add tests and IPs for all elements in NIST database

- previous list was incomplete
- remove iniabu from requirements

pyproject.toml

@@ -40,7 +40,6 @@ dev-dependencies = [
     "hypothesis>=6.97.1",
     "pytest-cov>=4.1.0",
     "requests>=2.31.0",
-    "iniabu>=1.1.2",
 ]
 
 [tool.rye.scripts]

requirements-dev.lock

@@ -25,7 +25,6 @@ fonttools==4.49.0
 hypothesis==6.98.13
 idna==3.6
     # via requests
-iniabu==1.1.2
 iniconfig==2.0.0
     # via pytest
 kiwisolver==1.4.5
@@ -34,7 +33,6 @@ matplotlib==3.8.3
     # via rimsschemedrawer
 numpy==1.26.4
     # via contourpy
-    # via iniabu
     # via matplotlib
     # via rimsschemedrawer
 packaging==23.2

scripts/ip_nist.json

@@ -41,6 +41,7 @@
     "Zr": 53507.832,
     "Nb": 54513.8,
     "Mo": 57204.3,
+    "Tc": 57421.68,
     "Ru": 59366.4,
     "Rh": 60160.1,
     "Pd": 67241.14,
@@ -58,6 +59,7 @@
     "Ce": 44672.0,
     "Pr": 44120.0,
     "Nd": 44562.0,
+    "Pm": 45020.8,
     "Sm": 45519.69,
     "Eu": 45734.74,
     "Gd": 49601.45,
@@ -80,6 +82,39 @@
     "Tl": 49266.66,
     "Pb": 59819.558,
     "Bi": 58761.65,
+    "Po": 67896.31,
+    "At": 75150.8,
+    "Rn": 86692.5,
+    "Fr": 32848.872,
+    "Ra": 42573.36,
+    "Ac": 43394.52,
     "Th": 50867.0,
-    "U": 49958.4
+    "Pa": 47500.0,
+    "U": 49958.4,
+    "Np": 50535.0,
+    "Pu": 48601.0,
+    "Am": 48182.0,
+    "Cm": 48330.68,
+    "Bk": 49989.0,
+    "Cf": 50666.76,
+    "Es": 51364.58,
+    "Fm": 52400.0,
+    "Md": 53100.0,
+    "No": 53444.0,
+    "Lr": 40005.0,
+    "Rf": 48580.0,
+    "Db": 55000.0,
+    "Sg": 63000.0,
+    "Bh": 62000.0,
+    "Hs": 61000.0,
+    "Mt": null,
+    "Ds": null,
+    "Rg": null,
+    "Cn": null,
+    "Nh": null,
+    "Fl": null,
+    "Mc": null,
+    "Lv": null,
+    "Ts": null,
+    "Og": null
 }

scripts/ip_nist_reader.py

@@ -1,6 +1,24 @@
+"""Create json file with all ionization potentials.
+
+Elemental data read from the NIST database, which can be found here:
+https://physics.nist.gov/PhysRefData/ASD/levels_form.html
+
+2024-02-29: Currently, the following elements have no IP data associated with them:
+    - Mt
+    - Ds
+    - Rg
+    - Cn
+    - Nh
+    - Fl
+    - Mc
+    - Lv
+    - Ts
+    - Og
+"""
+
+
 import json
 
-from iniabu import ini
 import requests
 
 
@@ -31,11 +49,20 @@ def get_ip(ele: str) -> float:
     data = data.split("\n")
 
     # find limit line in data
+    limit_found = False
     for it, line in enumerate(data):
         if "Limit" in line:
             idx = it
+            limit_found = True
             break
 
+    if not limit_found:
+        try:
+            return manual_ips[ele]
+        except KeyError:
+            print(f"Could not find limit for {ele}")
+            return None
+
     line = data[idx].replace('"', "").replace("=", "").split(",")
     # print(line)
     ip = line[4]
@@ -44,12 +71,130 @@ def get_ip(ele: str) -> float:
     return float(ip)
 
 
-elements = ini.ele_dict.keys()  # list of all elements
-ele_ips = {}
-
-# print(elements)
+manual_ips = {}
+
+elements = [
+    "H",
+    "He",
+    "Li",
+    "Be",
+    "B",
+    "C",
+    "N",
+    "O",
+    "F",
+    "Ne",
+    "Na",
+    "Mg",
+    "Al",
+    "Si",
+    "P",
+    "S",
+    "Cl",
+    "Ar",
+    "K",
+    "Ca",
+    "Sc",
+    "Ti",
+    "V",
+    "Cr",
+    "Mn",
+    "Fe",
+    "Co",
+    "Ni",
+    "Cu",
+    "Zn",
+    "Ga",
+    "Ge",
+    "As",
+    "Se",
+    "Br",
+    "Kr",
+    "Rb",
+    "Sr",
+    "Y",
+    "Zr",
+    "Nb",
+    "Mo",
+    "Tc",
+    "Ru",
+    "Rh",
+    "Pd",
+    "Ag",
+    "Cd",
+    "In",
+    "Sn",
+    "Sb",
+    "Te",
+    "I",
+    "Xe",
+    "Cs",
+    "Ba",
+    "La",
+    "Ce",
+    "Pr",
+    "Nd",
+    "Pm",
+    "Sm",
+    "Eu",
+    "Gd",
+    "Tb",
+    "Dy",
+    "Ho",
+    "Er",
+    "Tm",
+    "Yb",
+    "Lu",
+    "Hf",
+    "Ta",
+    "W",
+    "Re",
+    "Os",
+    "Ir",
+    "Pt",
+    "Au",
+    "Hg",
+    "Tl",
+    "Pb",
+    "Bi",
+    "Po",
+    "At",
+    "Rn",
+    "Fr",
+    "Ra",
+    "Ac",
+    "Th",
+    "Pa",
+    "U",
+    "Np",
+    "Pu",
+    "Am",
+    "Cm",
+    "Bk",
+    "Cf",
+    "Es",
+    "Fm",
+    "Md",
+    "No",
+    "Lr",
+    "Rf",
+    "Db",
+    "Sg",
+    "Bh",
+    "Hs",
+    "Mt",
+    "Ds",
+    "Rg",
+    "Cn",
+    "Nh",
+    "Fl",
+    "Mc",
+    "Lv",
+    "Ts",
+    "Og",
+]
 
-# print(get_ip("Tb"))
+ele_ips = {}
 
 for ele in elements:
     print(f"{ele} is up")

src/rimsschemedrawer/utils.py

@@ -76,6 +76,7 @@
     "Zr": 53507.832,
     "Nb": 54513.8,
     "Mo": 57204.3,
+    "Tc": 57421.68,
     "Ru": 59366.4,
     "Rh": 60160.1,
     "Pd": 67241.14,
@@ -93,6 +94,7 @@
     "Ce": 44672.0,
     "Pr": 44120.0,
     "Nd": 44562.0,
+    "Pm": 45020.8,
     "Sm": 45519.69,
     "Eu": 45734.74,
     "Gd": 49601.45,
@@ -115,8 +117,31 @@
     "Tl": 49266.66,
     "Pb": 59819.558,
     "Bi": 58761.65,
+    "Po": 67896.31,
+    "At": 75150.8,
+    "Rn": 86692.5,
+    "Fr": 32848.872,
+    "Ra": 42573.36,
+    "Ac": 43394.52,
     "Th": 50867.0,
+    "Pa": 47500.0,
     "U": 49958.4,
+    "Np": 50535.0,
+    "Pu": 48601.0,
+    "Am": 48182.0,
+    "Cm": 48330.68,
+    "Bk": 49989.0,
+    "Cf": 50666.76,
+    "Es": 51364.58,
+    "Fm": 52400.0,
+    "Md": 53100.0,
+    "No": 53444.0,
+    "Lr": 40005.0,
+    "Rf": 48580.0,
+    "Db": 55000.0,
+    "Sg": 63000.0,
+    "Bh": 62000.0,
+    "Hs": 61000.0,
 }
 
 

tests/data/ti_old_style.json

@@ -0,0 +1,40 @@
+{
+    "scheme": {
+        "gs_level": "0",
+        "gs_term": "3F2",
+        "ip_level": "55070",
+        "ip_term": "",
+        "step_level0": "170.15",
+        "step_level1": "386.88",
+        "step_level2": "21469.5",
+        "step_level3": "45498.85",
+        "step_level4": "56844.45",
+        "step_lowlying0": true,
+        "step_lowlying1": true,
+        "step_lowlying2": false,
+        "step_lowlying3": false,
+        "step_lowlying4": false,
+        "step_term0": "3F3",
+        "step_term1": "3F4",
+        "step_term2": "3G3",
+        "step_term3": "3G4",
+        "step_term4": "",
+        "unit": "cm<sup>-1</sup>"
+    },
+    "settings": {
+        "arrow_head_width": "0.6",
+        "arrow_width": "0.2",
+        "fig_height": "8",
+        "fig_width": "5",
+        "fs_axes": "12",
+        "fs_axes_labels": "14",
+        "fs_labels": "12",
+        "fs_title": "14",
+        "headspace": "2700",
+        "ip_label_pos": "Top",
+        "line_breaks": false,
+        "plot_title": "",
+        "prec_level": "0",
+        "prec_wavelength": "3"
+    }
+}

tests/test_plotter.py

@@ -1,4 +1,6 @@
 # Test the plotter
+import pytest
+
 import rimsschemedrawer.json_parser
 from rimsschemedrawer.plotter import Plotter
 
@@ -13,3 +15,12 @@ def test_plotter(data_path, tmp_path):
     fig.savefig(fname)
 
     assert fname.exists()
+
+
+def test_plotter_old_style(data_path):
+    """Raise warning when old style file is detected."""
+    fin = data_path.joinpath("ti_old_style.json")
+    data = rimsschemedrawer.json_parser.json_reader(fin)
+
+    with pytest.warns(UserWarning, match="Ti"):
+        _ = Plotter(data)

tests/test_utils.py

@@ -13,6 +13,15 @@ def test_cm_2_to_nm():
     assert ut.cm_2_to_nm(3.3333333333333335e6) == 3
 
 
+def test_get_elements():
+    """Check that elements are in list."""
+    eles = ut.get_elements()
+    assert "H" in eles
+    assert "He" in eles
+    assert "U" in eles
+    assert "Pu" in eles
+
+
 def test_get_ip():
     """Check that the ionization potentials are correct."""
     assert ut.get_ip("H") == 109678.77174307