Merge

.github/workflows/CI.yml

@@ -7,6 +7,8 @@ on:
   pull_request:
     branches:
       - master
+  schedule:
+    - cron: "9 16 * * 1"
 
 jobs:
   build:
@@ -19,60 +21,88 @@ 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: 3.6
+            python-version: 3.8
             label: ANI
             runs-on: ubuntu-latest
+            pytest: ""
 
           - conda-env: openmm
-            python-version: 3.6
+            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: 3.6
+            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:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v3
       with:
         fetch-depth: 0
 
@@ -83,9 +113,15 @@ jobs:
         environment-file: devtools/conda-envs/${{ matrix.cfg.conda-env }}.yaml
         python-version: ${{ matrix.cfg.python-version }}
         auto-activate-base: false
+        show-channel-urls: true
+        miniforge-variant: Mambaforge
+        use-mamba: true
+        add-pip-as-python-dependency: true
+        # note: conda-forge chnl req'd for Mambaforge, but we'll spec in file, not here `channels: conda-forge,...`
+        # 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
 
@@ -94,15 +130,29 @@ jobs:
       run: |
         qcore --accept-license
 
+    - 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 == 'Psi4-1.6') || (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
+
     - name: Environment Information
       run: |
-        conda info
-        conda list --show-channel-urls
+        mamba info
+        mamba list
 
     - name: Install QCEngine
       run: |
@@ -117,10 +167,10 @@ 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@v1
+      uses: codecov/codecov-action@v3
 
   release_sphinx:
     needs: [build]
@@ -140,7 +190,7 @@ jobs:
     runs-on: ${{ matrix.cfg.runs-on }}
 
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v3
 
     - name: Create Environment
       uses: conda-incubator/setup-miniconda@v2
@@ -149,11 +199,15 @@ jobs:
         environment-file: devtools/conda-envs/${{ matrix.cfg.conda-env }}.yaml
         python-version: ${{ matrix.cfg.python-version }}
         auto-activate-base: false
+        miniforge-variant: Mambaforge
+        use-mamba: true
+        add-pip-as-python-dependency: true
+        channels: conda-forge
 
     - name: Environment Information
       run: |
-        conda info
-        conda list --show-channel-urls
+        mamba info
+        mamba list --show-channel-urls
 
     - name: Build Documentation
       run: |

.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

.github/workflows/codeql.yml

@@ -0,0 +1,41 @@
+name: "CodeQL"
+
+on:
+  push:
+    branches: [ "master", "gh-pages" ]
+  pull_request:
+    branches: [ "master" ]
+  schedule:
+    - cron: "8 16 * * 2"
+
+jobs:
+  analyze:
+    name: Analyze
+    runs-on: ubuntu-latest
+    permissions:
+      actions: read
+      contents: read
+      security-events: write
+
+    strategy:
+      fail-fast: false
+      matrix:
+        language: [ python ]
+
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v3
+
+      - name: Initialize CodeQL
+        uses: github/codeql-action/init@v2
+        with:
+          languages: ${{ matrix.language }}
+          queries: +security-and-quality
+
+      - name: Autobuild
+        uses: github/codeql-action/autobuild@v2
+
+      - name: Perform CodeQL Analysis
+        uses: github/codeql-action/analyze@v2
+        with:
+          category: "/language:${{ matrix.language }}"

README.md

@@ -1,11 +1,11 @@
 QCEngine
 ========
-[![Travis build](https://img.shields.io/travis/MolSSI/QCEngine/master.svg?logo=linux&logoColor=white)](https://travis-ci.org/MolSSI/QCEngine)
+[![Build Status](https://github.com/MolSSI/QCEngine/workflows/CI/badge.svg?branch=master)](https://github.com/MolSSI/QCEngine/actions?query=workflow%3ACI)
 [![codecov](https://img.shields.io/codecov/c/github/MolSSI/QCEngine.svg?logo=Codecov&logoColor=white)](https://codecov.io/gh/MolSSI/QCEngine)
-[![Language grade: Python](https://img.shields.io/lgtm/grade/python/g/MolSSI/QCEngine.svg?logo=lgtm&logoWidth=18)](https://lgtm.com/projects/g/MolSSI/QCEngine/context:python)
-[![Documentation Status](https://img.shields.io/github/workflow/status/MolSSI/QCEngine/CI/master?label=docs&logo=readthedocs&logoColor=white)](http://docs.qcarchive.molssi.org/projects/qcengine/en/latest/)
+[![Documentation Status](https://img.shields.io/github/actions/workflow/status/MolSSI/QCEngine/CI.yml?label=docs&logo=readthedocs&logoColor=white)](https://molssi.github.io/QCEngine/)
 [![Conda (channel only)](https://img.shields.io/conda/vn/conda-forge/qcengine?color=blue&logo=anaconda&logoColor=white)](https://anaconda.org/conda-forge/qcengine)
 [![Chat on Slack](https://img.shields.io/badge/chat-on_slack-808493.svg?longCache=true&style=flat&logo=slack)](https://join.slack.com/t/qcarchive/shared_invite/enQtNDIzNTQ2OTExODk0LTE3MWI0YzBjNzVhNzczNDM0ZTA5MmQ1ODcxYTc0YTA1ZDQ2MTk1NDhlMjhjMmQ0YWYwOGMzYzJkZTM2NDlmOGM)
+![python](https://img.shields.io/badge/python-3.7+-blue.svg)
 
 <!--[![Azure Build Status](https://dev.azure.com/MolSSI/QCArchive/_apis/build/status/MolSSI.QCEngine?branchName=master)](https://dev.azure.com/MolSSI/QCArchive/_build/latest?definitionId=5&branchName=master)-->
 Quantum chemistry program executor and IO standardizer ([QCSchema](https://github.com/MolSSI/QCSchema)) for quantum chemistry.
@@ -52,7 +52,7 @@ The results contain a complete record of the computation:
 Intel(R) Core(TM) i7-7820HQ CPU @ 2.90GHz
 ```
 
-See the [documentation](https://qcengine.readthedocs.io/en/latest/) for more information.
+See the [documentation](https://molssi.github.io/QCEngine/) for more information.
 
 # License
 

devtools/conda-envs/adcc.yaml

@@ -1,21 +1,19 @@
 name: test
 channels:
-  - adcc
-  - psi4/label/dev
+  #- adcc
   - conda-forge
+  - nodefaults
 dependencies:
   - adcc>=0.15.7
-  - psi4
-  - blas=*=mkl  # not needed but an example of disuading solver from openblas and old psi
-  - intel-openmp!=2019.5
+  - psi4>=1.8.1
+  - conda-forge/label/libint_dev::libint
 
   # Core
   - python
-  - pyyaml
   - py-cpuinfo
   - psutil
   - qcelemental >=0.24.0
-  - pydantic>=1.0.0
+  - pydantic=1
   - msgpack-python
 
     # Testing

devtools/conda-envs/docs-cf.yaml

@@ -5,7 +5,7 @@ channels:
 dependencies:
   - python
   - networkx
-  - pydantic
+  - pydantic=1
   - numpy
   - pint
 

devtools/conda-envs/mrchem.yaml

@@ -2,7 +2,9 @@ name: test
 channels:
   - conda-forge
 dependencies:
-  - mrchem=1=*openmpi*_1
+  - mrchem >=1.1=*openmpi*
+  - geometric
+  - optking
 
     # Core
   - python
@@ -17,3 +19,7 @@ dependencies:
   - pytest
   - pytest-cov
   - codecov
+
+  - pip
+  - pip:
+    - pyberny

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

devtools/conda-envs/openmm.yaml

@@ -16,7 +16,8 @@ dependencies:
   - py-cpuinfo
   - psutil
   - qcelemental >=0.11.1
-  - pydantic >=0.30.1
+  - pydantic >=1.8.2
+  - pint <0.22
 
     # Testing
   - pytest