Address JOSS comments + prepare for v1.0 release

doc/basic_usage.md

@@ -11,13 +11,16 @@ ae.visualization.plot_impedance_combo(freq, Z)
 
 # Perform automated EIS analysis
 circuits = ae.perform_full_analysis(freq, Z, iters=24, parallel=True)
-print(circuits)
 
-# Print summary of the results
-mcmcs, status = circuits["MCMC (chain)"], circuits["MCMC (status)"]
-for mcmc, stat, circuit in zip(mcmcs, status, circuits.circuitstring):
-    if stat == 0:
+# Print summary of the inference for each circuit model
+for i, row in circuits.iterrows():
+    circuit = row["circuit"]
+    mcmc = row["MCMC"]
+    if row["success"]:
         ae.visualization.print_summary_statistics(mcmc, circuit)
+
+# Print summary of all circuit models
+ae.visualization.print_inference_results(circuits)
 ```
 
 :::{seealso}

doc/examples.rst

@@ -11,4 +11,6 @@ AutoEIS is still under development, and we will add more examples as we make pro
     :maxdepth: 1
 
     examples/circuit_basics
+    examples/circuit_generation
     examples/basic_workflow
+    examples/parallel_inference

examples/circuit_basics.ipynb

@@ -4,7 +4,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "# Circuit models 101\n",
+    "# Circuit Models 101\n",
     "\n",
     "In this notebook, we will explore the basics of circuit models in AutoEIS. We will start by importing the necessary libraries."
    ]
@@ -311,11 +311,11 @@
     {
      "data": {
       "text/plain": [
-       "array([1.31224604-3.15463527e+02j, 1.30870746-6.79460179e+01j,\n",
-       "       1.35630867-1.45662084e+01j, 1.45656166-3.12402983e+00j,\n",
-       "       1.44771251-7.23602325e-01j, 1.34794177-2.66541669e-01j,\n",
-       "       1.21918839-1.06364114e-01j, 1.17811049-4.72247543e-02j,\n",
-       "       1.14814457-3.18940068e-02j, 1.12181823-2.52094831e-02j])"
+       "array([0.85089852-1.64798029e+02j, 0.85081614-3.54974344e+01j,\n",
+       "       0.85810555-7.61382811e+00j, 0.94485726-1.56968312e+00j,\n",
+       "       1.00846777-3.85588331e-01j, 0.88255519-1.91496795e-01j,\n",
+       "       0.77938056-9.66334080e-02j, 0.71046522-6.71223724e-02j,\n",
+       "       0.65790512-4.10276536e-02j, 0.63191817-2.00368082e-02j])"
       ]
      },
      "execution_count": 10,

pyproject.toml

@@ -28,7 +28,8 @@ dependencies = [
     "click",
     "deprecated",
     "dill",
-    "impedance",
+    # "impedance",
+    "impedance @ git+https://github.com/ma-sadeghi/impedance.py@fix-numpy2",
     "ipython",
     "ipykernel",
     "ipywidgets",
@@ -102,6 +103,9 @@ path = "src/autoeis/version.py"
 [tool.hatch.build.targets.sdist]
 include = ["src/autoeis"]
 
+[tool.hatch.metadata]
+allow-direct-references = true
+
 [tool.pytest.ini_options]
 minversion = "6.0"
 addopts = "-ra -vv --durations=5"