From 2385bf416e3608c37e89ca5218a356d0a880576e Mon Sep 17 00:00:00 2001 From: theorashid Date: Sun, 28 Jul 2024 18:23:48 +0100 Subject: [PATCH 01/20] do not need pylintrc since we have ruff --- .pylintrc | 372 ------------------------------------------------------ 1 file changed, 372 deletions(-) delete mode 100644 .pylintrc diff --git a/.pylintrc b/.pylintrc deleted file mode 100644 index 952050ed8..000000000 --- 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 From e967ff089fdaf98b87514eee7051bc5037544253 Mon Sep 17 00:00:00 2001 From: theorashid Date: Sun, 28 Jul 2024 19:30:30 +0100 Subject: [PATCH 02/20] simplify project build and package installation from setup.py to pyproject, including the versioning using __version__ attribute --- pymc_extras/__init__.py | 11 +++++++ pyproject.toml | 69 +++++++++++++++++++++++++++++++++++++++++ requirements-dev.txt | 5 --- requirements-docs.txt | 4 --- setupegg.py | 21 ------------- 5 files changed, 80 insertions(+), 30 deletions(-) delete mode 100644 requirements-dev.txt delete mode 100644 requirements-docs.txt delete mode 100755 setupegg.py diff --git a/pymc_extras/__init__.py b/pymc_extras/__init__.py index 0ff07bd65..8589820a3 100644 --- a/pymc_extras/__init__.py +++ b/pymc_extras/__init__.py @@ -31,3 +31,14 @@ if len(_log.handlers) == 0: handler = logging.StreamHandler() _log.addHandler(handler) + + +__all__ = [ + "distributions", + "gp", + "statespace", + "utils", + "fit", + "MarginalModel", + "as_model", +] diff --git a/pyproject.toml b/pyproject.toml index df7752cb1..7cc3d7852 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 a28518d8e..000000000 --- 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 185288a8b..000000000 --- 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/setupegg.py b/setupegg.py deleted file mode 100755 index 168c05b99..000000000 --- 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()) From e2c02ba32eecaf23e68413b3cacf6de83b9fa9b8 Mon Sep 17 00:00:00 2001 From: theorashid Date: Sun, 28 Jul 2024 21:04:01 +0100 Subject: [PATCH 03/20] remove .txt files from rtd and gitpod --- .gitpod.yml | 2 +- .readthedocs.yaml | 4 ++-- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/.gitpod.yml b/.gitpod.yml index d18bb225a..c9ece7559 100644 --- a/.gitpod.yml +++ b/.gitpod.yml @@ -8,7 +8,7 @@ tasks: conda env update -f conda-envs/environment-test.yml -p env conda activate /workspace/pymc-extras/env pip install -r requirements-dev.txt - pip install -e . + pip install -e ."[dev]" command: | conda init bash && echo "conda activate /workspace/pymc-extras/env" >> ~/.bashrc && source ~/.bashrc diff --git a/.readthedocs.yaml b/.readthedocs.yaml index 4002dca20..fd04542aa 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 From c5800f77812c5680ed86a4bd5ce18630622e0cbf Mon Sep 17 00:00:00 2001 From: Jesse Grabowski Date: Mon, 5 May 2025 11:49:09 +0800 Subject: [PATCH 04/20] rename experimental -> extras --- pyproject.toml | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/pyproject.toml b/pyproject.toml index 7cc3d7852..a65c90d64 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -3,7 +3,7 @@ requires = ["setuptools>=61.0"] build-backend = "setuptools.build_meta" [project] -name = "pymc_experimental" +name = "pymc_extras" authors = [ {name = "PyMC Developers", email = "pymc.devs@gmail.com"}, ] @@ -53,19 +53,19 @@ docs = [ ] [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" +Documentation = "https://www.pymc.io/projects/extras/" +Repository = "https://github.com/pymc-devs/pymc-extras.git" +Issues = "https://github.com/pymc-devs/pymc-extras/issues" [tool.setuptools.packages.find] where = ["."] -include = ["pymc_experimental"] +include = ["pymc_extras"] exclude = ["tests", "notebooks"] # Additional install requirements for running tests namespaces = false [tool.setuptools.dynamic] -version = {attr = "pymc_experimental.__version__"} +version = {attr = "pymc_extras.__version__"} [tool.pytest.ini_options] minversion = "6.0" From fb98b48b96b0571da4fbc184ec569660bcf8c89b Mon Sep 17 00:00:00 2001 From: Jesse Grabowski Date: Mon, 5 May 2025 11:58:48 +0800 Subject: [PATCH 05/20] Adjustment to requirements --- pyproject.toml | 17 +++++++++++------ 1 file changed, 11 insertions(+), 6 deletions(-) diff --git a/pyproject.toml b/pyproject.toml index a65c90d64..54f761cef 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -3,11 +3,11 @@ requires = ["setuptools>=61.0"] build-backend = "setuptools.build_meta" [project] -name = "pymc_extras" +name = "pymc-extras" 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." +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." classifiers = [ "Development Status :: 5 - Production/Stable", "Programming Language :: Python", @@ -34,15 +34,20 @@ keywords = [ license = {file = "LICENSE"} dynamic = ["version"] # specify the version in the __init__.py file dependencies = [ - "pymc>=5.16.1", + "pymc>=5.21.1", "scikit-learn", + "better-optimize" ] [project.optional-dependencies] +complete = [ + "dask[complete]<2025.1.1", + "xhistogram", +] dev = [ "pytest>=6.0", - "dask[all]", - "blackjax>1.0.0", + "dask[all]<2025.1.1", + "blackjax", "statsmodels", ] docs = [ @@ -53,7 +58,7 @@ docs = [ ] [project.urls] -Documentation = "https://www.pymc.io/projects/extras/" +Documentation = "https://pymc-extras.readthedocs.io/" Repository = "https://github.com/pymc-devs/pymc-extras.git" Issues = "https://github.com/pymc-devs/pymc-extras/issues" From 4f61f120c44bebde6789a3da47fdefc8431417cf Mon Sep 17 00:00:00 2001 From: Jesse Grabowski Date: Mon, 5 May 2025 12:01:31 +0800 Subject: [PATCH 06/20] remove __all__ --- pymc_extras/__init__.py | 11 ----------- 1 file changed, 11 deletions(-) diff --git a/pymc_extras/__init__.py b/pymc_extras/__init__.py index 8589820a3..0ff07bd65 100644 --- a/pymc_extras/__init__.py +++ b/pymc_extras/__init__.py @@ -31,14 +31,3 @@ if len(_log.handlers) == 0: handler = logging.StreamHandler() _log.addHandler(handler) - - -__all__ = [ - "distributions", - "gp", - "statespace", - "utils", - "fit", - "MarginalModel", - "as_model", -] From e7c41fcca83a07a9e776646c24091fb40ead7662 Mon Sep 17 00:00:00 2001 From: Jesse Grabowski Date: Mon, 5 May 2025 12:13:04 +0800 Subject: [PATCH 07/20] Adjust setup.py --- setup.py | 65 +------------------------------------------------------- 1 file changed, 1 insertion(+), 64 deletions(-) diff --git a/setup.py b/setup.py index c7bd5945e..f7f434a57 100644 --- a/setup.py +++ b/setup.py @@ -12,60 +12,12 @@ # 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-extras" -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-extras" -LICENSE = "Apache-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", - "Programming Language :: Python :: 3.13", - "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]<2025.1.1", "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__)) @@ -78,20 +30,5 @@ def read_version(): setup( name="pymc-extras", 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, + packages=find_packages(exclude=["tests*"]), ) From e7ff2740bca4b42b0593d974d73bd75422a99b7f Mon Sep 17 00:00:00 2001 From: Jesse Grabowski Date: Mon, 5 May 2025 12:36:22 +0800 Subject: [PATCH 08/20] Add numpy to build-system requires --- pyproject.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pyproject.toml b/pyproject.toml index 54f761cef..ec41ac231 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,5 +1,5 @@ [build-system] -requires = ["setuptools>=61.0"] +requires = ["setuptools>=61.0", "numpy"] build-backend = "setuptools.build_meta" [project] From a3daeca4528b9f9b83dcb6dd65e6d02f933718a2 Mon Sep 17 00:00:00 2001 From: Jesse Grabowski Date: Mon, 5 May 2025 12:44:08 +0800 Subject: [PATCH 09/20] remove requirements.txt --- requirements.txt | 3 --- 1 file changed, 3 deletions(-) delete mode 100644 requirements.txt diff --git a/requirements.txt b/requirements.txt deleted file mode 100644 index 49c7d88af..000000000 --- a/requirements.txt +++ /dev/null @@ -1,3 +0,0 @@ -pymc>=5.21.1 -scikit-learn -better-optimize From 4d85378d86a6aeb248039bac8346833b513f15d0 Mon Sep 17 00:00:00 2001 From: Jesse Grabowski Date: Mon, 5 May 2025 13:03:33 +0800 Subject: [PATCH 10/20] Read dynamic version from text file --- pyproject.toml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/pyproject.toml b/pyproject.toml index ec41ac231..116f97bef 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,5 +1,5 @@ [build-system] -requires = ["setuptools>=61.0", "numpy"] +requires = ["setuptools>=61.0"] build-backend = "setuptools.build_meta" [project] @@ -70,7 +70,7 @@ exclude = ["tests", "notebooks"] namespaces = false [tool.setuptools.dynamic] -version = {attr = "pymc_extras.__version__"} +version = {file = "pymc_extras/version.txt"} [tool.pytest.ini_options] minversion = "6.0" From 5e6492694e75c8b21d8bdca107997a6b7cb7cab7 Mon Sep 17 00:00:00 2001 From: Jesse Grabowski Date: Mon, 5 May 2025 13:28:05 +0800 Subject: [PATCH 11/20] Delete .gitattributes --- .gitattributes | 1 - 1 file changed, 1 deletion(-) delete mode 100644 .gitattributes diff --git a/.gitattributes b/.gitattributes deleted file mode 100644 index 0aabb9c28..000000000 --- a/.gitattributes +++ /dev/null @@ -1 +0,0 @@ -pymc_extras/_version.py export-subst From 979499dd91bd68dbfc375c121391702aae33517c Mon Sep 17 00:00:00 2001 From: Jesse Grabowski Date: Mon, 5 May 2025 13:28:24 +0800 Subject: [PATCH 12/20] Move `conftest.py` to tests folder --- conftest.py => tests/conftest.py | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename conftest.py => tests/conftest.py (100%) diff --git a/conftest.py b/tests/conftest.py similarity index 100% rename from conftest.py rename to tests/conftest.py From eaba16591140ccf294b22abb6e7d048ef4987e4b Mon Sep 17 00:00:00 2001 From: Jesse Grabowski Date: Mon, 5 May 2025 14:25:29 +0800 Subject: [PATCH 13/20] Simplify setup.py --- setup.py | 20 ++------------------ 1 file changed, 2 insertions(+), 18 deletions(-) diff --git a/setup.py b/setup.py index f7f434a57..8f8434a07 100644 --- a/setup.py +++ b/setup.py @@ -12,23 +12,7 @@ # See the License for the specific language governing permissions and # limitations under the License. -import os - -from codecs import open - -from setuptools import find_packages, setup - - -def read_version(): - here = os.path.abspath(os.path.dirname(__file__)) - with open(os.path.join(here, "pymc_extras", "version.txt")) as f: - version = f.read().strip() - return version - +from setuptools import setup if __name__ == "__main__": - setup( - name="pymc-extras", - version=read_version(), - packages=find_packages(exclude=["tests*"]), - ) + setup() From cb0a0c8b258bb457c40de806d9a6c1502090cf22 Mon Sep 17 00:00:00 2001 From: Jesse Grabowski Date: Mon, 5 May 2025 15:41:08 +0800 Subject: [PATCH 14/20] Switch to `hatchling` based build --- .pre-commit-config.yaml | 1 - MANIFEST.in | 5 ----- pymc_extras/__init__.py | 1 - pymc_extras/version.py | 11 ----------- pymc_extras/version.txt | 1 - pyproject.toml | 29 +++++++++++++++++++---------- setup.py | 18 ------------------ 7 files changed, 19 insertions(+), 47 deletions(-) delete mode 100644 MANIFEST.in delete mode 100644 pymc_extras/version.py delete mode 100644 pymc_extras/version.txt delete mode 100644 setup.py diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index b405033ba..efde98625 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -26,5 +26,4 @@ repos: rev: 0.4.1 hooks: - id: no-print-statements - exclude: _version.py files: ^pymc_extras/ diff --git a/MANIFEST.in b/MANIFEST.in deleted file mode 100644 index f5b9908c8..000000000 --- a/MANIFEST.in +++ /dev/null @@ -1,5 +0,0 @@ -include requirements*.txt -include *.md *.rst -include LICENSE -include README.md -include pymc_extras/version.txt diff --git a/pymc_extras/__init__.py b/pymc_extras/__init__.py index 0ff07bd65..8fa130414 100644 --- a/pymc_extras/__init__.py +++ b/pymc_extras/__init__.py @@ -22,7 +22,6 @@ recover_marginals, ) from pymc_extras.model.model_api import as_model -from pymc_extras.version import __version__ _log = logging.getLogger("pmx") diff --git a/pymc_extras/version.py b/pymc_extras/version.py deleted file mode 100644 index cc0aacca5..000000000 --- a/pymc_extras/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_extras/version.txt b/pymc_extras/version.txt deleted file mode 100644 index 3a4036fb4..000000000 --- a/pymc_extras/version.txt +++ /dev/null @@ -1 +0,0 @@ -0.2.5 diff --git a/pyproject.toml b/pyproject.toml index 116f97bef..7a987cf4c 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,6 +1,6 @@ [build-system] -requires = ["setuptools>=61.0"] -build-backend = "setuptools.build_meta" +requires = ["hatchling", "hatch-vcs"] +build-backend = "hatchling.build" [project] name = "pymc-extras" @@ -62,15 +62,24 @@ Documentation = "https://pymc-extras.readthedocs.io/" Repository = "https://github.com/pymc-devs/pymc-extras.git" Issues = "https://github.com/pymc-devs/pymc-extras/issues" -[tool.setuptools.packages.find] -where = ["."] -include = ["pymc_extras"] -exclude = ["tests", "notebooks"] -# Additional install requirements for running tests -namespaces = false +[tool.hatch.version] +source = 'vcs' -[tool.setuptools.dynamic] -version = {file = "pymc_extras/version.txt"} +[tool.hatch.build.hooks.vcs] +version-file = "_version.py" + +[tool.hatch.build.targets.sdist] +exclude = [ + '/.github', + '/notebooks', + '/tests' +] + +[tool.hatch.build.targets.wheel] +packages = ["pymc_extras"] + +[tool.hatch.metadata] +allow-direct-references = true [tool.pytest.ini_options] minversion = "6.0" diff --git a/setup.py b/setup.py deleted file mode 100644 index 8f8434a07..000000000 --- a/setup.py +++ /dev/null @@ -1,18 +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. - -from setuptools import setup - -if __name__ == "__main__": - setup() From ee17badd732aea99eec6c6a8cde6337e4819cc39 Mon Sep 17 00:00:00 2001 From: Jesse Grabowski <48652735+jessegrabowski@users.noreply.github.com> Date: Mon, 5 May 2025 15:56:45 +0800 Subject: [PATCH 15/20] Include tests in sdist Co-authored-by: Ben Mares --- pyproject.toml | 1 - 1 file changed, 1 deletion(-) diff --git a/pyproject.toml b/pyproject.toml index 7a987cf4c..fdae5b703 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -72,7 +72,6 @@ version-file = "_version.py" exclude = [ '/.github', '/notebooks', - '/tests' ] [tool.hatch.build.targets.wheel] From c146880cb463dee9801825d9c36652124dedf37a Mon Sep 17 00:00:00 2001 From: Jesse Grabowski Date: Mon, 5 May 2025 16:03:23 +0800 Subject: [PATCH 16/20] Build project with `hatch` in `pypi.yml` --- .github/workflows/pypi.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/pypi.yml b/.github/workflows/pypi.yml index 3b8a57e61..92e887ec9 100644 --- a/.github/workflows/pypi.yml +++ b/.github/workflows/pypi.yml @@ -20,8 +20,8 @@ jobs: python-version: "3.10" - name: Build the sdist and the wheel run: | - pip install build - python3 -m build + pip install hatch + python3 -m hatch build - name: Check the sdist installs and imports run: | mkdir -p test-sdist From 9a5276b0d11cc9422cca7c5ef714effe17859463 Mon Sep 17 00:00:00 2001 From: Jesse Grabowski Date: Mon, 5 May 2025 16:12:13 +0800 Subject: [PATCH 17/20] Back to build in the pypi CI --- .github/workflows/pypi.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/pypi.yml b/.github/workflows/pypi.yml index 92e887ec9..3b8a57e61 100644 --- a/.github/workflows/pypi.yml +++ b/.github/workflows/pypi.yml @@ -20,8 +20,8 @@ jobs: python-version: "3.10" - name: Build the sdist and the wheel run: | - pip install hatch - python3 -m hatch build + pip install build + python3 -m build - name: Check the sdist installs and imports run: | mkdir -p test-sdist From c902e861f528505d0323aca98f5c70fa576ae764 Mon Sep 17 00:00:00 2001 From: Jesse Grabowski Date: Mon, 5 May 2025 16:12:45 +0800 Subject: [PATCH 18/20] Add `__version__` to `__init__.py` --- pymc_extras/__init__.py | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/pymc_extras/__init__.py b/pymc_extras/__init__.py index 8fa130414..cee0ffeb5 100644 --- a/pymc_extras/__init__.py +++ b/pymc_extras/__init__.py @@ -13,6 +13,8 @@ # limitations under the License. import logging +from importlib.metadata import version + from pymc_extras import gp, statespace, utils from pymc_extras.distributions import * from pymc_extras.inference import find_MAP, fit, fit_laplace, fit_pathfinder @@ -30,3 +32,6 @@ if len(_log.handlers) == 0: handler = logging.StreamHandler() _log.addHandler(handler) + + +__version__ = version("pymc-extras") From 228a5c6a0be0d48460e6a93945a7a68666db255c Mon Sep 17 00:00:00 2001 From: Ben Mares Date: Mon, 5 May 2025 11:06:02 +0200 Subject: [PATCH 19/20] Add Python 3.13 classifier --- pyproject.toml | 1 + 1 file changed, 1 insertion(+) diff --git a/pyproject.toml b/pyproject.toml index fdae5b703..c8db81e7c 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -15,6 +15,7 @@ classifiers = [ "Programming Language :: Python :: 3.10", "Programming Language :: Python :: 3.11", "Programming Language :: Python :: 3.12", + "Programming Language :: Python :: 3.13", "License :: OSI Approved :: Apache Software License", "Intended Audience :: Science/Research", "Topic :: Scientific/Engineering", From 4bcab4b02d515dfd70ebbaa6e5fafae56011f0be Mon Sep 17 00:00:00 2001 From: Ben Mares Date: Mon, 5 May 2025 11:06:36 +0200 Subject: [PATCH 20/20] Add missing histogram and dask_histogram extras --- pyproject.toml | 7 +++++++ 1 file changed, 7 insertions(+) diff --git a/pyproject.toml b/pyproject.toml index c8db81e7c..bf9a34a4c 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -57,6 +57,13 @@ docs = [ "sphinx>=4.0", "pymc-sphinx-theme@git+https://github.com/pymc-devs/pymc-sphinx-theme", ] +dask_histogram = [ + "dask[complete]<2025.1.1", + "xhistogram", +] +histogram = [ + "xhistogram", +] [project.urls] Documentation = "https://pymc-extras.readthedocs.io/"