Add experiment planner

.github/workflows/python-test.yml

@@ -26,12 +26,12 @@ jobs:
 
     - name: Test with pytest and coverage
       run: |
-        pytest --cov=analyzer_tools --cov-report=xml --cov-report=html --cov-report=term-missing --cov-fail-under=0
+        pytest --cov=analyzer_tools --cov-report=xml --cov-report=html --cov-report=term-missing
 
     - name: Upload coverage reports to Codecov
       uses: codecov/codecov-action@v5
       with:
-        file: ./coverage.xml
+        files: ./coverage.xml
         flags: unittests
         name: codecov-umbrella
         fail_ci_if_error: false

.gitignore

@@ -1,5 +1,6 @@
 data/
 reports/
+results/
 
 # Coverage reports
 coverage.xml
@@ -209,3 +210,4 @@ cython_debug/
 marimo/_static/
 marimo/_lsp/
 __marimo__/
+optimization_results.json

analyzer_tools/planner/README.md

@@ -0,0 +1,10 @@
+# Experiment planning tool
+
+# TODO: add nested sampler
+In some cases the information gain can be comparable in different scenarios.
+For instance in the case of a CuOx layer on top of copper, both a protiated and 
+deuterated electrolyte will lead to similar information gains. But the protiated 
+electrolyte model looks very close to a simpler model without an oxide, as the
+oxide is lost in the roughness. Using a nested sampler to compare two models (with and without an oxide) might give us better insight into what deuteration ratio is best.
+
+We could do this by adding an alternate model to the experiment planner.