diff --git a/pixi.lock b/pixi.lock index 94512ae1..5aa8274a 100644 --- a/pixi.lock +++ b/pixi.lock @@ -6,6 +6,8 @@ environments: - url: https://conda.anaconda.org/Auto-Mech/ indexes: - https://pypi.org/simple + options: + pypi-prerelease-mode: if-necessary-or-explicit packages: linux-64: - conda: https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2 @@ -17,9 +19,9 @@ environments: - conda: https://conda.anaconda.org/conda-forge/noarch/astor-0.8.1-pyhd8ed1ab_1.conda - conda: https://conda.anaconda.org/conda-forge/noarch/asttokens-3.0.1-pyhd8ed1ab_0.conda - conda: https://conda.anaconda.org/conda-forge/noarch/attrs-25.4.0-pyh71513ae_0.conda - - conda: https://conda.anaconda.org/Auto-Mech/noarch/autochem-0.2025.0-pyh4616a5c_0.conda + - conda: https://conda.anaconda.org/Auto-Mech/noarch/autochem-0.2026.2-pyh4616a5c_0.conda - conda: https://conda.anaconda.org/Auto-Mech/noarch/autofile-0.2025.0-pyh4616a5c_0.conda - - conda: https://conda.anaconda.org/Auto-Mech/noarch/autoio-0.2025.0-pyh4616a5c_0.conda + - 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- conda: https://conda.anaconda.org/Auto-Mech/noarch/autochem-0.2025.0-pyh4616a5c_0.conda + - conda: https://conda.anaconda.org/Auto-Mech/noarch/autochem-0.2026.2-pyh4616a5c_0.conda - conda: https://conda.anaconda.org/Auto-Mech/noarch/autofile-0.2025.0-pyh4616a5c_0.conda - - conda: https://conda.anaconda.org/Auto-Mech/noarch/autoio-0.2025.0-pyh4616a5c_0.conda + - conda: https://conda.anaconda.org/Auto-Mech/noarch/autoio-0.2026.0-pyh4616a5c_0.conda - conda: https://conda.anaconda.org/conda-forge/linux-64/brotli-1.2.0-h41a2e66_0.conda - conda: https://conda.anaconda.org/conda-forge/linux-64/brotli-bin-1.2.0-hf2c8021_0.conda - conda: https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-hda65f42_8.conda @@ -591,8 +597,8 @@ environments: - conda: https://conda.anaconda.org/conda-forge/noarch/matplotlib-inline-0.2.1-pyhd8ed1ab_0.conda - conda: https://conda.anaconda.org/conda-forge/noarch/mdit-py-plugins-0.5.0-pyhd8ed1ab_0.conda - conda: https://conda.anaconda.org/conda-forge/noarch/mdurl-0.1.2-pyhd8ed1ab_1.conda - 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conda: https://conda.anaconda.org/conda-forge/noarch/asttokens-3.0.1-pyhd8ed1ab_0.conda - conda: https://conda.anaconda.org/conda-forge/noarch/attrs-25.4.0-pyh71513ae_0.conda - - conda: https://conda.anaconda.org/Auto-Mech/noarch/autochem-0.2025.0-pyh4616a5c_0.conda + - conda: https://conda.anaconda.org/Auto-Mech/noarch/autochem-0.2026.2-pyh4616a5c_0.conda - conda: https://conda.anaconda.org/Auto-Mech/noarch/autofile-0.2025.0-pyh4616a5c_0.conda - - conda: https://conda.anaconda.org/Auto-Mech/noarch/autoio-0.2025.0-pyh4616a5c_0.conda + - conda: https://conda.anaconda.org/Auto-Mech/noarch/autoio-0.2026.0-pyh4616a5c_0.conda - conda: https://conda.anaconda.org/conda-forge/linux-64/brotli-1.2.0-h41a2e66_0.conda - conda: https://conda.anaconda.org/conda-forge/linux-64/brotli-bin-1.2.0-hf2c8021_0.conda - conda: https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-hda65f42_8.conda @@ -835,8 +843,8 @@ environments: - conda: https://conda.anaconda.org/conda-forge/noarch/matplotlib-inline-0.2.1-pyhd8ed1ab_0.conda - conda: https://conda.anaconda.org/conda-forge/noarch/mdit-py-plugins-0.5.0-pyhd8ed1ab_0.conda - conda: https://conda.anaconda.org/conda-forge/noarch/mdurl-0.1.2-pyhd8ed1ab_1.conda - - conda: https://conda.anaconda.org/Auto-Mech/noarch/mechanalyzer-0.2025.0-pyh4616a5c_0.conda - - conda: https://conda.anaconda.org/Auto-Mech/noarch/mess-static-2025.9.0-h4616a5c_0.conda + - conda: https://conda.anaconda.org/Auto-Mech/noarch/mechanalyzer-0.2026.0-pyh4616a5c_0.conda + - conda: https://conda.anaconda.org/Auto-Mech/noarch/mess-static-2026.2.4-h4616a5c_0.conda - conda: https://conda.anaconda.org/conda-forge/noarch/more-itertools-10.8.0-pyhd8ed1ab_0.conda - conda: https://conda.anaconda.org/conda-forge/noarch/munkres-1.1.4-pyhd8ed1ab_1.conda - conda: https://conda.anaconda.org/conda-forge/noarch/narwhals-2.12.0-pyhcf101f3_0.conda @@ -948,6 +956,8 @@ environments: - url: https://conda.anaconda.org/Auto-Mech/ indexes: - https://pypi.org/simple + options: + pypi-prerelease-mode: if-necessary-or-explicit packages: linux-64: - conda: https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2 @@ -958,9 +968,9 @@ environments: - conda: https://conda.anaconda.org/conda-forge/linux-64/arpack-3.9.1-nompi_hf03ea27_102.conda - conda: https://conda.anaconda.org/conda-forge/noarch/asttokens-3.0.1-pyhd8ed1ab_0.conda - conda: https://conda.anaconda.org/conda-forge/noarch/attrs-25.4.0-pyh71513ae_0.conda - - conda: https://conda.anaconda.org/Auto-Mech/noarch/autochem-0.2025.0-pyh4616a5c_0.conda + - conda: https://conda.anaconda.org/Auto-Mech/noarch/autochem-0.2026.2-pyh4616a5c_0.conda - conda: https://conda.anaconda.org/Auto-Mech/noarch/autofile-0.2025.0-pyh4616a5c_0.conda - - conda: https://conda.anaconda.org/Auto-Mech/noarch/autoio-0.2025.0-pyh4616a5c_0.conda + - conda: https://conda.anaconda.org/Auto-Mech/noarch/autoio-0.2026.0-pyh4616a5c_0.conda - conda: https://conda.anaconda.org/conda-forge/linux-64/brotli-1.2.0-h41a2e66_0.conda - conda: https://conda.anaconda.org/conda-forge/linux-64/brotli-bin-1.2.0-hf2c8021_0.conda - conda: https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-hda65f42_8.conda @@ -1070,8 +1080,8 @@ environments: - conda: https://conda.anaconda.org/conda-forge/linux-64/matplotlib-3.10.8-py313h78bf25f_0.conda - conda: https://conda.anaconda.org/conda-forge/linux-64/matplotlib-base-3.10.8-py313h683a580_0.conda - conda: https://conda.anaconda.org/conda-forge/noarch/matplotlib-inline-0.2.1-pyhd8ed1ab_0.conda - - conda: https://conda.anaconda.org/Auto-Mech/noarch/mechanalyzer-0.2025.0-pyh4616a5c_0.conda - - conda: https://conda.anaconda.org/Auto-Mech/noarch/mess-static-2025.9.0-h4616a5c_0.conda + - conda: https://conda.anaconda.org/Auto-Mech/noarch/mechanalyzer-0.2026.0-pyh4616a5c_0.conda + - conda: https://conda.anaconda.org/Auto-Mech/noarch/mess-static-2026.2.4-h4616a5c_0.conda - conda: https://conda.anaconda.org/conda-forge/noarch/more-itertools-10.8.0-pyhd8ed1ab_0.conda - conda: https://conda.anaconda.org/conda-forge/noarch/munkres-1.1.4-pyhd8ed1ab_1.conda - conda: https://conda.anaconda.org/conda-forge/noarch/narwhals-2.12.0-pyhcf101f3_0.conda @@ -1294,13 +1304,12 @@ packages: timestamp: 1759762331492 - pypi: ../autochem name: autochem - version: 0.2025.0 - sha256: 98f664d3cc0fda39b817ac99a2598477c133218fac3940e4ae80d6ccca7b0381 + version: 0.2026.2 + sha256: 9501bbbefb1adb15bcc4cec731548c452e7643e31510a2d7c2d0d5f453819ade requires_python: '>=3.11' - editable: true -- conda: https://conda.anaconda.org/Auto-Mech/noarch/autochem-0.2025.0-pyh4616a5c_0.conda - sha256: 56535f3e7f30ed02b2b65d65f49ee60b00f558757dd07e51d7d9339aff0066ca - md5: c1905a59367f1750ebf58384c3ad2015 +- conda: https://conda.anaconda.org/Auto-Mech/noarch/autochem-0.2026.2-pyh4616a5c_0.conda + sha256: ac66a659c2b1da738582acc23bd4c3831da5db572d6e5032d35fb689c507766c + md5: 51d360511a3d07803176ad44f5401beb depends: - altair >=5.5.0 - ipython >=8.15 @@ -1317,14 +1326,13 @@ packages: - xarray >=2023.8 - python >=3.11 - python * - size: 610723 - timestamp: 1763746042074 + size: 610491 + timestamp: 1772739572046 - pypi: ../autofile name: autofile version: 0.2025.0 sha256: 1158420897d789f9aa7bc3d2053412f840d1f377d567c78ca1c1fbc98ed8faf0 requires_python: '>=3.11' - editable: true - conda: https://conda.anaconda.org/Auto-Mech/noarch/autofile-0.2025.0-pyh4616a5c_0.conda sha256: 027fed4c146c65bb3d55a237c331ff4a4534964e9771c09e7220bce99a208a3d md5: b7bfb6a4fcf15eb0d4ec20dc69dc9f58 @@ -1339,13 +1347,12 @@ packages: timestamp: 1763748110716 - pypi: ../autoio name: autoio - version: 0.2025.0 - sha256: 9720401e7f430caa3b97ef6d736d056eed1eeb9fc08ab5e04d3b132882a216af + version: 0.2026.0 + sha256: b554f06265eb5e8204bc87e109b9dba5df8b8a42163ad747fe0213439cb4c49c requires_python: '>=3.11' - editable: true -- conda: https://conda.anaconda.org/Auto-Mech/noarch/autoio-0.2025.0-pyh4616a5c_0.conda - sha256: 38f151908a4e4595df7a90bc16d41f71549220ceb3ecd2a1fd7afe121266dbf5 - md5: e8117f81ed6caf696bdc033fed6e9d93 +- conda: https://conda.anaconda.org/Auto-Mech/noarch/autoio-0.2026.0-pyh4616a5c_0.conda + sha256: 0dd0d28a368b55cf775b231e7710e1309491b1db79bcad5b334056afe636f6a6 + md5: 8f97347f404687644c579ac99bae3f7d depends: - mako >=1.3.10 - more-itertools >=10.8.0 @@ -1357,8 +1364,8 @@ packages: - autochem >=0.2025.0,<2.0.0 - python >=3.11 - python * - size: 5285348 - timestamp: 1763747126180 + size: 5284910 + timestamp: 1772762271687 - conda: https://conda.anaconda.org/conda-forge/linux-64/brotli-1.2.0-h41a2e66_0.conda sha256: 33239a07f7685917cac25646dd33798ee93e61f83504a0c938d86c507e05d7c9 md5: 4ddfd44e473c676cb8e80548ba4aa704 @@ -3189,13 +3196,12 @@ packages: timestamp: 1733255681319 - pypi: ../mechanalyzer name: mechanalyzer - version: 0.2025.0 - sha256: ae648c05f2a528eeda61f591dee818e43aad5e046148c2b7a9bb070da1b801a8 + version: 0.2026.0 + sha256: 363ca1cad51d90753262a652999083d551e70f20286cea794df088877ee219da requires_python: '>=3.11' - editable: true -- conda: https://conda.anaconda.org/Auto-Mech/noarch/mechanalyzer-0.2025.0-pyh4616a5c_0.conda - sha256: dddf3523678cbc77b69c03521e04698ad543fd2077d587b4d1f1c66bb054d57c - md5: 10d551318ec5f7adb4ac58d347bcc9e9 +- conda: https://conda.anaconda.org/Auto-Mech/noarch/mechanalyzer-0.2026.0-pyh4616a5c_0.conda + sha256: 19a62baba6c137f47e7538511ce00682e9102be412ddd548e4750837f93eedb6 + md5: 0670a4dc8844b832866fc5e4a3dac4e2 depends: - click >=8.2.1 - mako >=1.3.10 @@ -3211,21 +3217,20 @@ packages: - autofile >=0.2025.0,<2.0.0 - python >=3.11 - python * - size: 2729114 - timestamp: 1763750488901 + size: 2731032 + timestamp: 1772765088653 - pypi: ./ name: mechdriver version: 0.2025.0 - sha256: 2e82d94200ce04596d1b6e47b5502d1e0bd2f5b55fa1e71c6184bb79a1bbfa32 + sha256: f92d97fc3ecfd0c06ab555c96ff9f8f82a613a5dc8bbf21026d8c299d95c311c requires_dist: - hyperqueue requires_python: '>=3.11,<3.14' - editable: true -- conda: https://conda.anaconda.org/Auto-Mech/noarch/mess-static-2025.9.0-h4616a5c_0.conda - sha256: bf49bc57d60cbcda20f57e6a6e63edbb6204396946703224f9ecd9e49c78e50f - md5: d7dee2b3a30813504691abd00da40943 - size: 42798128 - timestamp: 1758816360707 +- conda: https://conda.anaconda.org/Auto-Mech/noarch/mess-static-2026.2.4-h4616a5c_0.conda + sha256: 73cf524ed5a9f5a34f5c68e0309de084c9dcad833bdfcb3c7f288b48f45ac22d + md5: 962375844fd512acf2d0305a46fcd8f3 + size: 42835440 + timestamp: 1770225035248 - conda: https://conda.anaconda.org/conda-forge/noarch/more-itertools-10.8.0-pyhd8ed1ab_0.conda sha256: fabe81c8f8f3e1d0ef227fc1306526c76189b3f1175f12302c707e0972dd707c md5: d7620a15dc400b448e1c88a981b23ddd diff --git a/pyproject.toml b/pyproject.toml index 75312869..dbf2199a 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -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}"', -] \ No newline at end of file +] diff --git a/src/mechdriver/subtasks/_2run.py b/src/mechdriver/subtasks/_2run.py index baaf7d8e..6844991a 100644 --- a/src/mechdriver/subtasks/_2run.py +++ b/src/mechdriver/subtasks/_2run.py @@ -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 diff --git a/src/mechdriver/subtasks/util.py b/src/mechdriver/subtasks/util.py index 1b7df7ca..36f3f8be 100644 --- a/src/mechdriver/subtasks/util.py +++ b/src/mechdriver/subtasks/util.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: diff --git a/src/mechroutines/models/build.py b/src/mechroutines/models/build.py index aff761bc..f0427be1 100644 --- a/src/mechroutines/models/build.py +++ b/src/mechroutines/models/build.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, diff --git a/tests/archive.tgz b/tests/archive.tgz index 5b4f5477..3e579810 100644 Binary files a/tests/archive.tgz and b/tests/archive.tgz differ