Created intial working SinglePoint and FileInput calculations. Create…

…d FileAdapter and TeraChemAdapter. Created packaged setup, CI/CD, etc. Verified working with TeraChem and using Psi4 via the QCEngine compatibility layer.

.github/workflows/basic-code-quality.yaml

@@ -0,0 +1,85 @@
+name: Basic Code Quality
+
+on: [push]
+
+env:
+  POETRY_VIRTUALENVS_CREATE: false
+
+jobs:
+  ruff:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+      - name: Set up Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: "3.8"
+      - name: Install ruff
+        run: pip install ruff
+      - name: ruff
+        run: ruff check .
+
+  mypy:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+      - name: Set up Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: "3.8"
+      - name: Install poetry
+        run: pip install poetry
+      - name: Install repo
+        run: poetry install --no-interaction --no-ansi
+      - name: mypy
+        run: mypy .
+
+  black:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+      - name: Set up Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: "3.8"
+      - name: Install black
+        run: pip install black
+      - name: Check code formatting with black
+        run: black --check .
+
+  isort:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+      - name: Set up Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: "3.8"
+      - name: Install poetry
+        run: pip install poetry
+      - name: Install repo
+        run: poetry install --no-interaction --no-ansi
+      - name: Check import formatting with isort
+        run: isort --check-only --diff .
+
+  detect-secrets:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+      - name: Set up Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: "3.8"
+      - name: Install detect secrets
+        run: pip install detect-secrets
+      - name: Look for secrets
+        run: git ls-files -z | xargs -0 detect-secrets-hook -v
+
+  typos:
+    name: "spell check"
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+      - uses: crate-ci/typos@master
+        with:
+          files: .

.github/workflows/publish-to-pypi.yaml

@@ -0,0 +1,40 @@
+# https://github.com/marketplace/actions/pypi-publish
+
+name: Publish to PyPI
+
+on:
+  push:
+    tags: # Only publish on tagged commits
+      - "*"
+
+jobs:
+  build-and-publish:
+    name: Build and publish Python 🐍 distributions 📦 to PyPI
+    runs-on: ubuntu-latest
+    environment:
+      name: pypi
+      url: https://pypi.org/project/qcop/
+    permissions:
+      id-token: write # IMPORTANT: this permission is mandatory for trusted publishing
+
+    steps:
+      - name: Check out source repository
+        uses: actions/checkout@v2
+
+      - name: Set up Python
+        uses: actions/setup-python@v2
+        with:
+          python-version: 3.8
+
+      - name: Install poetry
+        run: |
+          curl -sSL https://install.python-poetry.org | python3 -
+
+      - name: Install dependencies
+        run: poetry install --no-interaction --no-ansi
+
+      - name: Build distribution 📦
+        run: poetry build
+
+      - name: Publish package 📤 to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1

.github/workflows/test.yaml

@@ -0,0 +1,24 @@
+name: Tests
+
+on: [push]
+
+jobs:
+  tests:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+      - uses: actions/setup-python@v4
+        name: Set up Python
+        with:
+          python-version: "3.8"
+      - name: Install poetry
+        run: pip install poetry
+      - name: Install repo
+        run: poetry install --no-interaction --no-ansi
+      - name: Run tests
+        run: bash scripts/tests.sh
+      - name: Upload coverage HTML
+        uses: actions/upload-artifact@v3
+        with:
+          name: htmlcov
+          path: htmlcov

.gitignore

@@ -158,3 +158,11 @@ cython_debug/
 #  and can be added to the global gitignore or merged into this file.  For a more nuclear
 #  option (not recommended) you can uncomment the following to ignore the entire idea folder.
 #.idea/
+
+# qcop specific ignores
+# TeraChem scratch files
+scr.*
+tc.in
+*.xyz
+# Psi4 scratch files
+*.dat

.pre-commit-config.yaml

@@ -0,0 +1,45 @@
+# See https://pre-commit.com for more information
+# See https://pre-commit.com/hooks.html for more hooks
+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.4.0
+    hooks:
+      - id: check-yaml
+      - id: check-added-large-files
+        args: ["--maxkb=250"]
+        exclude: caffeine.frequencies.out
+  - repo: https://github.com/Yelp/detect-secrets
+    rev: v1.4.0
+    hooks:
+      - id: detect-secrets
+        stages: [commit]
+        exclude: poetry.lock
+  - repo: https://github.com/charliermarsh/ruff-pre-commit
+    # Ruff version.
+    rev: "v0.0.272"
+    hooks:
+      - id: ruff
+        args: [--fix, --exit-non-zero-on-fix]
+  - repo: https://github.com/PyCQA/isort
+    rev: 5.12.0
+    hooks:
+      - id: isort
+  - repo: https://github.com/psf/black
+    rev: 23.1.0
+    hooks:
+      - id: black
+  - repo: https://github.com/pre-commit/mirrors-mypy
+    rev: v1.1.1
+    hooks:
+      - id: mypy
+        additional_dependencies:
+          [tokenize-rt==3.2.0, pydantic>=1.0.0, types-paramiko]
+  - repo: local
+    hooks:
+      - id: tests
+        name: tests
+        stages: [push]
+        language: system
+        entry: poetry run pytest
+        types: [python]
+        pass_filenames: false

.vscode/settings.json

@@ -0,0 +1,14 @@
+{
+    "cSpell.words": [
+        "allclose",
+        "dockerized",
+        "hostcpus",
+        "htmlcov",
+        "qcio",
+        "qcop",
+        "qcparse",
+        "spinmult",
+        "terachem",
+        "terachemd"
+    ]
+}

CHANGELOG.md

@@ -0,0 +1,16 @@
+# Changelog
+
+All notable changes to this project will be documented in this file.
+
+The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/), and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
+
+## [unreleased]
+
+### Added
+
+- Core compute capabilities exposed in top-level `compute()` function, including `QCEngine` fallback for programs without a `qcop` adapter.
+- Created adapter for TeraChem.
+- Exposed general purpose computing for any subprocess with `FileAdaptor`
+
+[unreleased]: https://github.com/coltonbh/qcop/compare/0.1.0...HEAD
+[0.1.0]: https://github.com/coltonbh/qcop/releases/tag/0.1.0

CONTRIBUTING.md

@@ -0,0 +1,21 @@
+# Contributing
+
+## Running Test
+
+- Run all tests (except integration test). See coverage report afterwards by opening `htmlcov/index.html`
+
+```sh
+bash scripts/tests.sh
+```
+
+- To run integration test:
+
+```sh
+pytest -m integration
+```
+
+- To run all tests + integration tests (skipping those where `program` is not installed)
+
+```sh
+pytest -m 'not not_integration'
+```

LICENSE

@@ -0,0 +1,21 @@
+The MIT License (MIT)
+
+Copyright (c) 2021 Colton Hicks
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+THE SOFTWARE.

README.md

@@ -0,0 +1,10 @@
+# Quantum Chemistry Operate
+
+A package for operating Quantum Chemistry programs using [qcio](https://github.com/coltonbh/qcio) standardized data structures.
+
+[![image](https://img.shields.io/pypi/v/qcop.svg)](https://pypi.python.org/pypi/qcop)
+[![image](https://img.shields.io/pypi/l/qcop.svg)](https://pypi.python.org/pypi/qcop)
+[![image](https://img.shields.io/pypi/pyversions/qcop.svg)](https://pypi.python.org/pypi/qcop)
+[![Actions status](https://github.com/coltonbh/qcop/workflows/Tests/badge.svg)](https://github.com/coltonbh/qcop/actions)
+[![Actions status](https://github.com/coltonbh/qcop/workflows/Basic%20Code%20Quality/badge.svg)](https://github.com/coltonbh/qcop/actions)
+[![Ruff](https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/charliermarsh/ruff/main/assets/badge/v1.json)](https://github.com/charliermarsh/ruff)

docs/dev-decisions.md

@@ -0,0 +1,22 @@
+# Dev Decisions and Research
+
+## Switching to pydantic v2
+
+- geomeTRIC does not rely up on any QCElemental objects--only a dictionary with the corresponding structure. So I don't loose `geometric_run_json` support if I drop `qcel`.
+- `psi4` does use `pydantic` and specifically the `qcel` `ProtoObject` and `pydantic` `validator` in its `driver` code `psi4/driver/task_base.py` and other `psi4/driver/*` files. It's not clear if this code gets executed if you run `psi4` in executable mode rather than python API mode.
+
+## Parsing Output files
+
+- `QChem` requires text parsing, no structured output according to Dip. This leads me to think `tcparse` needs to become `qcparse` and work for more packages.
+
+## Open Questions
+
+- Consider changing signature of `BaseAdaptor.compute` to `def compute(inp_obj: InputBase, **kwargs)` to make things less redundant across adaptors. Loose some clarity, save a bunch of redundancy in specifying a signature over and over again. This caused issues
+
+## Publishing Checklist
+
+- Update `CHANGELOG.md`
+- Bump version in `pyproject.toml`
+- Tag commit with a version and GitHub Actions will publish it to pypi if tag is on `master` branch.
+- `git push`
+- `git push --tags`