Merge pull request #5 from mwbrulhardt/main

Added poetry for setup and workflow

.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"
+}

.devcontainer/post-create.sh

@@ -0,0 +1,11 @@
+#!/usr/bin/env bash
+set -e
+
+# Setup poetry and install
+poetry config virtualenvs.in-project true
+poetry install --with dev
+
+# Setup and install pre-commit
+cd /workspace
+source .venv/bin/activate
+pre-commit install

.github/workflows/python-app.yml

@@ -23,17 +23,23 @@ jobs:
       uses: actions/setup-python@v3
       with:
         python-version: "3.10"
+
+    - name: Install poetry
+      uses: snok/install-poetry@v1
+      with:
+        version: 1.8.2
+        virtualenvs-create: true
+        virtualenvs-in-project: true
+
     - name: Install dependencies
-      run: |
-        python -m pip install --upgrade pip
-        pip install flake8 pytest
-        if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
+      run: poetry install --with dev
+
     - 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
+        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 . --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

.gitignore

@@ -0,0 +1,163 @@
+# 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/
+
+# Ruff
+.ruff_cache/

pylambertw/_version.py

@@ -1,3 +1,3 @@
 """Version."""
 
-__version__ = "0.0.3"
+__version__ = "0.0.4"

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, :]

pyproject.toml

@@ -1,8 +1,36 @@
+[tool.poetry]
+name = "pylambertw"
+version = "0.0.4"
+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 <im@gmge.org>"]
+homepage = "https://github.com/gmgeorg/pylambertw.git"
+
+[tool.poetry.dependencies]
+python = "^3.9"
+
+dataclasses = ">=0.6"
+matplotlib = ">=3.3.0"
+numpy = ">=1.0.1"
+pandas = ">=1.0.0"
+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]
+flake8 = "^7.0.0"
+pre-commit = "^3.7.0"
+pytest = ">=6.1.1"
+ruff = "^0.3.7"
+
 [tool.ruff]
 line-length = 100
 
 fix = true
 
-
-[tool.ruff.per-file-ignores]
-"setup.py" = ['E501']  # line length violations
+[build-system]
+requires = ["poetry-core>=1.0.0"]
+build-backend = "poetry.core.masonry.api"