pymc-extras 0.2.0__tar.gz

pymc_extras-0.2.0/CODE_OF_CONDUCT.md

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+# PyMC Code of Conduct
+
+## Our Pledge
+
+In the interest of fostering an open and welcoming environment, we as
+contributors and maintainers pledge to making participation in our project and
+our community a harassment-free experience for everyone, regardless of age, body
+size, disability, ethnicity, sex characteristics, gender identity and expression,
+level of experience, education, socio-economic status, nationality, personal
+appearance, race, religion, or sexual identity and orientation.
+
+## Our Standards
+
+Examples of behavior that contributes to creating a positive environment
+include:
+
+* Using welcoming and inclusive language
+* Being respectful of differing viewpoints and experiences
+* Gracefully accepting constructive criticism
+* Focusing on what is best for the community
+* Showing empathy towards other community members
+
+Examples of unacceptable behavior by participants include:
+
+* The use of sexualized language or imagery and unwelcome sexual attention or
+  advances
+* Trolling, insulting/derogatory comments, and personal or political attacks
+* Public or private harassment
+* Publishing others' private information, such as a physical or electronic
+  address, without explicit permission
+* Other conduct which could reasonably be considered inappropriate in a
+  professional setting
+
+## Our Responsibilities
+
+Project maintainers are responsible for clarifying the standards of acceptable
+behavior and are expected to take appropriate and fair corrective action in
+response to any instances of unacceptable behavior.
+
+Project maintainers have the right and responsibility to remove, edit, or
+reject comments, commits, code, wiki edits, issues, and other contributions
+that are not aligned to this Code of Conduct, or to ban temporarily or
+permanently any contributor for other behaviors that they deem inappropriate,
+threatening, offensive, or harmful.
+
+## Scope
+
+This Code of Conduct applies both within project spaces and in public spaces
+when an individual is representing the project or its community. Examples of
+representing a project or community include using an official project e-mail
+address, posting via an official social media account, or acting as an appointed
+representative at an online or offline event. Representation of a project may be
+further defined and clarified by project maintainers.
+
+## Enforcement
+
+Instances of abusive, harassing, or otherwise unacceptable behavior may be
+reported by contacting PyMC developer Christopher Fonnesbeck via email
+(chris.fonnesbeck@vanderbilt.edu) or phone (615-955-0380). Alternatively, you
+may also contact NumFOCUS Executive Director Leah Silen (512-222-5449) or
+fill an anonymous report using [NumFOCUS Typeform](https://numfocus.typeform.com/to/ynjGdT).
+As PyMC is a member of NumFOCUS and subscribes to their code of conduct as a
+precondition for continued membership. All complaints will be reviewed and
+investigated and will result in a response that is deemed necessary and
+appropriate to the circumstances. The project team is obligated to maintain
+confidentiality with regard to the reporter of an incident. Further details of
+specific enforcement policies may be posted separately.
+
+Project maintainers who do not follow or enforce the Code of Conduct in good
+faith may face temporary or permanent repercussions as determined by other
+members of the project's leadership.
+
+## Attribution
+
+This Code of Conduct is adapted from the [Contributor Covenant][homepage], version 1.4,
+available at https://www.contributor-covenant.org/version/1/4/code-of-conduct.html
+
+[homepage]: https://www.contributor-covenant.org

pymc_extras-0.2.0/CONTRIBUTING.md

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+# Contributing guide
+
+Page in construction, for now go to https://github.com/pymc-devs/pymc-extras#questions.

pymc_extras-0.2.0/LICENSE

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+=======
+License
+=======
+
+PyMC is distributed under the Apache License, Version 2.0
+
+Copyright (c) 2006 Christopher J. Fonnesbeck (Academic Free License)
+Copyright (c) 2007-2008 Christopher J. Fonnesbeck, Anand Prabhakar Patil, David Huard (Academic Free License)
+Copyright (c) 2009-2017 The PyMC developers (see contributors to pymc-devs on GitHub)
+All rights reserved.
+
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pymc_extras-0.2.0/MANIFEST.in

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+include requirements*.txt
+include *.md *.rst
+include LICENSE
+include README.md
+include pymc_extras/version.txt

pymc_extras-0.2.0/PKG-INFO

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+Metadata-Version: 2.1
+Name: pymc-extras
+Version: 0.2.0
+Summary: 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.
+Home-page: http://github.com/pymc-devs/pymc-extras
+Maintainer: PyMC Developers
+Maintainer-email: pymc.devs@gmail.com
+License: Apache License, Version 2.0
+Classifier: Development Status :: 5 - Production/Stable
+Classifier: Programming Language :: Python
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: License :: OSI Approved :: Apache Software License
+Classifier: Intended Audience :: Science/Research
+Classifier: Topic :: Scientific/Engineering
+Classifier: Topic :: Scientific/Engineering :: Mathematics
+Classifier: Operating System :: OS Independent
+Requires-Python: >=3.10
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: pymc>=5.19.1
+Requires-Dist: scikit-learn
+Provides-Extra: dask-histogram
+Requires-Dist: dask[complete]; extra == "dask-histogram"
+Requires-Dist: xhistogram; extra == "dask-histogram"
+Provides-Extra: histogram
+Requires-Dist: xhistogram; extra == "histogram"
+Provides-Extra: complete
+Requires-Dist: dask[complete]; extra == "complete"
+Requires-Dist: xhistogram; extra == "complete"
+Provides-Extra: dev
+Requires-Dist: dask[all]; extra == "dev"
+Requires-Dist: blackjax; extra == "dev"
+Requires-Dist: statsmodels; extra == "dev"
+
+# Welcome to `pymc-extras`
+<a href="https://gitpod.io/#https://github.com/pymc-devs/pymc-extras">
+  <img
+    src="https://img.shields.io/badge/Contribute%20with-Gitpod-908a85?logo=gitpod"
+    alt="Contribute with Gitpod"
+  />
+</a>
+<img
+  src="https://codecov.io/gh/pymc-devs/pymc-extras/branch/main/graph/badge.svg"
+  alt="Codecov Badge"
+/>
+
+As PyMC continues to mature and expand its functionality to accommodate more domains of application, we increasingly see cutting-edge methodologies, highly specialized statistical distributions, and complex models appear.
+While this adds to the functionality and relevance of the project, it can also introduce instability and impose a burden on testing and quality control.
+To reduce the burden on the main `pymc` repository, this `pymc-extras` repository can become the aggregator and testing ground for new additions to PyMC.
+This may include unusual probability distributions, advanced model fitting algorithms, innovative yet not fully tested methods, or niche functionality that might not fit in the main PyMC repository, but still may be of interest to users.
+
+The `pymc-extras` repository can be understood as the first step in the PyMC development pipeline, where all novel code is introduced until it is obvious that it belongs in the main repository.
+We hope that this organization improves the stability and streamlines the testing overhead of the `pymc` repository, while allowing users and developers to test and evaluate cutting-edge methods and not yet fully mature features.
+
+`pymc-extras` would be designed to mirror the namespaces in `pymc` to make usage and migration as easy as possible.
+For example, a `ParabolicFractal` distribution could be used analogously to those in `pymc`:
+
+```python
+import pymc as pm
+import pymc_extras as pmx
+
+with pm.Model():
+
+    alpha = pmx.ParabolicFractal('alpha', b=1, c=1)
+
+    ...
+
+```
+
+## Questions
+
+### What belongs in `pymc-extras`?
+
+- newly-implemented statistical methods, for example step methods or model construction helpers
+- distributions that are tricky to sample from or test
+- infrequently-used fitting methods or distributions
+- any code that requires additional optimization before it can be used in practice
+
+
+### What does not belong in `pymc-extras`?
+- Case studies
+- Implementations that cannot be applied generically, for example because they are tied to variables from a toy example
+
+
+### Should there be more than one add-on repository?
+
+Since there is a lot of code that we may not want in the main repository, does it make sense to have more than one additional repository?
+For example, `pymc-extras` may just include methods that are not fully developed, tested and trusted, while code that is known to work well and has adequate test coverage, but is still too specialized to become part of `pymc` could reside in a `pymc-extras` (or similar) repository.
+
+
+### Unanswered questions & ToDos
+This project is still young and many things have not been answered or implemented.
+Please get involved!
+
+* What are guidelines for organizing submodules?
+  * Proposal: No default imports of WIP/unstable submodules. By importing manually we can avoid breaking the package if a submodule breaks, for example because of an updated dependency.

pymc_extras-0.2.0/README.md

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+# Welcome to `pymc-extras`
+<a href="https://gitpod.io/#https://github.com/pymc-devs/pymc-extras">
+  <img
+    src="https://img.shields.io/badge/Contribute%20with-Gitpod-908a85?logo=gitpod"
+    alt="Contribute with Gitpod"
+  />
+</a>
+<img
+  src="https://codecov.io/gh/pymc-devs/pymc-extras/branch/main/graph/badge.svg"
+  alt="Codecov Badge"
+/>
+
+As PyMC continues to mature and expand its functionality to accommodate more domains of application, we increasingly see cutting-edge methodologies, highly specialized statistical distributions, and complex models appear.
+While this adds to the functionality and relevance of the project, it can also introduce instability and impose a burden on testing and quality control.
+To reduce the burden on the main `pymc` repository, this `pymc-extras` repository can become the aggregator and testing ground for new additions to PyMC.
+This may include unusual probability distributions, advanced model fitting algorithms, innovative yet not fully tested methods, or niche functionality that might not fit in the main PyMC repository, but still may be of interest to users.
+
+The `pymc-extras` repository can be understood as the first step in the PyMC development pipeline, where all novel code is introduced until it is obvious that it belongs in the main repository.
+We hope that this organization improves the stability and streamlines the testing overhead of the `pymc` repository, while allowing users and developers to test and evaluate cutting-edge methods and not yet fully mature features.
+
+`pymc-extras` would be designed to mirror the namespaces in `pymc` to make usage and migration as easy as possible.
+For example, a `ParabolicFractal` distribution could be used analogously to those in `pymc`:
+
+```python
+import pymc as pm
+import pymc_extras as pmx
+
+with pm.Model():
+
+    alpha = pmx.ParabolicFractal('alpha', b=1, c=1)
+
+    ...
+
+```
+
+## Questions
+
+### What belongs in `pymc-extras`?
+
+- newly-implemented statistical methods, for example step methods or model construction helpers
+- distributions that are tricky to sample from or test
+- infrequently-used fitting methods or distributions
+- any code that requires additional optimization before it can be used in practice
+
+
+### What does not belong in `pymc-extras`?
+- Case studies
+- Implementations that cannot be applied generically, for example because they are tied to variables from a toy example
+
+
+### Should there be more than one add-on repository?
+
+Since there is a lot of code that we may not want in the main repository, does it make sense to have more than one additional repository?
+For example, `pymc-extras` may just include methods that are not fully developed, tested and trusted, while code that is known to work well and has adequate test coverage, but is still too specialized to become part of `pymc` could reside in a `pymc-extras` (or similar) repository.
+
+
+### Unanswered questions & ToDos
+This project is still young and many things have not been answered or implemented.
+Please get involved!
+
+* What are guidelines for organizing submodules?
+  * Proposal: No default imports of WIP/unstable submodules. By importing manually we can avoid breaking the package if a submodule breaks, for example because of an updated dependency.

pymc_extras-0.2.0/pymc_extras/__init__.py

@@ -0,0 +1,29 @@
+#   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 logging
+
+from pymc_extras import gp, statespace, utils
+from pymc_extras.distributions import *
+from pymc_extras.inference.fit import fit
+from pymc_extras.model.marginal.marginal_model import MarginalModel, marginalize
+from pymc_extras.model.model_api import as_model
+from pymc_extras.version import __version__
+
+_log = logging.getLogger("pmx")
+
+if not logging.root.handlers:
+    _log.setLevel(logging.INFO)
+    if len(_log.handlers) == 0:
+        handler = logging.StreamHandler()
+        _log.addHandler(handler)

pymc_extras-0.2.0/pymc_extras/distributions/__init__.py

@@ -0,0 +1,40 @@
+#   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.
+
+# coding: utf-8
+"""
+Experimental probability distributions for stochastic nodes in PyMC.
+"""
+
+from pymc_extras.distributions.continuous import Chi, GenExtreme, Maxwell
+from pymc_extras.distributions.discrete import (
+    BetaNegativeBinomial,
+    GeneralizedPoisson,
+    Skellam,
+)
+from pymc_extras.distributions.histogram_utils import histogram_approximation
+from pymc_extras.distributions.multivariate import R2D2M2CP
+from pymc_extras.distributions.timeseries import DiscreteMarkovChain
+
+__all__ = [
+    "Chi",
+    "Maxwell",
+    "DiscreteMarkovChain",
+    "GeneralizedPoisson",
+    "BetaNegativeBinomial",
+    "GenExtreme",
+    "R2D2M2CP",
+    "Skellam",
+    "histogram_approximation",
+]