polyclustx 1.4.1__tar.gz

polyclustx-1.4.1/.readthedocs.yaml

@@ -0,0 +1,17 @@
+# Read the Docs configuration
+# See https://docs.readthedocs.io/en/stable/config-file/v2.html
+
+version: 2
+
+build:
+  os: ubuntu-24.04
+  tools:
+    python: "3.11"
+
+sphinx:
+  configuration: docs/conf.py
+  fail_on_warning: true
+
+python:
+  install:
+    - requirements: docs/requirements.txt

polyclustx-1.4.1/LICENSE

@@ -0,0 +1,133 @@
+MIT License
+
+Copyright (c) 2025-2026 Abdelheq Mokhtari
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.
+
+------------------------------------------------------------------------
+Third-party notices and asset exclusions
+------------------------------------------------------------------------
+
+# Algorithm references and notices
+
+## Institutional marks
+
+`src/polyclustx/display/assets/borelli.png` (Centre Borelli) and
+`src/polyclustx/display/assets/paris_cite.png` (Université Paris Cité) were
+supplied by the repository owner. They are reproduced unchanged to identify
+research affiliations, not as a claim of institutional endorsement.
+These marks are not licensed under the software's MIT license; rights remain
+with their respective institutions. Reuse must follow institutional requirements:
+
+- https://centreborelli.ens-paris-saclay.fr/fr
+- https://u-paris.fr/charte-graphique-et-outils/
+
+The separate PolyClustX project mark is an original AI-generated transparent
+X-and-nodes design. It is not an institutional mark.
+
+## Algorithm adaptations
+
+CONAN, DGF and G-CoMVKM are framework-native adaptations informed by their
+reference implementations. The copyright notices and MIT license below apply
+to the respective derived portions:
+
+- CONAN: https://github.com/Guanzhou-Ke/conan — Copyright (c) 2021 ihades
+- DGF: https://github.com/HaoranZ99/DGF — Copyright (c) 2026 Haoran Zheng
+- G-CoMVKM: https://github.com/KristinaP09/G-CoMVKM — Copyright (c) 2025 Kristina P. Sinaga
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.
+
+SGLA and UMC are independent implementations of their published formulations;
+their unlicensed standalone source files, pretrained networks and datasets
+are not redistributed. UMC deliberately operates on user-supplied features.
+
+The Co-EM and co-training spectral estimators are framework-native PyTorch
+adaptations informed by mvlearn (https://github.com/mvlearn/mvlearn).
+COMPLETER's architecture and objective are adapted from the XLearning reference
+(https://github.com/XLearning-SCU/2021-CVPR-Completer). Their MIT notices follow.
+
+IDEC, DCP and MFLVC are reimplementations of their published clustering
+objectives using polyclustx's shared building blocks. Original standalone scripts,
+datasets and pretrained weights are not redistributed. Paper and reference
+implementation links, scope and deliberate differences are documented in
+docs/background/algorithms.md and docs/user_guide/clustering_models.md.
+
+## mvlearn
+
+The MIT License
+
+Copyright (c) 2020 The mvlearn developers.
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.
+
+## COMPLETER
+
+MIT License
+
+Copyright (c) 2021 XLearning Group
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

polyclustx-1.4.1/MANIFEST.in

@@ -0,0 +1,9 @@
+include README.md LICENSE .readthedocs.yaml
+include Makefile
+recursive-include scripts *.py
+recursive-include notebooks *.ipynb
+recursive-include docs *.rst *.md *.py *.txt *.css *.html Makefile make.bat
+prune docs/_build
+recursive-include examples *.yaml
+recursive-include tests *.py
+recursive-include src/polyclustx/display/assets *.png

polyclustx-1.4.1/Makefile

@@ -0,0 +1,119 @@
+.PHONY: help guide cli run search list-datasets list-models \
+        install test lint fix format build docs docs-build docs-serve docs-deploy clean version bump release
+
+PYTHON ?= python
+PORT ?= 8000
+RTD_PROJECT ?= polyclustx
+RTD_VERSION ?= latest
+
+# ── Help ──────────────────────────────────────────────────────────
+
+help:            ## Show this list of targets
+	@grep -hE '^[a-zA-Z_-]+:.*?## ' $(MAKEFILE_LIST) \
+		| awk 'BEGIN {FS = ":.*?## "}; {printf "  %-16s %s\n", $$1, $$2}'
+
+# ── Development ───────────────────────────────────────────────────
+
+install:         ## Install the complete package, including the interface
+	$(PYTHON) -m pip install .
+
+test:            ## Run the test suite
+	$(PYTHON) -m pytest $(ARGS)
+
+lint:            ## Lint with ruff
+	$(PYTHON) -m ruff check src/ tests/
+
+fix:             ## Auto-fix lint issues
+	$(PYTHON) -m ruff check --fix src/ tests/
+
+format:          ## Format code (Black-compatible)
+	$(PYTHON) -m ruff format src/ tests/
+
+build:           ## Build wheel and sdist
+	$(PYTHON) -m build
+
+docs: docs-build  ## Alias for docs-build
+
+docs-build:      ## Install documentation tools and build HTML
+	$(PYTHON) -m pip install -r docs/requirements.txt
+	$(PYTHON) -m sphinx -W --keep-going -b html docs docs/_build/html
+
+docs-serve:      ## Serve existing HTML without rebuilding at http://127.0.0.1:8000
+	@test -f docs/_build/html/index.html || { echo "Run make docs-build first."; exit 1; }
+	$(PYTHON) -m http.server $(PORT) --directory docs/_build/html --bind 127.0.0.1
+
+docs-deploy:     ## Trigger Read the Docs; requires READTHEDOCS_TOKEN in the environment
+	$(PYTHON) scripts/deploy_docs.py --project $(RTD_PROJECT) --version $(RTD_VERSION)
+
+clean:           ## Remove build, cache and docs artifacts
+	rm -rf build dist src/polyclustx.egg-info docs/_build .pytest_cache .ruff_cache .coverage htmlcov test-results.xml
+	find src tests docs scripts -name __pycache__ -type d -prune -exec rm -rf {} +
+
+# ── CLI helpers ───────────────────────────────────────────────────
+
+guide:           ## Show short command-line help
+	@$(PYTHON) -m polyclustx.command
+
+cli:             ## Forward arguments, e.g. make cli ARGS="models idec"
+	@$(PYTHON) -m polyclustx.command $(ARGS)
+
+run:             ## Run a model: make run DATASET=acm MODEL=lmgec ARGS="--runs 3"
+	@$(PYTHON) -m polyclustx.command run $(DATASET) --model $(or $(MODEL),multiview_kmeans) $(ARGS)
+
+search:          ## Tune a model: pass --strategy and --vary through ARGS
+	@$(PYTHON) -m polyclustx.command search $(DATASET) --model $(or $(MODEL),multiview_kmeans) $(ARGS)
+
+list-datasets:   ## List dataset families
+	@$(PYTHON) -m polyclustx.command datasets
+
+list-models:     ## List registered models
+	@$(PYTHON) -m polyclustx.command models
+
+# ── Release ───────────────────────────────────────────────────────
+
+version:         ## Show the current library version
+	@$(PYTHON) -m polyclustx --version
+
+bump:            ## Bump version using commitizen (updates version files)
+	@echo "Bumping version with commitizen..."
+	cz bump
+	@echo ""
+	@echo "Version bumped. Files updated:"
+	@echo "  - pyproject.toml  (project.version + tool.commitizen.version)"
+	@echo "  - src/polyclustx/__init__.py  (__version__)"
+	@echo ""
+	@echo "Run  make release  to merge into main and push tags."
+
+release:         ## Full release: bump -> merge develop -> main, push tags
+	@echo "Starting release process..."
+
+	@if [ "$$(git branch --show-current)" != "develop" ]; then \
+		echo "Error: You must run this from the develop branch"; \
+		exit 1; \
+	fi
+
+	@if [ -n "$$(git status --porcelain)" ]; then \
+		echo "Error: Working tree is dirty. Commit or stash changes first."; \
+		exit 1; \
+	fi
+
+	@echo "Bumping version (commitizen -> version files)"
+	cz bump
+
+	@echo "Switching to main"
+	git checkout main
+
+	@echo "Pulling latest main"
+	git pull origin main
+
+	@echo "Merging develop"
+	git merge --no-ff develop -m "release: merge develop into main"
+
+	@echo "Pushing changes"
+	git push origin main
+	git push origin develop
+	git push origin --tags
+
+	@echo ""
+	@echo "Release completed successfully"
+	@$(PYTHON) -m polyclustx --version