Change names of calc and conf easyxtb modules

about.py

@@ -57,7 +57,7 @@
         # Do nothing to data other than add message with version and path info
         output["message"] = (
             "avo_xtb plugin\n"
-            + f"easyxtb version: {easyxtb.conf.easyxtb_VERSION}\n"
+            + f"easyxtb version: {easyxtb.configuration.easyxtb_VERSION}\n"
             + f"xtb version: {xtb_version}\n"
             + f"xtb path: {easyxtb.XTB_BIN}\n"
             + f"CREST version: {crest_version}\n"

config.py

@@ -134,7 +134,7 @@
         # Save change to user_dir if there has been one
         if avo_input["user_dir"] != str(easyxtb.CALC_DIR):
             easyxtb.CALC_DIR = Path(avo_input["user_dir"])
-            easyxtb.conf.TEMP_DIR = easyxtb.CALC_DIR / "last"
+            easyxtb.configuration.TEMP_DIR = easyxtb.CALC_DIR / "last"
             try:
                 easyxtb.TEMP_DIR.mkdir(parents=True, exist_ok=True)
             except PermissionError:
@@ -171,4 +171,4 @@
         # Update optimization level
         easyxtb.config["opt_lvl"] = avo_input["opt_lvl"]
 
-        easyxtb.conf.save_config()
+        easyxtb.configuration.save_config()

conformers.py

@@ -155,7 +155,7 @@
             solvation = avo_input["solvent"]
 
         # Run calculation; returns set of conformers as well as Calculation object
-        conformers, calc = easyxtb.calc.conformers(
+        conformers, calc = easyxtb.calculate.conformers(
             geom,
             solvation=solvation,
             method=2,

deprotonate.py

@@ -42,7 +42,7 @@
         geom = easyxtb.Geometry.from_cjson(avo_input["cjson"])
 
         # Run calculation; returns set of tautomers as well as Calculation object
-        tautomers, calc = easyxtb.calc.deprotonate(
+        tautomers, calc = easyxtb.calculate.deprotonate(
             geom,
             solvation=easyxtb.config["solvent"],
             method=2,

easyxtb/README.md

@@ -48,7 +48,7 @@ Note that `easyxtb` follows the convention used by `xtb` itself, where `spin` is
 The package provides a function API for basic xtb calculation types (`energy`, `optimize`, `frequencies`, `opt_freq`, `orbitals`):
 
 ```python
->>> optimized = py_xtb.calc.optimize(input_geom, solvation="water", method=2, level="normal")
+>>> optimized = py_xtb.calculate.optimize(input_geom, solvation="water", method=2, level="normal")
 >>> for atom in optimized:
 ...     print(atom)
 ... 
@@ -78,7 +78,7 @@ The xtb team recommend generally using the `ohess` (optimization followed by a f
 The `opt_freq()` calculation function takes advantage of this and will continue reoptimizing using these distorted geometries until a minimum is reached, so is more reliable in getting what we want:
 
 ```python
->>> output_geom, output_freqs, calc = py_xtb.calc.opt_freq(input_geom, solvation="water", return_calc=True)
+>>> output_geom, output_freqs, calc = py_xtb.calculate.opt_freq(input_geom, solvation="water", return_calc=True)
 >>> output_freqs[0]
 {'mode': 1, 'symmetry': 'a', 'frequency': 70.0622, 'reduced_mass': 13.4154, 'ir_intensity': 6.422, 'raman_scattering_activity': 0.0, 'eigenvectors': [[0.0, 0.0, -0.28], [-0.0, 0.0, -0.0], [-0.0, -0.0, 0.25], [0.0, -0.0, 0.04], [0.0, -0.0, -0.24], [-0.0, 0.0, -0.0], [-0.0, 0.0, 0.29], [-0.0, 0.0, 0.15], [0.0, -0.0, 0.02], [0.0, -0.0, -0.12], [0.0, 0.0, -0.15], [0.0, -0.0, 0.55], [0.0, 0.01, -0.56], [0.0, 0.0, -0.19]]}
 ```

easyxtb/src/easyxtb/__init__.py

@@ -1,10 +1,10 @@
 import logging
 
-from .conf import config, config_file
-from .conf import PLUGIN_DIR, CALC_DIR, TEMP_DIR, BIN_DIR, XTB_BIN, CREST_BIN
+from .configuration import config, config_file
+from .configuration import PLUGIN_DIR, CALC_DIR, TEMP_DIR, BIN_DIR, XTB_BIN, CREST_BIN
 from .geometry import Atom, Geometry
-from .calc import Calculation
-from . import calc, conf, convert, format
+from .calculate import Calculation
+from . import calculate, configuration, convert, format
 
 
 logger = logging.getLogger(__name__)

easyxtb/src/easyxtb/calc.py → easyxtb/src/easyxtb/calculate.py

@@ -20,7 +20,7 @@
 from pathlib import Path
 from shutil import rmtree
 
-from .conf import config, XTB_BIN, CREST_BIN, TEMP_DIR
+from .configuration import config, XTB_BIN, CREST_BIN, TEMP_DIR
 from .geometry import Geometry
 from .parse import parse_energy, parse_g98_frequencies
 

easyxtb/tests/test_calc.py

@@ -3,7 +3,7 @@
 
 from pathlib import Path
 
-from easyxtb import Geometry, calc, parse
+from easyxtb import Geometry, calculate, parse
 from . import equal_geom
 
 
@@ -23,7 +23,7 @@
 def test_opt_neutral_singlet():
     for mol in ["acetic_acid", "acetone", "benzene"]:
         in_geom = Geometry.from_file(input_dir / f"{mol}.cjson")
-        out_geom = calc.optimize(in_geom)
+        out_geom = calculate.optimize(in_geom)
         ref_geom = Geometry.from_file(results_dir / f"{mol}_opt.xyz")
         print(f"Testing {mol}:")
         assert equal_geom(out_geom, ref_geom)
@@ -32,7 +32,7 @@ def test_opt_neutral_singlet():
 def test_opt_charged():
     for mol in ["benzoate", "bu4n"]:
         in_geom = Geometry.from_file(input_dir / f"{mol}.cjson")
-        out_geom = calc.optimize(in_geom)
+        out_geom = calculate.optimize(in_geom)
         ref_geom = Geometry.from_file(results_dir / f"{mol}_opt.xyz")
         print(f"Testing {mol}:")
         assert equal_geom(out_geom, ref_geom)
@@ -41,7 +41,7 @@ def test_opt_charged():
 def test_opt_doublet():
     for mol in ["tempo"]:
         in_geom = Geometry.from_file(input_dir / f"{mol}.cjson")
-        out_geom = calc.optimize(in_geom)
+        out_geom = calculate.optimize(in_geom)
         ref_geom = Geometry.from_file(results_dir / f"{mol}_opt.xyz")
         print(f"Testing {mol}:")
         assert equal_geom(out_geom, ref_geom)
@@ -50,7 +50,7 @@ def test_opt_doublet():
 def test_freq_neutral_singlet():
     for mol in ["acetic_acid", "acetone", "benzene"]:
         opt_geom = Geometry.from_file(results_dir / f"{mol}_opt.xyz")
-        freqs = calc.frequencies(opt_geom)
+        freqs = calculate.frequencies(opt_geom)
         with open(results_dir / f"{mol}_g98.out", encoding="utf-8") as f:
             ref_freqs = parse.parse_g98_frequencies(f.read())
         print(f"Testing {mol}:")
@@ -60,7 +60,7 @@ def test_freq_neutral_singlet():
 def test_freq_anion():
     for mol in ["benzoate"]:
         opt_geom = Geometry.from_file(results_dir / f"{mol}_opt.xyz", charge=-1)
-        freqs = calc.frequencies(opt_geom)
+        freqs = calculate.frequencies(opt_geom)
         with open(results_dir / f"{mol}_g98.out", encoding="utf-8") as f:
             ref_freqs = parse.parse_g98_frequencies(f.read())
         print(f"Testing {mol}:")
@@ -70,7 +70,7 @@ def test_freq_anion():
 def test_freq_cation():
     for mol in ["bu4n"]:
         opt_geom = Geometry.from_file(results_dir / f"{mol}_opt.xyz", charge=1)
-        freqs = calc.frequencies(opt_geom)
+        freqs = calculate.frequencies(opt_geom)
         with open(results_dir / f"{mol}_g98.out", encoding="utf-8") as f:
             ref_freqs = parse.parse_g98_frequencies(f.read())
         print(f"Testing {mol}:")
@@ -80,7 +80,7 @@ def test_freq_cation():
 def test_freq_doublet():
     for mol in ["tempo"]:
         opt_geom = Geometry.from_file(results_dir / f"{mol}_opt.xyz", spin=1)
-        freqs = calc.frequencies(opt_geom)
+        freqs = calculate.frequencies(opt_geom)
         with open(results_dir / f"{mol}_g98.out", encoding="utf-8") as f:
             ref_freqs = parse.parse_g98_frequencies(f.read())
         print(f"Testing {mol}:")

energy.py

@@ -42,7 +42,7 @@
 
         # Run calculation; returns energy as float in hartree
         logger.debug("avo_xtb is requesting a single point energy calculation")
-        energy_hartree = easyxtb.calc.energy(
+        energy_hartree = easyxtb.calculate.energy(
             geom,
             solvation=easyxtb.config["solvent"],
             method=easyxtb.config["method"],

freq.py

@@ -42,7 +42,7 @@
 
         # Run calculation; returns set of frequency data
         logger.debug("avo_xtb is requesting a frequency calculation")
-        freqs = easyxtb.calc.frequencies(
+        freqs = easyxtb.calculate.frequencies(
             geom,
             solvation=easyxtb.config["solvent"],
             method=easyxtb.config["method"],

install.py

@@ -101,7 +101,7 @@ def link_xtb_bin(xtb_folder):
     # Add to config
     easyxtb.config["xtb_bin"] = str(easyxtb.XTB_BIN)
     # Save config
-    easyxtb.conf.save_config()
+    easyxtb.configuration.save_config()
 
 
 def link_crest_bin(crest_folder):
@@ -116,7 +116,7 @@ def link_crest_bin(crest_folder):
     # Add to config
     easyxtb.config["crest_bin"] = str(easyxtb.CREST_BIN)
     # Save config
-    easyxtb.conf.save_config()
+    easyxtb.configuration.save_config()
 
 
 if __name__ == "__main__":
@@ -157,7 +157,7 @@ def link_crest_bin(crest_folder):
                 "install_dir": {
                     "type": "string",
                     "label": "Install in",
-                    "default": str(easyxtb.conf.BIN_DIR),
+                    "default": str(easyxtb.configuration.BIN_DIR),
                     "order": 5.0,
                 },
                 "notice": {

ohess.py

@@ -43,7 +43,7 @@
 
         # Run calculation; returns path to Gaussian file containing frequencies
         logger.debug("avo_xtb is requesting an opt+freq calculation")
-        opt_geom, freqs, calc = easyxtb.calc.opt_freq(
+        opt_geom, freqs, calc = easyxtb.calculate.opt_freq(
             geom,
             solvation=easyxtb.config["solvent"],
             method=easyxtb.config["method"],

opt.py

@@ -61,7 +61,7 @@ def cleanup_after_opt(cjson: dict) -> dict:
 
         # Run calculation; returns optimized geometry as well as Calculation object
         logger.debug("avo_xtb is requesting a geometry optimization")
-        opt_geom, calc = easyxtb.calc.optimize(
+        opt_geom, calc = easyxtb.calculate.optimize(
             geom,
             solvation=easyxtb.config["solvent"],
             method=easyxtb.config["method"],

orbitals.py

@@ -42,7 +42,7 @@
 
         # Run calculation; returns Molden output file as string
         logger.debug("avo_xtb is requesting a molecular orbitals calculation")
-        molden_string = easyxtb.calc.orbitals(
+        molden_string = easyxtb.calculate.orbitals(
             geom,
             solvation=easyxtb.config["solvent"],
             method=easyxtb.config["method"],

protonate.py

@@ -55,7 +55,7 @@ def cleanup_after_taut(cjson: dict) -> dict:
         geom = easyxtb.Geometry.from_cjson(avo_input["cjson"])
 
         # Run calculation; returns set of tautomers as well as Calculation object
-        tautomers, calc = easyxtb.calc.protonate(
+        tautomers, calc = easyxtb.calculate.protonate(
             geom,
             solvation=easyxtb.config["solvent"],
             method=2,