Merge branch 'postgres_test_fix' into 'master'

Modify tests to use Postgres, not SQL lite and update documentation and readme Closes #173 See merge request mass-spectrometry/corems!137
EMSL-Computing · Nov 14, 2024 · 14c062a · 14c062a
2 parents b4d4c7e + c62789a
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diff --git a/.gitlab-ci.yml b/.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

diff --git a/README.md b/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
 
 ```
 

diff --git a/docs/corems.html b/docs/corems.html
diff --git a/docs/corems/chroma_peak/calc/ChromaPeakCalc.html b/docs/corems/chroma_peak/calc/ChromaPeakCalc.html
diff --git a/docs/corems/chroma_peak/factory/chroma_peak_classes.html b/docs/corems/chroma_peak/factory/chroma_peak_classes.html
diff --git a/docs/corems/encapsulation/constant.html b/docs/corems/encapsulation/constant.html
diff --git a/docs/corems/encapsulation/factory/parameters.html b/docs/corems/encapsulation/factory/parameters.html
diff --git a/docs/corems/encapsulation/factory/processingSetting.html b/docs/corems/encapsulation/factory/processingSetting.html
diff --git a/docs/corems/encapsulation/input/parameter_from_json.html b/docs/corems/encapsulation/input/parameter_from_json.html
diff --git a/docs/corems/encapsulation/output/parameter_to_dict.html b/docs/corems/encapsulation/output/parameter_to_dict.html
diff --git a/docs/corems/encapsulation/output/parameter_to_json.html b/docs/corems/encapsulation/output/parameter_to_json.html
diff --git a/docs/corems/mass_spectra/calc/GC_Calc.html b/docs/corems/mass_spectra/calc/GC_Calc.html
diff --git a/docs/corems/mass_spectra/calc/GC_Deconvolution.html b/docs/corems/mass_spectra/calc/GC_Deconvolution.html
diff --git a/docs/corems/mass_spectra/calc/GC_RI_Calibration.html b/docs/corems/mass_spectra/calc/GC_RI_Calibration.html
diff --git a/docs/corems/mass_spectra/calc/LC_Calc.html b/docs/corems/mass_spectra/calc/LC_Calc.html
diff --git a/docs/corems/mass_spectra/calc/MZSearch.html b/docs/corems/mass_spectra/calc/MZSearch.html
diff --git a/docs/corems/mass_spectra/calc/SignalProcessing.html b/docs/corems/mass_spectra/calc/SignalProcessing.html
diff --git a/docs/corems/mass_spectra/factory/GC_Class.html b/docs/corems/mass_spectra/factory/GC_Class.html
diff --git a/docs/corems/mass_spectra/factory/LC_Class.html b/docs/corems/mass_spectra/factory/LC_Class.html
diff --git a/docs/corems/mass_spectra/factory/chromat_data.html b/docs/corems/mass_spectra/factory/chromat_data.html
diff --git a/docs/corems/mass_spectra/input/andiNetCDF.html b/docs/corems/mass_spectra/input/andiNetCDF.html
diff --git a/docs/corems/mass_spectra/input/boosterHDF5.html b/docs/corems/mass_spectra/input/boosterHDF5.html
@@ -317,7 +317,7 @@ <h1 class="modulename">
 </span><span id="L-210"><a href="#L-210"><span class="linenos">210</span></a><span class="sd">        Get the LCMS object.</span>
 </span><span id="L-211"><a href="#L-211"><span class="linenos">211</span></a>
 </span><span id="L-212"><a href="#L-212"><span class="linenos">212</span></a><span class="sd">        &quot;&quot;&quot;</span>
-</span><span id="L-213"><a href="#L-213"><span class="linenos">213</span></a>        <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">lcms</span><span class="p">)</span><span class="o">&gt;</span><span class="mi">0</span><span class="p">:</span>
+</span><span id="L-213"><a href="#L-213"><span class="linenos">213</span></a>        <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">lcms</span><span class="p">)</span> <span class="o">&gt;</span> <span class="mi">0</span><span class="p">:</span>
 </span><span id="L-214"><a href="#L-214"><span class="linenos">214</span></a>            <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">lcms</span>
 </span><span id="L-215"><a href="#L-215"><span class="linenos">215</span></a>        <span class="k">else</span><span class="p">:</span>
 </span><span id="L-216"><a href="#L-216"><span class="linenos">216</span></a>            <span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="s2">&quot;Returning an empty LCMS class&quot;</span><span class="p">)</span>
@@ -532,7 +532,7 @@ <h1 class="modulename">
 </span><span id="ReadHDF_BoosterMassSpectra-211"><a href="#ReadHDF_BoosterMassSpectra-211"><span class="linenos">211</span></a><span class="sd">        Get the LCMS object.</span>
 </span><span id="ReadHDF_BoosterMassSpectra-212"><a href="#ReadHDF_BoosterMassSpectra-212"><span class="linenos">212</span></a>
 </span><span id="ReadHDF_BoosterMassSpectra-213"><a href="#ReadHDF_BoosterMassSpectra-213"><span class="linenos">213</span></a><span class="sd">        &quot;&quot;&quot;</span>
-</span><span id="ReadHDF_BoosterMassSpectra-214"><a href="#ReadHDF_BoosterMassSpectra-214"><span class="linenos">214</span></a>        <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">lcms</span><span class="p">)</span><span class="o">&gt;</span><span class="mi">0</span><span class="p">:</span>
+</span><span id="ReadHDF_BoosterMassSpectra-214"><a href="#ReadHDF_BoosterMassSpectra-214"><span class="linenos">214</span></a>        <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">lcms</span><span class="p">)</span> <span class="o">&gt;</span> <span class="mi">0</span><span class="p">:</span>
 </span><span id="ReadHDF_BoosterMassSpectra-215"><a href="#ReadHDF_BoosterMassSpectra-215"><span class="linenos">215</span></a>            <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">lcms</span>
 </span><span id="ReadHDF_BoosterMassSpectra-216"><a href="#ReadHDF_BoosterMassSpectra-216"><span class="linenos">216</span></a>        <span class="k">else</span><span class="p">:</span>
 </span><span id="ReadHDF_BoosterMassSpectra-217"><a href="#ReadHDF_BoosterMassSpectra-217"><span class="linenos">217</span></a>            <span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="s2">&quot;Returning an empty LCMS class&quot;</span><span class="p">)</span>
@@ -1000,7 +1000,7 @@ <h6 id="parameters">Parameters</h6>
 </span><span id="ReadHDF_BoosterMassSpectra.get_lcms_obj-211"><a href="#ReadHDF_BoosterMassSpectra.get_lcms_obj-211"><span class="linenos">211</span></a><span class="sd">        Get the LCMS object.</span>
 </span><span id="ReadHDF_BoosterMassSpectra.get_lcms_obj-212"><a href="#ReadHDF_BoosterMassSpectra.get_lcms_obj-212"><span class="linenos">212</span></a>
 </span><span id="ReadHDF_BoosterMassSpectra.get_lcms_obj-213"><a href="#ReadHDF_BoosterMassSpectra.get_lcms_obj-213"><span class="linenos">213</span></a><span class="sd">        &quot;&quot;&quot;</span>
-</span><span id="ReadHDF_BoosterMassSpectra.get_lcms_obj-214"><a href="#ReadHDF_BoosterMassSpectra.get_lcms_obj-214"><span class="linenos">214</span></a>        <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">lcms</span><span class="p">)</span><span class="o">&gt;</span><span class="mi">0</span><span class="p">:</span>
+</span><span id="ReadHDF_BoosterMassSpectra.get_lcms_obj-214"><a href="#ReadHDF_BoosterMassSpectra.get_lcms_obj-214"><span class="linenos">214</span></a>        <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">lcms</span><span class="p">)</span> <span class="o">&gt;</span> <span class="mi">0</span><span class="p">:</span>
 </span><span id="ReadHDF_BoosterMassSpectra.get_lcms_obj-215"><a href="#ReadHDF_BoosterMassSpectra.get_lcms_obj-215"><span class="linenos">215</span></a>            <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">lcms</span>
 </span><span id="ReadHDF_BoosterMassSpectra.get_lcms_obj-216"><a href="#ReadHDF_BoosterMassSpectra.get_lcms_obj-216"><span class="linenos">216</span></a>        <span class="k">else</span><span class="p">:</span>
 </span><span id="ReadHDF_BoosterMassSpectra.get_lcms_obj-217"><a href="#ReadHDF_BoosterMassSpectra.get_lcms_obj-217"><span class="linenos">217</span></a>            <span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="s2">&quot;Returning an empty LCMS class&quot;</span><span class="p">)</span>