update actions to dependent on reuiqrements file

this fixes the versions so tests do not fail. Will add dependabot to
update the reuqirements file

.github/workflows/ci.yml

@@ -9,8 +9,8 @@ jobs:
       matrix:
         os: [ubuntu-latest]
           #os: [ubuntu-latest, windows-latest, macos-latest] # remove mac tests
-        # Latest pyOpenMS supports Python 3.10, and 3.11
-        python-version: ["3.10", "3.11"]
+        # Requirements file generated with python=3.11 
+        python-version: ["3.11"]
     steps:
     - uses: actions/checkout@v4
 
@@ -21,8 +21,7 @@ jobs:
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip
-        pip install pytest
-        pip install pytest-regtest
+        pip install -r requirements.txt # test with requirements file so can easily bump with dependabot
         pip install .
 
     - name: Compile cython module

requirements.txt

@@ -0,0 +1,118 @@
+#
+# This file is autogenerated by pip-compile with Python 3.11
+# by the following command:
+#
+#    pip-compile --all-extras --output-file=requirements.txt
+#
+click==8.1.7
+    # via pyprophet (setup.py)
+cloudpickle==3.1.0
+    # via hyperopt
+contourpy==1.3.0
+    # via matplotlib
+cycler==0.12.1
+    # via matplotlib
+cython==3.0.11
+    # via pyprophet (setup.py)
+duckdb==1.1.3
+    # via
+    #   duckdb-extension-sqlite-scanner
+    #   duckdb-extensions
+    #   pyprophet (setup.py)
+duckdb-extension-sqlite-scanner==1.1.3
+    # via pyprophet (setup.py)
+duckdb-extensions==1.1.3
+    # via pyprophet (setup.py)
+fonttools==4.55.0
+    # via matplotlib
+future==1.0.0
+    # via hyperopt
+hyperopt==0.2.7
+    # via pyprophet (setup.py)
+iniconfig==2.0.0
+    # via pytest
+joblib==1.4.2
+    # via scikit-learn
+kiwisolver==1.4.7
+    # via matplotlib
+matplotlib==3.9.2
+    # via pyprophet (setup.py)
+networkx==3.2.1
+    # via hyperopt
+numexpr==2.10.1
+    # via pyprophet (setup.py)
+numpy==2.0.2
+    # via
+    #   contourpy
+    #   hyperopt
+    #   matplotlib
+    #   numexpr
+    #   pandas
+    #   patsy
+    #   pyprophet (setup.py)
+    #   scikit-learn
+    #   scipy
+    #   statsmodels
+    #   xgboost
+nvidia-nccl-cu12==2.23.4
+    # via xgboost
+packaging==24.2
+    # via
+    #   matplotlib
+    #   pytest
+    #   statsmodels
+pandas==2.2.3
+    # via
+    #   pyprophet (setup.py)
+    #   statsmodels
+patsy==1.0.1
+    # via statsmodels
+pillow==11.0.0
+    # via matplotlib
+pluggy==1.5.0
+    # via pytest
+py4j==0.10.9.7
+    # via hyperopt
+pyarrow==18.0.0
+    # via pyprophet (setup.py)
+pyparsing==3.2.0
+    # via matplotlib
+pypdf==5.1.0
+    # via pyprophet (setup.py)
+pytest==8.3.3
+    # via
+    #   pyprophet (setup.py)
+    #   pytest-regtest
+pytest-regtest==2.3.3
+    # via pyprophet (setup.py)
+python-dateutil==2.9.0.post0
+    # via
+    #   matplotlib
+    #   pandas
+pytz==2024.2
+    # via pandas
+scikit-learn==1.5.2
+    # via pyprophet (setup.py)
+scipy==1.13.1
+    # via
+    #   hyperopt
+    #   pyprophet (setup.py)
+    #   scikit-learn
+    #   statsmodels
+    #   xgboost
+six==1.16.0
+    # via
+    #   hyperopt
+    #   python-dateutil
+statsmodels==0.14.4
+    # via pyprophet (setup.py)
+tabulate==0.9.0
+    # via pyprophet (setup.py)
+threadpoolctl==3.5.0
+    # via scikit-learn
+tqdm==4.67.0
+    # via hyperopt
+tzdata==2024.2
+    # via pandas
+xgboost==2.1.2
+    # via pyprophet (setup.py)