changelog and GHA CI (from upstream) (#286)

* changelog and GHA CI, take 1

* fix syntax error

* take 2

* take 3

* take 4

* take 5

* nwchem wants xenial?

* remove, then install

* small docs update

* try mostly bionic

* cleanup

* update changelog, misc.

* bit more GHA

* remove travis file

* codecov tests so can see what's not covered by the various CI lanes

* changelog

.codecov.yml

@@ -1,6 +1,5 @@
 coverage:
   ignore:
-    - qcengine/test/.*
     - qcengine/programs/util/.*
     - qcengine/programs/cfour/.*
     - qcengine/programs/gamess/.*

.github/workflows/CI.yml

@@ -0,0 +1,121 @@
+name: CI
+
+on:
+  push:
+    branches:
+      - master
+  pull_request:
+    branches:
+      - master
+
+jobs:
+  build:
+    defaults:
+      run:
+        shell: bash -l {0}
+    strategy:
+      matrix:
+        cfg:
+          - conda-env: psi
+            python-version: 3.6
+            label: Psi4-release
+            runs-on: ubuntu-latest
+
+          - conda-env: psi-nightly
+            python-version: 3.9
+            label: Psi4-nightly
+            runs-on: ubuntu-latest
+
+          - conda-env: torchani
+            python-version: 3.6
+            label: ANI
+            runs-on: ubuntu-latest
+
+          - conda-env: openmm
+            python-version: 3.6
+            label: OpenMM
+            runs-on: ubuntu-latest
+
+          - conda-env: xtb
+            python-version: 3.6
+            label: xTB
+            runs-on: ubuntu-latest
+
+          - conda-env: qcore
+            python-version: 3.7
+            label: QCore
+            runs-on: ubuntu-latest
+
+          - conda-env: nwchem
+            python-version: 3.6
+            label: NWChem
+            runs-on: ubuntu-16.04
+
+          - conda-env: mrchem
+            python-version: 3.6
+            label: MRChem
+            runs-on: ubuntu-latest
+
+          - conda-env: adcc
+            python-version: 3.8
+            label: ADCC
+            runs-on: ubuntu-latest
+
+          # - conda-env:
+          #   python-version:
+          #   label:
+          #   runs-on: ubuntu-latest
+
+    name: "🐍 ${{ matrix.cfg.python-version }} • ${{ matrix.cfg.label }}" # • ${{ matrix.cfg.runs-on }}"
+    runs-on: ${{ matrix.cfg.runs-on }}
+
+    steps:
+    - uses: actions/checkout@v2
+      with:
+        fetch-depth: 0
+
+    - name: Create Environment
+      uses: conda-incubator/setup-miniconda@v2
+      with:
+        activate-environment: test
+        environment-file: devtools/conda-envs/${{ matrix.cfg.conda-env }}.yaml
+        python-version: ${{ matrix.cfg.python-version }}
+        auto-activate-base: false
+
+    - name: Special Config - NWChem
+      if: "(matrix.cfg.label == 'NWChem')"
+      run: |
+        sudo apt-get -y install nwchem
+
+    - name: Special Config - QCore
+      if: "(matrix.cfg.label == 'QCore')"
+      run: |
+        qcore --accept-license
+
+    - name: Special Config - QCEngine Dep
+      if: "(matrix.cfg.label == 'Psi4-nightly') || (matrix.cfg.label == 'ADCC')"
+      run: |
+        conda remove qcengine --force
+
+    - name: Environment Information
+      run: |
+        conda info
+        conda list --show-channel-urls
+
+    - name: Install QCEngine
+      run: |
+        python -m pip install . --no-deps
+
+    - name: QCEngineRecords
+      run: |
+        qcengine info
+        export QCER_VER=`python -c "import qcengine.testing; print(qcengine.testing.QCENGINE_RECORDS_COMMIT)"`
+        pip install git+https://github.com/MolSSI/QCEngineRecords.git@${QCER_VER}#egg=qcenginerecords
+        python -c "import qcengine; print(qcengine.config.global_repr())"
+
+    - name: PyTest
+      run: |
+        pytest -rws -v --cov=qcengine --color=yes --cov-report=xml qcengine/
+
+    - name: CodeCov
+      uses: codecov/codecov-action@v1

.github/workflows/Lint.yml

@@ -1,6 +1,12 @@
 name: Lint
 
-on: [push, pull_request]
+on:
+  push:
+    branches:
+      - master
+  pull_request:
+    branches:
+      - master
 
 jobs:
   build:

codemeta.json

@@ -306,6 +306,14 @@
             "affiliation": "Inria Paris and CERMICS, \u00C9cole des Ponts ParisTech",
             "@id": "https://orcid.org/0000-0003-0378-7921",
             "identifier": "https://github.com/mfherbst"
+        },
+        {
+            "@type": "Person",
+            "givenName": "Holger",
+            "familyName": "Kruse",
+            "affiliation": "Institute of Biophysics of the CAS, v.v.i., Czech Republic",
+            "@id": "https://orcid.org/0000-0002-0560-1513",
+            "identifier": "https://github.com/hokru"
         }
     ],
     "developmentStatus": "active",

docs/source/changelog.rst

@@ -1,7 +1,7 @@
 Changelog
 =========
 
-.. vX.Y.0 / 2020-MM-DD
+.. vX.Y.0 / 2021-MM-DD
 .. --------------------
 ..
 .. New Features
@@ -14,6 +14,31 @@ Changelog
 .. +++++++++
 
 
+v0.18.0 / 2021-MM-DD
+--------------------
+
+New Features
+++++++++++++
+.. - (:pr:`206`) OptKing - new procedure harness for OptKing optimizer.
+- (:pr:`269`) MRChem - new multiresolution chemistry program harness.
+- (:pr:`277`) ADCC - new program harness for ADC-connect. (Requires Psi4 for SCF.)
+- (:pr:`278`) gCP - new program harness for geometric counterpoise.
+- (:pr:`280`) Add framework to register identifying known outfile errors, modify input schema, and rerun.
+- (:pr:`281`) NWChem - new procedure harness to use NWChem's DRIVER geometry optimizer with NWChem's program harness gradients.
+- (:pr:`282`) DFTD3 - added D3m and D3m(bj) parameters for SAPT0/HF. Allow pairwise analysis to be returned.
+.. - (:pr:`xxx`) TeraChem - new harness for "Server Mode".
+
+Enhancements
+++++++++++++
+- (:pr:`274`) Entos/Qcore - renamed harness and updated to new Python bindings.
+- (:pr:`283`) OpenMM - transition harness from `openforcefield` packages on omnia channel to `openff.toolkit` packages on conda-forge channel.
+- (:pr:`286`) CI - moves from Travis-CI to GHA for open-source testing.
+
+Bug Fixes
++++++++++
+- (:pr:`273`) TeraChem - fixed bug of missing method field.
+
+
 v0.17.0 / 2020-10-02
 --------------------
 

docs/source/program_overview.rst

@@ -8,7 +8,7 @@ Quantum Chemistry
 -----------------
 
 +---------------+------------+---+---+---+------------+--------------+
-| Program       | Production | E | G | H | Properties | Wavefunction +
+| Program       | Production | E | G | H | Properties | Wavefunction |
 +===============+============+===+===+===+============+==============+
 | adcc          | ✘          | ✓ | ✘ | ✘ | ✓          | ✘            |
 +---------------+------------+---+---+---+------------+--------------+
@@ -70,7 +70,7 @@ Analytical Corrections
 +------------+------------+---+---+---+------------+
 | Program    | Production | E | G | H | Properties |
 +============+============+===+===+===+============+
-| DFTD3      | ✓          | ✓ | ✓ | ✘ | ✓          |
+| DFTD3      | ✓          | ✓ | ✓ | ✘ | ✘          |
 +------------+------------+---+---+---+------------+
 | gCP        | ✘          | ✓ | ✓ | ✘ | ✘          |
-+------------+------------+---+---+---+------------+
++------------+------------+---+---+---+------------+

qcengine/programs/model.py

@@ -84,7 +84,7 @@ def parse_output(self, outfiles: Dict[str, str], input_model: "AtomicInput") ->
 class ErrorCorrectionProgramHarness(ProgramHarness, abc.ABC):
     """Base class for Harnesses that include logic to correct common errors
 
-    Classes which implement this Hardness must override the :meth:`_compute` method
+    Classes which implement this Harness must override the :meth:`_compute` method
     rather than :meth:`compute`. The ``compute`` method from this class will make
     calls to ``_compute`` with different actions as it attempts to correct errors in the
     input files.

setup.py

@@ -48,6 +48,8 @@
             "Programming Language :: Python :: 3",
             "Programming Language :: Python :: 3.6",
             "Programming Language :: Python :: 3.7",
+            "Programming Language :: Python :: 3.8",
+            "Programming Language :: Python :: 3.9",
         ],
         zip_safe=False,
         long_description=long_description,