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In the near future, more dashboards will be added to this repo +This project brings dashboards to ArviZ enabling users to compare different visualizations in the +same view and interact with them. ## Installation + +### Contributor installation + +We will use `mamba` to create a virtual environment where we will install a development version of +ArviZ Dashboard. The first step is to follow the instructions here +[https://github.com/conda-forge/miniforge#mambaforge](https://github.com/conda-forge/miniforge#mambaforge) +to install the correct version of `mamba` for your operating system. **Note** that if you have +`conda` installed already, you can exchange the command `mamba` for `conda` with the same results. + +```bash +mamba create --name arviz-dashboard pip python +mamba activate arviz-dashboard ``` -git clone the REPO + +Once the virtual environment has been created, and you have activated it with the above commands, +you can install the development requirements for `arviz_dashboard` with the following commands. + +```bash +git clone the https://github.com/arviz-devs/arviz_dashboard cd arviz_dashboard -pip install -e . +pip install --editable .[dev,examples] +``` + +### Contributor installation test + +TBD + +```bash +pytest ``` ## Usage -Dashboard usually includes multiple visualizations with different purposes. If you have any problems with certain visualization, you can find more explanations for the ArviZ visualizations in [ArvZ](https://arviz-devs.github.io/arviz/examples/index.html) and [Bayesian Modeling and Computation in Python](https://bayesiancomputationbook.com/welcome.html) +Dashboard usually includes multiple visualizations with different purposes. If you have any problems +with certain visualization, you can find more explanations for the ArviZ visualizations in +[ArvZ](https://arviz-devs.github.io/arviz/examples/index.html) and +[Bayesian Modeling and Computation in Python](https://bayesiancomputationbook.com/welcome.html) ## Sponsors -[![NumFOCUS](https://www.numfocus.org/wp-content/uploads/2017/07/NumFocus_LRG.png)](https://numfocus.org) \ No newline at end of file + +[![NumFOCUS](https://www.numfocus.org/wp-content/uploads/2017/07/NumFocus_LRG.png)](https://numfocus.org) diff --git a/pyproject.toml b/pyproject.toml new file mode 100644 index 0000000..762fe56 --- /dev/null +++ b/pyproject.toml @@ -0,0 +1,86 @@ +[build-system] +build-backend = "hatchling.build" +requires = ["hatchling"] + +[project] +authors = [{name = "arviz-devs"}] +classifiers = [ + "Development Status :: 1 - Planning", + "Intended Audience :: Science/Research", + "Intended Audience :: Education", + "License :: OSI Approved :: Apache Software License", + "Programming Language :: Python", + "Programming Language :: Python :: 3", + "Programming Language :: Python :: 3.9", + "Programming Language :: Python :: 3.10", + "Programming Language :: Python :: 3.11", + "Topic :: Scientific/Engineering", + "Topic :: Scientific/Engineering :: Visualization", + "Topic :: Scientific/Engineering :: Mathematics", +] +dependencies = ["arviz", "jupyterlab", "panel"] +description = "Bayesian Dashboards built on top of Panel" +dynamic = ["version"] +keywords = [] +license = {file = "LICENSE.txt"} +maintainers = [] +name = "arviz_dashboard" +readme = {file = "README.md", content-type = "text/markdown"} +requires-python = ">3.9" + +[project.optional-dependencies] +dev = [ + # Automation + "pre-commit", + + # Python code formatting + "absolufy-imports", # use only absolute imports, no `from .module import method` + "black", # code formatting + "isort", # sort imports + + # Python code linting + "flake8", + "flake8-builtins", # ensure python builtins are not used as variables + "flake8-debugger", # remove ipdb or pdb statements + "flake8-eradicate", # remove unused code + "flake8-docstrings", # ensure docstrings exist + "Flake8-pyproject", # allow configs for flake8 in the pyproject.toml file + "pycln", # remove unused import statements + "ruff", # lint python code + + # Python code testing + "pytest", + "pytest-cov", + + # Python type checking + "pyre-check", + + # Python docstring style checking + "pydocstyle", + + # Markdown code formatting + "mdformat", + "mdformat-myst", +] +examples = ["pymc"] + +[project.urls] +"Bug Tracker" = "https://github.com/arviz-devs/arviz_dashboard/issues" +"Homepage" = "https://github.com/arviz-devs/arviz_dashboard" +"Source Code" = "https://github.com/arviz-devs/arviz_dashboard" + +[tool.hatch.version] +path = "src/arviz_dashboard/__init__.py" + +[tool.flake8] +ignore = ["D100"] +max-line-length = 100 +per-file-ignores = ["__init__.py:D104"] + +[tool.isort] +force_grid_wrap = 0 +include_trailing_comma = true +line_length = 100 +multi_line_output = 3 +profile = "black" +use_parentheses = true diff --git a/requirements.txt b/requirements.txt deleted file mode 100644 index b24cf97..0000000 --- a/requirements.txt +++ /dev/null @@ -1,3 +0,0 @@ -arviz -jupyterlab -panel < 1.0.0 diff --git a/setup.py b/setup.py deleted file mode 100644 index c636398..0000000 --- a/setup.py +++ /dev/null @@ -1,62 +0,0 @@ -import codecs -import os -import re - -import setuptools -from setuptools import find_packages, setup -from setuptools.command.develop import develop -from setuptools.command.install import install - -PROJECT_ROOT = os.path.dirname(os.path.realpath(__file__)) -REQUIREMENTS_FILE = os.path.join(PROJECT_ROOT, "requirements.txt") -README_FILE = os.path.join(PROJECT_ROOT, "README.md") -VERSION_FILE = os.path.join(PROJECT_ROOT, "arviz_dashboard", "__init__.py") - - -def get_requirements(): - with codecs.open(REQUIREMENTS_FILE) as buff: - return buff.read().splitlines() - - -def get_long_description(): - with codecs.open(README_FILE, "rt") as buff: - return buff.read() - - -def get_version(): - lines = open(VERSION_FILE, "rt").readlines() - version_regex = r"^__version__ = ['\"]([^'\"]*)['\"]" - for line in lines: - mo = re.search(version_regex, line, re.M) - if mo: - return mo.group(1) - raise RuntimeError("Unable to find version in %s." % (VERSION_FILE,)) - - -setup( - name="arviz_dashboard", - license="Apache-2.0", - version=get_version(), - description="Bayesian Dashboards built on top of Panel", - author="ArviZ Developers", - url="http://github.com/arviz-devs/arviz_dashboard", - packages=find_packages(), - install_requires=get_requirements(), - long_description=get_long_description(), - long_description_content_type="text/markdown", - include_package_data=True, - classifiers=[ - "Development Status :: 1 - Planning", - "Intended Audience :: Science/Research", - "Intended Audience :: Education", - "License :: OSI Approved :: Apache Software License", - "Programming Language :: Python", - "Programming Language :: Python :: 3", - "Programming Language :: Python :: 3.6", - "Programming Language :: Python :: 3.7", - "Programming Language :: Python :: 3.8", - "Topic :: Scientific/Engineering", - "Topic :: Scientific/Engineering :: Visualization", - "Topic :: Scientific/Engineering :: Mathematics", - ], -) diff --git a/arviz_dashboard/__init__.py b/src/arviz_dashboard/__init__.py similarity index 100% rename from arviz_dashboard/__init__.py rename to src/arviz_dashboard/__init__.py diff --git a/arviz_dashboard/dashboards.py b/src/arviz_dashboard/dashboards.py similarity index 100% rename from arviz_dashboard/dashboards.py rename to src/arviz_dashboard/dashboards.py diff --git a/arviz_dashboard/elpd.py b/src/arviz_dashboard/elpd.py similarity index 98% rename from arviz_dashboard/elpd.py rename to src/arviz_dashboard/elpd.py index a7e7959..81da3ca 100644 --- a/arviz_dashboard/elpd.py +++ b/src/arviz_dashboard/elpd.py @@ -124,8 +124,8 @@ def get_stacked_bar_plot(model_selection1, model_selection2, thre_slider, ic_gro p = figure( x_range=standard, - plot_height=300, - plot_width=200, + height=300, + width=200, title="Summary of Observations", tooltips=tooltips, toolbar_location=None, diff --git a/arviz_dashboard/forest.py b/src/arviz_dashboard/forest.py similarity index 100% rename from arviz_dashboard/forest.py rename to src/arviz_dashboard/forest.py diff --git a/arviz_dashboard/marginal/__init__.py b/src/arviz_dashboard/marginal/__init__.py similarity index 100% rename from arviz_dashboard/marginal/__init__.py rename to src/arviz_dashboard/marginal/__init__.py diff --git a/arviz_dashboard/marginal/one_d.py b/src/arviz_dashboard/marginal/one_d.py similarity index 100% rename from arviz_dashboard/marginal/one_d.py rename to src/arviz_dashboard/marginal/one_d.py diff --git a/arviz_dashboard/plots.py b/src/arviz_dashboard/plots.py similarity index 100% rename from arviz_dashboard/plots.py rename to src/arviz_dashboard/plots.py diff --git a/arviz_dashboard/ppc.py b/src/arviz_dashboard/ppc.py similarity index 100% rename from arviz_dashboard/ppc.py rename to src/arviz_dashboard/ppc.py diff --git a/arviz_dashboard/trace/__init__.py b/src/arviz_dashboard/trace/__init__.py similarity index 100% rename from arviz_dashboard/trace/__init__.py rename to src/arviz_dashboard/trace/__init__.py diff --git a/arviz_dashboard/trace/trace.py b/src/arviz_dashboard/trace/trace.py similarity index 100% rename from arviz_dashboard/trace/trace.py rename to src/arviz_dashboard/trace/trace.py diff --git a/arviz_dashboard/widgets.py b/src/arviz_dashboard/widgets.py similarity index 100% rename from arviz_dashboard/widgets.py rename to src/arviz_dashboard/widgets.py