aegiss 0.1.0__tar.gz

aegiss-0.1.0/.git_archival.txt

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+node: $Format:%H$
+node-date: $Format:%cI$
+describe-name: $Format:%(describe:tags=true,match=*[0-9]*)$

aegiss-0.1.0/.gitattributes

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+.git_archival.txt  export-subst

aegiss-0.1.0/.gitignore

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+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[codz]
+*$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/
+
+# 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
+
+# UV
+#   Similar to Pipfile.lock, it is generally recommended to include uv.lock in version control.
+#   This is especially recommended for binary packages to ensure reproducibility, and is more
+#   commonly ignored for libraries.
+#uv.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
+#poetry.toml
+
+# pdm
+#   Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control.
+#   pdm recommends including project-wide configuration in pdm.toml, but excluding .pdm-python.
+#   https://pdm-project.org/en/latest/usage/project/#working-with-version-control
+#pdm.lock
+#pdm.toml
+.pdm-python
+.pdm-build/
+
+# pixi
+#   Similar to Pipfile.lock, it is generally recommended to include pixi.lock in version control.
+#pixi.lock
+#   Pixi creates a virtual environment in the .pixi directory, just like venv module creates one
+#   in the .venv directory. It is recommended not to include this directory in version control.
+.pixi
+
+# 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/
+
+# Abstra
+# Abstra is an AI-powered process automation framework.
+# Ignore directories containing user credentials, local state, and settings.
+# Learn more at https://abstra.io/docs
+.abstra/
+
+# Visual Studio Code
+#  Visual Studio Code specific template is maintained in a separate VisualStudioCode.gitignore
+#  that can be found at https://github.com/github/gitignore/blob/main/Global/VisualStudioCode.gitignore
+#  and can be added to the global gitignore or merged into this file. However, if you prefer,
+#  you could uncomment the following to ignore the entire vscode folder
+.vscode/
+
+# Ruff stuff:
+.ruff_cache/
+
+# PyPI configuration file
+.pypirc
+
+# Cursor
+#  Cursor is an AI-powered code editor. `.cursorignore` specifies files/directories to
+#  exclude from AI features like autocomplete and code analysis. Recommended for sensitive data
+#  refer to https://docs.cursor.com/context/ignore-files
+.cursorignore
+.cursorindexingignore
+
+# Marimo
+marimo/_static/
+marimo/_lsp/
+__marimo__/
+
+# macOS
+.DS_Store
+
+# AEGISS runtime scratch/output (SCRATCH_DIR default, OutputConfig default)
+/tmp/
+aegiss_output/
+
+# Local developer scratch scripts and their DMRG scratch dir — never pushed.
+# Also excluded from ruff via [tool.ruff] exclude in pyproject.toml.
+/scripts/
+
+# Written by `just sbom`
+/sbom/
+
+# Local, never-pushed working files (generated cubes/plots, FCIDUMPs, test runs).
+/local/
+
+# Written by hatch-vcs at build time
+src/aegiss/_version.py
+
+# nix-direnv state (.envrc itself is tracked: it loads the Nix dev shell)
+.direnv/

aegiss-0.1.0/.grant.yaml

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+# License policy for the runtime dependencies, checked by `just sbom-check` with anchore/grant
+# (https://oss.anchore.com/docs/guides/license/policies/) against the SBOMs from `just sbom`.
+#
+# AEGISS is released under Apache-2.0: allow what an Apache-2.0 library may depend on. Matching is
+# case-sensitive and `*` is a glob. A package must match on every license it declares.
+
+allow:
+  # Permissive
+  - 0BSD
+  - Apache-2.0
+  - BSD-*-Clause
+  - CC0-1.0
+  - ISC
+  - MIT
+  - MIT-CMU
+  - PSF-2.0
+  - Python-2.0
+  - Unlicense
+  - Zlib
+  # Weak copyleft: fine for unmodified dependencies installed alongside AEGISS, not for code
+  # copied into it.
+  - LGPL-2.1-only
+  - LGPL-2.1-or-later
+  - LGPL-3.0-only
+  - LGPL-3.0-or-later
+  - MPL-2.0
+  # Trove classifiers, for packages that declare no SPDX identifier
+  - "License :: OSI Approved :: Apache Software License"
+  - "License :: OSI Approved :: BSD License"
+  - "License :: OSI Approved :: MIT License"
+  - "License :: OSI Approved :: Mozilla Public License 2.0 (MPL 2.0)"
+
+# Reviewed by hand. Every entry needs the reason it passes; drop it when the reason goes.
+ignore-packages:
+  # GPL-3.0-only. AEGISS runs `block2main` as a separate program and exchanges only files
+  # (FCIDUMP and input in, density matrices out); it never imports or links block2, so the
+  # GPL does not reach AEGISS (https://www.gnu.org/licenses/gpl-faq.html#MereAggregation).
+  # See the note at the top of src/aegiss/wavefunction/dmrg_subprocess.py. Anything that
+  # ships block2 itself (a container image, a frozen bundle) must meet the GPL for block2.
+  - block2
+  # `LGPL-3.0-only OR GPL-2.0-only OR GPL-3.0-only`: we take the LGPL-3.0 option. grant
+  # checks each alternative of an OR expression, so it denies the GPL ones.
+  - PySide6_Essentials
+  - shiboken6
+  # Public domain and BSD-2-Clause. Its GPL classifier covers tools/editors/emacs/rst.el
+  # alone, which the wheel does not ship (https://docutils.sourceforge.io/COPYING.html).
+  - docutils
+
+require-license: true

aegiss-0.1.0/.mailmap

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+# Entries in this file are made for two reasons:
+# 1) to merge multiple git commit authors that correspond to a single author
+# 2) to change the canonical name and/or email address of an author.
+#
+# See `git help mailmap` for the format.
+
+Fabio Tarocco <fabio.tarocco@algorithmiq.fi> FabioTarocco <fabio.tarocco.vr@gmail.com>
+Fabio Tarocco <fabio.tarocco@algorithmiq.fi> FabioTarocco <54395661+FabioTarocco@users.noreply.github.com>

aegiss-0.1.0/.python-version

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+3.12

aegiss-0.1.0/CHANGELOG.md

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+# Changelog
+
+All notable changes to this project are listed here.
+
+## 0.1.0 (2026-10-28)
+
+### Features
+
+- Additional localization procedure (#46)
+- Added format  (#54)
+- Added resolution space without SOE (#55)
+- Added beta components to `plot_ao_contributions` (#58)
+- Add `mo_composition` (#59)
+- Add `clusters` grouping to mo_ao_contributions (#61)
+- Simple `chemcore` core identification; (#57)
+- Started UHF integration (#62)
+- Orbital index mutable setup (#65)
+
+### Fixes
+
+- Improved plateau visibility
+- Expose AO contributions and update outdated tutorials (#71)
+- Use mulliken as default pop_method for Pipek-Mezey (#72)
+- IAO shape, Pipek-Mezey occupied pop_method and plot output names (#76)
+- **scf:** Log the mean-field energy after the SCF (#86)
+
+### Documentation
+
+- Refining `mkdocs` (#64)
+- **localization:** Explain why the DMRG window is not a frontier window for localized orbitals (#75)
+- Fix docstrings that no longer match the code (#79)
+- **plotting:** Explain how to use the MI plots with an external mutual-information matrix (#81)
+- Trim the README to an entry point and fix stale docs pages (#77)
+- **tutorials:** Use a CAS(18,18) window in 03/04 and fix stale tutorial text (#78)
+- Deploy the site, run the doc code blocks and add a developer guide (#88)
+- **uhf:** Validate the entropies against PySCF FCI instead of pyblock2 (#93)
+- **site:** Show the Apache licence on the docs site (#101)
+- **citing:** Cite AEGISS and the work it builds on (#102)
+- **contributing:** Document the Apache-2.0 licence header (#104)