diff --git a/.gitpod.yml b/.gitpod.yml index 7343f54d..e8ad6dd6 100644 --- a/.gitpod.yml +++ b/.gitpod.yml @@ -7,8 +7,7 @@ tasks: conda init bash && source ~/.bashrc conda env update -f conda-envs/environment-test.yml -p env conda activate /workspace/pymc-experimental/env - pip install -r requirements-dev.txt - pip install -e . + pip install -e ."[dev]" command: | conda init bash && echo "conda activate /workspace/pymc-experimental/env" >> ~/.bashrc && source ~/.bashrc diff --git a/.pylintrc b/.pylintrc deleted file mode 100644 index 952050ed..00000000 --- a/.pylintrc +++ /dev/null @@ -1,372 +0,0 @@ -[MASTER] -# Use multiple processes to speed up Pylint. -jobs=1 - -# Allow loading of arbitrary C extensions. Extensions are imported into the -# active Python interpreter and may run arbitrary code. -unsafe-load-any-extension=no - -# Allow optimization of some AST trees. This will activate a peephole AST -# optimizer, which will apply various small optimizations. For instance, it can -# be used to obtain the result of joining multiple strings with the addition -# operator. Joining a lot of strings can lead to a maximum recursion error in -# Pylint and this flag can prevent that. It has one side effect, the resulting -# AST will be different than the one from reality. -optimize-ast=no - -[MESSAGES CONTROL] - -# Only show warnings with the listed confidence levels. Leave empty to show -# all. Valid levels: HIGH, INFERENCE, INFERENCE_FAILURE, UNDEFINED -confidence= - -# Disable the message, report, category or checker with the given id(s). You -# can either give multiple identifiers separated by comma (,) or put this -# option multiple times (only on the command line, not in the configuration -# file where it should appear only once).You can also use "--disable=all" to -# disable everything first and then reenable specific checks. For example, if -# you want to run only the similarities checker, you can use "--disable=all -# --enable=similarities". If you want to run only the classes checker, but have -# no Warning level messages displayed, use"--disable=all --enable=classes -# --disable=W" -disable=all - -# Enable the message, report, category or checker with the given id(s). You can -# either give multiple identifier separated by comma (,) or put this option -# multiple time. See also the "--disable" option for examples. -enable=import-self, - reimported, - wildcard-import, - misplaced-future, - relative-import, - deprecated-module, - unpacking-non-sequence, - invalid-all-object, - undefined-all-variable, - used-before-assignment, - cell-var-from-loop, - global-variable-undefined, - dangerous-default-value, - # redefined-builtin, - redefine-in-handler, - unused-import, - unused-wildcard-import, - global-variable-not-assigned, - undefined-loop-variable, - global-statement, - global-at-module-level, - bad-open-mode, - redundant-unittest-assert, - boolean-datetime, - # unused-variable - - -[REPORTS] - -# Set the output format. Available formats are text, parseable, colorized, msvs -# (visual studio) and html. You can also give a reporter class, eg -# mypackage.mymodule.MyReporterClass. -output-format=parseable - -# Put messages in a separate file for each module / package specified on the -# command line instead of printing them on stdout. Reports (if any) will be -# written in a file name "pylint_global.[txt|html]". -files-output=no - -# Tells whether to display a full report or only the messages -reports=no - -# Python expression which should return a note less than 10 (10 is the highest -# note). You have access to the variables errors warning, statement which -# respectively contain the number of errors / warnings messages and the total -# number of statements analyzed. This is used by the global evaluation report -# (RP0004). -evaluation=10.0 - ((float(5 * error + warning + refactor + convention) / statement) * 10) - -[BASIC] - -# List of builtins function names that should not be used, separated by a comma -bad-functions=map,filter,input - -# Good variable names which should always be accepted, separated by a comma -good-names=i,j,k,ex,Run,_ - -# Bad variable names which should always be refused, separated by a comma -bad-names=foo,bar,baz,toto,tutu,tata - -# Colon-delimited sets of names that determine each other's naming style when -# the name regexes allow several styles. -name-group= - -# Include a hint for the correct naming format with invalid-name -include-naming-hint=yes - -# Regular expression matching correct method names -method-rgx=[a-z_][a-z0-9_]{2,30}$ - -# Naming hint for method names -method-name-hint=[a-z_][a-z0-9_]{2,30}$ - -# Regular expression matching correct function names -function-rgx=[a-z_][a-z0-9_]{2,30}$ - -# Naming hint for function names -function-name-hint=[a-z_][a-z0-9_]{2,30}$ - -# Regular expression matching correct module names -module-rgx=(([a-z_][a-z0-9_]*)|([A-Z][a-zA-Z0-9]+))$ - -# Naming hint for module names -module-name-hint=(([a-z_][a-z0-9_]*)|([A-Z][a-zA-Z0-9]+))$ - -# Regular expression matching correct attribute names -attr-rgx=[a-z_][a-z0-9_]{2,30}$ - -# Naming hint for attribute names -attr-name-hint=[a-z_][a-z0-9_]{2,30}$ - -# Regular expression matching correct class attribute names -class-attribute-rgx=([A-Za-z_][A-Za-z0-9_]{2,30}|(__.*__))$ - -# Naming hint for class attribute names -class-attribute-name-hint=([A-Za-z_][A-Za-z0-9_]{2,30}|(__.*__))$ - -# Regular expression matching correct constant names -const-rgx=(([A-Z_][A-Z0-9_]*)|(__.*__))$ - -# Naming hint for constant names -const-name-hint=(([A-Z_][A-Z0-9_]*)|(__.*__))$ - -# Regular expression matching correct class names -class-rgx=[A-Z_][a-zA-Z0-9]+$ - -# Naming hint for class names -class-name-hint=[A-Z_][a-zA-Z0-9]+$ - -# Regular expression matching correct argument names -argument-rgx=[a-z_][a-z0-9_]{2,30}$ - -# Naming hint for argument names -argument-name-hint=[a-z_][a-z0-9_]{2,30}$ - -# Regular expression matching correct inline iteration names -inlinevar-rgx=[A-Za-z_][A-Za-z0-9_]*$ - -# Naming hint for inline iteration names -inlinevar-name-hint=[A-Za-z_][A-Za-z0-9_]*$ - -# Regular expression matching correct variable names -variable-rgx=[a-z_][a-z0-9_]{2,30}$ - -# Naming hint for variable names -variable-name-hint=[a-z_][a-z0-9_]{2,30}$ - -# Regular expression which should only match function or class names that do -# not require a docstring. -no-docstring-rgx=^_ - -# Minimum line length for functions/classes that require docstrings, shorter -# ones are exempt. -docstring-min-length=-1 - - -[ELIF] - -# Maximum number of nested blocks for function / method body -max-nested-blocks=5 - - -[FORMAT] - -# Maximum number of characters on a single line. -max-line-length=100 - -# Regexp for a line that is allowed to be longer than the limit. -ignore-long-lines=^\s*(# )??$ - -# Allow the body of an if to be on the same line as the test if there is no -# else. -single-line-if-stmt=no - -# List of optional constructs for which whitespace checking is disabled. `dict- -# separator` is used to allow tabulation in dicts, etc.: {1 : 1,\n222: 2}. -# `trailing-comma` allows a space between comma and closing bracket: (a, ). -# `empty-line` allows space-only lines. -no-space-check=trailing-comma,dict-separator - -# Maximum number of lines in a module -max-module-lines=1000 - -# String used as indentation unit. This is usually " " (4 spaces) or "\t" (1 -# tab). -indent-string=' ' - -# Number of spaces of indent required inside a hanging or continued line. -indent-after-paren=4 - -# Expected format of line ending, e.g. empty (any line ending), LF or CRLF. -expected-line-ending-format= - - -[LOGGING] - -# Logging modules to check that the string format arguments are in logging -# function parameter format -logging-modules=logging - - -[MISCELLANEOUS] - -# List of note tags to take in consideration, separated by a comma. -notes=FIXME,XXX,TODO - - -[SIMILARITIES] - -# Minimum lines number of a similarity. -min-similarity-lines=4 - -# Ignore comments when computing similarities. -ignore-comments=yes - -# Ignore docstrings when computing similarities. -ignore-docstrings=yes - -# Ignore imports when computing similarities. -ignore-imports=no - - -[SPELLING] - -# Spelling dictionary name. Available dictionaries: none. To make it working -# install python-enchant package. -spelling-dict= - -# List of comma separated words that should not be checked. -spelling-ignore-words= - -# A path to a file that contains private dictionary; one word per line. -spelling-private-dict-file= - -# Tells whether to store unknown words to indicated private dictionary in -# --spelling-private-dict-file option instead of raising a message. -spelling-store-unknown-words=no - - -[TYPECHECK] - -# Tells whether missing members accessed in mixin class should be ignored. A -# mixin class is detected if its name ends with "mixin" (case insensitive). -ignore-mixin-members=yes - -# List of module names for which member attributes should not be checked -# (useful for modules/projects where namespaces are manipulated during runtime -# and thus existing member attributes cannot be deduced by static analysis. It -# supports qualified module names, as well as Unix pattern matching. -ignored-modules= - -# List of classes names for which member attributes should not be checked -# (useful for classes with attributes dynamically set). This supports can work -# with qualified names. -ignored-classes= - -# List of members which are set dynamically and missed by pylint inference -# system, and so shouldn't trigger E1101 when accessed. Python regular -# expressions are accepted. -generated-members= - - -[VARIABLES] - -# Tells whether we should check for unused import in __init__ files. -init-import=no - -# A regular expression matching the name of dummy variables (i.e. expectedly -# not used). -dummy-variables-rgx=_$|dummy - -# List of additional names supposed to be defined in builtins. Remember that -# you should avoid to define new builtins when possible. -additional-builtins= - -# List of strings which can identify a callback function by name. A callback -# name must start or end with one of those strings. -callbacks=cb_,_cb - - -[CLASSES] - -# List of method names used to declare (i.e. assign) instance attributes. -defining-attr-methods=__init__,__new__,setUp - -# List of valid names for the first argument in a class method. -valid-classmethod-first-arg=cls - -# List of valid names for the first argument in a metaclass class method. -valid-metaclass-classmethod-first-arg=mcs - -# List of member names, which should be excluded from the protected access -# warning. -exclude-protected=_asdict,_fields,_replace,_source,_make - - -[DESIGN] - -# Maximum number of arguments for function / method -max-args=5 - -# Argument names that match this expression will be ignored. Default to name -# with leading underscore -ignored-argument-names=_.* - -# Maximum number of locals for function / method body -max-locals=15 - -# Maximum number of return / yield for function / method body -max-returns=6 - -# Maximum number of branch for function / method body -max-branches=12 - -# Maximum number of statements in function / method body -max-statements=50 - -# Maximum number of parents for a class (see R0901). -max-parents=7 - -# Maximum number of attributes for a class (see R0902). -max-attributes=7 - -# Minimum number of public methods for a class (see R0903). -min-public-methods=2 - -# Maximum number of public methods for a class (see R0904). -max-public-methods=20 - -# Maximum number of boolean expressions in a if statement -max-bool-expr=5 - - -[IMPORTS] - -# Deprecated modules which should not be used, separated by a comma -deprecated-modules=optparse - -# Create a graph of every (i.e. internal and external) dependencies in the -# given file (report RP0402 must not be disabled) -import-graph= - -# Create a graph of external dependencies in the given file (report RP0402 must -# not be disabled) -ext-import-graph= - -# Create a graph of internal dependencies in the given file (report RP0402 must -# not be disabled) -int-import-graph= - - -[EXCEPTIONS] - -# Exceptions that will emit a warning when being caught. Defaults to -# "Exception" -overgeneral-exceptions=Exception diff --git a/.readthedocs.yaml b/.readthedocs.yaml index 4002dca2..fd04542a 100644 --- a/.readthedocs.yaml +++ b/.readthedocs.yaml @@ -9,10 +9,10 @@ build: python: install: - - requirements: requirements-docs.txt - - requirements: requirements.txt - method: pip path: . + extra_requirements: + - docs sphinx: fail_on_warning: false diff --git a/MANIFEST.in b/MANIFEST.in deleted file mode 100644 index 9b37dee9..00000000 --- a/MANIFEST.in +++ /dev/null @@ -1,4 +0,0 @@ -include requirements*.txt -include *.md *.rst -include LICENSE -include pymc_experimental/version.txt diff --git a/pymc_experimental/__init__.py b/pymc_experimental/__init__.py index d519ff3d..1541e677 100644 --- a/pymc_experimental/__init__.py +++ b/pymc_experimental/__init__.py @@ -17,7 +17,8 @@ from pymc_experimental.inference.fit import fit from pymc_experimental.model.marginal_model import MarginalModel from pymc_experimental.model.model_api import as_model -from pymc_experimental.version import __version__ + +__version__ = "1.1.0" _log = logging.getLogger("pmx") @@ -36,5 +37,4 @@ "fit", "MarginalModel", "as_model", - "__version__", ] diff --git a/pymc_experimental/version.py b/pymc_experimental/version.py deleted file mode 100644 index cc0aacca..00000000 --- a/pymc_experimental/version.py +++ /dev/null @@ -1,11 +0,0 @@ -import os - - -def get_version(): - version_file = os.path.join(os.path.dirname(os.path.abspath(__file__)), "version.txt") - with open(version_file) as f: - version = f.read().strip() - return version - - -__version__ = get_version() diff --git a/pymc_experimental/version.txt b/pymc_experimental/version.txt deleted file mode 100644 index 17e51c38..00000000 --- a/pymc_experimental/version.txt +++ /dev/null @@ -1 +0,0 @@ -0.1.1 diff --git a/pyproject.toml b/pyproject.toml index 1fb70104..55b7b5c5 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,3 +1,72 @@ +[build-system] +requires = ["setuptools>=61.0"] +build-backend = "setuptools.build_meta" + +[project] +name = "pymc_experimental" +authors = [ + {name = "PyMC Developers", email = "pymc.devs@gmail.com"}, +] +description = "A home for new additions to PyMC, which may include unusual probability distributions, advanced model fitting algorithms, or any code that may be inappropriate to include in the pymc repository, but may want to be made available to users." +classifiers = [ + "Development Status :: 5 - Production/Stable", + "Programming Language :: Python", + "Programming Language :: Python :: 3", + "Programming Language :: Python :: 3.10", + "Programming Language :: Python :: 3.11", + "Programming Language :: Python :: 3.12", + "License :: OSI Approved :: Apache Software License", + "Intended Audience :: Science/Research", + "Topic :: Scientific/Engineering", + "Topic :: Scientific/Engineering :: Mathematics", + "Operating System :: OS Independent", +] +readme = "README.md" +requires-python = ">=3.10" +keywords = [ + "probability", + "machine learning", + "statistics", + "mcmc", + "sampling", + "bayesian", +] +license = {file = "LICENSE"} +dynamic = ["version"] # specify the version in the __init__.py file +dependencies = [ + "pymc>=5.16.1", + "scikit-learn", +] + +[project.optional-dependencies] +dev = [ + "pytest>=6.0", + "dask[all]", + "blackjax>1.0.0", + "statsmodels", +] +docs = [ + "nbsphinx>=0.4.2", + "pydata-sphinx-theme>=0.6.3", + "sphinx>=4.0", + "pymc-sphinx-theme@git+https://github.com/pymc-devs/pymc-sphinx-theme", +] + +[project.urls] +Documentation = "https://www.pymc.io/projects/experimental/" +Repository = "https://github.com/pymc-devs/pymc-experimental.git" +Issues = "https://github.com/pymc-devs/pymc-experimental/issues" + +[tool.setuptools.packages.find] +where = ["."] +include = ["pymc_experimental"] +exclude = ["tests", "notebooks"] +# Additional install requirements for running tests +namespaces = false + +[tool.setuptools.dynamic] +version = {attr = "pymc_experimental.__version__"} + [tool.pytest.ini_options] minversion = "6.0" xfail_strict = true diff --git a/requirements-dev.txt b/requirements-dev.txt deleted file mode 100644 index a28518d8..00000000 --- a/requirements-dev.txt +++ /dev/null @@ -1,5 +0,0 @@ -dask[all] -blackjax - -# Used as benchmark for statespace models -statsmodels diff --git a/requirements-docs.txt b/requirements-docs.txt deleted file mode 100644 index 185288a8..00000000 --- a/requirements-docs.txt +++ /dev/null @@ -1,4 +0,0 @@ -nbsphinx>=0.4.2 -pydata-sphinx-theme>=0.6.3 -sphinx>=4 -git+https://github.com/pymc-devs/pymc-sphinx-theme diff --git a/requirements.txt b/requirements.txt deleted file mode 100644 index a7141a82..00000000 --- a/requirements.txt +++ /dev/null @@ -1,2 +0,0 @@ -pymc>=5.16.1 -scikit-learn diff --git a/setup.py b/setup.py deleted file mode 100644 index 404e0411..00000000 --- a/setup.py +++ /dev/null @@ -1,96 +0,0 @@ -# Copyright 2022 The PyMC Developers -# -# Licensed under the Apache License, Version 2.0 (the "License"); -# you may not use this file except in compliance with the License. -# You may obtain a copy of the License at -# -# http://www.apache.org/licenses/LICENSE-2.0 -# -# Unless required by applicable law or agreed to in writing, software -# distributed under the License is distributed on an "AS IS" BASIS, -# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -# See the License for the specific language governing permissions and -# limitations under the License. - -import itertools -import os - -from codecs import open -from os.path import dirname, join, realpath - -from setuptools import find_packages, setup - -DISTNAME = "pymc-experimental" -DESCRIPTION = "A home for new additions to PyMC, which may include unusual probability distribitions, advanced model fitting algorithms, or any code that may be inappropriate to include in the pymc repository, but may want to be made available to users." -AUTHOR = "PyMC Developers" -AUTHOR_EMAIL = "pymc.devs@gmail.com" -URL = "http://github.com/pymc-devs/pymc-experimental" -LICENSE = "Apache License, Version 2.0" - -classifiers = [ - "Development Status :: 5 - Production/Stable", - "Programming Language :: Python", - "Programming Language :: Python :: 3", - "Programming Language :: Python :: 3.10", - "Programming Language :: Python :: 3.11", - "Programming Language :: Python :: 3.12", - "License :: OSI Approved :: Apache Software License", - "Intended Audience :: Science/Research", - "Topic :: Scientific/Engineering", - "Topic :: Scientific/Engineering :: Mathematics", - "Operating System :: OS Independent", -] - -PROJECT_ROOT = dirname(realpath(__file__)) - -# Get the long description from the README file -with open(join(PROJECT_ROOT, "README.md"), encoding="utf-8") as buff: - LONG_DESCRIPTION = buff.read() - -REQUIREMENTS_FILE = join(PROJECT_ROOT, "requirements.txt") -DEV_REQUIREMENTS_FILE = join(PROJECT_ROOT, "requirements-dev.txt") - -with open(REQUIREMENTS_FILE) as f: - install_reqs = f.read().splitlines() - - -with open(DEV_REQUIREMENTS_FILE) as f: - dev_install_reqs = f.read().splitlines() - - -extras_require = dict( - dask_histogram=["dask[complete]", "xhistogram"], - histogram=["xhistogram"], -) -extras_require["complete"] = sorted(set(itertools.chain.from_iterable(extras_require.values()))) -extras_require["dev"] = dev_install_reqs - - -def read_version(): - here = os.path.abspath(os.path.dirname(__file__)) - with open(os.path.join(here, "pymc_experimental", "version.txt")) as f: - version = f.read().strip() - return version - - -if __name__ == "__main__": - setup( - name="pymc-experimental", - version=read_version(), - maintainer=AUTHOR, - maintainer_email=AUTHOR_EMAIL, - description=DESCRIPTION, - license=LICENSE, - url=URL, - long_description=LONG_DESCRIPTION, - long_description_content_type="text/markdown", - packages=find_packages(), - # because of an upload-size limit by PyPI, we're temporarily removing docs from the tarball. - # Also see MANIFEST.in - # package_data={'docs': ['*']}, - include_package_data=True, - classifiers=classifiers, - python_requires=">=3.10", - install_requires=install_reqs, - extras_require=extras_require, - ) diff --git a/setupegg.py b/setupegg.py deleted file mode 100755 index 168c05b9..00000000 --- a/setupegg.py +++ /dev/null @@ -1,21 +0,0 @@ -# Copyright 2020 The PyMC Developers -# -# Licensed under the Apache License, Version 2.0 (the "License"); -# you may not use this file except in compliance with the License. -# You may obtain a copy of the License at -# -# http://www.apache.org/licenses/LICENSE-2.0 -# -# Unless required by applicable law or agreed to in writing, software -# distributed under the License is distributed on an "AS IS" BASIS, -# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -# See the License for the specific language governing permissions and -# limitations under the License. - -#!/usr/bin/env python -""" -A setup.py script to use setuptools, which gives egg goodness, etc. -""" - -with open("setup.py") as s: - exec(s.read())