diff --git a/.github/workflows/docs.yaml b/.github/workflows/docs.yaml deleted file mode 100644 index 87946a92..00000000 --- a/.github/workflows/docs.yaml +++ /dev/null @@ -1,38 +0,0 @@ -name: Quarto documents - -on: - pull_request: - branches: [main] - push: - branches: [main] - -jobs: - render-docs: - runs-on: ubuntu-latest - steps: - - uses: actions/checkout@v4 - - - uses: quarto-dev/quarto-actions/setup@v2 - - - uses: actions/setup-python@v5 - with: - python-version: "3.12" - - - name: cache poetry - uses: actions/cache@v4 - with: - path: ~/.local - key: ${{ runner.os }}-poetry - - - name: install poetry - run: pip install poetry - - - name: install package - run: poetry install --with dev -C model - - - name: Render documents - run: | - cd model - for file in $(find docs -name '*.qmd'); do - poetry run quarto render $file - done diff --git a/.github/workflows/website.yaml b/.github/workflows/website.yaml index d6bdc36a..493bd6f8 100644 --- a/.github/workflows/website.yaml +++ b/.github/workflows/website.yaml @@ -15,7 +15,46 @@ permissions: id-token: write jobs: + render-docs: + runs-on: ubuntu-latest + steps: + - uses: actions/checkout@v4 + + - uses: quarto-dev/quarto-actions/setup@v2 + + - uses: actions/setup-python@v5 + with: + python-version: "3.12" + + - name: cache poetry + uses: actions/cache@v4 + with: + path: ~/.local + key: ${{ runner.os }}-poetry + + - name: install poetry + run: pip install poetry + + - name: install package + run: poetry install --with dev -C model + + - name: Render documents + run: | + cd model + mkdir _compiled + for file in $(find docs -name '*.qmd'); do + poetry run quarto render $file --to rst --output-dir ../_compiled + done + + # Upload + - name: Upload artifacts + uses: actions/upload-artifact@v3 + with: + name: tutorials + path: model/_compiled/ + build: + needs: render-docs runs-on: ubuntu-latest permissions: contents: write @@ -26,6 +65,13 @@ jobs: - name: Setup Pages uses: actions/configure-pages@v4 + # Load the artifact github-pages-tutorials + - name: Download artifacts + uses: actions/download-artifact@v3 + with: + name: tutorials + path: docs/source/tutorials/ + - name: Set up Python uses: actions/setup-python@v5 with: @@ -67,4 +113,4 @@ jobs: uses: actions/deploy-pages@v4 with: artifact_name: github-pages - preview: false # Not yet available to the public. + preview: true # Not yet available to the public. diff --git a/README.md b/README.md index 06ad7253..fd1e4875 100755 --- a/README.md +++ b/README.md @@ -7,7 +7,6 @@ [![installation and testing pipeline](https://github.com/CDCgov/multisignal-epi-inference/actions/workflows/pipeline.yaml/badge.svg)](https://github.com/CDCgov/multisignal-epi-inference/actions/workflows/pipeline.yaml) [![Docs: model](https://github.com/CDCgov/multisignal-epi-inference/actions/workflows/website.yaml/badge.svg)](https://github.com/CDCgov/multisignal-epi-inference/actions/workflows/website.yaml) [![codecov (model)](https://codecov.io/gh/CDCgov/multisignal-epi-inference/graph/badge.svg?token=7Z06HOMYR1)](https://codecov.io/gh/CDCgov/multisignal-epi-inference) -[![Quarto documents](https://github.com/CDCgov/multisignal-epi-inference/actions/workflows/docs.yaml/badge.svg)](https://github.com/CDCgov/multisignal-epi-inference/actions/workflows/docs.yaml) This repo hosts the multisignal (*a.k.a.* signal fusion) renewal project: an internal forecasting model that leverages multiple data sources for enhancing epidemiological modeling of infectious disease outbreaks. diff --git a/docs/build/doctrees/bugs.doctree b/docs/build/doctrees/bugs.doctree deleted file mode 100644 index 25ddfa3f..00000000 Binary files a/docs/build/doctrees/bugs.doctree and /dev/null differ diff --git a/docs/build/doctrees/contribute.doctree b/docs/build/doctrees/contribute.doctree deleted file mode 100644 index ca43dfd2..00000000 Binary files a/docs/build/doctrees/contribute.doctree and /dev/null differ diff --git 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a/docs/build/doctrees/test_reference/test_regression.doctree b/docs/build/doctrees/test_reference/test_regression.doctree deleted file mode 100644 index e7bfb707..00000000 Binary files a/docs/build/doctrees/test_reference/test_regression.doctree and /dev/null differ diff --git a/docs/build/doctrees/test_reference/test_transforms.doctree b/docs/build/doctrees/test_reference/test_transforms.doctree deleted file mode 100644 index 505bb02a..00000000 Binary files a/docs/build/doctrees/test_reference/test_transforms.doctree and /dev/null differ diff --git a/docs/build/doctrees/usage.doctree b/docs/build/doctrees/usage.doctree deleted file mode 100644 index 40eccbe5..00000000 Binary files a/docs/build/doctrees/usage.doctree and /dev/null differ diff --git a/docs/build/html/.buildinfo b/docs/build/html/.buildinfo deleted file mode 100644 index a7284647..00000000 --- a/docs/build/html/.buildinfo +++ /dev/null @@ -1,4 +0,0 @@ -# Sphinx build info version 1 -# This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done. -config: 901af503b84dff1464beaf13282c3a02 # pragma: allowlist secret -tags: 645f666f9bcd5a90fca523b33c5a78b7 # pragma: allowlist secret diff --git a/docs/build/html/.nojekyll b/docs/build/html/.nojekyll deleted file mode 100644 index e69de29b..00000000 diff --git a/docs/build/html/_sources/bugs.rst.txt b/docs/build/html/_sources/bugs.rst.txt deleted file mode 100644 index 67e7f4b9..00000000 --- a/docs/build/html/_sources/bugs.rst.txt +++ /dev/null @@ -1,52 +0,0 @@ -Reporting Issues -================ - -To report issues and work on bugs, please head to ``. Please adopt the following template in making issues. This template should be used as an outline. It may not be necessary to fill out every section. Delete this block of text and fill in anything in brackets. - -Make sure you follow the project's standards specified in `this adr doc ` (private link) - -Goal ----- - -[1-3 sentence summary of the issue or feature request. E.g. "We want to be able to ..."] - -Context -------- - -[Short paragraph describing how the issue arose and constraints imposed by the existing code architecture] - -Required features ------------------ - -- [Describe each thing you need the code to do to achieve the goal] -- [Example 1: Use a config to set input and output paths] -- [Example 2: Read in some-dataset and output some-transformed-dataset] -- etc... - -Specifications --------------- - -[A checklist to keep track of details for each feature. At least one specification per feature is recommended. Edit the example below:] - -- [ ] EX2: A function that reads data from the `some-api` API and returns the dataset -- [ ] EX2: Another function that inputs the dataset, performs $x$ transform, and outputs $y$ -- [ ] EX1: A script that runs the workflow from a config -- [ ] All functions should follow PEP8 package conventions with blah, blah, blah -- [ ] The workflow should run in the VAP from `directory` -- [ ] All functions should have associated unit tests -- [ ] etc. etc. - -Out of scope ------------- - -- [Things out of scope from this issue/PR] - -Related documents ------------------ - -- [Link to related scripts, functions, issues, PRs, conversations, datasets, etc.] - - -Note: [this page is a work in progress; the above text was taken from `https://github.com/CDCgov/multisignal-epi-inference `_ on 2024/03/25] - -.. todo:: Get baseline, accurate version of the Reporting Issues page. diff --git a/docs/build/html/_sources/contribute.rst.txt b/docs/build/html/_sources/contribute.rst.txt deleted file mode 100644 index 96f2ec1d..00000000 --- a/docs/build/html/_sources/contribute.rst.txt +++ /dev/null @@ -1,10 +0,0 @@ -Contributing To MSEI -==================== - -Anyone is encouraged to contribute to the repository by `forking `_ and submitting a pull request. (If you are new to GitHub, you might start with a `basic tutorial `_.) By contributing to this project, you grant a world-wide, royalty-free, perpetual, irrevocable, non-exclusive, transferable license to all users under the terms of the `Apache Software License v2 `_) or later. - -All comments, messages, pull requests, and other submissions received through CDC including this GitHub page may be subject to applicable federal law, including but not limited to the Federal Records Act, and may be archived. Learn more at `http://www.cdc.gov/other/privacy.html `_. - -Note: [this page is a work in progress; the above text was taken from `https://github.com/CDCgov/multisignal-epi-inference `_ on 2024/03/25] - -.. todo:: Get baseline, accurate version of the CONTRIBUTING page. diff --git a/docs/build/html/_sources/ctoc.rst.txt b/docs/build/html/_sources/ctoc.rst.txt deleted file mode 100644 index 9f4ed5f1..00000000 --- a/docs/build/html/_sources/ctoc.rst.txt +++ /dev/null @@ -1,12 +0,0 @@ -Complete Table Of Contents -========================== - -.. toctree:: - :maxdepth: 4 - - msei_reference/index - test_reference/index - genindex - modindex - search - glossary diff --git a/docs/build/html/_sources/faq.rst.txt b/docs/build/html/_sources/faq.rst.txt deleted file mode 100644 index 61030d9d..00000000 --- a/docs/build/html/_sources/faq.rst.txt +++ /dev/null @@ -1,6 +0,0 @@ -FAQ -=== - -Note: [this page is a work in progress; this page is a placeholder] - -.. todo:: Get baseline, accurate version of the Frequently Asked Questions (FAQ) page. diff --git a/docs/build/html/_sources/general/bugs.rst.txt b/docs/build/html/_sources/general/bugs.rst.txt deleted file mode 100644 index 67e7f4b9..00000000 --- a/docs/build/html/_sources/general/bugs.rst.txt +++ /dev/null @@ -1,52 +0,0 @@ -Reporting Issues -================ - -To report issues and work on bugs, please head to ``. Please adopt the following template in making issues. This template should be used as an outline. It may not be necessary to fill out every section. Delete this block of text and fill in anything in brackets. - -Make sure you follow the project's standards specified in `this adr doc ` (private link) - -Goal ----- - -[1-3 sentence summary of the issue or feature request. E.g. "We want to be able to ..."] - -Context -------- - -[Short paragraph describing how the issue arose and constraints imposed by the existing code architecture] - -Required features ------------------ - -- [Describe each thing you need the code to do to achieve the goal] -- [Example 1: Use a config to set input and output paths] -- [Example 2: Read in some-dataset and output some-transformed-dataset] -- etc... - -Specifications --------------- - -[A checklist to keep track of details for each feature. At least one specification per feature is recommended. Edit the example below:] - -- [ ] EX2: A function that reads data from the `some-api` API and returns the dataset -- [ ] EX2: Another function that inputs the dataset, performs $x$ transform, and outputs $y$ -- [ ] EX1: A script that runs the workflow from a config -- [ ] All functions should follow PEP8 package conventions with blah, blah, blah -- [ ] The workflow should run in the VAP from `directory` -- [ ] All functions should have associated unit tests -- [ ] etc. etc. - -Out of scope ------------- - -- [Things out of scope from this issue/PR] - -Related documents ------------------ - -- [Link to related scripts, functions, issues, PRs, conversations, datasets, etc.] - - -Note: [this page is a work in progress; the above text was taken from `https://github.com/CDCgov/multisignal-epi-inference `_ on 2024/03/25] - -.. todo:: Get baseline, accurate version of the Reporting Issues page. diff --git a/docs/build/html/_sources/general/contribute.rst.txt b/docs/build/html/_sources/general/contribute.rst.txt deleted file mode 100644 index 96f2ec1d..00000000 --- a/docs/build/html/_sources/general/contribute.rst.txt +++ /dev/null @@ -1,10 +0,0 @@ -Contributing To MSEI -==================== - -Anyone is encouraged to contribute to the repository by `forking `_ and submitting a pull request. (If you are new to GitHub, you might start with a `basic tutorial `_.) By contributing to this project, you grant a world-wide, royalty-free, perpetual, irrevocable, non-exclusive, transferable license to all users under the terms of the `Apache Software License v2 `_) or later. - -All comments, messages, pull requests, and other submissions received through CDC including this GitHub page may be subject to applicable federal law, including but not limited to the Federal Records Act, and may be archived. Learn more at `http://www.cdc.gov/other/privacy.html `_. - -Note: [this page is a work in progress; the above text was taken from `https://github.com/CDCgov/multisignal-epi-inference `_ on 2024/03/25] - -.. todo:: Get baseline, accurate version of the CONTRIBUTING page. diff --git a/docs/build/html/_sources/general/ctoc.rst.txt b/docs/build/html/_sources/general/ctoc.rst.txt deleted file mode 100644 index 41df0b16..00000000 --- a/docs/build/html/_sources/general/ctoc.rst.txt +++ /dev/null @@ -1,21 +0,0 @@ -Complete Table Of Contents -========================== - -.. toctree:: - :maxdepth: 4 - - ../msei_reference/index - ../test_reference/index - ../genindex - ../modindex - ../search - faq - glossary - license - notices - state - usage - contribute - bugs - -.. todo:: Change order and naming of these toctree entities diff --git a/docs/build/html/_sources/general/faq.rst.txt b/docs/build/html/_sources/general/faq.rst.txt deleted file mode 100644 index 61030d9d..00000000 --- a/docs/build/html/_sources/general/faq.rst.txt +++ /dev/null @@ -1,6 +0,0 @@ -FAQ -=== - -Note: [this page is a work in progress; this page is a placeholder] - -.. todo:: Get baseline, accurate version of the Frequently Asked Questions (FAQ) page. diff --git a/docs/build/html/_sources/general/glossary.rst.txt b/docs/build/html/_sources/general/glossary.rst.txt deleted file mode 100644 index 2ed37067..00000000 --- a/docs/build/html/_sources/general/glossary.rst.txt +++ /dev/null @@ -1,12 +0,0 @@ -Glossary -======== - -.. glossary:: - - Term 1 - Definition for term 1 etc... - - Term 2 - Definition for term 2 etc... - -..todo:: Populate the glossary with terms (e.g., from model_definition.md) diff --git a/docs/build/html/_sources/general/license.rst.txt b/docs/build/html/_sources/general/license.rst.txt deleted file mode 100644 index 32a2b660..00000000 --- a/docs/build/html/_sources/general/license.rst.txt +++ /dev/null @@ -1,17 +0,0 @@ -License -======= - -This repository is licensed under ASL v2 or later. - -This source code in this repository is free: you can redistribute it and/or modify it under the terms of the Apache Software License version 2, or (at your option) any later version. - -This source code in this repository is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the Apache Software License for more details. - -You should have received a copy of the Apache Software License along with this program. If not, see `http://www.apache.org/licenses/LICENSE-2.0.html `_ - -The source code forked from other open source projects will inherit its license. - - -Note: [this page is a work in progress; the above text was taken from `https://github.com/CDCgov/multisignal-epi-inference `_ on 2024/03/25] - -.. todo:: Get baseline, accurate version of the License page. diff --git a/docs/build/html/_sources/general/notices.rst.txt b/docs/build/html/_sources/general/notices.rst.txt deleted file mode 100644 index 7972d6db..00000000 --- a/docs/build/html/_sources/general/notices.rst.txt +++ /dev/null @@ -1,37 +0,0 @@ -Other Notices -============= - -General Disclaimer ------------------- - -This repository was created for use by CDC programs to collaborate on public health related projects in support of the `CDC mission `_. GitHub is not hosted by the CDC, but is a third party website used by CDC and its partners to share information and collaborate on software. CDC use of GitHub does not imply an endorsement of any one particular service, product, or enterprise. - -Public Domain Standard Notice ------------------------------ - -This repository constitutes a work of the United States Government and is not subject to domestic copyright protection under 17 USC § 105. This repository is in the public domain within the United States, and copyright and related rights in the work worldwide are waived through the `CC0 1.0 Universal public domain dedication `_. All contributions to this repository will be released under the CC0 dedication. By submitting a pull request you are agreeing to comply with this waiver of copyright interest. - -Privacy Standard Notice ------------------------ - -This repository contains only non-sensitive, publicly available data and information. All material and community participation is covered by the `Disclaimer `_` and `Code of Conduct `_. For more information about CDC's privacy policy, please visit `http://www.cdc.gov/other/privacy.html `_. - -Records Management Standard Notice ----------------------------------- - -This repository is not a source of government records but is a copy to increase collaboration and collaborative potential. All government records will be published through the `CDC web site `. - -Additional Standard Notices ---------------------------- - -Please refer to `CDC's Template Repository `_ for more information about `contributing to this repository `_, `public domain notices and disclaimers `_, and `code of conduct `_. - - -Final Notes ------------ - -Please refer, under Meta Information, the License and Reporting Issues pages for other standard notices. - -Note: [this page is a work in progress; the above text was taken from `https://github.com/CDCgov/multisignal-epi-inference `_ on 2024/03/25] - -.. todo:: Get baseline, accurate version of the Notices page. diff --git a/docs/build/html/_sources/general/state.rst.txt b/docs/build/html/_sources/general/state.rst.txt deleted file mode 100644 index e5932b77..00000000 --- a/docs/build/html/_sources/general/state.rst.txt +++ /dev/null @@ -1,6 +0,0 @@ -State Of Development -==================== - -Note: [this page is a work in progress; this page is a placeholder] - -.. todo:: Get baseline, accurate version of the State Of Development page. diff --git a/docs/build/html/_sources/general/usage.rst.txt b/docs/build/html/_sources/general/usage.rst.txt deleted file mode 100644 index 6fabafd6..00000000 --- a/docs/build/html/_sources/general/usage.rst.txt +++ /dev/null @@ -1,6 +0,0 @@ -Setup & Usage -============= - -Note: [this page is a work in progress; this page is a placeholder] - -.. todo:: Get baseline, accurate version of the Setup & Usage page. diff --git a/docs/build/html/_sources/genindex.rst.txt b/docs/build/html/_sources/genindex.rst.txt deleted file mode 100644 index a04b8d29..00000000 --- a/docs/build/html/_sources/genindex.rst.txt +++ /dev/null @@ -1,4 +0,0 @@ -General Index -============= - -:ref:`genindex` diff --git a/docs/build/html/_sources/glossary.rst.txt b/docs/build/html/_sources/glossary.rst.txt deleted file mode 100644 index 2ed37067..00000000 --- a/docs/build/html/_sources/glossary.rst.txt +++ /dev/null @@ -1,12 +0,0 @@ -Glossary -======== - -.. glossary:: - - Term 1 - Definition for term 1 etc... - - Term 2 - Definition for term 2 etc... - -..todo:: Populate the glossary with terms (e.g., from model_definition.md) diff --git a/docs/build/html/_sources/index.rst.txt b/docs/build/html/_sources/index.rst.txt deleted file mode 100644 index ce3e3920..00000000 --- a/docs/build/html/_sources/index.rst.txt +++ /dev/null @@ -1,91 +0,0 @@ -.. CFA Multisignal Renewal documentation master file, created by - sphinx-quickstart on Sun Mar 17 15:31:47 2024. - You can adapt this file completely to your liking, but it should at least - contain the root `toctree` directive. - -CFA Multisignal Renewal Documentation -===================================== - -Welcome to the CFA's `Multisignal Epidemiological Inference `_ (MSEI) project (*a.k.a.* signal fusion project), which consists of an internal forecasting model that leverages multiple data sources for enhancing epidemiological modeling of infectious disease outbreaks. - -This repository is composed of two parts: - -1. **Model development** (`model folder `_). -2. **Analysis pipeline** (`pipeline folder `_). - -Overview of the project follows: - -.. mermaid:: - - flowchart TD - %% Main diagram - io((P1: I/O\nDefinition)) --> |Dependency of| model((P2: Model\nPackage)) - io --> |Is used by| etl[[P3: ETL]] - model --> |Is used in| run - io -.-> |Possible\ndependency of|ww((Wastewater\nPackage)) - - %% Definition of the pipe - subgraph pipeline["Pipeline\n(Azure + GHA)"] - etl --> |Feeds| run[["P4: Run the\nmodel"]] - end - run --> |Feeds| Outputs - - %% Definition of the outputs - subgraph Outputs - direction TB - postp[[P5: Post\nProduction]] - retro[[P6: Retrospective\nTesting]] - bench[[P7: Benchmarking\n&A/B testing]] - end - - %% Connections to the outputs - io --> |Is used by| Outputs - postp --> manual[[Manual review]] - manual --> share[[Share publicly]] - - - %% Tagging sub-projects - classDef tealNode fill:teal,color:white,stroke:white; - class io,model,etl,run,postp,retro,bench,project,process tealNode; - -Documentation Components -======================== - -.. toctree:: - :maxdepth: 1 - - msei_reference/index - test_reference/index - general/state - general/faq - general/usage - - -Indices And Tables -================== - -.. toctree:: - :maxdepth: 1 - - genindex - modindex - search - general/glossary - general/ctoc - -Meta Information -================ - -.. toctree:: - :maxdepth: 1 - - general/contribute - general/bugs - general/license - general/notices - -.. todo:: Have docs folder exist in main, deploy using GHA. - -.. todo:: Add [State, Usage, Help, Tutorials/index, FAQ, HOWTOs/index] pages in Documentation Components. - -.. todo:: Add [About, History, Download, Copyright] pages in Meta Information. diff --git a/docs/build/html/_sources/license.rst.txt b/docs/build/html/_sources/license.rst.txt deleted file mode 100644 index 32a2b660..00000000 --- a/docs/build/html/_sources/license.rst.txt +++ /dev/null @@ -1,17 +0,0 @@ -License -======= - -This repository is licensed under ASL v2 or later. - -This source code in this repository is free: you can redistribute it and/or modify it under the terms of the Apache Software License version 2, or (at your option) any later version. - -This source code in this repository is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the Apache Software License for more details. - -You should have received a copy of the Apache Software License along with this program. If not, see `http://www.apache.org/licenses/LICENSE-2.0.html `_ - -The source code forked from other open source projects will inherit its license. - - -Note: [this page is a work in progress; the above text was taken from `https://github.com/CDCgov/multisignal-epi-inference `_ on 2024/03/25] - -.. todo:: Get baseline, accurate version of the License page. diff --git a/docs/build/html/_sources/modindex.rst.txt b/docs/build/html/_sources/modindex.rst.txt deleted file mode 100644 index c2e9e67d..00000000 --- a/docs/build/html/_sources/modindex.rst.txt +++ /dev/null @@ -1,4 +0,0 @@ -Module Index -============ - -:ref:`modindex` diff --git a/docs/build/html/_sources/msei_reference/basic.rst.txt b/docs/build/html/_sources/msei_reference/basic.rst.txt deleted file mode 100644 index 1ba9d4c0..00000000 --- a/docs/build/html/_sources/msei_reference/basic.rst.txt +++ /dev/null @@ -1,9 +0,0 @@ -Basic Renewal Model Module -========================== - -.. automodule:: pyrenew.basic - :members: - :undoc-members: - :show-inheritance: - -.. todo:: Describe the `basic` module in greater detail. diff --git a/docs/build/html/_sources/msei_reference/convolve.rst.txt b/docs/build/html/_sources/msei_reference/convolve.rst.txt deleted file mode 100644 index b6b19acc..00000000 --- a/docs/build/html/_sources/msei_reference/convolve.rst.txt +++ /dev/null @@ -1,7 +0,0 @@ -Convolution Utility Module -========================== - -.. automodule:: pyrenew.convolve - :members: - :undoc-members: - :show-inheritance: diff --git a/docs/build/html/_sources/msei_reference/distutil.rst.txt b/docs/build/html/_sources/msei_reference/distutil.rst.txt deleted file mode 100644 index 16ae2d15..00000000 --- a/docs/build/html/_sources/msei_reference/distutil.rst.txt +++ /dev/null @@ -1,7 +0,0 @@ -Distribution Utility Module -=========================== - -.. automodule:: pyrenew.distutil - :members: - :undoc-members: - :show-inheritance: diff --git a/docs/build/html/_sources/msei_reference/index.rst.txt b/docs/build/html/_sources/msei_reference/index.rst.txt deleted file mode 100644 index a50d944f..00000000 --- a/docs/build/html/_sources/msei_reference/index.rst.txt +++ /dev/null @@ -1,15 +0,0 @@ -MSEI Reference -============== - -.. toctree:: - :maxdepth: 3 - - observation - process - latent - model - msei - -.. todolist:: - -.. todo:: Determine order and naming of the above toctree entities. diff --git a/docs/build/html/_sources/msei_reference/infection.rst.txt b/docs/build/html/_sources/msei_reference/infection.rst.txt deleted file mode 100644 index 8ba4f3f5..00000000 --- a/docs/build/html/_sources/msei_reference/infection.rst.txt +++ /dev/null @@ -1,7 +0,0 @@ -Infection Module -================ - -.. automodule:: pyrenew.infection - :members: - :undoc-members: - :show-inheritance: diff --git a/docs/build/html/_sources/msei_reference/latent.rst.txt b/docs/build/html/_sources/msei_reference/latent.rst.txt deleted file mode 100644 index 6d11dc1b..00000000 --- a/docs/build/html/_sources/msei_reference/latent.rst.txt +++ /dev/null @@ -1,28 +0,0 @@ -Latent MSEI Components -====================== - -Hospital Admissions -------------------- - -.. automodule:: pyrenew.latent.hospitaladmissions - :members: - :undoc-members: - :show-inheritance: - -Infections ----------- - -.. automodule:: pyrenew.latent.infections - :members: - :undoc-members: - :show-inheritance: - -Infection Functions -------------------- - -.. automodule:: pyrenew.latent.infection_functions - :members: - :undoc-members: - :show-inheritance: - -.. todo:: Determine and naming order of these modules. diff --git a/docs/build/html/_sources/msei_reference/math.rst.txt b/docs/build/html/_sources/msei_reference/math.rst.txt deleted file mode 100644 index 58e64c3a..00000000 --- a/docs/build/html/_sources/msei_reference/math.rst.txt +++ /dev/null @@ -1,7 +0,0 @@ -Math Utility Module -=================== - -.. automodule:: pyrenew.math - :members: - :undoc-members: - :show-inheritance: diff --git a/docs/build/html/_sources/msei_reference/model.rst.txt b/docs/build/html/_sources/msei_reference/model.rst.txt deleted file mode 100644 index 21109cc4..00000000 --- a/docs/build/html/_sources/msei_reference/model.rst.txt +++ /dev/null @@ -1,20 +0,0 @@ -MSEI Model -========== - -Hospital Admissions -------------------- - -.. automodule:: pyrenew.model.admissionsmodel - :members: - :undoc-members: - :show-inheritance: - -Reproduction Number Renewal Infections --------------------------------------- - -.. automodule:: pyrenew.model.rtinfectionsrenewalmodel - :members: - :undoc-members: - :show-inheritance: - -.. todo:: Determine and naming order of these modules. diff --git a/docs/build/html/_sources/msei_reference/msei.rst.txt b/docs/build/html/_sources/msei_reference/msei.rst.txt deleted file mode 100644 index 8322fed0..00000000 --- a/docs/build/html/_sources/msei_reference/msei.rst.txt +++ /dev/null @@ -1,61 +0,0 @@ -General MSEI Support -==================== - -Metaclass Module -================ - -.. automodule:: pyrenew.metaclass - :members: - :undoc-members: - :show-inheritance: - -Convolution Utility Module --------------------------- - -.. automodule:: pyrenew.convolve - :members: - :undoc-members: - :show-inheritance: - -Mathematics Utilities Module ----------------------------- - -.. automodule:: pyrenew.math - :members: - :undoc-members: - :show-inheritance: - -Transform Utility Module ------------------------- - -.. automodule:: pyrenew.transform - :members: - :undoc-members: - :show-inheritance: - -Regression Module ------------------ - -.. automodule:: pyrenew.regression - :members: - :undoc-members: - :show-inheritance: - - -MCMC Utilities Module ---------------------- - -.. automodule:: pyrenew.mcmcutils - :members: - :undoc-members: - :show-inheritance: - -Distributions Utility Module ----------------------------- - -.. automodule:: pyrenew.distutil - :members: - :undoc-members: - :show-inheritance: - -.. todo:: Determine and naming order of these modules. diff --git a/docs/build/html/_sources/msei_reference/observation.rst.txt b/docs/build/html/_sources/msei_reference/observation.rst.txt deleted file mode 100644 index 7ea62d46..00000000 --- a/docs/build/html/_sources/msei_reference/observation.rst.txt +++ /dev/null @@ -1,20 +0,0 @@ -Observation Processes -===================== - -Negative Binomial ------------------ - -.. automodule:: pyrenew.observation.negativebinomial - :members: - :undoc-members: - :show-inheritance: - -Poisson -------- - -.. automodule:: pyrenew.observation.poisson - :members: - :undoc-members: - :show-inheritance: - -.. todo:: Determine order of these modules. diff --git a/docs/build/html/_sources/msei_reference/process.rst.txt b/docs/build/html/_sources/msei_reference/process.rst.txt deleted file mode 100644 index 15b9dd20..00000000 --- a/docs/build/html/_sources/msei_reference/process.rst.txt +++ /dev/null @@ -1,36 +0,0 @@ -Process MSEI -============ - -AR Processes ------------- - -.. automodule:: pyrenew.process.ar - :members: - :undoc-members: - :show-inheritance: - -First Difference (AR) ---------------------- - -.. automodule:: pyrenew.process.firstdifferencear - :members: - :undoc-members: - :show-inheritance: - -Reproduction Number Random Walk -------------------------------- - -.. automodule:: pyrenew.process.rtrandomwalk - :members: - :undoc-members: - :show-inheritance: - -Simple Random Walk ------------------- - -.. automodule:: pyrenew.process.simplerandomwalk - :members: - :undoc-members: - :show-inheritance: - -.. todo:: Determine order and naming of these modules. diff --git a/docs/build/html/_sources/msei_reference/regression.rst.txt b/docs/build/html/_sources/msei_reference/regression.rst.txt deleted file mode 100644 index 379c0ce6..00000000 --- a/docs/build/html/_sources/msei_reference/regression.rst.txt +++ /dev/null @@ -1,7 +0,0 @@ -Regression Module -================== - -.. automodule:: pyrenew.regression - :members: - :undoc-members: - :show-inheritance: diff --git a/docs/build/html/_sources/msei_reference/transform.rst.txt b/docs/build/html/_sources/msei_reference/transform.rst.txt deleted file mode 100644 index 14ea482c..00000000 --- a/docs/build/html/_sources/msei_reference/transform.rst.txt +++ /dev/null @@ -1,7 +0,0 @@ -Transform Utility Module -======================== - -.. automodule:: pyrenew.transform - :members: - :undoc-members: - :show-inheritance: diff --git a/docs/build/html/_sources/notices.rst.txt b/docs/build/html/_sources/notices.rst.txt deleted file mode 100644 index 7972d6db..00000000 --- a/docs/build/html/_sources/notices.rst.txt +++ /dev/null @@ -1,37 +0,0 @@ -Other Notices -============= - -General Disclaimer ------------------- - -This repository was created for use by CDC programs to collaborate on public health related projects in support of the `CDC mission `_. GitHub is not hosted by the CDC, but is a third party website used by CDC and its partners to share information and collaborate on software. CDC use of GitHub does not imply an endorsement of any one particular service, product, or enterprise. - -Public Domain Standard Notice ------------------------------ - -This repository constitutes a work of the United States Government and is not subject to domestic copyright protection under 17 USC § 105. This repository is in the public domain within the United States, and copyright and related rights in the work worldwide are waived through the `CC0 1.0 Universal public domain dedication `_. All contributions to this repository will be released under the CC0 dedication. By submitting a pull request you are agreeing to comply with this waiver of copyright interest. - -Privacy Standard Notice ------------------------ - -This repository contains only non-sensitive, publicly available data and information. All material and community participation is covered by the `Disclaimer `_` and `Code of Conduct `_. For more information about CDC's privacy policy, please visit `http://www.cdc.gov/other/privacy.html `_. - -Records Management Standard Notice ----------------------------------- - -This repository is not a source of government records but is a copy to increase collaboration and collaborative potential. All government records will be published through the `CDC web site `. - -Additional Standard Notices ---------------------------- - -Please refer to `CDC's Template Repository `_ for more information about `contributing to this repository `_, `public domain notices and disclaimers `_, and `code of conduct `_. - - -Final Notes ------------ - -Please refer, under Meta Information, the License and Reporting Issues pages for other standard notices. - -Note: [this page is a work in progress; the above text was taken from `https://github.com/CDCgov/multisignal-epi-inference `_ on 2024/03/25] - -.. todo:: Get baseline, accurate version of the Notices page. diff --git a/docs/build/html/_sources/observation.rst.txt b/docs/build/html/_sources/observation.rst.txt deleted file mode 100644 index 5be0e912..00000000 --- a/docs/build/html/_sources/observation.rst.txt +++ /dev/null @@ -1,7 +0,0 @@ -Observation Module -================== - -.. automodule:: pyrenew.observation - :members: - :undoc-members: - :show-inheritance: diff --git a/docs/build/html/_sources/reference.rst.txt b/docs/build/html/_sources/reference.rst.txt deleted file mode 100644 index 4065f555..00000000 --- a/docs/build/html/_sources/reference.rst.txt +++ /dev/null @@ -1,7 +0,0 @@ -API Reference -============== - -.. toctree:: - :maxdepth: 4 - - observation diff --git a/docs/build/html/_sources/reference/index.rst.txt b/docs/build/html/_sources/reference/index.rst.txt deleted file mode 100644 index 4065f555..00000000 --- a/docs/build/html/_sources/reference/index.rst.txt +++ /dev/null @@ -1,7 +0,0 @@ -API Reference -============== - -.. toctree:: - :maxdepth: 4 - - observation diff --git a/docs/build/html/_sources/reference/observation.rst.txt b/docs/build/html/_sources/reference/observation.rst.txt deleted file mode 100644 index 5be0e912..00000000 --- a/docs/build/html/_sources/reference/observation.rst.txt +++ /dev/null @@ -1,7 +0,0 @@ -Observation Module -================== - -.. automodule:: pyrenew.observation - :members: - :undoc-members: - :show-inheritance: diff --git a/docs/build/html/_sources/search.rst.txt b/docs/build/html/_sources/search.rst.txt deleted file mode 100644 index 24d8a887..00000000 --- a/docs/build/html/_sources/search.rst.txt +++ /dev/null @@ -1,4 +0,0 @@ -Search Page -=========== - -:ref:`search` diff --git a/docs/build/html/_sources/state.rst.txt b/docs/build/html/_sources/state.rst.txt deleted file mode 100644 index e5932b77..00000000 --- a/docs/build/html/_sources/state.rst.txt +++ /dev/null @@ -1,6 +0,0 @@ -State Of Development -==================== - -Note: [this page is a work in progress; this page is a placeholder] - -.. todo:: Get baseline, accurate version of the State Of Development page. diff --git a/docs/build/html/_sources/test_reference/index.rst.txt b/docs/build/html/_sources/test_reference/index.rst.txt deleted file mode 100644 index 79924955..00000000 --- a/docs/build/html/_sources/test_reference/index.rst.txt +++ /dev/null @@ -1,14 +0,0 @@ -Test Reference -============== - -.. toctree:: - :maxdepth: 3 - - test_ar_process - test_first_difference_ar - test_logistic_susceptibility_adjustment - test_random_walk - test_process_asymptotics - test_transforms - test_regression - test_leslie_matrix diff --git a/docs/build/html/_sources/test_reference/test_ar_process.rst.txt b/docs/build/html/_sources/test_reference/test_ar_process.rst.txt deleted file mode 100644 index 8cd482f4..00000000 --- a/docs/build/html/_sources/test_reference/test_ar_process.rst.txt +++ /dev/null @@ -1,4 +0,0 @@ -AR Process Testing Functions -============================ - -.. autofunction:: test.test_ar_process.test_ar_can_be_sampled diff --git a/docs/build/html/_sources/test_reference/test_first_difference_ar.rst.txt b/docs/build/html/_sources/test_reference/test_first_difference_ar.rst.txt deleted file mode 100644 index 2213dada..00000000 --- a/docs/build/html/_sources/test_reference/test_first_difference_ar.rst.txt +++ /dev/null @@ -1,4 +0,0 @@ -AR First Difference Testing Functions -===================================== - -.. autofunction:: test.test_first_difference_ar.test_fd_ar_can_be_sampled diff --git a/docs/build/html/_sources/test_reference/test_leslie_matrix.rst.txt b/docs/build/html/_sources/test_reference/test_leslie_matrix.rst.txt deleted file mode 100644 index 84a0421e..00000000 --- a/docs/build/html/_sources/test_reference/test_leslie_matrix.rst.txt +++ /dev/null @@ -1,4 +0,0 @@ -Leslie Matrix Testing Functions -=============================== - -.. autofunction:: test.test_leslie_matrix.test_get_leslie diff --git a/docs/build/html/_sources/test_reference/test_logistic_susceptibility_adjustment.rst.txt b/docs/build/html/_sources/test_reference/test_logistic_susceptibility_adjustment.rst.txt deleted file mode 100644 index 970b16b0..00000000 --- a/docs/build/html/_sources/test_reference/test_logistic_susceptibility_adjustment.rst.txt +++ /dev/null @@ -1,4 +0,0 @@ -Logistic Susceptibility Testing Functions -========================================= - -.. autofunction:: test.test_logistic_susceptibility_adjustment.test_logistic_susceptibility_adjustment diff --git a/docs/build/html/_sources/test_reference/test_process_asymptotics.rst.txt b/docs/build/html/_sources/test_reference/test_process_asymptotics.rst.txt deleted file mode 100644 index 7595f5b8..00000000 --- a/docs/build/html/_sources/test_reference/test_process_asymptotics.rst.txt +++ /dev/null @@ -1,4 +0,0 @@ -Processed Asymptomatic Testing Functions -======================================== - -.. autofunction:: test.test_process_asymptotics.test_asymptotic_properties diff --git a/docs/build/html/_sources/test_reference/test_random_walk.rst.txt b/docs/build/html/_sources/test_reference/test_random_walk.rst.txt deleted file mode 100644 index 022aec1c..00000000 --- a/docs/build/html/_sources/test_reference/test_random_walk.rst.txt +++ /dev/null @@ -1,7 +0,0 @@ -Random Walk Testing Functions -============================= - -.. autofunction:: test.test_random_walk.test_rw_can_be_sampled - - -.. autofunction:: test.test_random_walk.test_rw_samples_correctly_distributed diff --git a/docs/build/html/_sources/test_reference/test_regression.rst.txt b/docs/build/html/_sources/test_reference/test_regression.rst.txt deleted file mode 100644 index 07910bc7..00000000 --- a/docs/build/html/_sources/test_reference/test_regression.rst.txt +++ /dev/null @@ -1,4 +0,0 @@ -Regression Testing Functions -============================ - -.. autofunction:: test.test_regression.test_glm_prediction diff --git a/docs/build/html/_sources/test_reference/test_transforms.rst.txt b/docs/build/html/_sources/test_reference/test_transforms.rst.txt deleted file mode 100644 index b19a5752..00000000 --- a/docs/build/html/_sources/test_reference/test_transforms.rst.txt +++ /dev/null @@ -1,6 +0,0 @@ -Transforms Testing Functions -============================ - -.. autofunction:: test.test_transforms.generic_inversion_test - -.. autofunction:: test.test_transforms.test_invert_dists diff --git a/docs/build/html/_sources/usage.rst.txt b/docs/build/html/_sources/usage.rst.txt deleted file mode 100644 index 6fabafd6..00000000 --- a/docs/build/html/_sources/usage.rst.txt +++ /dev/null @@ -1,6 +0,0 @@ -Setup & Usage -============= - -Note: [this page is a work in progress; this page is a placeholder] - -.. todo:: Get baseline, accurate version of the Setup & Usage page. diff --git a/docs/build/html/_static/alabaster.css b/docs/build/html/_static/alabaster.css deleted file mode 100644 index 4c276908..00000000 --- a/docs/build/html/_static/alabaster.css +++ /dev/null @@ -1,708 +0,0 @@ -@import url("basic.css"); - -/* -- page layout ----------------------------------------------------------- */ - -body { - font-family: Georgia, serif; - font-size: 17px; - background-color: #fff; - color: #000; - margin: 0; - padding: 0; -} - - -div.document { - width: 940px; - margin: 30px auto 0 auto; -} - -div.documentwrapper { - float: left; - width: 100%; -} - -div.bodywrapper { - margin: 0 0 0 220px; -} - -div.sphinxsidebar { - width: 220px; - font-size: 14px; - line-height: 1.5; -} - -hr { - border: 1px solid #B1B4B6; -} - -div.body { - background-color: #fff; - color: #3E4349; - padding: 0 30px 0 30px; -} - -div.body > .section { - text-align: left; -} - -div.footer { - width: 940px; - margin: 20px auto 30px auto; - font-size: 14px; - color: #888; - text-align: right; -} - -div.footer a { - color: #888; -} - -p.caption { - font-family: inherit; - font-size: inherit; -} - - -div.relations { - display: none; -} - - -div.sphinxsidebar { - max-height: 100%; - overflow-y: auto; -} - -div.sphinxsidebar a { - color: #444; - text-decoration: none; - border-bottom: 1px dotted #999; -} - -div.sphinxsidebar a:hover { - border-bottom: 1px solid #999; -} - -div.sphinxsidebarwrapper { - padding: 18px 10px; -} - -div.sphinxsidebarwrapper p.logo { - padding: 0; - margin: -10px 0 0 0px; - text-align: center; -} - -div.sphinxsidebarwrapper h1.logo { - margin-top: -10px; - text-align: center; - margin-bottom: 5px; - text-align: left; -} - -div.sphinxsidebarwrapper h1.logo-name { - margin-top: 0px; -} - -div.sphinxsidebarwrapper p.blurb { - margin-top: 0; - font-style: normal; -} - -div.sphinxsidebar h3, -div.sphinxsidebar h4 { - font-family: Georgia, serif; - color: #444; - font-size: 24px; 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- -ms-hyphens: manual; - -webkit-hyphens: manual; - hyphens: manual; -} - -table.footnote td.label { - width: .1px; - padding: 0.3em 0 0.3em 0.5em; -} - -table.footnote td { - padding: 0.3em 0.5em; -} - -dl { - margin-left: 0; - margin-right: 0; - margin-top: 0; - padding: 0; -} - -dl dd { - margin-left: 30px; -} - -blockquote { - margin: 0 0 0 30px; - padding: 0; -} - -ul, ol { - /* Matches the 30px from the narrow-screen "li > ul" selector below */ - margin: 10px 0 10px 30px; - padding: 0; -} - -pre { - background: #EEE; - padding: 7px 30px; - margin: 15px 0px; - line-height: 1.3em; -} - -div.viewcode-block:target { - background: #ffd; -} - -dl pre, blockquote pre, li pre { - margin-left: 0; - padding-left: 30px; -} - -tt, code { - background-color: #ecf0f3; - color: #222; - /* padding: 1px 2px; */ -} - -tt.xref, code.xref, a tt { - background-color: #FBFBFB; - border-bottom: 1px solid #fff; -} - -a.reference { - text-decoration: none; - border-bottom: 1px dotted #004B6B; -} - -/* Don't put an underline on images */ -a.image-reference, a.image-reference:hover { - border-bottom: none; 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- padding: 20px 30px; - } - - div.documentwrapper { - float: none; - background: #fff; - } - - div.sphinxsidebar { - display: block; - float: none; - width: 102.5%; - margin: 50px -30px -20px -30px; - padding: 10px 20px; - background: #333; - color: #FFF; - } - - div.sphinxsidebar h3, div.sphinxsidebar h4, div.sphinxsidebar p, - div.sphinxsidebar h3 a { - color: #fff; - } - - div.sphinxsidebar a { - color: #AAA; - } - - div.sphinxsidebar p.logo { - display: none; - } - - div.document { - width: 100%; - margin: 0; - } - - div.footer { - display: none; - } - - div.bodywrapper { - margin: 0; - } - - div.body { - min-height: 0; - padding: 0; - } - - .rtd_doc_footer { - display: none; - } - - .document { - width: auto; - } - - .footer { - width: auto; - } - - .footer { - width: auto; - } - - .github { - display: none; - } -} - - -/* misc. */ - -.revsys-inline { - display: none!important; -} - -/* Hide ugly table cell borders in ..bibliography:: directive output */ -table.docutils.citation, table.docutils.citation td, table.docutils.citation th { - border: none; - /* Below needed in some edge cases; if not applied, bottom shadows appear */ - -moz-box-shadow: none; - -webkit-box-shadow: none; - box-shadow: none; -} - - -/* relbar */ - -.related { - line-height: 30px; - width: 100%; - font-size: 0.9rem; -} - -.related.top { - border-bottom: 1px solid #EEE; - margin-bottom: 20px; -} - -.related.bottom { - border-top: 1px solid #EEE; -} - -.related ul { - padding: 0; - margin: 0; - list-style: none; -} - -.related li { - display: inline; -} - -nav#rellinks { - float: right; -} - -nav#rellinks li+li:before { - content: "|"; -} - -nav#breadcrumbs li+li:before { - content: "\00BB"; -} - -/* Hide certain items when printing */ -@media print { - div.related { - display: none; - } -} diff --git a/docs/build/html/_static/basic.css b/docs/build/html/_static/basic.css deleted file mode 100644 index 16e1d1e6..00000000 --- a/docs/build/html/_static/basic.css +++ /dev/null @@ -1,925 +0,0 @@ -/* - * basic.css - * ~~~~~~~~~ - * - * Sphinx stylesheet -- basic theme. - * - * :copyright: Copyright 2007-2023 by the Sphinx team, see AUTHORS. - * :license: BSD, see LICENSE for details. - * - */ - -/* -- main layout ----------------------------------------------------------- */ - -div.clearer { - clear: both; 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- margin-left: auto; - margin-right: auto; -} - -table.contentstable p.biglink { - line-height: 150%; -} - -a.biglink { - font-size: 1.3em; -} - -span.linkdescr { - font-style: italic; - padding-top: 5px; - font-size: 90%; -} - -/* -- general index --------------------------------------------------------- */ - -table.indextable { - width: 100%; -} - -table.indextable td { - text-align: left; - vertical-align: top; -} - -table.indextable ul { - margin-top: 0; - margin-bottom: 0; - list-style-type: none; -} - -table.indextable > tbody > tr > td > ul { - padding-left: 0em; -} - -table.indextable tr.pcap { - height: 10px; -} - -table.indextable tr.cap { - margin-top: 10px; - background-color: #f2f2f2; -} - -img.toggler { - margin-right: 3px; - margin-top: 3px; - cursor: pointer; -} - -div.modindex-jumpbox { - border-top: 1px solid #ddd; - border-bottom: 1px solid #ddd; - margin: 1em 0 1em 0; - padding: 0.4em; -} - -div.genindex-jumpbox { - border-top: 1px solid #ddd; - border-bottom: 1px solid #ddd; - margin: 1em 0 1em 0; - padding: 0.4em; -} - -/* -- domain module index --------------------------------------------------- */ - -table.modindextable td { - padding: 2px; - border-collapse: collapse; -} - -/* -- general body styles --------------------------------------------------- */ - -div.body { - min-width: 360px; - max-width: 800px; -} - -div.body p, div.body dd, div.body li, div.body blockquote { - -moz-hyphens: auto; - -ms-hyphens: auto; - -webkit-hyphens: auto; - hyphens: auto; -} - -a.headerlink { - visibility: hidden; -} - -a:visited { - color: #551A8B; -} - -h1:hover > a.headerlink, -h2:hover > a.headerlink, -h3:hover > a.headerlink, -h4:hover > a.headerlink, -h5:hover > a.headerlink, -h6:hover > a.headerlink, -dt:hover > a.headerlink, -caption:hover > a.headerlink, -p.caption:hover > a.headerlink, -div.code-block-caption:hover > a.headerlink { - visibility: visible; -} - -div.body p.caption { - text-align: inherit; -} - -div.body td { - text-align: left; -} - -.first { - margin-top: 0 !important; -} - -p.rubric { - margin-top: 30px; - font-weight: bold; -} - -img.align-left, figure.align-left, .figure.align-left, object.align-left { - clear: left; - float: left; - margin-right: 1em; -} - -img.align-right, figure.align-right, .figure.align-right, object.align-right { - clear: right; - float: right; - margin-left: 1em; -} - -img.align-center, figure.align-center, .figure.align-center, object.align-center { - display: block; - margin-left: auto; - margin-right: auto; -} - -img.align-default, figure.align-default, .figure.align-default { - display: block; - margin-left: auto; - margin-right: auto; -} - -.align-left { - text-align: left; -} - -.align-center { - text-align: center; -} - -.align-default { - text-align: center; -} - -.align-right { - text-align: right; -} - -/* -- sidebars -------------------------------------------------------------- */ - -div.sidebar, -aside.sidebar { - margin: 0 0 0.5em 1em; - border: 1px solid #ddb; - padding: 7px; - background-color: #ffe; - width: 40%; - float: right; - clear: right; - overflow-x: auto; -} - -p.sidebar-title { - font-weight: bold; -} - -nav.contents, -aside.topic, -div.admonition, div.topic, blockquote { - clear: left; -} - -/* -- topics ---------------------------------------------------------------- */ - -nav.contents, -aside.topic, -div.topic { - border: 1px solid #ccc; - padding: 7px; - margin: 10px 0 10px 0; -} - -p.topic-title { - font-size: 1.1em; - font-weight: bold; - margin-top: 10px; -} - -/* -- admonitions ----------------------------------------------------------- */ - -div.admonition { - margin-top: 10px; - margin-bottom: 10px; - padding: 7px; -} - -div.admonition dt { - font-weight: bold; -} - -p.admonition-title { - margin: 0px 10px 5px 0px; - font-weight: bold; -} - -div.body p.centered { - text-align: center; - margin-top: 25px; -} - -/* -- content of sidebars/topics/admonitions -------------------------------- */ - -div.sidebar > :last-child, -aside.sidebar > :last-child, -nav.contents > :last-child, -aside.topic > :last-child, -div.topic > :last-child, -div.admonition > :last-child { - margin-bottom: 0; -} - -div.sidebar::after, -aside.sidebar::after, -nav.contents::after, -aside.topic::after, -div.topic::after, -div.admonition::after, -blockquote::after { - display: block; - content: ''; - clear: both; -} - -/* -- tables ---------------------------------------------------------------- */ - -table.docutils { - margin-top: 10px; - margin-bottom: 10px; - border: 0; - border-collapse: collapse; -} - -table.align-center { - margin-left: auto; - margin-right: auto; -} - -table.align-default { - margin-left: auto; - margin-right: auto; -} - -table caption span.caption-number { - font-style: italic; -} - -table caption span.caption-text { -} - -table.docutils td, table.docutils th { - padding: 1px 8px 1px 5px; - border-top: 0; - border-left: 0; - border-right: 0; - border-bottom: 1px solid #aaa; -} - -th { - text-align: left; - padding-right: 5px; -} - -table.citation { - border-left: solid 1px gray; - margin-left: 1px; -} - -table.citation td { - border-bottom: none; -} - -th > :first-child, -td > :first-child { - margin-top: 0px; -} - -th > :last-child, -td > :last-child { - margin-bottom: 0px; -} - -/* -- figures --------------------------------------------------------------- */ - -div.figure, figure { - margin: 0.5em; - padding: 0.5em; -} - -div.figure p.caption, figcaption { - padding: 0.3em; -} - -div.figure p.caption span.caption-number, -figcaption span.caption-number { - font-style: italic; -} - -div.figure p.caption span.caption-text, -figcaption span.caption-text { -} - -/* -- field list styles ----------------------------------------------------- */ - -table.field-list td, table.field-list th { - border: 0 !important; -} - -.field-list ul { - margin: 0; - padding-left: 1em; -} - -.field-list p { - margin: 0; -} - -.field-name { - -moz-hyphens: manual; - -ms-hyphens: manual; - -webkit-hyphens: manual; - hyphens: manual; -} - -/* -- hlist styles ---------------------------------------------------------- */ - -table.hlist { - margin: 1em 0; -} - -table.hlist td { - vertical-align: top; -} - -/* -- object description styles --------------------------------------------- */ - -.sig { - font-family: 'Consolas', 'Menlo', 'DejaVu Sans Mono', 'Bitstream Vera Sans Mono', monospace; -} - -.sig-name, code.descname { - background-color: transparent; - font-weight: bold; -} - -.sig-name { - font-size: 1.1em; -} - -code.descname { - font-size: 1.2em; -} - -.sig-prename, code.descclassname { - background-color: transparent; -} - -.optional { - font-size: 1.3em; -} - -.sig-paren { - font-size: larger; -} - -.sig-param.n { - font-style: italic; -} - -/* C++ specific styling */ - -.sig-inline.c-texpr, -.sig-inline.cpp-texpr { - font-family: unset; -} - -.sig.c .k, .sig.c .kt, -.sig.cpp .k, .sig.cpp .kt { - color: #0033B3; -} - -.sig.c .m, -.sig.cpp .m { - color: #1750EB; -} - -.sig.c .s, .sig.c .sc, -.sig.cpp .s, .sig.cpp .sc { - color: #067D17; -} - - -/* -- other body styles ----------------------------------------------------- */ - -ol.arabic { - list-style: decimal; -} - -ol.loweralpha { - list-style: lower-alpha; -} - -ol.upperalpha { - list-style: upper-alpha; -} - -ol.lowerroman { - list-style: lower-roman; -} - -ol.upperroman { - list-style: upper-roman; -} - -:not(li) > ol > li:first-child > :first-child, -:not(li) > ul > li:first-child > :first-child { - margin-top: 0px; -} - -:not(li) > ol > li:last-child > :last-child, -:not(li) > ul > li:last-child > :last-child { - margin-bottom: 0px; -} - -ol.simple ol p, -ol.simple ul p, -ul.simple ol p, -ul.simple ul p { - margin-top: 0; -} - -ol.simple > li:not(:first-child) > p, -ul.simple > li:not(:first-child) > p { - margin-top: 0; -} - -ol.simple p, -ul.simple p { - margin-bottom: 0; -} - -aside.footnote > span, -div.citation > span { - float: left; -} -aside.footnote > span:last-of-type, -div.citation > span:last-of-type { - padding-right: 0.5em; -} -aside.footnote > p { - margin-left: 2em; -} -div.citation > p { - margin-left: 4em; -} -aside.footnote > p:last-of-type, -div.citation > p:last-of-type { - margin-bottom: 0em; -} -aside.footnote > p:last-of-type:after, -div.citation > p:last-of-type:after { - content: ""; - clear: both; -} - -dl.field-list { - display: grid; - grid-template-columns: fit-content(30%) auto; -} - -dl.field-list > dt { - font-weight: bold; - word-break: break-word; - padding-left: 0.5em; - padding-right: 5px; -} - -dl.field-list > dd { - padding-left: 0.5em; - margin-top: 0em; - margin-left: 0em; - margin-bottom: 0em; -} - -dl { - margin-bottom: 15px; -} - -dd > :first-child { - margin-top: 0px; -} - -dd ul, dd table { - margin-bottom: 10px; -} - -dd { - margin-top: 3px; - margin-bottom: 10px; - margin-left: 30px; -} - -.sig dd { - margin-top: 0px; - margin-bottom: 0px; -} - -.sig dl { - margin-top: 0px; - margin-bottom: 0px; -} - -dl > dd:last-child, -dl > dd:last-child > :last-child { - margin-bottom: 0; -} - -dt:target, span.highlighted { - background-color: #fbe54e; -} - -rect.highlighted { - fill: #fbe54e; -} - -dl.glossary dt { - font-weight: bold; - font-size: 1.1em; -} - -.versionmodified { - font-style: italic; -} - -.system-message { - background-color: #fda; - padding: 5px; - border: 3px solid red; -} - -.footnote:target { - background-color: #ffa; -} - -.line-block { - display: block; - margin-top: 1em; - margin-bottom: 1em; -} - -.line-block .line-block { - margin-top: 0; - margin-bottom: 0; - margin-left: 1.5em; -} - -.guilabel, .menuselection { - font-family: sans-serif; -} - -.accelerator { - text-decoration: underline; -} - -.classifier { - font-style: oblique; -} - -.classifier:before { - font-style: normal; - margin: 0 0.5em; - content: ":"; - display: inline-block; -} - -abbr, acronym { - border-bottom: dotted 1px; - cursor: help; -} - -.translated { - background-color: rgba(207, 255, 207, 0.2) -} - -.untranslated { - background-color: rgba(255, 207, 207, 0.2) -} - -/* -- code displays --------------------------------------------------------- */ - -pre { - overflow: auto; - overflow-y: hidden; /* fixes display issues on Chrome browsers */ -} - -pre, div[class*="highlight-"] { - clear: both; -} - -span.pre { - -moz-hyphens: none; - -ms-hyphens: none; - -webkit-hyphens: none; - hyphens: none; - white-space: nowrap; -} - -div[class*="highlight-"] { - margin: 1em 0; -} - -td.linenos pre { - border: 0; - background-color: transparent; - color: #aaa; -} - -table.highlighttable { - display: block; -} - -table.highlighttable tbody { - display: block; -} - -table.highlighttable tr { - display: flex; -} - -table.highlighttable td { - margin: 0; - padding: 0; -} - -table.highlighttable td.linenos { - padding-right: 0.5em; -} - -table.highlighttable td.code { - flex: 1; - overflow: hidden; -} - -.highlight .hll { - display: block; -} - -div.highlight pre, -table.highlighttable pre { - margin: 0; -} - -div.code-block-caption + div { - margin-top: 0; -} - -div.code-block-caption { - margin-top: 1em; - padding: 2px 5px; - font-size: small; -} - -div.code-block-caption code { - background-color: transparent; -} - -table.highlighttable td.linenos, -span.linenos, -div.highlight span.gp { /* gp: Generic.Prompt */ - user-select: none; - -webkit-user-select: text; /* Safari fallback only */ - -webkit-user-select: none; /* Chrome/Safari */ - -moz-user-select: none; /* Firefox */ - -ms-user-select: none; /* IE10+ */ -} - -div.code-block-caption span.caption-number { - padding: 0.1em 0.3em; - font-style: italic; -} - -div.code-block-caption span.caption-text { -} - -div.literal-block-wrapper { - margin: 1em 0; -} - -code.xref, a code { - background-color: transparent; - font-weight: bold; -} - -h1 code, h2 code, h3 code, h4 code, h5 code, h6 code { - background-color: transparent; -} - -.viewcode-link { - float: right; -} - -.viewcode-back { - float: right; - font-family: sans-serif; -} - -div.viewcode-block:target { - margin: -1px -10px; - padding: 0 10px; -} - -/* -- math display ---------------------------------------------------------- */ - -img.math { - vertical-align: middle; -} - -div.body div.math p { - text-align: center; -} - -span.eqno { - float: right; -} - -span.eqno a.headerlink { - position: absolute; - z-index: 1; -} - -div.math:hover a.headerlink { - visibility: visible; -} - -/* -- printout stylesheet --------------------------------------------------- */ - -@media print { - div.document, - div.documentwrapper, - div.bodywrapper { - margin: 0 !important; - width: 100%; - } - - div.sphinxsidebar, - div.related, - div.footer, - #top-link { - display: none; - } -} diff --git a/docs/build/html/_static/classic.css b/docs/build/html/_static/classic.css deleted file mode 100644 index 292e7c72..00000000 --- a/docs/build/html/_static/classic.css +++ /dev/null @@ -1,269 +0,0 @@ -/* - * classic.css_t - * ~~~~~~~~~~~~~ - * - * Sphinx stylesheet -- classic theme. - * - * :copyright: Copyright 2007-2023 by the Sphinx team, see AUTHORS. - * :license: BSD, see LICENSE for details. - * - */ - -@import url("basic.css"); - -/* -- page layout ----------------------------------------------------------- */ - -html { - /* CSS hack for macOS's scrollbar (see #1125) */ - background-color: #FFFFFF; -} - -body { - font-family: sans-serif; - font-size: 100%; - background-color: #11303d; - color: #000; - margin: 0; - padding: 0; -} - -div.document { - display: flex; - background-color: #1c4e63; -} - -div.documentwrapper { - float: left; - width: 100%; -} - -div.bodywrapper { - margin: 0 0 0 230px; -} - -div.body { - background-color: #ffffff; - color: #000000; - padding: 0 20px 30px 20px; -} - -div.footer { - color: #ffffff; - width: 100%; - padding: 9px 0 9px 0; - text-align: center; - font-size: 75%; -} - -div.footer a { - color: #ffffff; - text-decoration: underline; -} - -div.related { - background-color: #133f52; - line-height: 30px; - color: #ffffff; -} - -div.related a { - color: #ffffff; -} - -div.sphinxsidebar { -} - -div.sphinxsidebar h3 { - font-family: 'Trebuchet MS', sans-serif; - color: #ffffff; - font-size: 1.4em; - font-weight: normal; - margin: 0; - padding: 0; -} - -div.sphinxsidebar h3 a { - color: #ffffff; -} - -div.sphinxsidebar h4 { - font-family: 'Trebuchet MS', sans-serif; - color: #ffffff; - font-size: 1.3em; - font-weight: normal; - margin: 5px 0 0 0; - padding: 0; -} - -div.sphinxsidebar p { - color: #ffffff; -} - -div.sphinxsidebar p.topless { - margin: 5px 10px 10px 10px; -} - -div.sphinxsidebar ul { - margin: 10px; - padding: 0; - color: #ffffff; -} - -div.sphinxsidebar a { - color: #98dbcc; -} - -div.sphinxsidebar input { - border: 1px solid #98dbcc; - font-family: sans-serif; - font-size: 1em; -} - - - -/* -- hyperlink styles ------------------------------------------------------ */ - -a { - color: #355f7c; - text-decoration: none; -} - -a:visited { - color: #551a8b; - text-decoration: none; -} - -a:hover { - text-decoration: underline; -} - - - -/* -- body styles ----------------------------------------------------------- */ - -div.body h1, -div.body h2, -div.body h3, -div.body h4, -div.body h5, -div.body h6 { - font-family: 'Trebuchet MS', sans-serif; - background-color: #f2f2f2; - font-weight: normal; - color: #20435c; - border-bottom: 1px solid #ccc; - margin: 20px -20px 10px -20px; - padding: 3px 0 3px 10px; -} - -div.body h1 { margin-top: 0; font-size: 200%; } -div.body h2 { font-size: 160%; } -div.body h3 { font-size: 140%; } -div.body h4 { font-size: 120%; } -div.body h5 { font-size: 110%; } -div.body h6 { font-size: 100%; } - -a.headerlink { - color: #c60f0f; - font-size: 0.8em; - padding: 0 4px 0 4px; - text-decoration: none; -} - -a.headerlink:hover { - background-color: #c60f0f; - color: white; -} - -div.body p, div.body dd, div.body li, div.body blockquote { - text-align: justify; - line-height: 130%; -} - -div.admonition p.admonition-title + p { - display: inline; -} - -div.admonition p { - margin-bottom: 5px; -} - -div.admonition pre { - margin-bottom: 5px; -} - -div.admonition ul, div.admonition ol { - margin-bottom: 5px; -} - -div.note { - background-color: #eee; - border: 1px solid #ccc; -} - -div.seealso { - background-color: #ffc; - border: 1px solid #ff6; -} - -nav.contents, -aside.topic, -div.topic { - background-color: #eee; -} - -div.warning { - background-color: #ffe4e4; - border: 1px solid #f66; -} - -p.admonition-title { - display: inline; -} - -p.admonition-title:after { - content: ":"; -} - -pre { - padding: 5px; - background-color: unset; - color: unset; - line-height: 120%; - border: 1px solid #ac9; - border-left: none; - border-right: none; -} - -code { - background-color: #ecf0f3; - padding: 0 1px 0 1px; - font-size: 0.95em; -} - -th, dl.field-list > dt { - background-color: #ede; -} - -.warning code { - background: #efc2c2; -} - -.note code { - background: #d6d6d6; -} - -.viewcode-back { - font-family: sans-serif; -} - -div.viewcode-block:target { - background-color: #f4debf; - border-top: 1px solid #ac9; - border-bottom: 1px solid #ac9; -} - -div.code-block-caption { - color: #efefef; - background-color: #1c4e63; -} diff --git a/docs/build/html/_static/custom.css b/docs/build/html/_static/custom.css deleted file mode 100644 index 2a924f1d..00000000 --- a/docs/build/html/_static/custom.css +++ /dev/null @@ -1 +0,0 @@ -/* This file intentionally left blank. */ diff --git a/docs/build/html/_static/doctools.js b/docs/build/html/_static/doctools.js deleted file mode 100644 index d06a71d7..00000000 --- a/docs/build/html/_static/doctools.js +++ /dev/null @@ -1,156 +0,0 @@ -/* - * doctools.js - * ~~~~~~~~~~~ - * - * Base JavaScript utilities for all Sphinx HTML documentation. - * - * :copyright: Copyright 2007-2023 by the Sphinx team, see AUTHORS. - * :license: BSD, see LICENSE for details. - * - */ -"use strict"; - -const BLACKLISTED_KEY_CONTROL_ELEMENTS = new Set([ - "TEXTAREA", - "INPUT", - "SELECT", - "BUTTON", -]); - -const _ready = (callback) => { - if (document.readyState !== "loading") { - callback(); - } else { - document.addEventListener("DOMContentLoaded", callback); - } -}; - -/** - * Small JavaScript module for the documentation. - */ -const Documentation = { - init: () => { - Documentation.initDomainIndexTable(); - Documentation.initOnKeyListeners(); - }, - - /** - * i18n support - */ - TRANSLATIONS: {}, - PLURAL_EXPR: (n) => (n === 1 ? 0 : 1), - LOCALE: "unknown", - - // gettext and ngettext don't access this so that the functions - // can safely bound to a different name (_ = Documentation.gettext) - gettext: (string) => { - const translated = Documentation.TRANSLATIONS[string]; - switch (typeof translated) { - case "undefined": - return string; // no translation - case "string": - return translated; // translation exists - default: - return translated[0]; // (singular, plural) translation tuple exists - } - }, - - ngettext: (singular, plural, n) => { - const translated = Documentation.TRANSLATIONS[singular]; - if (typeof translated !== "undefined") - return translated[Documentation.PLURAL_EXPR(n)]; - return n === 1 ? singular : plural; - }, - - addTranslations: (catalog) => { - Object.assign(Documentation.TRANSLATIONS, catalog.messages); - Documentation.PLURAL_EXPR = new Function( - "n", - `return (${catalog.plural_expr})` - ); - Documentation.LOCALE = catalog.locale; - }, - - /** - * helper function to focus on search bar - */ - focusSearchBar: () => { - document.querySelectorAll("input[name=q]")[0]?.focus(); - }, - - /** - * Initialise the domain index toggle buttons - */ - initDomainIndexTable: () => { - const toggler = (el) => { - const idNumber = el.id.substr(7); - const toggledRows = document.querySelectorAll(`tr.cg-${idNumber}`); - if (el.src.substr(-9) === "minus.png") { - el.src = `${el.src.substr(0, el.src.length - 9)}plus.png`; - toggledRows.forEach((el) => (el.style.display = "none")); - } else { - el.src = `${el.src.substr(0, el.src.length - 8)}minus.png`; - toggledRows.forEach((el) => (el.style.display = "")); - } - }; - - const togglerElements = document.querySelectorAll("img.toggler"); - togglerElements.forEach((el) => - el.addEventListener("click", (event) => toggler(event.currentTarget)) - ); - togglerElements.forEach((el) => (el.style.display = "")); - if (DOCUMENTATION_OPTIONS.COLLAPSE_INDEX) togglerElements.forEach(toggler); - }, - - initOnKeyListeners: () => { - // only install a listener if it is really needed - if ( - !DOCUMENTATION_OPTIONS.NAVIGATION_WITH_KEYS && - !DOCUMENTATION_OPTIONS.ENABLE_SEARCH_SHORTCUTS - ) - return; - - document.addEventListener("keydown", (event) => { - // bail for input elements - if (BLACKLISTED_KEY_CONTROL_ELEMENTS.has(document.activeElement.tagName)) return; - // bail with special keys - if (event.altKey || event.ctrlKey || event.metaKey) return; - - if (!event.shiftKey) { - switch (event.key) { - case "ArrowLeft": - if (!DOCUMENTATION_OPTIONS.NAVIGATION_WITH_KEYS) break; - - const prevLink = document.querySelector('link[rel="prev"]'); - if (prevLink && prevLink.href) { - window.location.href = prevLink.href; - event.preventDefault(); - } - break; - case "ArrowRight": - if (!DOCUMENTATION_OPTIONS.NAVIGATION_WITH_KEYS) break; - - const nextLink = document.querySelector('link[rel="next"]'); - if (nextLink && nextLink.href) { - window.location.href = nextLink.href; - event.preventDefault(); - } - break; - } - } - - // some keyboard layouts may need Shift to get / - switch (event.key) { - case "/": - if (!DOCUMENTATION_OPTIONS.ENABLE_SEARCH_SHORTCUTS) break; - Documentation.focusSearchBar(); - event.preventDefault(); - } - }); - }, -}; - -// quick alias for translations -const _ = Documentation.gettext; - -_ready(Documentation.init); diff --git a/docs/build/html/_static/documentation_options.js b/docs/build/html/_static/documentation_options.js deleted file mode 100644 index 7e0cecce..00000000 --- a/docs/build/html/_static/documentation_options.js +++ /dev/null @@ -1,13 +0,0 @@ -const DOCUMENTATION_OPTIONS = { - VERSION: '0.0.1', - LANGUAGE: 'en', - COLLAPSE_INDEX: false, - BUILDER: 'html', - FILE_SUFFIX: '.html', - LINK_SUFFIX: '.html', - HAS_SOURCE: true, - SOURCELINK_SUFFIX: '.txt', - NAVIGATION_WITH_KEYS: false, - SHOW_SEARCH_SUMMARY: true, - ENABLE_SEARCH_SHORTCUTS: true, -}; diff --git a/docs/build/html/_static/graphviz.css b/docs/build/html/_static/graphviz.css deleted file mode 100644 index 8d81c02e..00000000 --- a/docs/build/html/_static/graphviz.css +++ /dev/null @@ -1,19 +0,0 @@ -/* - * graphviz.css - * ~~~~~~~~~~~~ - * - * Sphinx stylesheet -- graphviz extension. - * - * :copyright: Copyright 2007-2023 by the Sphinx team, see AUTHORS. - * :license: BSD, see LICENSE for details. - * - */ - -img.graphviz { - border: 0; - max-width: 100%; -} - -object.graphviz { - max-width: 100%; -} diff --git a/docs/build/html/_static/language_data.js b/docs/build/html/_static/language_data.js deleted file mode 100644 index 68b9e83a..00000000 --- a/docs/build/html/_static/language_data.js +++ /dev/null @@ -1,198 +0,0 @@ -/* - * language_data.js - * ~~~~~~~~~~~~~~~~ - * - * This script contains the language-specific data used by searchtools.js, - * namely the list of stopwords, stemmer, scorer and splitter. - * - * :copyright: Copyright 2007-2023 by the Sphinx team, see AUTHORS. - * :license: BSD, see LICENSE for details. - * - */ - -var stopwords = ["a", "and", "are", "as", "at", "be", "but", "by", "for", "if", "in", "into", "is", "it", "near", "no", "not", "of", "on", "or", "such", "that", "the", "their", "then", "there", "these", "they", "this", "to", "was", "will", "with"]; - - -/* Non-minified version is copied as a separate JS file, is available */ - -/** - * Porter Stemmer - */ -var Stemmer = function() { - - var step2list = { - ational: 'ate', - tional: 'tion', - enci: 'ence', - anci: 'ance', - izer: 'ize', - bli: 'ble', - alli: 'al', - entli: 'ent', - eli: 'e', - ousli: 'ous', - ization: 'ize', - ation: 'ate', - ator: 'ate', - alism: 'al', - iveness: 'ive', - fulness: 'ful', - ousness: 'ous', - aliti: 'al', - iviti: 'ive', - biliti: 'ble', - logi: 'log' - }; - - var step3list = { - icate: 'ic', - ative: '', - alize: 'al', - iciti: 'ic', - ical: 'ic', - ful: '', - ness: '' - }; - - var c = "[^aeiou]"; // consonant - var v = "[aeiouy]"; // vowel - var C = c + "[^aeiouy]*"; // consonant sequence - var V = v + "[aeiou]*"; // vowel sequence - - var mgr0 = "^(" + C + ")?" + V + C; // [C]VC... is m>0 - var meq1 = "^(" + C + ")?" + V + C + "(" + V + ")?$"; // [C]VC[V] is m=1 - var mgr1 = "^(" + C + ")?" + V + C + V + C; // [C]VCVC... is m>1 - var s_v = "^(" + C + ")?" + v; // vowel in stem - - this.stemWord = function (w) { - var stem; - var suffix; - var firstch; - var origword = w; - - if (w.length < 3) - return w; - - var re; - var re2; - var re3; - var re4; - - firstch = w.substr(0,1); - if (firstch == "y") - w = firstch.toUpperCase() + w.substr(1); - - // Step 1a - re = /^(.+?)(ss|i)es$/; - re2 = /^(.+?)([^s])s$/; - - if (re.test(w)) - w = w.replace(re,"$1$2"); - else if (re2.test(w)) - w = w.replace(re2,"$1$2"); - - // Step 1b - re = /^(.+?)eed$/; - re2 = /^(.+?)(ed|ing)$/; - if (re.test(w)) { - var fp = re.exec(w); - re = new RegExp(mgr0); - if (re.test(fp[1])) { - re = /.$/; - w = w.replace(re,""); - } - } - else if (re2.test(w)) { - var fp = re2.exec(w); - stem = fp[1]; - re2 = new RegExp(s_v); - if (re2.test(stem)) { - w = stem; - re2 = /(at|bl|iz)$/; - re3 = new RegExp("([^aeiouylsz])\\1$"); - re4 = new RegExp("^" + C + v + "[^aeiouwxy]$"); - if (re2.test(w)) - w = w + "e"; - else if (re3.test(w)) { - re = /.$/; - w = w.replace(re,""); - } - else if (re4.test(w)) - w = w + "e"; - } - } - - // Step 1c - re = /^(.+?)y$/; - if (re.test(w)) { - var fp = re.exec(w); - stem = fp[1]; - re = new RegExp(s_v); - if (re.test(stem)) - w = stem + "i"; - } - - // Step 2 - re = /^(.+?)(ational|tional|enci|anci|izer|bli|alli|entli|eli|ousli|ization|ation|ator|alism|iveness|fulness|ousness|aliti|iviti|biliti|logi)$/; - if (re.test(w)) { - var fp = re.exec(w); - stem = fp[1]; - suffix = fp[2]; - re = new RegExp(mgr0); - if (re.test(stem)) - w = stem + step2list[suffix]; - } - - // Step 3 - re = /^(.+?)(icate|ative|alize|iciti|ical|ful|ness)$/; - if (re.test(w)) { - var fp = re.exec(w); - stem = fp[1]; - suffix = fp[2]; - re = new RegExp(mgr0); - if (re.test(stem)) - w = stem + step3list[suffix]; - } - - // Step 4 - re = /^(.+?)(al|ance|ence|er|ic|able|ible|ant|ement|ment|ent|ou|ism|ate|iti|ous|ive|ize)$/; - re2 = /^(.+?)(s|t)(ion)$/; - if (re.test(w)) { - var fp = re.exec(w); - stem = fp[1]; - re = new RegExp(mgr1); - if (re.test(stem)) - w = stem; - } - else if (re2.test(w)) { - var fp = re2.exec(w); - stem = fp[1] + fp[2]; - re2 = new RegExp(mgr1); - if (re2.test(stem)) - w = stem; - } - - // Step 5 - re = /^(.+?)e$/; - if (re.test(w)) { - var fp = re.exec(w); - stem = fp[1]; - re = new RegExp(mgr1); - re2 = new RegExp(meq1); - re3 = new RegExp("^" + C + v + "[^aeiouwxy]$"); - if (re.test(stem) || (re2.test(stem) && !(re3.test(stem)))) - w = stem; - } - re = /ll$/; - re2 = new RegExp(mgr1); - if (re.test(w) && re2.test(w)) { - re = /.$/; - w = w.replace(re,""); - } - - // and turn initial Y back to y - if (firstch == "y") - w = firstch.toLowerCase() + w.substr(1); - return w; - } -} diff --git a/docs/build/html/_static/msei.css b/docs/build/html/_static/msei.css deleted file mode 100644 index 92a7888e..00000000 --- a/docs/build/html/_static/msei.css +++ /dev/null @@ -1,5 +0,0 @@ -@import url('https://your-font-hosting-url.com/path/to/iosevka.css'); - -body { - font-family: 'Iosevka', monospace; -} diff --git a/docs/build/html/_static/pygments.css b/docs/build/html/_static/pygments.css deleted file mode 100644 index ebe2a901..00000000 --- a/docs/build/html/_static/pygments.css +++ /dev/null @@ -1,75 +0,0 @@ -pre { line-height: 125%; } -td.linenos .normal { color: inherit; background-color: transparent; padding-left: 5px; padding-right: 5px; } -span.linenos { color: inherit; background-color: transparent; padding-left: 5px; padding-right: 5px; } -td.linenos .special { color: #000000; background-color: #ffffc0; padding-left: 5px; padding-right: 5px; } -span.linenos.special { color: #000000; background-color: #ffffc0; padding-left: 5px; padding-right: 5px; } -.highlight .hll { background-color: #ffffcc } -.highlight { background: #eeffcc; } -.highlight .c { color: #408090; font-style: italic } /* Comment */ -.highlight .err { border: 1px solid #FF0000 } /* Error */ -.highlight .k { color: #007020; font-weight: bold } /* Keyword */ -.highlight .o { color: #666666 } /* Operator */ -.highlight .ch { color: #408090; font-style: italic } /* Comment.Hashbang */ -.highlight .cm { color: #408090; font-style: italic } /* Comment.Multiline */ -.highlight .cp { color: #007020 } /* Comment.Preproc */ -.highlight .cpf { color: #408090; 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- -/** - * Simple result scoring code. - */ -if (typeof Scorer === "undefined") { - var Scorer = { - // Implement the following function to further tweak the score for each result - // The function takes a result array [docname, title, anchor, descr, score, filename] - // and returns the new score. - /* - score: result => { - const [docname, title, anchor, descr, score, filename] = result - return score - }, - */ - - // query matches the full name of an object - objNameMatch: 11, - // or matches in the last dotted part of the object name - objPartialMatch: 6, - // Additive scores depending on the priority of the object - objPrio: { - 0: 15, // used to be importantResults - 1: 5, // used to be objectResults - 2: -5, // used to be unimportantResults - }, - // Used when the priority is not in the mapping. - objPrioDefault: 0, - - // query found in title - title: 15, - partialTitle: 7, - // query found in terms - term: 5, - partialTerm: 2, - }; -} - -const _removeChildren = (element) => { - while (element && element.lastChild) element.removeChild(element.lastChild); -}; - -/** - * See https://developer.mozilla.org/en-US/docs/Web/JavaScript/Guide/Regular_Expressions#escaping - */ -const _escapeRegExp = (string) => - string.replace(/[.*+\-?^${}()|[\]\\]/g, "\\$&"); // $& means the whole matched string - -const _displayItem = (item, searchTerms, highlightTerms) => { - const docBuilder = DOCUMENTATION_OPTIONS.BUILDER; - const docFileSuffix = DOCUMENTATION_OPTIONS.FILE_SUFFIX; - const docLinkSuffix = DOCUMENTATION_OPTIONS.LINK_SUFFIX; - const showSearchSummary = DOCUMENTATION_OPTIONS.SHOW_SEARCH_SUMMARY; - const contentRoot = document.documentElement.dataset.content_root; - - const [docName, title, anchor, descr, score, _filename] = item; - - let listItem = document.createElement("li"); - let requestUrl; - let linkUrl; - if (docBuilder === "dirhtml") { - // dirhtml builder - let dirname = docName + "/"; - if (dirname.match(/\/index\/$/)) - dirname = dirname.substring(0, dirname.length - 6); - else if (dirname === "index/") dirname = ""; - requestUrl = contentRoot + dirname; - linkUrl = requestUrl; - } else { - // normal html builders - requestUrl = contentRoot + docName + docFileSuffix; - linkUrl = docName + docLinkSuffix; - } - let linkEl = listItem.appendChild(document.createElement("a")); - linkEl.href = linkUrl + anchor; - linkEl.dataset.score = score; - linkEl.innerHTML = title; - if (descr) { - listItem.appendChild(document.createElement("span")).innerHTML = - " (" + descr + ")"; - // highlight search terms in the description - if (SPHINX_HIGHLIGHT_ENABLED) // set in sphinx_highlight.js - highlightTerms.forEach((term) => _highlightText(listItem, term, "highlighted")); - } - else if (showSearchSummary) - fetch(requestUrl) - .then((responseData) => responseData.text()) - .then((data) => { - if (data) - listItem.appendChild( - Search.makeSearchSummary(data, searchTerms) - ); - // highlight search terms in the summary - if (SPHINX_HIGHLIGHT_ENABLED) // set in sphinx_highlight.js - highlightTerms.forEach((term) => _highlightText(listItem, term, "highlighted")); - }); - Search.output.appendChild(listItem); -}; -const _finishSearch = (resultCount) => { - Search.stopPulse(); - Search.title.innerText = _("Search Results"); - if (!resultCount) - Search.status.innerText = Documentation.gettext( - "Your search did not match any documents. Please make sure that all words are spelled correctly and that you've selected enough categories." - ); - else - Search.status.innerText = _( - `Search finished, found ${resultCount} page(s) matching the search query.` - ); -}; -const _displayNextItem = ( - results, - resultCount, - searchTerms, - highlightTerms, -) => { - // results left, load the summary and display it - // this is intended to be dynamic (don't sub resultsCount) - if (results.length) { - _displayItem(results.pop(), searchTerms, highlightTerms); - setTimeout( - () => _displayNextItem(results, resultCount, searchTerms, highlightTerms), - 5 - ); - } - // search finished, update title and status message - else _finishSearch(resultCount); -}; - -/** - * Default splitQuery function. Can be overridden in ``sphinx.search`` with a - * custom function per language. - * - * The regular expression works by splitting the string on consecutive characters - * that are not Unicode letters, numbers, underscores, or emoji characters. - * This is the same as ``\W+`` in Python, preserving the surrogate pair area. - */ -if (typeof splitQuery === "undefined") { - var splitQuery = (query) => query - .split(/[^\p{Letter}\p{Number}_\p{Emoji_Presentation}]+/gu) - .filter(term => term) // remove remaining empty strings -} - -/** - * Search Module - */ -const Search = { - _index: null, - _queued_query: null, - _pulse_status: -1, - - htmlToText: (htmlString) => { - const htmlElement = new DOMParser().parseFromString(htmlString, 'text/html'); - htmlElement.querySelectorAll(".headerlink").forEach((el) => { el.remove() }); - const docContent = htmlElement.querySelector('[role="main"]'); - if (docContent !== undefined) return docContent.textContent; - console.warn( - "Content block not found. Sphinx search tries to obtain it via '[role=main]'. Could you check your theme or template." - ); - return ""; - }, - - init: () => { - const query = new URLSearchParams(window.location.search).get("q"); - document - .querySelectorAll('input[name="q"]') - .forEach((el) => (el.value = query)); - if (query) Search.performSearch(query); - }, - - loadIndex: (url) => - (document.body.appendChild(document.createElement("script")).src = url), - - setIndex: (index) => { - Search._index = index; - if (Search._queued_query !== null) { - const query = Search._queued_query; - Search._queued_query = null; - Search.query(query); - } - }, - - hasIndex: () => Search._index !== null, - - deferQuery: (query) => (Search._queued_query = query), - - stopPulse: () => (Search._pulse_status = -1), - - startPulse: () => { - if (Search._pulse_status >= 0) return; - - const pulse = () => { - Search._pulse_status = (Search._pulse_status + 1) % 4; - Search.dots.innerText = ".".repeat(Search._pulse_status); - if (Search._pulse_status >= 0) window.setTimeout(pulse, 500); - }; - pulse(); - }, - - /** - * perform a search for something (or wait until index is loaded) - */ - performSearch: (query) => { - // create the required interface elements - const searchText = document.createElement("h2"); - searchText.textContent = _("Searching"); - const searchSummary = document.createElement("p"); - searchSummary.classList.add("search-summary"); - searchSummary.innerText = ""; - const searchList = document.createElement("ul"); - searchList.classList.add("search"); - - const out = document.getElementById("search-results"); - Search.title = out.appendChild(searchText); - Search.dots = Search.title.appendChild(document.createElement("span")); - Search.status = out.appendChild(searchSummary); - Search.output = out.appendChild(searchList); - - const searchProgress = document.getElementById("search-progress"); - // Some themes don't use the search progress node - if (searchProgress) { - searchProgress.innerText = _("Preparing search..."); - } - Search.startPulse(); - - // index already loaded, the browser was quick! - if (Search.hasIndex()) Search.query(query); - else Search.deferQuery(query); - }, - - /** - * execute search (requires search index to be loaded) - */ - query: (query) => { - const filenames = Search._index.filenames; - const docNames = Search._index.docnames; - const titles = Search._index.titles; - const allTitles = Search._index.alltitles; - const indexEntries = Search._index.indexentries; - - // stem the search terms and add them to the correct list - const stemmer = new Stemmer(); - const searchTerms = new Set(); - const excludedTerms = new Set(); - const highlightTerms = new Set(); - const objectTerms = new Set(splitQuery(query.toLowerCase().trim())); - splitQuery(query.trim()).forEach((queryTerm) => { - const queryTermLower = queryTerm.toLowerCase(); - - // maybe skip this "word" - // stopwords array is from language_data.js - if ( - stopwords.indexOf(queryTermLower) !== -1 || - queryTerm.match(/^\d+$/) - ) - return; - - // stem the word - let word = stemmer.stemWord(queryTermLower); - // select the correct list - if (word[0] === "-") excludedTerms.add(word.substr(1)); - else { - searchTerms.add(word); - highlightTerms.add(queryTermLower); - } - }); - - if (SPHINX_HIGHLIGHT_ENABLED) { // set in sphinx_highlight.js - localStorage.setItem("sphinx_highlight_terms", [...highlightTerms].join(" ")) - } - - // console.debug("SEARCH: searching for:"); - // console.info("required: ", [...searchTerms]); - // console.info("excluded: ", [...excludedTerms]); - - // array of [docname, title, anchor, descr, score, filename] - let results = []; - _removeChildren(document.getElementById("search-progress")); - - const queryLower = query.toLowerCase(); - for (const [title, foundTitles] of Object.entries(allTitles)) { - if (title.toLowerCase().includes(queryLower) && (queryLower.length >= title.length/2)) { - for (const [file, id] of foundTitles) { - let score = Math.round(100 * queryLower.length / title.length) - results.push([ - docNames[file], - titles[file] !== title ? `${titles[file]} > ${title}` : title, - id !== null ? "#" + id : "", - null, - score, - filenames[file], - ]); - } - } - } - - // search for explicit entries in index directives - for (const [entry, foundEntries] of Object.entries(indexEntries)) { - if (entry.includes(queryLower) && (queryLower.length >= entry.length/2)) { - for (const [file, id] of foundEntries) { - let score = Math.round(100 * queryLower.length / entry.length) - results.push([ - docNames[file], - titles[file], - id ? "#" + id : "", - null, - score, - filenames[file], - ]); - } - } - } - - // lookup as object - objectTerms.forEach((term) => - results.push(...Search.performObjectSearch(term, objectTerms)) - ); - - // lookup as search terms in fulltext - results.push(...Search.performTermsSearch(searchTerms, excludedTerms)); - - // let the scorer override scores with a custom scoring function - if (Scorer.score) results.forEach((item) => (item[4] = Scorer.score(item))); - - // now sort the results by score (in opposite order of appearance, since the - // display function below uses pop() to retrieve items) and then - // alphabetically - results.sort((a, b) => { - const leftScore = a[4]; - const rightScore = b[4]; - if (leftScore === rightScore) { - // same score: sort alphabetically - const leftTitle = a[1].toLowerCase(); - const rightTitle = b[1].toLowerCase(); - if (leftTitle === rightTitle) return 0; - return leftTitle > rightTitle ? -1 : 1; // inverted is intentional - } - return leftScore > rightScore ? 1 : -1; - }); - - // remove duplicate search results - // note the reversing of results, so that in the case of duplicates, the highest-scoring entry is kept - let seen = new Set(); - results = results.reverse().reduce((acc, result) => { - let resultStr = result.slice(0, 4).concat([result[5]]).map(v => String(v)).join(','); - if (!seen.has(resultStr)) { - acc.push(result); - seen.add(resultStr); - } - return acc; - }, []); - - results = results.reverse(); - - // for debugging - //Search.lastresults = results.slice(); // a copy - // console.info("search results:", Search.lastresults); - - // print the results - _displayNextItem(results, results.length, searchTerms, highlightTerms); - }, - - /** - * search for object names - */ - performObjectSearch: (object, objectTerms) => { - const filenames = Search._index.filenames; - const docNames = Search._index.docnames; - const objects = Search._index.objects; - const objNames = Search._index.objnames; - const titles = Search._index.titles; - - const results = []; - - const objectSearchCallback = (prefix, match) => { - const name = match[4] - const fullname = (prefix ? prefix + "." : "") + name; - const fullnameLower = fullname.toLowerCase(); - if (fullnameLower.indexOf(object) < 0) return; - - let score = 0; - const parts = fullnameLower.split("."); - - // check for different match types: exact matches of full name or - // "last name" (i.e. last dotted part) - if (fullnameLower === object || parts.slice(-1)[0] === object) - score += Scorer.objNameMatch; - else if (parts.slice(-1)[0].indexOf(object) > -1) - score += Scorer.objPartialMatch; // matches in last name - - const objName = objNames[match[1]][2]; - const title = titles[match[0]]; - - // If more than one term searched for, we require other words to be - // found in the name/title/description - const otherTerms = new Set(objectTerms); - otherTerms.delete(object); - if (otherTerms.size > 0) { - const haystack = `${prefix} ${name} ${objName} ${title}`.toLowerCase(); - if ( - [...otherTerms].some((otherTerm) => haystack.indexOf(otherTerm) < 0) - ) - return; - } - - let anchor = match[3]; - if (anchor === "") anchor = fullname; - else if (anchor === "-") anchor = objNames[match[1]][1] + "-" + fullname; - - const descr = objName + _(", in ") + title; - - // add custom score for some objects according to scorer - if (Scorer.objPrio.hasOwnProperty(match[2])) - score += Scorer.objPrio[match[2]]; - else score += Scorer.objPrioDefault; - - results.push([ - docNames[match[0]], - fullname, - "#" + anchor, - descr, - score, - filenames[match[0]], - ]); - }; - Object.keys(objects).forEach((prefix) => - objects[prefix].forEach((array) => - objectSearchCallback(prefix, array) - ) - ); - return results; - }, - - /** - * search for full-text terms in the index - */ - performTermsSearch: (searchTerms, excludedTerms) => { - // prepare search - const terms = Search._index.terms; - const titleTerms = Search._index.titleterms; - const filenames = Search._index.filenames; - const docNames = Search._index.docnames; - const titles = Search._index.titles; - - const scoreMap = new Map(); - const fileMap = new Map(); - - // perform the search on the required terms - searchTerms.forEach((word) => { - const files = []; - const arr = [ - { files: terms[word], score: Scorer.term }, - { files: titleTerms[word], score: Scorer.title }, - ]; - // add support for partial matches - if (word.length > 2) { - const escapedWord = _escapeRegExp(word); - Object.keys(terms).forEach((term) => { - if (term.match(escapedWord) && !terms[word]) - arr.push({ files: terms[term], score: Scorer.partialTerm }); - }); - Object.keys(titleTerms).forEach((term) => { - if (term.match(escapedWord) && !titleTerms[word]) - arr.push({ files: titleTerms[word], score: Scorer.partialTitle }); - }); - } - - // no match but word was a required one - if (arr.every((record) => record.files === undefined)) return; - - // found search word in contents - arr.forEach((record) => { - if (record.files === undefined) return; - - let recordFiles = record.files; - if (recordFiles.length === undefined) recordFiles = [recordFiles]; - files.push(...recordFiles); - - // set score for the word in each file - recordFiles.forEach((file) => { - if (!scoreMap.has(file)) scoreMap.set(file, {}); - scoreMap.get(file)[word] = record.score; - }); - }); - - // create the mapping - files.forEach((file) => { - if (fileMap.has(file) && fileMap.get(file).indexOf(word) === -1) - fileMap.get(file).push(word); - else fileMap.set(file, [word]); - }); - }); - - // now check if the files don't contain excluded terms - const results = []; - for (const [file, wordList] of fileMap) { - // check if all requirements are matched - - // as search terms with length < 3 are discarded - const filteredTermCount = [...searchTerms].filter( - (term) => term.length > 2 - ).length; - if ( - wordList.length !== searchTerms.size && - wordList.length !== filteredTermCount - ) - continue; - - // ensure that none of the excluded terms is in the search result - if ( - [...excludedTerms].some( - (term) => - terms[term] === file || - titleTerms[term] === file || - (terms[term] || []).includes(file) || - (titleTerms[term] || []).includes(file) - ) - ) - break; - - // select one (max) score for the file. - const score = Math.max(...wordList.map((w) => scoreMap.get(file)[w])); - // add result to the result list - results.push([ - docNames[file], - titles[file], - "", - null, - score, - filenames[file], - ]); - } - return results; - }, - - /** - * helper function to return a node containing the - * search summary for a given text. keywords is a list - * of stemmed words. - */ - makeSearchSummary: (htmlText, keywords) => { - const text = Search.htmlToText(htmlText); - if (text === "") return null; - - const textLower = text.toLowerCase(); - const actualStartPosition = [...keywords] - .map((k) => textLower.indexOf(k.toLowerCase())) - .filter((i) => i > -1) - .slice(-1)[0]; - const startWithContext = Math.max(actualStartPosition - 120, 0); - - const top = startWithContext === 0 ? "" : "..."; - const tail = startWithContext + 240 < text.length ? "..." : ""; - - let summary = document.createElement("p"); - summary.classList.add("context"); - summary.textContent = top + text.substr(startWithContext, 240).trim() + tail; - - return summary; - }, -}; - -_ready(Search.init); diff --git a/docs/build/html/_static/sidebar.js b/docs/build/html/_static/sidebar.js deleted file mode 100644 index 1e24d7b1..00000000 --- a/docs/build/html/_static/sidebar.js +++ /dev/null @@ -1,70 +0,0 @@ -/* - * sidebar.js - * ~~~~~~~~~~ - * - * This script makes the Sphinx sidebar collapsible. - * - * .sphinxsidebar contains .sphinxsidebarwrapper. This script adds - * in .sphixsidebar, after .sphinxsidebarwrapper, the #sidebarbutton - * used to collapse and expand the sidebar. - * - * When the sidebar is collapsed the .sphinxsidebarwrapper is hidden - * and the width of the sidebar and the margin-left of the document - * are decreased. When the sidebar is expanded the opposite happens. - * This script saves a per-browser/per-session cookie used to - * remember the position of the sidebar among the pages. - * Once the browser is closed the cookie is deleted and the position - * reset to the default (expanded). - * - * :copyright: Copyright 2007-2023 by the Sphinx team, see AUTHORS. - * :license: BSD, see LICENSE for details. - * - */ - -const initialiseSidebar = () => { - - - - - // global elements used by the functions. - const bodyWrapper = document.getElementsByClassName("bodywrapper")[0] - const sidebar = document.getElementsByClassName("sphinxsidebar")[0] - const sidebarWrapper = document.getElementsByClassName('sphinxsidebarwrapper')[0] - const sidebarButton = document.getElementById("sidebarbutton") - const sidebarArrow = sidebarButton.querySelector('span') - - // for some reason, the document has no sidebar; do not run into errors - if (typeof sidebar === "undefined") return; - - const flipArrow = element => element.innerText = (element.innerText === "»") ? "«" : "»" - - const collapse_sidebar = () => { - bodyWrapper.style.marginLeft = ".8em"; - sidebar.style.width = ".8em" - sidebarWrapper.style.display = "none" - flipArrow(sidebarArrow) - sidebarButton.title = _('Expand sidebar') - window.localStorage.setItem("sidebar", "collapsed") - } - - const expand_sidebar = () => { - bodyWrapper.style.marginLeft = "" - sidebar.style.removeProperty("width") - sidebarWrapper.style.display = "" - flipArrow(sidebarArrow) - sidebarButton.title = _('Collapse sidebar') - window.localStorage.setItem("sidebar", "expanded") - } - - sidebarButton.addEventListener("click", () => { - (sidebarWrapper.style.display === "none") ? expand_sidebar() : collapse_sidebar() - }) - - if (!window.localStorage.getItem("sidebar")) return - const value = window.localStorage.getItem("sidebar") - if (value === "collapsed") collapse_sidebar(); - else if (value === "expanded") expand_sidebar(); -} - -if (document.readyState !== "loading") initialiseSidebar() -else document.addEventListener("DOMContentLoaded", initialiseSidebar) diff --git a/docs/build/html/_static/sphinx_highlight.js b/docs/build/html/_static/sphinx_highlight.js deleted file mode 100644 index 8a96c69a..00000000 --- a/docs/build/html/_static/sphinx_highlight.js +++ /dev/null @@ -1,154 +0,0 @@ -/* Highlighting utilities for Sphinx HTML documentation. */ -"use strict"; - -const SPHINX_HIGHLIGHT_ENABLED = true - -/** - * highlight a given string on a node by wrapping it in - * span elements with the given class name. - */ -const _highlight = (node, addItems, text, className) => { - if (node.nodeType === Node.TEXT_NODE) { - const val = node.nodeValue; - const parent = node.parentNode; - const pos = val.toLowerCase().indexOf(text); - if ( - pos >= 0 && - !parent.classList.contains(className) && - !parent.classList.contains("nohighlight") - ) { - let span; - - const closestNode = parent.closest("body, svg, foreignObject"); - const isInSVG = closestNode && closestNode.matches("svg"); - if (isInSVG) { - span = document.createElementNS("http://www.w3.org/2000/svg", "tspan"); - } else { - span = document.createElement("span"); - span.classList.add(className); - } - - span.appendChild(document.createTextNode(val.substr(pos, text.length))); - const rest = document.createTextNode(val.substr(pos + text.length)); - parent.insertBefore( - span, - parent.insertBefore( - rest, - node.nextSibling - ) - ); - node.nodeValue = val.substr(0, pos); - /* There may be more occurrences of search term in this node. So call this - * function recursively on the remaining fragment. - */ - _highlight(rest, addItems, text, className); - - if (isInSVG) { - const rect = document.createElementNS( - "http://www.w3.org/2000/svg", - "rect" - ); - const bbox = parent.getBBox(); - rect.x.baseVal.value = bbox.x; - rect.y.baseVal.value = bbox.y; - rect.width.baseVal.value = bbox.width; - rect.height.baseVal.value = bbox.height; - rect.setAttribute("class", className); - addItems.push({ parent: parent, target: rect }); - } - } - } else if (node.matches && !node.matches("button, select, textarea")) { - node.childNodes.forEach((el) => _highlight(el, addItems, text, className)); - } -}; -const _highlightText = (thisNode, text, className) => { - let addItems = []; - _highlight(thisNode, addItems, text, className); - addItems.forEach((obj) => - obj.parent.insertAdjacentElement("beforebegin", obj.target) - ); -}; - -/** - * Small JavaScript module for the documentation. - */ -const SphinxHighlight = { - - /** - * highlight the search words provided in localstorage in the text - */ - highlightSearchWords: () => { - if (!SPHINX_HIGHLIGHT_ENABLED) return; // bail if no highlight - - // get and clear terms from localstorage - const url = new URL(window.location); - const highlight = - localStorage.getItem("sphinx_highlight_terms") - || url.searchParams.get("highlight") - || ""; - localStorage.removeItem("sphinx_highlight_terms") - url.searchParams.delete("highlight"); - window.history.replaceState({}, "", url); - - // get individual terms from highlight string - const terms = highlight.toLowerCase().split(/\s+/).filter(x => x); - if (terms.length === 0) return; // nothing to do - - // There should never be more than one element matching "div.body" - const divBody = document.querySelectorAll("div.body"); - const body = divBody.length ? divBody[0] : document.querySelector("body"); - window.setTimeout(() => { - terms.forEach((term) => _highlightText(body, term, "highlighted")); - }, 10); - - const searchBox = document.getElementById("searchbox"); - if (searchBox === null) return; - searchBox.appendChild( - document - .createRange() - .createContextualFragment( - '

' + - '' + - _("Hide Search Matches") + - "

" - ) - ); - }, - - /** - * helper function to hide the search marks again - */ - hideSearchWords: () => { - document - .querySelectorAll("#searchbox .highlight-link") - .forEach((el) => el.remove()); - document - .querySelectorAll("span.highlighted") - .forEach((el) => el.classList.remove("highlighted")); - localStorage.removeItem("sphinx_highlight_terms") - }, - - initEscapeListener: () => { - // only install a listener if it is really needed - if (!DOCUMENTATION_OPTIONS.ENABLE_SEARCH_SHORTCUTS) return; - - document.addEventListener("keydown", (event) => { - // bail for input elements - if (BLACKLISTED_KEY_CONTROL_ELEMENTS.has(document.activeElement.tagName)) return; - // bail with special keys - if (event.shiftKey || event.altKey || event.ctrlKey || event.metaKey) return; - if (DOCUMENTATION_OPTIONS.ENABLE_SEARCH_SHORTCUTS && (event.key === "Escape")) { - SphinxHighlight.hideSearchWords(); - event.preventDefault(); - } - }); - }, -}; - -_ready(() => { - /* Do not call highlightSearchWords() when we are on the search page. - * It will highlight words from the *previous* search query. - */ - if (typeof Search === "undefined") SphinxHighlight.highlightSearchWords(); - SphinxHighlight.initEscapeListener(); -}); diff --git a/docs/build/html/objects.inv b/docs/build/html/objects.inv deleted file mode 100644 index bedaccaf..00000000 Binary files a/docs/build/html/objects.inv and /dev/null differ diff --git a/docs/build/html/searchindex.js b/docs/build/html/searchindex.js deleted file mode 100644 index 9d4dc6ae..00000000 --- a/docs/build/html/searchindex.js +++ /dev/null @@ -1 +0,0 @@ -Search.setIndex({"docnames": ["general/ctoc", "index", "msei_reference/index", "msei_reference/observation", "msei_reference/process"], "filenames": ["general/ctoc.rst", "index.rst", "msei_reference/index.rst", "msei_reference/observation.rst", "msei_reference/process.rst"], "titles": ["Complete Table Of Contents", "CFA Multisignal Renewal Documentation", "MSEI Reference", "Observation Processes", "Process MSEI"], "terms": {"msei": [0, 1], "refer": [0, 1], "observ": [0, 2], "process": [0, 2], "neg": [0, 2], "binomi": [0, 2], "negativebinomialobserv": [0, 2, 3], "poisson": [0, 2], "poissonobserv": [0, 2, 3], "ar": [0, 2], "arprocess": [0, 2, 4], "first": [0, 2], "differ": [0, 2], "firstdifferencearprocess": [0, 2, 4], "reproduct": [0, 2], "number": [0, 2], "random": [0, 2], "walk": [0, 2], "rtrandomwalkprocess": [0, 2, 4], "simpl": [0, 2], "simplerandomwalkprocess": [0, 2, 4], "latent": [0, 2], "compon": [0, 2], "hospit": [0, 2], "admiss": [0, 2], "hospadmissionssampl": [0, 2], "hospitaladmiss": [0, 2], "infect": [0, 2], "infectionssampl": [0, 2], "function": [0, 2], "logistic_susceptibility_adjust": [0, 2], "sample_infections_rt": [0, 2], "sample_infections_with_feedback": [0, 2], "model": [0, 1, 2], "hospmodelsampl": [0, 2], "hospitaladmissionsmodel": [0, 2], "renew": [0, 2], "rtinfectionsrenewalmodel": [0, 2], "rtinfectionsrenewalsampl": [0, 2], "gener": [0, 2, 4], "support": [0, 2], "metaclass": [0, 2], "modul": [0, 1, 2, 3, 4], "kernel": [0, 2], "mcmc": [0, 2], "print_summari": [0, 2], "run": [0, 2], "sampl": [0, 2, 3, 4], "spread_draw": [0, 2], "valid": [0, 2, 3, 4], "randomvari": [0, 2, 3, 4], "convolut": [0, 2], "util": [0, 2], "new_convolve_scann": [0, 2], "new_double_scann": [0, 2], "mathemat": [0, 2], "get_asymptotic_growth_r": [0, 2], "get_asymptotic_growth_rate_and_age_dist": [0, 2], "get_leslie_matrix": [0, 2], "get_stable_age_distribut": [0, 2], "transform": [0, 2, 4], "abstracttransform": [0, 2, 4], "identitytransform": [0, 2], "logtransform": [0, 2, 4], "logittransform": [0, 2], "scaledlogittransform": [0, 2], "regress": [0, 2], "abstractregressionpredict": [0, 2], "glmpredict": [0, 2], "distribut": [0, 2, 3, 4], "reverse_discrete_dist_vector": [0, 2], "validate_discrete_dist_vector": [0, 2], "test": [0, 1], "test_ar_can_be_sampl": 0, "test_fd_ar_can_be_sampl": 0, "logist": 0, "suscept": 0, 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"project": 1, "k": 1, "signal": 1, "fusion": 1, "which": [1, 3], "consist": 1, "an": [1, 4], "intern": 1, "forecast": 1, "leverag": 1, "multipl": 1, "data": 1, "sourc": [1, 2, 3, 4], "enhanc": 1, "infecti": 1, "diseas": 1, "outbreak": 1, "thi": 1, "repositori": 1, "i": [1, 2, 3, 4], "compos": 1, "two": 1, "part": 1, "folder": [1, 2], "analysi": 1, "pipelin": 1, "overview": 1, "follow": 1, "Of": [1, 2], "complet": 1, "content": 1, "have": [1, 2], "doc": [1, 2], "exist": [1, 2], "main": [1, 2], "deploi": [1, 2], "us": [1, 2], "gha": [1, 2], "add": [1, 2], "help": [1, 2], "tutori": [1, 2], "howto": [1, 2], "about": [1, 2], "histori": [1, 2], "download": [1, 2], "copyright": [1, 2], "get": 2, "baselin": 2, "accur": 2, "version": 2, "The": 2, "origin": 2, "entri": 2, "locat": 2, "user": 2, "trevormartin": 2, "github": 2, "multisign": 2, "epi": 2, "bug": 2, "rst": 2, "line": 2, "52": 2, "10": 2, "frequent": 2, "ask": 2, "question": 2, "6": 2, "17": 2, "37": 2, "determin": [2, 3, 4], "msei_refer": 2, "28": 2, "20": 2, "61": 2, "ctoc": 2, "21": 2, "87": 2, "89": 2, "meta": 2, "inform": 2, "91": 2, "abov": 2, "15": 2, "36": 2, "class": [3, 4], "pyrenew": [3, 4], "negativebinomi": 3, "concentration_prior": 3, "_supportsarrai": [3, 4], "dtype": [3, 4], "ani": [3, 4], "_nestedsequ": [3, 4], "bool": [3, 4], "int": [3, 4], "float": [3, 4], "complex": [3, 4], "str": [3, 4], "byte": [3, 4], "concentration_suffix": 3, "_concentr": 3, "parameter_nam": 3, "negbinom_rv": 3, "mean_varnam": 3, "mean": [3, 4], "counts_varnam": 3, "count": 3, "base": [3, 4], "random_vari": [3, 4], "dict": [3, 4], "constant": [3, 4], "none": [3, 4], "tupl": [3, 4], "from": [3, 4], "paramet": [3, 4], "option": [3, 4], "A": [3, 4], "dictionari": [3, 4], "contain": [3, 4], "possibli": 3, "pass": [3, 4], "ob": 3, "numpyro": [3, 4], "ignor": 3, "default": [3, 4], "return": [3, 4], "type": [3, 4], "static": [3, 4], "poisson_rv": 3, "rate_varnam": 3, "rate": [3, 4], "ep": 3, "1e": 3, "08": 3, "possibl": 3, "autoreg": 4, "noise_sd": 4, "object": 4, "repres": 4, "p": 4, "durat": 4, "init": 4, "length": 4, "sequenc": 4, "arraylik": 4, "initi": 4, "point": 4, "firstdifferencear": 4, "stochast": 4, "1": 4, "e": 4, "init_v": 4, "init_rate_of_chang": 4, "trend_rw": 4, "start": 4, "rtrandomwalk": 4, "rt0_dist": 4, "truncat": 4, "lefttruncateddistribut": 4, "rt_transform": 4, "rt_rw_dist": 4, "continu": 4, "normal": 4, "rt": 4, "randomwalk": 4, "rt0": 4, "n_timepoint": 4, "simplerandomwalk": 4, "error_distribut": 4, "markovian": 4, "arbitrari": 4, "step": 4}, "objects": {"pyrenew.observation": [[3, 0, 0, "-", "negativebinomial"], [3, 0, 0, "-", "poisson"]], "pyrenew.observation.negativebinomial": [[3, 1, 1, "", "NegativeBinomialObservation"]], "pyrenew.observation.negativebinomial.NegativeBinomialObservation": [[3, 2, 1, "", "sample"], [3, 2, 1, "", "validate"]], "pyrenew.observation.poisson": [[3, 1, 1, "", "PoissonObservation"]], "pyrenew.observation.poisson.PoissonObservation": [[3, 2, 1, "", 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description = "sphinxcontrib-applehelp is a Sphinx extension which outputs Apple help books" -category = "main" optional = false python-versions = ">=3.9" files = [ @@ -697,7 +1119,6 @@ test = ["pytest"] name = "sphinxcontrib-devhelp" version = "1.0.6" description = "sphinxcontrib-devhelp is a sphinx extension which outputs Devhelp documents" -category = "main" optional = false python-versions = ">=3.9" files = [ @@ -714,7 +1135,6 @@ test = ["pytest"] name = "sphinxcontrib-htmlhelp" version = "2.0.5" description = "sphinxcontrib-htmlhelp is a sphinx extension which renders HTML help files" -category = "main" optional = false python-versions = ">=3.9" files = [ @@ -731,7 +1151,6 @@ test = ["html5lib", "pytest"] name = "sphinxcontrib-jsmath" version = "1.0.1" description = "A sphinx extension which renders display math in HTML via JavaScript" -category = "main" optional = false python-versions = ">=3.5" files = [ @@ -746,7 +1165,6 @@ test = ["flake8", "mypy", "pytest"] name = "sphinxcontrib-mermaid" version = "0.9.2" description = "Mermaid diagrams in yours Sphinx powered docs" -category = "main" optional = false python-versions = ">=3.7" files = [ @@ -758,7 +1176,6 @@ files = [ name = "sphinxcontrib-qthelp" version = "1.0.7" description = "sphinxcontrib-qthelp is a sphinx extension which outputs QtHelp documents" -category = "main" optional = false python-versions = ">=3.9" files = [ @@ -775,7 +1192,6 @@ test = ["pytest"] name = "sphinxcontrib-serializinghtml" version = "1.1.10" description = "sphinxcontrib-serializinghtml is a sphinx extension which outputs \"serialized\" HTML files (json and pickle)" -category = "main" optional = false python-versions = ">=3.9" files = [ @@ -792,7 +1208,6 @@ test = ["pytest"] name = "tqdm" version = "4.66.2" description = "Fast, Extensible Progress Meter" -category = "main" optional = false python-versions = ">=3.7" files = [ @@ -813,7 +1228,6 @@ telegram = ["requests"] name = "urllib3" version = "2.2.1" description = "HTTP library with thread-safe connection pooling, file post, and more." -category = "main" optional = false python-versions = ">=3.8" files = [ @@ -830,4 +1244,4 @@ zstd = ["zstandard (>=0.18.0)"] [metadata] lock-version = "2.0" python-versions = "^3.11" -content-hash = "25331ede4706a442aaa2bdbe2d021ab55b224dd2b15dc5266cfa4a7fc6f74167" +content-hash = "13a69925b7d4754d7abdeb92ed748fe3ea9224a2dfa3dcc319469eb315259f85" diff --git a/docs/pyproject.toml b/docs/pyproject.toml index b94f121a..7f2885cd 100644 --- a/docs/pyproject.toml +++ b/docs/pyproject.toml @@ -4,7 +4,7 @@ version = "0.1.0" description = "This package contains the documentation for the CFA Multisignal Renewal project. This documentation leverages Sphinx." authors = ["R543hfer099JJfd <127630341+AFg6K7h4fhy2@users.noreply.github.com>"] license = "Apache 2.0" -readme = "README.md" +package-mode = false [tool.poetry.dependencies] python = "^3.11" @@ -14,6 +14,8 @@ jaxlib = "^0.4.25" numpyro = "^0.14.0" sphinxcontrib-mermaid = "^0.9.2" polars = "^0.20.16" +matplotlib = "^3.8.3" +sphinx-autodoc-typehints = "^2.1.0" [build-system] diff --git a/docs/source/conf.py b/docs/source/conf.py index 5805d6bc..c9c6133a 100644 --- a/docs/source/conf.py +++ b/docs/source/conf.py @@ -32,12 +32,24 @@ "sphinx.ext.viewcode", "sphinx.ext.mathjax", "sphinxcontrib.mermaid", + "sphinx_autodoc_typehints", ] +# Simplifies printing of type hints +set_type_checking_flag = True +typehints_fully_qualified = False + +# Avoid appending the full module name to the class name +add_module_names = False + templates_path = ["_templates"] exclude_patterns = [] -todo_include_todos = True +# Default deph for documentation +toc_deph = 2 + +# We don't want that explicitly +todo_include_todos = False # -- Options for HTML output ------------------------------------------------- diff --git a/docs/source/general/ctoc.rst b/docs/source/general/ctoc.rst index 41df0b16..02dd1693 100644 --- a/docs/source/general/ctoc.rst +++ b/docs/source/general/ctoc.rst @@ -2,10 +2,11 @@ Complete Table Of Contents ========================== .. toctree:: - :maxdepth: 4 + :maxdepth: 3 ../msei_reference/index ../test_reference/index + ../tutorials/index ../genindex ../modindex ../search diff --git a/docs/source/index.rst b/docs/source/index.rst index ce3e3920..06eb0a9a 100644 --- a/docs/source/index.rst +++ b/docs/source/index.rst @@ -56,6 +56,7 @@ Documentation Components msei_reference/index test_reference/index + tutorials/index general/state general/faq general/usage diff --git a/docs/source/tutorials/index.rst b/docs/source/tutorials/index.rst new file mode 100644 index 00000000..47c16476 --- /dev/null +++ b/docs/source/tutorials/index.rst @@ -0,0 +1,9 @@ +Tutorials +============== + +.. toctree:: + :maxdepth: 3 + + getting-started + example-with-datasets + pyrenew_demo diff --git a/model/docs/.gitignore b/model/docs/.gitignore index 4b7530c4..b31cd818 100644 --- a/model/docs/.gitignore +++ b/model/docs/.gitignore @@ -1,2 +1,4 @@ !*png *_files/libs + +/.quarto/ diff --git a/model/docs/example-with-datasets.qmd b/model/docs/example-with-datasets.qmd index 470614d3..91c27b8a 100644 --- a/model/docs/example-with-datasets.qmd +++ b/model/docs/example-with-datasets.qmd @@ -77,7 +77,7 @@ dat.head(5) Let's take a look at the daily prevalence of hospital admissions. ```{python} -#| label: plot-hospital admissions +#| label: fig-plot-hospital-admissions import matplotlib.pyplot as plt # Rotating the x-axis labels, and only showing ~10 labels @@ -95,7 +95,7 @@ plt.show() First, we will extract two datasets we will use as deterministic quantities: the generation interval and the infection to hospitalization interval. ```{python} -#| label: data-extract +#| label: fig-data-extract gen_int = datasets.load_generation_interval() inf_hosp_int = datasets.load_infection_admission_interval() @@ -184,9 +184,8 @@ with npro.handlers.seed(rng_seed = np.random.randint(1, timeframe)): ``` ```{python} -#| label: basic-fig +#| label: fig-basic #| fig-cap: Rt and Infections -#| fig-cap-location: bottom import matplotlib.pyplot as plt fig, axs = plt.subplots(1, 2) @@ -230,9 +229,8 @@ We can use the `plot_posterior` method to visualize the results[^capture]: [^capture]: The output is captured to avoid `quarto` from displaying the output twice. ```{python} -#| label: output-hospital admissions +#| label: fig-output-hospital-admissions #| fig-cap: Hospital Admissions posterior distribution -#| fig-cap-location: bottom out = hosp_model.plot_posterior( var="predicted_admissions", ylab="Hospital Admissions", @@ -269,9 +267,8 @@ hosp_model.run( And plotting the results: ```{python} -#| label: output-admissions-with-padding +#| label: fig-output-admissions-with-padding #| fig-cap: Hospital Admissions posterior distribution -#| fig-cap-location: bottom out = hosp_model.plot_posterior( var="predicted_admissions", ylab="Hospital Admissions", @@ -282,9 +279,8 @@ out = hosp_model.plot_posterior( We can also take a look at the latent infections: ```{python} -#| label: output-infections-with-padding +#| label: fig-output-infections-with-padding #| fig-cap: Hospital Admissions posterior distribution -#| fig-cap-location: bottom out2 = hosp_model.plot_posterior( var="latent_infections", ylab="Latent Infections" @@ -369,10 +365,8 @@ hosp_model_weekday.run( And plotting the results: ```{python} -#| label: output-admissions-padding-and-weekday +#| label: fig-output-admissions-padding-and-weekday #| fig-cap: Hospital Admissions posterior distribution -#| fig-cap-location: bottom -#| out = hosp_model_weekday.plot_posterior( var="predicted_admissions", ylab="Hospital Admissions", diff --git a/model/docs/getting-started.qmd b/model/docs/getting-started.qmd index d054e48d..8ab08f76 100644 --- a/model/docs/getting-started.qmd +++ b/model/docs/getting-started.qmd @@ -115,6 +115,7 @@ The following diagram summarizes how the modules interact via composition; notab ```{mermaid} %%| label: overview-of-RtInfectionsRenewalModel +%%| include: true flowchart TB genint["(1) gen_int\n(DetermnisticPMF)"] i0["(2) I0\n(Infections0)"] @@ -145,9 +146,8 @@ sim_data To understand what has been accomplished here, visualize an $R_t$ sample path (left panel) and infections over time (right panel): ```{python} -#| label: basic-fig +#| label: fig-basic #| fig-cap: Rt and Infections -#| fig-cap-location: bottom import matplotlib.pyplot as plt fig, axs = plt.subplots(1, 2) @@ -185,9 +185,8 @@ model1.run( Now, let's investigate the output, particularly the posterior distribution of the $R_t$ estimates: ```{python} -#| label: output-rt +#| label: fig-output-rt #| fig-cap: Rt posterior distribution -#| fig-cap-location: bottom import polars as pl samps = model1.spread_draws([('Rt', 'time')]) @@ -221,6 +220,7 @@ The first four are collections of instances of `RandomVariable`, and the last is ```{mermaid} %%| label: overview-of-RtInfectionsRenewalModel +%%| include: true flowchart LR rand((RandomVariable\nmetaclass)) models((Model\nmetaclass)) diff --git a/model/src/pyrenew/latent/hospitaladmissions.py b/model/src/pyrenew/latent/hospitaladmissions.py index 91d0fa81..bdd87322 100644 --- a/model/src/pyrenew/latent/hospitaladmissions.py +++ b/model/src/pyrenew/latent/hospitaladmissions.py @@ -13,15 +13,14 @@ class HospAdmissionsSample(NamedTuple): """ - A container for holding the output from HospAdmissionsSample.sample. - >>>>>>> origin/main + A container for holding the output from HospAdmissionsSample.sample. - Parameters - ---------- - infection_hosp_rate : float, optional - The infection-to-hospitalization rate. Defaults to None. - predicted : ArrayLike or None - The predicted number of hospital admissions. Defaults to None. + Parameters + ---------- + infection_hosp_rate : float, optional + The infection-to-hospitalization rate. Defaults to None. + predicted : ArrayLike or None + The predicted number of hospital admissions. Defaults to None. """ infection_hosp_rate: float | None = None