Merge pull request #604 from avcopan/dev

Turn off symmetry factor racemization, update dependencies, remove autochem dependency

Author: avcopan

pixi.lock

@@ -56,11 +56,11 @@ scipy = ">=1.12"
 pac99 = ">=1.6.0"
 projrot = ">=1.8.0"
 thermp = ">=0.7.0"
-mess-static = ">=2025.9.0"
-autochem = "==0.2025.0"
-autoio = "==0.2025.0"
+mess-static = ">=2026.2.4"
+autochem = "==0.2026.2"
+autoio = "==0.2026.0"
 autofile = "==0.2025.0"
-mechanalyzer = "==0.2025.0"
+mechanalyzer = "==0.2026.0"
 
 #   - Environments
 [tool.pixi.pypi-dependencies]
@@ -82,11 +82,11 @@ scipy = ">=1.12"
 pac99 = ">=1.6.0"
 projrot = ">=1.8.0"
 thermp = ">=0.7.0"
-mess-static = ">=2025.9.0"
-autochem = "==0.2025.0"
-autoio = "==0.2025.0"
+mess-static = ">=2026.2.4"
+autochem = "==0.2026.2"
+autoio = "==0.2026.0"
 autofile = "==0.2025.0"
-mechanalyzer = "==0.2025.0"
+mechanalyzer = "==0.2026.0"
 
 [tool.pixi.feature.build.dependencies]
 rattler-build = ">=0.47.1"
@@ -165,4 +165,4 @@ push = true
 ]
 "src/mechdriver/__init__.py" = [
     '__version__ = "{version}"',
-]
+]

pyproject.toml

@@ -1,5 +1,7 @@
 """Standalone script to run AutoMech subtasks in parallel using HyperQueue."""
 
+import sys
+import traceback
 import contextlib
 import functools
 import itertools
@@ -205,13 +207,13 @@ def assign_atomic_function(
     """Create a HyperQueue task to run automech."""
     run_ = run_automech
 
+    # Ignore errors if requested
+    run_ = ignore_error_wrapper(run_) if ignore_error else run_
+
     # Create lock file if requested
     lock_path = log_path.with_suffix(Extension.running)
     run_ = lock_wrapper(run_, lock_file=lock_path) if lock else run_
 
-    # Ignore errors if requested
-    run_ = ignore_error_wrapper(run_) if ignore_error else run_
-
     resources = hq.resource_request(cpus=cpus, mem=mem)
     stdout = stderr = str(log_path)
     return job.function(
@@ -232,8 +234,12 @@ def ignore_error_wrapper(func: Callable[..., None]) -> Callable[..., None]:
     def wrapper(*args, **kwargs) -> None:
         try:
             func(*args, **kwargs)
-        except Exception as err:
-            print(err)
+        except Exception as error:
+            trace = traceback.format_exc()
+            print(f"{error=}")
+            print("---traceback start---")
+            print(trace)
+            print("---traceback end---")
 
     return wrapper
 

src/mechdriver/subtasks/_2run.py

@@ -12,7 +12,7 @@
 import more_itertools as mit
 import pandas
 import pyparsing as pp
-from autochem.util.chemkin import parse_equation
+from chemkin_io.parser.reaction import rct_names, prd_names
 from pyparsing import common as ppc
 
 COMMENT_REGEX = re.compile(r"#.*$", flags=re.M)
@@ -360,9 +360,8 @@ def parse_mechanism_dat(mechanism_dat: str) -> dict[str, tuple[list[str], list[s
     for line in rxn_block_str.splitlines():
         line_match = re.search(r"\d\s*(!.*|# .*)?$", line)
         if line_match:
-            result = parse_equation(line)
-            reactants = result.reactants
-            products = result.products
+            reactants = list(rct_names(line))
+            products = list(prd_names(line))
             comment = line_match.group(1)
 
             if comment:

src/mechdriver/subtasks/util.py

@@ -381,7 +381,7 @@ def mol_data(spc_name, spc_dct,
             zma_locs = ts_zma_locs(spc_dct, spc_name, zma_fs)
             zma = zma_fs[-1].file.zmatrix.read(zma_locs)
 
-    racemic = True
+    racemic = False
     ioprinter.info_message('Setting symmetry factors as racemic=', racemic)
     sym_factor = symm.symmetry_factor(
         pf_filesystems, spc_mod_dct_i, spc_dct_i, rotors, grxn=zrxn, zma=zma,