Bump version patch and generate documentation

kheal · kheal · commit 136016bcdd99 · 2025-09-09T10:21:13.000-07:00
diff --git a/.bumpversion.cfg b/.bumpversion.cfg
@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 3.2.1
+current_version = 3.2.2
 commit = False
 tag = False
 
diff --git a/.bumpversion_lcmsmetab.cfg b/.bumpversion_lcmsmetab.cfg
@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 1.0.1
+current_version = 1.0.2
 commit = False
 tag = False
 
diff --git a/.bumpversion_lipid.cfg b/.bumpversion_lipid.cfg
@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 1.2.1
+current_version = 1.2.2
 commit = False
 tag = False
 
diff --git a/MAINTAINERS.md b/MAINTAINERS.md
@@ -45,9 +45,9 @@ To test a workflow before an associated docker image is pushed, you can run the
 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 3.2.1.
-The version of the lipid workflow is currently 1.2.1.
-The version of the LCMS metabolomics workflow is currently 1.0.1.
+The versioning of the repo, docker image and the GC/MS workflow are currently 3.2.2.
+The version of the lipid workflow is currently 1.2.2.
+The version of the LCMS metabolomics workflow is currently 1.0.2.
 
 To bump the repo *and all workflows*, run one of the following commands.  This will update the runtime version of all of the workflows, the version of the repo and the version of the docker image.
 
diff --git a/README.md b/README.md
@@ -10,7 +10,7 @@
 
 ## Current Version
 
-### `3.2.1`
+### `3.2.2`
 
 ## Available Workflows
 
diff --git a/docs/gcms_metabolomics/README_GCMS.md b/docs/gcms_metabolomics/README_GCMS.md
@@ -20,7 +20,7 @@
 
 ## Current Version
 
-### `3.2.1`
+### `3.2.2`
 
 ### Data input formats
 
diff --git a/docs/gcms_metabolomics/index.rst b/docs/gcms_metabolomics/index.rst
@@ -96,7 +96,7 @@ Outputs
 Version History
 ---------------
 
-- Current version is 3.2.1
+- Current version is 3.2.2
 
 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 (v1.2.1)
+# Lipidomics Workflow (v1.2.2)
 
 ![](lipid_workflow_v1.svg)
 
@@ -128,7 +128,7 @@ The following inputs are required (declared in the input json file):
 
 ## Version History
 
--   v1.2.1: Current release
+-   v1.2.2: Current release
 -   v1.0.0: 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-v1.2.1">Lipidomics Workflow (v1.2.1)</h1>
+<h1 id="lipidomics-workflow-v1.2.2">Lipidomics Workflow (v1.2.2)</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>v1.2.1: Current release</li>
+<li>v1.2.2: Current release</li>
 <li>v1.0.0: Initial release of the lipidomics workflow Jan 9, 2025</li>
 </ul>
 <h2 id="point-of-contact">Point of contact</h2>
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 (v1.2.1)
+Lipidomics Workflow (v1.2.2)
 ============================
 
 .. figure:: lipid_workflow_v1.svg
@@ -120,7 +120,7 @@ Outputs
 Version History
 ---------------
 
-- v1.2.1: Current release
+- v1.2.2: Current release
 - v1.0.0: Initial release of the lipidomics workflow Jan 9, 2025
 
 Point of contact
diff --git a/docs/lcms_metabolomics/README_LCMS_METABOLOMICS.md b/docs/lcms_metabolomics/README_LCMS_METABOLOMICS.md
@@ -2,7 +2,7 @@ github_url
 
 :   <https://github.com/microbiomedata/metaMS/blob/master/docs/index_lipid.rst>
 
-LC/MS Metabolomics Workflow (v1.0.1) ============================
+LC/MS Metabolomics Workflow (v1.0.2) ============================
 
 ![](lcms_metabolite_workflow.svg)
 
@@ -123,7 +123,7 @@ The following inputs are required (declared in the input json file):
 
 # Version History
 
--   v1.0.1: Current release
+-   v1.0.2: Current release
 -   v1.0.0: Initial release of the LC/MS metabolomics workflow June 24,
     2025
 
diff --git a/docs/lcms_metabolomics/index.html b/docs/lcms_metabolomics/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>
-<p>LC/MS Metabolomics Workflow (v1.0.1) ============================</p>
+<p>LC/MS Metabolomics Workflow (v1.0.2) ============================</p>
 <figure>
 <img src="lcms_metabolite_workflow.svg"
 alt="lcms_metabolite_workflow.svg" />
@@ -121,7 +121,7 @@ <h2 id="outputs">Outputs</h2>
 </ul>
 <h1 id="version-history">Version History</h1>
 <ul>
-<li>v1.0.1: Current release</li>
+<li>v1.0.2: Current release</li>
 <li>v1.0.0: Initial release of the LC/MS metabolomics workflow June 24,
 2025</li>
 </ul>
diff --git a/docs/lcms_metabolomics/index.rst b/docs/lcms_metabolomics/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
 
-LC/MS Metabolomics Workflow (v1.0.1)
+LC/MS Metabolomics Workflow (v1.0.2)
 ============================
 
 .. figure:: lcms_metabolite_workflow.svg
@@ -112,7 +112,7 @@ Outputs
 Version History
 ---------------
 
-- v1.0.1: Current release
+- v1.0.2: Current release
 - v1.0.0: Initial release of the LC/MS metabolomics workflow June 24, 2025
 
 Point of contact
diff --git a/docs/metaMS.html b/docs/metaMS.html
@@ -79,7 +79,7 @@ <h1 id="metams">MetaMS</h1>
 
 <h2 id="current-version">Current Version</h2>
 
-<h3 id="321"><code>3.2.1</code></h3>
+<h3 id="322"><code>3.2.2</code></h3>
 
 <h2 id="available-workflows">Available Workflows</h2>
 
@@ -122,7 +122,7 @@ <h2 id="disclaimer">Disclaimer</h2>
 
                         <label class="view-source-button" for="mod-metaMS-view-source"><span>View Source</span></label>
 
-                        <div class="pdoc-code codehilite"><pre><span></span><span id="L-1"><a href="#L-1"><span class="linenos"> 1</span></a><span class="n">__version__</span> <span class="o">=</span> <span class="s1">&#39;3.2.1&#39;</span>
+                        <div class="pdoc-code codehilite"><pre><span></span><span id="L-1"><a href="#L-1"><span class="linenos"> 1</span></a><span class="n">__version__</span> <span class="o">=</span> <span class="s1">&#39;3.2.2&#39;</span>
 </span><span id="L-2"><a href="#L-2"><span class="linenos"> 2</span></a>
 </span><span id="L-3"><a href="#L-3"><span class="linenos"> 3</span></a><span class="kn">import</span> <span class="nn">os</span>
 </span><span id="L-4"><a href="#L-4"><span class="linenos"> 4</span></a><span class="c1"># Get the path to the README file</span>
diff --git a/docs/search.js b/docs/search.js
diff --git a/metaMS/__init__.py b/metaMS/__init__.py
@@ -1,5 +1,5 @@
 
-__version__ = '3.2.1'
+__version__ = '3.2.2'
 
 import os
 # Get the path to the README file
diff --git a/setup.py b/setup.py
@@ -11,7 +11,7 @@
 # This call to setup() does all the work
 setup(
     name="metaMS",
-    version="3.2.1",
+    version="3.2.2",
     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:3.2.1'}"
+        docker: "~{if defined(docker_image) then docker_image else 'microbiomedata/metams:3.2.2'}"
     }
 }
diff --git a/wdl/metaMS_lcms_metabolomics.wdl b/wdl/metaMS_lcms_metabolomics.wdl
@@ -61,6 +61,6 @@ task runMetaMSLCMSMetabolomics {
     }
 
     runtime {
-        docker: "~{if defined(docker_image) then docker_image else 'microbiomedata/metams:3.2.1'}"
+        docker: "~{if defined(docker_image) then docker_image else 'microbiomedata/metams:3.2.2'}"
     }
 }
diff --git a/wdl/metaMS_lcmslipidomics.wdl b/wdl/metaMS_lcmslipidomics.wdl
@@ -61,6 +61,6 @@ task runMetaMSLCMSLipidomics {
     }
 
     runtime {
-        docker: "~{if defined(docker_image) then docker_image else 'microbiomedata/metams:3.2.1'}"
+        docker: "~{if defined(docker_image) then docker_image else 'microbiomedata/metams:3.2.2'}"
     }
 }
