diff --git a/Makefile b/Makefile index 733dee4f..043a67a2 100644 --- a/Makefile +++ b/Makefile @@ -2,23 +2,33 @@ SHELL = /bin/bash VENV = venv-hnx PYTHON3 = python3 -## Lint -.PHONY: lint -lint: pylint flake8 +############# Manage Environments ############# -.PHONY: pylint -pylint: - @$(PYTHON3) -m pylint --recursive=y --persistent=n --verbose hypernetx +## Environment using Pip +.PHONY: venv +venv: clean-venv + @$(PYTHON3) -m venv $(VENV); -# Todo: fix flake8 errors and remove --exit-zero -.PHONY: flake8 -flake8: - @$(PYTHON3) -m flake8 hypernetx --exit-zero +.PHONY: clean-venv +clean-venv: + rm -rf $(VENV) -.PHONY: pre-commit -pre-commit: - pre-commit install - pre-commit run --all-files +.PHONY: install-reqs +install-reqs: + @$(PYTHON3) -m pip install -r requirements.txt + +## Environment using Poetry + +.PHONY: develop +develop: clean-poetry-env + poetry install --all-extras --with test + poetry shell + +.PHONY: requirements.txt +requirements.txt: + poetry export --format requirements.txt --output requirements.txt --without-hashes --extras "contagion modularity" + +############# Running Tests, linters ############# ## Tests .PHONY: test @@ -34,8 +44,18 @@ test-tox: ### Tests using Poetry + Tox ### Used by Bamboo CI Pipeline, Github Workflows CI Pipeline -.PHONY: install-poetry -install-poetry: + +.PHONY: test-ci-github +test-ci-github: run-poetry-tox + +.PHONY: test-ci-stash +test-ci-stash: install-poetry-stash run-poetry-tox clean-poetry-env + +.PHONY: build-docs-stash +build-docs-stash: install-poetry-stash run-build-docs clean-poetry-env + +.PHONY: install-poetry-stash +install-poetry-stash: pip install poetry==1.8.2 poetry config virtualenvs.in-project true poetry run pip install tox @@ -44,64 +64,58 @@ install-poetry: run-poetry-tox: poetry run tox --parallel -.PHONY: clean-poetry -clean-poetry: - poetry env remove --all - -.PHONY: test-ci-stash -test-ci-stash: install-poetry run-poetry-tox clean-poetry +.PHONY: run-build-docs +run-build-docs: + poetry run tox -e build-docs -.PHONY: test-ci-github -test-ci-github: run-poetry-tox +.PHONY: clean-poetry-env +clean-poetry-env: + poetry env remove --all -.PHONY: run-poetry-tox-build-docs -run-poetry-tox-build-docs: - poetry run tox -e build-docs +## Lint +.PHONY: lint +lint: pylint flake8 -.PHONY: build-docs -build-docs: install-poetry run-poetry-tox-build-docs clean-poetry +.PHONY: pylint +pylint: + @$(PYTHON3) -m pylint --recursive=y --persistent=n --verbose hypernetx +# Todo: fix flake8 errors and remove --exit-zero +.PHONY: flake8 +flake8: + @$(PYTHON3) -m flake8 hypernetx --exit-zero +.PHONY: pre-commit +pre-commit: + pre-commit install + pre-commit run --all-files -## Publish to PyPi +############# Packaging and Publishing to PyPi ############# +## Uses Poetry to manage packaging and publishing ## Targets are included as a backup in case the Github Workflows CI can't publish to PyPi and we need to do it manually ## Assumes the following environment variables are set: PYPI_API_TOKEN .PHONY: publish-to-pypi -publish-to-pypi: build-dist +publish-to-pypi: build check-long-desc @echo "Publishing to PyPi" poetry config pypi-token.pypi PYPI_API_TOKEN poetry config repositories.pypi https://pypi.org/simple/ poetry publish --dry-run #poetry publish -.PHONY: build-dist -build-dist: clean - poetry run pip install twine +.PHONY: build +build: clean poetry build - poetry run twine check dist/* +.PHONY: check-long-desc +check-long-desc: + poetry run pip install twine + poetry run twine check dist/* -## Tutorials +############# Misc ############# .PHONY: tutorials tutorials: jupyter notebook tutorials - -## Environment -.PHONY: clean-venv -clean-venv: - rm -rf $(VENV) - -.PHONY: venv -venv: clean-venv - @$(PYTHON3) -m venv $(VENV); - -.PHONY: install-reqs -install-reqs: - @$(PYTHON3) -m pip install -r requirements.txt - - -## Clean .PHONY: clean clean: rm -rf .out .pytest_cache .tox *.egg-info dist build _build diff --git a/poetry.lock b/poetry.lock index 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packages = [ {include = "hypernetx"}, {include = "hypernetx/algorithms"}, @@ -23,14 +22,10 @@ packages = [ ] [tool.poetry.dependencies] -python = "^3.9,<3.12" -networkx = "^3.2.1" -numpy = "^1.26.4" -scipy = "^1.12.0" -pandas = "^2.2.1" -typing-extensions = "^4.10.0" # remove after 2.3 refactor -scikit-learn = "^1.4.1.post1" -matplotlib = "^3.8.3" +python = "^3.8,<3.12" +networkx = "^2.2" +pandas = "^1.5.3" +scikit-learn = "^1.3.2" celluloid = {version = "^0.2.0", optional = true} igraph = {version = "^0.11.4", optional = true} @@ -48,7 +43,7 @@ pytest-env = "^1.1.3" tox = "^4.14.2" nbmake = "^1.5.3" -# TODO: remove required python versions after HNX upgrade to 3.9 +# TODO: This optional dependency group requires Ptyhon >=3.9 [tool.poetry.group.lint] optional = true [tool.poetry.group.lint.dependencies] @@ -59,6 +54,7 @@ pylint-exit = "^1.2.0" pre-commit = {version = "^3.7.0", python = "^3.9"} mypy = "^1.9.0" +# TODO: This optional dependency group requires Ptyhon >=3.9 [tool.poetry.group.docs] optional = true [tool.poetry.group.docs.dependencies] diff --git a/requirements.txt b/requirements.txt index 55bd974f..ba1b80ad 100644 --- a/requirements.txt +++ b/requirements.txt @@ -1,177 +1,24 @@ -alabaster==0.7.16 -anyio==4.3.0 -appnope==0.1.4 -argon2-cffi==23.1.0 -argon2-cffi-bindings==21.2.0 -arrow==1.3.0 -astroid==3.1.0 -asttokens==2.4.1 -async-lru==2.0.4 -attrs==23.2.0 -Babel==2.14.0 -beautifulsoup4==4.12.3 -black==24.3.0 -bleach==6.1.0 -cachetools==5.3.3 -celluloid==0.2.0 -certifi==2024.2.2 -cffi==1.16.0 -cfgv==3.4.0 -chardet==5.2.0 -charset-normalizer==3.3.2 -click==8.1.7 -colorama==0.4.6 -comm==0.2.2 -contourpy==1.2.0 -coverage==7.4.4 -cycler==0.12.1 -debugpy==1.8.1 -decorator==5.1.1 -defusedxml==0.7.1 -dill==0.3.8 -distlib==0.3.8 -docutils==0.20.1 -execnet==2.0.2 -executing==2.0.1 -fastjsonschema==2.19.1 -filelock==3.13.3 -flake8==7.0.0 -fonttools==4.50.0 -fqdn==1.5.1 -h11==0.14.0 -hnxwidget==0.1.1b3 -httpcore==1.0.4 -httpx==0.27.0 -identify==2.5.35 -idna==3.6 -igraph==0.11.4 -imagesize==1.4.1 -iniconfig==2.0.0 -ipykernel==6.29.3 -ipython==8.18.0 -ipython-genutils==0.2.0 -ipywidgets==7.6.5 -isoduration==20.11.0 -isort==5.13.2 -jedi==0.19.1 -Jinja2==3.1.3 -joblib==1.3.2 -json5==0.9.24 -jsonpointer==2.4 -jsonschema==4.21.1 -jsonschema-specifications==2023.12.1 -jupyter==1.0.0 -jupyter-console==6.6.3 -jupyter-events==0.10.0 -jupyter-highlight-selected-word==0.2.0 -jupyter-lsp==2.2.4 -jupyter-nbextensions-configurator==0.6.3 -jupyter_client==8.6.1 -jupyter_contrib_core==0.4.2 -jupyter_contrib_nbextensions==0.7.0 -jupyter_core==5.7.2 -jupyter_server==2.13.0 -jupyter_server_terminals==0.5.3 -jupyterlab==4.1.5 -jupyterlab_pygments==0.3.0 -jupyterlab_server==2.25.4 -jupyterlab_widgets==3.0.10 -kiwisolver==1.4.5 -livereload==2.6.3 -lxml==5.1.0 -MarkupSafe==2.1.5 -matplotlib==3.8.3 -matplotlib-inline==0.1.6 -mccabe==0.7.0 -mistune==3.0.2 -mypy==1.9.0 -mypy-extensions==1.0.0 -nbclient==0.6.8 -nbconvert==7.16.3 -nbformat==5.10.3 -nbmake==1.5.3 -nest-asyncio==1.6.0 -networkx==3.2.1 -nodeenv==1.8.0 -notebook==7.1.2 -notebook_shim==0.2.4 -numpy==1.26.4 -overrides==7.7.0 -packaging==24.0 -pandas==2.2.1 -pandocfilters==1.5.1 -parso==0.8.3 -pathspec==0.12.1 -pexpect==4.9.0 -pillow==10.2.0 -platformdirs==4.2.0 -pluggy==1.4.0 -pre-commit==3.7.0 -prometheus_client==0.20.0 -prompt-toolkit==3.0.36 -psutil==5.9.8 -ptyprocess==0.7.0 -pure-eval==0.2.2 -pycodestyle==2.11.1 -pycparser==2.21 -pyflakes==3.2.0 -Pygments==2.17.2 -pylint==3.1.0 -pylint-exit==1.2.0 -pyparsing==3.1.2 -pyproject-api==1.6.1 -pytest==8.1.1 -pytest-cov==5.0.0 -pytest-env==1.1.3 -pytest-xdist==3.5.0 -python-dateutil==2.9.0.post0 -python-json-logger==2.0.7 -pytz==2024.1 -PyYAML==6.0.1 -pyzmq==25.1.2 -qtconsole==5.5.1 -QtPy==2.4.1 -referencing==0.34.0 -requests==2.31.0 -rfc3339-validator==0.1.4 -rfc3986-validator==0.1.1 -rpds-py==0.18.0 -scikit-learn==1.4.1.post1 -scipy==1.12.0 -Send2Trash==1.8.2 -shutup==0.2.0 -six==1.16.0 -sniffio==1.3.1 -snowballstemmer==2.2.0 -soupsieve==2.5 -Sphinx==7.2.6 -sphinx-autobuild==2024.2.4 -sphinx-copybutton==0.5.2 -sphinx-rtd-theme==2.0.0 -sphinxcontrib-applehelp==1.0.8 -sphinxcontrib-devhelp==1.0.6 -sphinxcontrib-htmlhelp==2.0.5 -sphinxcontrib-jquery==4.1 -sphinxcontrib-jsmath==1.0.1 -sphinxcontrib-qthelp==1.0.7 -sphinxcontrib-serializinghtml==1.1.10 -stack-data==0.6.3 -terminado==0.18.1 -texttable==1.7.0 -threadpoolctl==3.4.0 -tinycss2==1.2.1 -tomlkit==0.12.4 -tornado==6.4 -tox==4.14.2 -traitlets==5.14.2 -types-python-dateutil==2.9.0.20240316 -typing_extensions==4.10.0 -tzdata==2024.1 -uri-template==1.3.0 -urllib3==2.2.1 -virtualenv==20.25.1 -wcwidth==0.2.13 -webcolors==1.13 -webencodings==0.5.1 -websocket-client==1.7.0 -widgetsnbextension==3.5.2 +celluloid==0.2.0 ; python_version >= "3.8" and python_version < "3.12" +contourpy==1.1.1 ; python_version >= "3.8" and python_version < "3.12" +cycler==0.12.1 ; python_version >= "3.8" and python_version < "3.12" +fonttools==4.50.0 ; python_version >= "3.8" and python_version < "3.12" +igraph==0.11.4 ; python_version >= "3.8" and python_version < "3.12" +importlib-resources==6.4.0 ; python_version >= "3.8" and python_version < "3.10" +joblib==1.3.2 ; python_version >= "3.8" and python_version < "3.12" +kiwisolver==1.4.5 ; python_version >= "3.8" and python_version < "3.12" +matplotlib==3.7.5 ; python_version >= "3.8" and python_version < "3.12" +networkx==2.8.8 ; python_version >= "3.8" and python_version < "3.12" +numpy==1.24.4 ; python_version >= "3.8" and python_version < "3.9" +numpy==1.26.4 ; python_version >= "3.9" and python_version < "3.12" +packaging==24.0 ; python_version >= "3.8" and python_version < "3.12" +pandas==1.5.3 ; python_version >= "3.8" and python_version < "3.12" +pillow==10.3.0 ; python_version >= "3.8" and python_version < "3.12" +pyparsing==3.1.2 ; python_version >= "3.8" and python_version < "3.12" +python-dateutil==2.9.0.post0 ; python_version >= "3.8" and python_version < "3.12" +pytz==2024.1 ; python_version >= "3.8" and python_version < "3.12" +scikit-learn==1.3.2 ; python_version >= "3.8" and python_version < "3.12" +scipy==1.10.1 ; python_version >= "3.8" and python_version < "3.12" +six==1.16.0 ; python_version >= "3.8" and python_version < "3.12" +texttable==1.7.0 ; python_version >= "3.8" and python_version < "3.12" +threadpoolctl==3.4.0 ; python_version >= "3.8" and python_version < "3.12" +zipp==3.18.1 ; python_version >= "3.8" and python_version < "3.10"