FASTEN-cli 1.0.0__tar.gz

fasten_cli-1.0.0/.github/workflows/publish.yml

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+name: Publish FASTEN
+on: [push]
+
+jobs:
+  build:
+    name: Build distribution
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v6
+      with:
+        persist-credentials: false
+    - name: Set up Python
+      uses: actions/setup-python@v6
+      with:
+        python-version: "3.x"
+    - name: Install pypa/build
+      run: >-
+        python3 -m
+        pip install
+        build
+        --user
+    - name: Build a binary wheel and a source tarball
+      run: python3 -m build
+    - name: Store the distribution packages
+      uses: actions/upload-artifact@v5
+      with:
+        name: python-package-distributions
+        path: dist/
+  
+  publish:
+    name: Publish to PyPI
+    needs: build
+    runs-on: ubuntu-latest
+    environment:
+      name: pypi
+      url: https://pypi.org/p/fasten-cli
+    permissions:
+      id-token: write
+
+    steps:
+      - name: Download all the dists
+        uses: actions/download-artifact@v6
+        with:
+          name: python-package-distributions
+          path: dist/
+      - name: Publish distribution to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1

fasten_cli-1.0.0/LICENSE.md

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+MIT License
+
+Copyright (c) 2026 Kate Jackson
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

fasten_cli-1.0.0/PKG-INFO

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+Metadata-Version: 2.4
+Name: FASTEN-cli
+Version: 1.0.0
+Project-URL: Homepage, https://github.com/k1jackson/FASTEN
+Project-URL: Bug Tracker, https://github.com/k1jackson/FASTEN/issues
+Project-URL: Config Designer, https://k1jackson.github.io/FASTEN/
+License-File: LICENSE.md
+Requires-Dist: k-means-constrained
+Requires-Dist: matplotlib
+Requires-Dist: numpy>=2.1.1
+Requires-Dist: optuna
+Requires-Dist: pandas
+Requires-Dist: pydantic>=2.0
+Requires-Dist: rich
+Requires-Dist: scikit-learn
+Requires-Dist: scipy>=1.14.0
+Requires-Dist: torch
+Description-Content-Type: text/markdown
+
+# FASTEN
+
+[![License](https://img.shields.io/badge/license-MIT-blue.svg)](LICENSE.md)
+[![Version](https://img.shields.io/badge/version-1.0.0-brightgreen.svg)](CHANGELOG.md)
+
+
+<!-- Explain the *what* and *why* of your project in 2–4 sentences.
+     Answer: What problem does it solve? Who is it for? Why does it exist? -->
+
+FASTEN is a flexible and user-friendly framework for building PyTorch-based deep learning emulators for epidemic simulations with stochastic outputs. FASTEN provides three intuitive modules to (1) train deep neural networks on simulation data, (2) select optimal hyperparameters, and (3) generate predictions from unseen inputs. 
+
+
+## Installation
+
+
+FASTEN can be installed via ```pip```:
+
+```bash
+pip install fasten-cli
+```
+
+## Usage
+
+There are two primary components to FASTEN: the [configuration file designer](https://k1jackson.github.io/FASTEN/) and the command line tool.
+
+### Configuration File Designer
+Before executing a FASTEN, the user must construct a workflow configuration file that outlines the simulation data format and training hyperparameters. The [configuration file designer](https://k1jackson.github.io/FASTEN/) guides users through this process with contextual instructions and validation checks.
+
+### Command Line Tool
+The FASTEN workflow decomposes the model emulation process into three phases: (1)training, (2) hyperparameter tuning, and (3) output prediction. Each phase is invoked through a dedicated command line module, with a shared configuration file governing the underlying behavior. The command line tool can used as follows:
+
+**Training:**
+
+```bash
+usage: FASTEN train [-h] -c CONFIG -i INPUT [-o OUTPUT] [-m MODEL]
+
+options:
+  -h, --help           show this help message and exit
+  -c, --config CONFIG  JSON file defining configuration parameters
+  -i, --input INPUT    TSV file with simulation data
+  -o, --output OUTPUT  Folder to output model and figures (default: outputs)
+  -m, --model MODEL    ZIP file containing initial model (default: None)
+```
+
+**Hyperparameter Tuning:**
+
+```bash
+usage: FASTEN tune [-h] -c CONFIG -i INPUT [-o OUTPUT] [-n TRIALS] [--unique]
+
+options:
+  -h, --help           show this help message and exit
+  -c, --config CONFIG  JSON file defining configuration parameters
+  -i, --input INPUT    TSV file with simulation data
+  -o, --output OUTPUT  Folder to output optimal configs and figures (default: outputs)
+  -n, --trials TRIALS  Total number of optimation trials (default: 100)
+  --unique             Prevents re-training with duplicate hyperparameter sets (default: False)
+```
+
+**Output Prediction:**
+
+```bash
+usage: FASTEN predict [-h] -m MODEL -i INPUT [-o OUTPUT] [-n RUNS]
+
+options:
+  -h, --help           show this help message and exit
+  -m, --model MODEL    ZIP file containing model
+  -i, --input INPUT    TSV file with simulation inputs
+  -o, --output OUTPUT  TSV file to output predicted simulation data (default: outputs.tsv)
+  -n, --runs RUNS      Number of simulation runs per input (default: 0)
+```

fasten_cli-1.0.0/README.md

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+# FASTEN
+
+[![License](https://img.shields.io/badge/license-MIT-blue.svg)](LICENSE.md)
+[![Version](https://img.shields.io/badge/version-1.0.0-brightgreen.svg)](CHANGELOG.md)
+
+
+<!-- Explain the *what* and *why* of your project in 2–4 sentences.
+     Answer: What problem does it solve? Who is it for? Why does it exist? -->
+
+FASTEN is a flexible and user-friendly framework for building PyTorch-based deep learning emulators for epidemic simulations with stochastic outputs. FASTEN provides three intuitive modules to (1) train deep neural networks on simulation data, (2) select optimal hyperparameters, and (3) generate predictions from unseen inputs. 
+
+
+## Installation
+
+
+FASTEN can be installed via ```pip```:
+
+```bash
+pip install fasten-cli
+```
+
+## Usage
+
+There are two primary components to FASTEN: the [configuration file designer](https://k1jackson.github.io/FASTEN/) and the command line tool.
+
+### Configuration File Designer
+Before executing a FASTEN, the user must construct a workflow configuration file that outlines the simulation data format and training hyperparameters. The [configuration file designer](https://k1jackson.github.io/FASTEN/) guides users through this process with contextual instructions and validation checks.
+
+### Command Line Tool
+The FASTEN workflow decomposes the model emulation process into three phases: (1)training, (2) hyperparameter tuning, and (3) output prediction. Each phase is invoked through a dedicated command line module, with a shared configuration file governing the underlying behavior. The command line tool can used as follows:
+
+**Training:**
+
+```bash
+usage: FASTEN train [-h] -c CONFIG -i INPUT [-o OUTPUT] [-m MODEL]
+
+options:
+  -h, --help           show this help message and exit
+  -c, --config CONFIG  JSON file defining configuration parameters
+  -i, --input INPUT    TSV file with simulation data
+  -o, --output OUTPUT  Folder to output model and figures (default: outputs)
+  -m, --model MODEL    ZIP file containing initial model (default: None)
+```
+
+**Hyperparameter Tuning:**
+
+```bash
+usage: FASTEN tune [-h] -c CONFIG -i INPUT [-o OUTPUT] [-n TRIALS] [--unique]
+
+options:
+  -h, --help           show this help message and exit
+  -c, --config CONFIG  JSON file defining configuration parameters
+  -i, --input INPUT    TSV file with simulation data
+  -o, --output OUTPUT  Folder to output optimal configs and figures (default: outputs)
+  -n, --trials TRIALS  Total number of optimation trials (default: 100)
+  --unique             Prevents re-training with duplicate hyperparameter sets (default: False)
+```
+
+**Output Prediction:**
+
+```bash
+usage: FASTEN predict [-h] -m MODEL -i INPUT [-o OUTPUT] [-n RUNS]
+
+options:
+  -h, --help           show this help message and exit
+  -m, --model MODEL    ZIP file containing model
+  -i, --input INPUT    TSV file with simulation inputs
+  -o, --output OUTPUT  TSV file to output predicted simulation data (default: outputs.tsv)
+  -n, --runs RUNS      Number of simulation runs per input (default: 0)
+```

fasten_cli-1.0.0/docs/.github/workflows/jekyll-gh-pages.yml

@@ -0,0 +1,51 @@
+# Sample workflow for building and deploying a Jekyll site to GitHub Pages
+name: Deploy Jekyll with GitHub Pages dependencies preinstalled
+
+on:
+  # Runs on pushes targeting the default branch
+  push:
+    branches: ["main"]
+
+  # Allows you to run this workflow manually from the Actions tab
+  workflow_dispatch:
+
+# Sets permissions of the GITHUB_TOKEN to allow deployment to GitHub Pages
+permissions:
+  contents: read
+  pages: write
+  id-token: write
+
+# Allow only one concurrent deployment, skipping runs queued between the run in-progress and latest queued.
+# However, do NOT cancel in-progress runs as we want to allow these production deployments to complete.
+concurrency:
+  group: "pages"
+  cancel-in-progress: false
+
+jobs:
+  # Build job
+  build:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+      - name: Setup Pages
+        uses: actions/configure-pages@v5
+      - name: Build with Jekyll
+        uses: actions/jekyll-build-pages@v1
+        with:
+          source: ./
+          destination: ./_site
+      - name: Upload artifact
+        uses: actions/upload-pages-artifact@v3
+
+  # Deployment job
+  deploy:
+    environment:
+      name: github-pages
+      url: ${{ steps.deployment.outputs.page_url }}
+    runs-on: ubuntu-latest
+    needs: build
+    steps:
+      - name: Deploy to GitHub Pages
+        id: deployment
+        uses: actions/deploy-pages@v5

fasten_cli-1.0.0/docs/404.html

@@ -0,0 +1,25 @@
+---
+permalink: /404.html
+layout: page
+---
+
+<style type="text/css" media="screen">
+  .container {
+    margin: 10px auto;
+    max-width: 600px;
+    text-align: center;
+  }
+  h1 {
+    margin: 30px 0;
+    font-size: 4em;
+    line-height: 1;
+    letter-spacing: -1px;
+  }
+</style>
+
+<div class="container">
+  <h1>404</h1>
+
+  <p><strong>Page not found :(</strong></p>
+  <p>The requested page could not be found.</p>
+</div>

fasten_cli-1.0.0/docs/Gemfile

@@ -0,0 +1,22 @@
+source "https://rubygems.org"
+# gem "jekyll", "~> 4.4.1"
+# gem "minima", "~> 2.5"
+gem "github-pages", group: :jekyll_plugins
+group :jekyll_plugins do
+  gem "jekyll-feed", "~> 0.12"
+  gem "jekyll-remote-theme" 
+end
+
+# Windows and JRuby does not include zoneinfo files, so bundle the tzinfo-data gem
+# and associated library.
+platforms :mingw, :x64_mingw, :mswin, :jruby do
+  gem "tzinfo", ">= 1", "< 3"
+  gem "tzinfo-data"
+end
+
+# Performance-booster for watching directories on Windows
+gem "wdm", "~> 0.1", :platforms => [:mingw, :x64_mingw, :mswin]
+
+# Lock `http_parser.rb` gem to `v0.6.x` on JRuby builds since newer versions of the gem
+# do not have a Java counterpart.
+gem "http_parser.rb", "~> 0.6.0", :platforms => [:jruby]

fasten_cli-1.0.0/docs/Gemfile.lock

@@ -0,0 +1,301 @@
+GEM
+  remote: https://rubygems.org/
+  specs:
+    activesupport (7.1.6)
+      base64
+      benchmark (>= 0.3)
+      bigdecimal
+      concurrent-ruby (~> 1.0, >= 1.0.2)
+      connection_pool (>= 2.2.5)
+      drb
+      i18n (>= 1.6, < 2)
+      logger (>= 1.4.2)
+      minitest (>= 5.1)
+      mutex_m
+      securerandom (>= 0.3)
+      tzinfo (~> 2.0)
+    addressable (2.9.0)
+      public_suffix (>= 2.0.2, < 8.0)
+    base64 (0.3.0)
+    benchmark (0.5.0)
+    bigdecimal (4.1.1)
+    coffee-script (2.4.1)
+      coffee-script-source
+      execjs
+    coffee-script-source (1.12.2)
+    colorator (1.1.0)
+    commonmarker (0.23.12)
+    concurrent-ruby (1.3.6)
+    connection_pool (2.5.5)
+    csv (3.3.5)
+    dnsruby (1.73.1)
+      base64 (>= 0.2)
+      logger (~> 1.6)
+      simpleidn (~> 0.2.1)
+    drb (2.2.3)
+    em-websocket (0.5.3)
+      eventmachine (>= 0.12.9)
+      http_parser.rb (~> 0)
+    ethon (0.18.0)
+      ffi (>= 1.15.0)
+      logger
+    eventmachine (1.2.7)
+    execjs (2.10.1)
+    faraday (2.14.1)
+      faraday-net_http (>= 2.0, < 3.5)
+      json
+      logger
+    faraday-net_http (3.4.2)
+      net-http (~> 0.5)
+    ffi (1.17.4)
+    forwardable-extended (2.6.0)
+    gemoji (4.1.0)
+    github-pages (232)
+      github-pages-health-check (= 1.18.2)
+      jekyll (= 3.10.0)
+      jekyll-avatar (= 0.8.0)
+      jekyll-coffeescript (= 1.2.2)
+      jekyll-commonmark-ghpages (= 0.5.1)
+      jekyll-default-layout (= 0.1.5)
+      jekyll-feed (= 0.17.0)
+      jekyll-gist (= 1.5.0)
+      jekyll-github-metadata (= 2.16.1)
+      jekyll-include-cache (= 0.2.1)
+      jekyll-mentions (= 1.6.0)
+      jekyll-optional-front-matter (= 0.3.2)
+      jekyll-paginate (= 1.1.0)
+      jekyll-readme-index (= 0.3.0)
+      jekyll-redirect-from (= 0.16.0)
+      jekyll-relative-links (= 0.6.1)
+      jekyll-remote-theme (= 0.4.3)
+      jekyll-sass-converter (= 1.5.2)
+      jekyll-seo-tag (= 2.8.0)
+      jekyll-sitemap (= 1.4.0)
+      jekyll-swiss (= 1.0.0)
+      jekyll-theme-architect (= 0.2.0)
+      jekyll-theme-cayman (= 0.2.0)
+      jekyll-theme-dinky (= 0.2.0)
+      jekyll-theme-hacker (= 0.2.0)
+      jekyll-theme-leap-day (= 0.2.0)
+      jekyll-theme-merlot (= 0.2.0)
+      jekyll-theme-midnight (= 0.2.0)
+      jekyll-theme-minimal (= 0.2.0)
+      jekyll-theme-modernist (= 0.2.0)
+      jekyll-theme-primer (= 0.6.0)
+      jekyll-theme-slate (= 0.2.0)
+      jekyll-theme-tactile (= 0.2.0)
+      jekyll-theme-time-machine (= 0.2.0)
+      jekyll-titles-from-headings (= 0.5.3)
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+      kramdown (= 2.4.0)
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+      liquid (= 4.0.4)
+      mercenary (~> 0.3)
+      minima (= 2.5.1)
+      nokogiri (>= 1.16.2, < 2.0)
+      rouge (= 3.30.0)
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+      webrick (~> 1.8)
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+      addressable (~> 2.3)
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+      octokit (>= 4, < 8)
+      public_suffix (>= 3.0, < 6.0)
+      typhoeus (~> 1.3)
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+      coffee-script (~> 2.2)
+      coffee-script-source (~> 1.12)
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+      commonmarker (~> 0.22)
+    jekyll-commonmark-ghpages (0.5.1)
+      commonmarker (>= 0.23.7, < 1.1.0)
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+      forwardable-extended (~> 2.6)
+    public_suffix (5.1.1)
+    racc (1.8.1)
+    rb-fsevent (0.11.2)
+    rb-inotify (0.11.1)
+      ffi (~> 1.0)
+    rexml (3.4.4)
+    rouge (3.30.0)
+    rubyzip (2.4.1)
+    safe_yaml (1.0.5)
+    sass (3.7.4)
+      sass-listen (~> 4.0.0)
+    sass-listen (4.0.0)
+      rb-fsevent (~> 0.9, >= 0.9.4)
+      rb-inotify (~> 0.9, >= 0.9.7)
+    sawyer (0.9.3)
+      addressable (>= 2.3.5)
+      faraday (>= 0.17.3, < 3)
+    securerandom (0.3.2)
+    simpleidn (0.2.3)
+    terminal-table (1.8.0)
+      unicode-display_width (~> 1.1, >= 1.1.1)
+    typhoeus (1.6.0)
+      ethon (>= 0.18.0)
+    tzinfo (2.0.6)
+      concurrent-ruby (~> 1.0)
+    unicode-display_width (1.8.0)
+    uri (1.1.1)
+    webrick (1.9.2)
+
+PLATFORMS
+  arm64-darwin
+  ruby
+  x86_64-darwin
+  x86_64-linux
+
+DEPENDENCIES
+  github-pages
+  http_parser.rb (~> 0.6.0)
+  jekyll-feed (~> 0.12)
+  jekyll-remote-theme
+  tzinfo (>= 1, < 3)
+  tzinfo-data
+  wdm (~> 0.1)
+
+BUNDLED WITH
+   2.5.23

fasten_cli-1.0.0/docs/_config.yml

@@ -0,0 +1,57 @@
+# Welcome to Jekyll!
+#
+# This config file is meant for settings that affect your whole blog, values
+# which you are expected to set up once and rarely edit after that. If you find
+# yourself editing this file very often, consider using Jekyll's data files
+# feature for the data you need to update frequently.
+#
+# For technical reasons, this file is *NOT* reloaded automatically when you use
+# 'bundle exec jekyll serve'. If you change this file, please restart the server process.
+#
+# If you need help with YAML syntax, here are some quick references for you:
+# https://learn-the-web.algonquindesign.ca/topics/markdown-yaml-cheat-sheet/#yaml
+# https://learnxinyminutes.com/docs/yaml/
+#
+# Site settings
+# These are used to personalize your new site. If you look in the HTML files,
+# you will see them accessed via {{ site.title }}, {{ site.email }}, and so on.
+# You can create any custom variable you would like, and they will be accessible
+# in the templates via {{ site.myvariable }}.
+
+title: FASTEN Configuration File Designer
+baseurl: "/FASTEN"
+source: docs 
+url: "https://k1jackson.github.io"
+email: k1jackson@ucsd.edu
+# description: >- # this means to ignore newlines until "baseurl:"
+#   Write an awesome description for your new site here. You can edit this
+#   line in _config.yml. It will appear in your document head meta (for
+#   Google search results) and in your feed.xml site description.
+github_username:  k1jackson
+
+# Build settings
+# theme: pages-themes/cayman@v0.2.0
+remote_theme: pages-themes/cayman
+plugins:
+  - jekyll-remote-theme
+  - jekyll-feed
+
+# Exclude from processing.
+# The following items will not be processed, by default.
+# Any item listed under the `exclude:` key here will be automatically added to
+# the internal "default list".
+#
+# Excluded items can be processed by explicitly listing the directories or
+# their entries' file path in the `include:` list.
+#
+# exclude:
+#   - .sass-cache/
+#   - .jekyll-cache/
+#   - gemfiles/
+#   - Gemfile
+#   - Gemfile.lock
+#   - node_modules/
+#   - vendor/bundle/
+#   - vendor/cache/
+#   - vendor/gems/
+#   - vendor/ruby/