Merge master into lipid_wf_update

Author: kheal

.gitlab-ci.yml

@@ -3,14 +3,14 @@ include:
 
 
 services:
-  - postgres
+  - postgres:13
 
 variables:
   POSTGRES_DB: molformula
   POSTGRES_USER: coremsdb
   POSTGRES_PASSWORD: coremsmolform
   POSTGRES_HOST_AUTH_METHOD: trust
-  COREMS_DATABASE_URL: postgresql://coremsdb:coremsmolform@localhost:5432/molformula
+  COREMS_DATABASE_URL: postgresql://coremsdb:coremsmolform@postgres:5432/molformula
   PIP_CACHE_DIR: "$CI_PROJECT_DIR/.cache/pip"
 
 stages:
@@ -32,6 +32,7 @@ test-source:
     - python3 -m pip install --upgrade pip
     - python3 -m pip install -r requirements.txt
     - python3 -m pip install pytest pytest-cov
+    - python3 -m pip install psycopg2
     - python3 -c "import pathlib; [p.unlink() for p in pathlib.Path('.').rglob('tests/win_only/__init__.py')]"
     - export PYTHONNET_RUNTIME=coreclr
     - pytest --cache-clear

README.md

@@ -4,7 +4,7 @@
 
 <br>
 <br>
-<a href="https://doi.org/10.5281/zenodo.4641552"><img src="https://zenodo.org/badge/DOI/10.5281/zenodo.4641552.svg" alt="CoreMS DOI" style="width:150px"></a>
+<a href="https://doi.org/10.5281/zenodo.14009575"><img src="https://zenodo.org/badge/DOI/10.5281/zenodo.14009575.svg" alt="DOI"></a>
 <br>
 </div>
 
@@ -337,9 +337,9 @@ If you use CoreMS in your work, please use the following citation:
 
 Version [3.0.0 Release on GitHub](https://github.com/EMSL-Computing/CoreMS/releases/tag/v3.0.0), archived on Zenodo:  
 
-[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.4641552.svg)](https://doi.org/10.5281/zenodo.4641552)
+[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.14009575.svg)](https://doi.org/10.5281/zenodo.14009575)
 
-Yuri E. Corilo, William R. Kew, Lee Ann McCue (2021, March 27). EMSL-Computing/CoreMS: CoreMS 2.0.1 (Version v2.0.1), as developed on Github. Zenodo. http://doi.org/10.5281/zenodo.4641552
+Yuri E. Corilo, William R. Kew, Lee Ann McCue, Katherine R . Heal, James C. Carr (2024, October 29). EMSL-Computing/CoreMS: CoreMS 3.0.0 (Version v3.0.0), as developed on Github. Zenodo. http://doi.org/10.5281/zenodo.14009575
 
 ```
 

corems/__init__.py

@@ -8,9 +8,17 @@
 # Get the path to the README file
 readme_path = os.path.join(os.path.dirname(__file__), "..", "README.md")
 
-# Read the contents of the README file
-with open(readme_path, "r", encoding="utf-8") as readme_file:
-    __doc__ = readme_file.read()
+# Read the contents of the README file if it exists
+if os.path.exists(readme_path):
+    try:
+        with open(readme_path, "r", encoding="utf-8") as readme_file:
+            __doc__ = readme_file.read()
+    except Exception as e:
+        __doc__ = "CoreMS: A comprehensive mass spectrometry framework for software development and data analysis of small molecules analysis."
+        print(f"Warning: Could not read README.md file. Error: {e}")
+else:
+    __doc__ = "CoreMS: A comprehensive mass spectrometry framework for software development and data analysis of small molecules analysis."
+
 
 
 def timeit(method):