-04-27
 Authors@R:
     c(person(given = "Sigve",

diff --git a/pcgrr/vignettes/installation.Rmd b/pcgrr/vignettes/installation.Rmd
@@ -12,7 +12,7 @@ output: rmarkdown::html_document
   software requirements:
 
 ```bash
-PCGR_VERSION="1.4.1.9003"
+PCGR_VERSION="1.4.1.9004"
 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="1.4.1.9003"
+PCGR_VERSION="1.4.1.9004"
 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:1.4.1.9003 \
+    sigven/pcgr:1.4.1.9004 \
     pcgr \
       --input_vcf "/root/pcgr_inputs/tumor_sample.BRCA.vcf.gz" \
       --pcgr_dir "/root/pcgr_data" \

diff --git a/pyproject.toml b/pyproject.toml
@@ -5,7 +5,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "pcgr"
-version = "1.4.1.9003" # versioned by bump2version
+version = "1.4.1.9004" # versioned by bump2version
 description = "Personal Cancer Genome Reporter (PCGR) - variant interpretation for precision cancer medicine"
 authors = [
     {name = "Sigve Nakken", email = "sigven@gmail.com"},