From b6547796199194c7b17509964c8fe7209ff40fb6 Mon Sep 17 00:00:00 2001 From: wolfyds Date: Wed, 10 Apr 2024 18:53:48 +0000 Subject: [PATCH 1/9] Updated project installation to not depend on ssh, but instead on http. Updated build to be completely through poetry and simplified pre-commit. --- .devcontainer/devcontainer.json | 49 ++ .devcontainer/post-create.sh | 8 + .gitignore | 160 ++++ .pre-commit-config.yaml | 54 +- poetry.lock | 1399 +++++++++++++++++++++++++++++++ pylambertw/igmm.py | 4 +- pyproject.toml | 32 +- requirements.txt | 12 - setup.py | 39 - 9 files changed, 1659 insertions(+), 98 deletions(-) create mode 100644 .devcontainer/devcontainer.json create mode 100644 .devcontainer/post-create.sh create mode 100644 .gitignore create mode 100644 poetry.lock delete mode 100644 requirements.txt delete mode 100644 setup.py diff --git a/.devcontainer/devcontainer.json b/.devcontainer/devcontainer.json new file mode 100644 index 0000000..4a9542c --- /dev/null +++ b/.devcontainer/devcontainer.json @@ -0,0 +1,49 @@ +// For format details, see https://aka.ms/devcontainer.json. For config options, see the +// README at: https://github.com/devcontainers/templates/tree/main/src/docker-existing-dockerfile +{ + "name": "pylambertw", + "postCreateCommand": "bash .devcontainer/post-create.sh", + "workspaceFolder": "/workspace", + "workspaceMount": "source=${localWorkspaceFolder},target=/workspace,type=bind,consistency=cache", + "image": "mcr.microsoft.com/devcontainers/python:1-3.12-bookworm", + // Features to add to the dev container. More info: https://containers.dev/features. + "features": { + "ghcr.io/devcontainers/features/github-cli:1": {}, + "ghcr.io/devcontainers-contrib/features/poetry:2": {}, + "ghcr.io/devcontainers/features/python:1": { + "installTools": true, + "installJupyterlab": true, + "version": "3.12" + } + }, + // Use 'forwardPorts' to make a list of ports inside the container available locally. + "forwardPorts": [], + // Configure tool-specific properties. + "customizations": { + "vscode": { + "settings": { + "editor.formatOnSave": true, + "[python]": { + "editor.defaultFormatter": "charliermarsh.ruff" + }, + "editor.codeActionsOnSave": { + "source.organizeImports": true, + "source.fixAll": true + }, + "python.defaultInterpreterPath": "./.venv/bin/python" + }, + "extensions": [ + "ms-toolsai.jupyter", + "ms-toolsai.jupyter-keymap", + "ms-toolsai.jupyter-renderers", + "vscode-icons-team.vscode-icons", + "wayou.vscode-todo-highlight", + "timonwong.shellcheck", + "charliermarsh.ruff", + "ms-python.python" + ] + } + }, + // Uncomment to connect as an existing user other than the container default. More info: https://aka.ms/dev-containers-non-root. + "remoteUser": "vscode" +} \ No newline at end of file diff --git a/.devcontainer/post-create.sh b/.devcontainer/post-create.sh new file mode 100644 index 0000000..226b890 --- /dev/null +++ b/.devcontainer/post-create.sh @@ -0,0 +1,8 @@ +#!/usr/bin/env bash +set -e + +sudo chown vscode .venv || true + +poetry config virtualenvs.in-project true + +poetry install --with dev diff --git a/.gitignore b/.gitignore new file mode 100644 index 0000000..6769e21 --- /dev/null +++ b/.gitignore @@ -0,0 +1,160 @@ +# Byte-compiled / optimized / DLL files +__pycache__/ +*.py[cod] +*$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 + +# 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 + +# pdm +# Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control. +#pdm.lock +# pdm stores project-wide configurations in .pdm.toml, but it is recommended to not include it +# in version control. +# https://pdm.fming.dev/#use-with-ide +.pdm.toml + +# 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/ \ No newline at end of file diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 60f9f90..ba52824 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -1,44 +1,18 @@ repos: -- repo: https://github.com/psf/black - rev: 0a37888e79059018eef9293a724b14da59d3377a + - repo: https://github.com/astral-sh/ruff-pre-commit + # Ruff version. + rev: v0.2.1 hooks: - - id: black -- repo: https://github.com/pre-commit/pre-commit-hooks - rev: 848f775476419273bcb928a911170980f0124507 - hooks: - - id: trailing-whitespace - - id: end-of-file-fixer - - id: check-yaml - - id: check-added-large-files - - id: requirements-txt-fixer # Sorts entries in requirements.txt - - id: check-ast - - id: check-docstring-first - - id: check-merge-conflict - - id: end-of-file-fixer - - id: name-tests-test - args: [--pytest-test-first] - - id: trailing-whitespace -# - 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- ) + ]).reshape(1, -1) for kk in range(self.max_iter): current = tau_trace[kk, :] diff --git a/pyproject.toml b/pyproject.toml index eb08463..3da47f3 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,8 +1,30 @@ -[tool.ruff] -line-length = 100 +[tool.poetry] +name = "pylambertw" +version = "0.1.1" +description = "Python implementation of the Lambert W x F framework for analyzing skewed, heavy-tailed distribution with an sklearn interface and torch based maximum likelihood estimation (MLE)." +authors = ["Georg M. Goerg "] +homepage = "https://github.com/gmgeorg/pylambertw.git" -fix = true +[tool.poetry.dependencies] +python = ">=3.9,<3.13" +numpy = ">=1.0.1" +scipy = ">=1.6.0" +pandas = ">=1.0.0" +matplotlib = ">=3.3.0" +statsmodels = ">=0.12.0" +seaborn = ">=0.11.1" +tqdm = ">=4.62.3" +dataclasses = ">=0.6" +scikit-learn = ">=1.0.1" +torch = ">=2.0.1" +torchlambertw = { git = "https://github.com/gmgeorg/torchlambertw.git", rev = "v0.0.3" } + +[tool.poetry.group.dev.dependencies] +pytest = ">=6.1.1" +ruff = "^0.2.1" + +[build-system] +requires = ["poetry-core>=1.0.0"] +build-backend = "poetry.core.masonry.api" -[tool.ruff.per-file-ignores] -"setup.py" = ['E501'] # line length violations diff --git a/requirements.txt b/requirements.txt deleted file mode 100644 index c06d61a..0000000 --- a/requirements.txt +++ /dev/null @@ -1,12 +0,0 @@ -dataclasses>=0.6 -git+https://github.com/gmgeorg/torchlambertw.git -matplotlib>=3.3.0 -numpy>=1.0.1 -pandas>=1.0.0 -pytest>=6.1.1 -scikit-learn>=1.0.1 -scipy~=1.6.0 -seaborn>=0.11.1 -statsmodels>=0.12.0 -torch>=2.0.1 -tqdm>=4.62.3 diff --git a/setup.py b/setup.py deleted file mode 100644 index 2fbea8b..0000000 --- a/setup.py +++ /dev/null @@ -1,39 +0,0 @@ -from setuptools import find_packages, setup -import re - -_VERSION_FILE = "pylambertw/_version.py" -verstrline = open(_VERSION_FILE, "rt").read() -_VERSION = r"^__version__ = ['\"]([^'\"]*)['\"]" -mo = re.search(_VERSION, verstrline, re.M) -if mo: - verstr = mo.group(1) -else: - raise RuntimeError("Unable to find version string in %s." % (_VERSION_FILE,)) - -pkg_descr = """ -Python implementation of the Lambert W x F framework for analyzing skewed, heavy-tailed distribution -with an sklearn interface and torch based maximum likelihood estimation (MLE). -""" - -setup( - name="pylambertw", - version=verstr, - url="https://github.com/gmgeorg/pylambertw.git", - author="Georg M. Goerg", - author_email="im@gmge.org", - description=pkg_descr, - packages=find_packages(), - install_requires=[ - "numpy>=1.0.1", - "scipy~=1.6.0", - "pytest>=6.1.1", - "pandas>=1.0.0", - "matplotlib>=3.3.0", - "statsmodels>=0.12.0", - "seaborn>=0.11.1", - "tqdm>=4.46.1", - "dataclasses>=0.6", - "scikit-learn>=1.0.1", - "torchlambertw @ git+ssh://git@github.com/gmgeorg/torchlambertw.git#egg=torchlambertw-0.0.3", - ], -) From b3c3f09e3ead30a0ab410c200472ccfade752ac6 Mon Sep 17 00:00:00 2001 From: wolfyds Date: Wed, 10 Apr 2024 19:05:50 +0000 Subject: [PATCH 2/9] Fixed path for tests. --- .devcontainer/post-create.sh | 9 +- .pre-commit-config.yaml | 2 +- poetry.lock | 181 ++++++++++++++++++++++++++++++++++- pyproject.toml | 1 + 4 files changed, 188 insertions(+), 5 deletions(-) diff --git a/.devcontainer/post-create.sh b/.devcontainer/post-create.sh index 226b890..66183ab 100644 --- a/.devcontainer/post-create.sh +++ b/.devcontainer/post-create.sh @@ -1,8 +1,11 @@ #!/usr/bin/env bash set 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7fc9afc082acc794cc1be00d1029e323cd159d64 Mon Sep 17 00:00:00 2001 From: wolfyds Date: Wed, 10 Apr 2024 19:07:42 +0000 Subject: [PATCH 3/9] Reformated igmm file. --- pylambertw/igmm.py | 12 +++++++----- 1 file changed, 7 insertions(+), 5 deletions(-) diff --git a/pylambertw/igmm.py b/pylambertw/igmm.py index 07d54c8..8e0168e 100644 --- a/pylambertw/igmm.py +++ b/pylambertw/igmm.py @@ -216,11 +216,13 @@ def fit(self, data: np.ndarray): self._initialize_params(data) tau_trace = np.zeros(shape=(self.max_iter + 1, 3)) - tau_trace[0, :] = np.array([ - self.tau_init.loc, - self.tau_init.scale, - self.tau_init.lambertw_params.delta, - ]).reshape(1, -1) + tau_trace[0, :] = np.array( + [ + self.tau_init.loc, + self.tau_init.scale, + self.tau_init.lambertw_params.delta, + ] + ).reshape(1, -1) for kk in range(self.max_iter): current = tau_trace[kk, :] From 75a5b0fadea007f3f1469722b1569c821a9a5f6e Mon Sep 17 00:00:00 2001 From: wolfyds Date: Wed, 10 Apr 2024 19:11:10 +0000 Subject: [PATCH 4/9] Added poetry.lock to .gitignore. --- .devcontainer/devcontainer.json | 2 +- .gitignore | 4 +++- 2 files changed, 4 insertions(+), 2 deletions(-) diff --git a/.devcontainer/devcontainer.json b/.devcontainer/devcontainer.json index 4a9542c..1539605 100644 --- a/.devcontainer/devcontainer.json +++ b/.devcontainer/devcontainer.json @@ -5,7 +5,7 @@ "postCreateCommand": "bash .devcontainer/post-create.sh", "workspaceFolder": "/workspace", "workspaceMount": "source=${localWorkspaceFolder},target=/workspace,type=bind,consistency=cache", - "image": "mcr.microsoft.com/devcontainers/python:1-3.12-bookworm", + "image": "mcr.microsoft.com/devcontainers/python:1-3.12-bookworm", // Features to add to the dev container. More info: https://containers.dev/features. "features": { "ghcr.io/devcontainers/features/github-cli:1": {}, diff --git a/.gitignore b/.gitignore index 6769e21..bcc3d59 100644 --- a/.gitignore +++ b/.gitignore @@ -157,4 +157,6 @@ cython_debug/ # 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. 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- repo: https://github.com/astral-sh/ruff-pre-commit - # Ruff version. - rev: v0.2.1 +- repo: https://github.com/psf/black + rev: 0a37888e79059018eef9293a724b14da59d3377a hooks: - # Run the linter. - - id: ruff - # Run the formatter. - - id: ruff-format - - repo: local + - id: black +- repo: https://github.com/pre-commit/pre-commit-hooks + rev: 848f775476419273bcb928a911170980f0124507 + hooks: + - id: trailing-whitespace + - id: end-of-file-fixer + - id: check-yaml + - id: check-added-large-files + - id: requirements-txt-fixer # Sorts entries in requirements.txt + - id: check-ast + - id: check-docstring-first + - id: check-merge-conflict + - id: end-of-file-fixer + - id: name-tests-test + args: [--pytest-test-first] + - id: trailing-whitespace +# - repo: https://github.com/pre-commit/mirrors-mypy +# rev: v1.6.1 +# hooks: +# - id: mypy +# exclude: tests/ +- repo: https://github.com/pre-commit/mirrors-isort + rev: '32119baf69e913a72f2e1b1fbe0d56921b670ebb' # Use the revision sha / tag you want to point at + hooks: + - id: isort +- repo: local hooks: - - id: pytest - name: pytest - entry: ./.venv/bin/pytest pylambertw/tests + - id: run-unit-tests + name: Run unit tests + entry: npm run test language: system - type: [python] - pass_filenames: false - always_run: true \ No newline at end of file + stages: [push] +- repo: https://github.com/charliermarsh/ruff-pre-commit + rev: v0.0.183 + hooks: + - id: ruff +#- repo: https://github.com/pycqa/pydocstyle +# rev: 4.0.0 # pick a git hash / tag to point to + # hooks: + # - id: pydocstyle diff --git a/pyproject.toml b/pyproject.toml index 19d7496..cf80636 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -22,10 +22,8 @@ torchlambertw = { git = "https://github.com/gmgeorg/torchlambertw.git", rev = "v [tool.poetry.group.dev.dependencies] pytest = ">=6.1.1" -ruff = "^0.2.1" pre-commit = "^3.7.0" [build-system] requires = ["poetry-core>=1.0.0"] build-backend = "poetry.core.masonry.api" - From 3787937df083cb8d9ea958c509d1fa0438726af9 Mon Sep 17 00:00:00 2001 From: Matthew Brulhardt Date: Sat, 13 Apr 2024 19:50:07 -0400 Subject: [PATCH 7/9] Update python-app.yml --- .github/workflows/python-app.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/python-app.yml b/.github/workflows/python-app.yml index 7479843..c8b6b7f 100644 --- a/.github/workflows/python-app.yml +++ b/.github/workflows/python-app.yml @@ -37,9 +37,9 @@ jobs: - name: Lint with flake8 run: | # stop the build if there are Python syntax errors or undefined names - flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics + flake8 pylambertw --count --select=E9,F63,F7,F82 --show-source --statistics # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide - flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics --ignore=C901 + flake8 pylambertw --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics --ignore=C901 - name: Test with pytest run: | pytest From c7f9eec78e45465793f89610fc82088107ebeb46 Mon Sep 17 00:00:00 2001 From: Matthew Brulhardt Date: Sat, 13 Apr 2024 19:53:11 -0400 Subject: [PATCH 8/9] Update python-app.yml --- .github/workflows/python-app.yml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/.github/workflows/python-app.yml b/.github/workflows/python-app.yml index c8b6b7f..95744ae 100644 --- a/.github/workflows/python-app.yml +++ b/.github/workflows/python-app.yml @@ -37,9 +37,9 @@ jobs: - name: Lint with flake8 run: | # stop the build if there are Python syntax errors or undefined names - flake8 pylambertw --count --select=E9,F63,F7,F82 --show-source --statistics + poetry run flake8 pylambertw --count --select=E9,F63,F7,F82 --show-source --statistics # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide - flake8 pylambertw --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics --ignore=C901 + poetry run flake8 pylambertw --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics --ignore=C901 - name: Test with pytest run: | - pytest + poetry run pytest From 3b993d5382aa03baf726c97e46746e3e8b2880ee Mon Sep 17 00:00:00 2001 From: mwbrulhardt Date: Mon, 15 Apr 2024 13:06:25 +0000 Subject: [PATCH 9/9] Refactored dependencies to be in alphabetical order. --- .gitignore | 5 +++-- pyproject.toml | 14 +++++++------- 2 files changed, 10 insertions(+), 9 deletions(-) diff --git a/.gitignore b/.gitignore index bcc3d59..061c4f9 100644 --- a/.gitignore +++ b/.gitignore @@ -99,7 +99,7 @@ ipython_config.py # 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.lock # pdm # Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control. @@ -159,4 +159,5 @@ cython_debug/ # option (not recommended) you can uncomment the following to ignore the entire idea folder. #.idea/ -poetry.lock \ No newline at end of file +# Ruff +.ruff_cache/ diff --git a/pyproject.toml b/pyproject.toml index 6b81341..da08757 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -8,22 +8,22 @@ homepage = "https://github.com/gmgeorg/pylambertw.git" [tool.poetry.dependencies] python = "^3.9" +dataclasses = ">=0.6" +matplotlib = ">=3.3.0" numpy = ">=1.0.1" -scipy = ">=1.7.0" pandas = ">=1.0.0" -matplotlib = ">=3.3.0" -statsmodels = ">=0.12.0" -seaborn = ">=0.11.1" -tqdm = ">=4.62.3" -dataclasses = ">=0.6" scikit-learn = ">=1.0.1" +scipy = ">=1.7.0" +seaborn = ">=0.11.1" +statsmodels = ">=0.12.0" torch = ">=2.0.1" torchlambertw = { git = "https://github.com/gmgeorg/torchlambertw.git", rev = "v0.0.3" } +tqdm = ">=4.62.3" [tool.poetry.group.dev.dependencies] -pytest = ">=6.1.1" flake8 = "^7.0.0" pre-commit = "^3.7.0" +pytest = ">=6.1.1" ruff = "^0.3.7" [tool.ruff]