melite 0.1.11__tar.gz

melite-0.1.11/.gitignore

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+__pycache__/
+.venv/
+.vscode/
+.env
+data/
+output/
+raw/
+tests_output.txt
+*.npy
+*.npz
+*.py[cod]
+*.pkl
+*.joblib
+
+tests_output.txt
+
+site/
+
+.pytest_tmp
+
+dist/

melite-0.1.11/CHANGELOG.md

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+# Changelog
+
+All notable changes to MELITE will be documented in this file.
+
+The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.1.0/),
+and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
+
+---
+
+## [0.1.11] - 2026-05-26
+
+### Changed
+- Prepared documentation and package metadata for the first PyPI publication as
+  `melite`.
+- Updated release metadata to use final version `0.1.11` instead of development
+  or previous release references.
+- Clarified that MELITE is tabular at the modeling level: learning algorithms
+  consume numeric `X` and `y` arrays that may come from PCA, UMAP, fingerprints,
+  descriptors, clinical variables, experimental measurements, industrial
+  features, or manually selected numeric features.
+- Clarified that the current dataset orchestration still reflects MELITE's
+  PCA/UMAP origin and uses concepts such as reduction type and level.
+- Documented generalized `[datasets.*]` definitions as a future direction, not
+  current behavior.
+
+### Notes
+- No functional behavior changes were made to training, model selection,
+  cross-validation, export, prediction, dataset loading, or CLI commands.
+
+---
+
+## [0.1.10] - 2026-05-25
+
+### Changed
+- Renamed the project identity from MOSAIC to MELITE.
+- Renamed the Python import package from `mosaic` to `melite`.
+- Renamed the CLI command from `mosaic` to `melite`.
+- Renamed the PyPI distribution target from `mosaic-tabular` to `melite`.
+- Updated repository, documentation, CI, and publishing metadata for
+  `NanoBiostructuresRG/melite`.
+- Updated public API imports to remain the same symbols under `melite`.
+- Updated result report headers to use MELITE branding and current CLI commands.
+
+### Fixed
+- Replaced the duplicated SVC RBF `C = 0.02` grid value with `C = 0.2`.
+
+### Validation
+- `python -m pytest tests/ -v --basetemp=.review_pytest_tmp -o cache_dir=.review_pytest_cache` — 82 passed, 1 warning, 0 failed.
+- `melite --help`, `melite run --help`, `melite export --help`, and `melite --version` — passed.
+- Public API smoke test — `OK: 0.1.10`.
+- `python -m build` — `melite-0.1.10.tar.gz` and `.whl` built successfully.
+- `python -m twine check dist/*` — PASSED.
+- `mkdocs build --strict` — build succeeded with no errors.
+- Wheel includes `melite/`, `melite/config_default.toml`, metadata, and license files.
+- Sdist inspected; local virtual environments, caches, generated review/docs
+  artifacts, build folders, raw/data/output folders, egg-info, `.pkl`, and
+  `.joblib` artifacts were not present.
+
+---
+
+## [0.1.9] - 2026-05-25
+
+### Added
+- Added dedicated MkDocs pages for installation, quick start, CLI reference,
+  configuration, and release notes.
+- Added a home-page workflow diagram:
+  `X / y -> mosaic run -> results.csv -> mosaic export -> .pkl -> predict()`.
+- Added a "MOSAIC does / does not" scope table to clarify project boundaries.
+
+### Changed
+- Reworked `docs/index.md` into a concise project overview with links to the
+  dedicated documentation pages.
+- Updated `mkdocs.yml` navigation to expose the expanded documentation set.
+- Updated `README.md` for `dev/v0.1.9`, test-suite status, live documentation
+  links, and planned PyPI publication as `mosaic-tabular`.
+- Bumped version to `0.1.9` in `version.py` and `CITATION.cff`.
+
+### Validation
+- `mkdocs build --strict` — build succeeded with no errors.
+- `pytest tests/ -v` — 82 passed, 1 warning, 0 failed.
+- `python -m build` — `mosaic_tabular-0.1.9.tar.gz` and `.whl` built successfully.
+- `python -m twine check dist/*` — PASSED.
+- `mosaic --version` -> `MOSAIC 0.1.9`.
+- Wheel and sdist contents inspected; local virtual environments, caches,
+  generated review artifacts, build folders, raw/data/output folders,
+  egg-info, `.pkl`, and `.joblib` artifacts were not present.
+
+---
+
+## [0.1.8] - 2026-05-25
+
+### Added
+- Added `.github/workflows/publish-to-pypi.yml` — manual PyPI publish workflow
+  triggered via `workflow_dispatch`. Validates tag format, verifies package
+  version matches tag, builds wheel and sdist, checks distributions, and
+  publishes via trusted publishing (OIDC, no API token required).
+- Added `dist/` to `.gitignore`.
+
+### Changed
+- Renamed PyPI package from `mosaic-ml` to `mosaic-tabular` in `pyproject.toml`.
+- Updated `description` in `pyproject.toml` to:
+  `"Tabular classification benchmarking toolkit for model selection, repeated
+  stratified cross-validation, final model export, and artifact-based inference."`
+- Updated `docs/api.md` to include `predict` in the public API reference.
+- Updated `docs/index.md`: version badge, pre-stable note, four-card panel,
+  `predict` tab in Python API examples, `predict` in public API table.
+- Updated `docs/stylesheets/extra.css`: added `.ms-grid--four` layout class.
+- Updated `README.md`: corrected all references from `mosaic-ml` to
+  `mosaic-tabular`, replaced "inference" with "artifact-based inference"
+  throughout, updated roadmap and notes.
+- Bumped version to `0.1.8` in `version.py` and `CITATION.cff`.
+
+### Validation
+- `python -m build` — `mosaic_tabular-0.1.8.tar.gz` and `.whl` built successfully.
+- `python -m twine check dist/*` — PASSED.
+- `mkdocs build --strict` — build succeeded with no errors.
+- `pytest tests/ -v` — 80 passed, 1 warning, 0 failed.
+- `mosaic --version` → `MOSAIC 0.1.8`.
+
+---
+
+## [0.1.7] - 2026-05-25
+
+### Added
+- Added `mosaic/predict.py` — inference module exposing `predict()` as a stable
+  public API symbol. Loads a `.pkl` artifact, returns predictions and class
+  probabilities for a new feature matrix.
+- Added `predict` to `mosaic/__init__.py` and `__all__`.
+- Added `.github/workflows/ci.yml` — CI workflow: tests on Python 3.11 and 3.12,
+  public import boundary check, wheel and sdist smoke installs, docs build.
+- Added `.github/workflows/docs.yml` — deploys MkDocs site to GitHub Pages on
+  push to `main`.
+- Added synthetic example dataset under `examples/`:
+  - `sample_labels.npy` — 100 binary labels, balanced classes.
+  - `sample_PCA70.npz` — 100×37 feature matrix with `X` and `y` keys.
+  - `example_config.toml` — TOML config pointing to example files.
+  - `generate_sample_data.py` — reproducible generation script (seed=42).
+- Added `tests/test_predict.py` — 11 tests for the inference module.
+- Added `tests/test_examples.py` — 11 tests for example dataset integrity.
+- Added `tmp_model` fixture to `tests/conftest.py` — trained SVC saved as `.pkl`.
+- Added `.pytest_tmp` to `.gitignore`.
+
+### Changed
+- Updated `tests/test_public_api.py` — added `predict` import and `__all__` tests.
+  Total test count: **80 tests**.
+- Rewrote `README.md` combining outside-in user perspective with full developer
+  documentation.
+- Updated `mosaic/__init__.py` public API docstring to include `predict`.
+- Bumped version to `0.1.7` in `version.py` and `CITATION.cff`.
+
+### Validation
+- `pytest tests/ -v` — 80 passed, 1 warning, 0 failed.
+- `mosaic run --smoke --config examples/example_config.toml` — completed successfully.
+- `predict()` returns correct shapes for predictions and probabilities.
+- CI workflow passes on Python 3.11 and 3.12 (GitHub Actions).
+- `mkdocs build --strict` — build succeeded.
+
+---
+
+## [0.1.6] - 2026-05-23
+
+### Added
+- Added NumPy-style docstrings to all 10 modules: `__init__.py`, `version.py`,
+  `config.py`, `load_dataset.py`, `result_manager.py`, `plot_metrics.py`,
+  `model_training.py`, `export_best_model.py`, `main.py`, and `cli.py`.
+- Added MkDocs documentation site with `mkdocs-material` theme:
+  - `mkdocs.yml` — site configuration with MOSAIC steel-blue + amber palette.
+  - `docs/index.md` — home page with hero section, quick start, and Python API examples.
+  - `docs/api.md` — API Reference generated from docstrings via `mkdocstrings`.
+  - `docs/changelog.md` — changelog page (includes `CHANGELOG.md`).
+  - `docs/stylesheets/extra.css` — custom MOSAIC theme styles.
+
+### Changed
+- Bumped version to `0.1.6` in `version.py` and `CITATION.cff`.
+
+### Validation
+- `pytest tests/ -v` — 57 passed, 1 warning, 0 failed.
+- `mkdocs build --strict` — build succeeded with no errors.
+- `mkdocs serve` — site renders correctly locally.
+- `python -c "help(mosaic.Config)"` — docstring visible.
+
+---
+
+## [0.1.5] - 2026-05-23
+
+### Added
+- Defined stable public API in `mosaic/__init__.py`: `Config`, `load_dataset`,
+  `ResultManager`, `plot_cv_distributions`, and `__version__` are now importable
+  directly from `mosaic`.
+- Added `__all__` to all modules: `config.py`, `load_dataset.py`,
+  `result_manager.py`, `plot_metrics.py`, `model_training.py`,
+  `export_best_model.py`, and `cli.py`.
+- Added `tests/test_version.py` — 6 tests for version metadata.
+- Added `tests/test_public_api.py` — 7 tests for public API imports and `__all__`.
+- Added `tests/test_plot_metrics.py` — 5 tests for PNG output and directory creation.
+- Added `tests/test_cli.py` — 8 tests for CLI help and version output.
+- Added `pytest` to `environment.yml`.
+
+### Changed
+- `mosaic/__init__.py` now exposes the stable public API with explicit imports
+  and `__all__`. Users can do `from mosaic import Config, load_dataset`.
+- Bumped version to `0.1.5` in `version.py` and `CITATION.cff`.
+
+### Validation
+- `pytest tests/ -v` — 57 passed, 1 warning (expected Agg backend warning), 0 failed.
+- `from mosaic import Config, load_dataset, ResultManager, plot_cv_distributions, __version__` ✓
+- `mosaic.__all__` contains exactly the 5 expected public symbols ✓
+- CLI help and version tests pass via subprocess ✓
+
+---
+
+## [0.1.4] - 2026-05-22
+
+### Added
+- Added formal `pytest` suite under `tests/` with 31 tests covering
+  `Config`, `load_dataset`, `ResultManager`, and `Finalizer`.
+- Added `tests/conftest.py` with shared synthetic fixtures: labels, valid/invalid
+  `.npz` files, minimal `results.csv`, and a base `Config` instance.
+- Added `tests_output.txt` to `.gitignore`.
+
+### Fixed
+- Removed redundant `print()` progress calls from `main.py`; all progress now
+  goes through `logger.*` only. Smoke banner remains as `print()` (user-facing UI).
+- Changed smoke-mode `logger.warning()` to `logger.info()` in `main.py` to avoid
+  spurious output when `--verbose` is not passed.
+- Removed `logging.basicConfig(level=logging.INFO)` from `load_dataset.py` —
+  module-level `basicConfig` was overriding the package logger configuration.
+- Improved error message for missing `.npz` file: now includes full expected path
+  and an actionable hint.
+- Improved error message for missing `X` key in `.npz`: now raises `ValueError`
+  with filename and list of available keys.
+- Improved label mismatch error: now includes both array shapes and differing
+  element count.
+- Added guard in `Finalizer.__init__` for missing `results.csv`: raises
+  `FileNotFoundError` with path and actionable hint before attempting to read.
+- Bumped version to `0.1.4` in `version.py` and `CITATION.cff`.
+
+### Validation
+- `pytest tests/ -v` — 31 passed, 0 failed.
+- `mosaic run --smoke` — silent output (smoke banner only, no logger noise).
+- `mosaic run --smoke --verbose` — clean INFO logs, no duplicates.
+- `mosaic export --row 0` (missing CSV) — descriptive `FileNotFoundError`.
+
+---
+
+## [0.1.3] - 2026-05-22
+
+### Added
+- Added `pyproject.toml` with `hatchling` build backend and `[project.scripts]`
+  entry point: `mosaic = "mosaic.cli:main"`. Package is now installable via
+  `pip install -e .`.
+- Added unified CLI `mosaic/cli.py` with subcommands `mosaic run` and
+  `mosaic export`, replacing the two separate entry points.
+- Added global CLI flags: `--verbose` (INFO-level logging), `--config PATH`
+  (user TOML override), `--version`.
+- Added `mosaic/config_default.toml` with externalized configuration: paths,
+  reduction types, levels, random state, CV settings, and active models.
+- Added `Config.setup()` method to separate filesystem side effects from object
+  instantiation, enabling safe use in tests.
+- Added `ResultManager.write_csv()` method, consolidating all file I/O under
+  `ResultManager`.
+- Added `smoke` column to `results.csv` to mark runs generated in smoke mode.
+- Added smoke-mode export guard: `mosaic export` blocks export of smoke results
+  with exit code 1. Use `mosaic export --force` to override with a visible
+  warning.
+- Added package-level `NullHandler` logger in `mosaic/__init__.py`.
+
+### Changed
+- `Config` now reads `config_default.toml` as the base configuration.
+- `Config.__init__` no longer creates directories or sets random seeds.
+- `Config.PARAM_GRID` is now built by `_build_param_grid()`.
+- `main.py` now iterates over `config.REDUCTION_TYPES` instead of a hardcoded list.
+- `main.py` delegates CSV writing to `ResultManager.write_csv()`.
+- CLI logic centralized in `mosaic/cli.py`.
+- Bumped version to `0.1.3` in `version.py` and `CITATION.cff`.
+
+### Validation
+- `pip install -e .` succeeded in `mosaic_env`.
+- `mosaic --help`, `mosaic run --help`, `mosaic export --help` verified.
+- `mosaic --version` returns `MOSAIC 0.1.3`.
+- `mosaic run --smoke --verbose` completed full PCA + UMAP run with INFO logging.
+- `mosaic export --row 0 --force` exported with warning, `.pkl` artifact created.
+
+---
+
+## [0.1.2] - 2026-05-22
+
+### Changed
+- Moved all source modules into a `mosaic/` package directory.
+- Updated all intra-package imports to use the `mosaic.*` namespace.
+- `result_manager.py` now reads `__version__` from `mosaic.version`.
+- Updated `README.md` to reflect the `mosaic/` package structure.
+
+### Fixed
+- Bumped version string in `version.py` to `0.1.2`.
+
+### Added
+- Added `--smoke` flag to `mosaic.main` for lightweight benchmarking.
+- Added `argparse` CLI to `mosaic.main` with `--smoke` flag and `--help` support.
+
+### Validation
+- Python syntax validation passed for all modules under `mosaic/`.
+- Dataset loading smoke test passed: PCA70 labels and features loaded correctly.
+- SVC, Random Forest and XGBoost smoke tests passed; scores match v0.1.1 baseline.
+- PNG figure generation smoke test passed.
+
+---
+
+## [0.1.1] - 2025-05-22
+
+### Changed
+- Rewrote `README.md` to reflect the current pre-stable repository workflow.
+- Changed project license from MIT to GNU LGPL v3.0 or later.
+- Added GNU license files: `COPYING` and `COPYING.LESSER`.
+- Added SPDX license metadata: `LGPL-3.0-or-later`.
+
+### Fixed
+- Added validation to ensure embedded `.npz` labels match `raw/labels.npy`.
+- Ensured plot output directories are created automatically before saving figures.
+
+### Added
+- Added `version.py` with centralized project version metadata.
+- Added `CITATION.cff` for software citation metadata.
+- Added non-interactive model export support with `python export_best_model.py --row <index>`.
+
+### Validation
+- Python syntax validation passed.
+- PCA70 dataset loading passed.
+- Export CLI help validation passed.
+- Minimal SVC, Random Forest and XGBoost smoke tests passed in `mosaic_env`.
+
+---
+
+## [0.1.0] - 2025-05-22
+
+### Added
+- Initial corrected pre-stable version of MOSAIC.
+- Tabular classification benchmarking with PCA/UMAP reduced datasets.
+- Grid search support for SVC, Random Forest and XGBoost.
+- Repeated Stratified K-Fold evaluation.
+- TXT/CSV result export.
+- Final model export as `.pkl`.
+- Three-panel metric plotting for F1, Accuracy and AUC-ROC.

melite-0.1.11/CITATION.cff

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+cff-version: 1.2.0
+message: "If you use this software, please cite it as below."
+type: software
+title: "MELITE: Multi-model Evaluation and Learning for Inference-ready Tabular Experiments"
+version: "0.1.11"
+date-released: "2026-05-26"
+authors:
+  - family-names: "Contreras-Torres"
+    given-names: "Flavio F."
+    orcid: "https://orcid.org/0000-0003-2375-131X"
+    affiliation: "Tecnologico de Monterrey"
+  - family-names: "Murrieta"
+    given-names: "Ana C."
+    orcid: "https://orcid.org/0000-0002-7619-8880"
+    affiliation: "Tecnologico de Monterrey"
+repository-code: "https://github.com/NanoBiostructuresRG/melite"
+license: "LGPL-3.0-or-later"
+abstract: >-
+  MELITE is a pre-stable Python toolkit for tabular classification benchmarking,
+  model selection, repeated stratified cross-validation, final model export,
+  and artifact-based inference.
+  It operates at the tabular modeling level by consuming numeric feature
+  matrices and labels, benchmarks SVC, Random Forest and XGBoost classifiers,
+  evaluates model configurations with repeated stratified cross-validation,
+  exports tabular performance summaries, and supports final model retraining
+  and serialization as reusable model artifacts.
+keywords:
+  - machine learning
+  - tabular classification
+  - model benchmarking
+  - cross-validation
+  - PCA
+  - UMAP
+  - SVC
+  - random forest
+  - XGBoost
+  - cheminformatics