qccodec 0.7.6__tar.gz

qccodec-0.7.6/.github/ISSUE_TEMPLATE/bug_report.md

@@ -0,0 +1,27 @@
+---
+name: Bug report
+about: Create a report to help us improve
+title: "[BUG] - "
+labels: bug
+assignees: ''
+
+---
+
+**Describe the bug**
+A clear and concise description of what the bug is.
+
+**To Reproduce**
+Steps to reproduce the behavior. Please provide all necessary data and a runable python script that reproduces your error:
+1. Go to '...'
+2. Click on '....'
+3. Scroll down to '....'
+4. See error
+
+**Expected behavior**
+A clear and concise description of what you expected to happen.
+
+**Screenshots**
+If applicable, add screenshots to help explain your problem.
+
+**Additional context**
+Add any other context about the problem here.

qccodec-0.7.6/.github/ISSUE_TEMPLATE/feature_request.md

@@ -0,0 +1,20 @@
+---
+name: Feature request
+about: Suggest an idea for this project
+title: "[FEATURE] - "
+labels: enhancement
+assignees: ''
+
+---
+
+**Is your feature request related to a problem? Please describe.**
+A clear and concise description of what the problem is. Ex. I'm always frustrated when [...]
+
+**Describe the solution you'd like**
+A clear and concise description of what you want to happen.
+
+**Describe alternatives you've considered**
+A clear and concise description of any alternative solutions or features you've considered.
+
+**Additional context**
+Add any other context or screenshots about the feature request here.

qccodec-0.7.6/.github/workflows/basic-code-quality.yaml

@@ -0,0 +1,59 @@
+name: Basic Code Quality
+
+on:
+  push:
+    branches: [master]
+  pull_request:
+    branches: [master]
+
+
+jobs:
+  ruff:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version-file: ".python-version"
+      - 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@v5
+        with:
+          python-version-file: ".python-version"
+      - name: Install uv
+        uses: astral-sh/setup-uv@v5
+      - name: Install the project
+        run: uv sync --all-extras --dev
+      - name: mypy
+        run: uv run mypy .
+
+  detect-secrets:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version-file: ".python-version"
+      - 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: .

qccodec-0.7.6/.github/workflows/create-release.yaml

@@ -0,0 +1,39 @@
+name: Create Release
+
+on:
+  push:
+    tags:
+      - "*" # Match any tag
+  workflow_dispatch: # Enable manual triggering
+
+jobs:
+  create-release:
+    name: Create GitHub Release
+    runs-on: ubuntu-latest
+    environment: release # Link to the protected environment
+
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v4
+
+      - name: Extract Release Notes
+        id: extract_notes
+        run: |
+          VERSION=${{ github.ref_name }}
+          sed -n "/## \\[$VERSION\\]/,/## \\[/p" CHANGELOG.md | sed '$d' | sed "s/## \\[$VERSION\\]/## $VERSION/" > RELEASE_NOTES.md
+
+      - name: Create GitHub Release
+        id: create_release
+        uses: actions/create-release@v1
+        with:
+          tag_name: ${{ github.ref_name }}
+          release_name: Release ${{ github.ref_name }}
+          body_path: ./RELEASE_NOTES.md
+          draft: false
+          prerelease: false
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+
+      - name: Output release URL
+        run: |
+          echo "Release URL: ${{ steps.create_release.outputs.html_url }}"

qccodec-0.7.6/.github/workflows/publish-to-pypi.yaml

@@ -0,0 +1,36 @@
+# 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/qccodec/
+    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@v5
+        with:
+          python-version-file: ".python-version"
+
+      - name: Install uv
+        uses: astral-sh/setup-uv@v5
+
+      - name: Build distribution 📦
+        run: uv build
+
+      - name: Publish package 📤 to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1

qccodec-0.7.6/.github/workflows/test.yaml

@@ -0,0 +1,33 @@
+name: Tests
+
+on:
+  push:
+    branches: [master]
+  pull_request:
+    branches: [master]
+
+jobs:
+  tests:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version-file: ".python-version"
+
+      - name: Install uv
+        uses: astral-sh/setup-uv@v5
+
+      - name: Install repo
+        run: uv sync --all-extras --dev
+
+      - name: Run tests
+        run: bash scripts/tests.sh
+
+      - name: Upload coverage HTML
+        uses: actions/upload-artifact@v4
+        with:
+          name: htmlcov
+          path: htmlcov

qccodec-0.7.6/.gitignore

@@ -0,0 +1,161 @@
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+cover/
+!test/data/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+.pybuilder/
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+#   For a library or package, you might want to ignore these files since the code is
+#   intended to run in multiple environments; otherwise, check them in:
+# .python-version
+
+# pipenv
+#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+#   However, in case of collaboration, if having platform-specific dependencies or dependencies
+#   having no cross-platform support, pipenv may install dependencies that don't work, or not
+#   install all needed dependencies.
+#Pipfile.lock
+
+# poetry
+#   Similar to Pipfile.lock, it is generally recommended to include poetry.lock in version control.
+#   This is especially recommended for binary packages to ensure reproducibility, and is more
+#   commonly ignored for libraries.
+#   https://python-poetry.org/docs/basic-usage/#commit-your-poetrylock-file-to-version-control
+#poetry.lock
+
+# pdm
+#   Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control.
+#pdm.lock
+#   pdm stores project-wide configurations in .pdm.toml, but it is recommended to not include it
+#   in version control.
+#   https://pdm.fming.dev/#use-with-ide
+.pdm.toml
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow and github.com/pdm-project/pdm
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/
+
+# pytype static type analyzer
+.pytype/
+
+# Cython debug symbols
+cython_debug/
+
+# PyCharm
+#  JetBrains specific template is maintained in a separate JetBrains.gitignore that can
+#  be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore
+#  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/

qccodec-0.7.6/.pre-commit-config.yaml

@@ -0,0 +1,41 @@
+# 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: [pre-commit]
+        exclude: uv.lock
+  - repo: https://github.com/charliermarsh/ruff-pre-commit
+    # Ruff version.
+    rev: "v0.8.3"
+    hooks:
+      - id: ruff
+        args: [--fix, --exit-non-zero-on-fix]
+  - repo: https://github.com/pre-commit/mirrors-mypy
+    rev: v1.1.1
+    hooks:
+      - id: mypy
+        additional_dependencies:
+          [tokenize-rt==3.2.0, types-paramiko, types-toml, qcio>=0.14.0]
+  - repo: https://github.com/crate-ci/typos
+    rev: v1.24.5
+    hooks:
+      - id: typos
+  - repo: local
+    hooks:
+      - id: tests
+        name: tests
+        stages: [pre-push]
+        language: system
+        entry: uv run pytest
+        types: [python]
+        pass_filenames: false

qccodec-0.7.6/.python-version

@@ -0,0 +1 @@
+3.9

qccodec-0.7.6/.vscode/settings.json

@@ -0,0 +1,48 @@
+{
+    "python.formatting.provider": "black",
+    "cSpell.words": [
+        "allclose",
+        "calcinfo",
+        "calctype",
+        "calctypes",
+        "crestopt",
+        "CUDA",
+        "dataclasses",
+        "disp",
+        "ENGRAD",
+        "freqs",
+        "Hartree",
+        "htmlcov",
+        "maxiter",
+        "natom",
+        "natoms",
+        "ndarray",
+        "nmodes",
+        "nocuda",
+        "numhess",
+        "optim",
+        "OPTLOG",
+        "pathconf",
+        "psutil",
+        "qcel",
+        "qcio",
+        "qccodec",
+        "rotamer",
+        "rotamers",
+        "runtypes",
+        "singlepoint",
+        "spinmult",
+        "tcin",
+        "tcout",
+        "tcparse",
+        "tcstdout",
+        "tddft",
+        "tensorbox",
+        "Tera",
+        "terachem",
+        "topo",
+        "traj",
+        "wavenumber",
+        "wavenumbers"
+    ]
+}

qccodec-0.7.6/CHANGELOG.md

@@ -0,0 +1,221 @@
+# 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]
+
+## [0.7.6] - 2025-04-01
+
+### Added
+
+- Logging to `decode` clearly detail what parsing actions are being taken and why on various filetypes.
+
+### Changed
+
+- Renamed package from `qcparse` -> `qccodec`.
+- Removed `poetry` in favor of `hatchling` build system and `uv` for project management.
+- 🚨 Refactored top-level `parse` function to a new signature `decode(program: str, calctype: CalcType, *, stdout: Optional[str] = None, directory: Optional[Union[str, Path]] = None, input_data: Optional[StructuredInputs] = None) -> StructureResults`.
+- Changed parsers to no longer set data on a data collector object but to rather be pure functions returning their parsed data.
+- Renamed `@parser` decorator to `@register` and accept `target` kwarg that tells the registry where to place the parsed data on the data collector object.
+- `DataCollector` now inherits from `dict` rather than being a `SimpleNamespace`.
+- Switched classes from pydantic `BaseModel` to `dataclasses` since I'm not using any advanced validation logic.
+
+### Removed
+
+- 🚨 `get_file_contents` function since we no longer pass filenames to top-level `decode` (formerly `parse`) function.
+- 🚨 `parse_results` function previously kept for backwards compatibility.
+- `pydantic` dependency.
+
+## [0.7.5] - 2025-03-24
+
+### Added
+
+- TeraChem `parse_excited_states` function.
+
+## [0.7.4] - 2025-02-25
+
+### Changed
+
+- CREST encoder now selects `min(os.cpu_count(), 16)` for `threads` if not set by the user.
+
+## [0.7.3] - 2025-02-08
+
+### Fixed
+
+- Bug in parsing CREST's `g98.out` file for more than three frequencies.
+
+## [0.7.2] - 2025-02-05
+
+### Added
+
+- Parse CREST's `numhess` g98.out file for frequency and normal mode displacement vectors.
+
+## [0.7.1] - 2025-01-15
+
+### Changed
+
+- More flexibly defined `qcio` dependency version from `^0.11.8` to `>=0.12.1` to account for the missing `eval_type_backport` package.
+
+## [0.7.0] - 2024-12-20
+
+### Changed
+
+- 🚨 Dropped Python 3.8 support.
+
+### Removed
+
+- `black` and `isort` in favor of `ruff`.
+
+## [0.6.4] - 2024-10-01
+
+### Added
+
+- Encoders and parsers for CREST to support `energy`, `gradient`, `hessian`, and `optimization` calculations.
+
+## [0.6.3] - 2024-09-12
+
+### Added
+
+- `parse_optimization_dir(...) -> OptimizationResults` for TeraChem.
+
+## [0.6.2] - 2024-08-13
+
+### Added
+
+- `CREST` encoder and directory parser for conformer search output directories.
+
+## [0.6.1] - 2024-08-08
+
+### Added
+
+- Program version parser for `CREST` stdout.
+
+## [0.6.0] - 2024-06-10
+
+### Changed
+
+- Updated to `qcio 0.10.0` to use new `Structure` rather than `Molecule` nomenclature.
+
+## [0.5.3] - 2024-04-04
+
+### Changed
+
+- TeraChem `parse_git_commit` updated to `parse_version_control_details` to accommodate older versions of TeraChem compiled from the `Hg` days.
+
+### Removed
+
+- TeraChem `parse_version` parser. It was unused given the switch to only parsing `SinglePointResults` objects and not `Provenance` objects as well. The `parse_version_string` function is used by `qcop` to get the version of the program. We do not need to set the version of the program at `SinglePointResults.extras.program_version` anymore.
+
+## [0.5.2] - 2023-09-27
+
+### Removed
+
+- All input parsing details from the library.
+
+### Added
+
+- `encode` top level function and encoder for TeraChem input files.
+
+### Changed
+
+- Added `FileType.stdout` as default `filetype` argument to `parse` decorator to reduce boilerplate in parsers.
+
+## [0.5.1] - 2023-09-19
+
+### Changed
+
+- Dropped Python dependency from `^3.8.1` to `^3.8`. Can't remember what older dependency required `3.8.1` but it's not needed anymore.
+
+## [0.5.0] - 2023-08-31
+
+### Changed
+
+- Updated `pydantic` from `v1` -> `v2`.
+
+## [0.4.1] - 2023-07-19
+
+### Changed
+
+- Updated `qcio` from `0.3.0` -> `0.4.0`.
+
+## [0.4.0] - 2023-07-17
+
+### Changed
+
+- Updated to used `qcio>=0.3.0` flattened models and the `SinglePointResults`object.
+
+## [0.3.2] - 2023-06-29
+
+### Fixed
+
+- Updated package description in pyproject.toml from TeraChem specific parsing and MolSSI to all QC packages and qcio.
+
+## [0.3.1] - 2023-06-29
+
+### Added
+
+- Git commit parsing for TeraChem as part of version parsing
+
+### Changed
+
+- `qcio` `>=0.1.0` -> `>=0.2.0`
+
+## [0.3.0] - 2023-06-28
+
+### Changed
+
+- Dropped support for `QCSchema` models and changed to [qcio](https://github.com/coltonbh/qcio) data models.
+- `parse` function now raises `NotImplementedError` and the default use case is to use `parse_computed_prop` instead and ignore inputs and provenance data. This is the minimum spec since QC programs can be powered using structured inputs and [qcop](https://github.com/coltonbh/qcop). I may go back to parsing entire `SinglePointSuccess/FailedOutput` objects if use cases arise.
+
+## [0.2.1] - 2023-03-25
+
+### Changed
+
+- Generalized `CUDA error:` regex to catch all CUDA errors.
+
+## [0.2.0] - 2023-03-24
+
+### Added
+
+- `cli` interface for parsing TeraChem outputs from the command line.
+- `parse_natoms`, `parse_nmo`, `parse_total_charge`, `parse_spin_multiplicity`
+
+### Removed
+
+- Removed Hessian matrix dimension checking from `parse_hessian`. Dimension validation is already done via `pydantic` on the `AtomicResult` object.
+
+## [0.1.0] - 2023-03-23
+
+### Added
+
+- Basic parsers for energy, gradient, Hessian (frequencies) calculations.
+- Can return either `AtomicResult` or `FailedOperation` objects depending on whether calculation succeeded or failed.
+- Tests for all parsers and the main `parse` function.
+
+[unreleased]: https://github.com/coltonbh/qccodec/compare/0.7.6...HEAD
+[0.7.6]: https://github.com/coltonbh/qccodec/releases/tag/0.7.6
+[0.7.5]: https://github.com/coltonbh/qccodec/releases/tag/0.7.5
+[0.7.4]: https://github.com/coltonbh/qccodec/releases/tag/0.7.4
+[0.7.3]: https://github.com/coltonbh/qccodec/releases/tag/0.7.3
+[0.7.2]: https://github.com/coltonbh/qccodec/releases/tag/0.7.2
+[0.7.1]: https://github.com/coltonbh/qccodec/releases/tag/0.7.1
+[0.7.0]: https://github.com/coltonbh/qccodec/releases/tag/0.7.0
+[0.6.4]: https://github.com/coltonbh/qccodec/releases/tag/0.6.4
+[0.6.3]: https://github.com/coltonbh/qccodec/releases/tag/0.6.3
+[0.6.2]: https://github.com/coltonbh/qccodec/releases/tag/0.6.2
+[0.6.1]: https://github.com/coltonbh/qccodec/releases/tag/0.6.1
+[0.6.0]: https://github.com/coltonbh/qccodec/releases/tag/0.6.0
+[0.5.3]: https://github.com/coltonbh/qccodec/releases/tag/0.5.3
+[0.5.2]: https://github.com/coltonbh/qccodec/releases/tag/0.5.2
+[0.5.1]: https://github.com/coltonbh/qccodec/releases/tag/0.5.1
+[0.5.0]: https://github.com/coltonbh/qccodec/releases/tag/0.5.0
+[0.4.1]: https://github.com/coltonbh/qccodec/releases/tag/0.4.1
+[0.4.0]: https://github.com/coltonbh/qccodec/releases/tag/0.4.0
+[0.3.2]: https://github.com/coltonbh/qccodec/releases/tag/0.3.2
+[0.3.1]: https://github.com/coltonbh/qccodec/releases/tag/0.3.1
+[0.3.0]: https://github.com/coltonbh/qccodec/releases/tag/0.3.0
+[0.2.1]: https://github.com/coltonbh/qccodec/releases/tag/0.2.1
+[0.2.0]: https://github.com/coltonbh/qccodec/releases/tag/0.2.0
+[0.1.0]: https://github.com/coltonbh/qccodec/releases/tag/0.1.0