MAINT: address reviewer comments

* modify figures based on Mihee's feedback
* fix test coverage
* remove unnecessary string/Path coercions
* remove util function for determining axis ranges
* fix mypy type hints
* fix minor erros in docs, comments, etc.

Author: ajwitmer

neat_ml/data/Binary_Mixture_Phase_Information/PEO8K_Sodium_Citrate_Composition.csv

@@ -1,49 +1,49 @@
-,Group,Label,Sodium Citrate (wt%),PEO 8 kg/mol (wt%),Phase_Separation_1st,Phase_Separation_2nd
-0,A,E2,2.3734801323935453,29.69113889317625,0,0
-1,A,E3,2.308596012,19.985769835360305,0,0
-2,A,E4,2.3726026477842845,9.854187291306609,0,0
-3,A,E5,4.932783175828565,35.06721682417143,1,1
-4,A,E6,5.012942902837546,10.236269805938896,0,0
-5,A,E7,7.494500041353073,24.965346125217106,1,1
-6,A,E8,7.406083474001257,30.084400754642044,1,1
-7,A,E9,7.674131428762139,4.700463905,0,0
-8,A,E10,10.103698811096434,19.887714663143992,1,1
-9,A,E11,9.950719624,30.04928037596684,1,1
-10,A,E12,10.213265374555696,2.3801220575414126,0,0
-11,A,F1,12.274739120602202,10.274932962879202,1,1
-12,A,F3,12.73781549541021,19.62774500025358,1,1
-13,A,F4,14.961766925929574,9.876275803222736,1,1
-14,A,F5,15.346519602047193,19.53482087056399,1,1
+,Group,Label,Sodium citrate (wt%),PEO 8 kg/mol (wt%),Phase_Separation_1st,Phase_Separation_2nd
+0,A,E2,2.373480132,29.69113889,0,0
+1,A,E3,2.308596012,19.98576984,0,0
+2,A,E4,2.372602648,9.854187291,0,0
+3,A,E5,4.932783176,35.06721682,1,1
+4,A,E6,5.012942903,10.23626981,0,0
+5,A,E7,7.494500041,24.96534613,1,1
+6,A,E8,7.406083474,30.08440075,1,1
+7,A,E9,7.674131429,4.700463905,0,0
+8,A,E10,10.10369881,19.88771466,1,1
+9,A,E11,9.950719624,30.04928038,1,1
+10,A,E12,10.21326537,2.380122058,0,0
+11,A,F1,12.27473912,10.27493296,1,1
+12,A,F3,12.7378155,19.627745,1,1
+13,A,F4,14.96176693,9.876275803,1,1
+14,A,F5,15.3465196,19.53482087,1,1
 15,A,F2,20.11679024,9.986877501,1,1
-16,A,F6,20.033699226226503,19.966300773773494,1,1
-17,B,D2,2.5309876049580167,34.94002399040384,1,1
-18,B,D1,2.533076858743832,37.03604583089404,1,1
-19,B,F1,4.918882531134299,29.90912151,1,1
-20,B,A3,5.049249886346416,20.57348756545605,0,1
-21,B,D4,5.135108318174302,24.92806350256326,1,1
-22,B,D5,5.180779255496892,22.303682416627677,1,1
-23,B,B6,7.246757511081923,12.245608274503365,0,0
-24,B,B5,7.398102454181413,11.200505126032267,0,0
-25,B,F2,7.468094003512587,14.77427448356611,1,1
-26,B,A4,7.679688679403523,16.59459550128319,1,1
-27,B,D7,7.700477605958385,19.213787114658825,1,1
-28,B,D12,9.804337538145203,12.11116369392451,1,1
-29,B,A7,9.865017795345327,12.344885273326664,1,1
-30,B,B8,9.891342098734805,8.054246258,1,1
-31,B,A8,9.894325110523114,11.459562509244499,1,1
-32,B,A5,9.979039857806397,14.780756912654896,1,1
-33,B,B9,9.993780781,9.968903904661053,1,1
-34,B,E2,10.019688323822871,5.231754930423467,0,0
-35,B,A9,10.060618306728633,7.670909948137669,1,1
-36,B,A10,10.107457736110876,4.813429679,0,0
-37,B,F3,10.277668339642679,7.0491101252162585,1,1
-38,B,A6,10.357190457150471,12.791550046648007,1,1
-39,B,E4,12.377494253639364,5.2420133915187055,1,1
-40,B,A11,12.454726334603583,6.936229049337335,1,1
-41,B,B1,12.473667411426748,3.0695314731130408,1,1
-42,B,B3,12.723868638993373,0.901378042,0,0
-43,B,B2,12.779514063917732,3.656282555365124,1,1
-44,B,E7,15.084114635281601,1.1018019815147284,1,1
-45,B,B4,15.12884842,0.8746074733746491,1,1
-46,B,E10,19.98453260493969,0.5713063366955721,1,1
-47,B,E9,20.01746206941996,1.0312505148015747,1,1
+16,A,F6,20.03369923,19.96630077,1,1
+17,B,D2,2.530987605,34.94002399,1,1
+18,B,D1,2.533076859,37.03604583,1,1
+19,B,F1,4.918882531,29.90912151,1,1
+20,B,A3,5.049249886,20.57348757,0,1
+21,B,D4,5.135108318,24.9280635,1,1
+22,B,D5,5.180779255,22.30368242,1,1
+23,B,B6,7.246757511,12.24560827,0,0
+24,B,B5,7.398102454,11.20050513,0,0
+25,B,F2,7.468094004,14.77427448,1,1
+26,B,A4,7.679688679,16.5945955,1,1
+27,B,D7,7.700477606,19.21378711,1,1
+28,B,D12,9.804337538,12.11116369,1,1
+29,B,A7,9.865017795,12.34488527,1,1
+30,B,B8,9.891342099,8.054246258,1,1
+31,B,A8,9.894325111,11.45956251,1,1
+32,B,A5,9.979039858,14.78075691,1,1
+33,B,B9,9.993780781,9.968903905,1,1
+34,B,E2,10.01968832,5.23175493,0,0
+35,B,A9,10.06061831,7.670909948,1,1
+36,B,A10,10.10745774,4.813429679,0,0
+37,B,F3,10.27766834,7.049110125,1,1
+38,B,A6,10.35719046,12.79155005,1,1
+39,B,E4,12.37749425,5.242013392,1,1
+40,B,A11,12.45472633,6.936229049,1,1
+41,B,B1,12.47366741,3.069531473,1,1
+42,B,B3,12.72386864,0.901378042,0,0
+43,B,B2,12.77951406,3.656282555,1,1
+44,B,E7,15.08411464,1.101801982,1,1
+45,B,B4,15.12884842,0.874607473,1,1
+46,B,E10,19.9845326,0.571306337,1,1
+47,B,E9,20.01746207,1.031250515,1,1

neat_ml/data/figure_data/Titration_Figures/Figure_3_PEO8k_Sodium_Citrate.csv

@@ -1,4 +1,4 @@
-Sodium Citrate (wt%),PEO 8 kg/mol (wt%),Phase_Separation
+Sodium citrate (wt%),PEO 8 kg/mol (wt%),Phase_Separation
 14.39094,12.94952,1
 13.31245,11.97905,1
 12.15627,10.93867,1

neat_ml/plot_manuscript_figures.py

@@ -1,5 +1,5 @@
 from pathlib import Path
-from importlib.resources import files
+from importlib.resources import files, as_file
 from neat_ml.utils import lib_plotting
 
 if __name__ == "__main__":
@@ -9,27 +9,27 @@
     figures. The variables defined below are used as
     function arguments for lib_plotting.plot_figures()
     """
-
-    PHASE_COLS = ("Phase_Separation_1st", "Phase_Separation_2nd")
-    FIG_3_CSV = files("neat_ml.data.figure_data").joinpath("Titration_Figures")
-    FIG_6_CSV = files("neat_ml.data.figure_data").joinpath("Binodal_Comparison_Figures")
-    CSV_PHASE_DIR = files("neat_ml.data").joinpath("Binary_Mixture_Phase_Information")
-    OUT_DIR = Path("neat_ml/data/Figures_for_Manuscript")
-    OUT_DIR.mkdir(parents=True, exist_ok=True)
-    MAT_MODEL_CSV = files("neat_ml.data.Binary_Mixture_Phase_Information").joinpath("PEO8K_Sodium_Citrate_Composition.csv")
-    JSON_PATH = files("neat_ml").joinpath("data/mathematical_model_parameters.json")
-    MAT_MODEL_PNG = OUT_DIR / (
-        "PEO8K_Sodium_Citrate_Phase_Diagram_Experiment_Literature_Comparison.png"
-    )
+    with as_file(files("neat_ml.data")) as base_path:
+        PHASE_COLS = ("Phase_Separation_1st", "Phase_Separation_2nd")
+        FIG_3_CSV = base_path / "figure_data" / "Titration_Figures"
+        FIG_6_CSV = base_path / "figure_data" / "Binodal_Comparison_Figures"
+        CSV_PHASE_DIR = base_path / "Binary_Mixture_Phase_Information"
+        OUT_DIR = Path("neat_ml/data/Figures_for_Manuscript")
+        OUT_DIR.mkdir(parents=True, exist_ok=True)
+        MAT_MODEL_CSV = base_path / "Binary_Mixture_Phase_Information" / "PEO8K_Sodium_Citrate_Composition.csv"
+        JSON_PATH = base_path / "mathematical_model_parameters.json"
+        MAT_MODEL_PNG = OUT_DIR / (
+            "PEO8K_Sodium_Citrate_Phase_Diagram_Experiment_Literature_Comparison.png"
+        )
 
     lib_plotting.plot_figures(
-        titration_csv_dir=Path(str(FIG_3_CSV)),
-        binodal_csv_dir=Path(str(FIG_6_CSV)),
-        csv_phase_dir=Path(str(CSV_PHASE_DIR)),
+        titration_csv_dir=FIG_3_CSV,
+        binodal_csv_dir=FIG_6_CSV,
+        csv_phase_dir=CSV_PHASE_DIR,
         out_dir=OUT_DIR,
-        mat_model_csv=Path(str(MAT_MODEL_CSV)),
-        mat_model_png=Path(str(MAT_MODEL_PNG)),
-        json_path=Path(str(JSON_PATH)),
+        mat_model_csv=MAT_MODEL_CSV,
+        mat_model_png=MAT_MODEL_PNG,
+        json_path=JSON_PATH,
         phase_cols=PHASE_COLS,
         xrange=[0, 21],
         yrange=[0, 38]