Bump to version 3.1

EMSL-Computing · Feb 5, 2025 · 7836078 · 7836078
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commit 7836078
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Showing 14 changed files with 20 additions and 21 deletions.
diff --git a/.bumpversion.cfg b/.bumpversion.cfg
@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 3.0.0
+current_version = 3.1.0
 commit = False
 tag = False
 

diff --git a/.bumpversion_lipid.cfg b/.bumpversion_lipid.cfg
@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 1.0.0
+current_version = 1.1.0
 commit = False
 tag = False
 
@@ -12,9 +12,8 @@ values =
 	rc2
 	rc3
 
-# Updates the lipidomics  version number in the docs
 [bumpversion:file:docs/lcms_lipidomics/index.rst]
+
 [bumpversion:file:MAINTAINERS.md]
 
-# Updates the lipidomics version number in the metadata generator
 [bumpversion:file:metaMS/nmdc_lipidomics_metadata_generation/metadata_generator.py]
diff --git a/MAINTAINERS.md b/MAINTAINERS.md
@@ -36,8 +36,8 @@ 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 3.0.0.
-The version of the lipid workflow is currently 1.0.0.
+The versioning of the repo, docker image and the GC/MS workflow are currently 3.1.0.
+The version of the lipid workflow is currently 1.1.0.
 
 To bump *both* the repo and the lipid workflow, run one of the following commands.
 

diff --git a/README.md b/README.md
@@ -10,7 +10,7 @@
 
 ## Current Version
 
-### `3.0.0`
+### `3.1.0`
 
 ## Available Workflows
 

diff --git a/docs/gcms_metabolomics/README_GCMS.md b/docs/gcms_metabolomics/README_GCMS.md
@@ -20,7 +20,7 @@
 
 ## Current Version
 
-### `3.0.0`
+### `3.1.0`
 
 ### Data input formats
 

diff --git a/docs/gcms_metabolomics/index.rst b/docs/gcms_metabolomics/index.rst
@@ -95,7 +95,7 @@ Outputs
 Version History
 ---------------
 
-- 3.0.0
+- 3.1.0
 
 Point of contact
 ----------------

diff --git a/docs/lcms_lipidomics/README_LCMS_LIPID.md b/docs/lcms_lipidomics/README_LCMS_LIPID.md
@@ -2,7 +2,7 @@ github_url
 
 :   <https://github.com/microbiomedata/metaMS/blob/master/docs/index_lipid.rst>
 
-# Lipidomics Workflow (v1.0.0)
+# Lipidomics Workflow (v1.1.0)
 
 ![](lipid_workflow_v1.svg)
 
@@ -128,7 +128,7 @@ The following inputs are required (declared in the input json file):
 
 ## Version History
 
--   v1.0.0: Initial release of the lipidomics workflow Jan 9, 2025
+-   v1.1.0: Initial release of the lipidomics workflow Jan 9, 2025
 
 ## Point of contact
 

diff --git a/docs/lcms_lipidomics/index.html b/docs/lcms_lipidomics/index.html
@@ -5,7 +5,7 @@
 href="https://github.com/microbiomedata/metaMS/blob/master/docs/index_lipid.rst">https://github.com/microbiomedata/metaMS/blob/master/docs/index_lipid.rst</a></p>
 </dd>
 </dl>
-<h1 id="lipidomics-workflow-v1.0.0">Lipidomics Workflow (v1.0.0)</h1>
+<h1 id="lipidomics-workflow-v1.1.0">Lipidomics Workflow (v1.1.0)</h1>
 <figure>
 <img src="lipid_workflow_v1.svg" alt="lipid_workflow_v1.svg" />
 </figure>
@@ -126,7 +126,7 @@ <h3 id="outputs">Outputs</h3>
 </ul>
 <h2 id="version-history">Version History</h2>
 <ul>
-<li>v1.0.0: Initial release of the lipidomics workflow Jan 9, 2025</li>
+<li>v1.1.0: Initial release of the lipidomics workflow Jan 9, 2025</li>
 </ul>
 <h2 id="point-of-contact">Point of contact</h2>
 <p>Workflow maintainer: Katherine R. Heal &lt;<a

diff --git a/docs/lcms_lipidomics/index.rst b/docs/lcms_lipidomics/index.rst
@@ -6,7 +6,7 @@
          site the file is incorporated into. You can learn more about the `github_url` field at:
          https://sphinx-rtd-theme.readthedocs.io/en/stable/configuring.html#confval-github_url
 
-Lipidomics Workflow (v1.0.0)
+Lipidomics Workflow (v1.1.0)
 ============================
 
 .. figure:: lipid_workflow_v1.svg
@@ -120,7 +120,7 @@ Outputs
 Version History
 ---------------
 
-- v1.0.0: Initial release of the lipidomics workflow Jan 9, 2025
+- v1.1.0: Initial release of the lipidomics workflow Jan 9, 2025
 
 Point of contact
 ----------------

diff --git a/metaMS/__init__.py b/metaMS/__init__.py
@@ -1,5 +1,5 @@
 
-__version__ = '3.0.0'
+__version__ = '3.1.0'
 __doc__ = '''
 # Table of Contents  
 - Introduction
@@ -24,7 +24,7 @@
 
 ## Current Version
 
-### `3.0.0`
+### `3.1.0`
 
 ### Data input formats
 

diff --git a/metaMS/nmdc_lipidomics_metadata_generation/metadata_generator.py b/metaMS/nmdc_lipidomics_metadata_generation/metadata_generator.py
@@ -220,7 +220,7 @@ def __init__(
             "Analysis of raw mass spectrometry data for the annotation of lipids."
         )
         self.workflow_git_url = "https://github.com/microbiomedata/metaMS/wdl/metaMS_lipidomics.wdl"
-        self.workflow_version = "1.0.0"
+        self.workflow_version = "1.1.0"
         self.wf_config_process_data_category = "workflow_parameter_data"
         self.wf_config_process_data_obj_type = "Configuration toml"
         self.wf_config_process_data_description = (

diff --git a/setup.py b/setup.py
@@ -11,7 +11,7 @@
 # This call to setup() does all the work
 setup(
     name="metaMS",
-    version="3.0.0",
+    version="3.1.0",
     description="Data processing, and annotation for metabolomics analyses",
     long_description=README,
     long_description_content_type="text/markdown",

diff --git a/wdl/metaMS_gcms.wdl b/wdl/metaMS_gcms.wdl
@@ -49,6 +49,6 @@ task runMetaMSGCMS {
     }
 
     runtime {
-        docker: "~{if defined(docker_image) then docker_image else 'microbiomedata/metams:3.0.0'}"
+        docker: "~{if defined(docker_image) then docker_image else 'microbiomedata/metams:3.1.0'}"
     }
 }
diff --git a/wdl/metaMS_lcmslipidomics.wdl b/wdl/metaMS_lcmslipidomics.wdl
@@ -35,6 +35,6 @@ task runMetaMSLCMSLipidomics {
     }
 
     runtime {
-        docker: "microbiomedata/metams:3.0.0"
+        docker: "microbiomedata/metams:3.1.0"
     }
 }
-Original file line number
+Diff line change
@@ Expand Up / @@ -95,7 +95,7 @@ Outputs @@
     Version History
     ---------------
-    - 3.0.0
+    - 3.1.0
     Point of contact
     ----------------
@@ Expand Down @@