diff --git a/.clang-format b/.clang-format
deleted file mode 100644
index a71b20fb..00000000
--- a/.clang-format
+++ /dev/null
@@ -1,3 +0,0 @@
-BasedOnStyle: Google
-IndentWidth: 4
-SortIncludes: true
diff --git a/.github/test.yml b/.github/test.yml
new file mode 100644
index 00000000..e1a885ea
--- /dev/null
+++ b/.github/test.yml
@@ -0,0 +1,73 @@
+name: Test
+
+on:
+ pull_request:
+ types: [opened, synchronize, reopened, ready_for_review]
+ paths-ignore:
+ - "research/**"
+ - "**.ipynb"
+ - "**.md"
+ push:
+ branches:
+ - main
+ paths-ignore:
+ - "research/**"
+ - "**.ipynb"
+ - "**.md"
+jobs:
+ test:
+ if: github.event.pull_request.draft == false
+ timeout-minutes: 15
+ strategy:
+ fail-fast: false
+ matrix:
+ os: ["ubuntu-latest"]
+ python-version: ["3.10"]
+ name: Test (${{ matrix.python-version }}, ${{ matrix.os }})
+ runs-on: ${{ matrix.os }}
+ steps:
+
+ - uses: actions/checkout@v3
+
+ - name: Install poetry
+ run: pipx install poetry
+
+ - name: Set up Python ${{ matrix.python-version }}
+ uses: actions/setup-python@v4
+ with:
+ python-version: ${{ matrix.python-version }}
+ cache: 'poetry'
+
+ # Cache pre-commit files so it's fast!
+ # based on https://pre-commit.com/#github-actions-example
+ - name: set PY
+ run: echo "PY=$(python -VV | sha256sum | cut -d' ' -f1)" >> $GITHUB_ENV
+ - name: Cache pre-commit
+ uses: actions/cache@v3
+ with:
+ path: ~/.cache/pre-commit
+ key: pre-commit|${{ env.PY }}|${{ hashFiles('.pre-commit-config.yaml') }}
+ id: precommitcache
+
+ - name: Update environment
+ run: |
+ poetry env use ${{ matrix.python-version }} && poetry install --with=test,cloud
+
+ - name: Run all pre-commit checks on all files
+ run: poetry run pre-commit run --color=always -a
+
+ - name: Pytest
+ run: poetry run pytest -n auto -s
+
+ - name: Report failures on Slack
+ if: failure() && github.event.repository.default_branch == github.event.workflow_run.head_branch
+ id: slack
+ uses: slackapi/slack-github-action@v1.19.0
+ with:
+ # Slack channel id, channel name, or user id to post message.
+ # See also: https://api.slack.com/methods/chat.postMessage#channels
+ channel-id: C02TC2DAN74
+ # For posting a simple plain text message
+ slack-message: "*Build failure on default branch!* 😱\nhttps://github.com/${{github.repository}}/actions/runs/${{github.run_id}}"
+ env:
+ SLACK_BOT_TOKEN: ${{ secrets.SLACK_BOT_TOKEN }}
diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
deleted file mode 100644
index dd86c3ae..00000000
--- a/.github/workflows/test.yml
+++ /dev/null
@@ -1,77 +0,0 @@
-name: Test
-
-on:
- schedule:
- # Every day at 9:00 AM UTC
- - cron: "0 9 * * *"
- push:
-jobs:
- test:
- timeout-minutes: 15
- strategy:
- fail-fast: false
- matrix:
- os: ["ubuntu-latest"]
- python-version: ["3.9"]
- name: Test (${{ matrix.python-version }}, ${{ matrix.os }})
- runs-on: ${{ matrix.os }}
- defaults:
- run:
- shell: bash -l {0}
- # https://github.com/marketplace/actions/setup-miniconda#caching-environments
- steps:
- - uses: actions/checkout@v2
- - name: Setup Mambaforge
- uses: conda-incubator/setup-miniconda@v2
- with:
- miniforge-variant: Mambaforge
- miniforge-version: latest
- activate-environment: anaconda-client-env
- use-mamba: true
- python-version: ${{ matrix.python-version }}
- - name: Get Date
- id: get-date
- run: echo "::set-output name=today::$(/bin/date -u '+%Y%m%d')"
- shell: bash
- - name: Cache Dependencies
- uses: actions/cache@v2
- with:
- # Cache the Conda, Bazel, and Pre-commit files
- path: |
- ${{ env.CONDA }}/envs
- ~/.cache/pre-commit
- ~/.cache/bazel
- key: conda-${{ runner.os }}--${{ runner.arch }}--${{ steps.get-date.outputs.today }}-${{ hashFiles('environment.yml') }}-${{ env.CACHE_NUMBER }}
- env:
- # Increase this value to reset cache if environment.yml has not changed
- CACHE_NUMBER: 1
- id: cache
- - name: Update environment
- run: mamba env update -n anaconda-client-env -f environment.yml
- if: steps.cache.outputs.cache-hit != 'true'
- - name: Run all pre-commit checks on the full repo!
- run: |
- pre-commit run --all-files
- - name: Build and install pyimprint
- run: |
- ./generate_bazelrc
- bazel build -c dbg //python:pyimprint_wheel
- pip install --no-deps --force-reinstall bazel-bin/python/dist/*.whl
- - name: Bazel Test
- run: |
- bazel test -c dbg //...
- - name: Pytest
- run: |
- pytest .
- - name: Report failures on Slack
- if: failure() && github.event.repository.default_branch == github.event.workflow_run.head_branch
- id: slack
- uses: slackapi/slack-github-action@v1.19.0
- with:
- # Slack channel id, channel name, or user id to post message.
- # See also: https://api.slack.com/methods/chat.postMessage#channels
- channel-id: C02TC2DAN74
- # For posting a simple plain text message
- slack-message: "*Build failure on default branch!* 😱\nhttps://github.com/${{github.repository}}/actions/runs/${{github.run_id}}"
- env:
- SLACK_BOT_TOKEN: ${{ secrets.SLACK_BOT_TOKEN }}
\ No newline at end of file
diff --git a/.gitignore b/.gitignore
index e911b8cd..e665dc68 100644
--- a/.gitignore
+++ b/.gitignore
@@ -1,37 +1,48 @@
*.DS_Store
-
-build/
-/.vs
-.history/
-/imprint/CMakeSettings.json
-CMakeCache.txt
-CMakeFiles/
-imprintConfig.cmake
-imprintConfigVersion.cmake
-DartConfiguration.tcl
.env
-/python/dist/
-.spyproject/
+# python stuff
+__pycache__/
+*.py[cod]
+*$py.class
+
+# notebook stuff
+.ipynb_checkpoints
-# ignore rc because we are tracking generator now
-.bazelrc
-bazel
-bazel-*
-.vagrant/
-Vagrantfile
-.idea/
-compile_commands.json
+# profiler outputs
+*.lprof
+*.prof
-# python stuff
-__pycache__
+# python packaging outputs
+*.egg-info
# c++ extensions built in place within the source tree.
+.rendered.*.cpp
*.so
-# bazel outputs
-*pid*.log
+# poetry.toml should not be committed because it will vary between machines
+# (e.g. CI will want to use virtualenvs but locally we use conda)
+poetry.toml
+
+# various data
+*.pkl
+*.npy
+*.parquet
+*.db
+*.db.wal
+*.zip
+
+# anything else
+*.gitignore*
+!**/.gitignore
# Codespaces
oryx-build-commands.txt
venv
+
+# Cloud and AWS stuff, CDK
+.terraform
+.terraform.*
+terraform.*
+.cdk.staging/
+cdk.out/
diff --git a/.gitleaks.toml b/.gitleaks.toml
new file mode 100644
index 00000000..677cfcd8
--- /dev/null
+++ b/.gitleaks.toml
@@ -0,0 +1,21 @@
+# Title for the gitleaks configuration file.
+title = "Gitleaks title"
+
+# Extend the base (this) configuration. When you extend a configuration
+# the base rules take precendence over the extended rules. I.e, if there are
+# duplicate rules in both the base configuration and the extended configuration
+# the base rules will override the extended rules.
+# Another thing to know with extending configurations is you can chain together
+# multiple configuration files to a depth of 2. Allowlist arrays are appended
+# and can contain duplicates.
+# useDefault and path can NOT be used at the same time. Choose one.
+[extend]
+# useDefault will extend the base configuration with the default gitleaks config:
+# https://github.com/zricethezav/gitleaks/blob/master/config/gitleaks.toml
+useDefault = true
+
+[allowlist]
+paths = [
+ '''(.*?)(ipynb)$''',
+ '''tools/gitleaks-report.json'''
+]
\ No newline at end of file
diff --git a/.gitmodules b/.gitmodules
deleted file mode 100644
index d42ccde8..00000000
--- a/.gitmodules
+++ /dev/null
@@ -1,4 +0,0 @@
-[submodule "src/imprint/third_party/pybind11"]
- path = src/imprint/third_party/pybind11
- url = https://github.com/pybind/pybind11.git
- branch = stable
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index d8228843..c0798bca 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -1,34 +1,41 @@
fail_fast: false
repos:
- - repo: https://github.com/pocc/pre-commit-hooks
- rev: v1.3.5
+ # We have black here twice because the first black block runs black on
+ # Jupyter notebooks. And we don't want to run black on notebooks in the
+ # research folder because 1) it's slow. 2) it can overwrite a notebook in
+ # current use causing the session to be lost. 3) there's no reason, those
+ # notebooks are exploration anyway.
+ - repo: https://github.com/psf/black
+ rev: 22.10.0
hooks:
- - id: clang-format
- args: [-i]
- # - id: clang-tidy
+ - id: black-jupyter
+ language_version: python3
+ exclude: research/
- repo: https://github.com/psf/black
- rev: 22.3.0
+ rev: 22.10.0
hooks:
- id: black
- language_version: python3
- - repo: https://gitlab.com/pycqa/flake8
- rev: 3.8.4
+ - repo: https://github.com/pycqa/flake8
+ rev: 5.0.4
hooks:
- id: flake8
- repo: https://github.com/asottile/reorder_python_imports
- rev: v3.8.1
+ rev: v3.9.0
hooks:
- id: reorder-python-imports
- repo: https://github.com/mwouts/jupytext
- rev: v1.13.8
+ rev: v1.14.1
+ hooks:
+ - id: jupytext
+ args: [--from, ipynb, --to, "md"]
+ # Should run after jupytext so that secrets in ipynb files get properly scanned.
+ - repo: https://github.com/zricethezav/gitleaks
+ rev: v8.15.2
hooks:
- - id: jupytext
- args: [--from, ipynb, --to, "md"]
+ - id: gitleaks
+ args: [--baseline-path, tools/gitleaks-report.json]
- repo: https://github.com/pre-commit/pre-commit-hooks
- rev: v4.0.1
+ rev: v4.3.0
hooks:
- id: debug-statements
- - id: detect-aws-credentials
- args: [--allow-missing-credentials]
- - id: detect-private-key
- - id: forbid-new-submodules
+ - id: forbid-new-submodules
\ No newline at end of file
diff --git a/.vscode/build.sh b/.vscode/build.sh
deleted file mode 100755
index 914626ea..00000000
--- a/.vscode/build.sh
+++ /dev/null
@@ -1,5 +0,0 @@
-#!/bin/zsh
-eval "$(conda shell.zsh hook)"
-conda activate imprint
-bazel build //python:pyimprint/core.so
-ln -sf ./bazel-bin/python/pyimprint/core.so python/pyimprint/core.so
\ No newline at end of file
diff --git a/.vscode/c_cpp_properties.json b/.vscode/c_cpp_properties.json
deleted file mode 100644
index 186042d0..00000000
--- a/.vscode/c_cpp_properties.json
+++ /dev/null
@@ -1,35 +0,0 @@
-{
- "configurations": [
- {
- "name": "Linux",
- "includePath": [
- "${workspaceFolder}/**",
- "${workspaceFolder}/imprint/include",
- "${workspaceFolder}/bazel-imprint/external/eigen",
- "${workspaceFolder}/bazel-imprint/external/fmtlib/include",
- "${workspaceFolder}/bazel-imprint/external/com_github_scipy_boost/",
- "${workspaceFolder}/bazel-imprint/external/pybind11/include",
- "${workspaceFolder}/bazel-imprint/external/com_github_google_benchmark/include",
- "${workspaceFolder}/bazel-imprint/external/com_google_googletest/googletest/include"
- ],
- "defines": [],
- "compilerPath": "/usr/bin/clang",
- "cStandard": "c11",
- "cppStandard": "c++17",
- "intelliSenseMode": "linux-clang-x64",
- "compilerArgs": [],
- "mergeConfigurations": false,
- "browse": {
- "path": [
- "${workspaceFolder}/**"
- ],
- "limitSymbolsToIncludedHeaders": true
- },
- "forcedInclude": [
- "${workspaceFolder}/.vscode/eigen_fix.h"
- ],
- "compileCommands": "${workspaceFolder}/compile_commands.json"
- }
- ],
- "version": 4
-}
\ No newline at end of file
diff --git a/.vscode/eigen_fix.h b/.vscode/eigen_fix.h
deleted file mode 100644
index a70f248a..00000000
--- a/.vscode/eigen_fix.h
+++ /dev/null
@@ -1,10 +0,0 @@
-/*
- * Proposed fix with IntelliSense that keeps raising error with Eigen classes
- * about incomplete types.
- * https://github.com/microsoft/vscode-cpptools/issues/7413#issuecomment-1105063602
- * This file is force-included in c_cpp_properties.json.
- */
-#if __INTELLISENSE__
-#undef __ARM_NEON
-#undef __ARM_NEON__
-#endif
\ No newline at end of file
diff --git a/.vscode/launch.json b/.vscode/launch.json
deleted file mode 100644
index 306f58eb..00000000
--- a/.vscode/launch.json
+++ /dev/null
@@ -1,16 +0,0 @@
-{
- // Use IntelliSense to learn about possible attributes.
- // Hover to view descriptions of existing attributes.
- // For more information, visit: https://go.microsoft.com/fwlink/?linkid=830387
- "version": "0.2.0",
- "configurations": [
- {
- "name": "Python: Current File",
- "type": "python",
- "request": "launch",
- "program": "${file}",
- "console": "integratedTerminal",
- "justMyCode": true
- }
- ]
-}
\ No newline at end of file
diff --git a/.vscode/settings.json b/.vscode/settings.json
index af9b6d59..1c355f81 100644
--- a/.vscode/settings.json
+++ b/.vscode/settings.json
@@ -1,120 +1,18 @@
{
- "bazel-cpp-tools.compileCommands.targets": [
- "//...",
- ],
- "jupyter.jupyterServerType": "local",
- "files.associations": {
- "functional": "cpp",
- "*.evaluator": "cpp",
- "*.traits": "cpp",
- "fft": "cpp",
- "openglsupport": "cpp",
- "regex": "cpp",
- "tuple": "cpp",
- "type_traits": "cpp",
- "any": "cpp",
- "array": "cpp",
- "atomic": "cpp",
- "bit": "cpp",
- "*.tcc": "cpp",
- "bitset": "cpp",
- "cctype": "cpp",
- "chrono": "cpp",
- "cinttypes": "cpp",
- "clocale": "cpp",
- "cmath": "cpp",
- "codecvt": "cpp",
- "complex": "cpp",
- "condition_variable": "cpp",
- "cstdarg": "cpp",
- "cstddef": "cpp",
- "cstdint": "cpp",
- "cstdio": "cpp",
- "cstdlib": "cpp",
- "cstring": "cpp",
- "ctime": "cpp",
- "cwchar": "cpp",
- "cwctype": "cpp",
- "deque": "cpp",
- "forward_list": "cpp",
- "list": "cpp",
- "map": "cpp",
- "set": "cpp",
- "unordered_map": "cpp",
- "unordered_set": "cpp",
- "vector": "cpp",
- "exception": "cpp",
- "algorithm": "cpp",
- "iterator": "cpp",
- "memory": "cpp",
- "memory_resource": "cpp",
- "numeric": "cpp",
- "optional": "cpp",
- "random": "cpp",
- "ratio": "cpp",
- "string": "cpp",
- "string_view": "cpp",
- "system_error": "cpp",
- "utility": "cpp",
- "hash_map": "cpp",
- "fstream": "cpp",
- "future": "cpp",
- "initializer_list": "cpp",
- "iomanip": "cpp",
- "iosfwd": "cpp",
- "iostream": "cpp",
- "istream": "cpp",
- "limits": "cpp",
- "mutex": "cpp",
- "new": "cpp",
- "ostream": "cpp",
- "shared_mutex": "cpp",
- "sstream": "cpp",
- "stdexcept": "cpp",
- "streambuf": "cpp",
- "thread": "cpp",
- "typeinfo": "cpp",
- "valarray": "cpp",
- "variant": "cpp",
- "filesystem": "cpp",
- "locale": "cpp",
- "mprealsupport": "cpp",
- "nonlinearoptimization": "cpp",
- "dense": "cpp",
- "__bit_reference": "cpp",
- "__bits": "cpp",
- "__config": "cpp",
- "__debug": "cpp",
- "__errc": "cpp",
- "__hash_table": "cpp",
- "__locale": "cpp",
- "__mutex_base": "cpp",
- "__node_handle": "cpp",
- "__nullptr": "cpp",
- "__split_buffer": "cpp",
- "__string": "cpp",
- "__threading_support": "cpp",
- "__tree": "cpp",
- "__tuple": "cpp",
- "compare": "cpp",
- "concepts": "cpp",
- "ios": "cpp",
- "queue": "cpp",
- "stack": "cpp",
- "__functional_base": "cpp",
- "alignedvector3": "cpp",
- "typeindex": "cpp",
- "*.ipp": "cpp",
- "*.inc": "cpp",
- "core": "cpp",
- "geometry": "cpp",
- "qtalignedmalloc": "cpp",
- "matrixfunctions": "cpp",
- "bvh": "cpp"
- },
- "C_Cpp.errorSquiggles": "Enabled",
- "editor.formatOnSave": false,
- "cmake.configureOnOpen": false,
- "python.testing.unittestEnabled": false,
- "python.testing.pytestEnabled": true
+ "python.testing.unittestEnabled": false,
+ "python.testing.pytestEnabled": true,
+ "python.linting.pylintEnabled": false,
+ "python.linting.flake8Enabled": true,
+ "python.linting.flake8Args": ["--ignore=E1,E2,E3,E4,E5,W1,W2,W3,W4,W5"],
+ "python.linting.enabled": true,
+ "python.formatting.provider": "black",
+ "autoDocstring.docstringFormat": "google-notypes",
+ "r.bracketedPaste": true,
+ "r.plot.useHttpgd": true,
+ "search.exclude": {
+ "**/.git": true,
+ "**/node_modules": true,
+ "**/__pycache__": true,
+ "research/archive": true
+ }
}
diff --git a/.vscode/tasks.json b/.vscode/tasks.json
deleted file mode 100644
index 724e5d26..00000000
--- a/.vscode/tasks.json
+++ /dev/null
@@ -1,20 +0,0 @@
-{
- "version": "2.0.0",
- "tasks": [
- {
- "type": "shell",
- "label": "Build Python extension",
- "command": ".vscode/build.sh",
- "options": {
- "cwd": "${workspaceFolder}",
- },
- "problemMatcher": [
- "$gcc"
- ],
- "group": {
- "kind": "build",
- "isDefault": true
- }
- }
- ]
-}
\ No newline at end of file
diff --git a/BUILD.bazel b/BUILD.bazel
deleted file mode 100644
index 56fa8821..00000000
--- a/BUILD.bazel
+++ /dev/null
@@ -1,2 +0,0 @@
-# Dummy file just to appease Bazel.
-# .bzl requires the existence of a BUILD file.
diff --git a/LICENSE b/LICENSE
deleted file mode 100644
index cba20ac3..00000000
--- a/LICENSE
+++ /dev/null
@@ -1,29 +0,0 @@
-BSD 3-Clause License
-
-Copyright (c) 2022, Confirm Solutions, Inc.
-All rights reserved.
-
-Redistribution and use in source and binary forms, with or without
-modification, are permitted provided that the following conditions are met:
-
-1. Redistributions of source code must retain the above copyright notice, this
- list of conditions and the following disclaimer.
-
-2. Redistributions in binary form must reproduce the above copyright notice,
- this list of conditions and the following disclaimer in the documentation
- and/or other materials provided with the distribution.
-
-3. Neither the name of the copyright holder nor the names of its
- contributors may be used to endorse or promote products derived from
- this software without specific prior written permission.
-
-THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
-AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
-IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
-DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
-FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
-DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
-SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
-CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
-OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
-OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
diff --git a/README.md b/README.md
index 4b7e6c6d..e90004c3 100644
--- a/README.md
+++ b/README.md
@@ -4,20 +4,9 @@ Imprint is a library to validate clinical trial designs.
![example workflow](https://github.com/Confirm-Solutions/imprint/actions/workflows/test.yml/badge.svg)
-## Dependencies
+## Installing Imprint for development.
-The most important dependencies are:
-
-- [conda](https://docs.conda.io/projects/conda/en/latest/index.html)
- - [Anaconda](https://www.anaconda.com/)
- - [Miniconda](https://docs.conda.io/en/latest/miniconda.html)
-- [Python >= 3.9](https://www.python.org/)
-
-## Installing Imprint for development
-
-NOTE: In the future, we will produce PyPI and conda-forge packages to ease the installation process for users. This will reduce the installation process to one or two steps. The current process is oriented at a developer of imprint.
-
-Please run all the steps here to get a fully functional development environment.
+(Soon, we will have a separate pathway for users to install via PyPI/pip)
1. If you do not have conda installed already, please install it. There are
many ways to get conda. We recommend installing `Mambaforge` which is a
@@ -25,68 +14,34 @@ Please run all the steps here to get a fully functional development environment.
`conda-forge` as the default set of package repositories. [CLICK HERE for
installers and installation
instructions.](https://github.com/conda-forge/miniforge#mambaforge)
-2. Install Bazel. On Mac, you can just run `brew install bazelisk`. On Ubuntu
- Linux, please follow the [instructions
- here](https://docs.bazel.build/versions/main/install-ubuntu.html).
-3. Clone the git repo:
-
- ```bash
- git clone git@github.com:Confirm-Solutions/imprint.git
- ```
-
-4. Set up your imprint conda environment (note that you may substitute `mamba`
- here for `conda` and the install will be substantially faster). The list of
- packages that will be installed inside your conda environment can be seen in
- the [`environment.yml` file](../environment.yml).
-
- ```bash
- cd imprint/
- conda update -y conda
- conda env create
- conda activate imprint
- ```
-
-5. To set up pre-commit for this git repo:
-
- ```bash
- pre-commit install
- ```
-
-6. To set up your bazel configuration for building C++. **See below to install bazel.**
-
- ```bash
- ./generate_bazelrc
- ```
-
-7. Build and install the `pyimprint` package.
-
- ```bash
- bazel build //python:pyimprint_wheel
- pip install bazel-bin/python/dist/pyimprint-0.1-py3-none-any.whl
- ```
-
-8. (it's okay to skip this step if this is your first time installing imprint) To recompile and reinstall the pyimprint package after making changes to the C++ backend, run the following:
-
- ```bash
- bazel build //python:pyimprint_wheel
- pip install --force-reinstall bazel-bin/python/dist/pyimprint-0.1-py3-none-any.whl
- ```
-
-9. Finally, check that the installation process was successful by running one of our example scripts:
-
- ```bash
- bazel run -c opt //python/example:simple_selection -- main
- ```
+2. Clone the git repo:
+
+ ```bash
+ git clone git@github.com:Confirm-Solutions/imprint.git
+ ```
+
+3. Set up your imprint conda environment. The list of packages that will be
+ installed inside your conda environment can be seen
+ in [`pyproject.toml`](pyproject.toml).
+
+ ```bash
+ cd confirm/env
+ mamba update -y conda
+ # create a development virtual environment with useful tools
+ mamba env create
+ conda activate confirm
+ # install the confirm package plus development tools
+ poetry install --with=dev,test,cloud,cloud_dev
+ ```
+
+## Committing code
+
+In order to commit code and pass the pre-commit checks, you will need to install `go` and `gitleaks` with `brew install go gitleaks`.
## Getting started understanding imprint
-[Please check out the tutorial where we analyze a three arm basket trial here.](./research/berry/tutorial.ipynb)
-
-## Developing the Imprint C++ core engine
-
-Most users will not need to work directly with the core C++, instead working entirely through the Python interface.
+[Please check out the tutorial where we analyze a three arm basket trial here.](./tutorials/basket/basket.ipynb)
-[Instructions for developing the C++ core engine are available in the subfolder](./imprint/README.md)
## References
diff --git a/WORKSPACE b/WORKSPACE
deleted file mode 100644
index d218b638..00000000
--- a/WORKSPACE
+++ /dev/null
@@ -1,154 +0,0 @@
-load("@bazel_tools//tools/build_defs/repo:http.bzl", "http_archive")
-
-rules_python_version = "740825b7f74930c62f44af95c9a4c1bd428d2c53" # Latest @ 2021-06-23
-
-# Python rules
-http_archive(
- name = "rules_python",
- sha256 = "09a3c4791c61b62c2cbc5b2cbea4ccc32487b38c7a2cc8f87a794d7a659cc742",
- strip_prefix = "rules_python-{}".format(rules_python_version),
- url = "https://github.com/bazelbuild/rules_python/archive/{}.zip".format(rules_python_version),
-)
-
-# GoogleTest/GoogleMock framework. Used by most unit-tests
-http_archive(
- name = "com_google_googletest",
- sha256 = "205ddbea89a0dff059cd681f3ec9b0a6c12de7036a04cd57f0254105257593d9",
- strip_prefix = "googletest-13a433a94dd9c7e55907d7a9b75f44ff82f309eb",
- urls = ["https://github.com/google/googletest/archive/13a433a94dd9c7e55907d7a9b75f44ff82f309eb.zip"],
-)
-
-# Google benchmark
-http_archive(
- name = "com_github_google_benchmark",
- sha256 = "59f918c8ccd4d74b6ac43484467b500f1d64b40cc1010daa055375b322a43ba3",
- strip_prefix = "benchmark-16703ff83c1ae6d53e5155df3bb3ab0bc96083be",
- urls = ["https://github.com/google/benchmark/archive/16703ff83c1ae6d53e5155df3bb3ab0bc96083be.zip"],
-)
-
-# Rules CC
-http_archive(
- name = "rules_cc",
- sha256 = "9a446e9dd9c1bb180c86977a8dc1e9e659550ae732ae58bd2e8fd51e15b2c91d",
- strip_prefix = "rules_cc-262ebec3c2296296526740db4aefce68c80de7fa",
- urls = ["https://github.com/bazelbuild/rules_cc/archive/262ebec3c2296296526740db4aefce68c80de7fa.zip"],
-)
-
-# PyBind11 Bazel
-PYBIND_BAZEL_VERSION = "72cbbf1fbc830e487e3012862b7b720001b70672"
-
-PYBIND_VERSION = "2.9.1"
-
-http_archive(
- name = "pybind11_bazel",
- sha256 = "fec6281e4109115c5157ca720b8fe20c8f655f773172290b03f57353c11869c2",
- strip_prefix = "pybind11_bazel-{}".format(PYBIND_BAZEL_VERSION),
- urls = ["https://github.com/pybind/pybind11_bazel/archive/{}.zip".format(PYBIND_BAZEL_VERSION)],
-)
-
-# We still require the pybind library.
-http_archive(
- name = "pybind11",
- build_file = "@pybind11_bazel//:pybind11.BUILD",
- sha256 = "c6160321dc98e6e1184cc791fbeadd2907bb4a0ce0e447f2ea4ff8ab56550913",
- strip_prefix = "pybind11-{}".format(PYBIND_VERSION),
- urls = ["https://github.com/pybind/pybind11/archive/v{}.tar.gz".format(PYBIND_VERSION)],
-)
-
-load("@pybind11_bazel//:python_configure.bzl", "python_configure")
-
-python_configure(name = "local_config_python")
-
-# fmt
-http_archive(
- name = "fmtlib",
- patch_cmds = [
- "mv support/bazel/.bazelrc .bazelrc",
- "mv support/bazel/.bazelversion .bazelversion",
- "mv support/bazel/BUILD.bazel BUILD.bazel",
- "mv support/bazel/WORKSPACE.bazel WORKSPACE.bazel",
- ],
- sha256 = "23778bad8edba12d76e4075da06db591f3b0e3c6c04928ced4a7282ca3400e5d",
- strip_prefix = "fmt-8.1.1",
- urls = ["https://github.com/fmtlib/fmt/releases/download/8.1.1/fmt-8.1.1.zip"],
-)
-
-# ====================================
-# GOOGLE TCMALLOC + DEPENDENCIES
-# ====================================
-
-http_archive(
- name = "rules_fuzzing",
- sha256 = "a5734cb42b1b69395c57e0bbd32ade394d5c3d6afbfe782b24816a96da24660d",
- strip_prefix = "rules_fuzzing-0.1.1",
- urls = ["https://github.com/bazelbuild/rules_fuzzing/archive/v0.1.1.zip"],
-)
-
-# Protobuf
-load("@rules_fuzzing//fuzzing:repositories.bzl", "rules_fuzzing_dependencies")
-
-rules_fuzzing_dependencies()
-
-load("@rules_fuzzing//fuzzing:init.bzl", "rules_fuzzing_init")
-
-rules_fuzzing_init()
-
-http_archive(
- name = "com_google_absl",
- sha256 = "92d469a1a652fd1944398e560bd0d92ee8e3affbd61ed41fca89bb624b59109e",
- strip_prefix = "abseil-cpp-04bde89e5cb33bf4a714a5496fac715481fc48311",
- urls = ["https://github.com/abseil/abseil-cpp/archive/04bde89e5cb33bf4a714a5496fac715481fc48311.zip"],
-)
-
-http_archive(
- name = "com_google_tcmalloc",
- sha256 = "2e5e6755e02b0275b1333199c2a128a57c0d48ec8838fdca9baccf3b0e939ad6",
- strip_prefix = "tcmalloc-a3717bc4fcade63c642f9b991fbdd64299896762",
- urls = ["https://github.com/google/tcmalloc/archive/a3717bc4fcade63c642f9b991fbdd64299896762.zip"],
-)
-
-# ====================================
-# EIGEN
-# ====================================
-
-EIGEN_VERSION = "3.4.0"
-
-http_archive(
- name = "eigen",
- build_file_content =
- """
-# TODO(keir): Replace this with a better version, like from TensorFlow.
-# See https://github.com/ceres-solver/ceres-solver/issues/337.
-cc_library(
- name = 'eigen',
- srcs = [],
- includes = ['.'],
- hdrs = glob(['Eigen/**', 'unsupported/Eigen/**']),
- visibility = ['//visibility:public'],
-)
-""",
- sha256 = "8586084f71f9bde545ee7fa6d00288b264a2b7ac3607b974e54d13e7162c1c72",
- strip_prefix = "eigen-{}".format(EIGEN_VERSION),
- urls = ["https://gitlab.com/libeigen/eigen/-/archive/{0}/eigen-{0}.tar.gz".format(EIGEN_VERSION)],
-)
-
-_BOOST_COMMIT = "d8626c9d2d937abf6a38a844522714ad72e63281"
-
-http_archive(
- name = "com_github_scipy_boost",
- build_file_content =
- """
-cc_library(
- name = 'boost',
- srcs = [],
- includes = ['.'],
- hdrs = glob(['boost/**']),
- visibility = ['//visibility:public'],
-)
-""",
- sha256 = "496064bba545eb218179c0fa479304ac396ecca9f02ba6e0d3d4cc872f3569fa",
- strip_prefix = "boost-headers-only-%s" % _BOOST_COMMIT,
- urls = [
- "https://github.com/scipy/boost-headers-only/archive/%s.zip" % _BOOST_COMMIT,
- ],
-)
diff --git a/conftest.py b/conftest.py
new file mode 100644
index 00000000..72968bfe
--- /dev/null
+++ b/conftest.py
@@ -0,0 +1,10 @@
+import os
+
+from jax.config import config
+
+dir_path = os.path.dirname(os.path.realpath(__file__))
+# This avoids errors that occur when imprint is in a subtree.
+if dir_path == os.getcwd():
+ pytest_plugins = ["imprint.testing"]
+
+config.update("jax_enable_x64", True)
diff --git a/docs/.gitignore b/docs/.gitignore
deleted file mode 100644
index 3f31e8c8..00000000
--- a/docs/.gitignore
+++ /dev/null
@@ -1,7 +0,0 @@
-*.aux
-*.fdb_latexmk
-*.fls
-*.log
-*.synctex.gz
-*.bbl
-*.blg
diff --git a/docs/adagrid/.gitignore b/docs/adagrid/.gitignore
deleted file mode 100644
index c18dd8d8..00000000
--- a/docs/adagrid/.gitignore
+++ /dev/null
@@ -1 +0,0 @@
-__pycache__/
diff --git a/docs/adagrid/adagrid_1d.py b/docs/adagrid/adagrid_1d.py
deleted file mode 100644
index 54016a43..00000000
--- a/docs/adagrid/adagrid_1d.py
+++ /dev/null
@@ -1,66 +0,0 @@
-import matplotlib.pyplot as plt
-import numpy as np
-from scipy.stats import norm
-
-
-def f(x):
- return np.abs(
- np.cos(x) * 3 - np.sin(2 * x) - x + x**2 - 1 / 3.0 * x**3 * np.cos(x)
- )
-
-
-def adagrid_1d(lower, upper, f, sigma=1, n_batch=10, n_max=100, seed=0, tol=1e-2):
- # set seed
- np.random.seed(seed)
-
- # create initial values
- x = np.linspace(lower, upper, n_batch)
- fx = f(x)
- # sd = np.maximum(np.abs(fx), 1e-8)
- sd = sigma * np.ones(len(x))
- w_sum = np.sum(fx)
- w = fx / w_sum
-
- # compute loss-function
- p = np.array([np.dot(w, norm.pdf(xi, loc=x, scale=sd)) for xi in x])
- L = np.dot((p - w) ** 2, w)
- L_prev = np.Inf
-
- n_pts = n_batch
-
- while (n_pts < n_max) and (np.abs(L - L_prev) > L * tol):
- z_new = np.random.choice(len(w), size=n_batch, replace=True, p=w)
- mean_new = x[z_new]
- sd_new = sd[z_new]
- x_new = np.random.normal(loc=mean_new, scale=sd_new)
-
- for i in range(len(x_new)):
- while (x_new[i] < lower) or (x_new[i] > upper):
- x_new[i] = np.random.normal(mean_new[i], sd_new[i])
-
- fx_new = f(x_new)
- x = np.append(x, x_new)
- # sd = np.append(sd, 1./np.maximum(np.abs(fx_new), 1e-8))
- sd = sigma * np.ones(len(x))
- w_sum_new = np.sum(fx_new)
- w *= w_sum / (w_sum + w_sum_new)
- w_sum += w_sum_new
- w = np.append(w, fx_new / w_sum)
- n_pts += n_batch
-
- # compute loss-function
- p = np.array([np.dot(w, norm.pdf(xi, loc=x, scale=sd)) for xi in x])
- L_prev = L
- L = np.dot((p - w) ** 2, w)
-
- return x
-
-
-if __name__ == "__main__":
- x = adagrid_1d(-10, 10, f, sigma=1, n_batch=10, n_max=1000, tol=1e-2)
- print("len(x) = {n}".format(n=len(x)))
- x_ord = np.argsort(x)
- x_even = np.linspace(np.min(x), np.max(x), 1000)
- plt.plot(x[x_ord], f(x)[x_ord], ls="-", marker=".")
- plt.plot(x_even, f(x_even), ls="--")
- plt.show()
diff --git a/docs/adagrid/adagrid_2d.py b/docs/adagrid/adagrid_2d.py
deleted file mode 100644
index f532d067..00000000
--- a/docs/adagrid/adagrid_2d.py
+++ /dev/null
@@ -1,142 +0,0 @@
-# flake8: noqa
-# The above line should be removed, but currently the code in this file is
-# incorrect in several ways and it is unclear to me whether this is dead code or
-# simply temporarily broken.
-import queue
-
-import matplotlib.pyplot as plt
-import numpy as np
-from binomial import Binomial2Arm
-from gridpt import GridPt
-from scipy.stats import norm
-
-
-def adagrid_internal(gridpt, grid_q, grid_final, model, alpha, N_max):
- # store upper bound at current grid point
- model.upper_bd(gridpt)
-
- # get full upper bound
- ub = gridpt.create_upper()
-
- itr = 0
- while ub >= alpha and itr < 20:
- model.tune_gridpt(gridpt)
- ub = gridpt.create_upper()
- ++itr
-
- # delta_0' + delta_1' ~ N(delta_0 + delta_1, sigma^2)
- # sigma = sd([delta_0'_i + v^* delta_1'_i])
- # P(Ub > alpha) ~~ 1-NCDF((ub-alpha)/sigma) decrease
- while ((ub - alpha) / sigma) < norm.isf(0.05):
- model.tune_gridpt(gridpt)
- ub = gridpt.create_upper()
- # update sigma
-
- print(
- "{p}:\n\tub={ub}\n\tub_old={ub_old}".format(p=gridpt.pt, ub=ub, ub_old=ub_old)
- )
-
- # if we have to shrink grid
- if shrink_grid:
- d = len(gridpt.pt)
- bits = np.zeros(d)
- new_rad = gridpt.radius / 2
- for _ in range(2**d):
- new_pt = gridpt.pt + new_rad * (2 * bits - 1)
-
- # only add the new point if it's "viable".
- # The only check right now is if it's in the null
- if model.is_viable(new_pt):
- grid_q.put(GridPt(new_pt, new_rad, gridpt))
-
- # add 1 to bits
- for j in range(d - 1, -1, -1):
- carry = (bits[j] + 1) // 2
- bits[j] = (bits[j] + 1) % 2
- if carry == 0:
- break
- else:
- grid_final.append(gridpt)
-
-
-def adagrid(
- lower, upper, model, alpha=0.025, init_size=2, N_init=1000, N_max=100000, max_iter=2
-):
- # set-up root node for special behavior
- root_pt = GridPt(None, None, None)
- root_pt.N = N_init
- root_pt.delta_0 = np.Inf
- root_pt.delta_0_u = np.Inf
- root_pt.delta_1 = np.Inf
- root_pt.delta_1_u = np.Inf
- root_pt.delta_2_u = np.Inf
- root_pt.delta_0_ci_lower = np.Inf
- root_pt.delta_0_ci_upper = np.Inf
-
- # make initial 1d grid
- rnge = upper - lower
- radius = rnge / (2 * init_size)
- theta_grids = (
- np.arange(lower[i] + radius[i], upper[i], step=2 * radius[i])
- for i in range(len(lower))
- )
-
- # make full grid
- coords = np.meshgrid(*theta_grids)
- grid = np.concatenate([c.flatten().reshape(-1, 1) for c in coords], axis=1)
-
- grid_q = queue.Queue()
- for pt in grid:
- if model.is_viable(pt):
- grid_q.put(GridPt(pt, radius, root_pt))
-
- # Final list of nodes to actually compute upper bound for.
- # Essentially the leaves of the tree we are building.
- grid_final = list()
-
- itr = 0
- while (not grid_q.empty()) and (itr < max_iter):
- # TODO: all grid_plt related stuff is temporary
- grid_plt = []
-
- # run through current queue and update the queue
- grid_q_size = grid_q.qsize()
- for _ in range(grid_q_size):
- gridpt = grid_q.get()
- adagrid_internal(gridpt, grid_q, grid_final, model, alpha, N_max)
- # TODO
- grid_plt.append(gridpt)
- itr += 1
-
- # TODO: temporary code here
- # plot the upper bound for each of the points
- grid_plt = list(set().union(grid_final, grid_plt))
- pts = np.array([pt.pt for pt in grid_plt])
- z = np.array([gp.create_upper() for gp in grid_plt])
- fig, ax = plt.subplots(subplot_kw={"projection": "3d"})
- ax.plot_trisurf(pts[:, 0], pts[:, 1], z)
- plt.show()
-
- # If max iteration was reached, just output the current leaves
- # with the deepest nodes that we were supposed to prune further.
- if itr == max_iter:
- grid_final = list(set().union(grid_final, grid_q.queue))
-
- return np.array(grid_final)
-
-
-if __name__ == "__main__":
- model = Binomial2Arm()
- grid = adagrid(
- lower=np.array([-0.02, -0.02]),
- upper=np.array([0.02, 0.02]),
- model=model,
- alpha=0.025,
- init_size=16,
- max_iter=6,
- N_max=10000,
- )
- grid_raw = np.array([pt.pt for pt in grid])
- N_raw = np.array([pt.N for pt in grid])
- plt.scatter(grid_raw[:, 0], grid_raw[:, 1], s=1, alpha=N_raw / np.max(N_raw))
- plt.show()
diff --git a/docs/adagrid/adagrid_garbage_compactor.py b/docs/adagrid/adagrid_garbage_compactor.py
deleted file mode 100644
index 87f3e84a..00000000
--- a/docs/adagrid/adagrid_garbage_compactor.py
+++ /dev/null
@@ -1,223 +0,0 @@
-import queue
-
-import matplotlib.pyplot as plt
-import numpy as np
-from binomial import Binomial2Arm
-from gridpt import GridPt
-
-
-def adagrid_internal(gridpt, grid_q, grid_final, model, alpha, N_max, slack_factor=0.1):
- # store upper bound at current grid point
- model.upper_bd(gridpt)
-
- print(gridpt)
-
- # get full upper bound
- ub = gridpt.create_upper()
-
- # already a good estimate for ub: no need to tune N and eps further
- if (ub < alpha * (1 - slack_factor)) or (gridpt.N >= N_max):
- grid_final.append(gridpt)
- return
-
- # Compute z-score if N changed to N*2^d, d = dimension of gridpt
- N = gridpt.N
- d = len(gridpt.pt)
- N_factor = 2**d
- N_new = min(N * N_factor, N_max)
- N_ratio = N / N_new
- # sigma_dN = gridpt.sigma / np.sqrt(N_new)
- mu_dN = (
- gridpt.delta_0
- + gridpt.delta_1
- + (gridpt.delta_0_u + gridpt.delta_1_u) * np.sqrt(N_ratio)
- + gridpt.delta_2_u
- )
- # z_dN = (alpha - mu_dN) / sigma_dN
-
- # Compute z-score if eps changed to eps/2
- # sigma_deps = gridpt.sigma
- mu_deps = (
- gridpt.delta_0
- + gridpt.delta_1
- + gridpt.delta_0_u
- + gridpt.delta_1_u / 2.0
- + gridpt.delta_2_u / 4.0
- )
- # z_deps = (alpha - mu_deps) / sigma_deps
-
- # mu_dN < mu_deps
- # <=>
- # gridpt.delta_0_u > 3/2 * gridpt.delta_2_u
-
- # Compare z-scores: larger the z-score, the more likely UpperBound < alpha.
-
- # 1) increase N and push gridpt into grid_q
- if mu_dN < mu_deps:
- gridpt.N = N_new
- grid_q.put(gridpt)
-
- # 2) decrease eps by adding children gridpts into grid_q
- else:
- bits = np.zeros(d)
- new_rad = gridpt.radius / 2
- for _ in range(2**d):
- new_pt = gridpt.pt + new_rad * (2 * bits - 1)
-
- # only add the new point if it's "viable".
- # The only check right now is if it's in the null
- if model.is_viable(new_pt):
- grid_q.put(GridPt(new_pt, new_rad, gridpt))
-
- # add 1 to bits
- for j in range(d - 1, -1, -1):
- carry = (bits[j] + 1) // 2
- bits[j] = (bits[j] + 1) % 2
- if carry == 0:
- break
-
-
-def adagrid(lower, upper, model, alpha, init_size, max_iter, N_init, N_max):
- # set-up root node for special behavior
- root_pt = GridPt(None, None, None)
- root_pt.N = N_init
- root_pt.delta_0 = np.Inf
- root_pt.delta_0_u = np.Inf
- root_pt.delta_1 = np.Inf
- root_pt.delta_1_u = np.Inf
- root_pt.delta_2_u = np.Inf
- root_pt.delta_0_ci_lower = np.Inf
- root_pt.delta_0_ci_upper = np.Inf
-
- # make initial 1d grid
- rnge = upper - lower
- radius = rnge / (2 * init_size)
- theta_grids = (
- np.arange(lower[i] + radius[i], upper[i], step=2 * radius[i])
- for i in range(len(lower))
- )
-
- # make full grid
- coords = np.meshgrid(*theta_grids)
- grid = np.concatenate([c.flatten().reshape(-1, 1) for c in coords], axis=1)
-
- # create initial queue of potential gridpts to look into further
- grid_q = queue.Queue()
- for pt in grid:
- if model.is_viable(pt):
- grid_q.put(GridPt(pt, radius, root_pt))
-
- # initialize thresholds
- # Note: this assumes that we're doing an one-sided upper-tail test because
- # we're always taking the maximum of the thresholds as the conservative
- # lambda. This loop is just to get a reasonable estimate for the thresholds.
- # By construction, they always correspond to threshold such that
- # at all initial grid points,
- # alpha_hat, alpha_minus_hat <= true alpha, true alpha_minus.
- thr_minus = -np.Inf
- thr = -np.Inf
- for pt in grid_q.queue:
- thr_minus_new, thr_new = model.initial_thresh(pt)
- thr_minus = max(thr_minus_new, thr_minus)
- thr = max(thr_new, thr)
- model.da_dthresh = (model.alpha_target - model.alpha_minus_target) / (
- thr - thr_minus
- )
- model.thresh = thr
- model.thresh_minus = thr_minus
- print(
- "da_dthresh={dd}, alpha_t={at}, alpha_minus_t={amt}".format(
- dd=model.da_dthresh, at=model.alpha_target, amt=model.alpha_minus_target
- )
- )
-
- # Final list of nodes to actually compute upper bound for.
- # Essentially the leaves of the tree we are building.
- grid_final = list()
-
- itr = 0
- while (not grid_q.empty()) and (itr < max_iter):
- # TODO: just a nice ol print
- print(
- "thr={thr}, thr_minus={thr_minus}".format(
- thr=model.thresh, thr_minus=model.thresh_minus
- )
- )
-
- model.seed = itr
-
- # TODO: all grid_plt related stuff is temporary
- grid_plt = []
-
- # run through current queue and update the queue
- alpha_hat = 0
- alpha_minus_hat = 0
- grid_q_size = grid_q.qsize()
- N_crit = 0
- for _ in range(grid_q_size):
- gridpt = grid_q.get()
- adagrid_internal(gridpt, grid_q, grid_final, model, alpha, N_max)
-
- if gridpt.delta_0 > alpha_hat:
- alpha_hat = max(gridpt.delta_0, alpha_hat)
- N_crit = gridpt.N
- alpha_minus_hat = max(gridpt.delta_0_minus, alpha_minus_hat)
-
- # TODO
- grid_plt.append(gridpt)
-
- print(
- "alpha={alpha}, alpha_minus={alpha_minus}".format(
- alpha=alpha_hat, alpha_minus=alpha_minus_hat
- )
- )
- model.alpha_minus_target = max(
- model.alpha_target / 2,
- model.alpha_target
- - 2 * np.sqrt(model.alpha_target * (1 - model.alpha_target) / N_crit),
- )
-
- # update thresholds again
- model.da_dthresh = (alpha_hat - alpha_minus_hat) / (
- model.thresh - model.thresh_minus
- )
- model.thresh += (model.alpha_target - alpha_hat) / model.da_dthresh
- model.thresh_minus += (
- model.alpha_minus_target - alpha_minus_hat
- ) / model.da_dthresh
-
- itr += 1
-
- # TODO: temporary code here
- # plot the upper bound for each of the points
- grid_plt = list(set().union(grid_final, grid_plt))
- pts = np.array([pt.pt for pt in grid_plt])
- z = np.array([pt.create_upper() for pt in grid_plt])
- fig, ax = plt.subplots(subplot_kw={"projection": "3d"})
- ax.plot_trisurf(pts[:, 0], pts[:, 1], z)
- plt.show()
-
- # If max iteration was reached, just output the current leaves
- # with the deepest nodes that we were supposed to prune further.
- if itr == max_iter:
- grid_final = list(set().union(grid_final, grid_q.queue))
-
- return np.array(grid_final)
-
-
-if __name__ == "__main__":
- model = Binomial2Arm()
- grid = adagrid(
- lower=np.array([-2, -2]),
- upper=np.array([2, 2]),
- model=model,
- alpha=0.025,
- init_size=8,
- max_iter=8,
- N_init=1000,
- N_max=64000,
- )
- grid_raw = np.array([pt.pt for pt in grid])
- N_raw = np.array([pt.N for pt in grid])
- plt.scatter(grid_raw[:, 0], grid_raw[:, 1], s=1, alpha=N_raw / np.max(N_raw))
- plt.show()
diff --git a/docs/adagrid/binomial.py b/docs/adagrid/binomial.py
deleted file mode 100644
index 14efbc68..00000000
--- a/docs/adagrid/binomial.py
+++ /dev/null
@@ -1,154 +0,0 @@
-import numpy as np
-from scipy.stats import norm
-
-
-class Binomial2Arm:
- def __init__(self):
- self.n_sample = 250
- self.alpha_minus_target = None
-
- self.da_dthresh = None
- self.thresh = None
- self.thresh_minus = None
-
- self.null_hypo = lambda p: p[1] <= p[0]
- self.seed = 1324
- self.alpha_target = 0.025
- self.delta = 0.025
-
- @staticmethod
- def sigmoid(x):
- return 1.0 / (1.0 + np.exp(-x))
-
- def is_viable(self, theta):
- return self.null_hypo(Binomial2Arm.sigmoid(theta))
-
- def simulate_once(self, gridpt):
- # generate RNG
- unifs = np.random.uniform(size=(self.n_sample, 2))
-
- p = Binomial2Arm.sigmoid(gridpt.pt)
-
- # construct binomials
- x_control = np.sum(unifs[:, 0] < p[0])
- x_treat = np.sum(unifs[:, 1] < p[1])
-
- # construct z-stat
- p_control = x_control / self.n_sample
- p_treat = x_treat / self.n_sample
- var = (p_control * (1 - p_control) + p_treat * (1 - p_treat)) / self.n_sample
- z = p_treat - p_control
- if var <= 0:
- z = np.Inf * np.sign(z)
- else:
- z /= np.sqrt(var)
-
- return np.array([x_control, x_treat]), z
-
- def simulate(self, gridpt):
- # prepare some members of gridpt
- p = Binomial2Arm.sigmoid(gridpt.pt)
- if not self.null_hypo(p):
- return
-
- # set seed
- np.random.seed(self.seed)
-
- gridpt.grad = np.zeros(2)
- gridpt.grad_minus = np.zeros(2)
-
- # run through each simulation and update upper bound
- for i in range(gridpt.N):
- X, z = self.simulate_once(gridpt)
-
- ## accumulate upper bound quantities
-
- curr_grad = X - self.n_sample * p
-
- if z > self.thresh_minus:
- gridpt.delta_0_minus += 1
- gridpt.grad_minus += curr_grad
-
- # rejected if above thresh and is under null
- if z > self.thresh:
- gridpt.delta_0 += 1
- gridpt.grad += curr_grad
- gridpt.kernel_trick += np.outer(curr_grad, curr_grad)
-
- ## finalize upper bound
- gridpt.delta_0 /= gridpt.N
- gridpt.delta_0_minus /= gridpt.N
- gridpt.grad_minus /= gridpt.N
- gridpt.delta_1_minus = np.dot(gridpt.radius, np.abs(gridpt.grad_minus))
- gridpt.grad /= gridpt.N
- gridpt.kernel_trick /= gridpt.N
-
- def upper_bd(self, gridpt):
- # simulate
- self.simulate(gridpt)
-
- # mean parameter
- p = Binomial2Arm.sigmoid(gridpt.pt)
-
- gridpt.delta_0_u = norm.isf(self.delta / 2.0) * np.sqrt(
- gridpt.delta_0 * (1 - gridpt.delta_0) / gridpt.N
- )
-
- v_star = gridpt.radius * np.sign(gridpt.grad)
- gridpt.delta_1 = np.dot(gridpt.radius, np.abs(gridpt.grad))
-
- gridpt.delta_1_u = np.sqrt(
- np.dot(gridpt.radius**2, p * (1 - p))
- * self.n_sample
- * (2.0 / self.delta - 1.0)
- / gridpt.N
- )
-
- gridpt.delta_2_u = 0
- for k in range(len(p)):
- pk_lower = Binomial2Arm.sigmoid(gridpt.pt[k] - gridpt.radius[k])
- pk_upper = Binomial2Arm.sigmoid(gridpt.pt[k] + gridpt.radius[k])
- if pk_lower <= 0.5 and 0.5 <= pk_upper:
- gridpt.delta_2_u += 0.25 * gridpt.radius[k] ** 2
- else:
- lower = pk_lower - 0.5
- upper = pk_upper - 0.5
- max_at_upper = np.abs(upper) < np.abs(lower)
- max_endpt = pk_upper if max_at_upper else pk_lower
- gridpt.delta_2_u += max_endpt * (1 - max_endpt) * gridpt.radius[k] ** 2
- gridpt.delta_2_u *= self.n_sample / 2.0
-
- gridpt.delta_0_ci_lower = (
- gridpt.delta_0 - (2 * gridpt.delta_0 * (1 - gridpt.delta_0)) / gridpt.N
- )
- gridpt.delta_0_ci_upper = (
- gridpt.delta_0 + (2 * gridpt.delta_0 * (1 - gridpt.delta_0)) / gridpt.N
- )
-
- # 1/N sum_i (1_F_i + v^T df_hat_i)^2 - (mean)^2
- # = 1/N sum_i (1_F_i + 2v^T df_hat_i + v^T df_hat_i df_hat_i^T v) - (mean)^2
- # = delta_0 + 2*delta_1 + v^T (1/N sum_i df_hat_i df_hat_i^T) v - (mean)^2
- # mean = delta_0 + delta_1
- gridpt.sigma = np.sqrt(
- gridpt.delta_0
- + 2 * gridpt.delta_1
- + v_star.dot(gridpt.kernel_trick.dot(v_star))
- - (gridpt.delta_0 + gridpt.delta_1) ** 2
- )
-
- def initial_thresh(self, gridpt):
- p = Binomial2Arm.sigmoid(gridpt.pt)
- if not self.null_hypo(p):
- return
-
- # set seed
- np.random.seed(self.seed)
-
- z_vec = np.array([self.simulate_once(gridpt)[1] for _ in range(gridpt.N)])
- np.sort(z_vec)
- alpha = self.alpha_target
- self.alpha_minus_target = alpha - 2 * np.sqrt(alpha * (1 - alpha) / gridpt.N)
- thr = np.quantile(z_vec, 1 - alpha)
- thr_minus = np.quantile(z_vec, 1 - self.alpha_minus_target)
-
- return thr_minus, thr
diff --git a/docs/adagrid/gridpt.py b/docs/adagrid/gridpt.py
deleted file mode 100644
index 5984be40..00000000
--- a/docs/adagrid/gridpt.py
+++ /dev/null
@@ -1,47 +0,0 @@
-import numpy as np
-
-
-class GridPt:
- def __init__(self, pt, radius, parent):
- self.pt = pt
- self.parent = parent
- self.N = 0 if parent is None else parent.N
- self.radius = radius
- self.grad = None
- self.grad_minus = None
- self.delta_0 = 0
- self.delta_0_minus = 0
- self.delta_0_u = 0
- self.delta_1 = 0
- self.delta_1_minus = 0
- self.delta_1_u = 0
- self.delta_2_u = 0
- self.delta_0_ci_lower = 0
- self.delta_0_ci_upper = 0
- self.sigma = 0
- self.kernel_trick = (
- None if radius is None else np.zeros(shape=(len(radius), len(radius)))
- )
-
- def __repr__(self):
- return "{pt}, N={N}, deltas={deltas}, sigma={sigma}\n".format(
- pt=self.pt,
- N=self.N,
- deltas=[
- self.delta_0,
- self.delta_1,
- self.delta_0_u,
- self.delta_1_u,
- self.delta_2_u,
- ],
- sigma=self.sigma,
- )
-
- def create_upper(self):
- return (
- self.delta_0
- + self.delta_0_u
- + self.delta_1
- + self.delta_1_u
- + self.delta_2_u
- )
diff --git a/docs/design/grid/grid_range/grid_range.md b/docs/design/grid/grid_range/grid_range.md
deleted file mode 100644
index b6687d5b..00000000
--- a/docs/design/grid/grid_range/grid_range.md
+++ /dev/null
@@ -1,162 +0,0 @@
-# Grid Range
-
-In general, `imprint` requires a notion of "a set of grid-points"
-on which to simulate a given model.
-As it turns out, we require a few more additional detail
-to be able to integrate grid range into the framework.
-This document covers the specification and the API
-for our grid range class.
-
-## Overview
-
-A typical workflow of using a grid range is described below:
-```mermaid
-flowchart TB
- user([User])
-
- %% Grid range construction
- subgraph gr_subg [Grid Range Construction]
- get_gridpts[Create a list of grid-points]
- get_radii[Create a list of radii]
- get_ss[Create a list of simulation sizes]
- get_gr[Create a GridRange]
- get_null_hypos[Create a list of null hypothesis surface objects]
- get_tiles[Create tiles]
- prune[Prune the grid range]
-
- get_gridpts --> get_gr
- get_radii --> get_gr
- get_ss --> get_gr
- get_gr --> get_tiles
- get_null_hypos --> get_tiles
- get_tiles --> prune
- end
- user --> gr_subg
-
- gr_subg --> process([Use grid range])
-```
-
-The following sections discuss in further detail
-the subroutines depicted as rectangular tiles in the diagram above.
-
-## Grid Range Specification
-
-This section covers the required specification
-of a grid range concept.
-Throughout this section, we will illustrate many concepts
-using a running example of a user-defined grid-space.
-
-### Grid-points
-
-The first and foremost requirement is to store a list of grid-points.
-As mentioned in [Grid Range](#grid-range),
-this is the set of grid-points under which we simulate a given model.
-An example is shown below with blue dots representing the grid-points
-and the gray-space representing the grid-space of interest:
-
-
-
-
-
-Note that the context, or meaning, of these points is defined by the model of interest.
-See [Model](../model/model.md#attaching-gridrange) for more detail.
-The user is responsible for constructing a valid list of grid-points
-that adhere to the convention of the model of interest.
-
-However, regardless of the context,
-a range of grid-points is still a meaningful quantity
-for the rest of the framework.
-The framework only ever assumes that the grid-points lie in the space in which
-we apply the Taylor expansion of the function of interest (e.g. Type I error function)
-(see [ImprintBound](../../../math/bound/doc.pdf)).
-
-### Radii
-
-In [ImprintBound](../../../math/bound/doc.pdf),
-the Type I error guarantees originate from having control of a Taylor expansion
-around a small region `R` associated with each grid-point.
-While it is true that `R` need not contain the corresponding grid-point,
-accuracy is improved when it does.
-So, if a user has a grid-space they wish to get Type I error guarantees on,
-we will assume that the space has been first partitioned by a set of hypercubes
-where each hypercube is defined by a grid-point as in [Grid-points](#grid-points)
-as the center and a radius vector that defines the radius along each direction.
-The following pictures shows an example of a grid partitioned by
-hypercubes with the same radius:
-
-
-
-
-
-### Simulation Sizes
-
-For each grid-point that we wish to simulate under,
-we can associate it with a simulation size (number of simulations).
-In general, we would like to have different simulation sizes
-for each grid-point because some points will result in a higher Type I error than others
-and we wish to get a more accurate estimate in those regions.
-During simulation, we can keep track of the number of finished simulations
-and stop updating for those that reached the desired simulation size.
-
-### Null Hypothesis Surfaces
-
-A vector of "null-hypothesis surfaces" is needed to create tiles
-(see [Tiles](#tiles)).
-A null-hypothesis surface is a surface that splits a space
-into three portions: negative orientation, positive orientation, and boundary.
-The positive orientation and the boundary is one half of the space split by the surface
-that is assumed to be associated with the null-hypothesis.
-The negative orientation is the alternative space.
-The most common type of a null-hypothesis surface is a hyperplane.
-It is motivated by examples of the form `theta_i <= theta_0`,
-where the hyperplane is of the form `(1,0,...,0,-1,0,...)` where
-the `-1` is in the ith position (0-indexed) with a `0` shift.
-
-### Tiles
-
-Once the grid-point, radius, simulation size,
-and null hypothesis surface information are provided,
-we can construct tiles.
-A tile is simply a hypercube mentioned in [Radii](#radii)
-intersected by all null-hypothesis surfaces.
-Naturally, a vector of null-hypothesis surfaces partition
-the given grid space into disjoint tiles.
-These tiles are precisely the regions on which we Taylor-expand
-and compute our Imprint bounds.
-Associated with each tile is an _intersection hypothesis space_ (IHS)
-defined by the configuration of the null-hypothesis space.
-Since each tile belongs to one partition of the null-hypothesis surfaces,
-it is associated with exactly one of 2 configurations for each hypothesis
-(in the null vs. in the alternative).
-An IHS is simply the full configuration of all null-hypotheses
-(e.g. (1,0,1) represents 1st and 3rd hypotheses as null and the 2nd as alternative).
-The following is an example of a grid-range with 2 hyperplanes as null-hypothesis surfaces.
-
-
-
-
-
-The 2nd tile on the top has both hyperplanes cutting the hypercube
-with the 4 tiles labeled from 1-4.
-__Note: currently for simplicity, if more than one hyperplane cuts a tile,
-no further cutting occurs and the current tile simply gets copied and labeled
-as on the negative/positive orientation, respectively.
-This does not break the math - it simply makes it more conservative.__
-The neighboring tiles are only cut by one hyperplane.
-The right-most column of tiles are not cut by any of the hyperplanes.
-
-### Pruning
-
-After tiles have been created, the user has the option to prune the tiles/grid-points.
-Since tiles associated with fully-alternative configuration is completely
-unnecessary for studying the Type I error,
-we can preemptively prune those tiles out.
-Moreover, if there are no tiles associated with a grid-point,
-the grid-point itself can be pruned out, lowering the cost of simulation.
-The following diagram shows the positive orientation of each of the hyperplanes,
-the purple lines delineate the set of tiles which get pruned,
-and the purple dots denote the grid-points which get pruned out as well.
-
-
-
-
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diff --git a/docs/design/model/model.md b/docs/design/model/model.md
deleted file mode 100644
index fb9b044f..00000000
--- a/docs/design/model/model.md
+++ /dev/null
@@ -1,441 +0,0 @@
-# Model
-
-Model classes are at the heart of `imprint`
-as they define all simulation-specific routines,
-model-specific imprint bound quantities,
-and any global configurations for the model.
-This document will explain in detail the design of our model classes.
-
-## Table of Content
-
-- [Overview](#overview)
-- [Model Specification](#model-specification)
- - [Attaching `GridRange`](#attaching-gridrange)
- - [Simulating](#simulating)
- - [`Accumulator` Update](#accumulator-update)
- - [`ImprintBound` Update](#imprintbound-update)
-- [Model API](#model-api)
- - [`Distribution`](#distribution)
- - [`Model` and `ModelBase`](#model-and-modelbase)
- - [`SimGlobalState` and `SimGlobalStateBase`](#simglobalstate-and-simglobalstatebase)
- - [`SimState` and `SimStateBase`](#simstate-and-simstatebase)
- - [`ImprintBoundState` and `ImprintBoundStateBase`](#imprintboundstate-and-imprintboundstatebase)
- - [Virtual Members](#virtual-members)
-
-## Overview
-
-The following diagram shows how a `model` fits into the whole framework.
-For simplicity, we assume that the cloud only consists of one node with four cores.
-
-The first diagram depicts only the key parts of
-the simulation framework that interact with a `model`.
-```mermaid
-flowchart TB
- user([User])
-
- %% Fit subgraph
- user -->|pass model, GridRange| fit_driver([Fit Driver])
- subgraph fd_subg [Fit Mechanism]
- fit_driver --> set_grid_range[Attach model to GridRange]
- set_grid_range -->|simulate model on node| n([Node])
- n --> c1([Core 1])
- n --> c2([Core 2])
- n --> c3([Core 3])
- n --> c4([Core 4])
- end
-```
-We refer to [TODO: link a page about `GridRange`]()
-for more information about the `GridRange` class
-and terminologies.
-
-We see that nearly all of the interactions with `model` occurs in the cores.
-The following diagram shows a close-up flowchart of the core mechanism.
-```mermaid
-flowchart TB
- n([Node]);
-
- %% Core subgraph
- subgraph ft_subg [Core]
- set_rng([Initialize RNG])
- set_rng --> simulate[Simulate once for model]
- simulate --> is_update[Accumulate result]
- is_update -->|repeat n_sim times| simulate
- end
- n -->|pass attached model| ft_subg
-```
-
-Aside from the simulation mechanism,
-we also have the imprint-bound mechanism where the framework
-interacts with a `model` and an accumulator object
-that has accrued information from simulations with that `model`
-to compute the corresponding `ImprintBound` object.
-The following diagram describes this interaction:
-```mermaid
-flowchart LR
- model([Model])
- is_o([Accumulator])
- model --> ub[Compute ImprintBound]
- is_o --> ub
-```
-
-In the subsequent sections, we will discuss each of the
-subroutines in the diagrams depicted by the rectangular nodes
-to see how they interact with a `model`.
-Combining will give us a sketch of the `model` API.
-We will then describe our implementation of the API.
-
-## Model Specification
-
-This section will cover the subroutines mentioned in [Overview](#overview).
-
-### Attaching `GridRange`
-
-Every `model` should have the opportunity to cache information
-from the given `GridRange` object before any simulations occur.
-For example, if a `model` assumes the grid lies in some space
-that parametrizes the mean parameter space of the exponential family,
-it is usually advantageous to transform the grid-points
-into the mean parameters first before any simulations occur,
-since simulation-dependent quantities such as the log-partition function
-can usually be computed cheaply in terms of the mean parameters.
-[Simulating](#simulating) gives another justification
-for having `models` attach to a `GridRange`.
-
-As mentioned in the previous paragraph,
-a `model` defines the context of the grid-points.
-It is the user's responsibility to construct a `GridRange` object
-that adheres to the convention of the `model` they wish to simulate.
-For example, a `model` assuming exponentially distributed data
-may define the grid-points to lie in the log-hazard space
-rather than the natural parameter space (negative hazard).
-The user is then responsible for constructing grid-points
-in the log-hazard space.
-This promise is solely between the user and the `model` of interest;
-the rest of the `imprint` framework does not use the context of a `GridRange` object
-for a given `model`, since they must be agnostic to the `model` types.
-
-__In summary__:
-- The framework guarantees that a `model` will be attached
-to a `GridRange` on which it will simulate.
-- The attaching procedure gives the opportunity for a `model` to cache
-any information that can potentially speed-up the simulations.
-- A `model` defines the context of the grid-points.
-It is the user's responsibility to construct grid-points in the expected space that they belong.
-
-### Simulating
-
-A `model` needs to define the simulation procedure
-beginning with the data generation to computing the false rejections for each tile of `GridRange`.
-
-From an optimization point of view,
-it is important that the `model` is aware of the `GridRange` ahead of time.
-As a simple example, consider a (one-arm) binomial distribution with size `n`
-and parameters `p_i` for `i=1,...,d` (`d` grid-points).
-Using Skhorokhod's embedding, it is enough to sample
-_`n` uniform random variables_ `U_j` (`j=1,...,n`) and evaluate the indicators
-that `U_j < p_i`.
-This is because such an indicator follows a Bernoulli with parameter `p_i`
-and the sum over `j` will give us a binomial distribution with size `n`, parameter `p_i`.
-This certainly correlates the binomials for each of the parameters `p_i`,
-but this __does not__ invalidate our math.
-In fact, this correlation only helps smooth-out the Type I error profile.
-Furthermore, assuming `U_j` and `p_i` are sorted,
-we can compute _all_ binomials by reading `U` and `p` _exactly once_.
-Moreover, if the model assumes independent binomial draws for `k` arms
-and there are `d` grid-points,
-it is enough to only save the _unique_ parameter values for each arm,
-and hence, enough to only compute binomials for these unique parameters.
-For this particular binomial model, the number of unique parameter values
-is typically `O(log(d))`, which introduces massive memory and computation savings.
-Note that this optimization is only possible because
-a `model` is aware of the whole range of grid-points.
-
-After sampling the RNG,
-we typically have to further compute the sufficient statistic,
-e.g. for the binomial example, the binomials are the sufficient statistic.
-Note that an exponential family only depends on the data through the sufficient statistic,
-so the test statistic used to compute false rejections
-should (in principle) only depend on the sufficient statistic.
-However, it is entirely up to the user how to sample RNG and save the necessary information
-(sometimes we may need to save a quantity other than the sufficient statistic!).
-The user has complete autonomy in deciding what data structure is most
-beneficial for the simulation procedure.
-
-Lastly, the simulation procedure must
-compute the false rejections for all tiles in `GridRange`.
-Note that from the framework perspective,
-the model is free to choose the meaning of "false rejection"
-(e.g. controlling FWER).
-
-__In summary__:
-- A `model` is given an RNG and must provide a simulation function that (conceptually):
- - Generates data for each grid-point.
- - Saves any necessary information (usually sufficient statistic).
- - Computes "false rejection" (defined model-specifically) for each tile.
-
-### `Accumulator` Update
-
-An `Accumulator` object essentially stores the necessary simulation-specific information
-needed to compute its corresponding imprint-bound.
-Depending on the function of interest (e.g. Type I Error, bias, MSE),
-we may have different quantities in general that are needed to compute their respective imprint bound.
-As an example, Type I Error accumulator will save the sum of false rejections
-and the score estimates for each tile in the attached `GridRange` object of the `model`
-(see [TODO: link `Accumulator` page]() for more information).
-See [TODO: ImprintBound page instead?](../math/stats/imprint_bound/doc.pdf)
-for the mathematical details for why this the case.
-
-The false rejections per tile has already been discussed in [Simulating](#simulating).
-The only extra information needed from `model` is then the score estimates.
-
-__In summary__:
-- After a simulation of a `model`,
-the `Accumulator` object is updated to accrue simulation information.
-- As an example, Type I Error accumulator only requires:
- - False rejections for each tile.
- - Score estimates for each grid-point.
-
-### `ImprintBound` Update
-
-An `ImprintBound` object stores the components that comprise the imprint bound estimate.
-It is computed from a `model`, its attached `GridRange` object,
-and its corresponding `Accumulator` object that accrued information across all the simulations.
-The only model-specific quantities are:
-
-- Jacobian operator of the transformation that maps grid-points to natural parameters.
-- Quadratic form of the covariance of the sufficient statistic.
-- Imprint bound on the quadratic form of the hessian.
-
-We explain the reasoning at a high-level.
-The first quantity is required since a `model` defines
-the space in which the grid-points lie,
-and `ImprintBound` requires the Jacobian of the transform
-that maps grid-points to the natural parameters.
-Hence, this Jacobian is a model-specific quantity.
-The second and third quantities are obviously model-specific
-since a model assumes a particular data distribution
-and both quantities are dependent on that distribution.
-See [ImprintBound](../math/stats/imprint_bound/doc.pdf)
-for further mathematical details.
-See [Exponential Model](../math/model/exp_control_k_treatment/doc.pdf)
-for a concrete example of these specifications.
-
-## Model API
-
-In this section, we discuss the Model API and remark on the design choices.
-The following class diagram describes a typical model class `Model`.
-Note that the diagram is a simplification of our implementation;
-we only present the essential class members for our discussion.
-```mermaid
-classDiagram
-
-class Distribution {
- <>
-}
-
-class GridRange
-
-class ModelBase {
- -vec_t critical_values_
- +n_models() size_t
- +critical_values(crit_vals) void
- +critical_values() vec_t
-}
-
-class Model {
- +make_sim_global_state(grid_range) SimGlobalState
- +make_imprint_bound_state(grid_range) ImprintBoundState
-}
-
-class SimGlobalStateBase {
- +make_sim_state()* unique_ptr~SimStateBase~
-}
-
-class SimGlobalState
-
-class SimStateBase {
- +simulate(gen, rej_len)* void
- +score(gridpt_idx, out)* void
-}
-
-class SimState
-
-class ImprintBoundStateBase {
- +apply_eta_jacobian(gridpt_idx, v, out)* void
- +covar_quadform(gridpt_idx, v)* double
- +hessian_quadform_bound(gridpt_idx, tile_idx, v)* double
-}
-
-class ImprintBoundState
-
-%% Inheritance
-Distribution --|> ImprintBoundState
-Distribution --|> SimGlobalState
-Distribution --|> SimState
-ModelBase --|> Model : Inheritance
-SimStateBase --|> SimState
-ImprintBoundStateBase --|> ImprintBoundState
-SimGlobalStateBase --|> SimGlobalState
-
-%% Composition (up to reference)
-Model --* SimGlobalState
-GridRange --* SimGlobalState : Composition by Reference
-
-SimGlobalState --* SimState
-
-Model --* ImprintBoundState
-GridRange --* ImprintBoundState
-
-%% Type Dependency
-SimGlobalState ..> Model
-ImprintBoundState ..> Model: Type Dependency
-```
-
-We list the diagram notation definitions:
-- `-`: private.
-- `+`: public.
-- `: name`: `name` is the return type.
-- Italicized functions are `virtual` or `pure virtual`.
-- Arrows with triangular tips represent `Inheritance` (example shown).
-- Arrows with rhombus tips represent `Composition by Reference` (example shown).
-- Arrows with dashed lines and angled tips represent `Type Dependency` (example shown).
-- `Distribution`: a class with a static interface for computing quantities
-specific to a particular distribution (e.g. binomial).
-- `GridRange`: a grid range class.
-- `Model`: concrete model class.
-- `SimState`: concrete simulation state class associated with `Model`.
-- `SimGlobalState`: concrete simulation global state class associated with `Model`.
-- `ImprintBoundState`: concrete imprint bound state class associated with `Model`.
-- All class names of the form `FooBase` are base classes for
-their corresponding derived classes `Foo`.
-
-The following subsections will cover the design choices
-for the classes in the diagram.
-
-### `Distribution`
-
-`Distribution` is a class with a static interface for computing quantities
-specific to a particular distribution.
-The purpose of this class is to isolate and modularize
-the expressions for such quantities so that these expressions
-are not duplicated within the codebase.
-So, different models, which may assume the same distribution,
-do not have to re-implement the logic of distribution-specific quantities,
-such as the score function.
-
-In general, distribution-specific quantities are present in
-- `SimState` (e.g. score function)
-- `SimGlobalState` (e.g. natural parameter to mean parameter transformation)
-- `ImprintBoundState` (e.g. covariance quadratic form)
-
-### `Model` and `ModelBase`
-
-The `Model` class should be interpreted as a collection of policies.
-It is simply a dispatcher to create sibling classes for a particular routine
-and store any model-specific configuration data.
-Note that `Model` contains two member functions which create
-an instance of `SimGlobalState` and `ImprintBoundState`.
-These sibling classes will be discussed in further detail in the later sections,
-but at a high level, `SimGlobalState` is a class used in simulation
-and `ImprintBoundState` is a class used to construct an imprint bound estimate.
-`Model` itself does not interact with the framework otherwise.
-The sibling classes are constructed with an instance of a `GridRange` object,
-`grid_range`.
-It is precisely here where we "attach" a `GridRange` object to a model
-as discussed in [Attaching `GridRange`](#attaching-gridrange).
-
-Looking slightly ahead, we see that `Model`'s `make_*` functions
-return the derived classes themselves rather than `unique_ptr`s.
-Of course, we could have returned `unique_ptr`s,
-but here we can avoid the unnecessary heap-allocation,
-since we are not attempting to return abstract types.
-
-The `ModelBase` class is a base class to all model types.
-Currently, the only property in common among all model types is that
-we can define a __sequence of models__.
-For now, we enforce that a sequence of real numbers index this sequence of models.
-In particular, in all our use-cases, this sequence will represent the critical values
-for which we reject our test-statistic of a given model.
-__Note: the context of these critical values is _model-specific_!__
-Every concrete `Model` class decides its own meaning of these critical values
-(e.g. critical values associated with lower-sided, upper-sided, or two-sided test;
-scaling of the critical values, e.g. z-score values, chi-squared values, etc.).
-These critical values are only ever used within `Model`-related classes,
-so the user is free to decide the context;
-`Accumulator` and `ImprintBound` objects never work with these critical values directly.
-The critical values solely exist to define the sequence of models
-and to compute the false rejections during simulations.
-
-### `SimGlobalState` and `SimGlobalStateBase`
-
-`SimGlobalState` is a class that represents a concrete `Model` class
-attached to a `GridRange` object.
-The primary goal of this object is to cache any global information
-that can be used by all simulations to potentially speed them up
-(see [Simulating](#simulating)).
-__The user is free to choose the internal representation
-of these concrete `SimGlobalState` types
-and expose any members that are needed by `SimState`.__
-This class only interacts with `SimState`.
-
-`SimGlobalStateBase` is the corresponding base class.
-It instructs all derived classes to implement
-`make_sim_state`, which creates a new `SimState` object
-(casted down to the abstract base type `SimStateBase`).
-See [Virtual Members](#virtual-members) for why
-this function is made `virtual`.
-
-### `SimState` and `SimStateBase`
-
-`SimState` is a class that represents a simulation state
-for the `Model` class under the global cache of `SimGlobalState`.
-At a high level, this class contains any members that stores
-simulation-specific information and member functions that compute
-simulation-specific quantities using model-specific values
-and pre-computed information about the current `GridRange` object.
-__The user is free to choose the internal representation
-of these concrete `SimState` types.__
-
-`SimStateBase` is the corresponding base class.
-It instructs all derived classes to implement the virtual member functions:
-- `simulate`: runs one simulation and outputs the false rejections
-for each tile in the current `GridRange` object
-(see [Simulating](#simulating)).
-- `score`: computes the score function evaluated at a grid-point
-and one of the parameters
-(see [`Accumulator` Update](#accumulator-update)).
-
-### `ImprintBoundState` and `ImprintBoundStateBase`
-
-`ImprintBoundState` is a class associated with `Model`
-that is used to create an `ImprintBound` object.
-It implements the members of `ImprintBoundStateBase`,
-which are the only members needed to create an imprint bound estimate
-(see [`ImprintBound` Update](#imprintbound-update)).
-__The user is otherwise free to choose the internal representation
-of these concrete `ImprintBoundState` types.__
-
-### Virtual Members
-
-At first glance, it seems arbitrary that
-some member functions are declared `virtual` in a base class
-and others are not.
-However, the choice was deliberate.
-
-In our framework, there are C++ functions that must
-be able to interact with _any arbitrary model-related types_,
-e.g. different `SimState` types,
-and they are later exported to a higher-level language like Python.
-So ideally, we would like to expose only one declaration/overload for each of the functions.
-We would also like to be able to write model-related classes not just in C++
-but also in Python and still be able to seamlessly plug them into our framework.
-These exported C++ functions must then be able to take any
-Python model-related class objects as well.
-The only solution is to introduce polymorphism and ensure that
-all model-related classes (written in C++ or Python) that interact with these exported C++ functions
-override the necessary member functions.
-
-In summary, all `virtual` functions are functions that get called by
-these exported C++ functions that must be callable for arbitrary types.
-The non-`virtual` functions are either extra user-defined functions
-or functions that only get called at a higher-level stage.
diff --git a/docs/imprint_flowcharts.md b/docs/imprint_flowcharts.md
deleted file mode 100644
index f979c43c..00000000
--- a/docs/imprint_flowcharts.md
+++ /dev/null
@@ -1,37 +0,0 @@
-# Imprint Flowcharts
-
-## Main Flowchart
-```mermaid
-flowchart LR;
- user[User];
- style user fill:#006666,stroke:#f66,stroke-width:2px
- SQL[(SQL)];
- ubcomp(Compute UpperBound);
-
- ubcomp --> |request data| SQL;
- SQL --> |send data| ubcomp;
-
- user -->|model| driver;
- subgraph subg_sim [Simulation];
- driver(Driver);
- driver --> |Batch 1| Node1((Node1));
- driver --> |Batch 2| Node2((Node2));
- driver --> |Batch 3| Node3((Node3));
- driver --> |Batch 4| Node4((Node4));
- end;
- Node1 --> SQL;
- Node2 --> |update InterSum| SQL;
- Node3 --> SQL;
- Node4 --> SQL;
-
- user --> |request plot| visproc;
- subgraph subg_vis [Visualization];
- visproc(Process request);
- visualizer(Visualizer);
- visproc -->|UpperBound| visualizer;
- end;
- visproc --> |database ID| ubcomp;
- ubcomp --> |get UpperBound| visproc;
- visualizer --> |send plots| user;
-
-```
diff --git a/docs/latex/mathtools.tex b/docs/latex/mathtools.tex
deleted file mode 100644
index ee2471cc..00000000
--- a/docs/latex/mathtools.tex
+++ /dev/null
@@ -1,81 +0,0 @@
-\usepackage{amsmath}
-\usepackage{amssymb}
-\usepackage{amsfonts}
-\usepackage{amsthm}
-\usepackage{mathrsfs}
-\usepackage{mathtools}
-\usepackage{bbm}
-\usepackage{listings}
-\usepackage{enumitem} % reference enum item
-\usepackage{wasysym} % smiley faces!
-
-% COLORS
-\usepackage{color}
-\usepackage{xcolor}
-\definecolor{mygray}{rgb}{0.4,0.4,0.4}
-
-% Math Utils
-\newcommand{\inner}[2]{\langle#1,\,#2\rangle}
-\newcommand{\innerone}[1]{\langle#1\rangle}
-\newcommand{\paren}[1]{\left(#1\right)}
-\newcommand{\bracket}[1]{\left[#1\right]}
-\newcommand{\given}{\biggr\rvert}
-\newcommand{\PP}[1]{\mathbb{P}\paren{#1}}
-\newcommand{\PPB}[1]{\mathbb{P}\bracket{#1}}
-\newcommand{\PPP}{\mathbb{P}}
-\newcommand{\E}{\mathbb{E}}
-\newcommand{\EE}[1]{\mathbb{E}\paren{#1}}
-\newcommand{\EEB}[1]{\mathbb{E}\bracket{#1}}
-\newcommand{\Tr}[1]{\text{Tr}\paren{#1}}
-\newcommand{\R}{\mathbb{R}}
-\newcommand{\Z}{\mathbb{Z}}
-\newcommand{\Q}{\mathbb{Q}}
-\newcommand{\N}{\mathbb{N}}
-\newcommand{\xeq}[1]{\stackrel{#1}{=}}
-\newcommand{\indist}{\mathcal{D}}
-\newcommand{\inprob}{\mathcal{P}}
-\newcommand{\borel}{\mathcal{B}}
-\newcommand{\indic}[1]{\mathbbm{1}_{#1}}
-\newcommand\restr[2]{{% we make the whole thing an ordinary symbol
- \left.\kern-\nulldelimiterspace% automatically resize the bar with \right
- #1 % the function
- \vphantom{\big|} % pretend it's a little taller at normal size
- \right|_{#2} % this is the delimiter
- }}
-\newcommand{\im}{\text{Im}}
-\newcommand{\cov}[2]{\text{Cov}\paren{#1,#2}}
-\newcommand{\corr}[2]{\text{Corr}\paren{#1,#2}}
-\newcommand{\var}[1]{\text{Var}\paren{#1}}
-\newcommand{\abs}[1]{\left\lvert#1\right\rvert}
-\newcommand{\norm}[1]{\vert\vert#1\rvert\rvert}
-\newcommand{\grad}{\nabla}
-\newcommand{\varrow}{\overset{\rightharpoonup}}
-\newcommand{\diag}[1]{\text{diag}\paren{#1}}
-\newcommand{\mesh}{\text{mesh}}
-\newcommand{\sgn}[1]{\text{sgn}\paren{#1}}
-\newcommand{\set}[1]{\{#1\}}
-\newcommand{\swap}{\operatorname{swap}}
-
-\DeclareMathOperator*{\argmax}{arg\,max}
-\DeclareMathOperator*{\argmin}{arg\,min}
-\DeclareMathOperator*{\tv}{d_{TV}}
-
-\DeclarePairedDelimiter{\floor}{\lfloor}{\rfloor}
-\DeclarePairedDelimiter{\ceil}{\lceil}{\rceil}
-
-\newcommand\indep{\protect\mathpalette{\protect\independenT}{\perp}}
-\def\independenT#1#2{\mathrel{\rlap{$#1#2$}\mkern2mu{#1#2}}}
-
-\newcommand{\code}[1]{{\texttt{\textcolor{mygray}{\small #1}}}}
-
-% TODO highlighting
-\newcommand{\todo}[1]{\textcolor{red}{#1}}
-
-% Theorem stuff
-\newtheorem{theorem}{Theorem}[section]
-\newtheorem{definition}[theorem]{Definition}
-\newtheorem{corollary}{Corollary}[theorem]
-\newtheorem{lemma}[theorem]{Lemma}
-\newtheorem{exercise}{Exercise}[section]
-\newtheorem{remark}{Remark}[section]
-\newtheorem{example}{Example}[section]
diff --git a/docs/math/bound/doc.pdf b/docs/math/bound/doc.pdf
deleted file mode 100644
index a227b9a4..00000000
Binary files a/docs/math/bound/doc.pdf and /dev/null differ
diff --git a/docs/math/bound/doc.tex b/docs/math/bound/doc.tex
deleted file mode 100644
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--- a/docs/math/bound/doc.tex
+++ /dev/null
@@ -1,568 +0,0 @@
-\documentclass[10pt]{article}
-\usepackage{cite}
-\usepackage{fullpage}
-\input{../../latex/mathtools}
-
-\newcommand{\new}{\operatorname{new}}
-
-\begin{document}
-\title{Generalized Grid Upper Bound}
-\author{James Yang}
-\maketitle
-
-\section{Introduction}\label{sec:intro}
-
-The current formulation of the upper bound estimate assumes that the
-(rectangular) gridding occurs in the (canonical) natural parameter space $\Xi$.
-However, it is sometimes more suitable to grid
-a different space $\Theta$ that parametrizes $\Xi$.
-For example, an exponential model with the control and treatment arms assumed to be
-exponentially distributed with hazards $\lambda_c, \lambda_t$, respectively,
-equipped with the logrank test
-can be greatly optimized under the parametrization of $\lambda_{c}, h$
-where $h := \lambda_t / \lambda_c$ is the hazard rate.
-Moreover, for better scaling, we may want to grid
-the $(\log(\lambda_{c}), \log(h))$ space.
-Such a parametrization defines a mapping from
-\emph{the grid space} to the natural parameter space.
-We wish to construct the upper bound estimate under any
-such parametrization,
-provided that the mapping is sufficiently smooth.
-
-In the subsequent sections,
-we will use the notation $\theta \in \Theta \subseteq \R^s$ to denote
-a point in the grid space and $\eta = \eta(\theta) \in \Xi \subseteq \R^d$
-as the canonical natural parameter.
-
-\section{Original Upper Bound Estimate}\label{sec:orig-ub}
-
-For completion, we give a short overview of the old version
-of the upper bound estimate.
-
-We begin with a set of multiple hypotheses $H_1,\ldots, H_p$.
-We define a \emph{configuration} of the multiple hypotheses
-as an element of $\set{0,1}^p$ where the ith coordinate is 1
-if and only if $H_i$ is true.
-We assume that we have i.i.d. draws of $X^i \sim \PPP_\eta$
-where $\PPP_\eta$ forms an exponential family.
-For adaptive trials, we assume that there exists a finite time horizon $\tau_{\max}$
-so that $X^i \in \R^{\tau_{\max}}$, though we only observe up to a stopping time $\tau$.
-We denote $T_{t}$ as the sufficient statistic of $(X_1,\ldots,X_t)$.
-
-Let $f(\eta) := \PPP_{\eta}\paren{X \in A}$
-where $A$ is the event of false rejection.
-Since exponential families are sufficiently smooth,
-$f(\eta)$ is twice-continuously differentiable.
-A second-order Taylor expansion gives us
-\begin{align*}
- f(\eta)
- &=
- f(\eta_0)
- +
- \nabla f(\eta_0)^\top (\eta - \eta_0)
- +
- \int_0^1
- (1-\alpha)
- (\eta - \eta_0)^\top
- \nabla^2 f(\eta_0 + \alpha (\eta-\eta_0))
- (\eta - \eta_0)
- d\alpha
-\end{align*}
-Note that the derivatives are with respect to $\eta$.
-
-Given a bounded set of $\eta$ values, $R$,
-we obtain an upper bound of the true Type I error:
-\begin{align*}
- \sup\limits_{\eta \in R}
- f(\eta)
- &=
- f(\eta_0)
- +
- \sup\limits_{\eta \in R}
- \bracket{%
- \nabla f(\eta_0)^\top (\eta - \eta_0)
- +
- \int_0^1
- (1-\alpha)
- {(\eta - \eta_0)}^\top
- \nabla^2 f(\eta_0 + \alpha (\eta-\eta_0))
- (\eta - \eta_0)
- d\alpha
- }
- \\&\leq
- f(\eta_0)
- +
- \sup\limits_{v \in R-\eta_0}
- \bracket{%
- \nabla f(\eta_0)^\top v
- +
- \frac{1}{2}
- v^\top
- \sup\limits_{\eta \in R} \var{T_{\tau_{\max}}}_{\eta}
- v
- }
-\end{align*}
-where $R-\eta_0 := \set{\eta-\eta_0 : \eta \in R}$.
-
-An obvious estimate for $f(\eta_0)$ is simply
-\begin{align*}
- \hat{f}(\eta_0)
- :=
- \frac{1}{N}
- \sum\limits_{i=1}^N
- \indic{X^i \in A}
-\end{align*}
-and using Clopper-Pearson, for any $\delta_1 \in [0,1]$,
-we have an exact upper bound $\hat{\delta}_0^u$ for this estimate such that
-\begin{align*}
- \PPP_{\eta_0}\paren{%
- f(\eta_0) < \hat{f}(\eta_0) + \hat{\delta}_0^u
- }
- =
- 1-\delta_1
-\end{align*}
-
-From here, we further assume that $R$ is a convex hull of a finite set of points,
-$v_1,\ldots, v_M$ so that the supremum is attained at one of the points by convexity.
-Using Cantelli's inequality,
-we showed that for any fixed $\delta_2 \in [0,1]$,
-there exists random $\hat{c}_m$, $m=1,\ldots, M$,
-such that
-\begin{align*}
- \PPP_{\eta_0}\paren{%
- \sup\limits_{v\in R-\eta_0}
- \bracket{%
- \nabla f(\eta_0)^\top v
- +
- \frac{1}{2}
- v^\top
- \sup\limits_{\eta \in R} \var{T_{\tau_{\max}}}_{\eta}
- v
- }
- \leq
- \max\limits_{m=1,\ldots, M} \hat{c}_m
- }
- \geq
- 1-\delta_2
-\end{align*}
-In particular, we have
-\begin{align*}
- \hat{c}_m
- &=
- \widehat{\nabla f}(\eta_0)^\top v_m
- +
- \sqrt{%
- \frac{v_m^\top \var{T_{\tau_{\max}}}_{\eta_0} v_m}{N}
- \paren{\frac{1}{\delta_2}-1}
- }
- +
- \frac{1}{2}
- v_m^\top
- \sup\limits_{\eta \in R} \var{T_{\tau_{\max}}}_{\eta}
- v_m
-\end{align*}
-where
-\begin{align*}
- \widehat{\nabla f}(\eta_0)
- :=
- \frac{1}{N} \sum\limits_{i=1}^N
- (T(X^i) - \nabla A(\eta_0)) \indic{X^i \in A}
-\end{align*}
-
-Combining the two estimates,
-\begin{align*}
- &\PPP_{\eta_0}\paren{%
- \sup\limits_{\eta \in R} f(\eta)
- >
- \hat{f}(\eta_0) + \hat{\delta}_0^u
- +
- \max\limits_{m=1,\ldots, M} \hat{c}_m
- }
- \leq
- \\&\qquad
- \PPP_{\eta_0}\paren{%
- \hat{f}(\eta_0) + \hat{\delta}_0^u
- <
- f(\eta_0)
- }
- \\&\qquad +
- \PPP_{\eta_0}\paren{%
- \max\limits_{m=1,\ldots, M} \hat{c}_m
- <
- \sup\limits_{v\in R-\eta_0}
- \bracket{%
- \nabla f(\eta_0)^\top v
- +
- \frac{1}{2}
- v^\top
- \sup\limits_{\eta \in R} \var{T_{\tau_{\max}}}_{\eta}
- v
- }
- }
- \\&\qquad \leq
- \delta_1 + \delta_2
-\end{align*}
-
-Given a bounded subset of the natural parameter space $H \subseteq \Xi$
-and a finite disjoint covering of $H$, $\set{R_j}_{j=1}^M$,
-where, without loss of generality, each $R_j$ belongs to
-exactly one configuration of the multiple hypotheses,
-we construct the upper bound estimates on each $R_j$.
-This gives us a point-wise (in $\eta$) guarantee
-that the true Type I error at $\eta$ is no larger than the upper bound estimate
-with probability at least $ 1-\delta$
-where $\delta := \delta_1 + \delta_2$.
-
-We define a few notations before we conclude this section.
-For any given $\eta \in H$, if $R_0$ is a partition where $\eta \in R_0$,
-and $\eta_0$ is a simulation grid-point associated with $R_0$
-(note that $\eta_0$ need not be inside $R_0$),
-then the upper bound quantity is the sum of the following five quantities:
-\begin{align*}
- \hat{\delta}_0 &:= \hat{f}(\eta_0) \\
- \hat{\delta}_0^u &:= \text{(Clopper-Pearson upper bound with level $\delta_1$)} - \hat{\delta}_0 \\
- \hat{\delta}_1 &:= \widehat{\nabla f}(\eta_0)^\top v_{m^*} \\
- \hat{\delta}_1^u &:= \sqrt{%
- \frac{v_{m^*}^\top \var{T_{\tau_{\max}}}_{\eta_0} v_{m^*}}{N}
- \paren{\frac{1}{\delta_2}-1}
- } \\
- \hat{\delta}_2^u &:= \frac{1}{2}
- v_{m^*}^\top \sup\limits_{\eta \in R_0} \var{T_{\tau_{\max}}}_{\eta} v_{m^*}
-\end{align*}
-where $m^* = \argmax\limits_{m=1,\ldots, M} \hat{c}_m$.
-
-\section{Generalized Upper Bound Estimate}\label{sec:gen-ub}
-
-In Section~\ref{sec:orig-ub}, we discussed the old version of the upper bound estimate.
-Note that we assumed the gridding occured in the canonical natural parameter space.
-In this section, we extend this framework to allow gridding in a different space $\Theta$
-where there exists a twice-continuously differentiable mapping $\eta(\cdot) : \Theta \to \Xi$
-that maps from the grid space to the natural parameter space, $\Xi$.
-
-Since we changed the gridding space, we must change the Taylor expansion
-to be with respect to $\Theta$ space.
-We abuse notation by denoting $f(\theta)$ as $f(\eta(\theta))$
-and $f(\eta)$ as in Section~\ref{sec:orig-ub}.
-Then, for any $\theta, \theta_0$,
-\begin{align*}
- f(\theta)
- &=
- f(\theta_0)
- +
- \nabla f(\theta_0) (\theta - \theta_0)
- +
- \int_0^1 (1-\alpha)
- (\theta-\theta_0)^\top
- \nabla^2 f(\theta_0 + \alpha (\theta-\theta_0))
- (\theta-\theta_0)
- d\alpha
-\end{align*}
-Note that all derivatives are with respect to $\theta$.
-
-For now, assume we have a function $U_R(v)$ such that
-\begin{align*}
- \sup\limits_{\theta \in R}
- v^\top \nabla^2 f(\theta) v
- \leq
- U_R(v)
-\end{align*}
-for any $v$.
-In Section~\ref{ssec:hess-quadform-bound},
-we will propose ways of finding such a $U_R$.
-Then,
-\begin{align*}
- \int_0^1 (1-\alpha) v^\top \nabla^2 f(\theta_0 + \alpha v) v d\alpha
- \leq
- \frac{1}{2} U_R(v)
-\end{align*}
-where $v = \theta-\theta_0$.
-
-In summary, we have the bound:
-\begin{align*}
- \sup\limits_{\theta \in R}
- f(\theta)
- &=
- f(\theta_0)
- +
- \sup\limits_{v \in R-\theta_0}
- \bracket{%
- \nabla f(\theta_0)^\top v
- +
- \int_0^1 (1-\alpha)
- v^\top \nabla^2 f(\theta_0 + \alpha v) v
- d\alpha
- }
- \\&\leq
- f(\theta_0)
- +
- \sup\limits_{v \in R-\theta_0}
- \bracket{%
- \nabla f(\theta_0)^\top v
- +
- \frac{1}{2} U_R(v)
- }
-\end{align*}
-
-\subsection{Constant Order Terms: $\hat{\delta}_0, \hat{\delta}_0^u$}
-
-The Monte Carlo term $\hat{\delta}_0$ and its corresponding upper bound
-$\hat{\delta}_0^u$ need no change from reparametrization
-other than the initial evaluation of $\eta_0 := \eta(\theta_0)$.
-
-\subsection{First Order Term: $\hat{\delta}_1$}
-
-The first order terms are affected by the $\eta$ transformation.
-\begin{align*}
- \nabla f(\theta)
- :=
- \nabla_{\theta} P_\theta(A)
- &=
- \nabla_{\theta} \int_A \frac{P_{\theta}}{P_{\theta_0}} dP_{\theta_0}
- =
- \int_A \nabla_{\theta} \frac{P_{\theta}}{P_{\theta_0}} dP_{\theta_0}
- \\&=
- \int_A (D_{\theta}\eta)^\top
- \nabla_{\eta} \frac{P_{\eta}}{P_{\eta_0}} dP_{\eta_0}
-\end{align*}
-where $\eta_0 = \eta(\theta_0)$.
-If $\theta_0$ is the point at which we are Taylor expanding,
-it suffices to compute this gradient at $\theta = \theta_0$.
-This results in
-\begin{align*}
- \nabla_{\theta} P_{\theta_0}(A)
- &=
- \int_A (D_{\theta}\eta(\theta_0))^\top (T - \nabla_\eta A(\eta_0)) dP_{\eta_0}
-\end{align*}
-
-Hence, our new gradient Monte Carlo estimate will be
-\begin{align*}
- \widehat{\nabla f}(\theta_0)
- :=
- D_{\theta} \eta(\theta_0)^\top
- \frac{1}{N}
- \sum\limits_{i=1}^N
- (T(X^i)-\nabla_\eta A(\eta_0)) \indic{X^i \in A}
-\end{align*}
-
-Note that the Jacobian of $\eta$ is known when defining a model
-and is simulation-independent.
-Hence, we may save the same gradient estimate as in Section~\ref{sec:orig-ub}
-and later multiply by $D_{\theta} \eta(\theta_0)^\top$.
-
-\subsection{Higher Order Upper Bound Terms: $\hat{\delta}_1, \hat{\delta}_1^u, \hat{\delta}_2^u$}%
-\label{ssec:higher-order-ub-terms}
-
-Similar to Section~\ref{sec:orig-ub},
-once we can show for any $v_m = \theta_m - \theta_0$,
-where $\theta_m$ are the vertices of a convex hull $R \subseteq \Theta$,
-$m=1,\ldots, M$,
-there exists a corresponding random $\hat{c}_m$ such that
-\[
- \PPP_{\theta_0}\paren{%
- \nabla f(\theta_0)^\top v_m
- +
- \frac{1}{2}U_R(v_m)
- \leq
- \hat{c}_m
- }
- \geq 1-\delta_2
-\]
-then we have
-\[
- \PPP_{\theta_0}\paren{%
- \sup\limits_{v\in R-\theta_0}
- \bracket{%
- \nabla f(\theta_0)^\top v
- +
- \frac{1}{2}U_R(v)
- }
- \leq
- \max\limits_{m=1,\ldots, M} \hat{c}_m
- }
- \geq
- 1-\delta_2
-\]
-as soon as we further assume that $U_R$ is convex.
-
-Using Cantelli's inequality
-with $Y = \widehat{\nabla f}(\theta_0)^\top v_m = \frac{1}{N} \sum\limits_{i=1}^N \widehat{\nabla f}(\theta_0)_i^\top v_m$,
-we only need to provide an upper bound on the variance of $\widehat{\nabla f}(\theta_0)_i^\top v_m$,
-where $\widehat{\nabla f}(\theta_0)_i := D_\theta \eta(\theta_0)^\top (T(X^i)-\nabla_\eta A(\eta_0)) \indic{X^i \in A}$.
-In that endeavor,
-\begin{align*}
- \var{\widehat{\nabla f}(\theta)_i^\top v_m}
- &=
- v_m^\top \var{\widehat{\nabla f}(\theta)_i} v_m
- \leq
- v_m^\top (D_\theta \eta)^\top \var{T_{\tau_{\max}}} (D_\theta \eta) v_m
-\end{align*}
-The rest of the calculations remain the same.
-
-Hence,
-\begin{align*}
- \hat{c}_m
- :=
- \widehat{\nabla f}(\theta_0)^\top v_m
- +
- \sqrt{
- \frac{v_m^\top (D_\theta \eta(\theta_0))^\top \var{T_{\tau_{\max}}}_{\eta_0} (D_\theta \eta(\theta_0)) v_m}{N}
- \paren{\frac{1}{\delta_2} - 1}
- }
- +
- \frac{1}{2} U_R(v_m)
-\end{align*}
-
-This gives us our new upper bound estimates:
-\begin{align*}
- \hat{\delta}_{0, \new} &:= \hat{\delta}_0 \\
- \hat{\delta}_{0, \new}^u &:= \hat{\delta}_0^u \\
- \hat{\delta}_{1, \new} &:= v_{m^*}^\top D_\theta \eta(\theta_0)^\top \hat{\delta}_1 \\
- \hat{\delta}_{1, \new}^u &:= \sqrt{%
- \frac{v_{m^*}^\top D\eta(\theta_0)^\top \var{T_{\tau_{\max}}}_{\eta_0} D\eta(\theta_0) v_{m^*}}{N}
- \paren{\frac{1}{\delta_2}-1}
- } \\
- \hat{\delta}_{2, \new}^u &:=
- \frac{1}{2} U_R(v_{m^*})
-\end{align*}
-where $m^* = \argmax\limits_{m=1,\ldots, M} \hat{c}_m$.
-
-
-\subsection{Hessian Quadratic Form Bound}\label{ssec:hess-quadform-bound}
-
-As mentioned in Section~\ref{sec:gen-ub},
-we will now discuss a way to find the upper bound $U_R(v)$ to
-$\sup\limits_{\theta \in R} v^\top \nabla^2 f(\theta) v$.
-In Section~\ref{ssec:higher-order-ub-terms},
-we made the additional assumption that $U_R$ is convex,
-so it is crucial this assumption is met.
-
-We will first bound $\nabla^2 f(\theta)$.
-\begin{align*}
- \nabla^2 f(\theta)
- &=
- \int_A \nabla^2 P_\theta(x) dx
-\end{align*}
-Applying the multivariate chain-rule for the function
-$\theta \mapsto P_{\eta(\theta)}(x)$,
-we have that
-\begin{align*}
- \nabla^2 P_\theta(x)
- &=
- (D\eta)^\top \nabla^2 P_\eta(x) (D\eta)
- +
- \sum\limits_{k=1}^d
- \frac{\partial P_\eta}{\partial \eta_k}
- \nabla^2 \eta_k
-\end{align*}
-~\cite{skorski:2019:hess}.
-
-It is easy to see that
-\begin{align*}
- -\var{T_{\tau_{\max}}}_{\eta}
- \preceq
- \int_A \nabla^2 P_{\eta}(x) dx
- \preceq
- \var{T_{\tau_{\max}}}_{\eta}
-\end{align*}
-
-Note that if $S \preceq T$
-for any square matrices $S, T$,
-then we must have that for any matrix $A$,
-$A^\top S A \preceq A^\top T A$.
-This is because $S \preceq T$
-if and only if $T - S$ is positive semi-definite,
-and $A^\top (T-S) A$ is clearly positive semi-definite as well.
-Rearranging, we have our claim.
-Hence,
-\begin{align*}
- -(D\eta)^\top
- \var{T_{\tau_{\max}}}_{\eta}
- (D\eta)
- \preceq
- (D\eta)^\top
- \int_A \nabla^2 P_{\eta}(x) dx
- (D\eta)
- \preceq
- (D\eta)^\top
- \var{T_{\tau_{\max}}}_{\eta}
- (D\eta)
-\end{align*}
-
-This gives us the first bound:
-\begin{align}
- v^\top \nabla^2 f(\theta) v
- \leq
- v^\top (D\eta)^\top \var{T_{\tau_{\max}}}_{\eta} (D\eta) v
- +
- \sum\limits_{k=1}^d
- v^\top \nabla^2 \eta_k v
- \int_A (T(x) - \nabla A(\eta))_k P_\eta(x) dx
- \label{eq:hess-second-term}
-\end{align}
-
-We next bound the second term in Eq.~\ref{eq:hess-second-term}.
-\begin{align*}
- \int_A \abs{(T(x) - \nabla A(\eta))_k} P_\eta(x) dx
- &\leq
- \int \abs{(T(x) - \nabla A(\eta))_k} P_\eta(x) dx
- \\&\leq
- \paren{\int \abs{(T(x) - \nabla A(\eta))_k}^2 P_\eta(x) dx}^{1/2}
- \\&=
- \sqrt{\var{T_k}_\eta}
-\end{align*}
-
-Combining with Eq.~\ref{eq:hess-second-term},
-\begin{align*}
- \sup\limits_{\theta \in R}
- v^\top \nabla^2 f(\theta) v
- &\leq
- \sup\limits_{\theta \in R}
- \bracket{
- v^\top (D\eta(\theta))^\top \var{T_{\tau_{\max}}}_{\eta(\theta)} (D\eta(\theta)) v
- }
- +
- \sum\limits_{k=1}^d
- \sup\limits_{\theta \in R}
- \bracket{%
- \abs{v^\top \nabla^2 \eta_k(\theta) v}
- \sqrt{\var{T_k}_{\eta(\theta)}}
- }
- \\&\leq
- \sup\limits_{\theta \in R}
- \bracket{
- v^\top (D\eta(\theta))^\top \var{T_{\tau_{\max}}}_{\eta(\theta)} (D\eta(\theta)) v
- }
- +
- \norm{v}^2
- \sum\limits_{k=1}^d
- \sup\limits_{\theta \in R}
- \bracket{%
- \norm{\nabla^2 \eta_k(\theta)}_{op}
- \sqrt{\var{T_k}_{\eta(\theta)}}
- }
- \\&=:
- U_1(v) + U_2(v)
- =:
- U_R(v)
-\end{align*}
-where $U_i$ are defined to be the respective terms.
-Note that $U_R$ is convex.
-Also note that $U_2(v) = 0$ for any linear transformation $\eta$.
-In particular, for the identity transformation, it simplifies to
-\begin{align*}
- U_R(v) = U_1(v) = \sup\limits_{\theta \in R} v^\top \var{T_{\tau_{\max}}}_{\eta(\theta)} v
-\end{align*}
-which can be further bounded above by the usual formula
-\begin{align*}
- v^\top \sup\limits_{\theta \in R} \var{T_{\tau_{\max}}}_{\eta(\theta)} v
-\end{align*}
-where the sup is element-wise.
-Note that in general, we can make $U_R(v)$ even more conservative
-by taking further upper bounds to make the computations more tractable.
-The only constraint is that the resulting bound must be convex.
-
-
-\bibliography{references}{}
-\bibliographystyle{plain}
-
-\end{document}
diff --git a/docs/math/bound/references.bib b/docs/math/bound/references.bib
deleted file mode 100644
index 0b1caa07..00000000
--- a/docs/math/bound/references.bib
+++ /dev/null
@@ -1,14 +0,0 @@
-@article{skorski:2019:hess,
- author = {Maciej Skorski},
- title = {Chain Rules for Hessian and Higher Derivatives Made Easy by Tensor
- Calculus},
- journal = {CoRR},
- volume = {abs/1911.13292},
- year = {2019},
- url = {http://arxiv.org/abs/1911.13292},
- eprinttype = {arXiv},
- eprint = {1911.13292},
- timestamp = {Wed, 08 Jan 2020 15:28:22 +0100},
- biburl = {https://dblp.org/rec/journals/corr/abs-1911-13292.bib},
- bibsource = {dblp computer science bibliography, https://dblp.org}
-}
diff --git a/docs/math/model/exp_control_k_treatment/doc.pdf b/docs/math/model/exp_control_k_treatment/doc.pdf
deleted file mode 100644
index e9de5447..00000000
Binary files a/docs/math/model/exp_control_k_treatment/doc.pdf and /dev/null differ
diff --git a/docs/math/model/exp_control_k_treatment/doc.tex b/docs/math/model/exp_control_k_treatment/doc.tex
deleted file mode 100644
index a5feeb47..00000000
--- a/docs/math/model/exp_control_k_treatment/doc.tex
+++ /dev/null
@@ -1,267 +0,0 @@
-\documentclass[10pt, a4paper]{article}
-\input{../../../latex/mathtools}
-\usepackage{cite}
-\usepackage{fullpage}
-
-\begin{document}
-\title{Exponential Model}
-\author{James Yang}
-\maketitle
-
-\section{Introduction}
-
-The exponential model is one where each arm $i$ is assumed to follow
-an exponential distribution with hazard $\lambda_i$.
-Depending on the design procedure (the test statistic)
-there are numerous choices of grid spaces and parametrizations
-of the natural parameter space.
-This document will focus on the log-rank statistic with two arms
-(control and a treatment).
-
-\section{Model Assumptions}\label{sec:model}
-
-Assume that there are $n$ patients in each of the $d=2$ arms
-with independent $X_{ci} \sim E(\lambda_c), X_{ti} \sim E(\lambda_t)$,
-$i=1,\ldots, n$.
-$X_{c\cdot}$ are the samples for the control arm and
-$X_{t\cdot}$ are for the treatment arm.
-Then, the distribution of $X \in \R^{n \times 2}$ forms an exponential family
-with sufficient statistic $T(x) = \paren{\sum\limits_{i=1}^n x_{ci}, \sum\limits_{i=1}^n x_{ti}}$
-natural parameter $\eta = (-\lambda_c, -\lambda_t)$,
-and log-partition function $A(\eta) := -n\log(\eta_c \eta_t)$.
-
-\section{Grid Space}
-
-Since the log-rank statistic only depends on the hazard rate
-$h = \lambda_t / \lambda_c$,
-it is convenient to parametrize the natural parameter space
-as a function of $(\lambda_c, h)$.
-Moreover, we will see in Section~\ref{ssec:max-cov-quad-form}
-that we get major computation benefits of parametrizing in the log-space
-$\theta = (\log(\lambda_c), \log(h))$.
-
-This parametrization defines a mapping $\eta(\theta) = \paren{-e^{\theta_1}, -e^{\theta_1+\theta_2}}$
-from the grid space to the natural parameter space.
-We conclude this section with the Jacobian and hessian computations
-needed in the later sections.
-\begin{align}
- D_\theta \eta(\theta)
- &=
- \begin{bmatrix}
- -e^{\theta_1} & 0 \\
- -e^{\theta_1+\theta_2} & -e^{\theta_1+\theta_2}
- \end{bmatrix}
- \label{eq:eta-jac}
- \\
- \nabla^2_\theta \eta_1(\theta)
- &=
- -e^{\theta_1} e_1e_1^\top
- \label{eq:eta-1-hess}
- \\
- \nabla^2_\theta \eta_2(\theta)
- &=
- -e^{\theta_1+\theta_2} \vec{1} \vec{1}^\top
- \label{eq:eta-2-hess}
-\end{align}
-where $ e_i$ is the ith standard basis vector
-and $ \vec{1}$ is a vector of ones.
-
-\section{Upper Bound}
-
-For any model, we must be able to compute
-the upper bound estimate.
-The generalized upper bound estimate requires model-specific quantities,
-which are given by
-\begin{align*}
- \text{Gradient Term}&: T(x) - \nabla_\eta A(\eta) \\
- \text{$\eta$ transform}&: D_\theta\eta(\theta) v \\
- \text{Covariance quadratic form}&: u^\top \var{T}_{\eta} u \\
- \text{Max covariance quadratic form}&:
- \sup\limits_{\theta \in R} \bracket{v^\top (D\eta(\theta))^\top \var{T}_{\eta(\theta)} (D\eta(\theta)) v} \\
- \text{Max covariance and $\eta$ hessian}&:
- \norm{v}^2
- \sum\limits_{k=1}^d
- \sup\limits_{\theta \in R}
- \bracket{%
- \norm{\nabla^2 \eta_k(\theta)}_{op}
- \sqrt{\var{T_k}_{\eta(\theta)}}
- }
-\end{align*}
-for any $v, u \in \R^d$ and a bounded subset $R \subseteq \R^d$.
-
-The next few subsections will derive the formulas
-for each of the quantities above.
-
-\subsection{Gradient Term}
-
-As shown in Section~\ref{sec:model},
-we have the form for $T(x)$ and $A(\eta)$.
-\begin{align*}
- \nabla_\eta A(\eta)
- &=
- -n \paren{\eta_c^{-1}, \eta_t^{-1}}
- =
- n \paren{\lambda_c^{-1}, \lambda_t^{-1}}
-\end{align*}
-This gives us
-\begin{align*}
- T(x) - \nabla_\eta A(\eta)
- &=
- \paren{%
- \sum\limits_{i=1}^n x_{ci} - n\lambda_c^{-1},
- \sum\limits_{i=1}^n x_{ti} - n\lambda_t^{-1}
- }
-\end{align*}
-
-\subsection{$\eta$ Transform}
-
-Using Eq.~\ref{eq:eta-jac},
-for any $v \in \R^d$,
-\begin{align*}
- D_\theta \eta(\theta) v
- &=
- -
- \begin{bmatrix}
- e^{\theta_1} & 0 \\
- e^{\theta_1+\theta_2} & e^{\theta_1+\theta_2}
- \end{bmatrix}
- v
- =
- -
- \begin{bmatrix}
- e^{\theta_1} v_1 \\
- e^{\theta_1+\theta_2} (v_1+v_2)
- \end{bmatrix}
- =
- -
- \begin{bmatrix}
- \lambda_c v_1 \\
- \lambda_t (v_1+v_2)
- \end{bmatrix}
-\end{align*}
-
-\subsection{Covariance Quadratic Form}
-
-The covariance of $T$ is given by
-\begin{align}
- \var{T}_\eta &=
- n
- \begin{bmatrix}
- \eta_c^{-2} & 0 \\
- 0 & \eta_t^{-2}
- \end{bmatrix}
- =
- n
- \begin{bmatrix}
- \lambda_c^{-2} & 0 \\
- 0 & \lambda_t^{-2}
- \end{bmatrix}
- \label{eq:t-cov}
-\end{align}
-and so,
-\begin{align*}
- u^\top \var{T}_\eta u &=
- n (u_1^2 \lambda_c^{-2} + u_2^2 \lambda_t^{-2})
-\end{align*}
-
-\subsection{Max Covariance Quadratic Form}\label{ssec:max-cov-quad-form}
-
-Using Eq.~\ref{eq:eta-jac},~\ref{eq:t-cov},
-\begin{align*}
- D_\theta \eta(\theta)^\top
- \var{T}_\eta
- D_\theta \eta(\theta)
- &=
- n
- D_\theta \eta(\theta)^\top
- \begin{bmatrix}
- \eta_c^{-2} & 0 \\
- 0 & \eta_t^{-2}
- \end{bmatrix}
- \begin{bmatrix}
- e^{\theta_1} & 0 \\
- e^{\theta_1+\theta_2} & e^{\theta_1+\theta_2}
- \end{bmatrix}
- \\&=
- n
- D_\theta \eta(\theta)^\top
- \begin{bmatrix}
- e^{-2\theta_1} & 0 \\
- 0 & e^{-2(\theta_1+\theta_2)}
- \end{bmatrix}
- \begin{bmatrix}
- e^{\theta_1} & 0 \\
- e^{\theta_1+\theta_2} & e^{\theta_1+\theta_2}
- \end{bmatrix}
- \\&=
- n
- \begin{bmatrix}
- e^{\theta_1} & e^{\theta_1+\theta_2} \\
- 0 & e^{\theta_1+\theta_2}
- \end{bmatrix}
- \begin{bmatrix}
- e^{-\theta_1} & 0 \\
- e^{-(\theta_1+\theta_2)} & e^{-(\theta_1+\theta_2)}
- \end{bmatrix}
- \\&=
- n
- \begin{bmatrix}
- 2 & 1 \\
- 1 & 1
- \end{bmatrix}
-\end{align*}
-Note the incredible simplification due to our choice of the $\eta$ transformation.
-This gives us
-\begin{align*}
- \sup\limits_{\theta \in R} \bracket{%
- v^\top
- D_\theta \eta(\theta)^\top
- \var{T}_\eta
- D_\theta \eta(\theta)
- v
- }
- &=
- n v^\top
- \begin{bmatrix}
- 2 & 1 \\
- 1 & 1
- \end{bmatrix}
- v
-\end{align*}
-
-\subsection{Max Covariance and $\eta$ Hessian}
-
-From Eq.~\ref{eq:eta-1-hess},~\ref{eq:eta-2-hess},
-\begin{align*}
- \norm{\nabla^2 \eta_1(\theta)}_{op}
- &=
- e^{\theta_1} \norm{e_1 e_1^\top}_{op}
- =
- e^{\theta_1}
- \\
- \norm{\nabla^2 \eta_2(\theta)}_{op}
- &=
- e^{\theta_1+\theta_2} \norm{\vec{1}\vec{1}^\top}_{op}
- =
- e^{\theta_1+\theta_2} d
-\end{align*}
-
-This gives us
-\begin{align*}
- \norm{v}^2
- \sum\limits_{k=1}^d
- \sup\limits_{\theta \in R}
- \bracket{%
- \norm{\nabla^2 \eta_k(\theta)}_{op}
- \sqrt{\var{T_k}_{\eta(\theta)}}
- }
- &=
- \norm{v}^2
- \sqrt{n}
- \paren{%
- 1 + d
- }
-\end{align*}
-
-
-\end{document}
diff --git a/environment.yml b/environment.yml
index 6fd70176..60237bc1 100644
--- a/environment.yml
+++ b/environment.yml
@@ -2,43 +2,7 @@ name: imprint
channels:
- conda-forge
dependencies:
-# essentials
- - python
- - setuptools
- - jupyterlab
- - ipykernel
- - numpy
- - scipy
- - matplotlib
- - sympy
- - pandas
-
-# C++ toolchain
- - cxx-compiler
- - clang-tools
- - bazel
-
-# some more nice stuff for easy dev.
- - pytest
- - pre-commit
- - black
- - flake8
- - isort
- - jupytext
- - cython
- - line_profiler
+ - python=3.10
- pip
- - seaborn
-
-# numerical tools
- - jax==0.3.7
- - jaxlib==0.3.7
- - numpyro
-
-# dependencies only available from pip.
-# - cppimport is only used for a few things in the research folder so we don't
-# need to worry about it much. That code could be removed safely.
-# - pybind11[global] is only used by the same cppimport code.
- pip:
- - "pybind11[global]"
- - cppimport
\ No newline at end of file
+ - poetry==1.2.2
\ No newline at end of file
diff --git a/frontend/.gitignore b/frontend/.gitignore
index 95004389..d4bfd63c 100644
--- a/frontend/.gitignore
+++ b/frontend/.gitignore
@@ -44,3 +44,6 @@ yarn-error.log*
npm-debug.log*
yarn-debug.log*
yarn-error.log*
+
+# local folders
+my-app/
diff --git a/frontend/package-lock.json b/frontend/package-lock.json
index 33b406a3..c76d29ce 100644
--- a/frontend/package-lock.json
+++ b/frontend/package-lock.json
@@ -1,7 +1,7 @@
{
"name": "frontend",
"version": "0.1.0",
- "lockfileVersion": 2,
+ "lockfileVersion": 3,
"requires": true,
"packages": {
"": {
@@ -34,12 +34,18 @@
"@types/plotly.js-dist": "npm:@types/plotly.js@^1.54.20"
}
},
+ "node_modules/@adobe/css-tools": {
+ "version": "4.0.1",
+ "resolved": "https://registry.npmjs.org/@adobe/css-tools/-/css-tools-4.0.1.tgz",
+ "integrity": "sha512-+u76oB43nOHrF4DDWRLWDCtci7f3QJoEBigemIdIeTi1ODqjx6Tad9NCVnPRwewWlKkVab5PlK8DCtPTyX7S8g=="
+ },
"node_modules/@ampproject/remapping": {
- "version": "2.1.1",
- "resolved": "https://registry.npmjs.org/@ampproject/remapping/-/remapping-2.1.1.tgz",
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+ "resolved": "https://registry.npmjs.org/@ampproject/remapping/-/remapping-2.2.0.tgz",
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+ "@jridgewell/gen-mapping": "^0.1.0",
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},
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@@ -57,32 +63,32 @@
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+ "resolved": "https://registry.npmjs.org/@babel/compat-data/-/compat-data-7.20.5.tgz",
+ "integrity": "sha512-KZXo2t10+/jxmkhNXc7pZTqRvSOIvVv/+lJwHS+B2rErwOyjuVRh60yVpb7liQ1U5t7lLJ1bz+t8tSypUZdm0g==",
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}
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- "@babel/traverse": "^7.17.0",
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+ "resolved": "https://registry.npmjs.org/@babel/core/-/core-7.20.5.tgz",
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"debug": "^4.1.0",
"gensync": "^1.0.0-beta.2",
- "json5": "^2.1.2",
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},
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@@ -94,11 +100,11 @@
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+ "resolved": "https://registry.npmjs.org/@babel/eslint-parser/-/eslint-parser-7.19.1.tgz",
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- "eslint-scope": "^5.1.1",
+ "@nicolo-ribaudo/eslint-scope-5-internals": "5.1.1-v1",
"eslint-visitor-keys": "^2.1.0",
"semver": "^6.3.0"
},
@@ -110,18 +116,6 @@
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@@ -130,20 +124,12 @@
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+ "version": "7.20.5",
+ "resolved": "https://registry.npmjs.org/@babel/generator/-/generator-7.20.5.tgz",
+ "integrity": "sha512-jl7JY2Ykn9S0yj4DQP82sYvPU+T3g0HFcWTqDLqiuA9tGRNIj9VfbtXGAYTTkyNEnQk1jkMGOdYka8aG/lulCA==",
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- "@babel/types": "^7.18.7",
+ "@babel/types": "^7.20.5",
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"jsesc": "^2.5.1"
},
@@ -151,6 +137,19 @@
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}
},
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+ "version": "0.3.2",
+ "resolved": "https://registry.npmjs.org/@jridgewell/gen-mapping/-/gen-mapping-0.3.2.tgz",
+ "integrity": "sha512-mh65xKQAzI6iBcFzwv28KVWSmCkdRBWoOh+bYQGW3+6OZvbbN3TqMGo5hqYxQniRcH9F2VZIoJCm4pa3BPDK/A==",
+ "dependencies": {
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+ "@jridgewell/sourcemap-codec": "^1.4.10",
+ "@jridgewell/trace-mapping": "^0.3.9"
+ },
+ "engines": {
+ "node": ">=6.0.0"
+ }
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"resolved": "https://registry.npmjs.org/@babel/helper-annotate-as-pure/-/helper-annotate-as-pure-7.18.6.tgz",
@@ -163,25 +162,25 @@
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+ "version": "7.18.9",
+ "resolved": "https://registry.npmjs.org/@babel/helper-builder-binary-assignment-operator-visitor/-/helper-builder-binary-assignment-operator-visitor-7.18.9.tgz",
+ "integrity": "sha512-yFQ0YCHoIqarl8BCRwBL8ulYUaZpz3bNsA7oFepAzee+8/+ImtADXNOmO5vJvsPff3qi+hvpkY/NYBTrBQgdNw==",
"dependencies": {
- "@babel/helper-explode-assignable-expression": "^7.16.7",
- "@babel/types": "^7.16.7"
+ "@babel/helper-explode-assignable-expression": "^7.18.6",
+ "@babel/types": "^7.18.9"
},
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}
},
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- "resolved": "https://registry.npmjs.org/@babel/helper-compilation-targets/-/helper-compilation-targets-7.16.7.tgz",
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+ "version": "7.20.0",
+ "resolved": "https://registry.npmjs.org/@babel/helper-compilation-targets/-/helper-compilation-targets-7.20.0.tgz",
+ "integrity": "sha512-0jp//vDGp9e8hZzBc6N/KwA5ZK3Wsm/pfm4CrY7vzegkVxc65SgSn6wYOnwHe9Js9HRQ1YTCKLGPzDtaS3RoLQ==",
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- "@babel/helper-validator-option": "^7.16.7",
- "browserslist": "^4.17.5",
+ "@babel/compat-data": "^7.20.0",
+ "@babel/helper-validator-option": "^7.18.6",
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},
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@@ -192,16 +191,16 @@
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- "resolved": "https://registry.npmjs.org/@babel/helper-create-class-features-plugin/-/helper-create-class-features-plugin-7.18.6.tgz",
- "integrity": "sha512-YfDzdnoxHGV8CzqHGyCbFvXg5QESPFkXlHtvdCkesLjjVMT2Adxe4FGUR5ChIb3DxSaXO12iIOCWoXdsUVwnqw==",
+ "version": "7.20.5",
+ "resolved": "https://registry.npmjs.org/@babel/helper-create-class-features-plugin/-/helper-create-class-features-plugin-7.20.5.tgz",
+ "integrity": "sha512-3RCdA/EmEaikrhayahwToF0fpweU/8o2p8vhc1c/1kftHOdTKuC65kik/TLc+qfbS8JKw4qqJbne4ovICDhmww==",
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- "@babel/helper-environment-visitor": "^7.18.6",
- "@babel/helper-function-name": "^7.18.6",
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+ "@babel/helper-function-name": "^7.19.0",
+ "@babel/helper-member-expression-to-functions": "^7.18.9",
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- "@babel/helper-replace-supers": "^7.18.6",
+ "@babel/helper-replace-supers": "^7.19.1",
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},
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@@ -212,12 +211,12 @@
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+ "version": "7.20.5",
+ "resolved": "https://registry.npmjs.org/@babel/helper-create-regexp-features-plugin/-/helper-create-regexp-features-plugin-7.20.5.tgz",
+ "integrity": "sha512-m68B1lkg3XDGX5yCvGO0kPx3v9WIYLnzjKfPcQiwntEQa5ZeRkPmo2X/ISJc8qxWGfwUr+kvZAeEzAwLec2r2w==",
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- "@babel/helper-annotate-as-pure": "^7.16.7",
- "regexpu-core": "^5.0.1"
+ "@babel/helper-annotate-as-pure": "^7.18.6",
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},
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@@ -227,14 +226,12 @@
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- "@babel/helper-plugin-utils": "^7.13.0",
- "@babel/traverse": "^7.13.0",
+ "version": "0.3.3",
+ "resolved": "https://registry.npmjs.org/@babel/helper-define-polyfill-provider/-/helper-define-polyfill-provider-0.3.3.tgz",
+ "integrity": "sha512-z5aQKU4IzbqCC1XH0nAqfsFLMVSo22SBKUc0BxGrLkolTdPTructy0ToNnlO2zA4j9Q/7pjMZf0DSY+DSTYzww==",
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+ "@babel/helper-plugin-utils": "^7.16.7",
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@@ -245,31 +242,31 @@
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+ "version": "7.18.9",
+ "resolved": "https://registry.npmjs.org/@babel/helper-environment-visitor/-/helper-environment-visitor-7.18.9.tgz",
+ "integrity": "sha512-3r/aACDJ3fhQ/EVgFy0hpj8oHyHpQc+LPtJoY9SzTThAsStm4Ptegq92vqKoE3vD706ZVFWITnMnxucw+S9Ipg==",
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+ "resolved": "https://registry.npmjs.org/@babel/helper-explode-assignable-expression/-/helper-explode-assignable-expression-7.18.6.tgz",
+ "integrity": "sha512-eyAYAsQmB80jNfg4baAtLeWAQHfHFiR483rzFK+BhETlGZaQC9bsfrugfXDCbRHLQbIA7U5NxhhOxN7p/dWIcg==",
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+ "@babel/types": "^7.18.6"
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+ "resolved": "https://registry.npmjs.org/@babel/helper-function-name/-/helper-function-name-7.19.0.tgz",
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+ "@babel/template": "^7.18.10",
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@@ -287,11 +284,11 @@
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+ "resolved": "https://registry.npmjs.org/@babel/helper-member-expression-to-functions/-/helper-member-expression-to-functions-7.18.9.tgz",
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+ "@babel/types": "^7.18.9"
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@@ -309,18 +306,18 @@
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+ "resolved": "https://registry.npmjs.org/@babel/helper-module-transforms/-/helper-module-transforms-7.20.2.tgz",
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@@ -338,58 +335,62 @@
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+ "version": "7.20.2",
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@@ -584,11 +594,11 @@
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},
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@@ -851,6 +861,20 @@
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}
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+ "resolved": "https://registry.npmjs.org/@babel/plugin-syntax-import-assertions/-/plugin-syntax-import-assertions-7.20.0.tgz",
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"resolved": "https://registry.npmjs.org/@babel/plugin-syntax-import-meta/-/plugin-syntax-import-meta-7.10.4.tgz",
@@ -874,11 +898,11 @@
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+ "resolved": "https://registry.npmjs.org/@babel/plugin-syntax-jsx/-/plugin-syntax-jsx-7.18.6.tgz",
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+ "version": "7.20.0",
+ "resolved": "https://registry.npmjs.org/@babel/plugin-syntax-typescript/-/plugin-syntax-typescript-7.20.0.tgz",
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+ "@babel/helper-plugin-utils": "^7.19.0"
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+ "resolved": "https://registry.npmjs.org/@babel/plugin-transform-arrow-functions/-/plugin-transform-arrow-functions-7.18.6.tgz",
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+ "@babel/helper-plugin-utils": "^7.18.6"
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+ "resolved": "https://registry.npmjs.org/@babel/plugin-transform-async-to-generator/-/plugin-transform-async-to-generator-7.18.6.tgz",
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+ "resolved": "https://registry.npmjs.org/@babel/plugin-transform-block-scoping/-/plugin-transform-block-scoping-7.20.5.tgz",
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+ "@babel/helper-plugin-utils": "^7.20.2"
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+ "resolved": "https://registry.npmjs.org/@babel/plugin-transform-classes/-/plugin-transform-classes-7.20.2.tgz",
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@@ -1075,11 +1100,11 @@
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+ "resolved": "https://registry.npmjs.org/@babel/plugin-transform-computed-properties/-/plugin-transform-computed-properties-7.18.9.tgz",
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+ "resolved": "https://registry.npmjs.org/@babel/plugin-transform-destructuring/-/plugin-transform-destructuring-7.20.2.tgz",
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@@ -1118,11 +1143,11 @@
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+ "resolved": "https://registry.npmjs.org/@babel/plugin-transform-duplicate-keys/-/plugin-transform-duplicate-keys-7.18.9.tgz",
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@@ -1132,12 +1157,12 @@
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@@ -1147,11 +1172,11 @@
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@@ -1286,11 +1308,12 @@
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@@ -1329,11 +1352,11 @@
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@@ -1417,12 +1440,12 @@
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@@ -1432,11 +1455,12 @@
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@@ -1446,11 +1470,11 @@
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@@ -1522,11 +1546,11 @@
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@@ -1536,11 +1560,11 @@
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@@ -1550,13 +1574,13 @@
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@@ -1566,11 +1590,11 @@
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@@ -1580,12 +1604,12 @@
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@@ -1595,36 +1619,37 @@
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@@ -1732,54 +1757,54 @@
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+ "minimatch": "^3.0.5"
},
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}
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@@ -2244,6 +2410,14 @@
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@@ -2600,6 +2774,17 @@
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+ "integrity": "sha512-/l/VWsdt/aBXgjshLWOFyFt3IVdYypu5y2Wn2rOO1un6nkqIn8SLXzgIMYXFyYsRWDyF5EthmKJMIdJvk08grg==",
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}
@@ -2854,32 +3038,60 @@
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}
},
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- "resolved": "https://registry.npmjs.org/@mui/base/-/base-5.0.0-alpha.68.tgz",
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- "@popperjs/core": "^2.4.4",
- "clsx": "^1.1.1",
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- "react-is": "^17.0.2"
+ "version": "5.0.0-alpha.109",
+ "resolved": "https://registry.npmjs.org/@mui/base/-/base-5.0.0-alpha.109.tgz",
+ "integrity": "sha512-UQxoONPI3ntzxcD/cbFHl+Lp2xsVj6HpKmU9QhUZ2kZ2K2yej2QJyU1gnADoWl/Hu94VrvwSSRnjTjR3HvXO/g==",
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+ "react-is": "^18.2.0"
},
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@@ -2889,9 +3101,9 @@
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},
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- "@types/react": "^16.8.6 || ^17.0.0",
- "react": "^17.0.0",
- "react-dom": "^17.0.0"
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+ "react": "^17.0.0 || ^18.0.0",
+ "react-dom": "^17.0.0 || ^18.0.0"
},
"peerDependenciesMeta": {
"@types/react": {
@@ -2899,23 +3111,32 @@
}
}
},
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+ "version": "5.10.17",
+ "resolved": "https://registry.npmjs.org/@mui/core-downloads-tracker/-/core-downloads-tracker-5.10.17.tgz",
+ "integrity": "sha512-iNwUuMA30nrN0tiEkeD3zaczv7Tk2jlZIDbXRnijAsYXkZtl/xEzQsVRIPYRDuyEz6D18vQJhV8h7gPUXEubTg==",
+ "funding": {
+ "type": "opencollective",
+ "url": "https://opencollective.com/mui"
+ }
+ },
"node_modules/@mui/material": {
- "version": "5.4.1",
- "resolved": "https://registry.npmjs.org/@mui/material/-/material-5.4.1.tgz",
- "integrity": "sha512-SxAT43UAjFTBBpJrN+oGrv40xP1uCa5Z49NfHt3m93xYeFzbxKOk0V9IKU7zlUjbsaVQ0i+o24yF5GULZmynlA==",
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- "prop-types": "^15.7.2",
- "react-is": "^17.0.2",
- "react-transition-group": "^4.4.2"
+ "version": "5.10.17",
+ "resolved": "https://registry.npmjs.org/@mui/material/-/material-5.10.17.tgz",
+ "integrity": "sha512-Kuqgv1qI5HXnc/Xu426xhCGYBSKzplb+xFNLitbnIb92Qx8jmcpfNpFlDJa2kD2H6qP66rr/m4c/zMUfGX/xBQ==",
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+ "@mui/base": "5.0.0-alpha.109",
+ "@mui/core-downloads-tracker": "^5.10.17",
+ "@mui/system": "^5.10.17",
+ "@mui/types": "^7.2.2",
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+ "react-is": "^18.2.0",
+ "react-transition-group": "^4.4.5"
},
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@@ -2927,9 +3148,9 @@
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- "@types/react": "^16.8.6 || ^17.0.0",
- "react": "^17.0.0",
- "react-dom": "^17.0.0"
+ "@types/react": "^17.0.0 || ^18.0.0",
+ "react": "^17.0.0 || ^18.0.0",
+ "react-dom": "^17.0.0 || ^18.0.0"
},
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@@ -2944,13 +3165,13 @@
}
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- "resolved": "https://registry.npmjs.org/@mui/private-theming/-/private-theming-5.4.1.tgz",
- "integrity": "sha512-Xbc4MXFZxv0A3hoc4TSDBhzjhstppKfc+gQcTMqqBZQP7KjnmxF+wO7rEPQuYRBihjCqQBdrHIGMLsKWrhkZkQ==",
+ "version": "5.10.16",
+ "resolved": "https://registry.npmjs.org/@mui/private-theming/-/private-theming-5.10.16.tgz",
+ "integrity": "sha512-0MArkJaOHRCKqL/GWjngGZmyOeRz+uxffhx82bKcewr8swqV7xx7EFP02pk0L/gLdfcvYdqwH4YTVjG/+TaKrg==",
"dependencies": {
- "@babel/runtime": "^7.17.0",
- "@mui/utils": "^5.4.1",
- "prop-types": "^15.7.2"
+ "@babel/runtime": "^7.20.1",
+ "@mui/utils": "^5.10.16",
+ "prop-types": "^15.8.1"
},
"engines": {
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@@ -2960,8 +3181,8 @@
"url": "https://opencollective.com/mui"
},
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- "@types/react": "^16.8.6 || ^17.0.0",
- "react": "^17.0.0"
+ "@types/react": "^17.0.0 || ^18.0.0",
+ "react": "^17.0.0 || ^18.0.0"
},
"peerDependenciesMeta": {
"@types/react": {
@@ -2970,13 +3191,14 @@
}
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- "resolved": "https://registry.npmjs.org/@mui/styled-engine/-/styled-engine-5.4.1.tgz",
- "integrity": "sha512-CFLNJkopRoAuShkgUZOTBVxdTlKu4w6L4kOwPi4r3QB2XXS6O5kyLHSsg9huUbtOYk5Dv5UZyUSc5pw4J7ezdg==",
+ "version": "5.10.16",
+ "resolved": "https://registry.npmjs.org/@mui/styled-engine/-/styled-engine-5.10.16.tgz",
+ "integrity": "sha512-ZMSjXvtiGwGDKqrSlXhpxK2voUaF2/lpC/pSTfFmZvKH9j9a9h1/iwo3ybgjFVYGgbfNeW4h0xEchiRohu9xsw==",
"dependencies": {
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- "@emotion/cache": "^11.7.1",
- "prop-types": "^15.7.2"
+ "@babel/runtime": "^7.20.1",
+ "@emotion/cache": "^11.10.5",
+ "csstype": "^3.1.1",
+ "prop-types": "^15.8.1"
},
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@@ -2988,7 +3210,7 @@
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+ "react": "^17.0.0 || ^18.0.0"
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@@ -3000,27 +3222,27 @@
}
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- "resolved": "https://registry.npmjs.org/@mui/styles/-/styles-5.4.1.tgz",
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- "@mui/types": "^7.1.1",
- "@mui/utils": "^5.4.1",
- "clsx": "^1.1.1",
- "csstype": "^3.0.10",
+ "version": "5.10.16",
+ "resolved": "https://registry.npmjs.org/@mui/styles/-/styles-5.10.16.tgz",
+ "integrity": "sha512-GYxY9pAx/mIAF3l9QJhTfWyUdT18UyjXHRmfPFgDupphTyHumrVE4rgYoTFordmzMWr+1kaS0mAUvDfziGncGA==",
+ "dependencies": {
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+ "@emotion/hash": "^0.9.0",
+ "@mui/private-theming": "^5.10.16",
+ "@mui/types": "^7.2.2",
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- "jss-plugin-global": "^10.8.2",
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- "jss-plugin-rule-value-function": "^10.8.2",
- "jss-plugin-vendor-prefixer": "^10.8.2",
- "prop-types": "^15.7.2"
+ "jss": "^10.9.2",
+ "jss-plugin-camel-case": "^10.9.2",
+ "jss-plugin-default-unit": "^10.9.2",
+ "jss-plugin-global": "^10.9.2",
+ "jss-plugin-nested": "^10.9.2",
+ "jss-plugin-props-sort": "^10.9.2",
+ "jss-plugin-rule-value-function": "^10.9.2",
+ "jss-plugin-vendor-prefixer": "^10.9.2",
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@@ -3030,7 +3252,7 @@
"url": "https://opencollective.com/mui"
},
"peerDependencies": {
- "@types/react": "^16.8.6 || ^17.0.0",
+ "@types/react": "^17.0.0",
"react": "^17.0.0"
},
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@@ -3040,18 +3262,18 @@
}
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- "resolved": "https://registry.npmjs.org/@mui/system/-/system-5.4.1.tgz",
- "integrity": "sha512-07JBYf9iQdxIHZU8cFOLoxBnkQDUPLb7UBhNxo4998yEqpWFJ00WKgEVYBKvPl0X+MRU/20wqFz6yGIuCx4AeA==",
+ "version": "5.10.17",
+ "resolved": "https://registry.npmjs.org/@mui/system/-/system-5.10.17.tgz",
+ "integrity": "sha512-UYzAOSK7uxkMsUssqrIUW3lnOuQpU8vqh4hLwfSw+GYAnQo3qjK4m4NhlDx+pFpsjjiGnr3K+vrSH+aIAMbcLg==",
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- "@mui/utils": "^5.4.1",
- "clsx": "^1.1.1",
- "csstype": "^3.0.10",
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+ "@mui/styled-engine": "^5.10.16",
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+ "clsx": "^1.2.1",
+ "csstype": "^3.1.1",
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@@ -3063,8 +3285,8 @@
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- "@types/react": "^16.8.6 || ^17.0.0",
- "react": "^17.0.0"
+ "@types/react": "^17.0.0 || ^18.0.0",
+ "react": "^17.0.0 || ^18.0.0"
},
"peerDependenciesMeta": {
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@@ -3079,9 +3301,9 @@
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- "resolved": "https://registry.npmjs.org/@mui/types/-/types-7.1.1.tgz",
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+ "version": "7.2.2",
+ "resolved": "https://registry.npmjs.org/@mui/types/-/types-7.2.2.tgz",
+ "integrity": "sha512-siex8cZDtWeC916cXOoUOnEQQejuMYmHtc4hM6VkKVYaBICz3VIiqyiAomRboTQHt2jchxQ5Q5ATlbcDekTxDA==",
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},
@@ -3092,15 +3314,15 @@
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+ "version": "5.10.16",
+ "resolved": "https://registry.npmjs.org/@mui/utils/-/utils-5.10.16.tgz",
+ "integrity": "sha512-3MB/SGsgiiu9Z55CFmAfiONUoR7AAue/H4F6w3mc2LnhFQCsoVvXhioDPcsiRpUMIQr34jDPzGXdCuqWooPCXQ==",
"dependencies": {
- "@babel/runtime": "^7.17.0",
- "@types/prop-types": "^15.7.4",
+ "@babel/runtime": "^7.20.1",
+ "@types/prop-types": "^15.7.5",
"@types/react-is": "^16.7.1 || ^17.0.0",
- "prop-types": "^15.7.2",
- "react-is": "^17.0.2"
+ "prop-types": "^15.8.1",
+ "react-is": "^18.2.0"
},
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@@ -3110,7 +3332,35 @@
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},
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- "react": "^17.0.0"
+ "react": "^17.0.0 || ^18.0.0"
+ }
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+ "node_modules/@nicolo-ribaudo/eslint-scope-5-internals": {
+ "version": "5.1.1-v1",
+ "resolved": "https://registry.npmjs.org/@nicolo-ribaudo/eslint-scope-5-internals/-/eslint-scope-5-internals-5.1.1-v1.tgz",
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+ "dependencies": {
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+ }
+ },
+ "node_modules/@nicolo-ribaudo/eslint-scope-5-internals/node_modules/eslint-scope": {
+ "version": "5.1.1",
+ "resolved": "https://registry.npmjs.org/eslint-scope/-/eslint-scope-5.1.1.tgz",
+ "integrity": "sha512-2NxwbF/hZ0KpepYN0cNbo+FN6XoK7GaHlQhgx/hIZl6Va0bF45RQOOwhLIy8lQDbuCiadSLCBnH2CFYquit5bw==",
+ "dependencies": {
+ "esrecurse": "^4.3.0",
+ "estraverse": "^4.1.1"
+ },
+ "engines": {
+ "node": ">=8.0.0"
+ }
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+ "node_modules/@nicolo-ribaudo/eslint-scope-5-internals/node_modules/estraverse": {
+ "version": "4.3.0",
+ "resolved": "https://registry.npmjs.org/estraverse/-/estraverse-4.3.0.tgz",
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+ "engines": {
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}
},
"node_modules/@nodelib/fs.scandir": {
@@ -3146,17 +3396,17 @@
}
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- "resolved": "https://registry.npmjs.org/@pmmmwh/react-refresh-webpack-plugin/-/react-refresh-webpack-plugin-0.5.4.tgz",
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+ "version": "0.5.10",
+ "resolved": "https://registry.npmjs.org/@pmmmwh/react-refresh-webpack-plugin/-/react-refresh-webpack-plugin-0.5.10.tgz",
+ "integrity": "sha512-j0Ya0hCFZPd4x40qLzbhGsh9TMtdb+CJQiso+WxLOPNasohq9cc5SNUcwsZaRH6++Xh91Xkm/xHCkuIiIu0LUA==",
"dependencies": {
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"common-path-prefix": "^3.0.0",
- "core-js-pure": "^3.8.1",
+ "core-js-pure": "^3.23.3",
"error-stack-parser": "^2.0.6",
"find-up": "^5.0.0",
"html-entities": "^2.1.0",
- "loader-utils": "^2.0.0",
+ "loader-utils": "^2.0.4",
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@@ -3167,7 +3417,7 @@
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"react-refresh": ">=0.10.0 <1.0.0",
"sockjs-client": "^1.4.0",
- "type-fest": ">=0.17.0 <3.0.0",
+ "type-fest": ">=0.17.0 <4.0.0",
"webpack": ">=4.43.0 <6.0.0",
"webpack-dev-server": "3.x || 4.x",
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@@ -3195,17 +3445,17 @@
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+ "version": "0.7.4",
+ "resolved": "https://registry.npmjs.org/source-map/-/source-map-0.7.4.tgz",
+ "integrity": "sha512-l3BikUxvPOcn5E74dZiq5BGsTb5yEwhaTSzccU6t4sDOH8NWJCstKO5QT2CvtFoK6F0saL7p9xHAqHOlCPJygA==",
"engines": {
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}
},
"node_modules/@popperjs/core": {
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- "resolved": "https://registry.npmjs.org/@popperjs/core/-/core-2.11.2.tgz",
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+ "version": "2.11.6",
+ "resolved": "https://registry.npmjs.org/@popperjs/core/-/core-2.11.6.tgz",
+ "integrity": "sha512-50/17A98tWUfQ176raKiOGXuYpLyyVMkxxG6oylzL3BPOlA6ADGdK7EYunSa4I064xerltq9TGXs8HmOk5E+vw==",
"funding": {
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"url": "https://opencollective.com/popperjs"
@@ -3286,14 +3536,19 @@
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},
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+ "version": "1.2.0",
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+ },
+ "node_modules/@sinclair/typebox": {
+ "version": "0.24.51",
+ "resolved": "https://registry.npmjs.org/@sinclair/typebox/-/typebox-0.24.51.tgz",
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@@ -4403,12 +4587,26 @@
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- "funding": {
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+ "resolved": "https://registry.npmjs.org/caniuse-lite/-/caniuse-lite-1.0.30001439.tgz",
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+ "funding": [
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+ "type": "opencollective",
+ "url": "https://opencollective.com/browserslist"
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- "integrity": "sha1-2Klr13/Wjfd5OnMDajug1UBdR3s="
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"resolved": "https://registry.npmjs.org/type-check/-/type-check-0.3.2.tgz",
- "integrity": "sha1-WITKtRLPHTVeP7eE8wgEsrUg23I=",
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"dependencies": {
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},
@@ -7158,12 +7293,14 @@
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- "resolved": "https://registry.npmjs.org/eslint/-/eslint-8.11.0.tgz",
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- "@eslint/eslintrc": "^1.2.1",
- "@humanwhocodes/config-array": "^0.9.2",
+ "version": "8.29.0",
+ "resolved": "https://registry.npmjs.org/eslint/-/eslint-8.29.0.tgz",
+ "integrity": "sha512-isQ4EEiyUjZFbEKvEGJKKGBwXtvXX+zJbkVKCgTuB9t/+jUBcy8avhkEwWJecI15BkRkOYmvIM5ynbhRjEkoeg==",
+ "dependencies": {
+ "@eslint/eslintrc": "^1.3.3",
+ "@humanwhocodes/config-array": "^0.11.6",
+ "@humanwhocodes/module-importer": "^1.0.1",
+ "@nodelib/fs.walk": "^1.2.8",
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"chalk": "^4.0.0",
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@@ -7173,30 +7310,32 @@
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"eslint-utils": "^3.0.0",
"eslint-visitor-keys": "^3.3.0",
- "espree": "^9.3.1",
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"esquery": "^1.4.0",
"esutils": "^2.0.2",
"fast-deep-equal": "^3.1.3",
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- "glob-parent": "^6.0.1",
- "globals": "^13.6.0",
+ "find-up": "^5.0.0",
+ "glob-parent": "^6.0.2",
+ "globals": "^13.15.0",
+ "grapheme-splitter": "^1.0.4",
"ignore": "^5.2.0",
"import-fresh": "^3.0.0",
"imurmurhash": "^0.1.4",
"is-glob": "^4.0.0",
+ "is-path-inside": "^3.0.3",
+ "js-sdsl": "^4.1.4",
"js-yaml": "^4.1.0",
"json-stable-stringify-without-jsonify": "^1.0.1",
"levn": "^0.4.1",
"lodash.merge": "^4.6.2",
- "minimatch": "^3.0.4",
+ "minimatch": "^3.1.2",
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"optionator": "^0.9.1",
"regexpp": "^3.2.0",
"strip-ansi": "^6.0.1",
"strip-json-comments": "^3.1.0",
- "text-table": "^0.2.0",
- "v8-compile-cache": "^2.0.3"
+ "text-table": "^0.2.0"
},
"bin": {
"eslint": "bin/eslint.js"
@@ -7253,15 +7392,19 @@
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+ "version": "2.7.4",
+ "resolved": "https://registry.npmjs.org/eslint-module-utils/-/eslint-module-utils-2.7.4.tgz",
+ "integrity": "sha512-j4GT+rqzCoRKHwURX7pddtIPGySnX9Si/cgMI5ztrcqOPtk5dDEeZ34CQVPphnqkJytlc97Vuk05Um2mJ3gEQA==",
"dependencies": {
- "debug": "^3.2.7",
- "find-up": "^2.1.0"
+ "debug": "^3.2.7"
},
"engines": {
"node": ">=4"
+ },
+ "peerDependenciesMeta": {
+ "eslint": {
+ "optional": true
+ }
}
},
"node_modules/eslint-module-utils/node_modules/debug": {
@@ -7272,67 +7415,6 @@
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}
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- },
- "engines": {
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- "node_modules/eslint-module-utils/node_modules/locate-path": {
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- "resolved": "https://registry.npmjs.org/locate-path/-/locate-path-2.0.0.tgz",
- "integrity": "sha512-NCI2kiDkyR7VeEKm27Kda/iQHyKJe1Bu0FlTbYp3CqJu+9IFe9bLyAjMxf5ZDDbEg+iMPzB5zYyUTSm8wVTKmA==",
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- "path-exists": "^3.0.0"
- },
- "engines": {
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- }
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- "node_modules/eslint-module-utils/node_modules/p-limit": {
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- "integrity": "sha512-vvcXsLAJ9Dr5rQOPk7toZQZJApBl2K4J6dANSsEuh6QI41JYcsS/qhTGa9ErIUUgK3WNQoJYvylxvjqmiqEA9Q==",
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- "node_modules/eslint-module-utils/node_modules/p-try": {
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- "node_modules/eslint-module-utils/node_modules/path-exists": {
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- "integrity": "sha512-bpC7GYwiDYQ4wYLe+FA8lhRjhQCMcQGuSgGGqDkg/QerRWw9CmGRT0iSOVRSZJ29NMLZgIzqaljJ63oaL4NIJQ==",
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"resolved": "https://registry.npmjs.org/eslint-plugin-flowtype/-/eslint-plugin-flowtype-8.0.3.tgz",
@@ -7424,20 +7506,20 @@
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- "resolved": "https://registry.npmjs.org/eslint-plugin-jsx-a11y/-/eslint-plugin-jsx-a11y-6.6.0.tgz",
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+ "version": "6.6.1",
+ "resolved": "https://registry.npmjs.org/eslint-plugin-jsx-a11y/-/eslint-plugin-jsx-a11y-6.6.1.tgz",
+ "integrity": "sha512-sXgFVNHiWffBq23uiS/JaP6eVR622DqwB4yTzKvGZGcPq6/yZ3WmOZfuBks/vHWo9GaFOqC2ZK4i6+C35knx7Q==",
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+ "@babel/runtime": "^7.18.9",
"aria-query": "^4.2.2",
"array-includes": "^3.1.5",
"ast-types-flow": "^0.0.7",
- "axe-core": "^4.4.2",
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"axobject-query": "^2.2.0",
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"emoji-regex": "^9.2.2",
"has": "^1.0.3",
- "jsx-ast-utils": "^3.3.1",
+ "jsx-ast-utils": "^3.3.2",
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"minimatch": "^3.1.2",
"semver": "^6.3.0"
@@ -7449,25 +7531,38 @@
"eslint": "^3 || ^4 || ^5 || ^6 || ^7 || ^8"
}
},
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+ "version": "4.2.2",
+ "resolved": "https://registry.npmjs.org/aria-query/-/aria-query-4.2.2.tgz",
+ "integrity": "sha512-o/HelwhuKpTj/frsOsbNLNgnNGVIFsVP/SW2BSF14gVl7kAfMOJ6/8wUAUvG1R1NHKrfG+2sHZTu0yauT1qBrA==",
+ "dependencies": {
+ "@babel/runtime": "^7.10.2",
+ "@babel/runtime-corejs3": "^7.10.2"
+ },
+ "engines": {
+ "node": ">=6.0"
+ }
+ },
"node_modules/eslint-plugin-react": {
- "version": "7.30.1",
- "resolved": "https://registry.npmjs.org/eslint-plugin-react/-/eslint-plugin-react-7.30.1.tgz",
- "integrity": "sha512-NbEvI9jtqO46yJA3wcRF9Mo0lF9T/jhdHqhCHXiXtD+Zcb98812wvokjWpU7Q4QH5edo6dmqrukxVvWWXHlsUg==",
+ "version": "7.31.11",
+ "resolved": "https://registry.npmjs.org/eslint-plugin-react/-/eslint-plugin-react-7.31.11.tgz",
+ "integrity": "sha512-TTvq5JsT5v56wPa9OYHzsrOlHzKZKjV+aLgS+55NJP/cuzdiQPC7PfYoUjMoxlffKtvijpk7vA/jmuqRb9nohw==",
"dependencies": {
- "array-includes": "^3.1.5",
- "array.prototype.flatmap": "^1.3.0",
+ "array-includes": "^3.1.6",
+ "array.prototype.flatmap": "^1.3.1",
+ "array.prototype.tosorted": "^1.1.1",
"doctrine": "^2.1.0",
"estraverse": "^5.3.0",
"jsx-ast-utils": "^2.4.1 || ^3.0.0",
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- "object.entries": "^1.1.5",
- "object.fromentries": "^2.0.5",
- "object.hasown": "^1.1.1",
- "object.values": "^1.1.5",
+ "object.entries": "^1.1.6",
+ "object.fromentries": "^2.0.6",
+ "object.hasown": "^1.1.2",
+ "object.values": "^1.1.6",
"prop-types": "^15.8.1",
"resolve": "^2.0.0-next.3",
"semver": "^6.3.0",
- "string.prototype.matchall": "^4.0.7"
+ "string.prototype.matchall": "^4.0.8"
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"node": ">=4"
@@ -7515,9 +7610,9 @@
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- "resolved": "https://registry.npmjs.org/eslint-plugin-testing-library/-/eslint-plugin-testing-library-5.5.1.tgz",
- "integrity": "sha512-plLEkkbAKBjPxsLj7x4jNapcHAg2ernkQlKKrN2I8NrQwPISZHyCUNvg5Hv3EDqOQReToQb5bnqXYbkijJPE/g==",
+ "version": "5.9.1",
+ "resolved": "https://registry.npmjs.org/eslint-plugin-testing-library/-/eslint-plugin-testing-library-5.9.1.tgz",
+ "integrity": "sha512-6BQp3tmb79jLLasPHJmy8DnxREe+2Pgf7L+7o09TSWPfdqqtQfRZmZNetr5mOs3yqZk/MRNxpN3RUpJe0wB4LQ==",
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},
@@ -7575,15 +7670,15 @@
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- "resolved": "https://registry.npmjs.org/eslint-webpack-plugin/-/eslint-webpack-plugin-3.1.1.tgz",
- "integrity": "sha512-xSucskTN9tOkfW7so4EaiFIkulWLXwCB/15H917lR6pTv0Zot6/fetFucmENRb7J5whVSFKIvwnrnsa78SG2yg==",
+ "version": "3.2.0",
+ "resolved": "https://registry.npmjs.org/eslint-webpack-plugin/-/eslint-webpack-plugin-3.2.0.tgz",
+ "integrity": "sha512-avrKcGncpPbPSUHX6B3stNGzkKFto3eL+DKM4+VyMrVnhPc3vRczVlCq3uhuFOdRvDHTVXuzwk1ZKUrqDQHQ9w==",
"dependencies": {
- "@types/eslint": "^7.28.2",
- "jest-worker": "^27.3.1",
- "micromatch": "^4.0.4",
+ "@types/eslint": "^7.29.0 || ^8.4.1",
+ "jest-worker": "^28.0.2",
+ "micromatch": "^4.0.5",
"normalize-path": "^3.0.0",
- "schema-utils": "^3.1.1"
+ "schema-utils": "^4.0.0"
},
"engines": {
"node": ">= 12.13.0"
@@ -7597,6 +7692,90 @@
"webpack": "^5.0.0"
}
},
+ "node_modules/eslint-webpack-plugin/node_modules/ajv": {
+ "version": "8.11.2",
+ "resolved": "https://registry.npmjs.org/ajv/-/ajv-8.11.2.tgz",
+ "integrity": "sha512-E4bfmKAhGiSTvMfL1Myyycaub+cUEU2/IvpylXkUu7CHBkBj1f/ikdzbD7YQ6FKUbixDxeYvB/xY4fvyroDlQg==",
+ "dependencies": {
+ "fast-deep-equal": "^3.1.1",
+ "json-schema-traverse": "^1.0.0",
+ "require-from-string": "^2.0.2",
+ "uri-js": "^4.2.2"
+ },
+ "funding": {
+ "type": "github",
+ "url": "https://github.com/sponsors/epoberezkin"
+ }
+ },
+ "node_modules/eslint-webpack-plugin/node_modules/ajv-keywords": {
+ "version": "5.1.0",
+ "resolved": "https://registry.npmjs.org/ajv-keywords/-/ajv-keywords-5.1.0.tgz",
+ "integrity": "sha512-YCS/JNFAUyr5vAuhk1DWm1CBxRHW9LbJ2ozWeemrIqpbsqKjHVxYPyi5GC0rjZIT5JxJ3virVTS8wk4i/Z+krw==",
+ "dependencies": {
+ "fast-deep-equal": "^3.1.3"
+ },
+ "peerDependencies": {
+ "ajv": "^8.8.2"
+ }
+ },
+ "node_modules/eslint-webpack-plugin/node_modules/has-flag": {
+ "version": "4.0.0",
+ "resolved": "https://registry.npmjs.org/has-flag/-/has-flag-4.0.0.tgz",
+ "integrity": "sha512-EykJT/Q1KjTWctppgIAgfSO0tKVuZUjhgMr17kqTumMl6Afv3EISleU7qZUzoXDFTAHTDC4NOoG/ZxU3EvlMPQ==",
+ "engines": {
+ "node": ">=8"
+ }
+ },
+ "node_modules/eslint-webpack-plugin/node_modules/jest-worker": {
+ "version": "28.1.3",
+ "resolved": "https://registry.npmjs.org/jest-worker/-/jest-worker-28.1.3.tgz",
+ "integrity": "sha512-CqRA220YV/6jCo8VWvAt1KKx6eek1VIHMPeLEbpcfSfkEeWyBNppynM/o6q+Wmw+sOhos2ml34wZbSX3G13//g==",
+ "dependencies": {
+ "@types/node": "*",
+ "merge-stream": "^2.0.0",
+ "supports-color": "^8.0.0"
+ },
+ "engines": {
+ "node": "^12.13.0 || ^14.15.0 || ^16.10.0 || >=17.0.0"
+ }
+ },
+ "node_modules/eslint-webpack-plugin/node_modules/json-schema-traverse": {
+ "version": "1.0.0",
+ "resolved": "https://registry.npmjs.org/json-schema-traverse/-/json-schema-traverse-1.0.0.tgz",
+ "integrity": "sha512-NM8/P9n3XjXhIZn1lLhkFaACTOURQXjWhV4BA/RnOv8xvgqtqpAX9IO4mRQxSx1Rlo4tqzeqb0sOlruaOy3dug=="
+ },
+ "node_modules/eslint-webpack-plugin/node_modules/schema-utils": {
+ "version": "4.0.0",
+ "resolved": "https://registry.npmjs.org/schema-utils/-/schema-utils-4.0.0.tgz",
+ "integrity": "sha512-1edyXKgh6XnJsJSQ8mKWXnN/BVaIbFMLpouRUrXgVq7WYne5kw3MW7UPhO44uRXQSIpTSXoJbmrR2X0w9kUTyg==",
+ "dependencies": {
+ "@types/json-schema": "^7.0.9",
+ "ajv": "^8.8.0",
+ "ajv-formats": "^2.1.1",
+ "ajv-keywords": "^5.0.0"
+ },
+ "engines": {
+ "node": ">= 12.13.0"
+ },
+ "funding": {
+ "type": "opencollective",
+ "url": "https://opencollective.com/webpack"
+ }
+ },
+ "node_modules/eslint-webpack-plugin/node_modules/supports-color": {
+ "version": "8.1.1",
+ "resolved": "https://registry.npmjs.org/supports-color/-/supports-color-8.1.1.tgz",
+ "integrity": "sha512-MpUEN2OodtUzxvKQl72cUF7RQ5EiHsGvSsVG0ia9c5RbWGL2CI4C7EpPS8UTBIplnlzZiNuV56w+FuNxy3ty2Q==",
+ "dependencies": {
+ "has-flag": "^4.0.0"
+ },
+ "engines": {
+ "node": ">=10"
+ },
+ "funding": {
+ "url": "https://github.com/chalk/supports-color?sponsor=1"
+ }
+ },
"node_modules/eslint/node_modules/ansi-styles": {
"version": "4.3.0",
"resolved": "https://registry.npmjs.org/ansi-styles/-/ansi-styles-4.3.0.tgz",
@@ -7647,21 +7826,10 @@
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"integrity": "sha512-dOy+3AuW3a2wNbZHIuMZpTcgjGuLU/uBL/ubcZF9OXbDo8ff4O8yVp5Bf0efS8uEoYo5q4Fx7dY9OgQGXgAsQA=="
},
- "node_modules/eslint/node_modules/escape-string-regexp": {
- "version": "4.0.0",
- "resolved": "https://registry.npmjs.org/escape-string-regexp/-/escape-string-regexp-4.0.0.tgz",
- "integrity": "sha512-TtpcNJ3XAzx3Gq8sWRzJaVajRs0uVxA2YAkdb1jm2YkPz4G6egUFAyA3n5vtEIZefPk5Wa4UXbKuS5fKkJWdgA==",
- "engines": {
- "node": ">=10"
- },
- "funding": {
- "url": "https://github.com/sponsors/sindresorhus"
- }
- },
"node_modules/eslint/node_modules/globals": {
- "version": "13.13.0",
- "resolved": "https://registry.npmjs.org/globals/-/globals-13.13.0.tgz",
- "integrity": "sha512-EQ7Q18AJlPwp3vUDL4mKA0KXrXyNIQyWon6T6XQiBQF0XHvRsiCSrWmmeATpUzdJN2HhWZU6Pdl0a9zdep5p6A==",
+ "version": "13.18.0",
+ "resolved": "https://registry.npmjs.org/globals/-/globals-13.18.0.tgz",
+ "integrity": "sha512-/mR4KI8Ps2spmoc0Ulu9L7agOF0du1CZNQ3dke8yItYlyKNmGrkONemBbd6V8UTc1Wgcqn21t3WYB7dbRmh6/A==",
"dependencies": {
"type-fest": "^0.20.2"
},
@@ -7714,16 +7882,19 @@
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- "resolved": "https://registry.npmjs.org/espree/-/espree-9.3.1.tgz",
- "integrity": "sha512-bvdyLmJMfwkV3NCRl5ZhJf22zBFo1y8bYh3VYb+bfzqNB4Je68P2sSuXyuFquzWLebHpNd2/d5uv7yoP9ISnGQ==",
+ "version": "9.4.1",
+ "resolved": "https://registry.npmjs.org/espree/-/espree-9.4.1.tgz",
+ "integrity": "sha512-XwctdmTO6SIvCzd9810yyNzIrOrqNYV9Koizx4C/mRhf9uq0o4yHoCEU/670pOxOL/MSraektvSAji79kX90Vg==",
"dependencies": {
- "acorn": "^8.7.0",
- "acorn-jsx": "^5.3.1",
+ "acorn": "^8.8.0",
+ "acorn-jsx": "^5.3.2",
"eslint-visitor-keys": "^3.3.0"
},
"engines": {
"node": "^12.22.0 || ^14.17.0 || >=16.0.0"
+ },
+ "funding": {
+ "url": "https://opencollective.com/eslint"
}
},
"node_modules/esprima": {
@@ -7784,7 +7955,7 @@
"node_modules/etag": {
"version": "1.8.1",
"resolved": "https://registry.npmjs.org/etag/-/etag-1.8.1.tgz",
- "integrity": "sha1-Qa4u62XvpiJorr/qg6x9eSmbCIc=",
+ "integrity": "sha512-aIL5Fx7mawVa300al2BnEE4iNvo1qETxLrPI/o05L7z6go7fCw1J6EQmbK4FmJ2AS7kgVF/KEZWufBfdClMcPg==",
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@@ -7792,7 +7963,7 @@
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+ "url": "https://github.com/sponsors/feross"
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+ "url": "https://www.patreon.com/feross"
+ },
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@@ -14864,10 +15464,18 @@
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"resolved": "https://registry.npmjs.org/sprintf-js/-/sprintf-js-1.0.3.tgz",
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- "integrity": "sha1-Fhx9rBd2Wf2YEfQ3cfqZOBR4Yow=",
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}
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@@ -15312,11 +15904,11 @@
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+ "version": "5.1.1",
+ "resolved": "https://registry.npmjs.org/stylehacks/-/stylehacks-5.1.1.tgz",
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- "browserslist": "^4.16.6",
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- "cosmiconfig": "^7.0.1",
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@@ -15509,74 +16103,14 @@
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@@ -15637,13 +16171,13 @@
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@@ -15654,15 +16188,15 @@
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+ "version": "5.3.6",
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@@ -15686,27 +16220,11 @@
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"resolved": "https://registry.npmjs.org/test-exclude/-/test-exclude-6.0.0.tgz",
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"resolved": "https://registry.npmjs.org/text-table/-/text-table-0.2.0.tgz",
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+ "integrity": "sha512-N+8UisAXDGk8PFXP4HAzVR9nbfmVJ3zYLAWiTIoqC5v5isinhr+r5uaO8+7r3BMfuNIufIsA7RdpVgacC2cSpw=="
},
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"resolved": "https://registry.npmjs.org/tiny-warning/-/tiny-warning-1.0.3.tgz",
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@@ -15787,22 +16300,23 @@
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+ "version": "4.1.2",
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"punycode": "^2.1.1",
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+ "universalify": "^0.2.0",
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},
"engines": {
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}
},
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+ "version": "0.2.0",
+ "resolved": "https://registry.npmjs.org/universalify/-/universalify-0.2.0.tgz",
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+ "version": "2.4.1",
+ "resolved": "https://registry.npmjs.org/tslib/-/tslib-2.4.1.tgz",
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@@ -15933,9 +16447,9 @@
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+ "version": "4.9.4",
+ "resolved": "https://registry.npmjs.org/typescript/-/typescript-4.9.4.tgz",
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"bin": {
"tsc": "bin/tsc",
"tsserver": "bin/tsserver"
@@ -15979,17 +16493,17 @@
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+ "version": "2.1.0",
+ "resolved": "https://registry.npmjs.org/unicode-match-property-value-ecmascript/-/unicode-match-property-value-ecmascript-2.1.0.tgz",
+ "integrity": "sha512-qxkjQt6qjg/mYscYMC0XKRn3Rh0wFPlfxB0xkt9CfyTvpX1Ra0+rAmdX2QyAobptSEvuy4RtpPRui6XkV+8wjA==",
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+ "version": "2.1.0",
+ "resolved": "https://registry.npmjs.org/unicode-property-aliases-ecmascript/-/unicode-property-aliases-ecmascript-2.1.0.tgz",
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"resolved": "https://registry.npmjs.org/unpipe/-/unpipe-1.0.0.tgz",
- "integrity": "sha1-sr9O6FFKrmFltIF4KdIbLvSZBOw=",
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@@ -16024,7 +16538,7 @@
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"resolved": "https://registry.npmjs.org/unquote/-/unquote-1.1.1.tgz",
- "integrity": "sha1-j97XMk7G6IoP+LkF58CYzcCG1UQ="
+ "integrity": "sha512-vRCqFv6UhXpWxZPyGDh/F3ZpNv8/qo7w6iufLpQg9aKnQ71qM4B5KiI7Mia9COcjEhrO9LueHpMYjYzsWH3OIg=="
},
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"version": "1.2.0",
@@ -16035,6 +16549,31 @@
"yarn": "*"
}
},
+ "node_modules/update-browserslist-db": {
+ "version": "1.0.10",
+ "resolved": "https://registry.npmjs.org/update-browserslist-db/-/update-browserslist-db-1.0.10.tgz",
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+ "funding": [
+ {
+ "type": "opencollective",
+ "url": "https://opencollective.com/browserslist"
+ },
+ {
+ "type": "tidelift",
+ "url": "https://tidelift.com/funding/github/npm/browserslist"
+ }
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+ "dependencies": {
+ "escalade": "^3.1.1",
+ "picocolors": "^1.0.0"
+ },
+ "bin": {
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+ },
+ "peerDependencies": {
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+ }
+ },
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"version": "4.4.1",
"resolved": "https://registry.npmjs.org/uri-js/-/uri-js-4.4.1.tgz",
@@ -16043,23 +16582,31 @@
"punycode": "^2.1.0"
}
},
+ "node_modules/url-parse": {
+ "version": "1.5.10",
+ "resolved": "https://registry.npmjs.org/url-parse/-/url-parse-1.5.10.tgz",
+ "integrity": "sha512-WypcfiRhfeUP9vvF0j6rw0J3hrWrw6iZv3+22h6iRMJ/8z1Tj6XfLP4DsUix5MhMPnXpiHDoKyoZ/bdCkwBCiQ==",
+ "dependencies": {
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+ "requires-port": "^1.0.0"
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- "resolved": "https://registry.npmjs.org/util/-/util-0.12.4.tgz",
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+ "version": "0.12.5",
+ "resolved": "https://registry.npmjs.org/util/-/util-0.12.5.tgz",
+ "integrity": "sha512-kZf/K6hEIrWHI6XqOFUiiMa+79wE/D8Q+NCNAWclkyg3b4d2k7s0QGepNjiABc+aR3N1PAyHL7p6UcLY6LmrnA==",
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}
},
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"version": "1.0.2",
"resolved": "https://registry.npmjs.org/util-deprecate/-/util-deprecate-1.0.2.tgz",
- "integrity": "sha1-RQ1Nyfpw3nMnYvvS1KKJgUGaDM8="
+ "integrity": "sha512-EPD5q1uXyFxJpCrLnCc1nHnq3gOa6DZBocAIiI2TaSCA7VCJ1UJDMagCzIkXNsUYfD1daK//LTEQ8xiIbrHtcw=="
},
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@@ -16078,12 +16625,12 @@
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"resolved": "https://registry.npmjs.org/utila/-/utila-0.4.0.tgz",
- "integrity": "sha1-ihagXURWV6Oupe7MWxKk+lN5dyw="
+ "integrity": "sha512-Z0DbgELS9/L/75wZbro8xAnT50pBVFQZ+hUEueGDU5FN51YSCYM+jdxsfCiHjwNP/4LCDD0i/graKpeBnOXKRA=="
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- "integrity": "sha1-n5VxD1CiZ5R7LMwSR0HBAoQn5xM=",
+ "integrity": "sha512-pMZTvIkT1d+TFGvDOqodOclx0QWkkgi6Tdoa8gC8ffGAAqz9pzPTZWAybbsHHoED/ztMtkv/VoYTYyShUn81hA==",
"engines": {
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}
@@ -16096,11 +16643,6 @@
"uuid": "dist/bin/uuid"
}
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- },
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"resolved": "https://registry.npmjs.org/v8-to-istanbul/-/v8-to-istanbul-8.1.1.tgz",
@@ -16115,9 +16657,9 @@
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- "integrity": "sha512-CkCj6giN3S+n9qrYiBTX5gystlENnRW5jZeNLHpe6aue+SrHcG5VYwujhW9s4dY31mEGsxBDrHR6oI69fTXsaQ==",
+ "version": "0.7.4",
+ "resolved": "https://registry.npmjs.org/source-map/-/source-map-0.7.4.tgz",
+ "integrity": "sha512-l3BikUxvPOcn5E74dZiq5BGsTb5yEwhaTSzccU6t4sDOH8NWJCstKO5QT2CvtFoK6F0saL7p9xHAqHOlCPJygA==",
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}
@@ -16125,7 +16667,7 @@
"node_modules/vary": {
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"resolved": "https://registry.npmjs.org/vary/-/vary-1.1.2.tgz",
- "integrity": "sha1-IpnwLG3tMNSllhsLn3RSShj2NPw=",
+ "integrity": "sha512-BNGbWLfd0eUPabhkXUVm0j8uuvREyTh5ovRa/dyow/BqAbZJyC+5fU+IzQOzmAKzYqYRAISoRhdQr3eIZ/PXqg==",
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@@ -16134,6 +16676,7 @@
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+ "deprecated": "Use your platform's native performance.now() and performance.timeOrigin.",
"dependencies": {
"browser-process-hrtime": "^1.0.0"
}
@@ -16158,9 +16701,9 @@
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- "resolved": "https://registry.npmjs.org/watchpack/-/watchpack-2.3.1.tgz",
- "integrity": "sha512-x0t0JuydIo8qCNctdDrn1OzH/qDzk2+rdCOC3YzumZ42fiMqmQ7T3xQurykYMhYfHaPHTp4ZxAx2NfUo1K6QaA==",
+ "version": "2.4.0",
+ "resolved": "https://registry.npmjs.org/watchpack/-/watchpack-2.4.0.tgz",
+ "integrity": "sha512-Lcvm7MGST/4fup+ifyKi2hjyIAwcdI4HRgtvTpIUxBRhB+RFtUh8XtDOxUfctVCnhVi+QQj49i91OyvzkJl6cg==",
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@@ -16191,33 +16734,33 @@
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- "integrity": "sha512-ZMWWy8CeuTTjCxbeaQI21xSswseF2oNOwc70QSKNePvmxE7XW36i7vpBMYZFAUHPwQiEbNGCEYIOOlyRbdGmxw==",
+ "version": "5.75.0",
+ "resolved": "https://registry.npmjs.org/webpack/-/webpack-5.75.0.tgz",
+ "integrity": "sha512-piaIaoVJlqMsPtX/+3KTTO6jfvrSYgauFVdt8cr9LTHKmcq/AMd4mhzsiP7ZF/PGRNPGA8336jldh9l2Kt2ogQ==",
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"@webassemblyjs/wasm-edit": "1.11.1",
"@webassemblyjs/wasm-parser": "1.11.1",
- "acorn": "^8.4.1",
+ "acorn": "^8.7.1",
"acorn-import-assertions": "^1.7.6",
"browserslist": "^4.14.5",
"chrome-trace-event": "^1.0.2",
- "enhanced-resolve": "^5.9.2",
+ "enhanced-resolve": "^5.10.0",
"es-module-lexer": "^0.9.0",
"eslint-scope": "5.1.1",
"events": "^3.2.0",
"glob-to-regexp": "^0.4.1",
"graceful-fs": "^4.2.9",
- "json-parse-better-errors": "^1.0.2",
+ "json-parse-even-better-errors": "^2.3.1",
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"mime-types": "^2.1.27",
"neo-async": "^2.6.2",
"schema-utils": "^3.1.0",
"tapable": "^2.1.1",
"terser-webpack-plugin": "^5.1.3",
- "watchpack": "^2.3.1",
+ "watchpack": "^2.4.0",
"webpack-sources": "^3.2.3"
},
"bin": {
@@ -16237,12 +16780,12 @@
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+ "version": "5.3.3",
+ "resolved": "https://registry.npmjs.org/webpack-dev-middleware/-/webpack-dev-middleware-5.3.3.tgz",
+ "integrity": "sha512-hj5CYrY0bZLB+eTO+x/j67Pkrquiy7kWepMHmUMoPsmcUaeEnQJqFzHJOyxgWlq746/wUuA64p9ta34Kyb01pA==",
"dependencies": {
"colorette": "^2.0.10",
- "memfs": "^3.4.1",
+ "memfs": "^3.4.3",
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@@ -16259,9 +16802,9 @@
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+ "version": "8.11.2",
+ "resolved": "https://registry.npmjs.org/ajv/-/ajv-8.11.2.tgz",
+ "integrity": "sha512-E4bfmKAhGiSTvMfL1Myyycaub+cUEU2/IvpylXkUu7CHBkBj1f/ikdzbD7YQ6FKUbixDxeYvB/xY4fvyroDlQg==",
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@@ -16308,38 +16851,37 @@
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+ "version": "4.11.1",
+ "resolved": "https://registry.npmjs.org/webpack-dev-server/-/webpack-dev-server-4.11.1.tgz",
+ "integrity": "sha512-lILVz9tAUy1zGFwieuaQtYiadImb5M3d+H+L1zDYalYoDl0cksAB1UNyuE5MMWJrG6zR1tXkCP2fitl7yoUJiw==",
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"@types/connect-history-api-fallback": "^1.3.5",
"@types/express": "^4.17.13",
"@types/serve-index": "^1.9.1",
+ "@types/serve-static": "^1.13.10",
"@types/sockjs": "^0.3.33",
- "@types/ws": "^8.2.2",
+ "@types/ws": "^8.5.1",
"ansi-html-community": "^0.0.8",
- "bonjour": "^3.5.0",
+ "bonjour-service": "^1.0.11",
"chokidar": "^3.5.3",
"colorette": "^2.0.10",
"compression": "^1.7.4",
- "connect-history-api-fallback": "^1.6.0",
+ "connect-history-api-fallback": "^2.0.0",
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- "del": "^6.0.0",
- "express": "^4.17.1",
+ "express": "^4.17.3",
"graceful-fs": "^4.2.6",
"html-entities": "^2.3.2",
- "http-proxy-middleware": "^2.0.0",
+ "http-proxy-middleware": "^2.0.3",
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- "workbox-precaching": "6.5.1",
- "workbox-routing": "6.5.1",
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- }
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- }
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- "requires": {
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- }
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- "workbox-streams": {
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- "resolved": "https://registry.npmjs.org/workbox-streams/-/workbox-streams-6.5.1.tgz",
- "integrity": "sha512-7jaTWm6HRGJ/ewECnhb+UgjTT50R42E0/uNCC4eTKQwnLO/NzNGjoXTdQgFjo4zteR+L/K6AtFAiYKH3ZJbAYw==",
- "requires": {
- "workbox-core": "6.5.1",
- "workbox-routing": "6.5.1"
- }
- },
- "workbox-sw": {
- "version": "6.5.1",
- "resolved": "https://registry.npmjs.org/workbox-sw/-/workbox-sw-6.5.1.tgz",
- "integrity": "sha512-hVrQa19yo9wzN1fQQ/h2JlkzFpkuH2qzYT2/rk7CLaWt6tLnTJVFCNHlGRRPhytZSf++LoIy7zThT714sowT/Q=="
- },
- "workbox-webpack-plugin": {
- "version": "6.5.1",
- "resolved": "https://registry.npmjs.org/workbox-webpack-plugin/-/workbox-webpack-plugin-6.5.1.tgz",
- "integrity": "sha512-SHtlQBpKruI16CAYhICDMkgjXE2fH5Yp+D+1UmBfRVhByZYzusVOykvnPm8ObJb9d/tXgn9yoppoxafFS7D4vQ==",
- "requires": {
- "fast-json-stable-stringify": "^2.1.0",
- "pretty-bytes": "^5.4.1",
- "upath": "^1.2.0",
- "webpack-sources": "^1.4.3",
- "workbox-build": "6.5.1"
- },
- "dependencies": {
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- "version": "0.6.1",
- "resolved": "https://registry.npmjs.org/source-map/-/source-map-0.6.1.tgz",
- "integrity": "sha512-UjgapumWlbMhkBgzT7Ykc5YXUT46F0iKu8SGXq0bcwP5dz/h0Plj6enJqjz1Zbq2l5WaqYnrVbwWOWMyF3F47g=="
- },
- "webpack-sources": {
- "version": "1.4.3",
- "resolved": "https://registry.npmjs.org/webpack-sources/-/webpack-sources-1.4.3.tgz",
- "integrity": "sha512-lgTS3Xhv1lCOKo7SA5TjKXMjpSM4sBjNV5+q2bqesbSPs5FjGmU6jjtBSkX9b4qW87vDIsCIlUPOEhbZrMdjeQ==",
- "requires": {
- "source-list-map": "^2.0.0",
- "source-map": "~0.6.1"
- }
- }
- }
- },
- "workbox-window": {
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- "resolved": "https://registry.npmjs.org/workbox-window/-/workbox-window-6.5.1.tgz",
- "integrity": "sha512-oRlun9u7b7YEjo2fIDBqJkU2hXtrEljXcOytRhfeQRbqXxjUOpFgXSGRSAkmDx1MlKUNOSbr+zfi8h5n7In3yA==",
- "requires": {
- "@types/trusted-types": "^2.0.2",
- "workbox-core": "6.5.1"
- }
- },
- "wrap-ansi": {
- "version": "7.0.0",
- "resolved": "https://registry.npmjs.org/wrap-ansi/-/wrap-ansi-7.0.0.tgz",
- "integrity": "sha512-YVGIj2kamLSTxw6NsZjoBxfSwsn0ycdesmc4p+Q21c5zPuZ1pl+NfxVdxPtdHvmNVOQ6XSYG4AUtyt/Fi7D16Q==",
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- "string-width": "^4.1.0",
- "strip-ansi": "^6.0.0"
- },
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- "y18n": "^5.0.5",
- "yargs-parser": "^20.2.2"
- }
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- "yargs-parser": {
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- "resolved": "https://registry.npmjs.org/yargs-parser/-/yargs-parser-20.2.9.tgz",
- "integrity": "sha512-y11nGElTIV+CT3Zv9t7VKl+Q3hTQoT9a1Qzezhhl6Rp21gJ/IVTW7Z3y9EWXhuUBC2Shnf+DX0antecpAwSP8w=="
- },
- "yocto-queue": {
- "version": "0.1.0",
- "resolved": "https://registry.npmjs.org/yocto-queue/-/yocto-queue-0.1.0.tgz",
- "integrity": "sha512-rVksvsnNCdJ/ohGc6xgPwyN8eheCxsiLM8mxuE/t/mOVqJewPuO1miLpTHQiRgTKCLexL4MeAFVagts7HmNZ2Q=="
- }
}
}
diff --git a/frontend/src/App.tsx b/frontend/src/App.tsx
index 4fdc5d79..18ad427f 100644
--- a/frontend/src/App.tsx
+++ b/frontend/src/App.tsx
@@ -4,8 +4,8 @@ import React from 'react';
import './App.css';
import { FormControl, FormLabel, FormControlLabel, Radio, RadioGroup, Checkbox, Button, InputLabel, MenuItem, Select } from '@mui/material';
-const numLayers = 6;
-const layerNames = ["Monte Carlo Type I error estimates", "0th order upper bound", "Max gradient estimates", "1st order upper bound", "2nd order upper bound", "Total upper bound"]
+const numLayers = 4;
+const layerNames = ["Monte Carlo Type I error estimates", "Clopper-Pearson", "Tilt-Bound", "Total bound"]
function App() {
const [plotType, setPlotType] = React.useState("surface");
diff --git a/frontend/tsconfig.json b/frontend/tsconfig.json
index a273b0cf..f199ca8f 100644
--- a/frontend/tsconfig.json
+++ b/frontend/tsconfig.json
@@ -18,7 +18,7 @@
"resolveJsonModule": true,
"isolatedModules": true,
"noEmit": true,
- "jsx": "react-jsx"
+ "jsx": "preserve"
},
"include": [
"src"
diff --git a/generate_bazelrc b/generate_bazelrc
deleted file mode 100755
index 3ca67dc0..00000000
--- a/generate_bazelrc
+++ /dev/null
@@ -1,80 +0,0 @@
-#!/usr/bin/env python3
-import os
-import subprocess
-from sys import platform
-
-ROOT_DIR = os.path.dirname(os.path.abspath(__file__))
-OUT_PATH = os.path.join(ROOT_DIR, ".bazelrc")
-
-
-def run_cmd(cmd):
- try:
- output = subprocess.check_output(
- cmd.split(" "), stderr=subprocess.STDOUT
- ).decode()
- except subprocess.CalledProcessError as e:
- output = e.output.decode()
- raise RuntimeError(output)
- return output.rstrip()
-
-
-def main():
- with open(OUT_PATH, "w") as f:
- # TODO: add ubsan + msan builds also
- f.write(
- """
-build --cxxopt="-std=c++17"
-build --cxxopt="-Wall"
-build --cxxopt="-fopenmp"
-build --linkopt -fopenmp
-
-# ASAN build
-# TODO: add ubsan + msan builds also
-build:asan --strip=never
-build:asan --copt -fsanitize=address
-build:asan --copt -DADDRESS_SANITIZER
-build:asan --copt -O1
-build:asan --copt -g
-build:asan --copt -fno-omit-frame-pointer
-build:asan --linkopt -fsanitize=address
-"""
- )
-
- # MacOS
- if platform == "darwin":
- # get canonical brew path
- conda_prefix = os.environ["CONDA_PREFIX"]
- conda_bin = os.path.join(conda_prefix, "bin")
- conda_inc = os.path.join(conda_prefix, "include")
- conda_lib = os.path.join(conda_prefix, "lib")
-
- # get canonical omp path
- sdk_path = run_cmd("xcrun --sdk macosx --show-sdk-path")
- f.write(
- f"""
-# Use clang from conda-forge
-build --action_env=CC={conda_bin}/clang
-build --action_env=CXX={conda_bin}/clang++
-build --action_env=BAZEL_CXXOPTS=-isystem{conda_inc}
-build --action_env=BAZEL_LINKOPTS=-L{conda_lib}:-Wl,-rpath,{conda_lib}
-build --action_env=SDKROOT={sdk_path}
-# Tell Bazel not to use the full Xcode toolchain on Mac OS
-build --repo_env=BAZEL_USE_CPP_ONLY_TOOLCHAIN=1"""
- )
- else:
- # Linux
- f.write(
- """
-# Linux GCC
-build:gcc --action_env=CC=gcc
-build:gcc --action_env=CXX=g++
-
-# Linux Clang (default)
-build --action_env=CC=clang
-build --action_env=CXX=clang++
-"""
- )
-
-
-if __name__ == "__main__":
- main()
diff --git a/imprint/.gitignore b/imprint/.gitignore
deleted file mode 100644
index 6709bcd8..00000000
--- a/imprint/.gitignore
+++ /dev/null
@@ -1,2 +0,0 @@
-build/
-third_party/
diff --git a/imprint/BUILD.bazel b/imprint/BUILD.bazel
deleted file mode 100644
index 8f782d86..00000000
--- a/imprint/BUILD.bazel
+++ /dev/null
@@ -1,16 +0,0 @@
-cc_library(
- name = "imprint",
- hdrs = glob(["include/**"]),
- defines = [
- # force Eigen to not use openmp to parallelize
- # we will use openmp to divide up simulation jobs
- # so there is no room for Eigen to further parallelize
- "EIGEN_DONT_PARALLELIZE",
- ],
- includes = ["include"],
- visibility = ["//visibility:public"],
- deps = [
- "@com_github_scipy_boost//:boost",
- "@eigen",
- ],
-)
diff --git a/imprint/CMakeLists.txt b/imprint/CMakeLists.txt
deleted file mode 100644
index 521dd736..00000000
--- a/imprint/CMakeLists.txt
+++ /dev/null
@@ -1,117 +0,0 @@
-cmake_minimum_required(VERSION 3.7)
-
-project("imprint" VERSION 1.0.0
- DESCRIPTION "A bed of simulation tools.")
-
-option(IMPRINT_ENABLE_TEST "Enable unit tests to be built." ON)
-option(IMPRINT_ENABLE_EXAMPLE "Enable examples to be built." OFF)
-option(IMPRINT_ENABLE_BENCHMARK "Enable benchmarks to be built." OFF)
-option(IMPRINT_ENABLE_COVERAGE "Build glmnetpp with coverage" OFF)
-
-# Stoopid hack on windows
-if (WIN32)
- SET(CMAKE_FIND_LIBRARY_PREFIXES "")
- SET(CMAKE_FIND_LIBRARY_SUFFIXES ".lib" ".dll")
-endif()
-
-# Dependency on Eigen
-find_package(Eigen3 3.4 CONFIG REQUIRED
- HINTS ${CMAKE_CURRENT_SOURCE_DIR}/third_party/eigen-3.4.0/build/share/eigen3)
-message(STATUS "Eigen3 found at ${EIGEN3_INCLUDE_DIR}")
-
-# Set include dirs
-set(IMPRINT_INCLUDEDIR "${${PROJECT_NAME}_SOURCE_DIR}/include")
-set(IMPRINT_SOURCEDIR "${${PROJECT_NAME}_SOURCE_DIR}/src")
-
-# Add this library as interface (header-only)
-add_library(${PROJECT_NAME} INTERFACE)
-
-target_include_directories(${PROJECT_NAME} SYSTEM INTERFACE
- $
- $)
-
-# Set C++17 standard for project target
-target_compile_features(${PROJECT_NAME} INTERFACE cxx_std_17)
-
-# Set install destinations
-install(TARGETS ${PROJECT_NAME}
- EXPORT ${PROJECT_NAME}_Targets
- ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR}
- LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR}
- RUNTIME DESTINATION ${CMAKE_INSTALL_BINDIR})
-
-# Create GlmnetppConfigVersion.cmake which contains current project version
-# This is supposed to help with (major) version compatibility.
-include(CMakePackageConfigHelpers)
-write_basic_package_version_file("${PROJECT_NAME}ConfigVersion.cmake"
- VERSION ${PROJECT_VERSION}
- COMPATIBILITY SameMajorVersion)
-configure_package_config_file(
- "${PROJECT_SOURCE_DIR}/cmake/${PROJECT_NAME}Config.cmake.in"
- "${PROJECT_BINARY_DIR}/${PROJECT_NAME}Config.cmake"
- INSTALL_DESTINATION
- ${CMAKE_INSTALL_PREFIX}/${CMAKE_INSTALL_DATAROOTDIR}/${PROJECT_NAME}/cmake)
-
-install(EXPORT ${PROJECT_NAME}_Targets
- FILE ${PROJECT_NAME}Targets.cmake
- NAMESPACE ${PROJECT_NAME}::
- DESTINATION ${CMAKE_INSTALL_PREFIX}/${CMAKE_INSTALL_DATAROOTDIR}/${PROJECT_NAME}/cmake)
-
-install(FILES
- "${PROJECT_BINARY_DIR}/${PROJECT_NAME}Config.cmake"
- "${PROJECT_BINARY_DIR}/${PROJECT_NAME}ConfigVersion.cmake"
- DESTINATION ${CMAKE_INSTALL_PREFIX}/${CMAKE_INSTALL_DATAROOTDIR}/${PROJECT_NAME}/cmake)
-
-install(DIRECTORY ${PROJECT_SOURCE_DIR}/include DESTINATION ${CMAKE_INSTALL_PREFIX})
-
-# Automate the choosing of config
-# if CMAKE_BUILD_TYPE not defined
-if (NOT CMAKE_BUILD_TYPE)
- # if binary directory ends with "release", use release mode
- if (${PROJECT_BINARY_DIR} MATCHES "release$")
- set(CMAKE_BUILD_TYPE RELEASE)
- # otherwise, use debug mode
- else()
- set(CMAKE_BUILD_TYPE DEBUG)
- endif()
-endif()
-message(STATUS "Compiling in ${CMAKE_BUILD_TYPE} mode")
-
-# Find pthread
-if (NOT DEFINED IMPRINT_HAS_PTHREAD)
- find_package(Threads REQUIRED)
- if (CMAKE_USE_PTHREADS_INIT)
- set(IMPRINT_HAS_PTHREAD ON)
- endif()
- if (DEFINED IMPRINT_HAS_PTHREAD)
- set(IMPRINT_HAS_PTHREAD_MACRO "-DIMPRINT_HAS_PTHREAD")
- endif()
-endif()
-
-# Test subdirectory
-if (IMPRINT_ENABLE_TEST)
- # This will perform memcheck
- include(CTest)
- enable_testing()
-
- # Find googletest
- find_package(GTest 1.11 CONFIG REQUIRED)
-
- # add test subdirectory
- add_subdirectory(${PROJECT_SOURCE_DIR}/test ${PROJECT_BINARY_DIR}/test)
-endif()
-
-# Example subdirectory
-if (IMPRINT_ENABLE_EXAMPLE)
- # add example subdirectory
- add_subdirectory(${PROJECT_SOURCE_DIR}/example ${PROJECT_BINARY_DIR}/example)
-endif()
-
-# Benchmark subdirectory
-if (IMPRINT_ENABLE_BENCHMARK)
- find_package(benchmark REQUIRED
- HINTS ${CMAKE_CURRENT_SOURCE_DIR}/../../benchmark/build)
-
- # add benchmark subdirectory
- add_subdirectory(${PROJECT_SOURCE_DIR}/benchmark ${PROJECT_BINARY_DIR}/benchmark)
-endif()
diff --git a/imprint/README.md b/imprint/README.md
deleted file mode 100644
index 29d61837..00000000
--- a/imprint/README.md
+++ /dev/null
@@ -1,62 +0,0 @@
-# Imprint C++ Core Engine
-
-## Overview
-
-The Imprint C++ core engine, `imprint`, implements the core components of the
-system.
-
-## Dependencies
-
-If you have set up a conda environment following the instructions in the main repo README, you should already have a C++ toolchain installed along with Bazel. If not, we require a C++ toolchain that supports C++-17 and [OpenMP](https://www.openmp.org/) and an installation of [Bazel](https://bazel.build/)
-
-Suggested compilers:
-- [GCC >= 9.3.0](https://gcc.gnu.org/)
-- [Clang >= 11.0.0](https://clang.llvm.org/)
-
-## Build
-
-__Note: `CMake` build has been deprecated and is not maintained.__
-
-__Note: On Linux, it's best to specify whether you want to use `clang` or `gcc`.
-Add the appropriate flag to each `bazel` call below:
-```
-# For gcc
-# For clang
-bazel ... --config=gcc
-bazel ... --config=clang
-```
-
-__To build `imprint`__:
-```
-bazel build //imprint:imprint
-```
-Note that `imprint` is a header-only library,
-so this will simply collect all the headers and register its dependencies.
-For release mode, add the flag `-c opt` after `build`.
-For debug mode, add the flag `-c dbg` after `build`.
-
-__To run all tests__:
-```
-bazel test -c dbg //imprint/test/...
-```
-
-__To run a particular test__:
-```
-bazel test -c dbg //imprint/test:name-of-test
-```
-where `name-of-test` is the same name as the subdirectory in `test/`
-besides `testutil`.
-
-__To run the benchmarks__:
-```
-bazel run -c opt //imprint/benchmark:name-of-benchmark
-```
-where `name-of-benchmark` is the same name of
-the benchmark `.cpp` file in the `benchmark/` folder.
-
-## Supported Models
-
-| Model | Description |
-| ----- | ----------- |
-| Binomial Control + k Treatment | Phase II/III trial with `k+1` total number of arms (1 control, k treatments) and each patient modeled as a `Bernoulli(p_i)` where `p_i` is the null probability of response for arm `i`. Phase II makes a selection of the treatment arm with most number of responses and Phase III constructs the [unpaired z-test](https://en.wikipedia.org/wiki/Paired_difference_test#Power_of_the_paired_Z-test) between the selected and control arms. |
-| Exponential Control + k Treatment | Phase III trial with `k+1` total number of arms (1 control, k treatments) and each patient modeled as an `Exponential(lambda_i)` where `lambda_i` is the hazard for arm `i`. Currently, it only supports 1 treatment arm. Phase III makes a selection of the treatment arm with most number of responses and constructs the [logrank test](https://en.wikipedia.org/wiki/Logrank_test) between the treatment and control arms. |
diff --git a/imprint/__init__.py b/imprint/__init__.py
new file mode 100644
index 00000000..9b3684b0
--- /dev/null
+++ b/imprint/__init__.py
@@ -0,0 +1,9 @@
+from imprint.batching import batch
+from imprint.batching import batch_all
+from imprint.driver import calibrate
+from imprint.driver import validate
+from imprint.grid import cartesian_grid
+from imprint.grid import Grid
+from imprint.grid import hypo
+from imprint.grid import init_grid
+from imprint.nb_util import setup_nb
diff --git a/imprint/batching.py b/imprint/batching.py
new file mode 100644
index 00000000..be635beb
--- /dev/null
+++ b/imprint/batching.py
@@ -0,0 +1,218 @@
+import jax.numpy as jnp
+import numpy as np
+
+
+def _pad_arg(a, axis, n_pad: int, module):
+ """
+ Pads an array:
+ - along the specified axis.
+ - with the values at index 0
+ - by n_pad elements.
+ - using the library "module" (either jnp or np).
+
+ Padding with the values at index 0 avoids problems with using a placeholder
+ value like 0 in situations where the placeholder value would be invalid.
+ """
+ pad_element = module.take(a, indices=0, axis=axis)
+ pad_element = module.expand_dims(pad_element, axis=axis)
+ new_shape = tuple(a.shape[i] if i != axis else n_pad for i in range(a.ndim))
+ return module.concatenate((a, module.full(new_shape, pad_element)), axis=axis)
+
+
+def _create_batched_args(args, in_axes, start, end, n_pad=None):
+ """
+ Subsets and pads the arguments as specified in in_axes.
+ """
+
+ def arg_take_transform(arg, start, end, axis):
+ # It's very important to check if arg is a jax array or numpy because
+ # we don't want to copy arrays back and forth from GPU to CPU!
+ is_jax = isinstance(arg, jnp.DeviceArray)
+ module = jnp if is_jax else np
+ slc = [slice(None)] * len(arg.shape)
+ slc[axis] = slice(start, end)
+ arg_take = arg[tuple(slc)]
+ return (
+ _pad_arg(arg_take, axis, n_pad, module) if n_pad is not None else arg_take
+ )
+
+ return [
+ arg_take_transform(arg, start, end, axis) if axis is not None else arg
+ for arg, axis in zip(args, in_axes)
+ ]
+
+
+def batch_yield(f, batch_size: int, in_axes):
+ """
+ A generator that yields batches of output from the function f.
+
+ Args:
+ f: The function to be batched.
+ batch_size: The batch size.
+ in_axes: For each argument, the axis along which to batch. If None, the
+ argument is not batched.
+ """
+
+ def internal(*args):
+ dims = np.array(
+ [arg.shape[axis] for arg, axis in zip(args, in_axes) if axis is not None]
+ )
+ if len(dims) <= 0:
+ raise ValueError(
+ "f must take at least one argument "
+ "whose corresponding in_axes is not None."
+ )
+
+ if len(args) != len(in_axes):
+ raise ValueError(
+ "The number of arguments must match the number of in_axes."
+ )
+
+ dims_all_equal = np.sum(dims != dims[0]) == 0
+ if not dims_all_equal:
+ raise ValueError(
+ "All batched arguments must have the same dimension "
+ "along their corresopnding in_axes."
+ )
+
+ dim = dims[0]
+
+ # NOTE: i don't think we should shrink the batch size because that'll
+ # incur extra JIT overhead when a user calls with lots of different
+ # small sizes. but we could make this a configurable behavior.
+ # batch_size_new = min(batch_size, dim)
+ n_full_batches = dim // batch_size
+ remainder = dim % batch_size
+ n_pad = batch_size - remainder
+ pad_last = remainder > 0
+ start = 0
+ end = batch_size
+
+ for _ in range(n_full_batches):
+ batched_args = _create_batched_args(
+ args=args,
+ in_axes=in_axes,
+ start=start,
+ end=end,
+ )
+ yield (f(*batched_args), 0)
+ start += batch_size
+ end += batch_size
+
+ if pad_last:
+ batched_args = _create_batched_args(
+ args=args,
+ in_axes=in_axes,
+ start=start,
+ end=dim,
+ n_pad=n_pad,
+ )
+ yield (f(*batched_args), n_pad)
+
+ return internal
+
+
+def batch_all(f, batch_size: int, in_axes):
+ """
+ A function wrapper that batches calls to f.
+
+ Args:
+ f: Function to be batched.
+ batch_size: The batch size.
+ in_axes: For each argument, the axis along which to batch. If None, the
+ argument is not batched.
+
+ Returns:
+ The batched results.
+ """
+ f_batch = batch_yield(f, batch_size, in_axes)
+
+ def internal(*args):
+ outs = tuple(out for out in f_batch(*args))
+ return tuple(out[0] for out in outs), outs[-1][-1]
+
+ return internal
+
+
+def batch(f, batch_size: int, in_axes, out_axes=None):
+ """
+ Batch a function call and concatenate the output.
+
+ The API is intended to be similar to jax.vmap.
+ https://jax.readthedocs.io/en/latest/_modules/jax/_src/api.html#vmap
+
+ If the function has a single output, the output is concatenated along the
+ specified axis. If the function has multiple outputs, each output is
+ concatenated along the corresponding axis.
+
+ NOTE: In performance critical situations, it might be better to use batch_all
+ and decide for yourself how to concatenate or process the output.
+
+ Args:
+ f: Function to be batched.
+ batch_size: The batch size.
+ in_axes: For each argument, the axis along which to batch. If None, the
+ argument is not batched.
+ out_axes: The axis along which to concatenate function outputs.
+ Defaults to None which will concatenate along the first axis.
+
+ Returns:
+ A concatenated array or a tuple of concatenated arrays.
+ """
+ f_batch_all = batch_all(f, batch_size, in_axes)
+
+ def internal(*args):
+ outs, n_pad = f_batch_all(*args)
+
+ return_first = False
+ if isinstance(outs[0], np.ndarray) or isinstance(outs[0], jnp.DeviceArray):
+ return_first = True
+ outs = [[o] for o in outs]
+ internal_out_axes = (0,) if out_axes is None else out_axes
+ else:
+ internal_out_axes = (
+ out_axes
+ if out_axes is not None
+ else tuple(0 for _ in range(len(outs[0])))
+ )
+
+ # We should concatenate using the same library as the function output
+ # to avoid accidental GPU to CPU copies.
+ is_jax = isinstance(outs[0][0], jnp.DeviceArray)
+ module = jnp if is_jax else np
+
+ def entry(i, j):
+ arr = outs[j][i]
+
+ # if we're concatenating on an axis that doesn't exist, we need to
+ # create that axis.
+ if j == len(outs) - 1 and n_pad > 0:
+ axis = internal_out_axes[i]
+ slc = [slice(None)] * arr.ndim
+ # N = outs[-1][i].shape[axis]
+ # slc[axis] = slice(0, N - n_pad)
+ slc[axis] = slice(0, batch_size - n_pad)
+ arr = arr[tuple(slc)]
+
+ axis = internal_out_axes[i]
+ while axis >= arr.ndim:
+ arr = arr[..., None]
+
+ return arr
+
+ if len(outs) == 1:
+ return_vals = [entry(i, 0) for i in range(len(outs[0]))]
+ else:
+ return_vals = [
+ module.concatenate(
+ [entry(i, j) for j in range(len(outs))],
+ axis=internal_out_axes[i],
+ )
+ for i in range(len(outs[0]))
+ ]
+ if return_first:
+ return return_vals[0]
+ else:
+ return return_vals
+
+ return internal
diff --git a/imprint/benchmark/BUILD.bazel b/imprint/benchmark/BUILD.bazel
deleted file mode 100644
index b4b6b49f..00000000
--- a/imprint/benchmark/BUILD.bazel
+++ /dev/null
@@ -1,14 +0,0 @@
-[cc_binary(
- name = type_,
- srcs = ["{}.cpp".format(type_)],
- # See GH-64
- # malloc = "@com_google_tcmalloc//tcmalloc",
- deps = [
- "//imprint",
- "@com_github_google_benchmark//:benchmark_main",
- ],
-) for type_ in [
- "direct_bayes",
- "imprint_bound",
- "simple_selection_accum",
-]]
diff --git a/imprint/benchmark/CMakeLists.txt b/imprint/benchmark/CMakeLists.txt
deleted file mode 100644
index f326506e..00000000
--- a/imprint/benchmark/CMakeLists.txt
+++ /dev/null
@@ -1,15 +0,0 @@
-# All macro tests
-set(
- BENCHMARKS
- bench_binomial_2_arm
- binomial_control_k_treatment_tune
-)
-
-foreach( benchmark ${BENCHMARKS} )
- add_executable(${benchmark} ${CMAKE_CURRENT_SOURCE_DIR}/${benchmark}.cpp)
- target_compile_options(${benchmark} PRIVATE -std=c++17)
- target_link_libraries(${benchmark}
- ${PROJECT_NAME}
- benchmark::benchmark_main
- Eigen3::Eigen)
-endforeach()
diff --git a/imprint/benchmark/direct_bayes.cpp b/imprint/benchmark/direct_bayes.cpp
deleted file mode 100644
index 76e8b004..00000000
--- a/imprint/benchmark/direct_bayes.cpp
+++ /dev/null
@@ -1,115 +0,0 @@
-#include
-
-#include
-#include
-#include
-#include
-#include
-#include
-#include
-#include
-#include
-#include
-#include
-
-namespace imprint {
-namespace {
-
-using gen_t = std::mt19937;
-using value_t = double;
-using uint_t = uint32_t;
-using tile_t = grid::Tile;
-using gr_t = grid::GridRange;
-using model_t = model::binomial::DirectBayes;
-using sgs_t =
- typename model_t::template sim_global_state_t;
-using ss_t = typename sgs_t::sim_state_t;
-using vec_t = colvec_type;
-using acc_t = bound::TypeIErrorAccum;
-
-const Eigen::Vector critical_values{0.95};
-const value_t alpha_prior = 0.0005;
-const value_t beta_prior = 0.000005;
-const value_t mu_sig_sq = 0.1;
-const int n_integration_points = 16;
-const int n_arm_size = 27;
-const int n_arms = 4;
-const int n_thetas = 64;
-const size_t sim_size = 60 * 10;
-const value_t efficacy_threshold = 0.3;
-const auto [quadrature_points, weighted_density_logspace] =
- sgs_t::get_quadrature(alpha_prior, beta_prior, n_integration_points,
- n_arm_size);
-
-vec_t get_efficacy_thresholds() {
- Eigen::Vector efficacy_thresholds(n_arms);
- efficacy_thresholds.fill(efficacy_threshold);
- return efficacy_thresholds;
-}
-
-struct MockHyperPlane : grid::HyperPlane {
- using base_t = HyperPlane;
- using base_t::base_t;
-};
-
-static void BM_get_posterior_exceedance_probs(benchmark::State& state) {
- const auto phat = Eigen::Vector{28, 14, 33, 36}.array() / 50;
- for (auto _ : state) {
- const auto got = sgs_t::get_posterior_exceedance_probs(
- phat, quadrature_points, weighted_density_logspace,
- get_efficacy_thresholds(), n_arm_size, mu_sig_sq);
- }
-}
-
-BENCHMARK(BM_get_posterior_exceedance_probs);
-
-static void BM_rej_len(benchmark::State& state) {
- using hp_t = MockHyperPlane;
- auto theta_1d = grid::Gridder::make_grid(n_thetas, -1., 0.);
- auto radius = grid::Gridder::radius(n_thetas, -1., 0.);
-
- colvec_type normal(n_arms);
- std::vector hps;
- for (int i = 0; i < n_arms; ++i) {
- normal.setZero();
- normal(i) = -1;
- hps.emplace_back(normal, logit(efficacy_threshold));
- }
-
- // populate theta as the cartesian product of theta_1d
- gr_t grid_range(n_arms, ipow(n_thetas, n_arms));
- auto& thetas = grid_range.thetas();
- dAryInt bits(n_thetas, n_arms);
- for (size_t j = 0; j < grid_range.n_gridpts(); ++j) {
- for (size_t i = 0; i < n_arms; ++i) {
- thetas(i, j) = theta_1d[bits()[i]];
- }
- ++bits;
- }
-
- // populate radii as fixed radius
- grid_range.radii().array() = radius;
-
- // create tile information
- grid_range.create_tiles(hps);
- grid_range.prune();
-
- colvec_type efficacy_thresholds(n_arms);
- efficacy_thresholds.fill(efficacy_threshold);
- size_t n_threads = std::thread::hardware_concurrency();
- model_t model(n_arms, n_arm_size, critical_values, efficacy_thresholds);
-
- auto sgs =
- model.make_sim_global_state(grid_range);
- size_t seed = 3214;
- colvec_type rej_len(grid_range.n_tiles());
- acc_t acc_os(critical_values.size(), grid_range.n_tiles(), n_arms);
- for (auto _ : state) {
- driver::accumulate(sgs, grid_range, acc_os, sim_size, seed, n_threads);
- }
-}
-
-BENCHMARK(BM_rej_len);
-
-} // namespace
-} // namespace imprint
diff --git a/imprint/benchmark/imprint_bound.cpp b/imprint/benchmark/imprint_bound.cpp
deleted file mode 100644
index 7208b4c0..00000000
--- a/imprint/benchmark/imprint_bound.cpp
+++ /dev/null
@@ -1,56 +0,0 @@
-#include
-
-#include
-#include
-#include
-#include
-#include
-#include
-#include
-
-namespace imprint {
-namespace {
-
-static void BM_imprint_bound(benchmark::State& state) {
- using namespace model::binomial;
- using value_t = double;
- using uint_t = uint32_t;
- using tile_t = grid::Tile;
- using gr_t = grid::GridRange;
- using hp_t = grid::HyperPlane;
- using kbs_t = ImprintBoundStateFixedNDefault;
- using kb_t = bound::TypeIErrorBound;
- using acc_t = bound::TypeIErrorAccum;
-
- size_t n_models = 1;
- size_t n_tiles = 180000;
- size_t n_params = 3;
- size_t n_arm_samples = 21; // arbitrary
- value_t alpha = 0.025;
- value_t delta = 0.025;
-
- std::vector hps;
-
- gr_t gr(n_params, n_tiles);
- gr.create_tiles(hps);
-
- acc_t acc_o(n_models, n_tiles, n_params);
-
- auto& typeI_sum = acc_o.typeI_sum__();
- typeI_sum.setRandom();
- typeI_sum /= typeI_sum.maxCoeff() / alpha;
- auto& score_sum = acc_o.score_sum__();
- score_sum.setRandom();
-
- kbs_t kbs(n_arm_samples, gr);
- kb_t kb;
-
- for (auto _ : state) {
- kb.create(kbs, acc_o, gr, delta);
- }
-}
-
-BENCHMARK(BM_imprint_bound);
-
-} // namespace
-} // namespace imprint
diff --git a/imprint/benchmark/simple_selection_accum.cpp b/imprint/benchmark/simple_selection_accum.cpp
deleted file mode 100644
index e3366b5f..00000000
--- a/imprint/benchmark/simple_selection_accum.cpp
+++ /dev/null
@@ -1,86 +0,0 @@
-#include
-#include
-#include
-#include
-#include
-#include
-#include
-#include
-
-#include "benchmark/benchmark.h"
-
-namespace imprint {
-
-struct binomial_fixture : benchmark::Fixture {
- using gen_t = std::mt19937;
- using value_t = double;
- using uint_t = uint32_t;
- using grid_t = grid::Gridder;
- using tile_t = grid::Tile;
- using grid_range_t = grid::GridRange;
- using hp_t = grid::HyperPlane;
- using model_t = model::binomial::SimpleSelection;
- using acc_t = bound::TypeIErrorAccum;
-
- size_t n_thetas_1d = 64;
- double lower = -0.5;
- double upper = 0.5;
- size_t n_sim = 1e5;
- double alpha = 0.025;
- double delta = 0.025;
- size_t grid_dim = 3;
- size_t n_samples = 250;
- size_t ph2_size = 50;
- double thresh = 1.96;
- size_t n_threads = std::thread::hardware_concurrency();
-};
-
-BENCHMARK_DEFINE_F(binomial_fixture, bench_fit)(benchmark::State& state) {
- size_t grid_radius = grid_t::radius(n_thetas_1d, lower, upper);
-
- colvec_type theta_1d;
- Eigen::VectorXd thresholds;
-
- // initialize threshold
- thresholds.resize(1);
- thresholds << thresh;
-
- // define hyperplanes
- std::vector hps;
- for (size_t k = 1; k < grid_dim; ++k) {
- colvec_type normal(grid_dim);
- normal.setZero();
- normal[0] = 1;
- normal[k] = -1;
- hps.emplace_back(normal, 0);
- }
-
- // create grid
- theta_1d =
- grid_t::make_grid(n_thetas_1d, lower, upper).template cast();
- dAryInt bits(n_thetas_1d, grid_dim);
- grid_range_t grid_range(grid_dim, bits.n_unique());
- for (size_t j = 0; j < bits.n_unique(); ++j, ++bits) {
- for (size_t i = 0; i < grid_dim; ++i) {
- grid_range.thetas()(i, j) = theta_1d[bits()(i)];
- }
- }
- grid_range.radii().array() = grid_radius;
- grid_range.sim_sizes().array() = n_sim;
-
- grid_range.create_tiles(hps);
- grid_range.prune();
-
- model_t model(grid_dim, n_samples, ph2_size, thresholds);
- auto sgs = model.make_sim_global_state(grid_range);
-
- acc_t acc_o(model.n_models(), grid_range.n_tiles(), grid_range.n_params());
-
- for (auto _ : state) {
- driver::accumulate(sgs, grid_range, acc_o, n_sim, 0, n_threads);
- }
-}
-
-BENCHMARK_REGISTER_F(binomial_fixture, bench_fit);
-
-} // namespace imprint
diff --git a/imprint/bound/binomial.py b/imprint/bound/binomial.py
new file mode 100644
index 00000000..755b7ccf
--- /dev/null
+++ b/imprint/bound/binomial.py
@@ -0,0 +1,351 @@
+import jax
+import jax.numpy as jnp
+
+
+def logistic(t):
+ """
+ Numerically stable implementation of log(1 + e^t).
+ """
+ return jnp.maximum(t, 0) + jnp.log(1 + jnp.exp(-jnp.abs(t)))
+
+
+def logistic_secant(t, v, q, b):
+ """
+ Numerically stable implementation of the secant of logistic defined by:
+ (logistic(t + q * v) - logistic(b)) / q
+ defined for all t, v in R and q > 0.
+ It is only numerically stable if t, b are not too large in magnitude
+ and q is sufficiently away from 0.
+ """
+ t_div_q = t / q
+ ls_1 = jnp.maximum(t_div_q + v, 0) - jnp.maximum(b, 0) / q
+ ls_2 = jnp.log(1 + jnp.exp(-jnp.abs(t + q * v)))
+ ls_2 = ls_2 - jnp.log(1 + jnp.exp(-jnp.abs(b)))
+ ls_2 = ls_2 / q
+ return ls_1 + ls_2
+
+
+def A(n, t):
+ """
+ Log-partition function of a Bernoulli family with d-arms
+ where arm i has n Bernoullis with logit t_i.
+ """
+ return n * jnp.sum(logistic(t))
+
+
+def A_secant(n, t, v, q, b):
+ """
+ Numerically stable implementation of the secant of A:
+ (A(t + q * v) - A(b)) / q
+ """
+ return n * jnp.sum(logistic_secant(t, v, q, b))
+
+
+def dA(n, t):
+ """
+ Gradient of the log-partition function A.
+ """
+ return n * jax.nn.sigmoid(t)
+
+
+def _simple_bisection(f, m, M, tol):
+ def _cond_fun(args):
+ m, M = args
+ return (M - m) / M > tol
+
+ def _body_fun(args):
+ m, M = args
+ x = jnp.linspace(m, M, 4)
+ y = f(x)
+ i_star = jnp.argmin(y)
+ new_min = jnp.where(
+ i_star <= 1,
+ m,
+ x[i_star - 1],
+ )
+ new_max = jnp.where(
+ i_star <= 1,
+ x[i_star + 1],
+ M,
+ )
+ return (
+ new_min,
+ new_max,
+ )
+
+ _init_val = (m, M)
+ m, M = jax.lax.while_loop(
+ _cond_fun,
+ _body_fun,
+ _init_val,
+ )
+ return (M + m) / 2.0
+
+
+class BaseTileQCPSolver:
+ def __init__(self, n, m=1, M=1e7, tol=1e-5):
+ self.n = n
+ self.min = m
+ self.max = M
+ self.tol = tol
+
+
+class TileForwardQCPSolver(BaseTileQCPSolver):
+ r"""
+ Solves the following strictly quasi-convex optimization problem:
+ minimize_q max_{v \in S} L_v(q)
+ subject to q >= 1
+ where
+ L_v(q) = (psi(theta_0, v, q) - log(a)) / q - psi(theta_0, v, 1)
+ """
+
+ def obj_v(self, theta_0, v, q, loga):
+ secq = A_secant(
+ self.n,
+ theta_0,
+ v,
+ q,
+ theta_0,
+ )
+ sec1 = A_secant(
+ self.n,
+ theta_0,
+ v,
+ 1,
+ theta_0,
+ )
+ return secq - loga / q - sec1
+
+ def obj(self, theta_0, vs, q, loga):
+ _obj_each_vmap = jax.vmap(self.obj_v, in_axes=(None, 0, None, None))
+ return jnp.max(_obj_each_vmap(theta_0, vs, q, loga))
+
+ def obj_vmap(self, theta_0, vs, qs, loga):
+ return jax.vmap(
+ self.obj,
+ in_axes=(None, None, 0, None),
+ )(theta_0, vs, qs, loga)
+
+ def solve(self, theta_0, vs, a):
+ loga = jnp.log(a)
+ return jax.lax.cond(
+ loga < -1e10,
+ lambda: jnp.inf,
+ lambda: _simple_bisection(
+ lambda x: self.obj_vmap(theta_0, vs, x, loga),
+ self.min,
+ self.max,
+ self.tol,
+ ),
+ )
+
+
+class TileBackwardQCPSolver(BaseTileQCPSolver):
+ r"""
+ Solves the following strictly quasi-convex optimization problem:
+ minimize_q max_{v \in S} L_v(q)
+ subject to q >= 1
+ where
+ L_v(q) = (q/(q-1)) * (psi(theta_0, v, q) / q - psi(theta_0, v, 1) - log(a))
+ """
+
+ def obj_v(self, theta_0, v, q):
+ secq = A_secant(
+ self.n,
+ theta_0,
+ v,
+ q,
+ theta_0,
+ )
+ sec1 = A_secant(
+ self.n,
+ theta_0,
+ v,
+ 1,
+ theta_0,
+ )
+ return secq - sec1
+
+ def obj(self, theta_0, vs, q, loga):
+ p = 1.0 / (1.0 - 1.0 / q)
+ _obj_each_vmap = jax.vmap(self.obj_v, in_axes=(None, 0, None))
+ return p * (jnp.max(_obj_each_vmap(theta_0, vs, q)) - loga)
+
+ def obj_vmap(self, theta_0, vs, qs, loga):
+ return jax.vmap(
+ self.obj,
+ in_axes=(None, None, 0, None),
+ )(theta_0, vs, qs, loga)
+
+ def solve(self, theta_0, vs, a):
+ loga = jnp.log(a)
+ return jax.lax.cond(
+ loga < -1e10,
+ lambda: jnp.inf,
+ lambda: _simple_bisection(
+ lambda x: self.obj_vmap(theta_0, vs, x, loga),
+ self.min,
+ self.max,
+ self.tol,
+ ),
+ )
+
+
+def tilt_bound_fwd(
+ q,
+ n,
+ theta_0,
+ v,
+ f0,
+):
+ """
+ Computes the forward q-Holder bound given by:
+ f0 * exp[L(q) - (A(theta_0 + v) - A(theta_0))]
+ for fixed f0, n, theta_0, v,
+ where L, A are as given in ForwardQCPSolver.
+
+ Parameters:
+ -----------
+ q: q parameter.
+ n: scalar Binomial size parameter.
+ theta_0: d-array pivot point.
+ v: d-array displacement vector.
+ f0: probability value at theta_0.
+ """
+ expo = A_secant(n, theta_0, v, q, theta_0)
+ expo = expo - A_secant(n, theta_0, v, 1, theta_0)
+ return f0 ** (1 - 1 / q) * jnp.exp(expo)
+
+
+def tilt_bound_fwd_tile(
+ q,
+ n,
+ theta_0,
+ vs,
+ f0,
+):
+ """
+ Computes the forward q-Holder bound given by:
+ f0 * max_{v in vs} exp[L(q) - (A(theta_0 + v) - A(theta_0))]
+ for fixed f0, n, theta_0, vs,
+ where L, A are as given in ForwardQCPSolver.
+
+ Parameters:
+ -----------
+ q: q parameter.
+ n: scalar Binomial size parameter.
+ theta_0: d-array pivot point.
+ vs: (k, d)-array of displacement vectors
+ denoting the corners of a rectangle.
+ f0: probability value at theta_0.
+ """
+
+ def _expo(v):
+ expo = A_secant(n, theta_0, v, q, theta_0)
+ expo = expo - A_secant(n, theta_0, v, 1, theta_0)
+ return expo
+
+ max_expo = jnp.max(jax.vmap(_expo, in_axes=(0,))(vs))
+ return f0 ** (1 - 1 / q) * jnp.exp(max_expo)
+
+
+def tilt_bound_bwd(
+ q,
+ n,
+ theta_0,
+ v,
+ alpha,
+):
+ """
+ Computes the backward q-Holder bound given by:
+ exp(-L(q))
+ where L(q) is as given in BackwardQCPSolver.
+ The resulting value is alpha' such that
+ q_holder_bound_fwd(q, n, theta_0, v, alpha') = alpha
+
+ Parameters:
+ -----------
+ q: q parameter.
+ n: scalar Binomial size parameter.
+ theta_0: d-array pivot point.
+ v: d-array displacement from pivot point.
+ alpha: target level.
+ """
+
+ def _bound(q):
+ p = 1 / (1 - 1 / q)
+ slope_diff = A_secant(n, theta_0, v, q, theta_0)
+ slope_diff = slope_diff - A_secant(n, theta_0, v, 1, theta_0)
+ return (alpha * jnp.exp(-slope_diff)) ** p
+
+ return jax.lax.cond(
+ q <= 1,
+ lambda _: (alpha >= 1) + 0.0,
+ _bound,
+ q,
+ )
+
+
+def tilt_bound_bwd_tile(
+ q,
+ n,
+ theta_0,
+ vs,
+ alpha,
+):
+ """
+ Computes the backward q-Holder bound given by:
+ max_{v in vs} exp(-L(q))
+ where L(q) is as given in BackwardQCPSolver.
+
+ Parameters:
+ -----------
+ q: q parameter.
+ n: scalar Binomial size parameter.
+ theta_0: d-array pivot point.
+ vs: (k, d)-array displacement from pivot point.
+ These represent the corners of the rectangular tile.
+ alpha: target level.
+ """
+ p = 1 / (1 - 1 / q)
+
+ def _expo(v):
+ slope_diff = A_secant(n, theta_0, v, q, theta_0)
+ slope_diff = slope_diff - A_secant(n, theta_0, v, 1, theta_0)
+ return slope_diff
+
+ def _bound():
+ max_expo = jnp.max(jax.vmap(_expo, in_axes=(0,))(vs))
+ return (alpha * jnp.exp(-max_expo)) ** p
+
+ return jax.lax.cond(
+ q <= 1,
+ lambda: (alpha >= 1) + 0.0,
+ _bound,
+ )
+
+
+class BinomialBound:
+ @staticmethod
+ def get_backward_bound(family_params):
+ n = family_params["n"]
+ bwd_solver = TileBackwardQCPSolver(n)
+
+ def backward_bound(alpha_target, theta0, vertices):
+ v = vertices - theta0
+ q_opt = bwd_solver.solve(theta0, v, alpha_target)
+ return tilt_bound_bwd_tile(q_opt, n, theta0, v, alpha_target)
+
+ return jax.jit(jax.vmap(backward_bound, in_axes=(None, 0, 0)))
+
+ @staticmethod
+ def get_forward_bound(family_params):
+ n = family_params["n"]
+ fwd_solver = TileForwardQCPSolver(n)
+
+ def forward_bound(f0, theta0, vertices):
+ vs = vertices - theta0
+ q_opt = fwd_solver.solve(theta0, vs, f0)
+ return tilt_bound_fwd_tile(q_opt, n, theta0, vs, f0)
+
+ return jax.jit(jax.vmap(forward_bound))
diff --git a/imprint/bound/multivariate_normal.py b/imprint/bound/multivariate_normal.py
new file mode 100644
index 00000000..dbca3063
--- /dev/null
+++ b/imprint/bound/multivariate_normal.py
@@ -0,0 +1,100 @@
+import jax
+import jax.numpy as jnp
+
+
+def _quad_form(v, A):
+ return v.dot(A @ v)
+
+
+class ForwardQCPSolver:
+ """
+ Solves the minimization problem:
+ 0.5 * (q-1) * v^T cov v - log(f0) / q
+ with respect to q >= 1.
+ """
+
+ def __init__(self, cov):
+ self.cov = cov
+
+ def solve(self, v, f0):
+ logf0 = jnp.log(f0)
+ mv = _quad_form(v, self.cov)
+ q_opt = jnp.sqrt(-2 * logf0 / mv)
+ return jnp.maximum(q_opt, 1)
+
+
+class BackwardQCPSolver:
+ """
+ Solves the minimization problem:
+ 0.5 * q * v^T cov v - log(alpha) * q / (q-1)
+ with respect to q >= 1.
+ """
+
+ def __init__(self, cov):
+ self.cov = cov
+
+ def solve(self, v, alpha):
+ mv = _quad_form(v, self.cov)
+ return 1 + jnp.sqrt(-2 * jnp.log(alpha) / mv)
+
+
+class TileForwardQCPSolver:
+ """
+ Solves the minimization problem:
+ 0.5 * (q-1) * max_v v^T cov v - log(f0) / q
+ with respect to q >= 1.
+ """
+
+ def __init__(self, cov):
+ self.cov = cov
+
+ def solve(self, vs, f0):
+ logf0 = jnp.log(f0)
+ mv = jnp.max(jax.vmap(_quad_form, in_axes=(0, None))(vs, self.cov))
+ q_opt = jnp.sqrt(-2 * logf0 / mv)
+ return jnp.maximum(q_opt, 1)
+
+
+class TileBackwardQCPSolver:
+ """
+ Solves the minimization problem:
+ 0.5 * q * max_v v^T cov v - log(alpha) * q / (q-1)
+ with respect to q >= 1.
+ """
+
+ def __init__(self, cov):
+ self.cov = cov
+
+ def solve(self, vs, alpha):
+ mv = jnp.max(jax.vmap(_quad_form, in_axes=(0, None))(vs, self.cov))
+ return 1 + jnp.sqrt(-2 * jnp.log(alpha) / mv)
+
+
+def tilt_bound_fwd(q, cov, v, f0):
+ p_inv = 1 - 1 / q
+ expo = 0.5 * (q - 1) * _quad_form(v, cov)
+ return f0**p_inv * jnp.exp(expo)
+
+
+def tilt_bound_fwd_tile(q, cov, vs, f0):
+ def _compute_expo(v):
+ return 0.5 * (q - 1) * _quad_form(v, cov)
+
+ p_inv = 1 - 1 / q
+ max_expo = jnp.max(jax.vmap(_compute_expo, in_axes=(0,))(vs))
+ return f0**p_inv * jnp.exp(max_expo)
+
+
+def tilt_bound_bwd(q, cov, v, alpha):
+ p = 1 / (1 - 1 / q)
+ expo = 0.5 * (q - 1) * _quad_form(v, cov)
+ return (alpha * jnp.exp(-expo)) ** p
+
+
+def tilt_bound_bwd_tile(q, cov, vs, alpha):
+ def _compute_expo(v):
+ return 0.5 * (q - 1) * _quad_form(v, cov)
+
+ p = 1 / (1 - 1 / q)
+ max_expo = jnp.max(jax.vmap(_compute_expo, in_axes=(0,))(vs))
+ return (alpha * jnp.exp(-max_expo)) ** p
diff --git a/imprint/bound/normal.py b/imprint/bound/normal.py
new file mode 100644
index 00000000..74c61ec3
--- /dev/null
+++ b/imprint/bound/normal.py
@@ -0,0 +1,158 @@
+import jax
+import jax.numpy as jnp
+
+
+class ForwardQCPSolver:
+ """
+ Solves the minimization problem:
+ 0.5 * (q-1) * s_sq * v ** 2 - log(f0) / q
+ with respect to q >= 1.
+ """
+
+ def __init__(self, scale):
+ self.scale = scale
+
+ def solve(self, v, f0):
+ logf0 = jnp.log(f0)
+ mv_sqrt = self.scale * jnp.abs(v)
+ q_opt = jax.lax.cond(
+ mv_sqrt == 0,
+ lambda: jnp.inf,
+ lambda: jnp.sqrt(-2 * logf0) / mv_sqrt,
+ )
+ return jnp.maximum(q_opt, 1)
+
+
+class BackwardQCPSolver:
+ """
+ Solves the minimization problem:
+ 0.5 * q * s_sq * v ** 2 - log(alpha) * q / (q-1)
+ with respect to q >= 1.
+ """
+
+ def __init__(self, scale):
+ self.scale = scale
+
+ def solve(self, v, alpha):
+ mv_sqrt = self.scale * jnp.abs(v)
+ return jax.lax.cond(
+ mv_sqrt == 0,
+ lambda: jnp.inf,
+ lambda: 1 + jnp.sqrt(-2 * jnp.log(alpha)) / mv_sqrt,
+ )
+
+
+class TileForwardQCPSolver:
+ """
+ Solves the minimization problem:
+ 0.5 * (q-1) * s_sq * max_v v ** 2 - log(f0) / q
+ with respect to q >= 1.
+ """
+
+ def __init__(self, scale):
+ self.scale = scale
+
+ def solve(self, vs, f0):
+ logf0 = jnp.log(f0)
+ mv_sqrt = self.scale * jnp.max(jnp.abs(vs))
+ q_opt = jax.lax.cond(
+ mv_sqrt == 0,
+ lambda: jnp.inf,
+ lambda: jnp.sqrt(-2 * logf0) / mv_sqrt,
+ )
+ return jnp.maximum(q_opt, 1)
+
+
+class TileBackwardQCPSolver:
+ """
+ Solves the minimization problem:
+ 0.5 * q * s_sq * max_v v ** 2 - log(alpha) * q / (q-1)
+ with respect to q >= 1.
+ """
+
+ def __init__(self, scale):
+ self.scale = scale
+
+ def solve(self, vs, alpha):
+ mv_sqrt = self.scale * jnp.max(jnp.abs(vs))
+ return jax.lax.cond(
+ mv_sqrt == 0,
+ lambda: jnp.inf,
+ lambda: 1 + jnp.sqrt(-2 * jnp.log(alpha)) / mv_sqrt,
+ )
+
+
+def tilt_bound_fwd(q, scale, v, f0):
+ p_inv = 1 - 1 / q
+ expo = 0.5 * (q - 1) * (scale * v) ** 2
+ return jax.lax.cond(
+ (v == 0) | (scale == 0),
+ lambda: f0**p_inv,
+ lambda: jax.lax.cond(
+ q == jnp.inf,
+ lambda: jnp.inf,
+ lambda: f0**p_inv * jnp.exp(expo),
+ ),
+ )
+
+
+def tilt_bound_fwd_tile(q, scale, vs, f0):
+ p_inv = 1 - 1 / q
+ max_v = jnp.max(jnp.abs(vs))
+ max_expo = 0.5 * (q - 1) * (scale * max_v) ** 2
+ return jax.lax.cond(
+ (max_v == 0) | (scale == 0),
+ lambda: f0**p_inv,
+ lambda: jax.lax.cond(
+ q == jnp.inf,
+ lambda: jnp.inf,
+ lambda: f0**p_inv * jnp.exp(max_expo),
+ ),
+ )
+
+
+def tilt_bound_bwd(q, scale, v, alpha):
+ p = jax.lax.cond(q == 1, lambda _: jnp.inf, lambda q: 1 / (1 - 1 / q), q)
+ expo = jax.lax.cond(
+ (v == 0) | (scale == 0),
+ lambda: 0.0,
+ lambda: 0.5 * q * (scale * v) ** 2,
+ )
+ return alpha**p * jnp.exp(-expo)
+
+
+def tilt_bound_bwd_tile(q, scale, vs, alpha):
+ p = jax.lax.cond(q == 1, lambda _: jnp.inf, lambda q: 1 / (1 - 1 / q), q)
+ max_v = jnp.max(jnp.abs(vs))
+ max_expo = jax.lax.cond(
+ (max_v == 0) | (scale == 0),
+ lambda: 0.0,
+ lambda: 0.5 * q * (scale * max_v) ** 2,
+ )
+ return alpha**p * jnp.exp(-max_expo)
+
+
+class NormalBound:
+ @staticmethod
+ def get_backward_bound(family_params):
+ scale = family_params.get("scale", 1.0)
+ bwd_solver = TileBackwardQCPSolver(scale)
+
+ def backward_bound(alpha_target, theta0, vertices):
+ v = vertices - theta0
+ q_opt = bwd_solver.solve(v, alpha_target)
+ return tilt_bound_bwd_tile(q_opt, scale, v, alpha_target)
+
+ return jax.jit(jax.vmap(backward_bound, in_axes=(None, 0, 0)))
+
+ @staticmethod
+ def get_forward_bound(family_params):
+ scale = family_params.get("scale", 1.0)
+ fwd_solver = TileForwardQCPSolver(scale)
+
+ def forward_bound(f0, theta0, vertices):
+ vs = vertices - theta0
+ q_opt = fwd_solver.solve(vs, f0)
+ return tilt_bound_fwd_tile(q_opt, scale, vs, f0)
+
+ return jax.jit(jax.vmap(forward_bound))
diff --git a/imprint/cmake/imprintConfig.cmake.in b/imprint/cmake/imprintConfig.cmake.in
deleted file mode 100644
index 9c15f36a..00000000
--- a/imprint/cmake/imprintConfig.cmake.in
+++ /dev/null
@@ -1,4 +0,0 @@
-@PACKAGE_INIT@
-
-include("${CMAKE_CURRENT_LIST_DIR}/@PROJECT_NAME@Targets.cmake")
-check_required_components("@PROJECT_NAME@")
diff --git a/imprint/driver.py b/imprint/driver.py
new file mode 100644
index 00000000..58e2584c
--- /dev/null
+++ b/imprint/driver.py
@@ -0,0 +1,228 @@
+import copy
+
+import jax
+import jax.numpy as jnp
+import numpy as np
+import pandas as pd
+import scipy.stats
+
+from . import batching
+from . import grid
+
+
+# TODO: Need to clean up the interface from driver to the bounds.
+# - should the bound classes have staticmethods or should they be objects with
+# __init__?
+# - can we pass a single vertex array as a substitute for the many vertex case?
+def get_bound(family, family_params):
+ if family == "normal":
+ from imprint.bound.normal import NormalBound as bound_type
+ elif family == "binomial":
+ from imprint.bound.binomial import BinomialBound as bound_type
+ else:
+ raise Exception("unknown family")
+
+ return (
+ bound_type.get_forward_bound(family_params),
+ bound_type.get_backward_bound(family_params),
+ )
+
+
+def clopper_pearson(tie_sum, K, delta):
+ tie_cp_bound = scipy.stats.beta.ppf(1 - delta, tie_sum + 1, K - tie_sum)
+ # If typeI_sum == sim_sizes, scipy.stats outputs nan. Output 0 instead
+ # because there is no way to go higher than 1.0
+ return np.where(np.isnan(tie_cp_bound), 0, tie_cp_bound)
+
+
+def calc_tuning_threshold(sorted_stats, sorted_order, alpha):
+ K = sorted_stats.shape[0]
+ cv_idx = jnp.maximum(jnp.floor((K + 1) * jnp.maximum(alpha, 0)).astype(int) - 1, 0)
+ # indexing a sorted array with sorted indices results in a sorted array!!
+ return sorted_stats[sorted_order[cv_idx]]
+
+
+class Driver:
+ def __init__(self, model, *, tile_batch_size):
+ self.model = model
+ self.tile_batch_size = tile_batch_size
+ self.forward_boundv, self.backward_boundv = get_bound(
+ model.family, model.family_params if hasattr(model, "family_params") else {}
+ )
+
+ self.calibratev = jax.jit(
+ jax.vmap(
+ calc_tuning_threshold,
+ in_axes=(0, None, 0),
+ )
+ )
+
+ def _stats(self, K_df):
+ K = K_df["K"].iloc[0]
+ K_g = grid.Grid(K_df)
+ theta = K_g.get_theta()
+ # TODO: batching
+ stats = self.model.sim_batch(0, K, theta, K_g.get_null_truth())
+ return stats
+
+ def stats(self, df):
+ return df.groupby("K", group_keys=False).apply(self._stats)
+
+ def _batched_validate(self, K, theta, null_truth, lam):
+ stats = self.model.sim_batch(0, K, theta, null_truth)
+ return jnp.sum(stats < lam, axis=-1)
+
+ def _validate(self, K_df, lam, delta):
+ K = K_df["K"].iloc[0]
+ K_g = grid.Grid(K_df)
+ theta = K_g.get_theta()
+
+ tie_sum = batching.batch(
+ self._batched_validate,
+ self.tile_batch_size,
+ in_axes=(None, 0, 0, None),
+ )(K, theta, K_g.get_null_truth(), lam)
+
+ tie_cp_bound = clopper_pearson(tie_sum, K, delta)
+ theta, vertices = K_g.get_theta_and_vertices()
+ tie_bound = self.forward_boundv(tie_cp_bound, theta, vertices)
+
+ return pd.DataFrame(
+ dict(
+ tie_sum=tie_sum,
+ tie_est=tie_sum / K,
+ tie_cp_bound=tie_cp_bound,
+ tie_bound=tie_bound,
+ )
+ )
+
+ def validate(self, df, lam, *, delta=0.01):
+ # The execution trace of a driver:
+ # entry point: (validate)
+ # for each K: (_validate)
+ # for each batch of tiles: (_batched_validate)
+ # simulate
+ return (
+ df.groupby("K", group_keys=False)
+ .apply(lambda K_df: self._validate(K_df, lam, delta))
+ .reset_index(drop=True)
+ )
+
+ def _batched_calibrate(self, K, theta, vertices, null_truth, alpha):
+ stats = self.model.sim_batch(0, K, theta, null_truth)
+ sorted_stats = jnp.sort(stats, axis=-1)
+ alpha0 = self.backward_boundv(alpha, theta, vertices)
+ bootstrap_lams = self.calibratev(sorted_stats, np.arange(K), alpha0)
+ return bootstrap_lams
+
+ def _calibrate(self, K_df, alpha):
+ K = K_df["K"].iloc[0]
+ K_g = grid.Grid(K_df)
+
+ theta, vertices = K_g.get_theta_and_vertices()
+ bootstrap_lams = batching.batch(
+ self._batched_calibrate,
+ self.tile_batch_size,
+ in_axes=(None, 0, 0, 0, None),
+ )(K, theta, vertices, K_g.get_null_truth(), alpha)
+ return pd.DataFrame(bootstrap_lams, columns=["lams"])
+
+ def calibrate(self, df, alpha):
+ return (
+ df.groupby("K", group_keys=False)
+ .apply(lambda K_df: self._calibrate(K_df, alpha))
+ .reset_index(drop=True)
+ )
+
+
+def _setup(modeltype, g, model_seed, K, model_kwargs, tile_batch_size):
+ g = copy.deepcopy(g)
+ if K is not None:
+ g.df["K"] = K
+ else:
+ # If K is not specified we just use a default value that's a decent
+ # guess.
+ default_K = 2**14
+ if "K" not in g.df.columns:
+ g.df["K"] = default_K
+ g.df.loc[g.df["K"] == 0, "K"] = default_K
+
+ if model_kwargs is None:
+ model_kwargs = {}
+ model = modeltype(model_seed, g.df["K"].max(), **model_kwargs)
+ return Driver(model, tile_batch_size=tile_batch_size), g
+
+
+def validate(
+ modeltype,
+ g,
+ lam,
+ *,
+ delta=0.01,
+ model_seed=0,
+ K=None,
+ tile_batch_size=64,
+ model_kwargs=None
+):
+ """
+ Calculate the Type I Error bound.
+
+ Args:
+ modeltype: The model class.
+ g: The grid.
+ lam: The critical threshold in the rejection rule. Test statistics
+ below this value will be rejected.
+ delta: The bound will hold point-wise with probability 1 - delta.
+ Defaults to 0.01.
+ model_seed: The random seed. Defaults to 0.
+ K: The number of simulations. If this is unspecified, it is assumed
+ that the grid has a "K" column containing per-tile simulation counts.
+ Defaults to None.
+ tile_batch_size: The number of tiles to simulate in a single batch.
+ model_kwargs: Keyword arguments passed to the model constructor.
+ Defaults to None.
+
+ Returns:
+ A dataframe with the following columns:
+ - tie_sum: The number of test statistics below the critical threshold.
+ - tie_est: The estimated Type I Error at the simulation points.
+ - tie_cp_bound: The Clopper-Pearson bound on the Type I error at the
+ simulation point.
+ - tie_bound: The bound on the Type I error over the whole tile.
+ """
+ driver, g = _setup(modeltype, g, model_seed, K, model_kwargs, tile_batch_size)
+ rej_df = driver.validate(g.df, lam, delta=delta)
+ return rej_df
+
+
+def calibrate(
+ modeltype,
+ g,
+ *,
+ model_seed=0,
+ alpha=0.025,
+ K=None,
+ tile_batch_size=64,
+ model_kwargs=None
+):
+ """
+ calibrate the critical threshold for a given level of Type I Error control.
+
+ Args:
+ modeltype: The model class.
+ g: The grid.
+ model_seed: The random seed. Defaults to 0.
+ alpha: The Type I Error control level. Defaults to 0.025.
+ K: The number of simulations. If this is unspecified, it is assumed
+ that the grid has a "K" column containing per-tile simulation counts.
+ Defaults to None.
+ tile_batch_size: The number of tiles to simulate in a single batch.
+ model_kwargs: Keyword arguments passed to the model constructor.
+ Defaults to None.
+
+ Returns:
+ _description_
+ """
+ driver, g = _setup(modeltype, g, model_seed, K, model_kwargs, tile_batch_size)
+ calibrate_df = driver.calibrate(g.df, alpha)
+ return calibrate_df
diff --git a/imprint/example/BUILD.bazel b/imprint/example/BUILD.bazel
deleted file mode 100644
index b69b49fe..00000000
--- a/imprint/example/BUILD.bazel
+++ /dev/null
@@ -1,9 +0,0 @@
-[cc_binary(
- name = type_,
- srcs = ["{}.cpp".format(type_)],
- deps = [
- "//imprint",
- ],
-) for type_ in [
- "normal_simple",
-]]
diff --git a/imprint/example/normal_simple.cpp b/imprint/example/normal_simple.cpp
deleted file mode 100644
index edfbb666..00000000
--- a/imprint/example/normal_simple.cpp
+++ /dev/null
@@ -1,71 +0,0 @@
-#include
-#include
-#include
-#include
-#include
-#include
-
-int main() {
- using namespace imprint;
- using model_t = model::normal::Simple;
- using tile_t = grid::Tile;
- using gr_t = grid::GridRange;
- using hp_t = grid::HyperPlane;
-
- // configuration setting
- size_t n_gridpts = 100;
- size_t n_sims = 1e5;
- size_t seed = 0;
- double lower = -3.;
- double upper = 1.4;
- double alpha = 0.025;
-
- // initialize critical threshold
- colvec_type cvs(1);
- cvs << (upper + qnorm(1 - alpha));
-
- // empty null hypothesis surfaces
- // we will treat all grid-points as part of the null-space.
- std::vector null_hypos;
-
- // initialize a grid range
- gr_t gr(1, n_gridpts);
- gr.thetas().row(0) = grid::Gridder::make_grid(n_gridpts, lower, upper);
- auto radius = grid::Gridder::radius(n_gridpts, lower, upper);
- gr.radii().row(0).array() = radius;
- gr.sim_sizes().array() = n_sims;
-
- // create tiles and prune (shouldn't affect any internals)
- gr.create_tiles(null_hypos);
- gr.prune();
-
- std::cout << "n_tiles: " << gr.n_tiles() << std::endl;
-
- // create a model object
- model_t model(cvs);
-
- // create a simulation global state,
- // which caches any values to speed-up simulations.
- auto sgs = model.make_sim_global_state(gr);
-
- // create a simulation state,
- // which defines the simulation routine.
- auto ss = sgs.make_sim_state(seed);
-
- colvec_type rejection_length(gr.n_tiles());
- colvec_type rejection_sum(gr.n_tiles());
- rejection_sum.setZero();
-
- // simulate and accumulate rejection counts
- for (size_t i = 0; i < n_sims; ++i) {
- ss->simulate(rejection_length);
- rejection_sum += rejection_length;
- }
-
- // print the Type I Error estimate
- colvec_type type_I_err =
- rejection_sum.template cast() / n_sims;
- std::cout << type_I_err.transpose() << std::endl;
-
- return 0;
-}
diff --git a/imprint/grid.py b/imprint/grid.py
new file mode 100644
index 00000000..48ca7f52
--- /dev/null
+++ b/imprint/grid.py
@@ -0,0 +1,709 @@
+import copy
+import time
+import warnings
+from dataclasses import dataclass
+from dataclasses import field
+from itertools import product
+from typing import List
+
+import numpy as np
+import pandas as pd
+import sympy as sp
+
+
+@dataclass(eq=False)
+class HyperPlane:
+ """
+ A plane defined by:
+ x.dot(n) - c = 0
+
+ Sign convention: When used as the boundary between null hypothesis and
+ alternative, the normal should point towards the null hypothesis space.
+ """
+
+ n: np.ndarray
+ c: float
+
+ def __eq__(self, other):
+ if not isinstance(other, HyperPlane):
+ return NotImplemented
+ return np.allclose(self.n, other.n) and np.isclose(self.c, other.c)
+
+
+def hypo(str_expr):
+ """
+ Define a hyperplane from a sympy expression.
+
+ For example:
+ >>> hypo("2*theta1 < 1")
+ HyperPlane(n=array([ 0., -1.]), c=-0.5)
+
+ >>> hypo("x - y >= 0")
+ HyperPlane(n=array([ 0.70710678, -0.70710678]), c=0.0)
+
+ Valid comparison operators are <, >, <=, >=.
+
+ The left hand and right hand sides must be linear in theta.
+
+ Aliases:
+ - theta{i}: x{i}
+ - x: x0
+ - y: x1
+ - z: x2
+
+ Args:
+ str_expr: The expression defining the hypothesis plane.
+
+ Returns:
+ The HyperPlane object corresponding to the sympy expression.
+ """
+ alias = dict(
+ x="x0",
+ y="x1",
+ z="x2",
+ )
+ expr = sp.parsing.parse_expr(str_expr)
+ if isinstance(expr, sp.StrictLessThan) or isinstance(expr, sp.LessThan):
+ plane = expr.rhs - expr.lhs
+ elif isinstance(expr, sp.StrictGreaterThan) or isinstance(expr, sp.GreaterThan):
+ plane = expr.lhs - expr.rhs
+ else:
+ raise ValueError("Hypothesis expression must be an inequality.")
+
+ symbols = plane.free_symbols
+ coeffs = sp.Poly(plane, *symbols).coeffs()
+ if len(coeffs) > len(symbols):
+ c = -float(coeffs[-1])
+ coeffs = coeffs[:-1]
+ else:
+ c = 0
+
+ symbol_names = [alias.get(s.name, s.name).replace("theta", "x") for s in symbols]
+
+ if any([s[0] != "x" for s in symbol_names]):
+ raise ValueError(
+ f"Hypothesis contains invalid symbols: {symbols}."
+ " Valid symbols are x0..., theta0..., x, y, z."
+ )
+ try:
+ symbol_idxs = [int(s[1:]) for s in symbol_names]
+ except ValueError:
+ raise ValueError(
+ f"Hypothesis contains invalid symbols: {symbols}."
+ " Valid symbols are x0..., theta0..., x, y, z."
+ )
+ coeff_dict = dict(zip(symbol_idxs, coeffs))
+ max_idx = max(symbol_idxs)
+
+ n = [float(coeff_dict.get(i, 0)) for i in range(max_idx + 1)]
+ n_norm = np.linalg.norm(n)
+ n /= n_norm
+ c /= n_norm
+
+ return HyperPlane(np.array(n), c)
+
+
+@dataclass
+class Grid:
+ """
+ A grid is a collection of tiles, each of which is a hyperrectangle in
+ parameter space. The grid is stored as a pandas DataFrame, with one row per
+ tile. The columns are:
+ - id: A unique identifier for the tile. See gen_short_uuids for details on
+ these ids.
+ - active: Whether the tile is active. A tile is active if it has not been
+ split.
+ - parent_id: The id of the parent tile if the tile has been split. This is
+ 0 for tiles with no parent.
+ - theta{i} and radii{i}: The center and half-width of the tile in the i-th
+ dimension.
+
+ Other columns may be added by other code. All columns will automatically be
+ inherited in refinement and splitting operations.
+ """
+
+ df: pd.DataFrame
+ null_hypos: List[HyperPlane] = field(default_factory=lambda: [])
+
+ @property
+ def d(self):
+ if not hasattr(self, "_d"):
+ self._d = (
+ max([int(c[5:]) for c in self.df.columns if c.startswith("theta")]) + 1
+ )
+ return self._d
+
+ @property
+ def n_tiles(self):
+ return self.df.shape[0]
+
+ @property
+ def n_active_tiles(self):
+ return self.df["active"].sum()
+
+ def _add_null_hypo(self, H, inherit_cols):
+ eps = 1e-15
+
+ hypo_idx = len(self.null_hypos)
+ self.null_hypos.append(H)
+
+ ########################################
+ # Step 1: Assign tile centers
+ ########################################
+ # Assign tiles to the null/alt hypothesis space depending on which side
+ # of the plane the tile lies. At the moment, we only check the tile
+ # centers. Any tiles that intersect the plane will be handled next.
+ theta, vertices = self.get_theta_and_vertices()
+ radii = self.get_radii()
+ gridpt_dist = theta.dot(H.n) - H.c
+ self.df[f"null_truth{hypo_idx}"] = gridpt_dist >= 0
+
+ ########################################
+ # Step 2: Check for intersection
+ ########################################
+ # If a tile is close to the plane, we need to check for intersection.
+ # "close" is defined by whether the bounding ball of the tile
+ # intersects the plane.
+ close = np.abs(gridpt_dist) <= np.sqrt(np.sum(self.get_radii() ** 2, axis=-1))
+ # We ignore intersections of inactive tiles.
+ close &= self.df["active"].values
+
+ # For each tile that is close to the plane, we check each vertex to
+ # find which side of the plane the vertex lies on.
+ vertex_dist = vertices[close].dot(H.n) - H.c
+ all_above = (vertex_dist >= -eps).all(axis=-1)
+ all_below = (vertex_dist <= eps).all(axis=-1)
+ # If all vertices are above or all the vertices are below the plane, we
+ # can ignore the tile.
+ close_intersects = ~(all_above | all_below)
+ if close_intersects.sum() == 0:
+ return self
+ intersects = np.zeros(self.n_tiles, dtype=bool)
+ intersects[close] = close_intersects
+
+ ########################################
+ # Step 3: Split intersecting tiles
+ ########################################
+ new_theta, new_radii = split(
+ theta[intersects],
+ radii[intersects],
+ vertices[intersects],
+ vertex_dist[close_intersects],
+ H,
+ )
+
+ parent_id = np.repeat(self.df["id"].values[intersects], 2)
+ new_g = init_grid(new_theta, new_radii, parents=parent_id)
+ _inherit(new_g.df, self.df[intersects], 2, inherit_cols)
+ for i in range(hypo_idx):
+ new_g.df[f"null_truth{i}"] = np.repeat(
+ self.df[f"null_truth{i}"].values[intersects], 2
+ )
+ new_g.df[f"null_truth{hypo_idx}"] = True
+ new_g.df[f"null_truth{hypo_idx}"].values[1::2] = False
+
+ # Any tile that has been split should be ignored going forward.
+ # We're done with these tiles!
+ self.df["active"].values[intersects] = False
+
+ return self.concat(new_g)
+
+ def add_null_hypos(self, null_hypos, inherit_cols=[]):
+ """
+ Add null hypotheses to the grid. This will split any tiles that
+ intersect the null hypotheses and assign the tiles to the null/alt
+ hypothesis space depending on which side of the null hypothesis the
+ tile lies. These assignments will be stored in the null_truth{i}
+ columns in the tile dataframe.
+
+ Args:
+ null_hypos: The null hypotheses to add. List of HyperPlane objects.
+ inherit_cols: Columns that should be inherited by split
+ tiles (e.g. K). Defaults to [].
+
+ Returns:
+ The grid with the null hypotheses added.
+ """
+ g = Grid(self.df.copy(), copy.deepcopy(self.null_hypos))
+ for H in null_hypos:
+ Hn = np.asarray(H.n)
+ Hpad = HyperPlane(np.pad(Hn, (0, g.d - Hn.shape[0])), H.c)
+ g = g._add_null_hypo(Hpad, inherit_cols)
+ return g
+
+ def prune(self):
+ """
+ Remove tiles that are not in the null hypothesis space for any
+ hypothesis.
+
+ Returns:
+ The pruned grid.
+ """
+ if len(self.null_hypos) == 0:
+ return self
+ null_truth = self.get_null_truth()
+ which = (null_truth.any(axis=1)) | (null_truth.shape[1] == 0)
+ if np.all(which):
+ return self
+ return self.subset(which)
+
+ def add_cols(self, df):
+ return Grid(pd.concat((self.df, df), axis=1), self.null_hypos)
+
+ def subset(self, which):
+ """
+ Subset a grid by some indexer.
+
+ Args:
+ which: The indexer.
+
+ Returns:
+ The grid subset.
+ """
+ df = self.df.loc[which].reset_index(drop=True)
+ return Grid(df, self.null_hypos)
+
+ def active(self):
+ """
+ Get the active subset of the grid.
+
+ Returns:
+ A grid composed of only the active tiles.
+ """
+ return self.subset(self.df["active"])
+
+ def get_null_truth(self):
+ return self.df[
+ [
+ f"null_truth{i}"
+ for i in range(self.df.shape[1])
+ if f"null_truth{i}" in self.df.columns
+ ]
+ ].to_numpy()
+
+ def get_theta(self):
+ return self.df[[f"theta{i}" for i in range(self.d)]].to_numpy()
+
+ def get_radii(self):
+ return self.df[[f"radii{i}" for i in range(self.d)]].to_numpy()
+
+ def get_theta_and_vertices(self):
+ theta = self.get_theta()
+ return theta, (
+ theta[:, None, :]
+ + hypercube_vertices(self.d)[None, :, :] * self.get_radii()[:, None, :]
+ )
+
+ def refine(self, inherit_cols=[]):
+ refine_radii = self.get_radii()[:, None, :] * 0.5
+ refine_theta = self.get_theta()[:, None, :]
+ new_thetas = (
+ refine_theta + hypercube_vertices(self.d)[None, :, :] * refine_radii
+ ).reshape((-1, self.d))
+ new_radii = np.tile(refine_radii, (1, 2**self.d, 1)).reshape((-1, self.d))
+ parent_id = np.repeat(self.df["id"].values, 2**self.d)
+ out = init_grid(
+ new_thetas,
+ new_radii,
+ parents=parent_id,
+ )
+ _inherit(out.df, self.df, 2**self.d, inherit_cols)
+ return out
+
+ def concat(self, *others):
+ return Grid(
+ pd.concat((self.df, *[o.df for o in others]), axis=0, ignore_index=True),
+ self.null_hypos,
+ )
+
+
+def _inherit(child_df, parent_df, repeat, inherit_cols):
+ assert (child_df["parent_id"] == np.repeat(parent_df["id"].values, repeat)).all()
+ for col in inherit_cols:
+ if col in child_df.columns:
+ continue
+ child_df[col] = np.repeat(parent_df[col].values, repeat)
+ # NOTE: if we ever need a more complex parent-child relationship, we can
+ # use pandas merge.
+ # pd.merge(
+ # child_df,
+ # parent_df,
+ # left_on="parent_id",
+ # right_on="id",
+ # how='left',
+ # validate='many_to_one'
+ # )
+
+
+def init_grid(theta, radii, parents=None):
+ d = theta.shape[1]
+ indict = dict()
+ indict["id"] = gen_short_uuids(len(theta))
+
+ # Is this a terminal tile in the tree?
+ indict["active"] = True
+
+ indict["parent_id"] = (
+ parents.astype(np.uint64) if parents is not None else np.uint64(0)
+ )
+
+ for i in range(d):
+ indict[f"theta{i}"] = theta[:, i]
+ for i in range(d):
+ indict[f"radii{i}"] = radii[:, i]
+
+ return Grid(pd.DataFrame(indict), [])
+
+
+def cartesian_grid(theta_min, theta_max, *, n=None, null_hypos=None, prune=True):
+ """
+ Produce a grid of points in the hyperrectangle defined by theta_min and
+ theta_max.
+
+ Args:
+ theta_min: The minimum value of theta for each dimension.
+ theta_max: The maximum value of theta for each dimension.
+ n: The number of theta values to use in each dimension.
+ null_hypos: The null hypotheses to add. List of HyperPlane objects.
+ prune: Whether to prune the grid to only include tiles that are in the
+ null hypothesis space.
+
+ Returns:
+ The grid.
+ """
+ theta_min = np.asarray(theta_min)
+ theta_max = np.asarray(theta_max)
+
+ if n is None:
+ n = np.full(theta_min.shape[0], 2)
+ g = init_grid(*_cartesian_gridpts(theta_min, theta_max, n))
+ if null_hypos is not None:
+ g = g.add_null_hypos(null_hypos)
+ if prune:
+ g = g.prune()
+ return g
+
+
+def _cartesian_gridpts(theta_min, theta_max, n_theta_1d):
+ theta_min = np.asarray(theta_min)
+ theta_max = np.asarray(theta_max)
+ n_theta_1d = np.asarray(n_theta_1d)
+
+ n_arms = theta_min.shape[0]
+ theta1d = [
+ np.linspace(theta_min[i], theta_max[i], 2 * n_theta_1d[i] + 1)[1::2]
+ for i in range(n_arms)
+ ]
+ radii1d = [
+ np.full(
+ theta1d[i].shape[0], (theta_max[i] - theta_min[i]) / (2 * n_theta_1d[i])
+ )
+ for i in range(n_arms)
+ ]
+ theta = np.stack(np.meshgrid(*theta1d), axis=-1).reshape((-1, len(theta1d)))
+ radii = np.stack(np.meshgrid(*radii1d), axis=-1).reshape((-1, len(theta1d)))
+ return theta, radii
+
+
+def plot_grid(g: Grid, only_active=True, dims=(0, 1)):
+ """
+ Plot a 2D grid.
+
+ Args:
+ g: the grid
+ null_hypos: If provided, the function will plot red lines for the null
+ hypothesis boundaries. Defaults to [].
+ """
+ import matplotlib as mpl
+ import matplotlib.pyplot as plt
+
+ vertices = g.get_theta_and_vertices()[1][..., dims]
+
+ if only_active:
+ g = g.active()
+
+ polys = []
+ for i in range(vertices.shape[0]):
+ vs = vertices[i]
+ vs = vs[~np.isnan(vs).any(axis=1)]
+ centroid = np.mean(vs, axis=0)
+ angles = np.arctan2(vs[:, 1] - centroid[1], vs[:, 0] - centroid[0])
+ order = np.argsort(angles)
+ polys.append(mpl.patches.Polygon(vs[order], fill=None, edgecolor="k"))
+ plt.text(*centroid, str(i))
+
+ plt.gca().add_collection(
+ mpl.collections.PatchCollection(polys, match_original=True)
+ )
+
+ maxvs = np.max(vertices, axis=(0, 1))
+ minvs = np.min(vertices, axis=(0, 1))
+ view_center = 0.5 * (maxvs + minvs)
+ view_radius = (maxvs - minvs) * 0.55
+ xlims = view_center[0] + np.array([-1, 1]) * view_radius[0]
+ ylims = view_center[1] + np.array([-1, 1]) * view_radius[1]
+ plt.xlim(xlims)
+ plt.ylim(ylims)
+
+ for h in g.null_hypos:
+ if h.n[0] == 0:
+ xs = np.linspace(*xlims, 100)
+ ys = (h.c - xs * h.n[0]) / h.n[1]
+ else:
+ ys = np.linspace(*ylims, 100)
+ xs = (h.c - ys * h.n[1]) / h.n[0]
+ plt.plot(xs, ys, "r-")
+
+
+# https://stackoverflow.com/a/52229385/
+def hypercube_vertices(d):
+ """
+ The corners of a hypercube of dimension d.
+
+ >>> print(hypercube_vertices(1))
+ [[-1]
+ [ 1]]
+
+ >>> print(hypercube_vertices(2))
+ [[-1 -1]
+ [-1 1]
+ [ 1 -1]
+ [ 1 1]]
+
+ >>> print(hypercube_vertices(3))
+ [[-1 -1 -1]
+ [-1 -1 1]
+ [-1 1 -1]
+ [-1 1 1]
+ [ 1 -1 -1]
+ [ 1 -1 1]
+ [ 1 1 -1]
+ [ 1 1 1]]
+
+ Args:
+ d: the dimension
+
+ Returns:
+ a numpy array of shape (2**d, d) containing the vertices of the
+ hypercube.
+ """
+ return np.array(list(product((-1, 1), repeat=d)))
+
+
+def split(theta, radii, vertices, vertex_dist, H):
+ eps = 1e-15
+ d = theta.shape[1]
+
+ ########################################
+ # Step 1. Intersect tile edges with the hyperplane.
+ # This will identify the new vertices that we need to add.
+ ########################################
+ split_edges = get_edges(theta, radii)
+ # The first n_params columns of split_edges are the vertices from which
+ # the edge originates and the second n_params are the edge vector.
+ split_vs = split_edges[..., :d]
+ split_dir = split_edges[..., d:]
+
+ with warnings.catch_warnings():
+ warnings.simplefilter("ignore")
+ # Intersect each edge with the plane.
+ alpha = (H.c - split_vs.dot(H.n)) / (split_dir.dot(H.n))
+ # Now we need to identify the new tile vertices. We have three
+ # possible cases here:
+ # 1. Intersection: indicated by 0 < alpha < 1. We give a little
+ # eps slack to ignore intersections for null planes that just barely
+ # touch a corner of a tile. In this case, we
+ # 2. Non-intersection indicated by alpha not in [0, 1]. In this
+ # case, the new vertex will just be marked nan to be filtered out
+ # later.
+ # 3. Non-finite alpha which also indicates no intersection. Again,
+ # we produced a nan vertex to filter out later.
+ new_vs = split_vs + alpha[:, :, None] * split_dir
+ new_vs = np.where(
+ (np.isfinite(new_vs)) & ((alpha > eps) & (alpha < 1 - eps))[..., None],
+ new_vs,
+ np.nan,
+ )
+
+ ########################################
+ # Step 2. Construct the vertex array for the new tiles..
+ ########################################
+ # Create the array for the new vertices. We need to expand the
+ # original vertex array in both dimensions:
+ # 1. We create a new row for each tile that is being split using np.repeat.
+ # 2. We create a new column for each potential additional vertex from
+ # the intersection operation above using np.concatenate. This is
+ # more new vertices than necessary, but facilitates a nice
+ # vectorized implementation.. We will just filter out the
+ # unnecessary slots later.
+ split_vertices = np.repeat(vertices, 2, axis=0)
+ split_vertices = np.concatenate(
+ (
+ split_vertices,
+ np.full(
+ (split_vertices.shape[0], split_edges.shape[1], d),
+ np.nan,
+ ),
+ ),
+ axis=1,
+ )
+
+ # Now we need to fill in the new vertices:
+ # For each original tile vertex, we need to determine whether the tile
+ # lies in the new null tile or the new alt tile.
+ include_in_null_tile = vertex_dist >= -eps
+ include_in_alt_tile = vertex_dist <= eps
+
+ # Since we copied the entire tiles, we can "delete" vertices by
+ # multiply by nan
+ # note: ::2 traverses the range of new null hypo tiles
+ # 1::2 traverses the range of new alt hypo tiles
+ split_vertices[::2, : vertices.shape[1]] *= np.where(
+ include_in_null_tile, 1, np.nan
+ )[..., None]
+ split_vertices[1::2, : vertices.shape[1]] *= np.where(
+ include_in_alt_tile, 1, np.nan
+ )[..., None]
+
+ # The intersection vertices get added to both new tiles because
+ # they lie on the boundary between the two tiles.
+ split_vertices[::2, vertices.shape[1] :] = new_vs
+ split_vertices[1::2, vertices.shape[1] :] = new_vs
+
+ # Trim the new tile array:
+ # We now are left with an array of tile vertices that has many more
+ # vertex slots per tile than necessary with the unused slots filled
+ # with nan.
+ # To deal with this:
+ # 1. We sort along the vertices axis. This has the effect of
+ # moving all the nan vertices to the end of the list.
+ split_vertices = split_vertices[
+ np.arange(split_vertices.shape[0])[:, None],
+ np.argsort(np.sum(split_vertices, axis=-1), axis=-1),
+ ]
+
+ # 2. Identify the maximum number of vertices of any tile and trim the
+ # array so that is the new vertex dimension size
+ nonfinite_corners = (~np.isfinite(split_vertices)).all(axis=(0, 2))
+ # 3. If any corner is unused for all tiles, we should remove it.
+ # But, we can't trim smaller than the original vertices array.
+ if nonfinite_corners[-1]:
+ first_all_nan_corner = nonfinite_corners.argmax()
+ split_vertices = split_vertices[:, :first_all_nan_corner]
+
+ ########################################
+ # Step 3. Identify bounding boxes.
+ ########################################
+ min_val = np.nanmin(split_vertices, axis=1)
+ max_val = np.nanmax(split_vertices, axis=1)
+ new_theta = (min_val + max_val) / 2
+ new_radii = (max_val - min_val) / 2
+ return new_theta, new_radii
+
+
+def get_edges(theta, radii):
+ """
+ Construct an array indicating the edges of each hyperrectangle.
+ - edges[:, :, :n_params] are the vertices at the origin of the edges
+ - edges[:, :, n_params:] are the edge vectors pointing from the start to
+ the end of the edge
+
+ Args:
+ thetas: the centers of the hyperrectangles
+ radii: the half-width of the hyperrectangles
+
+ Returns:
+ edges: an array as specified in the docstring shaped like
+ (n_grid_pts, number of hypercube vertices, 2*n_params)
+ """
+
+ n_params = theta.shape[1]
+ unit_vs = hypercube_vertices(n_params)
+ n_vs = unit_vs.shape[0]
+ unit_edges = []
+ for i in range(n_vs):
+ for j in range(n_params):
+ if unit_vs[i, j] > 0:
+ continue
+ unit_edges.append(np.concatenate((unit_vs[i], np.identity(n_params)[j])))
+
+ edges = np.tile(np.array(unit_edges)[None, :, :], (theta.shape[0], 1, 1))
+ edges[:, :, :n_params] *= radii[:, None, :]
+ edges[:, :, n_params:] *= 2 * radii[:, None, :]
+ edges[:, :, :n_params] += theta[:, None, :]
+ return edges
+
+
+def uuid_timer():
+ return time.time()
+
+
+def gen_short_uuids(n, host_id=None, t=None):
+ """
+ Short UUIDs are a custom identifier created for imprint that should allow
+ for concurrent creation of tiles without having overlapping indices.
+
+ - The highest 28 bits are the time in seconds of creation. This will not
+ loop for 8.5 years. When we start running jobs that take longer than 8.5
+ years to complete, please send a message to me in the afterlife.
+ - The creation time is never re-used. If the creation time is going to
+ be reused because less than one second has passed since the previous
+ call to gen_short_uuids, then the creation time is incremented by
+ one.
+ - The next 18 bits are the index of the process. This is a pretty generous limit
+ on the number of processes. 2^18=262144.
+ - The lowest 18 bits are the index of the created tiles within this batch.
+ This allows for up to 2^18 = 262144 tiles to be created in a single
+ batch. This is not a problematic constraint, because we can just
+ increment the time by one and then grab another batch of IDs.
+
+ NOTE: This should be safe across processes but will not be safe across
+ threads within a single Python process because multithreaded programs share
+ globals.
+
+ Args:
+ n: The number of short uuids to generate.
+ host_id: The host id. It's okay to ignore this for non-concurrent jobs.
+ Defaults to None.
+ t: The time to impose (used for testing). Defaults to None.
+
+ Returns:
+ An array with dtype uint64 of length n containing short uuids.
+ """
+ n_max = 2 ** _gen_short_uuids.config[0] - 1
+ if n <= n_max:
+ return _gen_short_uuids(n, host_id, t)
+
+ out = np.empty(n, dtype=np.uint64)
+ for i in range(0, n, n_max):
+ chunk_size = min(n_max, n - i)
+ out[i : i + chunk_size] = _gen_short_uuids(chunk_size, host_id, t)
+ return out
+
+
+def _gen_short_uuids(n, host_id, t):
+ n_bits, host_bits = _gen_short_uuids.config
+ # time_bits = 64 - n_bits - host_bits
+ assert n < 2**n_bits
+
+ if host_id is None:
+ # host_id == 0 is skipped so that we can use 0 as a sentinel value
+ host_id = 1
+ assert host_id > 0
+ assert host_id < 2**host_bits
+
+ if t is None:
+ t = np.uint64(int(uuid_timer()))
+ if _gen_short_uuids.largest_t is not None and t <= _gen_short_uuids.largest_t:
+ t = np.uint64(_gen_short_uuids.largest_t + 1)
+ _gen_short_uuids.largest_t = t
+
+ return (
+ (t << np.uint64(n_bits + host_bits))
+ + np.uint64(host_id << n_bits)
+ + np.arange(n, dtype=np.uint64)
+ )
+
+
+_gen_short_uuids.config = (18, 18)
+_gen_short_uuids.largest_t = None
diff --git a/imprint/include/imprint_bits/bound/accumulator/typeI_error_accum.hpp b/imprint/include/imprint_bits/bound/accumulator/typeI_error_accum.hpp
deleted file mode 100644
index f699efee..00000000
--- a/imprint/include/imprint_bits/bound/accumulator/typeI_error_accum.hpp
+++ /dev/null
@@ -1,158 +0,0 @@
-#pragma once
-#include
-#include
-
-namespace imprint {
-namespace bound {
-
-/*
- * Accumulator for Type I error imprint bound.
- */
-template
-struct TypeIErrorAccum {
- using value_t = ValueType;
- using uint_t = UIntType;
-
- private:
- mat_type typeI_sum_; // Type I error sums.
- // typeI_sum_(i,j) = rejection accumulation
- // for model i at tile j.
- colvec_type
- score_sum_; // score sums.
- // score_sum_(i,j,k) = partial deriv accumulation w.r.t.
- // param j for model i at tile k.
- size_t n_params_; // dimension of a gridpoint.
-
- /* Buffer needed in update for one-time allocation */
- colvec_type score_buff_; // score vector buffer
-
- IMPRINT_STRONG_INLINE void update_internal(uint_t pos, uint_t rej_len_pos) {
- typeI_sum_.col(pos).tail(rej_len_pos).array() += 1;
-
- const auto slice_size = n_models() * n_params();
- Eigen::Map > score_pos(
- score_sum_.data() + pos * slice_size, n_models(), n_params());
- for (uint_t k = 0; k < n_params_; ++k) {
- auto score_pos_k = score_pos.col(k);
- score_pos_k.tail(rej_len_pos).array() += score_buff_(k);
- }
- }
-
- public:
- TypeIErrorAccum() = default;
- TypeIErrorAccum(size_t n_models, size_t n_tiles, size_t n_params)
- : typeI_sum_(n_models, n_tiles),
- score_sum_(n_models * n_params * n_tiles),
- n_params_(n_params),
- score_buff_(n_params) {
- typeI_sum_.setZero();
- score_sum_.setZero();
- }
-
- /*
- * Accumulates estimates based on current model SimState.
- * Increments typeI_sum by rejection indicators.
- * Increments score_sum by rejection indicators * (T - \nabla A).
- *
- * @param rej_len rej_len[i] = number of models that rejected
- * at tile i.
- * @param sim_state SimState-like object that was used to
- * produce rej_len. Assumes that the sequence of models considered is
- * ordered in ascending order, in the sense that if ith model rejects then
- * jth model rejects for all j >= i.
- * @param grid_range a grid range object on which sim_state ran
- * its simulation to produce rej_len.
- */
- template
- void update(const VecType& rej_len, const SimStateType& sim_state,
- const GridRangeType& grid_range) {
- assert(grid_range.n_tiles() == typeI_sum_.cols());
- assert(grid_range.n_params() == n_params_);
- assert(score_buff_.size() == n_params_);
-
- const auto& gr_view = grid_range;
- const uint_t n_gridpts = gr_view.n_gridpts();
-
- // update typeI_sum_ and score_sum_
- size_t pos = 0;
- for (uint_t i = 0; i < n_gridpts; ++i) {
- // if current gridpoint is regular,
- // only update if there is any rejection
- if (gr_view.is_regular(i)) {
- if (unlikely(rej_len[pos] != 0)) {
- sim_state.score(i, score_buff_);
- update_internal(pos, rej_len[pos]);
- }
- ++pos;
- continue;
- }
-
- // then iterate through all the tiles for update
- bool score_computed = false;
- const auto n_ts = gr_view.n_tiles(i);
- for (uint_t j = 0; j < n_ts; ++j, ++pos) {
- if (unlikely(rej_len[pos] == 0)) continue;
- if (!score_computed) {
- score_computed = true;
- sim_state.score(i, score_buff_);
- }
- update_internal(pos, rej_len[pos]);
- }
- }
- }
-
- /*
- * Pools quantities from another TypeIErrorAccum object, other,
- * as if the current object were additionally updated in the same way as in
- * other.
- *
- * @param other another TypeIErrorAccum to pool into current object.
- */
- void pool(const TypeIErrorAccum& other) {
- typeI_sum_ += other.typeI_sum_;
- score_sum_ += other.score_sum_;
- }
-
- /*
- * Pools with the raw sum and score from another accumulation. as if the
- * current object were additionally updated in the same way as in other.
- *
- * @param other_typeI_sum the other type I sum
- * @param other_typeI_score the other type I score
- */
- void pool_raw(const mat_type& other_typeI_sum,
- const colvec_type& other_typeI_score) {
- typeI_sum_ += other_typeI_sum;
- score_sum_ += other_typeI_score;
- }
-
- /*
- * Reset the size of internal data structures corresponding
- * to the new configuration n_models, n_tiles, n_params, n_acc.
- * The first three parameters must be positive.
- *
- * @param n_models number of models.
- * @param n_tiles number of tiles.
- * @param n_params number of parameters.
- */
- void reset(size_t n_models, size_t n_tiles, size_t n_params) {
- typeI_sum_.setZero(n_models, n_tiles);
- score_sum_.setZero(n_models * n_params * n_tiles);
- score_buff_.resize(n_params);
- n_params_ = n_params;
- }
-
- const mat_type& typeI_sum() const { return typeI_sum_; }
- const colvec_type& score_sum() const { return score_sum_; }
-
- constexpr size_t n_tiles() const { return typeI_sum_.cols(); }
- constexpr size_t n_params() const { return n_params_; }
- constexpr size_t n_models() const { return typeI_sum_.rows(); }
-
- // helper debug functions that should not be used by average users.
- mat_type& typeI_sum__() { return typeI_sum_; }
- colvec_type& score_sum__() { return score_sum_; }
-};
-
-} // namespace bound
-} // namespace imprint
diff --git a/imprint/include/imprint_bits/bound/typeI_error_bound.hpp b/imprint/include/imprint_bits/bound/typeI_error_bound.hpp
deleted file mode 100644
index 9597a491..00000000
--- a/imprint/include/imprint_bits/bound/typeI_error_bound.hpp
+++ /dev/null
@@ -1,247 +0,0 @@
-#pragma once
-#include
-#include
-#include
-#include
-//#include // third-party
-
-namespace imprint {
-namespace bound {
-
-/*
- * This class encapsulates the logic of constructing
- * a Type I error imprint bound.
- * It stores all necessary components of the imprint bound.
- *
- * @param ValueType underlying value type (usually double).
- */
-template
-struct TypeIErrorBound {
- using value_t = ValueType;
-
- private:
- // Components that make up the imprint bound.
- mat_type delta_0_; // 0th order (n_models x n_tiles)
- mat_type delta_0_u_; // 0th order upper bound (n_models x n_tiles)
- mat_type delta_1_; // 1st order (n_models x n_tiles)
- mat_type delta_1_u_; // 1st order upper bound (n_models x n_tiles)
- mat_type delta_2_u_; // 2nd order upper bound (n_models x n_tiles)
- mat_type full_; // full upper bound = sum of previous components
-
- colvec_type
- vertices_; // vertices that achieve the maximum of
- // delta_1_ + delta_1_u_ + delta_2_u_.
- // It is of shape (n_params, n_tiles, n_models).
- // Note that the structure is slightly different
- // from the accumulator score sum (3D) array
- // (n_models, n_params, n_tiles).
- // This ordering allows us to return a viewer of
- // each corner without making a copy,
- // and saving each corner can be vectorized.
-
- template
- void create_internal(KBSType&& kbs, const AccumType& acc_o,
- const GridRangeType& grid_range, value_t delta,
- value_t delta_prop_0to1, SaveCornerType save_corner) {
- // some aliases
- const auto n_models = acc_o.n_models();
- const auto n_gridpts = grid_range.n_gridpts();
- const auto n_tiles = acc_o.n_tiles(); // total number of tiles
- const auto n_params = grid_range.n_params();
- const auto n_nat_params =
- kbs.n_natural_params(); // number of natural params
- const auto slice_size = n_models * n_params;
- const auto& sim_sizes = grid_range.sim_sizes();
- const auto& typeIsum = acc_o.typeI_sum();
- const auto& thetas = grid_range.thetas();
- const auto& tiles = grid_range.tiles();
- constexpr value_t neg_inf = -std::numeric_limits::infinity();
-
- // pre-compute some constants
- const value_t d0u_factor = 1. - delta * delta_prop_0to1;
- const value_t d1u_factor =
- std::sqrt(1. / ((1.0 - delta_prop_0to1) * delta) - 1.);
-
- // populate 0th order and upper bound
- delta_0_.resize(n_models, n_tiles);
- delta_0_u_.resize(n_models, n_tiles);
- delta_1_.setZero(n_models, n_tiles);
- delta_1_u_.resize(n_models, n_tiles);
- delta_2_u_.resize(n_models, n_tiles);
-
- colvec_type d11u2u(n_models); // d1 + d1u + d2u for each model
- colvec_type v_diff(n_params); // buffer to store vertex-gridpt
- colvec_type deta_v_diff(n_nat_params); // Deta * v_diff
-
- size_t pos = 0;
- for (size_t gp = 0; gp < n_gridpts; ++gp) {
- const auto ss = sim_sizes[gp];
- const auto sqrt_ss = std::sqrt(ss);
- const auto d1u_factor_sqrt_ss = d1u_factor / sqrt_ss;
-
- for (size_t i = 0; i < grid_range.n_tiles(gp); ++i, ++pos) {
- // update 0th order
- auto delta_0_j = delta_0_.col(pos);
- auto typeIsum_j = typeIsum.col(pos);
- delta_0_j = typeIsum_j.template cast() / ss;
-
- // update 0th order upper
- auto delta_0_u_j = delta_0_u_.col(pos);
- for (int m = 0; m < delta_0_u_j.size(); ++m) {
- delta_0_u_j[m] = ibeta_inv(typeIsum_j[m] + 1,
- ss - typeIsum_j[m], d0u_factor) -
- delta_0_j[m];
- }
-
- // update 1st/1st upper/2nd upper
- const auto& tile = tiles[pos];
-
- // set current max value of d1 + d1u + d2u = -inf for all
- // models.
- d11u2u.fill(neg_inf);
-
- // iterate over all vertices of the tile
- // and update current max of d1 + d1u + d2u
- // and d1, d1u, d2u that achieve that max.
- if (grid_range.is_regular(gp)) {
- update_d11u2u(tile, tile.begin_full(), tile.end_full(),
- true, gp, pos, ss, d1u_factor_sqrt_ss, v_diff,
- deta_v_diff, thetas, kbs, n_models, n_params,
- slice_size, acc_o, d11u2u, save_corner);
- } else {
- update_d11u2u(tile, tile.begin(), tile.end(), false, gp,
- pos, ss, d1u_factor_sqrt_ss, v_diff,
- deta_v_diff, thetas, kbs, n_models, n_params,
- slice_size, acc_o, d11u2u, save_corner);
- }
- } // end for-loop on tiles
- }
- }
-
- template
- void update_d11u2u(const TileType& tile, Iter begin, Iter end, bool is_reg,
- size_t gp, size_t tile_pos, size_t ss,
- value_t d1u_factor_sqrt_ss, VDiffType& v_diff,
- DetaVDiffType& deta_v_diff, const ThetasType& thetas,
- KBSType&& kbs, size_t n_models, size_t n_params,
- size_t slice_size, const AccumType& acc_o,
- D11U2UType& d11u2u, SaveCornerType save_corner) {
- Eigen::Map > score_tile(
- acc_o.score_sum().data() + slice_size * tile_pos, n_models,
- n_params);
-
- for (; begin != end; ++begin) {
- auto&& v = *begin; // vertex
-
- auto center = thetas.col(gp);
- v_diff = v - center;
- kbs.apply_eta_jacobian(gp, v_diff, deta_v_diff);
- value_t d1u = std::sqrt(kbs.covar_quadform(gp, deta_v_diff)) *
- d1u_factor_sqrt_ss;
- value_t d2u =
- 0.5 * kbs.hessian_quadform_bound(gp, tile_pos, v_diff);
-
- for (size_t m = 0; m < n_models; ++m) {
- // compute current v^T Deta^T score
- value_t d1 = score_tile.row(m).dot(deta_v_diff) / ss;
-
- // check if we have new maximum
- value_t new_max = d1 + d1u + d2u;
- bool is_new = (new_max > d11u2u[m]);
-
- // save new maximum sum and the components
- if (is_new) {
- d11u2u[m] = new_max;
- delta_1_(m, tile_pos) = d1;
- delta_1_u_(m, tile_pos) = d1u;
- delta_2_u_(m, tile_pos) = d2u;
- save_corner(m, tile_pos, v);
- }
-
- } // end for-loop on models
- } // end for-loop on vertices
- }
-
- public:
- /*
- * Creates and stores the components of the imprint bound.
- *
- * @param kbs ImprintBoundState-like object.
- * @param acc_o Accumulator object for Type I error.
- * Assumes that this is an accumulation
- * of simulations for the SimState associated
- * with the same model class as the one that
- * generated kbs.
- * @param grid_range GridRange-like object.
- * Assumes that this is the same grid range
- * that acc_o was updated with and that kbs
- * is initialized with.
- * @param delta 1-confidence of provable upper bound.
- * @param delta_prop_0to1 proportion of delta to put
- * into 0th order upper bound.
- * Default is 0.5.
- * @param verbose if true, then more quantities will be saved.
- * Currently, it stores the corner points of
- * each tile that maximizes the
- * first order + first order upper bound + second order upper bound
- * Note that for regular gridpoints,
- * the saved vertices are undefined. Default is false.
- */
- template
- void create(KBStateType&& kbs, const KBSAccType& acc_o,
- const GridRangeType& grid_range, value_t delta,
- value_t delta_prop_0to1 = 0.5, bool verbose = false) {
- const auto n_params = grid_range.n_params();
- const auto n_tiles = grid_range.n_tiles();
- const auto n_models = acc_o.n_models();
-
- if (verbose) {
- const auto slice_size = n_params * n_tiles;
- vertices_.resize(slice_size * n_models);
- create_internal(kbs, acc_o, grid_range, delta, delta_prop_0to1,
- [&](size_t m, size_t pos, const auto& v) {
- Eigen::Map > cor_slice(
- vertices_.data() + slice_size * m, n_params,
- n_tiles);
- cor_slice.col(pos) = v;
- });
- } else {
- create_internal(kbs, acc_o, grid_range, delta, delta_prop_0to1,
- [](size_t, size_t, const auto&) {});
- }
-
- full_ = delta_0_ + delta_0_u_ + delta_1_ + delta_1_u_ + delta_2_u_;
- }
-
- /*
- * Returns the total upper bound computed from the components.
- */
- const mat_type& get() const { return full_; }
-
- /*
- * Returns the vertices that maximize
- * first order + first order upper bound + second order upper bound
- * for each model and tile.
- * The output is a vector representing a 3-D array of shape
- * (n_params, n_tiles, n_models), so that vertices()[:,j,k]
- * is the maximizing vertex at jth tile and kth model.
- */
- const colvec_type& vertices() const { return vertices_; }
-
- mat_type& delta_0() { return delta_0_; }
- mat_type& delta_0_u() { return delta_0_u_; }
- mat_type& delta_1() { return delta_1_; }
- mat_type& delta_1_u() { return delta_1_u_; }
- mat_type& delta_2_u() { return delta_2_u_; }
- const mat_type& delta_0() const { return delta_0_; }
- const mat_type& delta_0_u() const { return delta_0_u_; }
- const mat_type& delta_1() const { return delta_1_; }
- const mat_type& delta_1_u() const { return delta_1_u_; }
- const mat_type& delta_2_u() const { return delta_2_u_; }
-};
-
-} // namespace bound
-} // namespace imprint
diff --git a/imprint/include/imprint_bits/distribution/binomial.hpp b/imprint/include/imprint_bits/distribution/binomial.hpp
deleted file mode 100644
index 870a8d4c..00000000
--- a/imprint/include/imprint_bits/distribution/binomial.hpp
+++ /dev/null
@@ -1,69 +0,0 @@
-#pragma once
-#include
-#include
-#include
-
-namespace imprint {
-namespace distribution {
-
-template
-struct Binomial {
- using value_t = IntType;
-
- private:
- std::binomial_distribution binom_dist_;
-
- public:
- Binomial(value_t n, double p) : binom_dist_(n, p) {}
-
- /*
- * Samples a single Binomial sample with parameter n, p.
- */
- template
- auto sample(GenType&& gen) {
- return binom_dist_(gen);
- }
-
- /*
- * Computes the score of a binomial distribution with parameters n, p.
- * The score is given by:
- * t - n * p
- * where t is the count.
- * The parameters t, n, p are all array-like with the same underlying value
- * type.
- */
- template
- IMPRINT_STRONG_INLINE static auto score(const TType& t, const NType& n,
- const PType& p) {
- return t - n * p;
- }
-
- /*
- * Computes the quadratic form (of v) of the covariance matrix
- * of the count evaluated at p.
- * If n has length d, the function assumes a random variable of length d
- * with each component i representing the count from
- * sampling n[i] i.i.d. samples of Bernoulli from p[i].
- * This function assumes that the binomial r.v.'s are independent
- * with array-like parameters n, p, v with the same underlying value type.
- */
- template
- IMPRINT_STRONG_INLINE static auto covar_quadform(const NType& n,
- const PType& p,
- const VType& v) {
- return (n * v.square() * p * (1.0 - p)).sum();
- }
-
- /*
- * Computes the transformation from natural parameter to mean parameter.
- * nat is an array-like object with each component representing
- * a binomial natural parameter.
- */
- template
- IMPRINT_STRONG_INLINE static auto natural_to_mean(const NatType& nat) {
- return sigmoid(nat);
- }
-};
-
-} // namespace distribution
-} // namespace imprint
diff --git a/imprint/include/imprint_bits/distribution/exponential.hpp b/imprint/include/imprint_bits/distribution/exponential.hpp
deleted file mode 100644
index 7167df04..00000000
--- a/imprint/include/imprint_bits/distribution/exponential.hpp
+++ /dev/null
@@ -1,67 +0,0 @@
-#pragma once
-#include
-#include
-#include
-
-namespace imprint {
-namespace distribution {
-
-template
-struct Exponential {
- using value_t = ValueType;
-
- private:
- std::exponential_distribution exp_;
-
- public:
- Exponential(value_t scale) : exp_(scale) {}
-
- /*
- * Generates i.i.d. exponential samples using
- * the RNG gen of shape (m, n), and stores the result in out.
- */
- template
- IMPRINT_STRONG_INLINE void sample(size_t m, size_t n, GenType&& gen,
- OutType&& out) {
- out = out.NullaryExpr(m, n, [&](auto, auto) { return exp_(gen); });
- }
-
- /*
- * Computes the quadratic form (of v) of the covariance matrix
- * of the sufficient statistic evaluated at lmda.
- * If n has length d, the function assumes a random variable of length d
- * with each component i representing the sufficient statistic of
- * sampling n[i] i.i.d. samples from lmda[i].
- * It assumes array-like parameters n, lmda, v.
- */
- template
- IMPRINT_STRONG_INLINE static auto covar_quadform(const NType& n,
- const LmdaType& lmda,
- const VType& v) {
- return (n * (v.square() / lmda.square())).sum();
- }
-
- /*
- * Computes the score of exponential distribution for n[i] i.i.d.
- * draws of Exp(lmda[i]) with sufficient statistic t[i].
- * Returns an array-like expression with the score for each i.
- */
- template
- IMPRINT_STRONG_INLINE static auto score(const TType& t, const NType& n,
- const LmdaType& lmda) {
- return t - n * (1 / lmda);
- }
-
- /*
- * Computes the transformation from natural parameter to mean parameter.
- * nat is an array-like object with each component representing
- * an exponential natural parameter.
- */
- template
- IMPRINT_STRONG_INLINE static auto natural_to_mean(const NatType& nat) {
- return -nat;
- }
-};
-
-} // namespace distribution
-} // namespace imprint
diff --git a/imprint/include/imprint_bits/distribution/normal.hpp b/imprint/include/imprint_bits/distribution/normal.hpp
deleted file mode 100644
index bb1a244b..00000000
--- a/imprint/include/imprint_bits/distribution/normal.hpp
+++ /dev/null
@@ -1,29 +0,0 @@
-#pragma once
-#include
-#include
-
-namespace imprint {
-namespace distribution {
-
-template
-struct Normal {
- using value_t = ValueType;
-
- private:
- std::normal_distribution normal_dist_;
-
- public:
- Normal(value_t loc, value_t scale) : normal_dist_(loc, scale) {}
-
- /*
- * Samples a single univariate normal random variable
- * given an RNG gen.
- */
- template
- IMPRINT_STRONG_INLINE value_t sample(GenType&& gen) {
- return normal_dist_(gen);
- }
-};
-
-} // namespace distribution
-} // namespace imprint
diff --git a/imprint/include/imprint_bits/distribution/uniform.hpp b/imprint/include/imprint_bits/distribution/uniform.hpp
deleted file mode 100644
index 39a9edcc..00000000
--- a/imprint/include/imprint_bits/distribution/uniform.hpp
+++ /dev/null
@@ -1,31 +0,0 @@
-#pragma once
-#include
-#include
-#include
-
-namespace imprint {
-namespace distribution {
-
-template
-struct Uniform {
- using value_t = ValueType;
-
- private:
- std::uniform_real_distribution unif_;
-
- public:
- Uniform(value_t min, value_t max) : unif_(min, max) {}
-
- /*
- * Generates i.i.d. uniform samples using the distribution object unif
- * and the RNG gen of shape (m, n), and stores the result in out.
- */
- template
- IMPRINT_STRONG_INLINE void sample(size_t m, size_t n, GenType&& gen,
- OutType&& out) {
- out = out.NullaryExpr(m, n, [&](auto, auto) { return unif_(gen); });
- }
-};
-
-} // namespace distribution
-} // namespace imprint
diff --git a/imprint/include/imprint_bits/driver/accumulate.hpp b/imprint/include/imprint_bits/driver/accumulate.hpp
deleted file mode 100644
index 7c06ffdf..00000000
--- a/imprint/include/imprint_bits/driver/accumulate.hpp
+++ /dev/null
@@ -1,85 +0,0 @@
-#pragma once
-#include
-
-#include
-#include
-#include
-#include
-#include
-#include
-
-namespace imprint {
-namespace driver {
-
-template
-inline void accumulate_(const VecSSType& vec_ss,
- const GridRangeType& grid_range, AccumType& acc_o,
- size_t sim_size, size_t n_threads) {
- using acc_t = std::decay_t;
- using gr_t = GridRangeType;
- using uint_t = typename gr_t::uint_t;
-
- auto sim_size_thr = sim_size / n_threads;
- auto sim_size_rem = sim_size % n_threads;
-
- std::vector acc_os(n_threads, acc_o);
-
- assert(vec_ss.size() == n_threads);
-
-#pragma omp parallel for schedule(static) num_threads(n_threads)
- for (size_t t = 0; t < n_threads; ++t) {
- auto& sim_state = *vec_ss[t];
- colvec_type rej_len(grid_range.n_tiles());
- auto sim_size_t = sim_size_thr + (t < sim_size_rem);
- for (size_t i = 0; i < sim_size_t; ++i) {
- sim_state.simulate(rej_len);
- acc_os[t].update(rej_len, sim_state, grid_range);
- }
- }
-
- for (size_t j = 0; j < acc_os.size(); ++j) {
- acc_o.pool(acc_os[j]);
- }
-}
-
-/*
- * Runs a sim_size number of simulations using
- * the simulation global state object, sgs,
- * which stores common data for all simulations
- * and specifies the simulation routine via the
- * simulation state class.
- * The simulations are run on the
- * grid range specified by grid_range.
- * For each simulation, the accumulator acc_o
- * accumulates information from it.
- * acc_o must be initialized properly so that
- * acc_o.pool(acc_o) and acc_o.update(...) have a well-defined behavior.
- */
-template
-inline void accumulate(const SGSType& sgs, const GridRangeType& grid_range,
- AccumType& acc_o, size_t sim_size, size_t seed,
- size_t n_threads) {
- using sgs_t = SGSType;
- using ss_t = typename sgs_t::interface_t::sim_state_t;
-
- size_t max_threads = std::thread::hardware_concurrency();
-
- if (n_threads <= 0) {
- throw std::runtime_error("n_threads must be positive.");
- }
-
- if (n_threads > max_threads) {
- n_threads = max_threads;
- }
-
- std::vector> ss_s;
- ss_s.reserve(n_threads);
- for (size_t i = 0; i < n_threads; ++i) {
- ss_s.emplace_back(sgs.make_sim_state(seed + i));
- }
-
- accumulate_(ss_s, grid_range, acc_o, sim_size, n_threads);
-}
-
-} // namespace driver
-} // namespace imprint
diff --git a/imprint/include/imprint_bits/grid/adagrid_internal.hpp b/imprint/include/imprint_bits/grid/adagrid_internal.hpp
deleted file mode 100644
index dbbe7811..00000000
--- a/imprint/include/imprint_bits/grid/adagrid_internal.hpp
+++ /dev/null
@@ -1,194 +0,0 @@
-#pragma once
-#include
-#include
-#include
-#include
-#include
-
-namespace imprint {
-namespace grid {
-
-struct AdaGridInternal {
- private:
- /*
- * Flags to indicate which action to take.
- * - finalize_ = finalize
- * - N_ = change sim size
- * - eps_ = change radius
- */
- enum class action_type : char { finalize_, N_, eps_ };
-
- /*
- * Computes new simulation size based on old value N,
- * the factor to scale by, N_factor, and the max value, N_max.
- */
- IMPRINT_STRONG_INLINE
- constexpr static auto compute_new_sim_size(size_t N, size_t N_factor,
- size_t N_max) {
- return std::min(N * N_factor, N_max);
- }
-
- public:
- /*
- * Replaces grid_range with the new iteration of grid-points, and
- * populates grid_final with current iteration of finalized points,
- * based on the imprint bound ub.
- */
- template
- void update(const ImprintBoundType& ub, GridRangeType& grid_range,
- GridRangeType& grid_final, size_t N_max,
- ValueType finalize_thr) const {
- using value_t = ValueType;
- using gr_t = std::decay_t;
-
- // allocate aux data one-time.
- const auto d = grid_range.n_params(); // dimension of grid point
- dAryInt bits(2, d);
- colvec_type new_rad;
- colvec_type new_pt;
- std::vector actions(grid_range.n_tiles());
-
- // aliases and configuration
- const auto& ub_tot = ub.get();
- const auto N_factor = bits.n_unique(); // amount to increase sim size
- const auto n_new_pts =
- bits.n_unique(); // number of new points if eps changes
- size_t n_finalized = 0; // number of new finalized points
- size_t n_grid_range = 0; // number of new grid range points
-
- // aliases
- const auto& d0 = ub.delta_0();
- const auto& d0_u = ub.delta_0_u();
- const auto& d1 = ub.delta_1();
- const auto& d1_u = ub.delta_1_u();
- const auto& d2_u = ub.delta_2_u();
- const auto& N = grid_range.sim_sizes();
-
- // Note: ImprintBound rows small->large = model most->least
- // conservative. So, first row is for thr_minus and second is thr.
-
- // First pass through all grid points is just to determine
- // how many finalized/new grid range points we have.
- size_t pos = 0;
- for (size_t j = 0; j < grid_range.n_gridpts(); ++j) {
- // Compute Gaussian mean approximation of upper bound
- // if N changed to N*2^d, d = dimension of gridpt
- auto ss = N[j];
- auto N_new = compute_new_sim_size(ss, N_factor, N_max);
- auto N_ratio = static_cast(ss) / N_new;
-
- bool any_eps = false; // true if any tile require splitting
- bool any_N =
- false; // true if any tile require increase in sim_size
- bool all_finalize = true; // true if all tiles finalized
-
- for (size_t t = 0; t < grid_range.n_tiles(j); ++t, ++pos) {
- // Already a good estimate for ub: finalize_
- if ((ub_tot(1, pos) < finalize_thr) || (ss >= N_max)) continue;
-
- all_finalize = false;
-
- auto mu_dN =
- d0(1, pos) + d1(1, pos) +
- (d0_u(1, pos) + d1_u(1, pos)) * std::sqrt(N_ratio) +
- d2_u(1, pos);
-
- // Compute Gaussian mean approximation of upper bound
- // if eps changed to eps/2
- auto mu_deps = d0(1, pos) + d0_u(1, pos) +
- (d1(1, pos) + d1_u(1, pos)) / 2. +
- d2_u(1, pos) / 4.;
-
- // Compare Gaussian mean approximations:
- // smaller the mean, the more likely ImprintBound < alpha.
- bool do_N = (mu_dN < mu_deps);
- any_N = any_N || do_N;
- any_eps = any_eps || !do_N;
-
- } // end for-loop over tiles
-
- if (all_finalize) {
- actions[j] = action_type::finalize_;
- ++n_finalized;
- continue;
- }
-
- // prioritize splitting!
- if (any_eps) {
- actions[j] = action_type::eps_;
- n_grid_range += n_new_pts;
- continue;
- }
-
- // finally, if not finalize and no eps, then increase sim_size
- actions[j] = action_type::N_;
- n_grid_range += 1;
-
- } // end for-loop over gridpts
-
- // move the current grid ranges and setup for next range.
- const gr_t grid_range_old = std::move(grid_range);
- grid_range = gr_t(d, n_grid_range);
- grid_final = gr_t(d, n_finalized);
-
- const auto& theta_old = grid_range_old.thetas();
- const auto& radii_old = grid_range_old.radii();
- const auto& sim_sizes_old = grid_range_old.sim_sizes();
- auto& theta_new = grid_range.thetas();
- auto& radii_new = grid_range.radii();
- auto& sim_sizes_new = grid_range.sim_sizes();
- auto& theta_fin = grid_final.thetas();
- auto& radii_fin = grid_final.radii();
- auto& sim_sizes_fin = grid_final.sim_sizes();
-
- // Second pass through the grid points will actually
- // populate the new grid_range and grid_final.
- size_t new_j = 0;
- size_t fin_j = 0;
- for (size_t j = 0; j < grid_range_old.n_gridpts(); ++j) {
- auto theta_old_j = theta_old.col(j);
- auto radius_old_j = radii_old.col(j);
- auto sim_size_old_j = sim_sizes_old[j];
-
- // finalize the point
- switch (actions[j]) {
- case action_type::finalize_: {
- theta_fin.col(fin_j) = theta_old_j;
- radii_fin.col(fin_j) = radius_old_j;
- sim_sizes_fin[fin_j] = sim_size_old_j;
- ++fin_j;
- break;
- }
-
- case action_type::N_: {
- theta_new.col(new_j) = theta_old_j;
- radii_new.col(new_j) = radius_old_j;
- sim_sizes_new[new_j] =
- compute_new_sim_size(sim_size_old_j, N_factor, N_max);
- ++new_j;
- break;
- }
-
- case action_type::eps_: {
- bits.setZero();
- new_rad = radius_old_j / 2.;
- for (int k = 0; k < n_new_pts; ++k, ++bits) {
- new_pt.array() =
- theta_old_j.array() +
- new_rad.array() *
- (2 * bits().cast().array() - 1);
-
- theta_new.col(new_j) = new_pt;
- radii_new.col(new_j) = new_rad;
- sim_sizes_new[new_j] = sim_size_old_j;
- ++new_j;
- }
- break;
- }
- } // end switch
- }
- }
-};
-
-} // namespace grid
-} // namespace imprint
diff --git a/imprint/include/imprint_bits/grid/decl.hpp b/imprint/include/imprint_bits/grid/decl.hpp
deleted file mode 100644
index 558e85a0..00000000
--- a/imprint/include/imprint_bits/grid/decl.hpp
+++ /dev/null
@@ -1,22 +0,0 @@
-#pragma once
-#include
-
-namespace imprint {
-namespace grid {
-
-template
-struct Tile;
-
-template
-struct GridRange;
-
-struct Gridder;
-
-template
-struct HyperPlaneView;
-
-template
-struct HyperPlane;
-
-} // namespace grid
-} // namespace imprint
diff --git a/imprint/include/imprint_bits/grid/grid_range.hpp b/imprint/include/imprint_bits/grid/grid_range.hpp
deleted file mode 100644
index cd004ffb..00000000
--- a/imprint/include/imprint_bits/grid/grid_range.hpp
+++ /dev/null
@@ -1,390 +0,0 @@
-#pragma once
-#include
-#include
-#include
-#include
-#include
-#include
-
-namespace imprint {
-namespace grid {
-
-template
-struct GridRange {
- using value_t = ValueType;
- using uint_t = UIntType;
- using tile_t = TileType;
- using bits_t = unsigned char; // TODO: generalize?
-
- private:
- mat_type thetas_; // matrix of theta vectors
- mat_type radii_; // matrix of radius vectors
- colvec_type sim_sizes_; // vector of simulation sizes
-
- // updated via member functions
- std::vector cum_n_tiles_; // cum_n_tiles_[i] = cumulative number of
- // tiles for ith gridpoint
- std::vector bits_; // vector of bits to represent ISH of each tile
- std::vector
- tiles_; // vector of tiles (flattened across all gridpoints)
-
- bits_t all_alt_bits_;
-
- IMPRINT_STRONG_INLINE
- static constexpr bits_t compute_init_bits(size_t max_bits) { return 0; }
-
- IMPRINT_STRONG_INLINE
- static constexpr bits_t compute_all_alt_bits(size_t max_bits) {
- bits_t out = 0;
- bits_t pos = 1;
- for (size_t b = 0; b < max_bits; ++b, pos <<= 1) {
- out |= pos;
- }
- return out;
- }
-
- IMPRINT_STRONG_INLINE
- void set_null(bits_t& bits, size_t hypo, bool is_null = true) {
- unsigned char t = (static_cast(1) << hypo);
- auto true_bit = -is_null;
- bits = ((~true_bit) & (bits | t)) | (true_bit & (bits & (~t)));
- }
-
- IMPRINT_STRONG_INLINE
- bool is_all_alt(bits_t bits) const {
- return all_alt_bits_ && (bits == all_alt_bits_);
- }
-
- void reset_tiles_viewer() {
- // if tiles haven't been created yet
- if (tiles_.size() == 0) return;
-
- size_t pos = 0;
- for (size_t i = 0; i < n_gridpts(); ++i) {
- for (size_t j = 0; j < n_tiles(i); ++j, ++pos) {
- tiles_[pos].center(thetas_.col(i));
- tiles_[pos].radius(radii_.col(i));
- }
- }
- }
-
- public:
- GridRange() = default;
-
- GridRange(uint_t dim, uint_t size)
- : thetas_(dim, size), radii_(dim, size), sim_sizes_(size) {}
-
- GridRange(const Eigen::Ref>& thetas,
- const Eigen::Ref>& radii,
- const Eigen::Ref>& sim_sizes)
- : thetas_(thetas), radii_(radii), sim_sizes_(sim_sizes) {}
-
- template
- GridRange(const Eigen::Ref>& thetas,
- const Eigen::Ref>& radii,
- const Eigen::Ref>& sim_sizes,
- const VecSurfType& surfs, bool do_prune = true)
- : thetas_(thetas), radii_(radii), sim_sizes_(sim_sizes) {
- create_tiles(surfs);
- if (do_prune) prune();
- }
-
- GridRange(const GridRange& gr)
- : thetas_(gr.thetas_),
- radii_(gr.radii_),
- sim_sizes_(gr.sim_sizes_),
- cum_n_tiles_(gr.cum_n_tiles_),
- bits_(gr.bits_),
- tiles_(gr.tiles_) {
- reset_tiles_viewer();
- }
-
- GridRange(GridRange&& gr)
- : thetas_(std::move(gr.thetas_)),
- radii_(std::move(gr.radii_)),
- sim_sizes_(std::move(gr.sim_sizes_)),
- cum_n_tiles_(std::move(gr.cum_n_tiles_)),
- bits_(std::move(gr.bits_)),
- tiles_(std::move(gr.tiles_)) {
- reset_tiles_viewer();
- }
-
- GridRange& operator=(const GridRange& gr) {
- thetas_ = gr.thetas_;
- radii_ = gr.radii_;
- sim_sizes_ = gr.sim_sizes_;
- cum_n_tiles_ = gr.cum_n_tiles_;
- bits_ = gr.bits_;
- tiles_ = gr.tiles_;
- reset_tiles_viewer();
- return *this;
- }
-
- GridRange& operator=(GridRange&& gr) {
- thetas_ = std::move(gr.thetas_);
- radii_ = std::move(gr.radii_);
- sim_sizes_ = std::move(gr.sim_sizes_);
- cum_n_tiles_ = std::move(gr.cum_n_tiles_);
- bits_ = std::move(gr.bits_);
- tiles_ = std::move(gr.tiles_);
- reset_tiles_viewer();
- return *this;
- }
-
- /*
- * Creates the tile information based on current values of
- * gridpoints and radii information.
- *
- * It is undefined behavior if gridpoints and radii are not set.
- *
- * @param vec_surf vector of surface objects.
- * vec_surf[i] corresponds to the surface that
- * divides the parameter space to get ith null
- * hypothesis space. Assumed that the non-negative side of the surface is
- * the null-hypothesis region.
- */
- template
- void create_tiles(const VecSurfaceType& vec_surf) {
- cum_n_tiles_.resize(n_gridpts() + 1);
- cum_n_tiles_[0] = 0;
-
- bits_.reserve(n_gridpts());
- tiles_.reserve(
- n_gridpts()); // slight optimization
- // we know we need at least 1 for each gridpoint.
-
- const size_t max_bits = vec_surf.size(); // max number of bits allowed
- assert(max_bits <= sizeof(bits_t) * 8);
-
- // this represents all alternative hypothesis being true
- // note that there may be some padded bits which are
- // set to null hypothesis being true,
- // so if max_bits < sizeof(bits_t) * 8, this value is non-trivial.
- all_alt_bits_ = compute_all_alt_bits(max_bits);
-
- // this represents all null-hypothesis being true.
- const bits_t init_bits = compute_init_bits(max_bits);
-
- size_t tiles_begin = 0; // begin position of tiles_ for gridpt j
- for (int j = 0; j < thetas_.cols(); ++j) {
- auto theta_j = thetas_.col(j);
- auto radius_j = radii_.col(j);
-
- // start the queue of tiles with one (regular) tile
- bits_.emplace_back(init_bits); // sets current bit to init_bits
- tiles_.emplace_back(theta_j, radius_j);
-
- for (size_t s = 0; s < vec_surf.size(); ++s) {
- const auto& surf = vec_surf[s];
- size_t q_size = tiles_.size() - tiles_begin;
-
- // iterate over current queue of tiles for current gridpt
- for (size_t i = 0; i < q_size; ++i) {
- // if tile is on one side of surface
- orient_type ori;
- if (is_oriented(tiles_[tiles_begin + i], surf, ori)) {
- set_null(bits_[tiles_begin + i], s,
- (ori == orient_type::non_neg));
- continue;
- }
-
- // add new (regular) tile
- bits_.emplace_back();
- tiles_.emplace_back(theta_j, radius_j);
-
- auto& c_bits = bits_[tiles_begin + i];
- auto& tile =
- tiles_[tiles_begin + i]; // get ref here because
- // previous emplace_back may
- // invalidate any prior refs.
- auto& n_bits = bits_.back();
- auto& n_tile = tiles_.back();
- auto p_tile = n_tile;
-
- // copy ISH of tile into the new tiles
- n_bits = c_bits;
-
- // split the current tile via surf into two smaller tiles
- // - p_tile will be oriented non-negatively (surf null hyp
- // space)
- // - n_tile will be oriented non-positively
- intersect(tile, surf, p_tile, n_tile);
- tile = std::move(p_tile);
-
- // update ISH for the new tiles
- set_null(c_bits, s, true);
- set_null(n_bits, s, false);
- }
- }
-
- cum_n_tiles_[j + 1] = tiles_.size();
- tiles_begin += cum_n_tiles_[j + 1] - tiles_begin;
- }
-
- assert(tiles_begin == n_tiles());
- }
-
- /*
- * Prunes out gridpts and tiles where the ISH is all 0.
- * These correspond to totally alternative regions
- * where we should not even compute Type I error since no null is ever true.
- */
- void prune() {
- if (n_tiles() == 0) return;
-
- std::vector grid_idx;
- std::vector new_cum_n_tiles;
- std::vector new_bits;
- std::vector new_tiles;
-
- new_cum_n_tiles.reserve(n_gridpts() + 1);
- new_cum_n_tiles.push_back(0);
- new_bits.reserve(bits_.size());
- new_tiles.reserve(tiles_.size());
-
- size_t pos = 0;
- for (size_t g = 0; g < n_gridpts(); ++g) {
- size_t n_append = 0;
- for (size_t j = 0; j < n_tiles(g); ++j) {
- const auto& tile = tiles_[pos + j];
- auto bi = bits_[pos + j];
- if (is_all_alt(bi)) continue;
- ++n_append;
- new_bits.emplace_back(bi);
- new_tiles.emplace_back(std::move(tile));
- }
- if (n_append == 0) {
- grid_idx.push_back(g);
- } else {
- new_cum_n_tiles.push_back(n_append + new_cum_n_tiles.back());
- }
- pos += n_tiles(g);
- }
-
- std::swap(bits_, new_bits);
- std::swap(cum_n_tiles_, new_cum_n_tiles);
- std::swap(tiles_, new_tiles);
-
- mat_type new_thetas(thetas_.rows(),
- thetas_.cols() - grid_idx.size());
- mat_type new_radii(radii_.rows(),
- radii_.cols() - grid_idx.size());
- colvec_type new_sim_sizes(sim_sizes_.size() - grid_idx.size());
- {
- std::sort(grid_idx.begin(), grid_idx.end());
- int nj = 0;
- for (int j = 0; j < thetas_.cols(); ++j) {
- // if current column should be removed
- if (std::binary_search(grid_idx.begin(), grid_idx.end(), j))
- continue;
- new_thetas.col(nj) = thetas_.col(j);
- new_radii.col(nj) = radii_.col(j);
- new_sim_sizes(nj) = sim_sizes_(j);
- ++nj;
- }
- }
- thetas_.swap(new_thetas);
- radii_.swap(new_radii);
- sim_sizes_.swap(new_sim_sizes);
-
- // make sure to reset the viewers for the tile objects!
- reset_tiles_viewer();
- }
-
- /*
- * If these internal members' shapes are changed,
- * user MUST call create_tiles() before using any tile information again.
- */
- IMPRINT_STRONG_INLINE mat_type& thetas() { return thetas_; }
- IMPRINT_STRONG_INLINE const mat_type& thetas() const {
- return thetas_;
- }
- IMPRINT_STRONG_INLINE mat_type& radii() { return radii_; }
- IMPRINT_STRONG_INLINE const mat_type& radii() const {
- return radii_;
- }
- IMPRINT_STRONG_INLINE colvec_type& sim_sizes() {
- return sim_sizes_;
- }
- IMPRINT_STRONG_INLINE const colvec_type& sim_sizes() const {
- return sim_sizes_;
- }
-
- IMPRINT_STRONG_INLINE const std::vector& cum_n_tiles() const {
- return cum_n_tiles_;
- }
-
- // This function is only valid once create_tiles() has been called.
- IMPRINT_STRONG_INLINE uint_t n_tiles(size_t gridpt_idx) const {
- return cum_n_tiles_[gridpt_idx + 1] - cum_n_tiles_[gridpt_idx];
- }
- IMPRINT_STRONG_INLINE uint_t n_tiles() const { return tiles_.size(); }
- IMPRINT_STRONG_INLINE uint_t n_gridpts() const { return thetas_.cols(); }
- IMPRINT_STRONG_INLINE uint_t n_params() const { return thetas_.rows(); }
-
- /*
- * Returns true if the tile specified by tile_idx
- * has ISH configuration such that null hypothesis for hypo_idx is true.
- * This function is only valid once create_tiles() has been called.
- * It is well-defined for hypo_idx in the range [0, max_bits()).
- * If create_tiles() were called with a vector of surfaces of size k,
- * then, hypo_idx in the range [k, max_bits()) will return true,
- * i.e. by default, an "empty" hypothesis is assumed to be null.
- */
- IMPRINT_STRONG_INLINE
- bool check_null(size_t tile_idx, size_t hypo_idx) const {
- return (bits_[tile_idx] &
- (static_cast(1) << hypo_idx)) == 0;
- }
-
- IMPRINT_STRONG_INLINE
- bool check_null(size_t gridpt_idx, size_t rel_tile_idx,
- size_t hypo_idx) const {
- size_t tile_idx = n_tiles(gridpt_idx) + rel_tile_idx;
- return check_null(tile_idx, hypo_idx);
- }
-
- /*
- * Returns true if the gridpoint at idx
- * is associated with a regular tile, i.e. a rectangular tile.
- * This function is only valid once create_tiles() has been called.
- *
- * The note below marked with "XXXX" is about an optimization that has been
- * reverted due to incorrect behavior.
- * XXXX Note: this function originally did:
- * XXXX return tiles_[tile_idx].is_regular();
- * XXXX but benchmarking shows that there is a MASSIVE speed difference
- * XXXX from the current implementation. Cache is really important...
- * XXXX Idea is that tiles_ is a heterogenous structure which used to
- * contain
- * XXXX std::bitset<> and some Eigen objects.
- * XXXX Iterating through these makes pre-fetching hard
- * XXXX and there are more tiles than gridpoints, so not only does the
- * current
- * XXXX implementation pre-fetch more values at a time,
- * XXXX but also pre-fetches less in total.
- */
- bool is_regular(size_t idx) const {
- return tiles_[cum_n_tiles_[idx]].is_regular();
- }
-
- IMPRINT_STRONG_INLINE
- static constexpr size_t max_bits() { return sizeof(bits_t) * 8; }
-
- /*
- * Returns the vector of tiles.
- */
- IMPRINT_STRONG_INLINE const auto& tiles() const { return tiles_; }
-
- // Helper functions for pickling stuff
- IMPRINT_STRONG_INLINE auto& tiles__() { return tiles_; }
- IMPRINT_STRONG_INLINE auto& cum_n_tiles__() { return cum_n_tiles_; }
- IMPRINT_STRONG_INLINE auto& bits__() { return bits_; }
- IMPRINT_STRONG_INLINE const auto& cum_n_tiles__() const {
- return cum_n_tiles_;
- }
- IMPRINT_STRONG_INLINE const auto& bits__() const { return bits_; }
-};
-
-} // namespace grid
-} // namespace imprint
diff --git a/imprint/include/imprint_bits/grid/gridder.hpp b/imprint/include/imprint_bits/grid/gridder.hpp
deleted file mode 100644
index 76c54879..00000000
--- a/imprint/include/imprint_bits/grid/gridder.hpp
+++ /dev/null
@@ -1,40 +0,0 @@
-#pragma once
-#include
-#include
-#include
-
-namespace imprint {
-namespace grid {
-
-/*
- * This class is responsible for defining routines to easily
- * create a 1-dimensional grid.
- */
-struct Gridder {
- template
- static ValueType radius(size_t n, ValueType lower, ValueType upper) {
- assert(n);
- return (upper - lower) / (2 * n);
- }
-
- template
- static auto make_grid(size_t n, ValueType lower, ValueType upper) {
- using value_t = ValueType;
- using vec_t = Eigen::Matrix;
- auto r = radius(n, lower, upper);
- return ((2. * vec_t::LinSpaced(n, 0, n - 1).array() + 1.) * r + lower)
- .matrix();
- }
-
- template
- static auto make_endpts(size_t n, ValueType lower, ValueType upper) {
- using value_t = ValueType;
- using mat_t = Eigen::Matrix;
- auto r = radius(n, lower, upper);
- return mat_t::NullaryExpr(
- 2, n, [=](auto i, auto j) { return 2 * (j + i) * r + lower; });
- }
-};
-
-} // namespace grid
-} // namespace imprint
diff --git a/imprint/include/imprint_bits/grid/hyperplane.hpp b/imprint/include/imprint_bits/grid/hyperplane.hpp
deleted file mode 100644
index 0b3c3df9..00000000
--- a/imprint/include/imprint_bits/grid/hyperplane.hpp
+++ /dev/null
@@ -1,120 +0,0 @@
-#pragma once
-#include
-#include
-
-namespace imprint {
-namespace grid {
-
-template
-struct HyperPlaneView {
- using value_t = ValueType;
-
- private:
- Eigen::Map>
- normal_; // normal vector to hyperplane
- const value_t* shift_; // affine shift
-
- public:
- HyperPlaneView() : normal_(nullptr, 0), shift_(nullptr) {}
-
- HyperPlaneView(const Eigen::Ref>& normal,
- const value_t& shift)
- : normal_(normal.data(), normal.size()), shift_(&shift) {}
-
- /*
- * Finds the orientation of a vector v w.r.t.
- * the current hyperplane object.
- * Returns one of neg, on, pos if v is in the
- * negative, boundary, or positive side of hyperplane,
- * respectively.
- */
- template
- IMPRINT_STRONG_INLINE orient_type find_orient(const VecType& v) const {
- value_t ctv = normal_.dot(v);
- constexpr value_t tol = 1e-16;
- auto comp = ctv - *shift_;
- if (comp <= -tol) {
- return orient_type::neg;
- } else if (comp >= tol) {
- return orient_type::pos;
- }
- return orient_type::on;
- }
-
- /*
- * Finds the directional weight alpha to get
- * the intersected point: v + alpha * d.
- * Returns alpha in (0,1) if successful,
- * otherwise returns 0.
- */
- template
- IMPRINT_STRONG_INLINE value_t intersect(const VType& v,
- const DType& d) const {
- auto ntd = normal_.dot(d);
- if (ntd == 0) return 0;
- auto ntv = normal_.dot(v);
- return (*shift_ - ntv) / ntd;
- }
-
- IMPRINT_STRONG_INLINE auto normal() const { return normal_; }
- IMPRINT_STRONG_INLINE
- void normal(const Eigen::Ref>& n) {
- new (&normal_)
- Eigen::Map>(n.data(), n.size());
- }
- IMPRINT_STRONG_INLINE auto shift() const { return *shift_; }
- IMPRINT_STRONG_INLINE void shift(const value_t& s) { shift_ = &s; }
-};
-
-template
-struct HyperPlane : HyperPlaneView {
- private:
- using view_t = HyperPlaneView;
-
- public:
- using typename view_t::value_t;
-
- private:
- colvec_type normal_;
- value_t shift_;
-
- IMPRINT_STRONG_INLINE
- void reset_view() {
- this->normal(normal_);
- this->shift(shift_);
- }
-
- public:
- HyperPlane(const Eigen::Ref>& normal,
- const value_t& shift)
- : view_t(), normal_(normal), shift_(shift) {
- reset_view();
- }
-
- HyperPlane(const HyperPlane& hp)
- : view_t(), normal_(hp.normal_), shift_(hp.shift_) {
- reset_view();
- }
-
- HyperPlane(HyperPlane&& hp)
- : view_t(),
- normal_(std::move(hp.normal_)),
- shift_(std::move(hp.shift_)) {
- reset_view();
- }
-
- HyperPlane& operator=(const HyperPlane& hp) {
- normal_ = hp.normal_;
- shift_ = hp.shift_;
- reset_view();
- }
-
- HyperPlane& operator=(HyperPlane&& hp) {
- normal_ = std::move(hp.normal_);
- shift_ = std::move(hp.shift_);
- reset_view();
- }
-};
-
-} // namespace grid
-} // namespace imprint
diff --git a/imprint/include/imprint_bits/grid/tile.hpp b/imprint/include/imprint_bits/grid/tile.hpp
deleted file mode 100644
index f3bd1220..00000000
--- a/imprint/include/imprint_bits/grid/tile.hpp
+++ /dev/null
@@ -1,187 +0,0 @@
-#pragma once
-#include
-#include
-#include
-#include
-#include