Added a Linear TS search job adapter

.github/workflows/ci.yml

@@ -23,21 +23,21 @@ jobs:
           path: ARC
 
       - name: Clean Ubuntu Image
-        uses: jlumbroso/free-disk-space@main
+        uses: jlumbroso/free-disk-space@v1.3.1
         with:
           tool-cache: true
           android: true
           dotnet: true
           haskell: true
           large-packages: true
-          swap-storage: true
+          swap-storage: false
 
       - name: Set up micromamba (arc_env)
         uses: mamba-org/setup-micromamba@v3
         with:
           environment-name: arc_env
           environment-file: ARC/environment.yml
-          cache-environment: true
+          cache-environment: ${{ github.event_name != 'schedule' }}
           cache-downloads: true
           generate-run-shell: true
 
@@ -55,22 +55,6 @@ jobs:
           echo "PATH=$PATH:$PWD" >> "$GITHUB_ENV"
           echo "PYTHONPATH=$PYTHONPATH:$PWD" >> "$GITHUB_ENV"
 
-      - name: Install Julia 1.10
-        shell: micromamba-shell {0}
-        run: |
-          echo "::group::Install juliaup + Julia 1.10"
-          # 1) Bootstrap juliaup non-interactively (-y)
-          curl -fsSL https://install.julialang.org | sh -s -- -y
-          # 2) Make juliaup visible *now* (CI shells won’t re-source rc files)
-          export PATH="$HOME/.juliaup/bin:$PATH"
-          # 3) Install & select Julia 1.10
-          juliaup add 1.10
-          juliaup default 1.10
-          # 4) Persist for subsequent steps
-          echo "PATH=$HOME/.juliaup/bin:$PATH" >> "$GITHUB_ENV"
-          echo "::endgroup::"
-          julia --version # Check that Julia is installed correctly
-
       - name: Install all extras - CI
         shell: micromamba-shell {0}
         working-directory: ARC
@@ -103,7 +87,7 @@ jobs:
         run: |
           echo "Running Unit Tests..."
           export PYTHONPATH="${{ github.workspace }}/AutoTST:${{ github.workspace }}/KinBot:$PYTHONPATH"
-          pytest arc/ --cov --cov-report=xml -ra -vv -n auto
+          pytest arc/ --cov --cov-report=xml -ra -vv -n 6 --dist worksteal
 
       - name: Run Functional Tests
         shell: micromamba-shell {0}
@@ -115,7 +99,7 @@ jobs:
         run: |
           echo "Running Functional Tests from $(pwd)..."
           export PYTHONPATH="${{ github.workspace }}/AutoTST:${{ github.workspace }}/KinBot:$PYTHONPATH"
-          pytest functional/ --cov --cov-append --cov-report=xml -ra -vv -n auto
+          pytest functional/ --cov --cov-append --cov-report=xml -ra -vv -n 6 --dist loadfile
 
       - name: Upload coverage data
         uses: codecov/codecov-action@v6

.gitignore

@@ -56,6 +56,10 @@ timer.dat
 # .vscode
 .vscode
 
+# Claude
+CLAUDE.md
+.claude/*
+
 # .trunk folder
 .trunk
 

Makefile

@@ -62,15 +62,15 @@ install-all: install
 
 install:
 	@echo "Installing all external ARC dependencies..."
-	bash $(DEVTOOLS_DIR)/install_all.sh --rmg-rms
+	bash $(DEVTOOLS_DIR)/install_all.sh
 
 install-ci:
 	@echo "Installing all external ARC dependencies for CI (no clean)..."
 	bash $(DEVTOOLS_DIR)/install_all.sh --no-clean
 
 install-lite:
 	@echo "Installing ARC's lite version (no external dependencies)..."
-	bash $(DEVTOOLS_DIR)/install_all.sh --no-ext --rmg-rms
+	bash $(DEVTOOLS_DIR)/install_all.sh --no-ext
 
 install-rmg:
 	bash $(DEVTOOLS_DIR)/install_rmg.sh $(RMG_ARGS)

arc/common.py

@@ -31,7 +31,7 @@
 from arc.imports import settings
 
 if TYPE_CHECKING:
-    from arc.molecule.molecule import Molecule
+    from arc.molecule.molecule import Atom, Molecule
 
 logger = logging.getLogger('arc')
 logging.getLogger('matplotlib.font_manager').disabled = True
@@ -44,6 +44,8 @@
 
 R = 8.31446261815324  # J/(mol*K)
 EA_UNIT_CONVERSION = {'J/mol': 1, 'kJ/mol': 1e+3, 'cal/mol': 4.184, 'kcal/mol': 4.184e+3}
+FULL_CIRCLE = 360.0
+HALF_CIRCLE = 180.0
 
 default_job_types, servers, supported_ess = settings['default_job_types'], settings['servers'], settings['supported_ess']
 
@@ -825,7 +827,7 @@
     return sorted(bonds)
 
 
-def determine_top_group_indices(mol: 'Molecule', atom1: 'Atom', atom2: 'Atom', index: int = 1) -> tuple[list, bool]:
+def determine_top_group_indices(mol: Molecule, atom1: Atom, atom2: Atom, index: int = 1) -> tuple[list, bool]:
     """
     Determine the indices of a "top group" in a molecule.
     The top is defined as all atoms connected to atom2, including atom2, excluding the direction of atom1.
@@ -1507,14 +1509,11 @@
     return True
 
 
-FULL_CIRCLE = 360.0
-HALF_CIRCLE = 180.0
-
 def get_angle_in_180_range(angle: float,
                            round_to: int | None = 2,
                            ) -> float:
     """
-    Get the corresponding angle in the -180 to +180 degree range.
+    Get the corresponding angle in the -180 to +180 degree range, (-180,180]
 
     Args:
         angle (float): An angle in degrees.
@@ -1524,7 +1523,8 @@
     Returns:
         float: The corresponding angle in the -180 to +180 degree range.
     """
-    return (angle + HALF_CIRCLE) % FULL_CIRCLE - HALF_CIRCLE
+    wrapped = (angle + HALF_CIRCLE) % FULL_CIRCLE - HALF_CIRCLE
+    return round(wrapped, round_to) if round_to is not None else wrapped
 
 
 def signed_angular_diff(phi_1: float, phi_2: float) -> float:
@@ -1736,7 +1736,7 @@
             break
 
 
-def dfs(mol: 'Molecule',
+def dfs(mol: Molecule,
         start: int,
         sort_result: bool = True,
         ) -> list[int]:
@@ -1767,7 +1767,7 @@
     return visited
 
 
-def sort_atoms_in_descending_label_order(mol: 'Molecule') -> None:
+def sort_atoms_in_descending_label_order(mol: Molecule) -> None:
     """
     If all atoms in the molecule object have a label, this function reassign the
     .atoms in Molecule with a list of atoms with the orders based on the labels of the atoms.
@@ -1786,7 +1786,7 @@
         return None
 
 
-def is_xyz_mol_match(mol: 'Molecule',
+def is_xyz_mol_match(mol: Molecule,
                      xyz: dict) -> bool:
     """
     A helper function that matches RMG's Molecule object to an xyz,

arc/common_test.py

@@ -30,11 +30,33 @@
     """
     Contains unit tests for ARC's common module
     """
+    @classmethod
+    def _clean_globalized_restart_artifact(cls):
+        """Remove the globalized restart-paths artifact written by
+        :meth:`test_globalize_paths`.
+
+        Called from BOTH ``setUpClass`` (defensive: wipes a stale
+        artifact left behind by a previously interrupted run) and
+        ``tearDownClass`` (the normal cleanup path).  This makes the
+        cleanup self-healing: a Ctrl+C, ``kill``, or hard error during
+        a previous run cannot leave the next run inheriting the prior
+        ``restart_paths_globalized.yml``.
+        """
+        globalized_restart_path = os.path.join(
+            common.ARC_TESTING_PATH, 'restart', '4_globalized_paths',
+            'restart_paths_globalized.yml')
+        if os.path.isfile(globalized_restart_path):
+            try:
+                os.remove(path=globalized_restart_path)
+            except OSError:
+                pass
+
     @classmethod
     def setUpClass(cls):
         """
         A method that is run before all unit tests in this class.
         """
+        cls._clean_globalized_restart_artifact()
         cls.maxDiff = None
         cls.default_job_types = {'conf_opt': True,
                                  'opt': True,
@@ -1077,8 +1099,8 @@
         """Test the getting a corresponding angle in the -180 to +180 range"""
         self.assertEqual(common.get_angle_in_180_range(0), 0)
         self.assertEqual(common.get_angle_in_180_range(10), 10)
-        self.assertAlmostEqual(common.get_angle_in_180_range(-5.364589), -5.364589)
-        self.assertAlmostEqual(common.get_angle_in_180_range(-5.364589), -5.364589)
+        self.assertAlmostEqual(common.get_angle_in_180_range(-5.364589, round_to=None), -5.364589)
+        self.assertAlmostEqual(common.get_angle_in_180_range(-5.364589, round_to=None), -5.364589)
         self.assertEqual(common.get_angle_in_180_range(-120), -120)
         self.assertAlmostEqual(common.get_angle_in_180_range(179.999), 180, 2)
         self.assertEqual(common.get_angle_in_180_range(180), -180)
@@ -1098,6 +1120,7 @@
         self.assertEqual(common.get_angle_in_180_range(-270), 90)
         self.assertAlmostEqual(common.get_angle_in_180_range(45.5), 45.5, places=7)
         self.assertAlmostEqual(common.get_angle_in_180_range(719.9), -0.1, places=7)
+        self.assertAlmostEqual(common.get_angle_in_180_range(-5.364589, round_to=2), -5.36)
 
     def test_signed_angular_diff(self):
         """Test the signed angular difference between two angles"""
@@ -1396,10 +1419,7 @@
         """
         A function that is run ONCE after all unit tests in this class.
         """
-        globalized_restart_path = os.path.join(common.ARC_TESTING_PATH, 'restart', '4_globalized_paths',
-                                               'restart_paths_globalized.yml')
-        if os.path.isfile(globalized_restart_path):
-            os.remove(path=globalized_restart_path)
+        cls._clean_globalized_restart_artifact()
 
 
 if __name__ == '__main__':