diff --git a/CHANGELOG.md b/CHANGELOG.md index e7f1eb6..1731330 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -16,13 +16,13 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/), ### Added -- `ProgramInput.structures` and `DualProgramInput.structures` for additional named structures required by calculations with multiple complete structure inputs, while keeping `.structure` as the required primary/start/reference structure. [#103](https://github.com/coltonbh/qcdata/pull/103) by [@coltonbh](https://github.com/coltonbh). +- `ProgramInput.structures` and `DualProgramInput.structures` for additional named structures required by calculations with multiple complete structure inputs, while keeping `.structure` as the required primary/start/reference structure. [#103](https://github.com/atomsforhumanity/qcdata/pull/103) by [@coltonbh](https://github.com/coltonbh). ## [0.17.1] - 2026-04-21 ### Added -- `CalcType.scan` and `ScanData` [#102](https://github.com/coltonbh/qcdata/pull/102). +- `CalcType.scan` and `ScanData` [#102](https://github.com/atomsforhumanity/qcdata/pull/102). ## [0.17.0] - 2026-03-26 @@ -49,8 +49,8 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/), ### Added -- `@field_validator` to `Structure.connectivity` to ensure no duplicate bonds. [#93](https://github.com/coltonbh/qcdata/pull/93) -- `Structure.adjacency_matrix` property that returns an adjacency matrix from the `.connectivity` information. [#93](https://github.com/coltonbh/qcdata/pull/93) +- `@field_validator` to `Structure.connectivity` to ensure no duplicate bonds. [#93](https://github.com/atomsforhumanity/qcdata/pull/93) +- `Structure.adjacency_matrix` property that returns an adjacency matrix from the `.connectivity` information. [#93](https://github.com/atomsforhumanity/qcdata/pull/93) ## [0.16.0] - 2025-10-09 @@ -62,9 +62,9 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/), ### Removed -- 🚨Python 3.9 support. Minimum supported version is now 3.10. [#91](https://github.com/coltonbh/qcdata/pull/91) -- All constants and periodic table data moved to [qcconst](https://github.com/coltonbh/qcconst). -- All cheminformatics methods, including those that used `rdkit` and `openbabel` such as `rmsd` and `align`. Placed these algorithms into [qcinf](https://github.com/coltonbh/qcinf) so that `qcio` can remain purely about data structures. All future algorithms will go into `qcinf`. +- 🚨Python 3.9 support. Minimum supported version is now 3.10. [#91](https://github.com/atomsforhumanity/qcdata/pull/91) +- All constants and periodic table data moved to [qcconst](https://github.com/atomsforhumanity/qcconst). +- All cheminformatics methods, including those that used `rdkit` and `openbabel` such as `rmsd` and `align`. Placed these algorithms into [qcinf](https://github.com/atomsforhumanity/qcinf) so that `qcio` can remain purely about data structures. All future algorithms will go into `qcinf`. - `Structure.from_smiles()` method in favor of functional API using the `qcinf` `smiles_to_structure` function. ```python @@ -95,20 +95,20 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/), ### Changed - Package dependency system changed from `poetry` to `uv` and build system from `poetry` to `hatchling`. -- Renamed `ProgramOutput` -> `Results` to better match basic parlance ("The program produced these results"). [#90](https://github.com/coltonbh/qcdata/pull/90) -- Renamed `Results.results` (formerly `ProgramOutput.results`) attribute to `.data`. "The program produced this data." [#90](https://github.com/coltonbh/qcdata/pull/90) -- Renamed `Results.stdout` -> `Results.logs`. We are coalescing `stdout` and `stderr` logs anyways. Prefer using a common name scientists will understand. [#90](https://github.com/coltonbh/qcdata/pull/90) -- Renamed `SinglePointResults` -> `SinglePointData`. [#90](https://github.com/coltonbh/qcdata/pull/90) -- Renamed `OptimizationResults` -> `OptimizationData`. [#90](https://github.com/coltonbh/qcdata/pull/90) -- Renamed `ConformerSearchResults` -> `ConformerSearchData`. [#90](https://github.com/coltonbh/qcdata/pull/90) -- Added compatibility classes so old imports looking for these names still work but emit a `FutureWarning`. [#90](https://github.com/coltonbh/qcdata/pull/90) -- Renamed `QCIOModelBase` -> `QCIOBaseModel` to match `pydantic` semantics for `BaseModel`. [#90](https://github.com/coltonbh/qcdata/pull/90) -- Renamed `ProgramInput` -> `CalcSpec` and added a compatibility shim. [#90](https://github.com/coltonbh/qcdata/pull/90) -- Renamed `ProgramArgs` -> `CoreSpec` and added a compatibility shim. [#90](https://github.com/coltonbh/qcdata/pull/90) -- Renamed `ProgramArgsSub` -> `SubCalcSpec` and added a compatibility shim. [#90](https://github.com/coltonbh/qcdata/pull/90) -- Renamed `DualProgramInput` -> `CompositeCalcSpec` and added a compatibility shim. [#90](https://github.com/coltonbh/qcdata/pull/90) -- Renamed `FileInput` -> `FileSpec` and added a compatibility shim. [#90](https://github.com/coltonbh/qcdata/pull/90) -- Backwards compatibility shim updated from `Results.__init__` override to `@model_validator(mode="before")`. [#90](https://github.com/coltonbh/qcdata/pull/90) +- Renamed `ProgramOutput` -> `Results` to better match basic parlance ("The program produced these results"). [#90](https://github.com/atomsforhumanity/qcdata/pull/90) +- Renamed `Results.results` (formerly `ProgramOutput.results`) attribute to `.data`. "The program produced this data." [#90](https://github.com/atomsforhumanity/qcdata/pull/90) +- Renamed `Results.stdout` -> `Results.logs`. We are coalescing `stdout` and `stderr` logs anyways. Prefer using a common name scientists will understand. [#90](https://github.com/atomsforhumanity/qcdata/pull/90) +- Renamed `SinglePointResults` -> `SinglePointData`. [#90](https://github.com/atomsforhumanity/qcdata/pull/90) +- Renamed `OptimizationResults` -> `OptimizationData`. [#90](https://github.com/atomsforhumanity/qcdata/pull/90) +- Renamed `ConformerSearchResults` -> `ConformerSearchData`. [#90](https://github.com/atomsforhumanity/qcdata/pull/90) +- Added compatibility classes so old imports looking for these names still work but emit a `FutureWarning`. [#90](https://github.com/atomsforhumanity/qcdata/pull/90) +- Renamed `QCIOModelBase` -> `QCIOBaseModel` to match `pydantic` semantics for `BaseModel`. [#90](https://github.com/atomsforhumanity/qcdata/pull/90) +- Renamed `ProgramInput` -> `CalcSpec` and added a compatibility shim. [#90](https://github.com/atomsforhumanity/qcdata/pull/90) +- Renamed `ProgramArgs` -> `CoreSpec` and added a compatibility shim. [#90](https://github.com/atomsforhumanity/qcdata/pull/90) +- Renamed `ProgramArgsSub` -> `SubCalcSpec` and added a compatibility shim. [#90](https://github.com/atomsforhumanity/qcdata/pull/90) +- Renamed `DualProgramInput` -> `CompositeCalcSpec` and added a compatibility shim. [#90](https://github.com/atomsforhumanity/qcdata/pull/90) +- Renamed `FileInput` -> `FileSpec` and added a compatibility shim. [#90](https://github.com/atomsforhumanity/qcdata/pull/90) +- Backwards compatibility shim updated from `Results.__init__` override to `@model_validator(mode="before")`. [#90](https://github.com/atomsforhumanity/qcdata/pull/90) ## [0.14.0] - 2025-04-01 @@ -670,69 +670,69 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/), - `SinglePointComputedProperties` - `Wavefunction` -[unreleased]: https://github.com/coltonbh/qcdata/compare/0.18.0...HEAD -[0.18.0]: https://github.com/coltonbh/qcdata/releases/tag/0.18.0 -[0.17.2]: https://github.com/coltonbh/qcdata/releases/tag/0.17.2 -[0.17.1]: https://github.com/coltonbh/qcdata/releases/tag/0.17.1 -[0.17.0]: https://github.com/coltonbh/qcdata/releases/tag/0.17.0 -[0.16.2]: https://github.com/coltonbh/qcdata/releases/tag/0.16.2 -[0.16.1]: https://github.com/coltonbh/qcdata/releases/tag/0.16.1 -[0.16.0]: https://github.com/coltonbh/qcdata/releases/tag/0.16.0 -[0.15.0]: https://github.com/coltonbh/qcdata/releases/tag/0.15.0 -[0.14.0]: https://github.com/coltonbh/qcdata/releases/tag/0.14.0 -[0.13.1]: https://github.com/coltonbh/qcdata/releases/tag/0.13.1 -[0.13.0]: 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+[0.3.5]: https://github.com/atomsforhumanity/qcdata/releases/tag/0.3.5 +[0.3.4]: https://github.com/atomsforhumanity/qcdata/releases/tag/0.3.4 +[0.3.3]: https://github.com/atomsforhumanity/qcdata/releases/tag/0.3.3 +[0.3.2]: https://github.com/atomsforhumanity/qcdata/releases/tag/0.3.2 +[0.3.1]: https://github.com/atomsforhumanity/qcdata/releases/tag/0.3.1 +[0.3.0]: https://github.com/atomsforhumanity/qcdata/releases/tag/0.3.0 +[0.2.1]: https://github.com/atomsforhumanity/qcdata/releases/tag/0.2.1 +[0.2.0]: https://github.com/atomsforhumanity/qcdata/releases/tag/0.2.0 +[0.1.0]: https://github.com/atomsforhumanity/qcdata/releases/tag/0.1.0 diff --git a/README.md b/README.md index 114d50b..2bafe35 100644 --- a/README.md +++ b/README.md @@ -3,8 +3,8 @@ [![image](https://img.shields.io/pypi/v/qcdata.svg)](https://pypi.python.org/pypi/qcdata) [![image](https://img.shields.io/pypi/l/qcdata.svg)](https://pypi.python.org/pypi/qcdata) [![image](https://img.shields.io/pypi/pyversions/qcdata.svg)](https://pypi.python.org/pypi/qcdata) -[![Actions status](https://github.com/coltonbh/qcdata/workflows/Tests/badge.svg)](https://github.com/coltonbh/qcdata/actions) -[![Actions status](https://github.com/coltonbh/qcdata/workflows/Basic%20Code%20Quality/badge.svg)](https://github.com/coltonbh/qcdata/actions) +[![Actions status](https://github.com/atomsforhumanity/qcdata/workflows/Tests/badge.svg)](https://github.com/atomsforhumanity/qcdata/actions) +[![Actions status](https://github.com/atomsforhumanity/qcdata/workflows/Basic%20Code%20Quality/badge.svg)](https://github.com/atomsforhumanity/qcdata/actions) Elegant and intuitive data structures for quantum chemistry, featuring seamless Jupyter Notebook visualizations. @@ -12,11 +12,13 @@ Elegant and intuitive data structures for quantum chemistry, featuring seamless ## The QC Suite of Programs -- [qcconst](https://github.com/coltonbh/qcconst) - NIST/CODATA2022 core physical constants, conversion factors, and a periodic table with clear source information for every value. -- [qcdata](https://github.com/coltonbh/qcdata) - Elegant and intuitive data structures for quantum chemistry, featuring seamless Jupyter Notebook visualizations. [Documentation](https://qcdata.coltonhicks.com) - [qcinf](https://github.com/coltonbh/qcinf) - Cheminformatics algorithms and structure utilities such as `rmsd`, and alignment, using standardized [qcdata](https://qcdata.coltonhicks.com/) data structures. -- [qccodec](https://github.com/coltonbh/qccodec) - A translation layer between quantum chemistry program inputs and outputs and structured `qcdata` objects. -- [qcop](https://github.com/coltonbh/qcop) - A package for operating quantum chemistry programs using `qcdata` standardized data structures. Compatible with `TeraChem`, `psi4`, `QChem`, `NWChem`, `ORCA`, `Molpro`, `geomeTRIC` and many more. +The QC Suite works in harmony to provide fast, structured, and interoperable quantum chemistry tools. + +- [qcconst](https://github.com/atomsforhumanity/qcconst) - Physical constants, conversion factors, and a periodic table with clear source information for every value. +- [qcdata](https://github.com/atomsforhumanity/qcdata) - Elegant and intuitive data structures for quantum chemistry, featuring seamless Jupyter Notebook visualizations. [Documentation](https://qcdata.docs.atomsforhumanity.org) +- [qcinf](https://github.com/atomsforhumanity/qcinf) - Cheminformatics algorithms and structure utilities using standardized [qcdata](https://qcdata.docs.atomsforhumanity.org/) data structures. +- [qccodec](https://github.com/atomsforhumanity/qccodec) - A package for translating between standardized [qcdata](https://github.com/atomsforhumanity/qcdata) data structures and native QC program inputs and outputs. +- [qccompute](https://github.com/atomsforhumanity/qccompute) - A package for operating quantum chemistry programs using standardized [qcdata](https://qcdata.docs.atomsforhumanity.org/) data structures. Compatible with `TeraChem`, `psi4`, `QChem`, `NWChem`, `ORCA`, `Molpro`, `geomeTRIC` and many more. - [BigChem](https://github.com/mtzgroup/bigchem) - A distributed application for running quantum chemistry calculations at scale across clusters of computers or the cloud. Bring multi-node scaling to your favorite quantum chemistry program. - `ChemCloud` - A [web application](https://github.com/mtzgroup/chemcloud-server) and associated [Python client](https://github.com/mtzgroup/chemcloud-client) for exposing a BigChem cluster securely over the internet. @@ -192,4 +194,4 @@ uv sync --all-groups ## Support -If you have any issues with `qcdata` or would like to request a feature, please open an [issue](https://github.com/coltonbh/qcdata/issues). +If you have any issues with `qcdata` or would like to request a feature, please open an [issue](https://github.com/atomsforhumanity/qcdata/issues). diff --git a/docs/CNAME b/docs/CNAME index 5a521dd..7fff79e 100644 --- a/docs/CNAME +++ b/docs/CNAME @@ -1 +1 @@ -qcdata.coltonhicks.com \ No newline at end of file +qcdata.docs.atomsforhumanity.org diff --git a/docs/api/inputs.md b/docs/api/inputs.md index d8ee5a4..54505ae 100644 --- a/docs/api/inputs.md +++ b/docs/api/inputs.md @@ -4,7 +4,7 @@ A `DualProgramInput` is used when two inputs are required for a calculation. For `ProgramInput.structure` is always the primary/start/reference structure for the calculation. Calculations that require additional complete structures can provide them by role name with `ProgramInput.structures`, for example `structures={"product": product_structure}` for a nudged elastic band calculation where `structure` is the reactant endpoint. Calculation-specific tools should validate which structure names are required. -A `FileInput` is an escape hatch that allows you to run _any_ calculation in any QC program (or any program for that matter), even if it isn't a supported [`CalcType`](./calctype.md) in `qcdata` yet. You can use a `FileInput` to store the native input files (text and binary) for a QC program along with the relevant command line args. Using [qcop](https://github.com/coltonbh/qcop) you can submit a `FileInput` to a QC program and all output files and `logs` produced by that program will be collected and returned in a user-friendly [`ProgramOutput`](./outputs.md) object. `FileInput` allows you to continue to use `qcdata` even for calculations that haven't yet been standardized. +A `FileInput` is an escape hatch that allows you to run _any_ calculation in any QC program (or any program for that matter), even if it isn't a supported [`CalcType`](./calctype.md) in `qcdata` yet. You can use a `FileInput` to store the native input files (text and binary) for a QC program along with the relevant command line args. Using [qcop](https://github.com/atomsforhumanity/qccompute) you can submit a `FileInput` to a QC program and all output files and `logs` produced by that program will be collected and returned in a user-friendly [`ProgramOutput`](./outputs.md) object. `FileInput` allows you to continue to use `qcdata` even for calculations that haven't yet been standardized. ::: qcdata.Inputs diff --git a/docs/index.md b/docs/index.md index b1b1850..62f9c5e 100644 --- a/docs/index.md +++ b/docs/index.md @@ -3,8 +3,8 @@ [![image](https://img.shields.io/pypi/v/qcdata.svg)](https://pypi.python.org/pypi/qcdata) [![image](https://img.shields.io/pypi/l/qcdata.svg)](https://pypi.python.org/pypi/qcdata) [![image](https://img.shields.io/pypi/pyversions/qcdata.svg)](https://pypi.python.org/pypi/qcdata) -[![Actions status](https://github.com/coltonbh/qcdata/workflows/Tests/badge.svg)](https://github.com/coltonbh/qcdata/actions) -[![Actions status](https://github.com/coltonbh/qcdata/workflows/Basic%20Code%20Quality/badge.svg)](https://github.com/coltonbh/qcdata/actions) +[![Actions status](https://github.com/atomsforhumanity/qcdata/workflows/Tests/badge.svg)](https://github.com/atomsforhumanity/qcdata/actions) +[![Actions status](https://github.com/atomsforhumanity/qcdata/workflows/Basic%20Code%20Quality/badge.svg)](https://github.com/atomsforhumanity/qcdata/actions) Elegant and intuitive data structures for quantum chemistry, featuring seamless Jupyter Notebook visualizations. @@ -12,10 +12,10 @@ Elegant and intuitive data structures for quantum chemistry, featuring seamless ## The QC Suite of Programs -- [qcconst](https://github.com/coltonbh/qcconst) - NIST/CODATA2022 core physical constants, conversion factors, and a periodic table with clear source information for every value. -- [qcdata](https://github.com/coltonbh/qcdata) - Elegant and intuitive data structures for quantum chemistry, featuring seamless Jupyter Notebook visualizations. [Documentation](https://qcdata.coltonhicks.com) -- [qccodec](https://github.com/coltonbh/qccodec) - A translation layer between quantum chemistry program inputs and outputs and structured `qcdata` objects. -- [qcop](https://github.com/coltonbh/qcop) - A package for operating quantum chemistry programs using `qcdata` standardized data structures. Compatible with `TeraChem`, `psi4`, `QChem`, `NWChem`, `ORCA`, `Molpro`, `geomeTRIC` and many more. +- [qcconst](https://github.com/atomsforhumanity/qcconst) - NIST/CODATA2022 core physical constants, conversion factors, and a periodic table with clear source information for every value. +- [qcdata](https://github.com/atomsforhumanity/qcdata) - Elegant and intuitive data structures for quantum chemistry, featuring seamless Jupyter Notebook visualizations. [Documentation](https://qcdata.docs.atomsforhumanity.org) +- [qccodec](https://github.com/atomsforhumanity/qccodec) - A translation layer between quantum chemistry program inputs and outputs and structured `qcdata` objects. +- [qcop](https://github.com/atomsforhumanity/qccompute) - A package for operating quantum chemistry programs using `qcdata` standardized data structures. Compatible with `TeraChem`, `psi4`, `QChem`, `NWChem`, `ORCA`, `Molpro`, `geomeTRIC` and many more. - [BigChem](https://github.com/mtzgroup/bigchem) - A distributed application for running quantum chemistry calculations at scale across clusters of computers or the cloud. Bring multi-node scaling to your favorite quantum chemistry program. - `ChemCloud` - A [web application](https://github.com/mtzgroup/chemcloud-server) and associated [Python client](https://github.com/mtzgroup/chemcloud-client) for exposing a BigChem cluster securely over the internet. diff --git a/docs/why.md b/docs/why.md index a46ef72..03f5ddd 100644 --- a/docs/why.md +++ b/docs/why.md @@ -2,9 +2,9 @@ Other data structure package for quantum chemistry exist such as [QCElemental](https://github.com/MolSSI/QCElemental) and [Atomic Simulation Environment](https://wiki.fysik.dtu.dk/ase/index.html). I often found these libraries were too heavy weight or too feature poor for most of what I needed. I also found their APIs to be somewhat unintuitive and often cumbersome to use. `qcdata` is designed to be easy to use, easy to reason about, and provide a unified format for diverse quantum chemistry calculations. -`qcdata` is also the central package used by [`qcop`](https://github.com/coltonbh/qcop) to power interoperable quantum chemistry calculations across dozens of packages and [`bigchem`](https://github.com/mtzgroup/bigchem), which scales QC calculations across hundreds of nodes on academic clusters or the cloud. I needed robust and reliable data structures for powering these applications. `qcdata` is the result of thousands of hours of organizing quantum chemistry data into coherent data structures. +`qcdata` is also the central package used by [`qcop`](https://github.com/atomsforhumanity/qccompute) to power interoperable quantum chemistry calculations across dozens of packages and [`bigchem`](https://github.com/mtzgroup/bigchem), which scales QC calculations across hundreds of nodes on academic clusters or the cloud. I needed robust and reliable data structures for powering these applications. `qcdata` is the result of thousands of hours of organizing quantum chemistry data into coherent data structures. -It is my hope that you'll find `qcdata` to be intuitive and delightful to use. If you have any questions please open an [issue](https://github.com/coltonbh/qcdata/issues) on GitHub. Pull requests welcome :) +It is my hope that you'll find `qcdata` to be intuitive and delightful to use. If you have any questions please open an [issue](https://github.com/atomsforhumanity/qcdata/issues) on GitHub. Pull requests welcome :) ## Getting Started diff --git a/mkdocs.yml b/mkdocs.yml index 26f8558..e0d3bb0 100644 --- a/mkdocs.yml +++ b/mkdocs.yml @@ -1,5 +1,5 @@ site_name: Quantum Chemistry Data (qcdata) -site_url: https://qcdata.coltonhicks.com/ +site_url: https://qcdata.docs.atomsforhumanity.org/ theme: name: material palette: @@ -37,7 +37,7 @@ theme: icon: repo: fontawesome/brands/github-alt -repo_url: https://github.com/coltonbh/qcdata +repo_url: https://github.com/atomsforhumanity/qcdata edit_uri: edit/master/docs/ site_author: Colton Hicks plugins: @@ -122,4 +122,4 @@ nav: - Structure: visualizations/structure.ipynb - Results: visualizations/results.ipynb - Core Views: visualizations/coreviews.ipynb - - Changelog: https://github.com/coltonbh/qcdata/blob/master/CHANGELOG.md + - Changelog: https://github.com/atomsforhumanity/qcdata/blob/master/CHANGELOG.md diff --git a/pyproject.toml b/pyproject.toml index 6ecd980..a36129a 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -31,12 +31,12 @@ classifiers = [ "Topic :: Software Development :: Libraries", ] [project.urls] -Homepage = "https://github.com/coltonbh/qcdata" -Documentation = "https://qcdata.coltonhicks.com" -Source = "https://github.com/coltonbh/qcdata" -Changelog = "https://github.com/coltonbh/qcdata/blob/master/CHANGELOG.md" -"Bug Tracker" = "https://github.com/coltonbh/qcdata/issues" -repository = "https://github.com/coltonbh/qcdata" +Homepage = "https://github.com/atomsforhumanity/qcdata" +Documentation = "https://qcdata.docs.atomsforhumanity.org" +Source = "https://github.com/atomsforhumanity/qcdata" +Changelog = "https://github.com/atomsforhumanity/qcdata/blob/master/CHANGELOG.md" +"Bug Tracker" = "https://github.com/atomsforhumanity/qcdata/issues" +repository = "https://github.com/atomsforhumanity/qcdata" [project.optional-dependencies] diff --git a/uv.lock b/uv.lock index faf3ac2..67b9da6 100644 --- a/uv.lock +++ b/uv.lock @@ -2919,7 +2919,7 @@ wheels = [ [[package]] name = "qcdata" -version = "0.17.2" +version = "0.18.0" source = { editable = "." } dependencies = [ { name = "eval-type-backport" },