CI for py312 (#433)

* fix? * experiment * round * qcer * more sutff * next * asdf * alt * probe * fix * rework * spell * progress * more * deeper * explciit call * abc * prog * execute * ef * gh * fix h * ij * l * m * b1c1 * b1 * full tests * no hes2 * fixup * last win * escape * again * more * asdf * nwc * suff * more * log * new p4 packages * remove lane
MolSSI · Oct 30, 2023 · 1e771c6 · 1e771c6
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diff --git a/.github/workflows/CI.yml b/.github/workflows/CI.yml
@@ -21,56 +21,84 @@ jobs:
         cfg:
           - conda-env: psi
             python-version: 3.7
-            label: Psi4-release
+            label: Psi4-1.5
             runs-on: ubuntu-latest
+            pytest: ""
 
           - conda-env: psi-nightly
             python-version: "3.10"
-            label: Psi4-nightly
+            label: Psi4-1.6
             runs-on: ubuntu-latest
+            pytest: ""
+
+          - conda-env: psi-cf
+            python-version: "3.12"
+            label: Psi4-1.8
+            runs-on: windows-latest
+            pytest: "-k 'not (hes2 or qchem)'"
 
           - conda-env: torchani
             python-version: 3.8
             label: ANI
             runs-on: ubuntu-latest
+            pytest: ""
 
           - conda-env: openmm
             python-version: 3.8
             label: OpenMM
             runs-on: ubuntu-latest
+            pytest: ""
 
           - conda-env: xtb
             python-version: "3.10"
             label: xTB
             runs-on: ubuntu-latest
+            pytest: ""
 
           - conda-env: qcore
             python-version: 3.7
             label: QCore
             runs-on: ubuntu-latest
+            pytest: ""
 
           - conda-env: nwchem
             python-version: 3.8
-            label: NWChem
+            label: NWChem70
             runs-on: ubuntu-20.04
+            pytest: ""
             # formerly NWChem v6.6 with python-version: 3.6 & runs-on: ubuntu-16.04 but ubuntu env retired by GH Sep 2021
 
+          - conda-env: nwchem-cf
+            python-version: 3.12
+            label: NWChem
+            runs-on: ubuntu-latest
+            pytest: ""
+
           - conda-env: mrchem
             python-version: 3.8
             label: MRChem
             runs-on: ubuntu-latest
+            pytest: ""
 
           - conda-env: adcc
             python-version: 3.8
             label: ADCC
             runs-on: ubuntu-latest
+            pytest: ""
 
           - conda-env: opt-disp
             python-version: 3.8
             label: optimization-dispersion
             runs-on: ubuntu-latest
+            pytest: ""
+
+          - conda-env: opt-disp-cf
+            python-version: 3.11
+            label: optimization-dispersion
+            runs-on: windows-latest
+            pytest: "-k 'not (hes2 or qchem)'"
 
-    name: "🐍 ${{ matrix.cfg.python-version }} • ${{ matrix.cfg.label }}" # • ${{ matrix.cfg.runs-on }}"
+    name: "🐍 ${{ matrix.cfg.python-version }} • ${{ matrix.cfg.label }} • ${{ matrix.cfg.runs-on }}"
     runs-on: ${{ matrix.cfg.runs-on }}
 
     steps:
@@ -93,7 +121,7 @@ jobs:
         # note: any activate/deactivate use the conda cmd. other cmds use mamba cmd.
 
     - name: Special Config - NWChem
-      if: "(matrix.cfg.label == 'NWChem')"
+      if: "(matrix.cfg.label == 'NWChem70')"
       run: |
         sudo apt-get -y install nwchem
 
@@ -102,23 +130,22 @@ jobs:
       run: |
         qcore --accept-license
 
-    # note: psi4 on c-f pins to a single qcel and qcng, so this may be handy for solve-and-replace
-    #- name: Special Config - QCElemental Dep
-    #  if: (matrix.cfg.label == 'ADCC')
-    #  run: |
-    #    conda remove qcelemental --force
-    #    python -m pip install qcelemental>=0.26.0 --no-deps
+    - name: Special Config - QCElemental Dep
+      if: false
+      run: |
+        conda remove qcelemental --force
+        python -m pip install 'git+https://github.com/MolSSI/QCElemental.git@loriab-patch-2' --no-deps
 
       # note: conda remove --force, not mamba remove --force b/c https://github.com/mamba-org/mamba/issues/412
       #       alt. is micromamba but not yet ready for setup-miniconda https://github.com/conda-incubator/setup-miniconda/issues/75
     - name: Special Config - QCEngine Dep
-      if: "(matrix.cfg.label == 'Psi4-nightly') || (matrix.cfg.label == 'ADCC') || (matrix.cfg.label == 'optimization-dispersion')"
+      if: "(startsWith(matrix.cfg.label, 'Psi4')) || (matrix.cfg.label == 'ADCC') || (matrix.cfg.label == 'optimization-dispersion')"
       run: |
         conda remove qcengine --force
 
       # QCEngine CI and Psi4 are circularly dependent, so a hack is in order
     - name: Special Config - Faux Pydantic Upgrade
-      if: "(matrix.cfg.label == 'Psi4-nightly') || (matrix.cfg.label == 'optimization-dispersion')"
+      if: "((matrix.cfg.label == 'Psi4-1.6') || (matrix.cfg.label == 'optimization-dispersion')) && (runner.os != 'Windows')"
       run: |
         sed -i s/from\ pydantic\ /from\ pydantic.v1\ /g ${CONDA_PREFIX}/lib/python${{ matrix.cfg.python-version }}/site-packages/psi4/driver/*py
 
@@ -140,7 +167,7 @@ jobs:
 
     - name: PyTest
       run: |
-        pytest -rws -v --cov=qcengine --color=yes --cov-report=xml qcengine/
+        pytest -rws -v ${{ matrix.cfg.pytest }} --cov=qcengine --color=yes --cov-report=xml qcengine/
 
     - name: CodeCov
       uses: codecov/codecov-action@v3

diff --git a/.github/workflows/Lint.yml b/.github/workflows/Lint.yml
@@ -13,15 +13,15 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: [3.7]
+        python-version: ["3.10"]
 
     steps:
-    - uses: actions/checkout@v1
+    - uses: actions/checkout@v4
 
     - name: Python Setup
-      uses: actions/setup-python@v1
+      uses: actions/setup-python@v4
       with:
-        python-version: ${{ matrix.python-version }}
+        python-version: "${{ matrix.python-version }}"
 
     - name: Create Environment
       shell: bash

diff --git a/devtools/conda-envs/nwchem-cf.yaml b/devtools/conda-envs/nwchem-cf.yaml
@@ -0,0 +1,19 @@
+name: test
+channels:
+  - conda-forge
+dependencies:
+  - nwchem
+
+    # Core
+  - python
+  - pyyaml
+  - py-cpuinfo
+  - psutil
+  - qcelemental >=0.24.0
+  - pydantic>=1.0.0
+  - networkx>=2.4.0
+
+    # Testing
+  - pytest
+  - pytest-cov
+  - codecov
diff --git a/devtools/conda-envs/opt-disp-cf.yaml b/devtools/conda-envs/opt-disp-cf.yaml
@@ -0,0 +1,35 @@
+name: test
+channels:
+  - conda-forge/label/libint_dev
+  - conda-forge
+  - nodefaults
+dependencies:
+  - psi4
+  - rdkit
+  - mopac
+
+    # Mixed Tests
+  - dftd3-python
+  - dftd4-python
+  - gcp-correction
+  - geometric
+  - optking
+  - pymdi
+
+    # Core
+  - python
+  - pyyaml
+  - py-cpuinfo
+  - psutil
+  - qcelemental >=0.26.0
+  - pydantic=1.10.13
+  - msgpack-python
+
+    # Testing
+  - pytest
+  - pytest-cov
+  - codecov
+
+  - pip
+  - pip:
+    - pyberny
diff --git a/devtools/conda-envs/psi-cf.yaml b/devtools/conda-envs/psi-cf.yaml
@@ -0,0 +1,18 @@
+name: test
+channels:
+  - conda-forge
+  - conda-forge/label/libint_dev
+dependencies:
+  - psi4=1.8
+
+    # Core
+  - python
+  - pyyaml
+  - py-cpuinfo
+  - psutil
+  - msgpack-python
+
+    # Testing
+  - pytest
+  - pytest-cov
+  - codecov
diff --git a/devtools/conda-envs/psi-nightly.yaml b/devtools/conda-envs/psi-nightly.yaml
@@ -3,7 +3,7 @@ channels:
   - psi4/label/dev
   - conda-forge
 dependencies:
-  - psi4
+  - psi4=1.6
   - blas=*=mkl  # not needed but an example of disuading solver from openblas and old psi
 
     # Core

diff --git a/docs/source/changelog.rst b/docs/source/changelog.rst
@@ -25,11 +25,10 @@ Changelog
 .. WIP (Unmerged)
 .. ++++++++++++++
 .. - UNMERGED (:pr:`421`) GAMESS - error handling and memory @taylor-a-barnes
-.. - UNMERGED (:pr:`405`, :issue:`415`, :pr:`417`) Config - change default `jobs_per_node` from 2 to more expected 1 so a single job fills the node. Alter CPU count formula to return physical cores on Hyerthreading machines, affecting default `ncores`. The net effect (both changes) for default cores running on Hyperthreading machines is unchanged. @cvsik, @loriab
 .. - UNSOLVED (:issue:`397`) extras failed
 
 
-v0.28.2 / 2023-MM-DD (Unreleased)
+v0.29.0 / 2023-MM-DD (Unreleased)
 --------------------
 
 Breaking Changes
@@ -43,14 +42,21 @@ Enhancements
 
 Bug Fixes
 +++++++++
+- (:pr:`427`) Config - Once again, expand environment variables (now more flexibly) and newly expand ``~``
+  passed into TaskConfig. Particularly relevant for scratch setting. @yueyericardo
+- (:pr:`428`) MDI - Ensure that molecule orientation remains fixed for MDI. @taylor-a-barnes
+- (:pr:`405`, :issue:`415`, :pr:`417`) Config - change default ``jobs_per_node`` from 2 to more expected 1
+  so a single job fills the node. Alter CPU count formula to return physical cores on Hyerthreading
+  machines, affecting default ``ncores``. The net effect (both changes) for default cores running on
+  Hyperthreading machines is unchanged. @cvsik, @loriab
+UNMERGED - (:pr:`433`) Turbomole, Q-Chem - Use raw strings when needed to avoid py312 warnings.
 
 Misc.
 +++++
+UNMERGED - (:pr:`433`) CI - Check py312 and some Windows lanes.
 
 MUST (Unmerged)
 +++++++++++++++
-- UNMERGED (:pr:`427`) Config - Once again, expand environment variables (now more flexibly) and newly expand ``~``
-  passed into TaskConfig. Particularly relevant for scratch setting.
 
 
 v0.28.1 / 2023-08-18

diff --git a/qcengine/programs/qchem.py b/qcengine/programs/qchem.py
@@ -358,7 +358,7 @@ def _parse_logfile_common(self, outtext: str, input_dict: Dict[str, Any]):
 
         properties["calcinfo_natom"] = len(input_dict["molecule"]["symbols"])
 
-        mobj = re.search(r"\n\s*(\d+)\s+" + NUMBER + "\s+" + NUMBER + r"\s+Convergence criterion met\s*\n", outtext)
+        mobj = re.search(r"\n\s*(\d+)\s+" + NUMBER + r"\s+" + NUMBER + r"\s+Convergence criterion met\s*\n", outtext)
         if mobj:
             properties["scf_iterations"] = int(mobj.group(1))
 

diff --git a/qcengine/programs/tests/test_canonical_config.py b/qcengine/programs/tests/test_canonical_config.py
@@ -3,6 +3,7 @@
 """
 import pprint
 import re
+import sys
 import tempfile
 from pathlib import Path
 
@@ -182,6 +183,9 @@ def test_local_options_scratch(program, model, keywords):
         "nwchem": "E. Apra",  # freebie
         "psi4": rf"Scratch directory: {scratch_directory}/tmp\w+_psi_scratch/",
     }
+    if sys.platform.startswith("win"):
+        # too hard to regex Windows paths that need escape chars
+        stdout_ref["psi4"] = f"Scratch directory: "
 
     # a scratch file (preferrably output) expected after job if scratch not cleaned up
     scratch_sample = {