resolved Fe lines conflict

.isort.cfg

@@ -1,5 +1,4 @@
-[settings]
-known_third_party = astropy,dotmap,matplotlib,numpy,omegaconf,pkg_resources,pytest,rascal,scipy,setuptools,tqdm,yaml
+known_third_party = astropy,bs4,dotmap,matplotlib,numpy,omegaconf,pkg_resources,preprocess_nist,pytest,rascal,scipy,setuptools,tqdm,yaml
 
 [tool.isort]
 profile = "black"

src/rascal/arc_lines/.gitignore

@@ -0,0 +1,2 @@
+*.pkl
+*.txt

src/rascal/arc_lines/get_strong_lines.py

@@ -0,0 +1,173 @@
+import argparse
+import csv
+
+from preprocess_nist import get_elements, toInt, toRoman
+
+from rascal.util import air_to_vacuum_wavelength
+
+
+def get_strong_url(name):
+    return f"https://physics.nist.gov/PhysRefData/Handbook/Tables/{name.lower()}table2_a.htm"
+
+
+import os
+from urllib import request
+
+from bs4 import BeautifulSoup
+from tqdm.auto import tqdm
+
+elements = get_elements(short_name=False)
+elements_short = get_elements()
+
+
+def process_raw(element, data):
+    """
+    Process a dump of NIST's "strong lines" web page. Unfortunately no machine readable
+    format is provided and the rows have variable column lengths
+    so we have to bodge around it.
+
+    """
+    mode = "air"
+
+    out = []
+
+    for line in data:
+
+        line = line.strip()
+        cols = line.split(",")
+
+        if len(cols) == 1:
+            if "vacuum" in cols[0].lower():
+                mode = "vacuum"
+            elif "air" in cols[0].lower():
+                mode = "air"
+        else:
+            intensity = 0
+            note = []
+            if cols[0] == "Intensity":
+                continue
+            # If there are only 4 columns, then first item is wavelength
+            # otherwise it should always be intensity
+            elif len(cols) == 3:
+                wavelength, element, ref = cols
+
+                ionisation = "I"
+            elif len(cols) == 4:
+                wavelength, element, ionisation, ref = cols
+            else:
+
+                try:
+                    intensity = cols[0]
+                    intensity = int(str(intensity).replace("*", ""))
+                except:
+                    continue
+
+                # Grab single letter "other info"
+                cols = cols[1:]
+                while len(cols[0]) == 1:
+                    note.append(cols[0])
+                    cols = cols[1:]
+
+                try:
+                    wavelength, element, ionisation, ref = cols[:4]
+                except:
+                    continue
+
+            wavelength = float(wavelength)
+
+            if mode == "air":
+                wavelength = air_to_vacuum_wavelength(wavelength)
+
+            # Some of the state info is odd
+            state_int = -1
+            try:
+                state_int = toInt(ionisation)
+            except:
+                pass
+
+            out.append(
+                {
+                    "element": element,
+                    "intensity": intensity,
+                    "note": "".join(note),
+                    "wavelength": wavelength,
+                    "state": state_int,
+                    "reference": ref,
+                    "note": "".join(note),
+                    "acc": "",
+                    "source": "",
+                    "unit": "A",
+                }
+            )
+
+    return out
+
+
+def main(args):
+
+    os.makedirs("strong_lines", exist_ok=True)
+
+    if args.download:
+        for element in tqdm(elements):
+
+            try:
+                res = request.urlopen(get_strong_url(element))
+            except request.HTTPError:
+                print(f"Failed to download {element}")
+
+            data_str = res.read().decode()
+            soup = BeautifulSoup(data_str)
+
+            try:
+                with open(f"strong_lines/{element}.txt", "w") as fp:
+                    for row in soup.select("pre")[0].text.split("\r\n"):
+                        fp.write(",".join(row.split()))
+                        fp.write("\n")
+            except (TypeError, IndexError):
+                print(f"Failed to download {element}")
+
+    elements_short = get_elements()
+    for idx, element in enumerate(elements):
+        file = f"strong_lines/{element}.txt"
+
+        if not os.path.exists(file):
+            continue
+
+        with open(file, "r") as fp:
+            data = fp.readlines()
+
+            out = process_raw(elements_short[idx], data)
+
+        states = set([line["state"] for line in out if line["state"] >= 1])
+
+        for state in states:
+            with open(
+                f"strong_lines/{elements_short[idx]}_{toRoman(state)}.csv", "w"
+            ) as fp:
+                writer = csv.DictWriter(
+                    fp,
+                    fieldnames=[
+                        "element",
+                        "wavelength",
+                        "intensity",
+                        "acc",
+                        "state",
+                        "source",
+                        "note",
+                        "reference",
+                        "unit",
+                    ],
+                )
+                writer.writeheader()
+                writer.writerows(
+                    [line for line in out if line["state"] == state]
+                )
+
+
+if __name__ == "__main__":
+
+    parser = argparse.ArgumentParser()
+    parser.add_argument("--download", action="store_true")
+    args = parser.parse_args()
+
+    main(args)