Bump version to 3.0 in preparation for push to Dockerhub

EMSL-Computing · Jan 8, 2025 · 3be4c20 · 3be4c20
1 parent d6d4285
commit 3be4c20
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Showing 10 changed files with 19 additions and 18 deletions.
diff --git a/.bumpversion.cfg b/.bumpversion.cfg
@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 2.2.3
+current_version = 3.0.0
 commit = False
 tag = False
 
@@ -12,15 +12,18 @@ values =
 	rc2
 	rc3
 
-# Updates the repo version number in the README and setup.py
 [bumpversion:file:README.md]
+
 [bumpversion:file:setup.py]
+
 [bumpversion:file:metaMS/__init__.py]
 
-# Updates the GCMS version number in the docs
 [bumpversion:file:docs/gcms_metabolomics/index.rst]
+
+[bumpversion:file:docs/gcms_metabolomics/README_GCMS.md]
+
 [bumpversion:file:MAINTAINERS.md]
 
-# Updates the docker image version in the wdls
 [bumpversion:file:wdl/metaMS_gcms.wdl]
+
 [bumpversion:file:wdl/metaMS_lcmslipidomics.wdl]
diff --git a/MAINTAINERS.md b/MAINTAINERS.md
@@ -36,7 +36,7 @@ This guide provides instructions for developers working on the project. It cover
 The following steps should be followed in order
 
 ### Bump Version Numbers
-The versioning of the repo, docker image and the GC/MS workflow are currently 2.2.3.
+The versioning of the repo, docker image and the GC/MS workflow are currently 3.0.0.
 The version of the lipid workflow is currently 1.0.0.
 
 To bump *both* the repo and the lipid workflow, run one of the following commands.

diff --git a/Makefile b/Makefile
@@ -72,6 +72,9 @@ docker-nmdc:
 	@docker image tag microbiomedata/metams:$(version) microbiomedata/metams:latest
 	@docker push microbiomedata/metams:latest
 
+echo-version:
+	@echo $(version)
+
 docker-build:
 
 	docker build -t microbiomedata/metams:latest .
@@ -89,9 +92,6 @@ wdl-run-gcms :
 	 miniwdl run wdl/metaMS_gcms.wdl -i wdl/metams_input_gcms.json --verbose --no-cache --copy-input-files
 
 wdl-run-lipid :
-#TODO KRH: remove the docker-build-local when the docker image is available in dockerhub and
-# update the docker image in the wdl file.  Good to rebuild for each run while in development
-	 make docker-build-local
 	 miniwdl run wdl/metaMS_lcmslipidomics.wdl -i wdl/metams_input_lipidomics.json --verbose --no-cache --copy-input-files
 
 convert_lipid_rst_to_md:

diff --git a/README.md b/README.md
@@ -10,7 +10,7 @@
 
 ## Current Version
 
-### `2.2.3`
+### `3.0.0`
 
 ## Available Workflows
 

diff --git a/docs/gcms_metabolomics/README_GCMS.md b/docs/gcms_metabolomics/README_GCMS.md
@@ -20,7 +20,7 @@
 
 ## Current Version
 
-### `2.2.3`
+### `3.0.0`
 
 ### Data input formats
 

diff --git a/docs/gcms_metabolomics/index.rst b/docs/gcms_metabolomics/index.rst
@@ -99,7 +99,7 @@ Outputs
 Version History
 ---------------
 
-- 2.2.3
+- 3.0.0
 
 Point of contact
 ----------------

diff --git a/metaMS/__init__.py b/metaMS/__init__.py
@@ -1,5 +1,5 @@
 
-__version__ = '2.2.3'
+__version__ = '3.0.0'
 __doc__ = '''
 # Table of Contents  
 - Introduction
@@ -24,7 +24,7 @@
 
 ## Current Version
 
-### `2.2.3`
+### `3.0.0`
 
 ### Data input formats
 

diff --git a/setup.py b/setup.py
@@ -11,7 +11,7 @@
 # This call to setup() does all the work
 setup(
     name="metaMS",
-    version="2.2.3",
+    version="3.0.0",
     description="Data processing, and annotation for metabolomics analysis by low-resolution GC-MS",
     long_description=README,
     long_description_content_type="text/markdown",

diff --git a/wdl/metaMS_gcms.wdl b/wdl/metaMS_gcms.wdl
@@ -43,7 +43,6 @@ task runMetaMSGCMS {
     }
 
     runtime {
-        docker: "local-metams:latest"
-        #TODO KRH: Update to pushed version when available
+        docker: "microbiomedata/metams:3.0.0"
     }
 }
diff --git a/wdl/metaMS_lcmslipidomics.wdl b/wdl/metaMS_lcmslipidomics.wdl
@@ -35,7 +35,6 @@ task runMetaMSLCMSLipidomics {
     }
 
     runtime {
-        docker: "local-metams:latest"
-        #TODO KRH: Update to pushed version when available
+        docker: "microbiomedata/metams:3.0.0"
     }
 }
-Original file line number
+Diff line change
@@ Expand Up / @@ -99,7 +99,7 @@ Outputs @@
     Version History
     ---------------
-    - 2.2.3
+    - 3.0.0
     Point of contact
     ----------------
@@ Expand Down @@