Fix openbabel install to ensure q-chem tests run

.github/workflows/linting.yml

@@ -9,8 +9,6 @@ on:
 jobs:
   build:
     runs-on: ubuntu-latest
-    strategy:
-      max-parallel: 1
     steps:
       - uses: actions/checkout@v4
         with:

.github/workflows/test.yml

@@ -14,30 +14,36 @@ on:
 jobs:
   build:
     strategy:
-      max-parallel: 1
       matrix:
-        os: [ubuntu-latest]
-        python-version: ["3.10"]
+        os: [ubuntu-latest, windows-latest, macos-14]
+        # not testing on 3.9 because tests use glob("*", root_dir=TEST_FILES)
+        # and root_dir only added in 3.10
+        python-version: ["3.10", "3.12"]
 
     runs-on: ${{ matrix.os }}
+    defaults:
+      run:
+        shell: bash -l {0}
 
     steps:
       - uses: actions/checkout@v4
 
+      - uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+          cache: pip
+          cache-dependency-path: pyproject.toml
+
       - uses: conda-incubator/setup-miniconda@v3
         with:
           python-version: ${{ matrix.python-version }}
+          activate-environment: qchem
 
       - name: Install OpenBabel
-        shell: bash -l {0}
         run: conda install -c conda-forge openbabel
 
-      - uses: actions/setup-python@v5
-        with:
-          python-version: ${{ matrix.python-version }}
-
       - name: Install dependencies
-        run: pip install -e '.[dev]'
+        run: pip install '.[dev]'
 
       - name: pytest
         env:

custodian/qchem/handlers.py

@@ -380,6 +380,6 @@ def correct(self):
         ) and str(self.qcinp.geom_opt["initial_hessian"]).lower() == "read":
             del self.qcinp.geom_opt["initial_hessian"]
             actions.append({"initial_hessian": "deleted"})
-        os.rename(self.input_file, self.input_file + ".last")
+        os.replace(self.input_file, f"{self.input_file}.last")
         self.qcinp.write_file(self.input_file)
         return {"errors": self.errors, "warnings": self.warnings, "actions": actions}

custodian/qchem/jobs.py

@@ -590,7 +590,7 @@ def opt_with_frequency_flattener(
                                 else:
                                     good_child = copy.deepcopy(history[-1])
                                 if good_child["num_neg_freqs"] > 1:
-                                    raise Exception(
+                                    raise ValueError(
                                         "ERROR: Child with lower energy has more negative frequencies! Exiting..."
                                     )
                                 if good_child["energy"] < parent_hist["energy"] or (
@@ -602,17 +602,17 @@ def opt_with_frequency_flattener(
                                 ):
                                     make_good_child_next_parent = True
                                 else:
-                                    raise Exception("ERROR: Good child not good enough! Exiting...")
+                                    raise ValueError("ERROR: Good child not good enough! Exiting...")
                                 if make_good_child_next_parent:
                                     good_child["index"] = len(history)
                                     history.append(good_child)
                                     ref_mol = history[-1]["molecule"]
                                     geom_to_perturb = history[-1]["geometry"]
                                     negative_freq_vecs = history[-1]["frequency_mode_vectors"][perturb_index]
                             else:
-                                raise Exception("ERROR: Can't deal with multiple neg frequencies yet! Exiting...")
+                                raise ValueError("ERROR: Can't deal with multiple neg frequencies yet! Exiting...")
                         else:
-                            raise AssertionError("ERROR: Parent cannot have more than two children! Exiting...")
+                            raise ValueError("ERROR: Parent cannot have more than two children! Exiting...")
                     # Implicitly, if the number of negative frequencies decreased from parent to child,
                     # continue normally.
                 if standard:

tests/files/qchem/new_test_files/fileman_cpscf.qin

@@ -0,0 +1,98 @@
+$molecule
+ 0 2
+ O      0.2914152612     -4.5445442042      3.0161751692
+ O     -1.5304339813     -3.2367784149      2.9281824830
+ C      0.8295530097     -3.9366715322      4.2435768817
+ C     -0.1230659566     -4.2007068432      5.3950468933
+ C      2.1314679452     -4.6891692104      4.4343334880
+ C      1.0891180123     -2.4551760936      4.0360799358
+ C     -0.8605961838     -4.1422775145      2.4861350017
+ C     -1.2116960079     -4.9374875952      1.2364985602
+ C     -2.6517342220     -4.6163181541      0.8175486720
+ H     -0.3280027986     -5.2718477365      5.4811047398
+ H      0.3385752508     -3.8702900027      6.3302131252
+ H     -1.0648795958     -3.6651308672      5.2679406205
+ H      2.8060542012     -4.5134182893      3.5911657969
+ H      1.9470806743     -5.7639090000      4.5122126635
+ H      2.6262968839     -4.3565250871      5.3502869188
+ H      1.6558832285     -2.2928927340      3.1137215346
+ H      0.1610759990     -1.8839982580      3.9934806758
+ H      1.6896565513     -2.0812658626      4.8711834869
+ C     -1.0164727255     -6.4347242690      1.4797433050
+ H     -1.5581303737     -6.7836873265      2.3638647772
+ H      0.0398286180     -6.6745120675      1.6184484158
+ H     -1.3829909813     -6.9970496209      0.6140214151
+ C     -0.2642252347     -4.4709101412      0.1263230216
+ H     -0.3925640144     -3.4049115606     -0.0773598657
+ H     -0.4789826082     -5.0237708051     -0.7947386622
+ H      0.7815646456     -4.6470496024      0.3929852586
+ C     -3.7386359783     -5.1159593031      1.7522230896
+ H     -2.8000270794     -5.0438393410     -0.1827625673
+ H     -2.7338896931     -3.5296566953      0.7024878530
+ H     -3.7691013071     -6.2090022139      1.7949719714
+ H     -4.7241345868     -4.7791401993      1.4163909720
+ H     -3.5933064317     -4.7432620029      2.7707341718
+ S     -3.1095688405     -0.8338328120      1.9223394071
+ C     -1.4763090285     -0.6530852521      0.5550909541
+ C     -1.7891128457     -0.8441888555     -0.7833876727
+ H     -2.8272949027     -0.8142864366     -1.1170758647
+ C     -0.7598974121     -1.0500002977     -1.7040885688
+ H     -0.9909069977     -1.1779594339     -2.7596192371
+ C      0.5668601276     -1.0856329376     -1.2708524494
+ H      1.3694627147     -1.2422432626     -1.9871957374
+ C      0.8611607361     -0.9378379065      0.0855095498
+ H      1.8948169178     -0.9779391480      0.4236494734
+ C     -0.1682729563     -0.7392449587      1.0085213741
+ H      0.0565492183     -0.6401064636      2.0671273707
+ C     -2.3463554075     -0.1413857476      3.3511116054
+ C     -1.6861008228      1.0969952276      3.3571269080
+ C     -1.1464262498      1.5804639094      4.5468959620
+ H     -0.6384784857      2.5416032340      4.5463233852
+ C     -1.2451485056      0.8426672145      5.7244777657
+ H     -0.8196610583      1.2241103280      6.6487441345
+ C     -1.9004041859     -0.3950415761      5.7114055631
+ H     -1.9807860619     -0.9794453631      6.6245370395
+ C     -2.4557420740     -0.8829375023      4.5380818681
+ H     -2.9596492827     -1.8437276305      4.5221216535
+ C     -4.1249281175      0.4004756787      1.1655216406
+ C     -3.6353302924      1.6229046114      0.6843711827
+ H     -1.5667550440      1.6629973908      2.4414322262
+ C     -4.5234891084      2.5509004307      0.1444384244
+ H     -4.1442520184      3.5017916858     -0.2216525594
+ C     -5.8845872809      2.2671234587      0.0644736389
+ H     -6.5705578262      2.9985074190     -0.3548381451
+ C     -6.3661310487      1.0371574340      0.5275291796
+ H     -7.4256662542      0.8058548518      0.4619447035
+ C     -5.4944582701      0.1113707308      1.0849708426
+ H     -5.8630706203     -0.8369243514      1.4678940842
+ H     -2.5707192368      1.8246188792      0.6894404950
+$end
+
+$rem
+   job_type = freq
+   basis = def2-svpd
+   max_scf_cycles = 100
+   gen_scfman = true
+   xc_grid = 3
+   thresh = 14
+   s2thresh = 16
+   scf_algorithm = diis
+   resp_charges = true
+   symmetry = false
+   sym_ignore = true
+   method = b97mv
+   solvent_method = pcm
+   mem_total = 170000
+$end
+
+$pcm
+   heavypoints 194
+   hpoints 194
+   radii uff
+   theory cpcm
+   vdwscale 1.1
+$end
+
+$solvent
+   dielectric 78.39
+$end