Bump corems version

kheal · kheal · commit ceaeacf16007 · 2025-10-22T17:11:03.000-07:00
diff --git a/.bumpversion.cfg b/.bumpversion.cfg
@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 3.3.2
+current_version = 3.3.3
 commit = False
 tag = False
 
diff --git a/.bumpversion_lcmsmetab.cfg b/.bumpversion_lcmsmetab.cfg
@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 1.1.2
+current_version = 1.1.3
 commit = False
 tag = False
 
diff --git a/.bumpversion_lipid.cfg b/.bumpversion_lipid.cfg
@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 1.3.2
+current_version = 1.3.3
 commit = False
 tag = False
 
diff --git a/Dockerfile b/Dockerfile
@@ -21,7 +21,7 @@ COPY metaMS/ /metams/metaMS/
 COPY README.md disclaimer.txt Makefile requirements.txt setup.py /metams/
 
 # Install the correct version of CoreMS from github
-RUN pip install git+https://github.com/EMSL-Computing/CoreMS.git@v3.9.2
+RUN pip install git+https://github.com/EMSL-Computing/CoreMS.git@v3.9.3
 
 # Install the MetaMS package in editable mode
 RUN pip3 install --editable .
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 3.3.2.
-The version of the lipid workflow is currently 1.3.2.
-The version of the LCMS metabolomics workflow is currently 1.1.2.
+The versioning of the repo, docker image and the GC/MS workflow are currently 3.3.3.
+The version of the lipid workflow is currently 1.3.3.
+The version of the LCMS metabolomics workflow is currently 1.1.3.
 
 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/Makefile b/Makefile
@@ -129,7 +129,7 @@ get-lipid-test-data:
 	@echo "Downloading test data for lipidomics"
 	@mkdir -p test_data
 	@mkdir -p test_data/test_lipid_data
-	@curl --retry 3 --retry-delay 5 --connect-timeout 30 --max-time 300 -L -o test_data/test_lipid_data.zip https://nmdcdemo.emsl.pnnl.gov/lipidomics/test_data/metams_lipid_test_data/test_lipid_data.zip
+	@curl --retry 3 --retry-delay 5 --connect-timeout 30 --max-time 600 -L -o test_data/test_lipid_data.zip https://nmdcdemo.emsl.pnnl.gov/lipidomics/test_data/metams_lipid_test_data/test_lipid_data.zip
 	@unzip test_data/test_lipid_data.zip -d test_data/test_lipid_data/
 	@rm test_data/test_lipid_data.zip
 	@echo "Test data downloaded and unzipped"
@@ -138,9 +138,9 @@ get-lcms-metab-test-data:
 	@echo "Downloading test data for LC-MS metabolomics"
 	@mkdir -p test_data
 	@mkdir -p test_data/test_lcms_metab_data
-	@curl --retry 3 --retry-delay 5 --connect-timeout 30 --max-time 300 -L -o test_data/test_lcms_metab_data/lcms_test_data1.mzML https://nmdcdemo.emsl.pnnl.gov/metabolomics/test_data/metams_lcms_metab_test_data/lcms_test_data1.mzML
-	@curl --retry 3 --retry-delay 5 --connect-timeout 30 --max-time 300 -L -o test_data/test_lcms_metab_data/lcms_test_data2.mzML https://nmdcdemo.emsl.pnnl.gov/metabolomics/test_data/metams_lcms_metab_test_data/lcms_test_data2.mzML
-	@curl --retry 3 --retry-delay 5 --connect-timeout 30 --max-time 300 -L -o test_data/test_lcms_metab_data/lcms_test_data3.mzML https://nmdcdemo.emsl.pnnl.gov/metabolomics/test_data/metams_lcms_metab_test_data/lcms_test_data3.mzML
+	@curl --retry 3 --retry-delay 5 --connect-timeout 30 --max-time 600 -L -o test_data/test_lcms_metab_data/lcms_test_data1.mzML https://nmdcdemo.emsl.pnnl.gov/metabolomics/test_data/metams_lcms_metab_test_data/lcms_test_data1.mzML
+	@curl --retry 3 --retry-delay 5 --connect-timeout 30 --max-time 600 -L -o test_data/test_lcms_metab_data/lcms_test_data2.mzML https://nmdcdemo.emsl.pnnl.gov/metabolomics/test_data/metams_lcms_metab_test_data/lcms_test_data2.mzML
+	@curl --retry 3 --retry-delay 5 --connect-timeout 30 --max-time 600 -L -o test_data/test_lcms_metab_data/lcms_test_data3.mzML https://nmdcdemo.emsl.pnnl.gov/metabolomics/test_data/metams_lcms_metab_test_data/lcms_test_data3.mzML
 	@echo "LCMS test data downloaded"
 
 wdl-run-lipid :
diff --git a/README.md b/README.md
@@ -10,7 +10,7 @@
 
 ## Current Version
 
-### `3.3.2`
+### `3.3.3`
 
 ## Available Workflows
 
diff --git a/docs/gcms_metabolomics/README_GCMS.md b/docs/gcms_metabolomics/README_GCMS.md
@@ -20,7 +20,7 @@
 
 ## Current Version
 
-### `3.3.2`
+### `3.3.3`
 
 ### 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 3.3.2
+- Current version is 3.3.3
 
 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 (v1.3.2)
+# Lipidomics Workflow (v1.3.3)
 
 ![](lipid_workflow_v1.svg)
 
@@ -128,7 +128,7 @@ The following inputs are required (declared in the input json file):
 
 ## Version History
 
--   v1.3.2: Current release
+-   v1.3.3: 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-v1.3.2">Lipidomics Workflow (v1.3.2)</h1>
+<h1 id="lipidomics-workflow-v1.3.3">Lipidomics Workflow (v1.3.3)</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>v1.3.2: Current release</li>
+<li>v1.3.3: 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 (v1.3.2)
+Lipidomics Workflow (v1.3.3)
 ============================
 
 .. figure:: lipid_workflow_v1.svg
@@ -120,7 +120,7 @@ Outputs
 Version History
 ---------------
 
-- v1.3.2: Current release
+- v1.3.3: 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 (v1.1.2) ============================
+LC/MS Metabolomics Workflow (v1.1.3) ============================
 
 ![](lcms_metabolite_workflow.svg)
 
@@ -123,7 +123,7 @@ The following inputs are required (declared in the input json file):
 
 # Version History
 
--   v1.1.2: Current release
+-   v1.1.3: 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 (v1.1.2) ============================</p>
+<p>LC/MS Metabolomics Workflow (v1.1.3) ============================</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>v1.1.2: Current release</li>
+<li>v1.1.3: 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 (v1.1.2)
+LC/MS Metabolomics Workflow (v1.1.3)
 ============================
 
 .. figure:: lcms_metabolite_workflow.svg
@@ -112,7 +112,7 @@ Outputs
 Version History
 ---------------
 
-- v1.1.2: Current release
+- v1.1.3: 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="332"><code>3.3.2</code></h3>
+<h3 id="333"><code>3.3.3</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;3.3.2&#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;3.3.3&#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__ = '3.3.2'
+__version__ = '3.3.3'
 
 import os
 # Get the path to the README file
diff --git a/requirements.txt b/requirements.txt
@@ -1,3 +1,3 @@
-corems==3.9.2
+corems==3.9.3
 Click>=7.1.1
 requests
diff --git a/setup.py b/setup.py
@@ -11,7 +11,7 @@
 # This call to setup() does all the work
 setup(
     name="metaMS",
-    version="3.3.2",
+    version="3.3.3",
     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:3.3.2'}"
+        docker: "~{if defined(docker_image) then docker_image else 'microbiomedata/metams:3.3.3'}"
     }
 }
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:3.3.2'}"
+        docker: "~{if defined(docker_image) then docker_image else 'microbiomedata/metams:3.3.3'}"
     }
 }
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:3.3.2'}"
+        docker: "~{if defined(docker_image) then docker_image else 'microbiomedata/metams:3.3.3'}"
     }
 }
