Update install package

.github/workflows/tests.yml

@@ -0,0 +1,30 @@
+name: Tests
+
+on:
+  push:
+  pull_request:
+
+jobs:
+  test:
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ["3.11", "3.12", "3.13", "3.14"]
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v4
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install pytest jsonschema
+          pip install -e .
+
+      - name: Test with pytest
+        run: make test

.gitignore

@@ -3,6 +3,9 @@ __pycache__/
 *.py[cod]
 *$py.class
 
+.agents/
+.claude/
+
 # C extensions
 *.so
 
@@ -24,6 +27,8 @@ wheels/
 *.egg-info/
 .installed.cfg
 *.egg
+*.whl
+*.tar.gz
 
 # PyInstaller
 #  Usually these files are written by a python script from a template
@@ -103,3 +108,8 @@ ENV/
 
 # Dev schema
 docs/source/auto*rst
+
+
+# Agent workflow (local only, not tracked)
+.agents/
+

.pre-commit-config.yaml

@@ -0,0 +1,8 @@
+repos:
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.6.9
+    hooks:
+      - id: ruff
+        args: [--fix]
+      - id: ruff-format
+        args: [--line-length=120]

README.md

@@ -1,6 +1,5 @@
 # QCSchema
 
-[![Build Status](https://img.shields.io/travis/MolSSI/QCSchema/master.svg?logo=linux&logoColor=white)](https://travis-ci.org/MolSSI/QCSchema)
 [![Language grade: Python](https://img.shields.io/lgtm/grade/python/g/MolSSI/QCSchema.svg?logo=lgtm&logoWidth=18)](https://lgtm.com/projects/g/MolSSI/QCSchema/context:python)
 [![Documentation Status](https://readthedocs.org/projects/molssi-qc-schema/badge/?version=latest)](https://molssi-qc-schema.readthedocs.io/en/latest/?badge=latest)
 
@@ -11,5 +10,17 @@ chemistry packages to enable more complex workflows.  The core of this is to
 avoid parsing ASCII-based output files and place output variables, vectors,
 matrices in a consistent format that can be easily parsed.
 
-Please see the [website](http://molssi-qc-schema.readthedocs.io/en/latest/index.html#) for the current specification. 
+Please see the [website](http://molssi-qc-schema.readthedocs.io/en/latest/index.html#) for the current specification.
+
+## Development
+
+Install the package with development dependencies and set up pre-commit hooks:
+
+```bash
+pip install -e .
+pip install pre-commit
+pre-commit install
+```
+
+Pre-commit will automatically lint and format code on each commit using [ruff](https://github.com/astral-sh/ruff).
 

docs/source/conf.py

@@ -1,4 +1,3 @@
-# -*- coding: utf-8 -*-
 #
 # Configuration file for the Sphinx documentation builder.
 #
@@ -20,10 +19,10 @@
 # -- Project information -----------------------------------------------------
 
 # Super hacky auto gen
-import sys
 import os
+import sys
+
 sys.path.insert(1, os.path.dirname(__file__))
-import gen_schema_docs
 
 project = 'A schema for Quantum Chemistry'
 copyright = f'2018-{datetime.datetime.today().year}, The Molecular Sciences Software Institute'

docs/source/gen_schema_docs.py

@@ -1,12 +1,12 @@
 """
 Very hacky way to write out the schema (for demo purposes only)
 """
-import qcschema
-import textwrap
+import os
 
 # Import headers from this
 import sys
-import os
+
+import qcschema
 
 sys.path.insert(1, os.path.dirname(__file__))
 import schema_doc_helpers as sh

docs/source/schema_doc_helpers/writers.py

@@ -3,6 +3,7 @@
 """
 import textwrap
 
+
 def write_header(data, header):
     data.append("")
     data.append(header)
@@ -25,11 +26,11 @@ def write_key_table(top_file, properties, keys=None):
     fmt_string = '   | {:%s} | {:%s} | {:%s} |' % tuple(table_widths)
     dash_inds = tuple("-" * w for w in table_widths)
     equals_inds = tuple("=" * w for w in table_widths)
-   
+
     top_file.append("   +-{}-+-{}-+-{}-+".format(*dash_inds))
     top_file.append(fmt_string.format("Key Name", "Description", "Field Type"))
     top_file.append("   +={}=+={}=+={}=+".format(*equals_inds))
-  
+
     if keys is None:
         keys = properties.keys()
 

pyproject.toml

@@ -1,3 +1,66 @@
-[tool.black]
+[build-system]
+requires = ["setuptools>=45", "wheel"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "qcschema"
+version = "1"
+description = "A schema for quantum chemistry"
+readme = "README.md"
+requires-python = ">3.11"
+dependencies = [
+    "jsonschema",
+    "pathlib2; python_version < '3.5'",
+]
+
+[project.optional-dependencies]
+docs = [
+    "sphinx==1.2.3",
+    "sphinxcontrib-napoleon",
+    "sphinx_rtd_theme",
+    "numpydoc",
+]
+tests = [
+    "pytest",
+]
+
+[project.urls]
+Homepage = "https://github.com/MolSSI/QCSchema"
+
+[tool.setuptools]
+packages = [
+    "qcschema",
+    "qcschema.data",
+    "qcschema.data.v1",
+    "qcschema.data.v2",
+    "qcschema.dev",
+    "qcschema.dev.properties",
+    "qcschema.dev.wavefunction",
+]
+zip-safe = true
+
+[tool.setuptools.package-data]
+"qcschema.data.v1" = ["*.schema"]
+"qcschema.data.v2" = ["*.schema"]
+
+[tool.ruff]
+line-length = 120
+target-version = "py311"
+lint.select = [
+    "E",      # pycodestyle errors
+    "W",      # pycodestyle warnings
+    "F",      # Pyflakes
+    "I",      # isort
+    "B",      # flake8-bugbear
+    "C4",     # flake8-comprehensions
+    "UP",     # pyupgrade
+]
+lint.ignore = [
+    "E501",   # Line too long (handled by formatter)
+]
+
+[tool.ruff.lint.isort]
+known-first-party = ["qcschema"]
+
+[tool.ruff.format]
 line-length = 120
-target-version = ['py27', 'py36', 'py37', 'py38']

qcschema/dev/dev_schema.py

@@ -4,11 +4,7 @@
 
 import copy
 
-from . import molecule
-from . import definitions
-from . import properties
-from . import basis
-from . import wavefunction
+from . import basis, definitions, molecule, properties, wavefunction
 
 # The base schema definition
 base_schema = {

qcschema/dev/properties/cc_properties.py

@@ -134,4 +134,4 @@
     "type": "number",
     "multipleOf": 1.0,
     "description": "The number of CCSDTQ iterations taken before convergence."
-}
+}

qcschema/dev/properties/properties_base.py

@@ -2,10 +2,10 @@
 The base file for QC Schema properties.
 """
 
-from .scf_properties import scf_properties
-from .mp_properties import mp_properties
-from .cc_properties import cc_properties
 from .calcinfo_properties import calcinfo_properties
+from .cc_properties import cc_properties
+from .mp_properties import mp_properties
+from .scf_properties import scf_properties
 
 properties = {
     "type": "object",

qcschema/dev/wavefunction/__init__.py

@@ -1 +1 @@
-from .wavefunction_base import output_wavefunction
+from .wavefunction_base import output_wavefunction

qcschema/dev/wavefunction/wavefunction_base.py

@@ -2,11 +2,11 @@
 The base file for QC Schema properties.
 """
 
+from ..basis import basis
+from .core_wavefunction import core_wavefunction
+from .localized_wavefunction import localized_wavefunction
 from .result_wavefunction import result_wavefunction
 from .scf_wavefunction import scf_wavefunction
-from .localized_wavefunction import localized_wavefunction
-from .core_wavefunction import core_wavefunction
-from ..basis import basis
 
 output_wavefunction = {
     "type": "object",

qcschema/versions.py

@@ -42,7 +42,7 @@ def list_versions(schema_type):
         if schema_type.lower() in aliases:
             return _versions_list[sk]
 
-    raise KeyError("Schema type should be among {} (+aliases), not '{}'.".format(list(_aliases.keys()), schema_type))
+    raise KeyError(f"Schema type should be among {list(_aliases.keys())} (+aliases), not '{schema_type}'.")
 
 
 def get_schema(schema_type, version="dev"):
@@ -62,10 +62,10 @@ def get_schema(schema_type, version="dev"):
                     fname = "qc_schema_" + sk
                 break
             else:
-                raise KeyError("Schema version should be among {}, not '{}'.".format(_versions_list[sk], version))
+                raise KeyError(f"Schema version should be among {_versions_list[sk]}, not '{version}'.")
     else:
         raise KeyError(
-            "Schema type should be among {} (+aliases), not '{}'.".format(list(_aliases.keys()), schema_type)
+            f"Schema type should be among {list(_aliases.keys())} (+aliases), not '{schema_type}'."
         )
 
     fpath = _data_path / ("v" + str(version)) / (fname + ".schema")

tests/test_failures.py

@@ -1,11 +1,11 @@
 """
 Tests the JSON schema
 """
+
 import jsonschema
 import pytest
-import os
-
 import test_helpers
+
 import qcschema
 
 ### Test input validation errors
@@ -17,7 +17,7 @@
 def test_input_failures(version, testfile):
 
     example = test_helpers.get_test(testfile)
-    
+
     with pytest.raises(jsonschema.exceptions.ValidationError):
         qcschema.validate(example, "input")
 
@@ -30,7 +30,7 @@ def test_input_failures(version, testfile):
 def test_output_failures(version, testfile):
 
     example = test_helpers.get_test(testfile)
-    
+
     with pytest.raises(jsonschema.exceptions.ValidationError):
         qcschema.validate(example, "output")