Migrating ARC to Python 14 (#867)

Bump the target runtime from 3.12 to 3.14 and modernize the codebase
accordingly.
   
- Update Python, Cython (≥3.1), and RDKit (≥2026.03) pins across
environment.yml, requirements.txt, Dockerfile, and pyproject.toml
- Fix stale check_python() gate that still referenced Python 3.7 /
RMG-Py
- Remove dead from __future__ import print_function and deprecated
assertDictEqual
- Replace deprecated typing generics with built-in equivalents (list,
dict, X | None, X | Y, collections.abc) across 70+ files
RMG's separate Python 3.9 environment for suprocess scripts (e.g.
Arkane) is unchanged.

Author: alongd

.github/workflows/ci.yml

@@ -99,6 +99,7 @@ jobs:
         env:
           ARC_COVERAGE: 1
           CYTHON_TRACE: 1
+          COVERAGE_CORE: ctrace
         run: |
           echo "Running Unit Tests..."
           export PYTHONPATH="${{ github.workspace }}/AutoTST:${{ github.workspace }}/KinBot:$PYTHONPATH"
@@ -110,6 +111,7 @@ jobs:
         env:
           ARC_COVERAGE: 1
           CYTHON_TRACE: 1
+          COVERAGE_CORE: ctrace
         run: |
           echo "Running Functional Tests from $(pwd)..."
           export PYTHONPATH="${{ github.workspace }}/AutoTST:${{ github.workspace }}/KinBot:$PYTHONPATH"

.github/workflows/docker_build.yml

@@ -50,6 +50,8 @@ jobs:
           push: false
           load: true
           tags: arc:test
+          build-args: |
+            ARC_BRANCH=${{ github.head_ref || github.ref_name }}
           cache-from: type=gha
           cache-to: type=gha,mode=max
 

.github/workflows/gh-pages.yml

@@ -37,16 +37,19 @@ jobs:
         with:
           environment-name: arc_env
           environment-file: ARC/environment.yml
+          condarc: |
+            channels:
+              - conda-forge
+              - danagroup
           cache-environment: true
+          cache-environment-key: py314v3-arc-env
           cache-downloads: true
+          generate-run-shell: true
 
       # ── Complie ARC ──────────────────────
       - name: Build ARC in arc_env
-        run: micromamba run -n arc_env make compile -C ARC -j"$(nproc)"
-      
-      # ── Install pyrdl ──────────────────────
-      - name: Install pyrdl
-        run: micromamba run -n arc_env make install-pyrdl -C ARC -j"$(nproc)"
+        run: make compile -C ARC -j"$(nproc)"
+        shell: micromamba-shell {0}
 
       # ── minimal TeX for png‑math in Sphinx ──────────────────────
       - name: System TeX tools
@@ -57,6 +60,12 @@ jobs:
         run: micromamba install -y -n arc_env -c conda-forge libgfortran=3
         shell: micromamba-shell {0}
 
+      # ── ensure ase is installed (the danagroup channel and/or
+      #    libgfortran install can cause the solver to drop ase)
+      - name: Ensure ase is installed
+        run: pip install "ase>=3.22.1" && python -c "import ase; print(f'ase {ase.__version__} OK')"
+        shell: micromamba-shell {0}
+
       # ── build HTML docs ─────────────────────────────────────────
       - name: Set env vars & Build docs
         run: |

.gitignore

@@ -30,6 +30,7 @@ examples/
 
 # Unit test files
 .coverage
+.coverage.*
 testing/*
 htmlcov/*
 arc/testing/gcn_tst/

Dockerfile

@@ -55,7 +55,7 @@ RUN micromamba run -n rmg_env bash -c "\
     "
 
 WORKDIR /home/mambauser/Code/ARC
-RUN micromamba create -y -v -n arc_env python=3.12 -f environment.yml && \
+RUN micromamba create -y -v -n arc_env python=3.14 -c conda-forge -c danagroup -f environment.yml && \
     micromamba install -y -v -n arc_env -c conda-forge pytest && \
     micromamba clean --all -f -y
 

Makefile

@@ -7,7 +7,7 @@
 DEVTOOLS_DIR := devtools
 
 .PHONY: all help clean test test-unittests test-functional test-all \
-        install-all install-ci install-pyrdl install-rmg install-rmgdb install-autotst install-gcn \
+        install-all install-ci install-rmg install-rmgdb install-autotst install-gcn \
         install-gcn-cpu install-kinbot install-sella install-xtb install-torchani install-ob \
         lite check-env compile
 
@@ -27,7 +27,6 @@ help:
 	@echo "Installation:"
 	@echo "  install          Install all external dependencies"
 	@echo "  install-ci       Install all external dependencies for CI (no clean)"
-	@echo "  install-pyrdl    Install PyRDL"
 	@echo "  install-rmg      Install RMG (default: packaged, override via RMG_ARGS=...)"
 	@echo "  install-rmgdb    Install RMG-database"
 	@echo "  install-autotst  Install AutoTST"
@@ -73,9 +72,6 @@ install-lite:
 	@echo "Installing ARC's lite version (no external dependencies)..."
 	bash $(DEVTOOLS_DIR)/install_all.sh --no-ext --rmg-rms
 
-install-pyrdl:
-	bash $(DEVTOOLS_DIR)/install_pyrdl.sh
-
 install-rmg:
 	bash $(DEVTOOLS_DIR)/install_rmg.sh $(RMG_ARGS)
 

README.md

@@ -4,6 +4,7 @@
 [![codecov](https://codecov.io/gh/ReactionMechanismGenerator/ARC/branch/main/graph/badge.svg)](https://codecov.io/gh/ReactionMechanismGenerator/ARC)
 [![MIT license](http://img.shields.io/badge/license-MIT-brightgreen.svg)](http://opensource.org/licenses/MIT)
 ![Release](https://img.shields.io/badge/version-1.1.0-blue.svg)
+![Python](https://img.shields.io/badge/python-3.14-blue.svg)
 [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.3356849.svg)](https://doi.org/10.5281/zenodo.3356849)
 
 <img src="https://github.com/ReactionMechanismGenerator/ARC/blob/main/logo/ARC-logo-small.jpg" alt="ARC logo" width="200"/>

arc/checks/common.py

@@ -5,8 +5,6 @@
 
 import datetime
 
-from typing import List, Optional
-
 CONFORMER_JOB_TYPES = ('conf_opt', 'conf_sp')
 
 
@@ -23,7 +21,7 @@ def is_conformer_job(job_name: str) -> bool:
     return job_name.startswith(CONFORMER_JOB_TYPES)
 
 
-def sum_time_delta(timedelta_list: List[datetime.timedelta]) -> datetime.timedelta:
+def sum_time_delta(timedelta_list: list[datetime.timedelta]) -> datetime.timedelta:
     """
     A helper function for summing datetime.timedelta objects.
 
@@ -40,15 +38,15 @@ def sum_time_delta(timedelta_list: List[datetime.timedelta]) -> datetime.timedel
     return result
 
 
-def get_i_from_job_name(job_name: str) -> Optional[int]:
+def get_i_from_job_name(job_name: str) -> int | None:
     """
     Get the conformer or tsg index from the job name.
 
     Args:
         job_name (str): The job name, e.g., 'conformer12' or 'tsg5'.
 
     Returns:
-        Optional[int]: The corresponding conformer or tsg index.
+        int | None: The corresponding conformer or tsg index.
     """
     i = None
     for prefix in CONFORMER_JOB_TYPES: