├── .coveragerc ├── .github └── workflows │ ├── push.yml │ └── release.yml ├── .gitignore ├── LICENSE ├── MANIFEST.in ├── README.md ├── mypy.ini ├── setup.py ├── src ├── posteriordb.egg-info │ ├── PKG-INFO │ ├── SOURCES.txt │ ├── dependency_links.txt │ ├── not-zip-safe │ ├── requires.txt │ └── top_level.txt └── posteriordb │ ├── __init__.py │ ├── dataset.py │ ├── model.py │ ├── model_implementation_base.py │ ├── posterior.py │ ├── posterior_database.py │ ├── posterior_database_github.py │ ├── pymc3_model_implementation.py │ ├── stan_model_implementation.py │ └── util.py ├── tests ├── __init__.py ├── integrity_tests │ ├── __init__.py │ ├── helpers.py │ └── test_integrity.py └── test_pdb.py └── tox.ini /.coveragerc: -------------------------------------------------------------------------------- 1 | [report] 2 | show_missing = True 3 | exclude_lines = 4 | \#\s*pragma: no cover 5 | ^\s*raise NotImplementedError\b 6 | ^\s*return NotImplemented\b 7 | -------------------------------------------------------------------------------- /.github/workflows/push.yml: -------------------------------------------------------------------------------- 1 | name: Python 2 | 3 | on: 4 | push: 5 | branches: 6 | - "**" 7 | paths-ignore: 8 | - 'README.md' 9 | jobs: 10 | models: 11 | name: Run Tests 12 | runs-on: ${{ matrix.os }} 13 | strategy: 14 | matrix: 15 | os: [ubuntu-latest, macos-latest, windows-latest] 16 | python-version: [3.6, 3.7, 3.8, 3.9] 17 | fail-fast: false 18 | env: 19 | GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} 20 | steps: 21 | - name: Checkout python module repo 22 | uses: actions/checkout@v2 23 | with: 24 | fetch-depth: 0 25 | 26 | - name: Checkout posteriordb repo 27 | uses: actions/checkout@v2 28 | with: 29 | repository: stan-dev/posteriordb 30 | path: posteriordb 31 | fetch-depth: 0 32 | 33 | - name: Set up Python ${{ matrix.python-version }} 34 | uses: actions/setup-python@v1 35 | with: 36 | python-version: ${{ matrix.python-version }} 37 | 38 | - name: Install python dependencies 39 | run: | 40 | pip install --upgrade pip wheel 41 | pip install tox-gh-actions codecov 42 | - name: Tox 43 | run: | 44 | tox 45 | #codecov -------------------------------------------------------------------------------- /.github/workflows/release.yml: -------------------------------------------------------------------------------- 1 | name: Python 2 | 3 | on: 4 | pull_request: 5 | branches: 6 | - main 7 | types: [closed] 8 | paths-ignore: 9 | - 'README.md' 10 | 11 | jobs: 12 | models: 13 | name: Run Tests and Publish 14 | runs-on: ${{ matrix.os }} 15 | if: ${{ github.event.pull_request.merged }} 16 | strategy: 17 | matrix: 18 | os: [ubuntu-latest, macos-latest, windows-latest] 19 | python-version: [3.6, 3.7, 3.8, 3.9] 20 | fail-fast: false 21 | env: 22 | GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} 23 | steps: 24 | - name: Checkout python module repo 25 | uses: actions/checkout@v2 26 | with: 27 | fetch-depth: 0 28 | 29 | - name: Checkout posteriordb repo 30 | uses: actions/checkout@v2 31 | with: 32 | repository: stan-dev/posteriordb 33 | path: posteriordb 34 | fetch-depth: 0 35 | 36 | - name: Set up Python ${{ matrix.python-version }} 37 | uses: actions/setup-python@v1 38 | with: 39 | python-version: ${{ matrix.python-version }} 40 | 41 | - name: Install python dependencies 42 | run: | 43 | pip install --upgrade pip wheel 44 | pip install tox-gh-actions codecov 45 | - name: Tox 46 | run: | 47 | cd python 48 | tox 49 | #codecov 50 | - name: Build wheel 51 | run: | 52 | cd python 53 | python setup.py bdist_wheel 54 | - name: Install wheel 55 | if: matrix.os != 'windows-latest' 56 | run: | 57 | python -m pip install python/dist/*.whl 58 | - name: Install wheel [Windows] 59 | if: matrix.os == 'windows-latest' 60 | run: | 61 | $whl = Get-ChildItem -Path python/dist -Filter *.whl | Select-Object -First 1 62 | python -m pip install "$whl" 63 | - name: Show libraries 64 | run: | 65 | python -m pip freeze 66 | - uses: actions/upload-artifact@v2 67 | if: success() && matrix.os == 'ubuntu-latest' 68 | with: 69 | name: posteriordb_wheel 70 | path: python/dist/*.whl 71 | 72 | - name: Upload wheel to release 73 | uses: svenstaro/upload-release-action@v1-release 74 | if: success() && startsWith(github.ref, 'refs/tags/') && matrix.os == 'ubuntu-latest' 75 | with: 76 | repo_token: ${{ secrets.GITHUB_TOKEN }} 77 | file: python/dist/*.whl 78 | tag: ${{ github.ref }} 79 | overwrite: true 80 | file_glob: true 81 | 82 | - name: Upload to pypi 83 | if: success() && startsWith(github.ref, 'refs/tags/') && matrix.os == 'ubuntu-latest' 84 | env: 85 | TWINE_USERNAME: ${{ secrets.PYPI_USERNAME }} 86 | TWINE_PASSWORD: ${{ secrets.PYPI_PASSWORD }} 87 | run: | 88 | python -m pip install --no-cache-dir twine 89 | python -m twine upload -u ${TWINE_USERNAME} -p ${TWINE_PASSWORD} --skip-existing python/dist/* -------------------------------------------------------------------------------- /.gitignore: -------------------------------------------------------------------------------- 1 | .Rproj.user 2 | .Rhistory 3 | .RData 4 | .Ruserdata 5 | *.Rproj 6 | **/__pycache__ 7 | build/ -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- 1 | GNU GENERAL PUBLIC LICENSE 2 | Version 3, 29 June 2007 3 | 4 | Copyright (C) 2007 Free Software Foundation, Inc. 5 | Everyone is permitted to copy and distribute verbatim copies 6 | of this license document, but changing it is not allowed. 7 | 8 | Preamble 9 | 10 | The GNU General Public License is a free, copyleft license for 11 | software and other kinds of works. 12 | 13 | The licenses for most software and other practical works are designed 14 | to take away your freedom to share and change the works. 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If not, see . 649 | 650 | Also add information on how to contact you by electronic and paper mail. 651 | 652 | If the program does terminal interaction, make it output a short 653 | notice like this when it starts in an interactive mode: 654 | 655 | Copyright (C) 656 | This program comes with ABSOLUTELY NO WARRANTY; for details type `show w'. 657 | This is free software, and you are welcome to redistribute it 658 | under certain conditions; type `show c' for details. 659 | 660 | The hypothetical commands `show w' and `show c' should show the appropriate 661 | parts of the General Public License. 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But first, please read 674 | . 675 | -------------------------------------------------------------------------------- /MANIFEST.in: -------------------------------------------------------------------------------- 1 | include *.md 2 | include LICENSE 3 | -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- 1 | [![Python](https://github.com/stan-dev/posteriordb-python/actions/workflows/push.yml/badge.svg)](https://github.com/stan-dev/posteriordb-python/actions/workflows/push.yml) 2 | 3 | # `posteriordb-python`: a Python library to work with `posteriordb` 4 | 5 | This repository contains the Python package to efficiently work with the [posteriordb](https://github.com/stan-dev/posteriordb) repository. The R package includes convenience functions to access data, model code and information for individual posteriors, models, data and draws. 6 | 7 | > [!IMPORTANT] 8 | > This repository `posteriordb-python` only contains Python convience functions. The repository [`posteriordb`](https://github.com/stan-dev/posteriordb) contains the actual posteriors and associated models, data, and reference draws. 9 | 10 | ## Python versions 11 | 12 | Currently only Python 3.6+ is supported. Python 3.5+ support can be added if needed. Support is not planned for Python 2. 13 | 14 | ## Installation 15 | 16 | Installation from PyPI is recommended. 17 | 18 | ```bash 19 | pip install posteriordb 20 | ``` 21 | 22 | Installing from the local clone. 23 | 24 | ```bash 25 | git clone https://github.com/stan-dev/posteriordb-python 26 | cd posteriordb-python 27 | python setup.py bdist_wheel 28 | pip install . 29 | ``` 30 | 31 | ## Using the posterior database from Python 32 | 33 | The included database contains convenience functions to access data, model code, and information for individual posteriors. This database can be created with local or online access to `posteriordb`. 34 | 35 | For local access, ensure `posteriordb` is already dowloaded or clone it with: 36 | 37 | ```bash 38 | git clone https://github.com/stan-dev/posteriordb.git 39 | ``` 40 | 41 | Then create the database by setting `pdb_path`: 42 | 43 | ```python 44 | from posteriordb import PosteriorDatabase 45 | pdb_path = path_to_your_posteriordb 46 | my_pdb = PosteriorDatabase(pdb_path) 47 | ``` 48 | If you run this code in the same directory in which `posteriordb` was cloned, the path `pdb_path` will be `../posteriordb/posterior_database`. 49 | 50 | For online access, use the `PosteriorDatabaseGithub` class with a [GitHub Personal Access Token (PAT)](https://docs.github.com/en/free-pro-team@latest/github/authenticating-to-github/creating-a-personal-access-token) to interact with `posteriordb` remotely. We recommend creating the `GITHUB_PAT` with read-only permissions and setting it as an environmental variable (therefore the `GITHUB_PAT` is not shown in the examples below). 51 | 52 | If not explicitly defined, `PosteriorDatabase` and `PosteriorDatabaseGithub` will create a new (or use old database) located at `POSTERIOR_DB_PATH` if it's 53 | defined. `PosteriorDatabaseGithub` will finally use `$HOME/.posteriordb/posterior_database` as a fallback location if no environmental variables have been set. 54 | Each model and data is only downloaded and cached when needed. 55 | 56 | ```python 57 | >>> from posteriordb import PosteriorDatabaseGithub 58 | >>> import os 59 | >>> # It is recommended that GITHUB_PAT is added to the user environmental variables 60 | >>> # outside Python and not in a Python script as shown in this example code 61 | >>> os.environ["GITHUB_PAT"] = "token-string-here" 62 | >>> my_pdb = PosteriorDatabaseGithub() 63 | ``` 64 | 65 | To list the posteriors available, use `posterior_names`. 66 | 67 | ```python 68 | >>> pos = my_pdb.posterior_names() 69 | >>> pos[:5] 70 | 71 | ['roaches-roaches_negbin', 72 | 'syn_gmK2D1n200-gmm_diagonal_nonordered', 73 | 'radon_mn-radon_variable_intercept_centered', 74 | 'syn_gmK3D2n300-gmm_nonordered', 75 | 'radon-radon_hierarchical_intercept_centered'] 76 | 77 | ``` 78 | 79 | In the same fashion, we can list data and models included in the database as 80 | 81 | ```python 82 | >>> mn = my_pdb.model_names() 83 | >>> mn[:5] 84 | 85 | ['gmm_diagonal_nonordered', 86 | 'radon_pool', 87 | 'radon_partial_pool_noncentered', 88 | 'blr', 89 | 'radon_hierarchical_intercept_noncentered'] 90 | 91 | 92 | >>> dn = my_pdb.dataset_names() 93 | >>> dn[:5] 94 | 95 | ['radon_mn', 96 | 'wells_centered', 97 | 'radon', 98 | 'wells_centered_educ4_interact', 99 | 'wells_centered_educ4'] 100 | 101 | 102 | ``` 103 | 104 | The posterior's name is made up of the data and model fitted 105 | to the data. Together, these two uniquely define a posterior distribution. 106 | To access a posterior object we can use the posterior name. 107 | 108 | ```python 109 | >>> posterior = my_pdb.posterior("eight_schools-eight_schools_centered") 110 | ``` 111 | 112 | From the posterior we can access the dataset and the model 113 | 114 | ```python 115 | >>> model = posterior.model 116 | >>> data = posterior.data 117 | ``` 118 | 119 | We can also access the names of posteriors, models and datasets. 120 | 121 | ```python 122 | >>> posterior.name 123 | "eight_schools-eight_schools_centered" 124 | 125 | >>> model.name 126 | "eight_schools_centered" 127 | 128 | >>> data.name 129 | "eight_schools" 130 | 131 | ``` 132 | 133 | We can access the same model and dataset also directly from the posterior database 134 | ```python 135 | >>> model = my_pdb.model("eight_schools_centered") 136 | >>> data = my_pdb.data("eight_schools") 137 | ``` 138 | 139 | From the model we can access model code and information about the model 140 | 141 | ```python 142 | >>> model.code("stan") 143 | data { 144 | int J; // number of schools 145 | real y[J]; // estimated treatment 146 | real sigma[J]; // std of estimated effect 147 | } 148 | parameters { 149 | real theta[J]; // treatment effect in school j 150 | real mu; // hyper-parameter of mean 151 | real tau; // hyper-parameter of sdv 152 | } 153 | model { 154 | tau ~ cauchy(0, 5); // a non-informative prior 155 | theta ~ normal(mu, tau); 156 | y ~ normal(theta , sigma); 157 | mu ~ normal(0, 5); 158 | } 159 | 160 | >>> model.code_file_path("stan") 161 | '/home/eero/posterior_database/content/models/stan/eight_schools_centered.stan' 162 | 163 | >>> model.information 164 | {'keywords': ['bda3_example', 'hiearchical'], 165 | 'description': 'A centered hiearchical model for the 8 schools example of Rubin (1981)', 166 | 'urls': ['http://www.stat.columbia.edu/~gelman/arm/examples/schools'], 167 | 'title': 'A centered hiearchical model for 8 schools', 168 | 'references': ['rubin1981estimation', 'gelman2013bayesian'], 169 | 'added_by': 'Mans Magnusson', 170 | 'added_date': '2019-08-12'} 171 | ``` 172 | Note that the references are referencing to BibTeX items that can be found in `content/references/references.bib`. 173 | 174 | From the dataset we can access the data values and information about it 175 | 176 | ```python 177 | >>> data.values() 178 | {'J': 8, 179 | 'y': [28, 8, -3, 7, -1, 1, 18, 12], 180 | 'sigma': [15, 10, 16, 11, 9, 11, 10, 18]} 181 | 182 | >>> data.file_path() 183 | '/tmp/tmpx16edu0w' 184 | 185 | >>> data.information 186 | {'keywords': ['bda3_example'], 187 | 'description': 'A study for the Educational Testing Service to analyze the effects of\nspecial coaching programs on test scores. See Gelman et. al. (2014), Section 5.5 for details.', 188 | 'urls': ['http://www.stat.columbia.edu/~gelman/arm/examples/schools'], 189 | 'title': 'The 8 schools dataset of Rubin (1981)', 190 | 'references': ['rubin1981estimation', 'gelman2013bayesian'], 191 | 'added_by': 'Mans Magnusson', 192 | 'added_date': '2019-08-12'} 193 | ``` 194 | 195 | To access gold standard posterior draws we can use `reference_draws` as follows. 196 | 197 | ```python 198 | >>> posterior.reference_draws_info() 199 | {'name': 'eight_schools-eight_schools_noncentered', 200 | 'inference': {'method': 'stan_sampling', 201 | 'method_arguments': {'chains': 10, 202 | 'iter': 20000, 203 | 'warmup': 10000, 204 | 'thin': 10, 205 | 'seed': 4711, 206 | 'control': {'adapt_delta': 0.95}}}, 207 | 'diagnostics': {'diagnostic_information': {'names': ['mu', 208 | 'tau', 209 | 'theta[1]', 210 | ... 211 | 212 | >>> gs = posterior.reference_draws() 213 | >>> import pandas as pd 214 | >>> pd.DataFrame(gs) 215 | 216 | theta[1] theta[2] 217 | 0 [10.6802773011458, 6.45383910854259, -2.241629... [9.71770681295263, 4.41030824418493, 0.7617047... 218 | 1 [5.70891361633589, 10.3012059848039, 4.2439533... [-2.32310565394337, 14.8121789773659, 6.517256... 219 | 2 [7.23747096507585, -0.427831558524343, 9.14782... [7.35425759420389, 8.69579738064637, 8.9058764... 220 | 3 [4.44915522912766, 2.34711393762556, 17.680378... [2.4368039319606, 5.89809320808632, 8.63031558... 221 | ... 222 | ``` 223 | -------------------------------------------------------------------------------- /mypy.ini: -------------------------------------------------------------------------------- 1 | [mypy] 2 | ignore_missing_imports = True 3 | -------------------------------------------------------------------------------- /setup.py: -------------------------------------------------------------------------------- 1 | import os 2 | import re 3 | from setuptools import setup 4 | 5 | PROJECT_ROOT = os.path.dirname(os.path.realpath(__file__)) 6 | VERSION_FILE = os.path.join(PROJECT_ROOT, "src", "posteriordb", "__init__.py") 7 | README_FILE = os.path.join(PROJECT_ROOT, "README.md") 8 | 9 | 10 | def get_long_description(): 11 | with open(README_FILE, "rt") as buff: 12 | return buff.read() 13 | 14 | 15 | def get_version(): 16 | lines = open(VERSION_FILE, "rt").readlines() 17 | version_regex = r"^__version__ = ['\"]([^'\"]*)['\"]" 18 | for line in lines: 19 | mo = re.search(version_regex, line, re.M) 20 | if mo: 21 | return mo.group(1) 22 | raise RuntimeError("Unable to find version in %s." % (VERSION_FILE,)) 23 | 24 | 25 | setup( 26 | name="posteriordb", 27 | version=get_version(), 28 | description="python interface to posterior database", 29 | url="https://github.com/MansMeg/posteriordb", 30 | author="Eero Linna", 31 | author_email="eero.linna@aalto.fi", 32 | license="GPL", 33 | long_description=get_long_description(), 34 | long_description_content_type="text/markdown", 35 | packages=["posteriordb"], 36 | package_dir={"": "src"}, 37 | install_requires=["requests"], 38 | zip_safe=False, 39 | include_package_data=True, 40 | ) 41 | -------------------------------------------------------------------------------- /src/posteriordb.egg-info/PKG-INFO: -------------------------------------------------------------------------------- 1 | Metadata-Version: 2.1 2 | Name: posteriordb 3 | Version: 0.2.0 4 | Summary: python interface to posterior database 5 | Home-page: https://github.com/MansMeg/posteriordb 6 | Author: Eero Linna 7 | Author-email: eero.linna@aalto.fi 8 | License: GPL 9 | Description: 10 | # Currently under construction 11 | 12 | ## Python versions 13 | 14 | Currently only python 3.6+ is supported. Python 3.5+ support can be added if needed. We don't plan to support python 2. 15 | 16 | ## Installation 17 | 18 | Installation from PyPI is recommended. 19 | 20 | ```bash 21 | pip install posteriordb 22 | ``` 23 | 24 | Installing from the local clone. 25 | 26 | ```bash 27 | git clone https://github.com/pystan-dev/posteriordb-python 28 | cd posteriordb-python 29 | python setup.py bdist_wheel 30 | pip install python/ 31 | ``` 32 | 33 | ## Using the posterior database from python 34 | 35 | The included database contains convenience functions to access data, model code and information for individual posteriors. 36 | 37 | First we create the posterior database to use, here the cloned posterior database. 38 | 39 | ```python 40 | >>> from posteriordb import PosteriorDatabase 41 | >>> import os 42 | >>> pdb_path = os.path.join(os.getcwd(), "path/to/posterior_database") 43 | >>> my_pdb = PosteriorDatabase(pdb_path) 44 | ``` 45 | The above code requires you to specify the path to posterior_database folder in the posteriordb repository. If you clone it in the same folder as this repository, the path will be ../posteriordb/posterior_database. 46 | 47 | Online database can be used with the `PosteriorDatabaseGithub` class. Remember to create and set `GITHUB_PAT` environmental variable. 48 | It's recommended that users create a read-only (no extra permissions) [GitHub Personal Access Token (PAT)](https://docs.github.com/en/free-pro-team@latest/github/authenticating-to-github/creating-a-personal-access-token) for `posteriordb` use. It's also recommended that the 49 | `GITHUB_PAT` environmental variable is added to user environmental variables and it is not shown in Python script as in the example below. 50 | 51 | 52 | If not explicitly defined, `PosteriorDatabase` and `PosteriorDatabaseGithub` will create a new (or use old database) located at `POSTERIOR_DB_PATH` if it's 53 | defined. `PosteriorDatabaseGithub` will finally use `$HOME/.posteriordb/posterior_database` as a fallback location if no environmental variables have been set. 54 | Each model and data is only downloaded and cached when needed. 55 | 56 | ```python 57 | >>> from posteriordb import PosteriorDatabaseGithub 58 | >>> import os 59 | >>> # It is recommended that GITHUB_PAT is added to the user environmental variables 60 | >>> # outside python and not in a python script as shown in this example code 61 | >>> os.environ["GITHUB_PAT"] = "token-string-here" 62 | >>> my_pdb = PosteriorDatabaseGithub() 63 | ``` 64 | 65 | To list the posteriors available, use `posterior_names`. 66 | 67 | ```python 68 | >>> pos = my_pdb.posterior_names() 69 | >>> pos[:5] 70 | 71 | ['roaches-roaches_negbin', 72 | 'syn_gmK2D1n200-gmm_diagonal_nonordered', 73 | 'radon_mn-radon_variable_intercept_centered', 74 | 'syn_gmK3D2n300-gmm_nonordered', 75 | 'radon-radon_hierarchical_intercept_centered'] 76 | 77 | ``` 78 | 79 | In the same fashion, we can list data and models included in the database as 80 | 81 | ```python 82 | >>> mn = my_pdb.model_names() 83 | >>> mn[:5] 84 | 85 | ['gmm_diagonal_nonordered', 86 | 'radon_pool', 87 | 'radon_partial_pool_noncentered', 88 | 'blr', 89 | 'radon_hierarchical_intercept_noncentered'] 90 | 91 | 92 | >>> dn = my_pdb.dataset_names() 93 | >>> dn[:5] 94 | 95 | ['radon_mn', 96 | 'wells_centered', 97 | 'radon', 98 | 'wells_centered_educ4_interact', 99 | 'wells_centered_educ4'] 100 | 101 | 102 | ``` 103 | 104 | The posterior's name is made up of the data and model fitted 105 | to the data. Together, these two uniquely define a posterior distribution. 106 | To access a posterior object we can use the posterior name. 107 | 108 | ```python 109 | >>> posterior = my_pdb.posterior("eight_schools-eight_schools_centered") 110 | ``` 111 | 112 | From the posterior we can access the dataset and the model 113 | 114 | ```python 115 | >>> model = posterior.model 116 | >>> data = posterior.data 117 | ``` 118 | 119 | We can also access the names of posteriors, models and datasets. 120 | 121 | ```python 122 | >>> posterior.name 123 | "eight_schools-eight_schools_centered" 124 | 125 | >>> model.name 126 | "eight_schools_centered" 127 | 128 | >>> data.name 129 | "eight_schools" 130 | 131 | ``` 132 | 133 | We can access the same model and dataset also directly from the posterior database 134 | ```python 135 | >>> model = my_pdb.model("eight_schools_centered") 136 | >>> data = my_pdb.data("eight_schools") 137 | ``` 138 | 139 | From the model we can access model code and information about the model 140 | 141 | ```python 142 | >>> model.code("stan") 143 | data { 144 | int J; // number of schools 145 | real y[J]; // estimated treatment 146 | real sigma[J]; // std of estimated effect 147 | } 148 | parameters { 149 | real theta[J]; // treatment effect in school j 150 | real mu; // hyper-parameter of mean 151 | real tau; // hyper-parameter of sdv 152 | } 153 | model { 154 | tau ~ cauchy(0, 5); // a non-informative prior 155 | theta ~ normal(mu, tau); 156 | y ~ normal(theta , sigma); 157 | mu ~ normal(0, 5); 158 | } 159 | 160 | >>> model.code_file_path("stan") 161 | '/home/eero/posterior_database/content/models/stan/eight_schools_centered.stan' 162 | 163 | >>> model.information 164 | {'keywords': ['bda3_example', 'hiearchical'], 165 | 'description': 'A centered hiearchical model for the 8 schools example of Rubin (1981)', 166 | 'urls': ['http://www.stat.columbia.edu/~gelman/arm/examples/schools'], 167 | 'title': 'A centered hiearchical model for 8 schools', 168 | 'references': ['rubin1981estimation', 'gelman2013bayesian'], 169 | 'added_by': 'Mans Magnusson', 170 | 'added_date': '2019-08-12'} 171 | ``` 172 | Note that the references are referencing to BibTeX items that can be found in `content/references/references.bib`. 173 | 174 | From the dataset we can access the data values and information about it 175 | 176 | ```python 177 | >>> data.values() 178 | {'J': 8, 179 | 'y': [28, 8, -3, 7, -1, 1, 18, 12], 180 | 'sigma': [15, 10, 16, 11, 9, 11, 10, 18]} 181 | 182 | >>> data.file_path() 183 | '/tmp/tmpx16edu0w' 184 | 185 | >>> data.information 186 | {'keywords': ['bda3_example'], 187 | 'description': 'A study for the Educational Testing Service to analyze the effects of\nspecial coaching programs on test scores. See Gelman et. al. (2014), Section 5.5 for details.', 188 | 'urls': ['http://www.stat.columbia.edu/~gelman/arm/examples/schools'], 189 | 'title': 'The 8 schools dataset of Rubin (1981)', 190 | 'references': ['rubin1981estimation', 'gelman2013bayesian'], 191 | 'added_by': 'Mans Magnusson', 192 | 'added_date': '2019-08-12'} 193 | ``` 194 | 195 | To access gold standard posterior draws we can use `reference_draws` as follows. 196 | 197 | ```python 198 | >>> posterior.reference_draws_info() 199 | {'name': 'eight_schools-eight_schools_noncentered', 200 | 'inference': {'method': 'stan_sampling', 201 | 'method_arguments': {'chains': 10, 202 | 'iter': 20000, 203 | 'warmup': 10000, 204 | 'thin': 10, 205 | 'seed': 4711, 206 | 'control': {'adapt_delta': 0.95}}}, 207 | 'diagnostics': {'diagnostic_information': {'names': ['mu', 208 | 'tau', 209 | 'theta[1]', 210 | ... 211 | 212 | >>> gs = posterior.reference_draws() 213 | >>> import pandas as pd 214 | >>> pd.DataFrame(gs) 215 | 216 | theta[1] theta[2] 217 | 0 [10.6802773011458, 6.45383910854259, -2.241629... [9.71770681295263, 4.41030824418493, 0.7617047... 218 | 1 [5.70891361633589, 10.3012059848039, 4.2439533... [-2.32310565394337, 14.8121789773659, 6.517256... 219 | 2 [7.23747096507585, -0.427831558524343, 9.14782... [7.35425759420389, 8.69579738064637, 8.9058764... 220 | 3 [4.44915522912766, 2.34711393762556, 17.680378... [2.4368039319606, 5.89809320808632, 8.63031558... 221 | ... 222 | ``` 223 | 224 | Platform: UNKNOWN 225 | Description-Content-Type: text/markdown 226 | -------------------------------------------------------------------------------- /src/posteriordb.egg-info/SOURCES.txt: -------------------------------------------------------------------------------- 1 | LICENSE 2 | MANIFEST.in 3 | README.md 4 | setup.py 5 | src/posteriordb/__init__.py 6 | src/posteriordb/dataset.py 7 | src/posteriordb/model.py 8 | src/posteriordb/model_implementation_base.py 9 | src/posteriordb/posterior.py 10 | src/posteriordb/posterior_database.py 11 | src/posteriordb/posterior_database_github.py 12 | src/posteriordb/pymc3_model_implementation.py 13 | src/posteriordb/stan_model_implementation.py 14 | src/posteriordb/util.py 15 | src/posteriordb.egg-info/PKG-INFO 16 | src/posteriordb.egg-info/SOURCES.txt 17 | src/posteriordb.egg-info/dependency_links.txt 18 | src/posteriordb.egg-info/not-zip-safe 19 | src/posteriordb.egg-info/requires.txt 20 | src/posteriordb.egg-info/top_level.txt -------------------------------------------------------------------------------- /src/posteriordb.egg-info/dependency_links.txt: -------------------------------------------------------------------------------- 1 | 2 | -------------------------------------------------------------------------------- /src/posteriordb.egg-info/not-zip-safe: -------------------------------------------------------------------------------- 1 | 2 | -------------------------------------------------------------------------------- /src/posteriordb.egg-info/requires.txt: -------------------------------------------------------------------------------- 1 | requests 2 | -------------------------------------------------------------------------------- /src/posteriordb.egg-info/top_level.txt: -------------------------------------------------------------------------------- 1 | posteriordb 2 | -------------------------------------------------------------------------------- /src/posteriordb/__init__.py: -------------------------------------------------------------------------------- 1 | from .posterior_database import PosteriorDatabase 2 | from .posterior_database_github import PosteriorDatabaseGithub 3 | 4 | __version__ = "0.2.0" 5 | -------------------------------------------------------------------------------- /src/posteriordb/dataset.py: -------------------------------------------------------------------------------- 1 | import json 2 | import os 3 | import tempfile 4 | from typing import Union 5 | from zipfile import ZipFile 6 | 7 | from .posterior_database import PosteriorDatabase 8 | from .posterior_database_github import PosteriorDatabaseGithub 9 | from .util import drop_keys 10 | 11 | 12 | class Dataset: 13 | def __init__( 14 | self, name: str, posterior_db: Union[PosteriorDatabase, PosteriorDatabaseGithub] 15 | ): 16 | self.name = name 17 | self.posterior_db = posterior_db 18 | full_information = self.posterior_db.get_data_info(name=self.name) 19 | self.information = drop_keys(full_information, "data_file") 20 | 21 | def file_path(self): 22 | data = self.values() 23 | # make a temp file with unzipped data 24 | with tempfile.NamedTemporaryFile(mode="w", delete=False) as f: 25 | json.dump(data, f) 26 | file_name = f.name 27 | return file_name 28 | 29 | def values(self): 30 | # unzip the file on the fly 31 | # return contents 32 | path = self.posterior_db.get_dataset_path(self.name) 33 | with ZipFile(path) as zipfile: 34 | namelist = zipfile.namelist() 35 | n_archives = len(namelist) 36 | if n_archives != 1: 37 | raise ValueError( 38 | f"Expected a zip archive that contains one file, {path} has {n_archives} files in it" 39 | ) 40 | archive_file_name = namelist[0] 41 | with zipfile.open(archive_file_name) as f: 42 | data = json.load(f) 43 | return data 44 | -------------------------------------------------------------------------------- /src/posteriordb/model.py: -------------------------------------------------------------------------------- 1 | import os 2 | from typing import Union 3 | 4 | from .posterior_database import PosteriorDatabase 5 | from .posterior_database_github import PosteriorDatabaseGithub 6 | from .pymc3_model_implementation import PyMC3ModelImplementation 7 | from .stan_model_implementation import StanModelImplementation 8 | from .util import drop_keys 9 | 10 | implementations = {"stan": StanModelImplementation, "pymc3": PyMC3ModelImplementation} 11 | 12 | 13 | class Model: 14 | def __init__( 15 | self, name: str, posterior_db: Union[PosteriorDatabase, PosteriorDatabaseGithub] 16 | ): 17 | self.name = name 18 | self.posterior_db = posterior_db 19 | full_model_info = self.posterior_db.get_model_info(name=self.name) 20 | self.information = drop_keys(full_model_info, "model_implementations") 21 | self._implementations = full_model_info["model_implementations"] 22 | 23 | def code_file_path(self, framework: str): 24 | """ 25 | Returns filepath to model code file for `framework` 26 | """ 27 | # TODO assert that framework is a valid framework for this model 28 | return self.posterior_db.get_model_code_path(self.name, framework) 29 | 30 | def code(self, framework: str): 31 | """ 32 | Returns model code for `framework` as a string 33 | """ 34 | file_path = self.code_file_path(framework) 35 | with open(file_path) as f: 36 | contents = f.read() 37 | 38 | return contents 39 | 40 | def stan_code(self): 41 | return self.code("stan") 42 | 43 | def stan_code_file_path(self): 44 | return self.code_file_path("stan") 45 | 46 | def implementation(self, framework): 47 | implementation_info = self._implementations[framework] 48 | implementation_class = implementations[framework] 49 | implementation_obj = implementation_class( 50 | self.posterior_db, **implementation_info 51 | ) 52 | return implementation_obj 53 | -------------------------------------------------------------------------------- /src/posteriordb/model_implementation_base.py: -------------------------------------------------------------------------------- 1 | from abc import ABC 2 | from abc import abstractmethod 3 | 4 | 5 | class ModelImplementationBase(ABC): 6 | @abstractmethod 7 | def load(self): 8 | pass 9 | -------------------------------------------------------------------------------- /src/posteriordb/posterior.py: -------------------------------------------------------------------------------- 1 | import json 2 | from typing import Union 3 | from zipfile import ZipFile 4 | 5 | from .dataset import Dataset 6 | from .model import Model 7 | from .posterior_database import PosteriorDatabase 8 | from .posterior_database_github import PosteriorDatabaseGithub 9 | from .util import drop_keys 10 | 11 | 12 | class Posterior: 13 | def __init__( 14 | self, name: str, posterior_db: Union[PosteriorDatabase, PosteriorDatabaseGithub] 15 | ): 16 | self.name = name 17 | 18 | assert name in posterior_db.posterior_names() 19 | 20 | self.posterior_db = posterior_db 21 | 22 | self.posterior_info = posterior_db.get_posterior_info(name) 23 | 24 | self.model = Model(self.posterior_info["model_name"], posterior_db) 25 | 26 | self.data = Dataset(self.posterior_info["data_name"], posterior_db) 27 | 28 | self.information = drop_keys( 29 | self.posterior_info, 30 | ["name", "model_name", "data_name", "reference_posterior_name"], 31 | ) 32 | 33 | def reference_draws_info(self): 34 | return self.posterior_db.get_reference_draws_info(self.name) 35 | 36 | def reference_draws_file_path(self): 37 | return self.posterior_db.get_reference_draws_path(self.name) 38 | 39 | def reference_draws(self): 40 | reference_name = self.reference_draws_info()["name"] 41 | with ZipFile(self.reference_draws_file_path() + ".zip", "r") as z: 42 | with z.open(reference_name + ".json", "r") as f: 43 | return json.load(f) 44 | -------------------------------------------------------------------------------- /src/posteriordb/posterior_database.py: -------------------------------------------------------------------------------- 1 | import json 2 | import os 3 | from pathlib import Path 4 | 5 | 6 | def load_json_file(filepath): 7 | with open(filepath, encoding="utf-8") as f: 8 | return json.load(f) 9 | 10 | 11 | def load_info(path, assertion_function): 12 | info = load_json_file(path) 13 | assertion_function(info) 14 | return info 15 | 16 | 17 | def temporary_no_assertions(x): 18 | return x 19 | 20 | 21 | def filename(path): 22 | """Given a full file path return just the filename without extension """ 23 | # with_suffix is needed in case the file has multiple extensions 24 | return path.with_suffix("").stem 25 | 26 | 27 | def filenames_in_dir_no_extension(directory, extension): 28 | path = Path(directory) 29 | 30 | filenames = [filename(p) for p in path.glob("*" + extension)] 31 | return filenames 32 | 33 | 34 | class PosteriorDatabase: 35 | def __init__(self, path: str = None): 36 | if path is None: 37 | path = os.environ.get("POSTERIOR_DB_PATH") 38 | self.path = str(path) 39 | # TODO assert that path is a valid posterior database 40 | 41 | def full_path(self, path: str): 42 | return os.path.join(self.path, path) 43 | 44 | def posterior(self, name): 45 | # inline import needed to avoid import loop 46 | from .posterior import Posterior 47 | 48 | return Posterior(name, self) 49 | 50 | def model(self, name): 51 | # inline import needed to avoid import loop 52 | from .model import Model 53 | 54 | return Model(name, self) 55 | 56 | def data(self, name): 57 | # inline import needed to avoid import loop 58 | from .dataset import Dataset 59 | 60 | return Dataset(name, self) 61 | 62 | def posterior_info_path(self, name: str): 63 | file_path = os.path.join(self.path, "posteriors", name + ".json") 64 | return file_path 65 | 66 | def get_posterior_info(self, name: str): 67 | file_path = self.posterior_info_path(name) 68 | return load_info(file_path, temporary_no_assertions) 69 | 70 | def get_model_info(self, name: str): 71 | # load from the correct path 72 | file_name = name + ".info.json" 73 | file_path = os.path.join(self.path, "models", "info", file_name) 74 | 75 | return load_info(file_path, temporary_no_assertions) 76 | 77 | def get_data_info(self, name: str): 78 | file_name = name + ".info.json" 79 | file_path = os.path.join(self.path, "data", "info", file_name) 80 | 81 | return load_info(file_path, temporary_no_assertions) 82 | 83 | def get_reference_draws_path(self, name: str): 84 | reference_root = os.path.join(self.path, "reference_posteriors/draws/draws") 85 | reference_name = self.get_posterior_info(name)["reference_posterior_name"] 86 | assert reference_name is not None 87 | file_path = os.path.join(reference_root, reference_name + ".json") 88 | return file_path 89 | 90 | def get_reference_draws_info(self, name: str): 91 | reference_root = os.path.join(self.path, "reference_posteriors/draws/info") 92 | reference_name = self.get_posterior_info(name)["reference_posterior_name"] 93 | assert reference_name is not None 94 | file_path = os.path.join(reference_root, reference_name + ".info.json") 95 | return load_info(file_path, temporary_no_assertions) 96 | 97 | def get_model_code_path(self, name, framework): 98 | model_info = self.get_model_info(name) 99 | path_within_posterior_db = model_info["model_implementations"][framework][ 100 | "model_code" 101 | ] 102 | full_path = os.path.join(self.path, path_within_posterior_db) 103 | return full_path 104 | 105 | def get_dataset_path(self, name): 106 | data_info = self.get_data_info(name) 107 | path = os.path.join(self.path, data_info["data_file"] + ".zip") 108 | return path 109 | 110 | def posterior_names(self): 111 | directory = os.path.join(self.path, "posteriors") 112 | # walk directory, find json files 113 | # strip file extension 114 | return filenames_in_dir_no_extension(directory, ".json") 115 | 116 | def model_names(self): 117 | directory = os.path.join(self.path, "models", "info") 118 | return filenames_in_dir_no_extension(directory, ".info.json") 119 | 120 | def dataset_names(self): 121 | directory = os.path.join(self.path, "data", "info") 122 | return filenames_in_dir_no_extension(directory, ".info.json") 123 | 124 | def posteriors(self): 125 | names = self.posterior_names() 126 | # inline import needed to avoid import loop 127 | from .posterior import Posterior 128 | 129 | for name in names: 130 | yield Posterior(name, self) 131 | 132 | def models(self): 133 | names = self.model_names() 134 | # inline import needed to avoid import loop 135 | from .model import Model 136 | 137 | for name in names: 138 | yield Model(name, self) 139 | 140 | def datasets(self): 141 | names = self.dataset_names() 142 | # inline import needed to avoid import loop 143 | from .dataset import Dataset 144 | 145 | for name in names: 146 | yield Dataset(name, self) 147 | -------------------------------------------------------------------------------- /src/posteriordb/posterior_database_github.py: -------------------------------------------------------------------------------- 1 | import hashlib 2 | import json 3 | import os 4 | import tempfile 5 | from pathlib import Path 6 | import requests 7 | 8 | 9 | def temporary_no_assertions(x): 10 | return x 11 | 12 | 13 | def get_requests(*args, n=3, **kwargs): 14 | for _ in range(n): 15 | try: 16 | response = requests.get(*args, **kwargs) 17 | if response.ok: 18 | break 19 | except Exception as e: 20 | print(e) 21 | continue 22 | else: 23 | print("response:", response.json()) 24 | raise ValueError("response was not successful") 25 | return response 26 | 27 | 28 | def github_pat(): 29 | GITHUB_PAT = os.environ.get("GITHUB_PAT") 30 | headers = {} 31 | if GITHUB_PAT is not None: 32 | headers["Authorization"] = "token {}".format(GITHUB_PAT) 33 | else: 34 | print( 35 | "GitHub access token was not defined (env GITHUB_PAT not defined), using limited API rate limit." 36 | ) 37 | return headers 38 | 39 | 40 | def get_content(url, path=None, headers=None): 41 | """Download contents assuming GitHub API v3""" 42 | 43 | if headers is None: 44 | headers = github_pat() 45 | if path is not None: 46 | path = Path(path) 47 | verify = os.environ.get("REQUESTS_VERIFY", True) 48 | if str(verify).lower() in ("0", "false"): 49 | verify = False 50 | verify = bool(verify) 51 | 52 | response = get_requests(url, verify=verify, headers=headers) 53 | contents = {} 54 | 55 | for content in response.json(): 56 | try: 57 | if content["type"] == "dir": 58 | contents.update( 59 | get_content(content["_links"]["self"], path=path, headers=headers) 60 | ) 61 | else: 62 | if path: 63 | key = path / content["path"] 64 | else: 65 | key = content["path"] 66 | contents[key] = content 67 | except Exception as e: 68 | print("Invalid content:", content, "Exception was raised (and ignored):", e) 69 | continue 70 | return contents 71 | 72 | 73 | def download_file(url, path, overwrite=False, sha=None): 74 | """Download file with a requests. 75 | 76 | To manually disable requests verify 77 | set environmental variable REQUESTS_VERIFY to false. 78 | """ 79 | if (not overwrite) and path.exists(): 80 | return True 81 | if overwrite and (sha is not None) and path.exists(): 82 | if sha == get_sha1_hash(path): 83 | return True 84 | 85 | verify = os.environ.get("REQUESTS_VERIFY", True) 86 | if str(verify).lower() in ("0", "false"): 87 | verify = False 88 | verify = bool(verify) 89 | 90 | headers = github_pat() 91 | try: 92 | response = get_requests(url, verify=verify, headers=headers) 93 | 94 | path.parent.mkdir(parents=True, exist_ok=True) 95 | 96 | with path.open(mode="wb") as f: 97 | f.write(response.content) 98 | except Exception as e: 99 | print("Exception was raised (and ignored):", e) 100 | return False 101 | return True 102 | 103 | 104 | def get_sha1_hash(path): 105 | sha1_hash = hashlib.sha1() 106 | size = path.stat().st_size 107 | with path.open("rb") as f: 108 | sha1_hash.update(bytes("blob {}".format(size), encoding="utf-8") + b"\0") 109 | for byte_block in iter(lambda: f.read(4096), b""): 110 | sha1_hash.update(byte_block) 111 | return sha1_hash.hexdigest() 112 | 113 | 114 | def load_json_file(path, metadata, overwrite=False): 115 | if not path.exists(): 116 | if metadata is not None: 117 | download_file(metadata["download_url"], path) 118 | else: 119 | raise TypeError("File was not found in GitHub") 120 | elif overwrite: 121 | if metadata is not None: 122 | download_file(metadata["download_url"], path, sha=metadata["sha"]) 123 | with path.open(encoding="utf-8") as f: 124 | data = json.load(f) 125 | return data 126 | 127 | 128 | def load_info(path, assertion_function, metadata, overwrite=False): 129 | info = load_json_file(path, metadata, overwrite=overwrite) 130 | assertion_function(info) 131 | return info 132 | 133 | 134 | def filenames_in_dir_no_extension(directory, gh_directory, extension): 135 | path = Path(directory) 136 | 137 | filenames = [p.with_suffix("").stem for p in path.glob("*" + extension)] 138 | gh_filenames = [p.with_suffix("").stem for p in gh_directory] 139 | return sorted(set(filenames + gh_filenames)) 140 | 141 | 142 | class PosteriorDatabaseGithub: 143 | def __init__( 144 | self, 145 | path: str = None, 146 | repo="MansMeg/posteriordb", 147 | ref="master", 148 | refresh=True, 149 | overwrite=False, 150 | ): 151 | if path is None: 152 | path = os.environ.get("POSTERIOR_DB_PATH") 153 | if path is None: 154 | path = Path.home() / ".posteriordb" / "posterior_database" 155 | path.mkdir(parents=True, exist_ok=True) 156 | self.path = Path(path) 157 | 158 | self.overwrite = overwrite 159 | self._repo = repo 160 | self._ref = ref 161 | 162 | self.refresh_url() 163 | 164 | self._progressbar_width = 30 165 | self._progressbar_marker = b"\xe2\x96\xa0".decode("utf-8") 166 | 167 | if refresh: 168 | self.refresh_github() 169 | else: 170 | self._links = {} 171 | 172 | # TODO assert that path is a valid posterior database 173 | 174 | def refresh_url(self, repo=None, ref=None): 175 | if repo is not None: 176 | self._repo = repo 177 | if ref is not None: 178 | self._ref = ref 179 | 180 | self._url = "https://api.github.com/repos/{repo}/contents/posterior_database?ref={ref}".format( 181 | repo=self._repo, ref=self._ref 182 | ) 183 | 184 | def refresh_github(self): 185 | self._links = get_content(self._url, path=self.path.parent) 186 | 187 | def download_all(self, refresh=False, overwrite=None, show_progress=True): 188 | """Download all files for database.""" 189 | if refresh: 190 | self.refresh_github() 191 | if overwrite is None: 192 | overwrite = self.overwrite 193 | n = len(self._links) 194 | for i, (path, metadata) in enumerate(self._links.items(), 1): 195 | print( 196 | "\rDownloading {:<30} ({}/{})".format( 197 | self._progressbar_marker * int(i / n * self._progressbar_width), 198 | i, 199 | n, 200 | ), 201 | end="", 202 | flush=True, 203 | ) 204 | download_file( 205 | metadata["download_url"], path, overwrite=overwrite, sha=metadata["sha"] 206 | ) 207 | 208 | def full_path(self, path: str): 209 | return self.path / path 210 | 211 | def posterior(self, name): 212 | # inline import needed to avoid import loop 213 | from .posterior import Posterior 214 | 215 | return Posterior(name, self) 216 | 217 | def model(self, name): 218 | # inline import needed to avoid import loop 219 | from .model import Model 220 | 221 | return Model(name, self) 222 | 223 | def data(self, name): 224 | # inline import needed to avoid import loop 225 | from .dataset import Dataset 226 | 227 | return Dataset(name, self) 228 | 229 | def posterior_info_path(self, name: str): 230 | path = self.path / "posteriors" / (name + ".json") 231 | return path 232 | 233 | def get_posterior_info(self, name: str): 234 | path = self.posterior_info_path(name) 235 | return load_info( 236 | path, 237 | temporary_no_assertions, 238 | self._links.get(path), 239 | overwrite=self.overwrite, 240 | ) 241 | 242 | def get_model_info(self, name: str): 243 | # load from the correct path 244 | file_name = name + ".info.json" 245 | path = self.path / "models" / "info" / file_name 246 | 247 | return load_info( 248 | path, 249 | temporary_no_assertions, 250 | self._links.get(path), 251 | overwrite=self.overwrite, 252 | ) 253 | 254 | def get_data_info(self, name: str): 255 | file_name = name + ".info.json" 256 | path = self.path / "data" / "info" / file_name 257 | 258 | return load_info( 259 | path, 260 | temporary_no_assertions, 261 | self._links.get(path), 262 | overwrite=self.overwrite, 263 | ) 264 | 265 | def get_reference_draws_path(self, name: str): 266 | reference_root = self.path / "reference_posteriors" / "draws" / "draws" 267 | reference_name = self.get_posterior_info(name).get("reference_posterior_name") 268 | assert reference_name is not None 269 | path = reference_root / (reference_name + ".json") 270 | return path 271 | 272 | def get_reference_draws_info(self, name: str): 273 | reference_root = self.path / "reference_posteriors" / "draws" / "info" 274 | reference_name = self.get_posterior_info(name).get("reference_posterior_name") 275 | assert reference_name is not None 276 | path = reference_root / (reference_name + ".info.json") 277 | return load_info( 278 | path, 279 | temporary_no_assertions, 280 | self._links.get(path, None), 281 | overwrite=self.overwrite, 282 | ) 283 | 284 | def get_model_code_path(self, name, framework): 285 | model_info = self.get_model_info(name) 286 | path_within_posterior_db = model_info["model_implementations"][framework][ 287 | "model_code" 288 | ] 289 | path = self.path / path_within_posterior_db 290 | 291 | # download model code 292 | if not path.exists() or self.overwrite: 293 | download_file( 294 | self._links[path]["download_url"], 295 | path, 296 | overwrite=self.overwrite, 297 | sha=self._links[path]["sha"], 298 | ) 299 | 300 | return path 301 | 302 | def get_dataset_path(self, name): 303 | data_info = self.get_data_info(name) 304 | path = self.path / (data_info["data_file"] + ".zip") 305 | 306 | # download model code 307 | if not path.exists() or self.overwrite: 308 | download_file( 309 | self._links[path]["download_url"], 310 | path, 311 | overwrite=self.overwrite, 312 | sha=self._links[path]["sha"], 313 | ) 314 | 315 | return path 316 | 317 | def posterior_names(self): 318 | directory = self.path / "posteriors" 319 | # walk directory, find json files 320 | # strip file extension 321 | gh_directory = [ 322 | key for key in self._links if str(directory.resolve()) in str(key.resolve()) 323 | ] 324 | return filenames_in_dir_no_extension(directory, gh_directory, ".json") 325 | 326 | def model_names(self): 327 | directory = self.path / "models" / "info" 328 | gh_directory = [ 329 | key for key in self._links if str(directory.resolve()) in str(key.resolve()) 330 | ] 331 | return filenames_in_dir_no_extension(directory, gh_directory, ".info.json") 332 | 333 | def dataset_names(self): 334 | directory = self.path / "data" / "info" 335 | gh_directory = [ 336 | key for key in self._links if str(directory.resolve()) in str(key.resolve()) 337 | ] 338 | return filenames_in_dir_no_extension(directory, gh_directory, ".info.json") 339 | 340 | def posteriors(self): 341 | names = self.posterior_names() 342 | # inline import needed to avoid import loop 343 | from .posterior import Posterior 344 | 345 | for name in names: 346 | yield Posterior(name, self) 347 | 348 | def models(self): 349 | names = self.model_names() 350 | # inline import needed to avoid import loop 351 | from .model import Model 352 | 353 | for name in names: 354 | yield Model(name, self) 355 | 356 | def datasets(self): 357 | names = self.dataset_names() 358 | # inline import needed to avoid import loop 359 | from .dataset import Dataset 360 | 361 | for name in names: 362 | yield Dataset(name, self) 363 | -------------------------------------------------------------------------------- /src/posteriordb/pymc3_model_implementation.py: -------------------------------------------------------------------------------- 1 | import os 2 | import sys 3 | 4 | from .model_implementation_base import ModelImplementationBase 5 | 6 | 7 | class add_path: 8 | def __init__(self, path): 9 | self.path = path 10 | 11 | def __enter__(self): 12 | sys.path.insert(0, self.path) 13 | 14 | def __exit__(self, exc_type, exc_value, traceback): 15 | try: 16 | sys.path.remove(self.path) 17 | except ValueError: 18 | pass 19 | 20 | 21 | class PyMC3ModelImplementation(ModelImplementationBase): 22 | def __init__(self, posterior_db, *, model_code): 23 | self.posterior_db = posterior_db 24 | self.model_code = model_code 25 | 26 | def load(self): 27 | try: 28 | import pymc3 29 | except ImportError: 30 | raise ValueError("pymc3 needs to be installed") 31 | import importlib 32 | 33 | model_code_file = self.posterior_db.full_path(self.model_code) 34 | model_code_directory = os.path.dirname(model_code_file) 35 | with add_path(model_code_directory): 36 | model_code_module_name, _ = os.path.splitext( 37 | os.path.basename(model_code_file) 38 | ) 39 | module = importlib.import_module(model_code_module_name) 40 | 41 | return module.model 42 | -------------------------------------------------------------------------------- /src/posteriordb/stan_model_implementation.py: -------------------------------------------------------------------------------- 1 | from .model_implementation_base import ModelImplementationBase 2 | 3 | 4 | class StanModelImplementation(ModelImplementationBase): 5 | def __init__(self, posterior_db, *, model_code): 6 | self.posterior_db = posterior_db 7 | self.model_code = model_code 8 | 9 | def load(self): 10 | try: 11 | import pystan 12 | except ImportError: 13 | raise ValueError("`pystan` needs to be installed") 14 | model_code_file = self.posterior_db.full_path(self.model_code) 15 | stan_model = pystan.StanModel(file=model_code_file) 16 | return stan_model 17 | -------------------------------------------------------------------------------- /src/posteriordb/util.py: -------------------------------------------------------------------------------- 1 | def drop_keys(dct, keys_to_drop): 2 | if not isinstance(keys_to_drop, list): 3 | keys_to_drop = [keys_to_drop] 4 | 5 | new_dct = {k: v for (k, v) in dct.items() if k not in keys_to_drop} 6 | 7 | return new_dct 8 | -------------------------------------------------------------------------------- /tests/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/stan-dev/posteriordb-python/53731f5c88e000a12c44968cca41814c8a67450c/tests/__init__.py -------------------------------------------------------------------------------- /tests/integrity_tests/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/stan-dev/posteriordb-python/53731f5c88e000a12c44968cca41814c8a67450c/tests/integrity_tests/__init__.py -------------------------------------------------------------------------------- /tests/integrity_tests/helpers.py: -------------------------------------------------------------------------------- 1 | import collections 2 | 3 | import pytest 4 | 5 | 6 | def _ensure_all_distinct(dct, error_message_callable): 7 | reverse_mapping = collections.defaultdict(list) 8 | for key, val in dct.items(): 9 | reverse_mapping[val].append(key) 10 | 11 | duplicates = {k: v for (k, v) in reverse_mapping.items() if len(v) > 1} 12 | 13 | if len(duplicates) > 0: 14 | error_msgs = "\n".join( 15 | [ 16 | error_message_callable(duplicate_val, duplicate_names) 17 | for (duplicate_val, duplicate_names) in duplicates.items() 18 | ] 19 | ) 20 | pytest.fail(error_msgs) 21 | 22 | 23 | def ensure_model_codes_are_distinct(dct): 24 | def error_msg(code_path, names): 25 | return f"""Models {", ".join(names)} had the same stan code: {code_path}""" 26 | 27 | __tracebackhide__ = True 28 | 29 | _ensure_all_distinct(dct, error_msg) 30 | 31 | 32 | def ensure_dataset_paths_are_distinct(dct): 33 | def error_msg(data_file_path, names): 34 | return ( 35 | f"""Datasets {", ".join(names)} had the same data file: {data_file_path}""" 36 | ) 37 | 38 | __tracebackhide__ = True 39 | 40 | _ensure_all_distinct(dct, error_msg) 41 | -------------------------------------------------------------------------------- /tests/integrity_tests/test_integrity.py: -------------------------------------------------------------------------------- 1 | import os 2 | 3 | from . import helpers 4 | from posteriordb import PosteriorDatabase 5 | 6 | 7 | def get_posterior_db(): 8 | project_path = os.path.dirname( 9 | os.path.dirname(os.path.dirname(__file__)) 10 | ) 11 | pdb_path = os.path.join(project_path, "posteriordb", "posterior_database") 12 | pdb = PosteriorDatabase(pdb_path) 13 | assert len(pdb.posterior_names()) > 0 14 | return pdb 15 | 16 | 17 | def test_models_dont_have_same_model_code(): 18 | pdb = get_posterior_db() 19 | 20 | model_code_paths = { 21 | model.name: model.stan_code_file_path() for model in pdb.models() 22 | } 23 | 24 | helpers.ensure_model_codes_are_distinct(model_code_paths) 25 | 26 | 27 | def test_datasets_dont_have_same_data(): 28 | pdb = get_posterior_db() 29 | 30 | data_names = pdb.dataset_names() 31 | 32 | data_file_paths = {name: pdb.get_dataset_path(name) for name in data_names} 33 | 34 | helpers.ensure_dataset_paths_are_distinct(data_file_paths) 35 | -------------------------------------------------------------------------------- /tests/test_pdb.py: -------------------------------------------------------------------------------- 1 | import os 2 | import re 3 | 4 | from posteriordb import PosteriorDatabase, PosteriorDatabaseGithub 5 | from posteriordb.posterior_database_github import get_sha1_hash 6 | 7 | 8 | def test_posterior_database(): 9 | # path to ../../ which is the posterior database directory 10 | project_path = os.path.dirname(os.path.dirname(__file__)) 11 | pdb_path = os.path.join(project_path, "posteriordb", "posterior_database") 12 | pdb = PosteriorDatabase(pdb_path) 13 | 14 | model_names = pdb.model_names() 15 | assert len(model_names) > 0 16 | 17 | dataset_names = pdb.dataset_names() 18 | assert len(dataset_names) > 0 19 | 20 | posterior_names = pdb.posterior_names() 21 | 22 | assert len(posterior_names) > 0 23 | 24 | for name in posterior_names: 25 | posterior = pdb.posterior(name) 26 | 27 | assert posterior.name is not None 28 | 29 | # test dataset methods 30 | data = posterior.data 31 | assert data.name is not None 32 | 33 | assert data.values() is not None 34 | assert data.file_path() is not None 35 | 36 | assert data.information is not None 37 | 38 | # test that pdb.data works 39 | data2 = pdb.data(data.name) 40 | assert data2 is not None 41 | 42 | # test model methods 43 | model = posterior.model 44 | 45 | assert model.name is not None 46 | 47 | assert model.code("stan") is not None 48 | assert model.code_file_path("stan") is not None 49 | assert model.stan_code() is not None 50 | assert model.stan_code_file_path() is not None 51 | 52 | assert model.information is not None 53 | 54 | # test that pdb.model works 55 | model2 = pdb.model(model.name) 56 | assert model2 is not None 57 | 58 | posteriors = list(pdb.posteriors()) 59 | assert len(posteriors) > 0 60 | 61 | models = list(pdb.models()) 62 | assert len(models) > 0 63 | 64 | datasets = list(pdb.datasets()) 65 | assert len(datasets) > 0 66 | 67 | 68 | def test_posterior_database_github(): 69 | # Skip test if GITHUB_PAT not defined 70 | if os.environ.get("GITHUB_PAT") is None: 71 | if os.environ.get("CI"): 72 | raise TypeError("GITHUB_PAT environmental variable is missing") 73 | return 74 | 75 | kwargs = {} 76 | if os.environ.get("GITHUB_ACTIONS"): 77 | kwargs["repo"] = os.environ.get("GITHUB_REPOSITORY", "MansMeg/posteriordb") 78 | kwargs["ref"] = re.sub( 79 | "^refs/heads/", "", os.environ.get("GITHUB_REF", "master") 80 | ) 81 | pdb = PosteriorDatabaseGithub(**kwargs) 82 | 83 | model_names = pdb.model_names() 84 | assert len(model_names) > 0 85 | 86 | dataset_names = pdb.dataset_names() 87 | assert len(dataset_names) > 0 88 | 89 | posterior_names = pdb.posterior_names() 90 | 91 | assert len(posterior_names) > 0 92 | 93 | for name in posterior_names: 94 | posterior = pdb.posterior(name) 95 | 96 | assert posterior.name is not None 97 | 98 | # test dataset methods 99 | data = posterior.data 100 | assert data.name is not None 101 | 102 | assert data.values() is not None 103 | assert data.file_path() is not None 104 | 105 | assert data.information is not None 106 | 107 | # test that pdb.data works 108 | data2 = pdb.data(data.name) 109 | assert data2 is not None 110 | 111 | # test model methods 112 | model = posterior.model 113 | 114 | assert model.name is not None 115 | 116 | assert model.code("stan") is not None 117 | assert model.code_file_path("stan") is not None 118 | assert model.stan_code() is not None 119 | assert model.stan_code_file_path() is not None 120 | 121 | assert model.information is not None 122 | 123 | # test that pdb.model works 124 | model2 = pdb.model(model.name) 125 | assert model2 is not None 126 | 127 | # check sha1 128 | model_files = [ 129 | (key, item["sha"]) 130 | for key, item in pdb._links.items() 131 | if ( 132 | (key.with_suffix("").stem == model.name) 133 | and ("/models/" in key.as_posix()) 134 | ) 135 | ] 136 | for model_file_path, sha1_github in model_files: 137 | sha1_file = get_sha1_hash(model_file_path) 138 | assert sha1_file == sha1_github 139 | 140 | posteriors = list(pdb.posteriors()) 141 | assert len(posteriors) > 0 142 | 143 | models = list(pdb.models()) 144 | assert len(models) > 0 145 | 146 | datasets = list(pdb.datasets()) 147 | assert len(datasets) > 0 148 | -------------------------------------------------------------------------------- /tox.ini: -------------------------------------------------------------------------------- 1 | # tox (https://tox.readthedocs.io/) is a tool for running tests 2 | # in multiple virtualenvs. This configuration file will run the 3 | # test suite on all supported python versions. To use it, "pip install tox" 4 | # and then run "tox" from this directory. 5 | 6 | [tox] 7 | envlist = py36, py37, py38, py39 8 | 9 | [testenv] 10 | deps = 11 | pytest 12 | pytest-cov 13 | commands = 14 | pytest --cov=posteriordb --cov-append {posargs:-vv} --cov-report=term 15 | depends = 16 | {py36, py37, py38, py39}: clean-coverage 17 | report-coverage: py36, py37, py38, py39 18 | 19 | [testenv:clean-coverage] 20 | skip_install = true 21 | deps = coverage 22 | commands = coverage erase 23 | 24 | [testenv:report-coverage] 25 | skip_install = true 26 | deps = coverage 27 | commands = 28 | coverage html 29 | coverage report 30 | 31 | [testenv:linting] 32 | skip_install = True 33 | basepython = python3 34 | deps = pre-commit>=1.11.0 35 | commands = pre-commit run --all-files --show-diff-on-failure 36 | 37 | [gh-actions] 38 | python = 39 | 3.6: py36 40 | 3.7: py37 41 | 3.8: py38 42 | 3.9: py39 43 | --------------------------------------------------------------------------------