MatInGit · MatInGit · Jul 17, 2025 · Jul 8, 2025 · Jul 8, 2025 · Jul 8, 2025
diff --git a/.github/workflows/docs.yml b/.github/workflows/docs.yml
@@ -0,0 +1,57 @@
+name: Build & Deploy Sphinx Docs
+
+on:
+  push:
+    branches: [20-documentation]
+
+permissions:
+  contents: read
+  pages: write
+  id-token: write
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    steps:
+      - name: 📥 Checkout code
+        uses: actions/checkout@v3
+
+      - name: 🐍 Set up Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: '3.11'
+
+      - name: 📦 Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install sphinx furo sphinx-autodoc-typehints
+
+    #   - name: 🛠️ Build documentation #  we are just using the uploaded ones
+    #     run: |
+    #       cd docs
+    #       make html
+
+      - name: 📂 Upload artifact
+        uses: actions/upload-pages-artifact@v3
+        with:
+          path: docs/build/html/
+
+  deploy:
+    needs: build
+
+    # Grant GITHUB_TOKEN the permissions required to make a Pages deployment
+    permissions:
+      pages: write      # to deploy to Pages
+      id-token: write   # to verify the deployment originates from an appropriate source
+
+    # Deploy to the github-pages environment
+    environment:
+      name: github-pages
+      url: ${{ steps.deployment.outputs.page_url }}
+
+    # Specify runner + deployment step
+    runs-on: ubuntu-latest
+    steps:
+      - name: Deploy to GitHub Pages
+        id: deployment
+        uses: actions/deploy-pages@v4 # or specific "vX.X.X" version tag for this action
diff --git a/.gitignore b/.gitignore
@@ -22,7 +22,7 @@ test.ipynb
 image_model
 test.h5
 .vscode
-build
+/build
 env.json
 creds.json
 test.py

diff --git a/docs/Makefile b/docs/Makefile
@@ -0,0 +1,30 @@
+# Minimal makefile for Sphinx documentation
+
+# You can set these variables from the command line, and also
+# from the environment for the first two.
+SPHINXOPTS    ?=
+SPHINXBUILD   ?= sphinx-build
+SOURCEDIR     = source
+BUILDDIR      = build
+
+# Adjust this to point to your Python package directory (relative to this Makefile)
+APIDOCSRC     = ../poly_lithic
+APIDOCOUT     = $(SOURCEDIR)/api
+
+.PHONY: help Makefile apidoc
+
+# Default target: "make" is like "make help"
+help:
+	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+# Autogenerate .rst files from Python source using sphinx-apidoc
+apidoc:
+	sphinx-apidoc -o $(APIDOCOUT) $(APIDOCSRC) --force --no-toc --separate
+
+# Build HTML docs, running apidoc first
+html: apidoc
+	@$(SPHINXBUILD) -M html "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+# Catch-all target: route all unknown targets to Sphinx
+%: Makefile
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
diff --git a/docs/build/doctrees/api/poly_lithic.doctree b/docs/build/doctrees/api/poly_lithic.doctree
diff --git a/docs/build/doctrees/api/poly_lithic.pre_install.doctree b/docs/build/doctrees/api/poly_lithic.pre_install.doctree
diff --git a/docs/build/doctrees/api/poly_lithic.scripts.doctree b/docs/build/doctrees/api/poly_lithic.scripts.doctree
diff --git a/docs/build/doctrees/api/poly_lithic.scripts.main.doctree b/docs/build/doctrees/api/poly_lithic.scripts.main.doctree
diff --git a/docs/build/doctrees/api/poly_lithic.src.cli.doctree b/docs/build/doctrees/api/poly_lithic.src.cli.doctree
diff --git a/docs/build/doctrees/api/poly_lithic.src.config.config_object.doctree b/docs/build/doctrees/api/poly_lithic.src.config.config_object.doctree
diff --git a/docs/build/doctrees/api/poly_lithic.src.config.doctree b/docs/build/doctrees/api/poly_lithic.src.config.doctree
diff --git a/docs/build/doctrees/api/poly_lithic.src.config.parser.doctree b/docs/build/doctrees/api/poly_lithic.src.config.parser.doctree
diff --git a/docs/build/doctrees/api/poly_lithic.src.doctree b/docs/build/doctrees/api/poly_lithic.src.doctree
diff --git a/docs/build/doctrees/api/poly_lithic.src.interfaces.BaseInterface.doctree b/docs/build/doctrees/api/poly_lithic.src.interfaces.BaseInterface.doctree
diff --git a/docs/build/doctrees/api/poly_lithic.src.interfaces.doctree b/docs/build/doctrees/api/poly_lithic.src.interfaces.doctree
diff --git a/docs/build/doctrees/api/poly_lithic.src.interfaces.file_interface.doctree b/docs/build/doctrees/api/poly_lithic.src.interfaces.file_interface.doctree
diff --git a/docs/build/doctrees/api/poly_lithic.src.interfaces.k2eg_interface.doctree b/docs/build/doctrees/api/poly_lithic.src.interfaces.k2eg_interface.doctree
diff --git a/docs/build/doctrees/api/poly_lithic.src.interfaces.p4p_interface.doctree b/docs/build/doctrees/api/poly_lithic.src.interfaces.p4p_interface.doctree
diff --git a/docs/build/doctrees/api/poly_lithic.src.logging_utils.doctree b/docs/build/doctrees/api/poly_lithic.src.logging_utils.doctree
diff --git a/docs/build/doctrees/api/poly_lithic.src.logging_utils.make_logger.doctree b/docs/build/doctrees/api/poly_lithic.src.logging_utils.make_logger.doctree
diff --git a/docs/build/doctrees/api/poly_lithic.src.model_utils.LocalModelGetter.doctree b/docs/build/doctrees/api/poly_lithic.src.model_utils.LocalModelGetter.doctree
diff --git a/docs/build/doctrees/api/poly_lithic.src.model_utils.MlflowModelGetter.doctree b/docs/build/doctrees/api/poly_lithic.src.model_utils.MlflowModelGetter.doctree
diff --git a/docs/build/doctrees/api/poly_lithic.src.model_utils.ModelGetterBase.doctree b/docs/build/doctrees/api/poly_lithic.src.model_utils.ModelGetterBase.doctree
diff --git a/docs/build/doctrees/api/poly_lithic.src.model_utils.doctree b/docs/build/doctrees/api/poly_lithic.src.model_utils.doctree
diff --git a/docs/build/doctrees/api/poly_lithic.src.transformers.BaseTransformer.doctree b/docs/build/doctrees/api/poly_lithic.src.transformers.BaseTransformer.doctree
diff --git a/docs/build/doctrees/api/poly_lithic.src.transformers.BaseTransformers.doctree b/docs/build/doctrees/api/poly_lithic.src.transformers.BaseTransformers.doctree
diff --git a/docs/build/doctrees/api/poly_lithic.src.transformers.CompoundTransformer.doctree b/docs/build/doctrees/api/poly_lithic.src.transformers.CompoundTransformer.doctree
diff --git a/docs/build/doctrees/api/poly_lithic.src.transformers.doctree b/docs/build/doctrees/api/poly_lithic.src.transformers.doctree
diff --git a/docs/build/doctrees/api/poly_lithic.src.utils.builder.doctree b/docs/build/doctrees/api/poly_lithic.src.utils.builder.doctree
diff --git a/docs/build/doctrees/api/poly_lithic.src.utils.doctree b/docs/build/doctrees/api/poly_lithic.src.utils.doctree
diff --git a/docs/build/doctrees/api/poly_lithic.src.utils.lazyInterfaceLoader.doctree b/docs/build/doctrees/api/poly_lithic.src.utils.lazyInterfaceLoader.doctree
diff --git a/docs/build/doctrees/api/poly_lithic.src.utils.messaging.doctree b/docs/build/doctrees/api/poly_lithic.src.utils.messaging.doctree
diff --git a/docs/build/doctrees/config.doctree b/docs/build/doctrees/config.doctree
diff --git a/docs/build/doctrees/environment.pickle b/docs/build/doctrees/environment.pickle
diff --git a/docs/build/doctrees/index.doctree b/docs/build/doctrees/index.doctree
diff --git a/docs/build/doctrees/interfaces.doctree b/docs/build/doctrees/interfaces.doctree
diff --git a/docs/build/doctrees/transformers.doctree b/docs/build/doctrees/transformers.doctree
diff --git a/docs/build/html/.buildinfo b/docs/build/html/.buildinfo
@@ -0,0 +1,4 @@
+# Sphinx build info version 1
+# This file records the configuration used when building these files. When it is not found, a full rebuild will be done.
+config: f3fa5c90ff625fc0342352252d74e923
+tags: 645f666f9bcd5a90fca523b33c5a78b7
diff --git a/docs/build/html/.buildinfo.bak b/docs/build/html/.buildinfo.bak
@@ -0,0 +1,4 @@
+# Sphinx build info version 1
+# This file records the configuration used when building these files. When it is not found, a full rebuild will be done.
+config: 97716ac4656efbec94163cb968cb166f
+tags: 645f666f9bcd5a90fca523b33c5a78b7
diff --git a/docs/build/html/_modules/index.html b/docs/build/html/_modules/index.html
@@ -0,0 +1,191 @@
+<!DOCTYPE html>
+<html lang="en"
+      data-content_root="../"
+      x-data="{ darkMode: localStorage.getItem('darkMode') || localStorage.setItem('darkMode', 'system'), activeSection: '' }"
+      x-init="$watch('darkMode', val => localStorage.setItem('darkMode', val))"
+      class="scroll-smooth"
+      :class="{'dark': darkMode === 'dark' || (darkMode === 'system' && window.matchMedia('(prefers-color-scheme: dark)').matches)}"
+>
+<head>
+  <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+  <meta charset="utf-8" />
+  <meta name="theme-color" media="(prefers-color-scheme: light)" content="white" />
+  <meta name="theme-color" media="(prefers-color-scheme: dark)" content="black" />
+
+    <title>Overview: module code | Poly-Lithic  documentation</title>
+    <meta property="og:title" content="Overview: module code | Poly-Lithic  documentation" />
+    <meta name="twitter:title" content="Overview: module code | Poly-Lithic  documentation" />
+      <link rel="stylesheet" type="text/css" href="../_static/pygments.css?v=e72c8e07" />
+      <link rel="stylesheet" type="text/css" href="../_static/theme.css?v=42baaae4" />
+        <link rel="search" title="Search" href="../search.html" />
+        <link rel="index" title="Index" href="../genindex.html" />
+
+    <script>
+    <!-- Prevent Flash of wrong theme -->
+      const userPreference = localStorage.getItem('darkMode');
+      let mode;
+      if (userPreference === 'dark' || window.matchMedia('(prefers-color-scheme: dark)').matches) {
+        mode = 'dark';
+        document.documentElement.classList.add('dark');
+      } else {
+        mode = 'light';
+      }
+      if (!userPreference) {localStorage.setItem('darkMode', mode)}
+    </script>
+</head>
+  <body x-data="{ showSidebar: false, showScrollTop: false }" class="min-h-screen font-sans antialiased bg-background text-foreground" :class="{ 'overflow-hidden': showSidebar }">
+    <div x-cloak x-show="showSidebar" class="fixed inset-0 z-50 overflow-hidden bg-background/80 backdrop-blur-sm md:hidden" @click.self="showSidebar = false"></div><div id="page" class="relative flex flex-col min-h-screen"><a href="#content" class="absolute top-0 left-0 z-[100] block bg-background p-4 text-xl transition -translate-x-full opacity-0 focus:translate-x-0 focus:opacity-100">
+      Skip to content
+    </a><header
+  class="sticky top-0 z-40 w-full border-b shadow-sm border-border supports-backdrop-blur:bg-background/60 bg-background/95 backdrop-blur"><div class="container flex items-center h-14">
+    <div class="hidden mr-4 md:flex">
+      <a href="../index.html" class="flex items-center mr-6"><span class="hidden font-bold sm:inline-block text-clip whitespace-nowrap">Poly-Lithic  documentation</span>
+      </a></div><button
+      class="inline-flex items-center justify-center h-10 px-0 py-2 mr-2 text-base font-medium transition-colors rounded-md hover:text-accent-foreground hover:bg-transparent md:hidden"
+      type="button" @click="showSidebar = true">
+      <svg xmlns="http://www.w3.org/2000/svg" height="24" width="24" viewBox="0 96 960 960" aria-hidden="true"
+        fill="currentColor">
+        <path
+          d="M152.587 825.087q-19.152 0-32.326-13.174t-13.174-32.326q0-19.152 13.174-32.326t32.326-13.174h440q19.152 0 32.326 13.174t13.174 32.326q0 19.152-13.174 32.326t-32.326 13.174h-440Zm0-203.587q-19.152 0-32.326-13.174T107.087 576q0-19.152 13.174-32.326t32.326-13.174h320q19.152 0 32.326 13.174T518.087 576q0 19.152-13.174 32.326T472.587 621.5h-320Zm0-203.587q-19.152 0-32.326-13.174t-13.174-32.326q0-19.152 13.174-32.326t32.326-13.174h440q19.152 0 32.326 13.174t13.174 32.326q0 19.152-13.174 32.326t-32.326 13.174h-440ZM708.913 576l112.174 112.174q12.674 12.674 12.674 31.826t-12.674 31.826Q808.413 764.5 789.261 764.5t-31.826-12.674l-144-144Q600 594.391 600 576t13.435-31.826l144-144q12.674-12.674 31.826-12.674t31.826 12.674q12.674 12.674 12.674 31.826t-12.674 31.826L708.913 576Z" />
+      </svg>
+      <span class="sr-only">Toggle navigation menu</span>
+    </button>
+    <div class="flex items-center justify-between flex-1 space-x-2 sm:space-x-4 md:justify-end">
+      <div class="flex-1 w-full md:w-auto md:flex-none"><form id="searchbox"
+      action="../search.html"
+      method="get"
+      class="relative flex items-center group"
+      @keydown.k.window.meta="$refs.search.focus()">
+  <input x-ref="search"
+          name="q"
+          id="search-input"
+          type="search"
+          aria-label="Search the docs"
+          placeholder="Search ..."
+          class="inline-flex items-center font-medium transition-colors bg-transparent focus-visible:outline-none focus-visible:ring-2 focus-visible:ring-ring focus-visible:ring-offset-2 ring-offset-background border border-input hover:bg-accent focus:bg-accent hover:text-accent-foreground focus:text-accent-foreground hover:placeholder-accent-foreground py-2 px-4 relative h-9 w-full justify-start rounded-[0.5rem] text-sm text-muted-foreground sm:pr-12 md:w-40 lg:w-64" />
+  <kbd class="pointer-events-none absolute right-1.5 top-2 hidden h-5 select-none text-muted-foreground items-center gap-1 rounded border border-border bg-muted px-1.5 font-mono text-[10px] font-medium opacity-100 sm:flex group-hover:bg-accent group-hover:text-accent-foreground">
+    <span class="text-xs">⌘</span>
+    K
+  </kbd>
+</form>
+      </div>
+      <nav class="flex items-center space-x-1">
+        <button @click="darkMode = darkMode === 'light' ? 'dark' : 'light'"
+          class="relative inline-flex items-center justify-center px-0 text-sm font-medium transition-colors rounded-md hover:bg-accent hover:text-accent-foreground h-9 w-9"
+          type="button"
+          aria-label="Color theme switcher">
+          <svg xmlns="http://www.w3.org/2000/svg" height="24" width="24" viewBox="0 96 960 960" fill="currentColor"
+            class="absolute transition-all scale-100 rotate-0 dark:-rotate-90 dark:scale-0">
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+          </svg>
+          <svg xmlns="http://www.w3.org/2000/svg" height="24" width="24" viewBox="0 96 960 960" fill="currentColor"
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+          </svg>
+        </button>
+      </nav>
+    </div>
+  </div>
+</header>
+
+    <div class="flex-1"><div class="container flex-1 items-start md:grid md:grid-cols-[220px_minmax(0,1fr)] md:gap-6 lg:grid-cols-[240px_minmax(0,1fr)] lg:gap-10"><aside id="left-sidebar"
+  class="fixed inset-y-0 left-0 md:top-14 z-50 md:z-30 bg-background md:bg-transparent transition-all duration-100 -translate-x-full md:translate-x-0 ml-0 p-6 md:p-0 md:-ml-2 md:h-[calc(100vh-3.5rem)] w-5/6 md:w-full shrink-0 overflow-y-auto border-r border-border md:sticky"
+  :aria-hidden="!showSidebar" :class="{ 'translate-x-0': showSidebar }">
+
+    <a href="../index.html" class="!justify-start text-sm md:!hidden bg-background"><span class="font-bold text-clip whitespace-nowrap">Poly-Lithic  documentation</span>
+    </a>
+
+    <div class="relative overflow-hidden md:overflow-auto my-4 md:my-0 h-[calc(100vh-8rem)] md:h-auto">
+      <div class="overflow-y-auto h-full w-full relative pr-6"><nav class="table w-full min-w-full my-6 lg:my-8">
+  <p class="caption" role="heading"><span class="caption-text">User Guide:</span></p>
+<ul>
+<li class="toctree-l1"><a class="reference internal" href="../transformers.html">Transformers Guide</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../interfaces.html">Interfaces Guide</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../config.html">Configuration Guide</a></li>
+</ul>
+<p class="caption" role="heading"><span class="caption-text">API Reference:</span></p>
+<ul>
+<li class="toctree-l1"><a class="reference internal" href="../api/poly_lithic.src.html">poly_lithic.src package</a></li>
+</ul>
+
+</nav>
+      </div>
+    </div>
+    <button type="button" @click="showSidebar = false"
+      class="absolute md:hidden right-4 top-4 rounded-sm opacity-70 transition-opacity hover:opacity-100">
+      <svg xmlns="http://www.w3.org/2000/svg" height="24" width="24" viewBox="0 96 960 960" fill="currentColor"
+        stroke="none" class="h-4 w-4">
+        <path
+          d="M480 632 284 828q-11 11-28 11t-28-11q-11-11-11-28t11-28l196-196-196-196q-11-11-11-28t11-28q11-11 28-11t28 11l196 196 196-196q11-11 28-11t28 11q11 11 11 28t-11 28L536 576l196 196q11 11 11 28t-11 28q-11 11-28 11t-28-11L480 632Z" />
+      </svg>
+    </button>
+  </aside>
+        <main class="relative py-6 lg:gap-10 lg:py-8 xl:grid xl:grid-cols-[1fr_300px]">
+<div class="w-full min-w-0 mx-auto">
+<nav aria-label="breadcrumbs"
+     class="flex items-center mb-4 space-x-1 text-sm text-muted-foreground">
+  <a class="overflow-hidden text-ellipsis whitespace-nowrap hover:text-foreground"
+     href="../index.html">
+    <span class="hidden md:inline">Poly-Lithic  documentation</span>
+    <svg xmlns="http://www.w3.org/2000/svg"
+         height="18"
+         width="18"
+         viewBox="0 96 960 960"
+         aria-label="Home"
+         fill="currentColor"
+         stroke="none"
+         class="md:hidden">
+      <path d="M240 856h120V616h240v240h120V496L480 316 240 496v360Zm-80 80V456l320-240 320 240v480H520V696h-80v240H160Zm320-350Z" />
+    </svg>
+  </a>
+
+<div class="mr-1">/</div><span aria-current="page"
+        class="font-medium text-foreground overflow-hidden text-ellipsis whitespace-nowrap">Overview: module code</span>
+</nav>
+
+    <div id="content" role="main">
+      <h1>All modules for which code is available</h1>
+<ul><li><a href="poly_lithic/scripts/main.html">poly_lithic.scripts.main</a></li>
+<li><a href="poly_lithic/src/cli.html">poly_lithic.src.cli</a></li>
+<li><a href="poly_lithic/src/config/config_object.html">poly_lithic.src.config.config_object</a></li>
+<li><a href="poly_lithic/src/config/parser.html">poly_lithic.src.config.parser</a></li>
+<li><a href="poly_lithic/src/interfaces.html">poly_lithic.src.interfaces</a></li>
+<ul><li><a href="poly_lithic/src/interfaces/BaseInterface.html">poly_lithic.src.interfaces.BaseInterface</a></li>
+<li><a href="poly_lithic/src/interfaces/file_interface.html">poly_lithic.src.interfaces.file_interface</a></li>
+<li><a href="poly_lithic/src/interfaces/k2eg_interface.html">poly_lithic.src.interfaces.k2eg_interface</a></li>
+<li><a href="poly_lithic/src/interfaces/p4p_interface.html">poly_lithic.src.interfaces.p4p_interface</a></li>
+</ul><li><a href="poly_lithic/src/logging_utils/make_logger.html">poly_lithic.src.logging_utils.make_logger</a></li>
+<li><a href="poly_lithic/src/model_utils/LocalModelGetter.html">poly_lithic.src.model_utils.LocalModelGetter</a></li>
+<li><a href="poly_lithic/src/model_utils/MlflowModelGetter.html">poly_lithic.src.model_utils.MlflowModelGetter</a></li>
+<li><a href="poly_lithic/src/model_utils/ModelGetterBase.html">poly_lithic.src.model_utils.ModelGetterBase</a></li>
+<li><a href="poly_lithic/src/transformers.html">poly_lithic.src.transformers</a></li>
+<ul><li><a href="poly_lithic/src/transformers/BaseTransformer.html">poly_lithic.src.transformers.BaseTransformer</a></li>
+<li><a href="poly_lithic/src/transformers/BaseTransformers.html">poly_lithic.src.transformers.BaseTransformers</a></li>
+<li><a href="poly_lithic/src/transformers/CompoundTransformer.html">poly_lithic.src.transformers.CompoundTransformer</a></li>
+</ul><li><a href="poly_lithic/src/utils/builder.html">poly_lithic.src.utils.builder</a></li>
+<li><a href="poly_lithic/src/utils/lazyInterfaceLoader.html">poly_lithic.src.utils.lazyInterfaceLoader</a></li>
+<li><a href="poly_lithic/src/utils/messaging.html">poly_lithic.src.utils.messaging</a></li>
+</ul>
+    </div></div>
+        </main>
+      </div>
+    </div><footer class="py-6 border-t border-border md:py-0">
+    <div class="container flex flex-col items-center justify-between gap-4 md:h-24 md:flex-row">
+      <div class="flex flex-col items-center gap-4 px-8 md:flex-row md:gap-2 md:px-0">
+        <p class="text-sm leading-loose text-center text-muted-foreground md:text-left">© 2025, Matuesz Leputa - ISIS Neutron and Muon Source at RAL - Science and Technology Facilities Council&nbsp;Built with <a class="font-medium underline underline-offset-4"
+    href="https://www.sphinx-doc.org"
+    rel="noreferrer">Sphinx 8.2.3</a></p>
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+</footer>
+  </div>
+
+    <script src="../_static/documentation_options.js?v=5929fcd5"></script>
+    <script src="../_static/doctools.js?v=9bcbadda"></script>
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+</body>
+</html>
-Original file line number
+Diff line change
@@ Expand Up / @@ -22,7 +22,7 @@ test.ipynb @@
     image_model
     test.h5
     .vscode
-    build
+    /build
     env.json
     creds.json
     test.py
@@ Expand Down @@