Merge branch '197_metabref_compat' into 'master'

Modify MetabRef queries to remove reliance on header / token and add workflow for publishing to PyPi

Closes #197 and #196

See merge request mass-spectrometry/corems!153

Author: corilo

.bumpversion.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 3.2.1
+current_version = 3.3.0
 commit = False
 tag = False
 

.github/workflows/pypi_publish.yml

@@ -0,0 +1,32 @@
+name: Publish PyPi Package
+
+on:
+  release:
+    types: [created]
+
+jobs:
+  publish:
+    runs-on: ubuntu-latest
+    
+    steps:
+    - id: checkout
+      uses: actions/checkout@v3
+    
+    - id: python-setup
+      name: Set up Python
+      uses: actions/setup-python@v2
+      with:
+        python-version: '3.11'
+
+    - id: python-dependencies
+      name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install setuptools wheel twine
+    
+    - id: publish-pypi
+      env:
+        TWINE_USERNAME: __token__
+        TWINE_PASSWORD: ${{ secrets.PYPI_TOKEN }}
+      run: |
+            make pypi

README.md

@@ -49,7 +49,7 @@ CoreMS aims to provide
 
 ## Current Version
 
- `3.2.1`
+ `3.3.0`
 
 ***
 
@@ -335,11 +335,11 @@ UML (unified modeling language) diagrams for Direct Infusion FT-MS and GC-MS cla
 
 If you use CoreMS in your work, please use the following citation:
 
-Version [3.2.1 Release on GitHub](https://github.com/EMSL-Computing/CoreMS/releases/tag/v3.2.1), archived on Zenodo:  
+Version [3.3.0 Release on GitHub](https://github.com/EMSL-Computing/CoreMS/releases/tag/v3.3.0), archived on Zenodo:  
 
 [![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, Katherine R . Heal, James C. Carr (2024, October 29). EMSL-Computing/CoreMS: CoreMS 3.2.1 (Version v3.2.1), as developed on Github. Zenodo. http://doi.org/10.5281/zenodo.14009575
+Yuri E. Corilo, William R. Kew, Lee Ann McCue, Katherine R . Heal, James C. Carr (2024, October 29). EMSL-Computing/CoreMS: CoreMS 3.3.0 (Version v3.3.0), as developed on Github. Zenodo. http://doi.org/10.5281/zenodo.14009575
 
 ```
 

corems/__init__.py

@@ -1,5 +1,5 @@
 __author__ = "Yuri E. Corilo"
-__version__ = "3.2.1"
+__version__ = "3.3.0"
 import time
 import os
 import sys

corems/molecular_id/search/database_interfaces.py

@@ -92,14 +92,16 @@ def get_header(self):
 
         return header
 
-    def get_query(self, url):
+    def get_query(self, url, use_header=True):
         """
         Request payload from URL according to `get` protocol.
 
         Parameters
         ----------
         url : str
             URL for request.
+        use_header: bool
+            Whether or not the query should include the header
 
         Returns
         -------
@@ -109,7 +111,10 @@ def get_query(self, url):
         """
 
         # Query URL via `get`
-        response = requests.get(url, headers=self.get_header())
+        if use_header:
+            response = requests.get(url, headers=self.get_header())
+        else:
+            response = requests.get(url)
 
         # Check response
         response.raise_for_status()
@@ -352,6 +357,16 @@ def _dict_to_dataclass(self, metabref_lib, data_class):
             if key not in input_dict.keys():
                 input_dict[key] = None
         return data_class(**input_dict)
+    
+    def get_query(self, url, use_header=False):
+        """Overwrites the get_query method on the parent class to default to not use a header
+        
+        Notes
+        -----
+        As of January 2025, the metabref database no longer requires a token and therefore no header is needed
+
+        """
+        return super().get_query(url, use_header)
 
 
 class MetabRefGCInterface(MetabRefInterface):

docs/corems.html

@@ -154,7 +154,7 @@ <h1 id="corems">CoreMS</h1>
 
 <h2 id="current-version">Current Version</h2>
 
-<p><code>3.2.1</code></p>
+<p><code>3.3.0</code></p>
 
 <hr />
 
@@ -487,11 +487,11 @@ <h2 id="citing-corems">Citing CoreMS</h2>
 
 <p>If you use CoreMS in your work, please use the following citation:</p>
 
-<p>Version <a href="https://github.com/EMSL-Computing/CoreMS/releases/tag/v3.2.1">3.2.1 Release on GitHub</a>, archived on Zenodo:  </p>
+<p>Version <a href="https://github.com/EMSL-Computing/CoreMS/releases/tag/v3.3.0">3.3.0 Release on GitHub</a>, archived on Zenodo:  </p>
 
 <p><a href="https://doi.org/10.5281/zenodo.14009575"><img src="https://zenodo.org/badge/DOI/10.5281/zenodo.14009575.svg" alt="DOI" /></a></p>
 
-<p>Yuri E. Corilo, William R. Kew, Lee Ann McCue, Katherine R . Heal, James C. Carr (2024, October 29). EMSL-Computing/CoreMS: CoreMS 3.2.1 (Version v3.2.1), as developed on Github. Zenodo. <a href="http://doi.org/10.5281/zenodo.14009575">http://doi.org/10.5281/zenodo.14009575</a></p>
+<p>Yuri E. Corilo, William R. Kew, Lee Ann McCue, Katherine R . Heal, James C. Carr (2024, October 29). EMSL-Computing/CoreMS: CoreMS 3.3.0 (Version v3.3.0), as developed on Github. Zenodo. <a href="http://doi.org/10.5281/zenodo.14009575">http://doi.org/10.5281/zenodo.14009575</a></p>
 
 <p>```</p>
 
@@ -527,7 +527,7 @@ <h2 id="citing-corems">Citing CoreMS</h2>
                         <label class="view-source-button" for="mod-corems-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">__author__</span> <span class="o">=</span> <span class="s2">&quot;Yuri E. Corilo&quot;</span>
-</span><span id="L-2"><a href="#L-2"><span class="linenos"> 2</span></a><span class="n">__version__</span> <span class="o">=</span> <span class="s2">&quot;3.2.1&quot;</span>
+</span><span id="L-2"><a href="#L-2"><span class="linenos"> 2</span></a><span class="n">__version__</span> <span class="o">=</span> <span class="s2">&quot;3.3.0&quot;</span>
 </span><span id="L-3"><a href="#L-3"><span class="linenos"> 3</span></a><span class="kn">import</span> <span class="nn">time</span>
 </span><span id="L-4"><a href="#L-4"><span class="linenos"> 4</span></a><span class="kn">import</span> <span class="nn">os</span>
 </span><span id="L-5"><a href="#L-5"><span class="linenos"> 5</span></a><span class="kn">import</span> <span class="nn">sys</span>