Feature qcio

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

@@ -0,0 +1,58 @@
+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: "3.9"
+      - 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: "3.9"
+      - name: Install poetry
+        run: pip install poetry
+      - name: Install repo
+        run: poetry install --no-interaction --no-ansi
+      - name: mypy
+        run: mypy .
+
+  detect-secrets:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+      - name: Set up Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: "3.9"
+      - name: Install detect secrets
+        run: pip install detect-secrets
+      - name: Look for secrets
+        # Ignore jwt.txt; the token is supposed to be there.
+        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

@@ -24,13 +24,14 @@ jobs:
       - name: Set up Python
         uses: actions/setup-python@v2
         with:
-          python-version: 3.8
+          python-version: 3.9
 
-      - name: Install Flit
-        run: pip install flit
+      - name: Install poetry
+        run: |
+          curl -sSL https://install.python-poetry.org | python3 -
 
       - name: Build distribution 📦
-        run: flit build
+        run: poetry build
 
       - name: Publish package 📤 to PyPI
         uses: pypa/gh-action-pypi-publish@release/v1

.pre-commit-config.yaml

@@ -2,40 +2,40 @@
 # See https://pre-commit.com/hooks.html for more hooks
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v3.2.0
+    rev: v4.6.0
     hooks:
       - id: check-yaml
+        exclude: mkdocs.yml
       - id: check-added-large-files
         args: ["--maxkb=250"]
   - repo: https://github.com/Yelp/detect-secrets
-    rev: v0.14.3
+    rev: v1.5.0
     hooks:
       - id: detect-secrets
-        exclude: Pipfile.lock
-  - repo: https://github.com/PyCQA/isort
-    rev: 5.7.0
+        stages: [commit]
+        exclude: 'poetry\.lock|tests/jwt\.txt'
+  - repo: https://github.com/charliermarsh/ruff-pre-commit
+    rev: "v0.5.7"
     hooks:
-      - id: isort
-  - repo: https://github.com/psf/black
-    rev: 20.8b1
-    hooks:
-      - id: black
-  - repo: https://github.com/PyCQA/flake8
-    rev: 3.8.4
-    hooks:
-      - id: flake8
+      - id: ruff
+        args: [--fix, --exit-non-zero-on-fix]
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v0.812
+    rev: v1.11.2
     hooks:
       - id: mypy
-        additional_dependencies: [tokenize-rt==3.2.0, pydantic>=1.0.0]
-
+        additional_dependencies:
+          [tokenize-rt==3.2.0, pydantic>=2.0.0, types-protobuf]
+        pass_filenames: false
+  - repo: https://github.com/crate-ci/typos
+    rev: v1.23.6
+    hooks:
+      - id: typos
   - repo: local
     hooks:
       - id: tests
         name: tests
         stages: [push]
-        language: python
-        entry: pytest
+        language: system
+        entry: poetry run pytest
         types: [python]
         pass_filenames: false

.vscode/settings.json

@@ -1,14 +1,20 @@
 {
     "python.formatting.provider": "black",
     "cSpell.words": [
+        "calcinfo",
+        "calctypes",
         "casci",
         "httpx",
         "molden",
+        "nalpha",
+        "natoms",
+        "nbeta",
         "orba",
         "orbb",
         "Protobuf",
         "qcel",
         "qcelemental",
+        "qcio",
         "TCPB",
         "Tera",
         "terachem",

docs/CHANGELOG.md

@@ -6,6 +6,24 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 
 ## [unreleased]
 
+### Added
+
+- GitHub workflows for basic code quality.
+- `release.py` script.
+
+### Changed
+
+- Changed build system from `flit` to `poetry` to standardize with other `MtzGroup` lab projects.
+- 🚨 Updated minimum Python version from `3.7` -> `3.9`.
+- Updated package dependencies.
+- Updated devops system. Removed `black`, `isort`, `flake8` in favor of latest version of `ruff`.
+- Updated documentation dependencies.
+
+### Removed
+
+- Checks for `bond_order` in the tests as this value is no longer returned by default by the TeraChem server.
+- `TCFEKeywords` checks. Just passing arguments to the `TCFEClient.compute()` function now.
+
 ## [0.13.2]
 
 ### Fixed

docs/clients.md

@@ -1,5 +1,5 @@
 # clients.py
 
-::: tcpb.clients:TCFrontEndClient
+::: tcpb.clients.TCFrontEndClient
 
-::: tcpb.clients:TCProtobufClient
+::: tcpb.clients.TCProtobufClient

docs/keywords.md

@@ -11,6 +11,6 @@ All keywords for controlling the [TCFrontEndClient][tcpb.clients.TCFrontEndClien
 | `scratch_messy`       | `bool`      | If set to `True` the scratch directory will not be cleaned up (deleted) after a compute job                                                                                                                                                                                                                                      | `False`       |
 | `uploads_messy`       | `bool`      | If set to `True` the uploaded files will not be cleaned up (deleted) after a compute job                                                                                                                                                                                                                                         | `False`       |
 | `native_files`        | `list[str]` | If used in conjunction with `AtomicInput.protocols = {"native_files": "all"}` only the filenames listed in the array will be returned. This is useful when only a single file is needed and the overhead of downloading potentially many files is large.                                                                         | `None`        |
-| `c0` or `ca0 and cb0` | `binary`    | TeraChem's c0 file(s) to be put on the server as an initial guess wavefunction. If included, they will be automatically uploaded and the `AtomicInput` will be modified to pass the `guess` keyword to TeraChem referencing the wave function files. See [FrontEnd Guess Reuse](../Examples/frontend_guess_reuse) for an example | `None`        |
+| `c0` or `ca0 and cb0` | `binary`    | TeraChem's c0 file(s) to be put on the server as an initial guess wavefunction. If included, they will be automatically uploaded and the `AtomicInput` will be modified to pass the `guess` keyword to TeraChem referencing the wave function files. See [FrontEnd Guess Reuse](Examples/frontend_guess_reuse.md) for an example | `None`        |
 
-::: tcpb.config:TCFEKeywords
+::: tcpb.config.TCFEKeywords

examples/basic_energy.py

@@ -2,7 +2,7 @@
 # Basic energy calculation
 import sys
 
-from qcelemental.models import AtomicInput, Molecule
+from qcio import ProgramInput, Structure
 
 from tcpb import TCProtobufClient as TCPBClient
 
@@ -11,23 +11,18 @@
     exit(1)
 
 
-# Water system
-atoms = ["O", "H", "H"]
-geom = [0.0, 0.0, 0.0, 0.0, 1.5, 0.0, 0.0, 0.0, 1.5]  # in bohr
-
-molecule = Molecule(symbols=atoms, geometry=geom)
-atomic_input = AtomicInput(
-    molecule=molecule,
-    model={
-        "method": "b3lyp",
-        "basis": "6-31g",
-    },
-    driver="energy",
-    protocols={"wavefunction": "all"},
+structure = Structure(
+    symbols=["O", "H", "H"],
+    geometry=[[0.0, 0.0, 0.0], [0.0, 1.5, 0.0], [0.0, 0.0, 1.5]],
+)
+prog_inp = ProgramInput(
+    calctype="energy",  # type: ignore
+    structure=structure,
+    model={"method": "b3lyp", "basis": "6-31g"},  # type: ignore
 )
 
 with TCPBClient(host=sys.argv[1], port=int(sys.argv[2])) as client:
-    result = client.compute(atomic_input)
+    prog_output = client.compute(prog_inp)
 
-print(result)
-print(result.return_result)
+print(prog_output)
+print(prog_output.results.energy)

examples/frontend_example.py

@@ -2,43 +2,32 @@
 # Basic energy calculation
 import sys
 
-from qcelemental.models import AtomicInput, Molecule
+from qcio import ProgramInput, Structure
 
 from tcpb import TCFrontEndClient
-from tcpb.config import TCFEKeywords, settings
 
 if len(sys.argv) != 3:
     print(f"Usage: {sys.argv[0]} host port")
     exit(1)
 
 
-# Water system
-atoms = ["O", "H", "H"]
-geom = [0.0, 0.0, 0.0, 0.0, 1.5, 0.0, 0.0, 0.0, 1.5]  # in bohr
-
-molecule = Molecule(symbols=atoms, geometry=geom)
-atomic_input = AtomicInput(
-    molecule=molecule,
-    model={
-        "method": "b3lyp",
-        "basis": "6-31g",
-    },
-    driver="energy",
+structure = Structure(
+    symbols=["O", "H", "H"], geometry=[0.0, 0.0, 0.0, 0.0, 1.5, 0.0, 0.0, 0.0, 1.5]
+)
+atomic_input = ProgramInput(
+    structure=structure,
+    model={"method": "b3lyp", "basis": "6-31g"},  # type: ignore
+    calctype="energy",  # type: ignore
     keywords={"restricted": False},
-    # TCFrontEndClient can collect stdout
-    # TCFrontEnd can also collect native_files produced by TeraCHem from the computation
-    protocols={"wavefunction": "all", "stdout": True, "native_files": "all"},
-    # TCFrontEndClient will delete scratch unless scratch_messy: True
-    extras={settings.tcfe_keywords: {TCFEKeywords.scratch_messy: False}},
 )
 
 with TCFrontEndClient(host=sys.argv[1], port=int(sys.argv[2])) as client:
-    result = client.compute(atomic_input)
+    # Collect stdout and native files
+    prog_output = client.compute(atomic_input, collect_stdout=True, collect_files=True)
 
 # NOTE: Addition of stdout field possible with TCFrontendClient
-print(result.stdout)
-print(result)
-print(result.return_result)
-print(result.extras["job_extras"])
+print(prog_output.stdout)
+print(prog_output)
+print(prog_output.return_result)
 # native_files will contain orb1a/b files in binary form
-print(result.native_files.keys())
+print(prog_output.files.keys())

examples/guess_reuse_tcfe.py

@@ -1,48 +1,35 @@
 #!/usr/bin/env python
 # Basic energy calculation
 import sys
-from pprint import pprint
 
-from qcelemental.models import AtomicInput, Molecule
+from qcio import CalcType, ProgramInput, Structure
 
 from tcpb import TCFrontEndClient
-from tcpb.config import settings
 
 if len(sys.argv) != 3:
     print(f"Usage: {sys.argv[0]} host port")
     exit(1)
 
 
-# Water system
-atoms = ["O", "H", "H"]
-geom = [0.0, 0.0, 0.0, 0.0, 1.5, 0.0, 0.0, 0.0, 1.5]  # in bohr
-
-molecule = Molecule(symbols=atoms, geometry=geom)
-atomic_input = AtomicInput(
-    molecule=molecule,
-    model={
-        "method": "b3lyp",
-        "basis": "6-31g",
-    },
+struct = Structure(
+    symbols=["O", "H", "H"], geometry=[0.0, 0.0, 0.0, 0.0, 1.5, 0.0, 0.0, 0.0, 1.5]
+)
+prog_inp = ProgramInput(
+    calctype=CalcType.energy,
+    structure=struct,
+    model={"method": "b3lyp", "basis": "6-31g"},  # type: ignore
     # Density matrix purification appears buggy and messes with initial guess
     keywords={"purify": "no"},
-    driver="energy",
-    protocols={"wavefunction": "all", "stdout": True, "native_files": "all"},
 )
 
 with TCFrontEndClient(host=sys.argv[1], port=int(sys.argv[2])) as client:
-    result = client.compute(atomic_input)
+    prog_output = client.compute(prog_inp, collect_files=True)
 
-atomic_input_2 = atomic_input.dict()
-atomic_input_2["extras"] = {settings.tcfe_keywords: {}}
-atomic_input_2["extras"][settings.tcfe_keywords]["c0"] = result.native_files["c0"]
-atomic_input_2["extras"][settings.tcfe_keywords]["uploads_messy"] = False
+prog_inp_2 = prog_inp.model_dump()
+prog_inp_2["files"]["c0"] = prog_output.results.files["scr/c0"]
 
 with TCFrontEndClient(host=sys.argv[1], port=int(sys.argv[2])) as client:
-    result2 = client.compute(AtomicInput(**atomic_input_2))
-
-print(result)
-print(result.return_result)
+    prog_output_2 = client.compute(ProgramInput(**prog_inp_2))
 
-pprint(result.stdout)
-pprint(result2.stdout)
+print(prog_output.stdout)
+print(prog_output_2.stdout)