diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 97117abd..aeae3537 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -23,8 +23,6 @@ jobs: os: [ubuntu-latest] steps: - uses: actions/checkout@v2 - with: - submodules: true - uses: julia-actions/setup-julia@v1 with: version: ${{ matrix.julia-version }} diff --git a/.github/workflows/documenter.yml b/.github/workflows/documenter.yml index 3d87ddaa..dd6b59dd 100644 --- a/.github/workflows/documenter.yml +++ b/.github/workflows/documenter.yml @@ -17,8 +17,6 @@ jobs: runs-on: ubuntu-latest steps: - uses: actions/checkout@v2 - with: - submodules: true - uses: julia-actions/setup-julia@v1 - name: Cache CmdStan id: cache-cmdstan diff --git a/.github/workflows/futures.yml b/.github/workflows/futures.yml index 7ca57b6c..ad5a1ee6 100644 --- a/.github/workflows/futures.yml +++ b/.github/workflows/futures.yml @@ -28,8 +28,6 @@ jobs: arviz_version: "release" steps: - uses: actions/checkout@v2 - with: - submodules: true - uses: julia-actions/setup-julia@v1 with: version: ${{ matrix.julia-version }} diff --git a/.gitmodules b/.gitmodules deleted file mode 100644 index 51ccd388..00000000 --- a/.gitmodules +++ /dev/null @@ -1,3 +0,0 @@ -[submodule "deps/data/example_data"] - path = deps/data/example_data - url = https://github.com/arviz-devs/arviz_example_data diff --git a/deps/data/example_data b/deps/data/example_data deleted file mode 160000 index 594a6add..00000000 --- a/deps/data/example_data +++ /dev/null @@ -1 +0,0 @@ -Subproject commit 594a6addd3aeddbd5d03e1a59300a1dcf0491a68 diff --git a/deps/data/example_data/.gitignore b/deps/data/example_data/.gitignore new file mode 100644 index 00000000..b6e47617 --- /dev/null +++ b/deps/data/example_data/.gitignore @@ -0,0 +1,129 @@ +# Byte-compiled / optimized / DLL files +__pycache__/ +*.py[cod] +*$py.class + +# C extensions +*.so + +# Distribution / packaging +.Python +build/ +develop-eggs/ +dist/ +downloads/ +eggs/ +.eggs/ +lib/ +lib64/ +parts/ +sdist/ +var/ +wheels/ +pip-wheel-metadata/ +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/ + +# 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 +target/ + +# Jupyter Notebook +.ipynb_checkpoints + +# IPython +profile_default/ +ipython_config.py + +# pyenv +.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 + +# PEP 582; used by e.g. github.com/David-OConnor/pyflow +__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/ diff --git a/deps/data/example_data/LICENSE b/deps/data/example_data/LICENSE new file mode 100644 index 00000000..261eeb9e --- /dev/null +++ b/deps/data/example_data/LICENSE @@ -0,0 +1,201 @@ + Apache License + Version 2.0, January 2004 + http://www.apache.org/licenses/ + + TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION + + 1. Definitions. + + "License" shall mean the terms and conditions for use, reproduction, + and distribution as defined by Sections 1 through 9 of this document. + + "Licensor" shall mean the copyright owner or entity authorized by + the copyright owner that is granting the License. + + "Legal Entity" shall mean the union of the acting entity and all + other entities that control, are controlled by, or are under common + control with that entity. For the purposes of this definition, + "control" means (i) the power, direct or indirect, to cause the + direction or management of such entity, whether by contract or + otherwise, or (ii) ownership of fifty percent (50%) or more of the + outstanding shares, or (iii) beneficial ownership of such entity. + + "You" (or "Your") shall mean an individual or Legal Entity + exercising permissions granted by this License. + + "Source" form shall mean the preferred form for making modifications, + including but not limited to software source code, documentation + source, and configuration files. + + "Object" form shall mean any form resulting from mechanical + transformation or translation of a Source form, including but + not limited to compiled object code, generated documentation, + and conversions to other media types. + + "Work" shall mean the work of authorship, whether in Source or + Object form, made available under the License, as indicated by a + copyright notice that is included in or attached to the work + (an example is provided in the Appendix below). + + "Derivative Works" shall mean any work, whether in Source or Object + form, that is based on (or derived from) the Work and for which the + editorial revisions, annotations, elaborations, or other modifications + represent, as a whole, an original work of authorship. For the purposes + of this License, Derivative Works shall not include works that remain + separable from, or merely link (or bind by name) to the interfaces of, + the Work and Derivative Works thereof. + + "Contribution" shall mean any work of authorship, including + the original version of the Work and any modifications or additions + to that Work or Derivative Works thereof, that is intentionally + submitted to Licensor for inclusion in the Work by the copyright owner + or by an individual or Legal Entity authorized to submit on behalf of + the copyright owner. For the purposes of this definition, "submitted" + means any form of electronic, verbal, or written communication sent + to the Licensor or its representatives, including but not limited to + communication on electronic mailing lists, source code control systems, + and issue tracking systems that are managed by, or on behalf of, the + Licensor for the purpose of discussing and improving the Work, but + excluding communication that is conspicuously marked or otherwise + designated in writing by the copyright owner as "Not a Contribution." + + "Contributor" shall mean Licensor and any individual or Legal Entity + on behalf of whom a Contribution has been received by Licensor and + subsequently incorporated within the Work. + + 2. Grant of Copyright License. Subject to the terms and conditions of + this License, each Contributor hereby grants to You a perpetual, + worldwide, non-exclusive, no-charge, royalty-free, irrevocable + copyright license to reproduce, prepare Derivative Works of, + publicly display, publicly perform, sublicense, and distribute the + Work and such Derivative Works in Source or Object form. + + 3. Grant of Patent License. Subject to the terms and conditions of + this License, each Contributor hereby grants to You a perpetual, + worldwide, non-exclusive, no-charge, royalty-free, irrevocable + (except as stated in this section) patent license to make, have made, + use, offer to sell, sell, import, and otherwise transfer the Work, + where such license applies only to those patent claims licensable + by such Contributor that are necessarily infringed by their + Contribution(s) alone or by combination of their Contribution(s) + with the Work to which such Contribution(s) was submitted. If You + institute patent litigation against any entity (including a + cross-claim or counterclaim in a lawsuit) alleging that the Work + or a Contribution incorporated within the Work constitutes direct + or contributory patent infringement, then any patent licenses + granted to You under this License for that Work shall terminate + as of the date such litigation is filed. + + 4. Redistribution. You may reproduce and distribute copies of the + Work or Derivative Works thereof in any medium, with or without + modifications, and in Source or Object form, provided that You + meet the following conditions: + + (a) You must give any other recipients of the Work or + Derivative Works a copy of this License; and + + (b) You must cause any modified files to carry prominent notices + stating that You changed the files; and + + (c) You must retain, in the Source form of any Derivative Works + that You distribute, all copyright, patent, trademark, and + attribution notices from the Source form of the Work, + excluding those notices that do not pertain to any part of + the Derivative Works; and + + (d) If the Work includes a "NOTICE" text file as part of its + distribution, then any Derivative Works that You distribute must + include a readable copy of the attribution notices contained + within such NOTICE file, excluding those notices that do not + pertain to any part of the Derivative Works, in at least one + of the following places: within a NOTICE text file distributed + as part of the Derivative Works; within the Source form or + documentation, if provided along with the Derivative Works; or, + within a display generated by the Derivative Works, if and + wherever such third-party notices normally appear. The contents + of the NOTICE file are for informational purposes only and + do not modify the License. You may add Your own attribution + notices within Derivative Works that You distribute, alongside + or as an addendum to the NOTICE text from the Work, provided + that such additional attribution notices cannot be construed + as modifying the License. + + You may add Your own copyright statement to Your modifications and + may provide additional or different license terms and conditions + for use, reproduction, or distribution of Your modifications, or + for any such Derivative Works as a whole, provided Your use, + reproduction, and distribution of the Work otherwise complies with + the conditions stated in this License. + + 5. Submission of Contributions. Unless You explicitly state otherwise, + any Contribution intentionally submitted for inclusion in the Work + by You to the Licensor shall be under the terms and conditions of + this License, without any additional terms or conditions. + Notwithstanding the above, nothing herein shall supersede or modify + the terms of any separate license agreement you may have executed + with Licensor regarding such Contributions. + + 6. Trademarks. This License does not grant permission to use the trade + names, trademarks, service marks, or product names of the Licensor, + except as required for reasonable and customary use in describing the + origin of the Work and reproducing the content of the NOTICE file. + + 7. Disclaimer of Warranty. Unless required by applicable law or + agreed to in writing, Licensor provides the Work (and each + Contributor provides its Contributions) on an "AS IS" BASIS, + WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or + implied, including, without limitation, any warranties or conditions + of TITLE, NON-INFRINGEMENT, MERCHANTABILITY, or FITNESS FOR A + PARTICULAR PURPOSE. You are solely responsible for determining the + appropriateness of using or redistributing the Work and assume any + risks associated with Your exercise of permissions under this License. + + 8. Limitation of Liability. In no event and under no legal theory, + whether in tort (including negligence), contract, or otherwise, + unless required by applicable law (such as deliberate and grossly + negligent acts) or agreed to in writing, shall any Contributor be + liable to You for damages, including any direct, indirect, special, + incidental, or consequential damages of any character arising as a + result of this License or out of the use or inability to use the + Work (including but not limited to damages for loss of goodwill, + work stoppage, computer failure or malfunction, or any and all + other commercial damages or losses), even if such Contributor + has been advised of the possibility of such damages. + + 9. Accepting Warranty or Additional Liability. While redistributing + the Work or Derivative Works thereof, You may choose to offer, + and charge a fee for, acceptance of support, warranty, indemnity, + or other liability obligations and/or rights consistent with this + License. However, in accepting such obligations, You may act only + on Your own behalf and on Your sole responsibility, not on behalf + of any other Contributor, and only if You agree to indemnify, + defend, and hold each Contributor harmless for any liability + incurred by, or claims asserted against, such Contributor by reason + of your accepting any such warranty or additional liability. + + END OF TERMS AND CONDITIONS + + APPENDIX: How to apply the Apache License to your work. + + To apply the Apache License to your work, attach the following + boilerplate notice, with the fields enclosed by brackets "[]" + replaced with your own identifying information. (Don't include + the brackets!) The text should be enclosed in the appropriate + comment syntax for the file format. We also recommend that a + file or class name and description of purpose be included on the + same "printed page" as the copyright notice for easier + identification within third-party archives. + + Copyright [yyyy] [name of copyright owner] + + 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. diff --git a/deps/data/example_data/README.md b/deps/data/example_data/README.md new file mode 100644 index 00000000..f2962333 --- /dev/null +++ b/deps/data/example_data/README.md @@ -0,0 +1,8 @@ +# ArviZ `InferenceData` examples + +This repository contains metadata of ArviZ InferenceData examples and the code used to generate some of the examples. +Example models stored remotely are listed in `data_remote.json`. +Example models stored locally are listed in `data_local.json`, and the data themselves are stored in `data/`. +Inclusion of the code serves both as extra information on the models in the JSON files and to ease updating these examples whenever necessary. + +When applicable, code for a model should be added as an executable file (e.g. `.py` or `.ipynb`) to a directory in `code/` of the same name as the model. diff --git a/deps/data/example_data/data/centered_eight.nc b/deps/data/example_data/data/centered_eight.nc new file mode 100644 index 00000000..a22e183e Binary files /dev/null and b/deps/data/example_data/data/centered_eight.nc differ diff --git a/deps/data/example_data/data/non_centered_eight.nc b/deps/data/example_data/data/non_centered_eight.nc new file mode 100644 index 00000000..e48a3487 Binary files /dev/null and b/deps/data/example_data/data/non_centered_eight.nc differ diff --git a/deps/data/example_data/data_local.json b/deps/data/example_data/data_local.json new file mode 100644 index 00000000..23e8b360 --- /dev/null +++ b/deps/data/example_data/data_local.json @@ -0,0 +1,12 @@ +[ + { + "name": "centered_eight", + "filename": "centered_eight.nc", + "description": "A centered parameterization of the eight schools model. Provided as an example of a model that NUTS has trouble fitting. Compare to `non_centered_eight`.\n\nThe eight schools model is a hierarchical model used for an analysis of the effectiveness of classes that were designed to improve students' performance on the Scholastic Aptitude Test.\n\nSee Bayesian Data Analysis (Gelman et. al.) for more details." + }, + { + "name": "non_centered_eight", + "filename": "non_centered_eight.nc", + "description": "A non-centered parameterization of the eight schools model. This is a hierarchical model where sampling problems may be fixed by a non-centered parametrization. Compare to `centered_eight`.\n\nThe eight schools model is a hierarchical model used for an analysis of the effectiveness of classes that were designed to improve students' performance on the Scholastic Aptitude Test.\n\nSee Bayesian Data Analysis (Gelman et. al.) for more details." + } +] \ No newline at end of file diff --git a/deps/data/example_data/data_remote.json b/deps/data/example_data/data_remote.json new file mode 100644 index 00000000..f964f1a7 --- /dev/null +++ b/deps/data/example_data/data_remote.json @@ -0,0 +1,51 @@ +[ + { + "name": "radon", + "filename": "radon_hierarchical.nc", + "url": "http://ndownloader.figshare.com/files/24067472", + "checksum": "a9b2b4adf1bf9c5728e5bdc97107e69c4fc8d8b7d213e9147233b57be8b4587b", + "description": "Radon is a radioactive gas that enters homes through contact points with the ground. It is a carcinogen that is the primary cause of lung cancer in non-smokers. Radon levels vary greatly from household to household.\n\nThis example uses an EPA study of radon levels in houses in Minnesota to construct a model with a hierarchy over households within a county. The model includes estimates (gamma) for contextual effects of the uranium per household.\n\nSee Gelman and Hill (2006) for details on the example, or https://docs.pymc.io/notebooks/multilevel_modeling.html by Chris Fonnesbeck for details on this implementation." + }, + { + "name": "rugby", + "filename": "rugby.nc", + "url": "http://ndownloader.figshare.com/files/16254359", + "checksum": "9eecd2c6317e45b0388dd97ae6326adecf94128b5a7d15a52c9fcfac0937e2a6", + "description": "The Six Nations Championship is a yearly rugby competition between Italy, Ireland, Scotland, England, France and Wales. Fifteen games are played each year, representing all combinations of the six teams.\n\nThis example uses and includes results from 2014 - 2017, comprising 60 total games. It models latent parameters for each team's attack and defense, as well as a parameter for home team advantage.\n\nSee https://docs.pymc.io/notebooks/rugby_analytics.html by Peader Coyle for more details and references." + }, + { + "name": "regression1d", + "filename": "regression1d.nc", + "url": "http://ndownloader.figshare.com/files/16254899", + "checksum": "909e8ffe344e196dad2730b1542881ab5729cb0977dd20ba645a532ffa427278", + "description": "A synthetic one dimensional linear regression dataset with latent slope, intercept, and noise (\"eps\"). One hundred data points, fit with PyMC3.\n\nTrue slope and intercept are included as deterministic variables." + }, + { + "name": "regression10d", + "filename": "regression10d.nc", + "url": "http://ndownloader.figshare.com/files/16255736", + "checksum": "c6716ec7e19926ad2a52d6ae4c1d1dd5ddb747e204c0d811757c8e93fcf9f970", + "description": "A synthetic multi-dimensional (10 dimensions) linear regression dataset with latent weights (\"w\"), intercept, and noise (\"eps\"). Five hundred data points, fit with PyMC3.\n\nTrue weights and intercept are included as deterministic variables." + }, + { + "name": "classification1d", + "filename": "classification1d.nc", + "url": "http://ndownloader.figshare.com/files/16256678", + "checksum": "1cf3806e72c14001f6864bb69d89747dcc09dd55bcbca50aba04e9939daee5a0", + "description": "A synthetic one dimensional logistic regression dataset with latent slope and intercept, passed into a Bernoulli random variable. One hundred data points, fit with PyMC3.\n\nTrue slope and intercept are included as deterministic variables." + }, + { + "name": "classification10d", + "filename": "classification10d.nc", + "url": "http://ndownloader.figshare.com/files/16256681", + "checksum": "16c9a45e1e6e0519d573cafc4d266d761ba347e62b6f6a79030aaa8e2fde1367", + "description": "A synthetic multi dimensional (10 dimensions) logistic regression dataset with latent weights (\"w\") and intercept, passed into a Bernoulli random variable. Five hundred data points, fit with PyMC3.\n\nTrue weights and intercept are included as deterministic variables." + }, + { + "name": "glycan_torsion_angles", + "filename": "glycan_torsion_angles.nc", + "url": "http://ndownloader.figshare.com/files/22882652", + "checksum": "4622621fe7a1d3075c18c4c34af8cc57c59eabbb3501b20c6e2d9c6c4737034c", + "description": "Torsion angles phi and psi are critical for determining the three dimensional structure of bio-molecules. Combinations of phi and psi torsion angles that produce clashes between atoms in the bio-molecule result in high energy, unlikely structures.\n\nThis model uses a Von Mises distribution to propose torsion angles for the structure of a glycan molecule (pdb id: 2LIQ), and a Potential to estimate the proposed structure's energy. Said Potential is bound by Boltzman's law." + } +] \ No newline at end of file