Merge pull request #339 from duartegroup/v1.4.3

V1.4.3

.github/workflows/pytest.yml

@@ -22,7 +22,7 @@ jobs:
       fail-fast: true
       matrix:
         os: ["ubuntu-latest", "macos-latest", "windows-latest"]
-        python-version: ["3.8", "3.9", "3.10"]
+        python-version: ["3.8", "3.12"]
 
     defaults:
       run:
@@ -31,7 +31,7 @@ jobs:
     steps:
     - uses: actions/checkout@v3
 
-    - uses: conda-incubator/setup-miniconda@v2
+    - uses: conda-incubator/setup-miniconda@v3
       with:
         python-version: ${{ matrix.python-version }}
         activate-environment: test

.github/workflows/pytest_cov.yml

@@ -23,7 +23,7 @@ jobs:
       fail-fast: true
       matrix:
         os: ["ubuntu-latest", "windows-latest"]
-        python-version: ["3.10"]
+        python-version: ["3.11"]
 
     defaults:
       run:
@@ -32,7 +32,7 @@ jobs:
     steps:
     - uses: actions/checkout@v3
 
-    - uses: conda-incubator/setup-miniconda@v2
+    - uses: conda-incubator/setup-miniconda@v3
       with:
         python-version: ${{ matrix.python-version }}
         activate-environment: test
@@ -56,7 +56,8 @@ jobs:
       run: |
         pytest --cov=./ --cov-report=xml
 
-    - uses: codecov/codecov-action@v3
+    - uses: codecov/codecov-action@v4
       with:
         flags: unittests
         fail_ci_if_error: true
+        token: ${{ secrets.CODECOV_TOKEN }} # required

README.md

@@ -95,3 +95,5 @@ If **autodE** is used in a publication please consider citing the [paper](https:
 - Jonathon Vandezande ([@jevandezande](https://github.com/jevandezande))
 - Shoubhik Maiti ([@shoubhikraj](https://github.com/shoubhikraj))
 - Daniel Hollas ([@danielhollas](https://github.com/danielhollas))
+- Nils Heunemann ([@nilsheunemann](https://github.com/NilsHeunemann))
+- Sijie Fu ([@sijiefu](https://github.com/SijieFu))

autode/bracket/base.py

@@ -122,7 +122,7 @@ def _exceeded_maximum_iteration(self) -> bool:
         if self._micro_iter >= self._maxiter:
             logger.error(
                 f"Reached the maximum number of micro-iterations "
-                f"*{self._maxiter}"
+                f"*{self._maxiter}*"
             )
             return True
         else:
@@ -165,6 +165,9 @@ def _calculate(
 
         n_cores = Config.n_cores if n_cores is None else int(n_cores)
         self.imgpair.set_method_and_n_cores(method, n_cores)
+        self.imgpair.initialise_trj(
+            f"{self._name}_left_history.zip", f"{self._name}_right_history.zip"
+        )
         self._initialise_run()
 
         logger.info(f"Starting {self._name} method to find transition state")
@@ -205,7 +208,7 @@ def _calculate(
             f"iterations (optimiser steps). {self._name} is "
             f"{'converged' if self.converged else 'not converged'}"
         )
-
+        self.imgpair.close_trj()
         self.print_geometries()
         self.plot_energies()
         if self.converged and self.ts_guess is not None: