From 68c7f1bb8b409b3ba1c628541985d346cb8f0c21 Mon Sep 17 00:00:00 2001
From: Yin-Chi Chan <ycc39@cam.ac.uk>
Date: Sun, 5 May 2024 02:04:43 +0100
Subject: [PATCH] Rebuild docs

---
 docs/html/_modules/histopath_bim_des/bim.html                 | 2 +-
 docs/html/_modules/histopath_bim_des/config/arrivals.html     | 2 +-
 docs/html/_modules/histopath_bim_des/config/batching.html     | 2 +-
 docs/html/_modules/histopath_bim_des/config/config.html       | 2 +-
 .../html/_modules/histopath_bim_des/config/distributions.html | 2 +-
 docs/html/_modules/histopath_bim_des/config/global_vars.html  | 2 +-
 docs/html/_modules/histopath_bim_des/config/resources.html    | 2 +-
 docs/html/_modules/histopath_bim_des/config/runners.html      | 2 +-
 docs/html/_modules/histopath_bim_des/config/tasks.html        | 2 +-
 docs/html/_modules/histopath_bim_des/distribution.html        | 2 +-
 docs/html/_modules/histopath_bim_des/excel.html               | 2 +-
 docs/html/_modules/histopath_bim_des/model.html               | 2 +-
 docs/html/_modules/histopath_bim_des/process/core.html        | 2 +-
 .../_modules/histopath_bim_des/process/p10_reception.html     | 2 +-
 docs/html/_modules/histopath_bim_des/process/p20_cutup.html   | 2 +-
 .../_modules/histopath_bim_des/process/p30_processing.html    | 2 +-
 .../_modules/histopath_bim_des/process/p40_microtomy.html     | 2 +-
 .../html/_modules/histopath_bim_des/process/p50_staining.html | 2 +-
 .../_modules/histopath_bim_des/process/p60_labelling.html     | 2 +-
 .../html/_modules/histopath_bim_des/process/p70_scanning.html | 2 +-
 docs/html/_modules/histopath_bim_des/process/p80_qc.html      | 2 +-
 .../_modules/histopath_bim_des/process/p90_reporting.html     | 2 +-
 docs/html/_modules/histopath_bim_des/specimens.html           | 2 +-
 docs/html/_modules/index.html                                 | 2 +-
 docs/html/_sources/index.rst.txt                              | 2 +-
 docs/html/apidoc/histopath_bim_des.bim.html                   | 2 +-
 docs/html/apidoc/histopath_bim_des.config.arrivals.html       | 2 +-
 docs/html/apidoc/histopath_bim_des.config.batching.html       | 2 +-
 docs/html/apidoc/histopath_bim_des.config.config.html         | 2 +-
 docs/html/apidoc/histopath_bim_des.config.distributions.html  | 2 +-
 docs/html/apidoc/histopath_bim_des.config.global_vars.html    | 2 +-
 docs/html/apidoc/histopath_bim_des.config.html                | 2 +-
 docs/html/apidoc/histopath_bim_des.config.resources.html      | 2 +-
 docs/html/apidoc/histopath_bim_des.config.runners.html        | 2 +-
 docs/html/apidoc/histopath_bim_des.config.tasks.html          | 2 +-
 docs/html/apidoc/histopath_bim_des.distribution.html          | 2 +-
 docs/html/apidoc/histopath_bim_des.excel.html                 | 2 +-
 docs/html/apidoc/histopath_bim_des.html                       | 2 +-
 docs/html/apidoc/histopath_bim_des.model.html                 | 2 +-
 docs/html/apidoc/histopath_bim_des.process.core.html          | 2 +-
 docs/html/apidoc/histopath_bim_des.process.html               | 2 +-
 docs/html/apidoc/histopath_bim_des.process.p10_reception.html | 2 +-
 docs/html/apidoc/histopath_bim_des.process.p20_cutup.html     | 2 +-
 .../html/apidoc/histopath_bim_des.process.p30_processing.html | 2 +-
 docs/html/apidoc/histopath_bim_des.process.p40_microtomy.html | 2 +-
 docs/html/apidoc/histopath_bim_des.process.p50_staining.html  | 2 +-
 docs/html/apidoc/histopath_bim_des.process.p60_labelling.html | 2 +-
 docs/html/apidoc/histopath_bim_des.process.p70_scanning.html  | 2 +-
 docs/html/apidoc/histopath_bim_des.process.p80_qc.html        | 2 +-
 docs/html/apidoc/histopath_bim_des.process.p90_reporting.html | 2 +-
 docs/html/apidoc/histopath_bim_des.specimens.html             | 2 +-
 docs/html/apidoc/histopath_bim_des.util.html                  | 2 +-
 docs/html/apidoc/modules.html                                 | 2 +-
 docs/html/config.html                                         | 2 +-
 docs/html/genindex.html                                       | 2 +-
 docs/html/index.html                                          | 4 ++--
 docs/html/processes.html                                      | 2 +-
 docs/html/py-modindex.html                                    | 2 +-
 docs/html/search.html                                         | 2 +-
 docs/html/searchindex.js                                      | 2 +-
 docs/html/simulation.html                                     | 2 +-
 61 files changed, 62 insertions(+), 62 deletions(-)

diff --git a/docs/html/_modules/histopath_bim_des/bim.html b/docs/html/_modules/histopath_bim_des/bim.html
index d208ece..5ace3d1 100644
--- a/docs/html/_modules/histopath_bim_des/bim.html
+++ b/docs/html/_modules/histopath_bim_des/bim.html
@@ -46,7 +46,7 @@
 <li class="toctree-l1"><a class="reference internal" href="../../config.html">Model Configuration</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../../simulation.html">Simulation and KPI extraction</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../../processes.html">Histopathology processes</a></li>
-<li class="toctree-l1"><a class="reference external" href="`Jupyter notebooks &lt;https://github.com/yinchi/histopath-bim-des/tree/main/notebooks&gt;`_">`Jupyter notebooks &lt;https://github.com/yinchi/histopath-bim-des/tree/main/notebooks&gt;`_</a></li>
+<li class="toctree-l1"><a class="reference external" href="https://github.com/yinchi/histopath-bim-des/tree/main/notebooks">Jupyter notebooks</a></li>
 </ul>
 <p class="caption" role="heading"><span class="caption-text">API reference:</span></p>
 <ul>
diff --git a/docs/html/_modules/histopath_bim_des/config/arrivals.html b/docs/html/_modules/histopath_bim_des/config/arrivals.html
index 2a58eea..01e0f0b 100644
--- a/docs/html/_modules/histopath_bim_des/config/arrivals.html
+++ b/docs/html/_modules/histopath_bim_des/config/arrivals.html
@@ -46,7 +46,7 @@
 <li class="toctree-l1"><a class="reference internal" href="../../../config.html">Model Configuration</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../../../simulation.html">Simulation and KPI extraction</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../../../processes.html">Histopathology processes</a></li>
-<li class="toctree-l1"><a class="reference external" href="`Jupyter notebooks &lt;https://github.com/yinchi/histopath-bim-des/tree/main/notebooks&gt;`_">`Jupyter notebooks &lt;https://github.com/yinchi/histopath-bim-des/tree/main/notebooks&gt;`_</a></li>
+<li class="toctree-l1"><a class="reference external" href="https://github.com/yinchi/histopath-bim-des/tree/main/notebooks">Jupyter notebooks</a></li>
 </ul>
 <p class="caption" role="heading"><span class="caption-text">API reference:</span></p>
 <ul>
diff --git a/docs/html/_modules/histopath_bim_des/config/batching.html b/docs/html/_modules/histopath_bim_des/config/batching.html
index 32df9ba..19436e0 100644
--- a/docs/html/_modules/histopath_bim_des/config/batching.html
+++ b/docs/html/_modules/histopath_bim_des/config/batching.html
@@ -46,7 +46,7 @@
 <li class="toctree-l1"><a class="reference internal" href="../../../config.html">Model Configuration</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../../../simulation.html">Simulation and KPI extraction</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../../../processes.html">Histopathology processes</a></li>
-<li class="toctree-l1"><a class="reference external" href="`Jupyter notebooks &lt;https://github.com/yinchi/histopath-bim-des/tree/main/notebooks&gt;`_">`Jupyter notebooks &lt;https://github.com/yinchi/histopath-bim-des/tree/main/notebooks&gt;`_</a></li>
+<li class="toctree-l1"><a class="reference external" href="https://github.com/yinchi/histopath-bim-des/tree/main/notebooks">Jupyter notebooks</a></li>
 </ul>
 <p class="caption" role="heading"><span class="caption-text">API reference:</span></p>
 <ul>
diff --git a/docs/html/_modules/histopath_bim_des/config/config.html b/docs/html/_modules/histopath_bim_des/config/config.html
index f2cee05..f04e3ed 100644
--- a/docs/html/_modules/histopath_bim_des/config/config.html
+++ b/docs/html/_modules/histopath_bim_des/config/config.html
@@ -46,7 +46,7 @@
 <li class="toctree-l1"><a class="reference internal" href="../../../config.html">Model Configuration</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../../../simulation.html">Simulation and KPI extraction</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../../../processes.html">Histopathology processes</a></li>
-<li class="toctree-l1"><a class="reference external" href="`Jupyter notebooks &lt;https://github.com/yinchi/histopath-bim-des/tree/main/notebooks&gt;`_">`Jupyter notebooks &lt;https://github.com/yinchi/histopath-bim-des/tree/main/notebooks&gt;`_</a></li>
+<li class="toctree-l1"><a class="reference external" href="https://github.com/yinchi/histopath-bim-des/tree/main/notebooks">Jupyter notebooks</a></li>
 </ul>
 <p class="caption" role="heading"><span class="caption-text">API reference:</span></p>
 <ul>
diff --git a/docs/html/_modules/histopath_bim_des/config/distributions.html b/docs/html/_modules/histopath_bim_des/config/distributions.html
index 9e543ae..e6d0571 100644
--- a/docs/html/_modules/histopath_bim_des/config/distributions.html
+++ b/docs/html/_modules/histopath_bim_des/config/distributions.html
@@ -46,7 +46,7 @@
 <li class="toctree-l1"><a class="reference internal" href="../../../config.html">Model Configuration</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../../../simulation.html">Simulation and KPI extraction</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../../../processes.html">Histopathology processes</a></li>
-<li class="toctree-l1"><a class="reference external" href="`Jupyter notebooks &lt;https://github.com/yinchi/histopath-bim-des/tree/main/notebooks&gt;`_">`Jupyter notebooks &lt;https://github.com/yinchi/histopath-bim-des/tree/main/notebooks&gt;`_</a></li>
+<li class="toctree-l1"><a class="reference external" href="https://github.com/yinchi/histopath-bim-des/tree/main/notebooks">Jupyter notebooks</a></li>
 </ul>
 <p class="caption" role="heading"><span class="caption-text">API reference:</span></p>
 <ul>
diff --git a/docs/html/_modules/histopath_bim_des/config/global_vars.html b/docs/html/_modules/histopath_bim_des/config/global_vars.html
index 629bab0..532358c 100644
--- a/docs/html/_modules/histopath_bim_des/config/global_vars.html
+++ b/docs/html/_modules/histopath_bim_des/config/global_vars.html
@@ -46,7 +46,7 @@
 <li class="toctree-l1"><a class="reference internal" href="../../../config.html">Model Configuration</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../../../simulation.html">Simulation and KPI extraction</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../../../processes.html">Histopathology processes</a></li>
-<li class="toctree-l1"><a class="reference external" href="`Jupyter notebooks &lt;https://github.com/yinchi/histopath-bim-des/tree/main/notebooks&gt;`_">`Jupyter notebooks &lt;https://github.com/yinchi/histopath-bim-des/tree/main/notebooks&gt;`_</a></li>
+<li class="toctree-l1"><a class="reference external" href="https://github.com/yinchi/histopath-bim-des/tree/main/notebooks">Jupyter notebooks</a></li>
 </ul>
 <p class="caption" role="heading"><span class="caption-text">API reference:</span></p>
 <ul>
diff --git a/docs/html/_modules/histopath_bim_des/config/resources.html b/docs/html/_modules/histopath_bim_des/config/resources.html
index 05aa4bf..1af758a 100644
--- a/docs/html/_modules/histopath_bim_des/config/resources.html
+++ b/docs/html/_modules/histopath_bim_des/config/resources.html
@@ -46,7 +46,7 @@
 <li class="toctree-l1"><a class="reference internal" href="../../../config.html">Model Configuration</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../../../simulation.html">Simulation and KPI extraction</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../../../processes.html">Histopathology processes</a></li>
-<li class="toctree-l1"><a class="reference external" href="`Jupyter notebooks &lt;https://github.com/yinchi/histopath-bim-des/tree/main/notebooks&gt;`_">`Jupyter notebooks &lt;https://github.com/yinchi/histopath-bim-des/tree/main/notebooks&gt;`_</a></li>
+<li class="toctree-l1"><a class="reference external" href="https://github.com/yinchi/histopath-bim-des/tree/main/notebooks">Jupyter notebooks</a></li>
 </ul>
 <p class="caption" role="heading"><span class="caption-text">API reference:</span></p>
 <ul>
diff --git a/docs/html/_modules/histopath_bim_des/config/runners.html b/docs/html/_modules/histopath_bim_des/config/runners.html
index b2a82bc..218930b 100644
--- a/docs/html/_modules/histopath_bim_des/config/runners.html
+++ b/docs/html/_modules/histopath_bim_des/config/runners.html
@@ -46,7 +46,7 @@
 <li class="toctree-l1"><a class="reference internal" href="../../../config.html">Model Configuration</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../../../simulation.html">Simulation and KPI extraction</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../../../processes.html">Histopathology processes</a></li>
-<li class="toctree-l1"><a class="reference external" href="`Jupyter notebooks &lt;https://github.com/yinchi/histopath-bim-des/tree/main/notebooks&gt;`_">`Jupyter notebooks &lt;https://github.com/yinchi/histopath-bim-des/tree/main/notebooks&gt;`_</a></li>
+<li class="toctree-l1"><a class="reference external" href="https://github.com/yinchi/histopath-bim-des/tree/main/notebooks">Jupyter notebooks</a></li>
 </ul>
 <p class="caption" role="heading"><span class="caption-text">API reference:</span></p>
 <ul>
diff --git a/docs/html/_modules/histopath_bim_des/config/tasks.html b/docs/html/_modules/histopath_bim_des/config/tasks.html
index fe887bb..0f8053a 100644
--- a/docs/html/_modules/histopath_bim_des/config/tasks.html
+++ b/docs/html/_modules/histopath_bim_des/config/tasks.html
@@ -46,7 +46,7 @@
 <li class="toctree-l1"><a class="reference internal" href="../../../config.html">Model Configuration</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../../../simulation.html">Simulation and KPI extraction</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../../../processes.html">Histopathology processes</a></li>
-<li class="toctree-l1"><a class="reference external" href="`Jupyter notebooks &lt;https://github.com/yinchi/histopath-bim-des/tree/main/notebooks&gt;`_">`Jupyter notebooks &lt;https://github.com/yinchi/histopath-bim-des/tree/main/notebooks&gt;`_</a></li>
+<li class="toctree-l1"><a class="reference external" href="https://github.com/yinchi/histopath-bim-des/tree/main/notebooks">Jupyter notebooks</a></li>
 </ul>
 <p class="caption" role="heading"><span class="caption-text">API reference:</span></p>
 <ul>
diff --git a/docs/html/_modules/histopath_bim_des/distribution.html b/docs/html/_modules/histopath_bim_des/distribution.html
index dcba46d..98c9a3b 100644
--- a/docs/html/_modules/histopath_bim_des/distribution.html
+++ b/docs/html/_modules/histopath_bim_des/distribution.html
@@ -46,7 +46,7 @@
 <li class="toctree-l1"><a class="reference internal" href="../../config.html">Model Configuration</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../../simulation.html">Simulation and KPI extraction</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../../processes.html">Histopathology processes</a></li>
-<li class="toctree-l1"><a class="reference external" href="`Jupyter notebooks &lt;https://github.com/yinchi/histopath-bim-des/tree/main/notebooks&gt;`_">`Jupyter notebooks &lt;https://github.com/yinchi/histopath-bim-des/tree/main/notebooks&gt;`_</a></li>
+<li class="toctree-l1"><a class="reference external" href="https://github.com/yinchi/histopath-bim-des/tree/main/notebooks">Jupyter notebooks</a></li>
 </ul>
 <p class="caption" role="heading"><span class="caption-text">API reference:</span></p>
 <ul>
diff --git a/docs/html/_modules/histopath_bim_des/excel.html b/docs/html/_modules/histopath_bim_des/excel.html
index 4406349..16fa6cd 100644
--- a/docs/html/_modules/histopath_bim_des/excel.html
+++ b/docs/html/_modules/histopath_bim_des/excel.html
@@ -46,7 +46,7 @@
 <li class="toctree-l1"><a class="reference internal" href="../../config.html">Model Configuration</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../../simulation.html">Simulation and KPI extraction</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../../processes.html">Histopathology processes</a></li>
-<li class="toctree-l1"><a class="reference external" href="`Jupyter notebooks &lt;https://github.com/yinchi/histopath-bim-des/tree/main/notebooks&gt;`_">`Jupyter notebooks &lt;https://github.com/yinchi/histopath-bim-des/tree/main/notebooks&gt;`_</a></li>
+<li class="toctree-l1"><a class="reference external" href="https://github.com/yinchi/histopath-bim-des/tree/main/notebooks">Jupyter notebooks</a></li>
 </ul>
 <p class="caption" role="heading"><span class="caption-text">API reference:</span></p>
 <ul>
diff --git a/docs/html/_modules/histopath_bim_des/model.html b/docs/html/_modules/histopath_bim_des/model.html
index a126a34..32316ad 100644
--- a/docs/html/_modules/histopath_bim_des/model.html
+++ b/docs/html/_modules/histopath_bim_des/model.html
@@ -46,7 +46,7 @@
 <li class="toctree-l1"><a class="reference internal" href="../../config.html">Model Configuration</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../../simulation.html">Simulation and KPI extraction</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../../processes.html">Histopathology processes</a></li>
-<li class="toctree-l1"><a class="reference external" href="`Jupyter notebooks &lt;https://github.com/yinchi/histopath-bim-des/tree/main/notebooks&gt;`_">`Jupyter notebooks &lt;https://github.com/yinchi/histopath-bim-des/tree/main/notebooks&gt;`_</a></li>
+<li class="toctree-l1"><a class="reference external" href="https://github.com/yinchi/histopath-bim-des/tree/main/notebooks">Jupyter notebooks</a></li>
 </ul>
 <p class="caption" role="heading"><span class="caption-text">API reference:</span></p>
 <ul>
diff --git a/docs/html/_modules/histopath_bim_des/process/core.html b/docs/html/_modules/histopath_bim_des/process/core.html
index 97fc473..29e1062 100644
--- a/docs/html/_modules/histopath_bim_des/process/core.html
+++ b/docs/html/_modules/histopath_bim_des/process/core.html
@@ -46,7 +46,7 @@
 <li class="toctree-l1"><a class="reference internal" href="../../../config.html">Model Configuration</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../../../simulation.html">Simulation and KPI extraction</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../../../processes.html">Histopathology processes</a></li>
-<li class="toctree-l1"><a class="reference external" href="`Jupyter notebooks &lt;https://github.com/yinchi/histopath-bim-des/tree/main/notebooks&gt;`_">`Jupyter notebooks &lt;https://github.com/yinchi/histopath-bim-des/tree/main/notebooks&gt;`_</a></li>
+<li class="toctree-l1"><a class="reference external" href="https://github.com/yinchi/histopath-bim-des/tree/main/notebooks">Jupyter notebooks</a></li>
 </ul>
 <p class="caption" role="heading"><span class="caption-text">API reference:</span></p>
 <ul>
diff --git a/docs/html/_modules/histopath_bim_des/process/p10_reception.html b/docs/html/_modules/histopath_bim_des/process/p10_reception.html
index 21abb82..79764c1 100644
--- a/docs/html/_modules/histopath_bim_des/process/p10_reception.html
+++ b/docs/html/_modules/histopath_bim_des/process/p10_reception.html
@@ -46,7 +46,7 @@
 <li class="toctree-l1"><a class="reference internal" href="../../../config.html">Model Configuration</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../../../simulation.html">Simulation and KPI extraction</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../../../processes.html">Histopathology processes</a></li>
-<li class="toctree-l1"><a class="reference external" href="`Jupyter notebooks &lt;https://github.com/yinchi/histopath-bim-des/tree/main/notebooks&gt;`_">`Jupyter notebooks &lt;https://github.com/yinchi/histopath-bim-des/tree/main/notebooks&gt;`_</a></li>
+<li class="toctree-l1"><a class="reference external" href="https://github.com/yinchi/histopath-bim-des/tree/main/notebooks">Jupyter notebooks</a></li>
 </ul>
 <p class="caption" role="heading"><span class="caption-text">API reference:</span></p>
 <ul>
diff --git a/docs/html/_modules/histopath_bim_des/process/p20_cutup.html b/docs/html/_modules/histopath_bim_des/process/p20_cutup.html
index 91366c5..9753861 100644
--- a/docs/html/_modules/histopath_bim_des/process/p20_cutup.html
+++ b/docs/html/_modules/histopath_bim_des/process/p20_cutup.html
@@ -46,7 +46,7 @@
 <li class="toctree-l1"><a class="reference internal" href="../../../config.html">Model Configuration</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../../../simulation.html">Simulation and KPI extraction</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../../../processes.html">Histopathology processes</a></li>
-<li class="toctree-l1"><a class="reference external" href="`Jupyter notebooks &lt;https://github.com/yinchi/histopath-bim-des/tree/main/notebooks&gt;`_">`Jupyter notebooks &lt;https://github.com/yinchi/histopath-bim-des/tree/main/notebooks&gt;`_</a></li>
+<li class="toctree-l1"><a class="reference external" href="https://github.com/yinchi/histopath-bim-des/tree/main/notebooks">Jupyter notebooks</a></li>
 </ul>
 <p class="caption" role="heading"><span class="caption-text">API reference:</span></p>
 <ul>
diff --git a/docs/html/_modules/histopath_bim_des/process/p30_processing.html b/docs/html/_modules/histopath_bim_des/process/p30_processing.html
index 13c2040..b375b8b 100644
--- a/docs/html/_modules/histopath_bim_des/process/p30_processing.html
+++ b/docs/html/_modules/histopath_bim_des/process/p30_processing.html
@@ -46,7 +46,7 @@
 <li class="toctree-l1"><a class="reference internal" href="../../../config.html">Model Configuration</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../../../simulation.html">Simulation and KPI extraction</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../../../processes.html">Histopathology processes</a></li>
-<li class="toctree-l1"><a class="reference external" href="`Jupyter notebooks &lt;https://github.com/yinchi/histopath-bim-des/tree/main/notebooks&gt;`_">`Jupyter notebooks &lt;https://github.com/yinchi/histopath-bim-des/tree/main/notebooks&gt;`_</a></li>
+<li class="toctree-l1"><a class="reference external" href="https://github.com/yinchi/histopath-bim-des/tree/main/notebooks">Jupyter notebooks</a></li>
 </ul>
 <p class="caption" role="heading"><span class="caption-text">API reference:</span></p>
 <ul>
diff --git a/docs/html/_modules/histopath_bim_des/process/p40_microtomy.html b/docs/html/_modules/histopath_bim_des/process/p40_microtomy.html
index e12d1b3..430ff2f 100644
--- a/docs/html/_modules/histopath_bim_des/process/p40_microtomy.html
+++ b/docs/html/_modules/histopath_bim_des/process/p40_microtomy.html
@@ -46,7 +46,7 @@
 <li class="toctree-l1"><a class="reference internal" href="../../../config.html">Model Configuration</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../../../simulation.html">Simulation and KPI extraction</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../../../processes.html">Histopathology processes</a></li>
-<li class="toctree-l1"><a class="reference external" href="`Jupyter notebooks &lt;https://github.com/yinchi/histopath-bim-des/tree/main/notebooks&gt;`_">`Jupyter notebooks &lt;https://github.com/yinchi/histopath-bim-des/tree/main/notebooks&gt;`_</a></li>
+<li class="toctree-l1"><a class="reference external" href="https://github.com/yinchi/histopath-bim-des/tree/main/notebooks">Jupyter notebooks</a></li>
 </ul>
 <p class="caption" role="heading"><span class="caption-text">API reference:</span></p>
 <ul>
diff --git a/docs/html/_modules/histopath_bim_des/process/p50_staining.html b/docs/html/_modules/histopath_bim_des/process/p50_staining.html
index 9a34b24..00b7ca6 100644
--- a/docs/html/_modules/histopath_bim_des/process/p50_staining.html
+++ b/docs/html/_modules/histopath_bim_des/process/p50_staining.html
@@ -46,7 +46,7 @@
 <li class="toctree-l1"><a class="reference internal" href="../../../config.html">Model Configuration</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../../../simulation.html">Simulation and KPI extraction</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../../../processes.html">Histopathology processes</a></li>
-<li class="toctree-l1"><a class="reference external" href="`Jupyter notebooks &lt;https://github.com/yinchi/histopath-bim-des/tree/main/notebooks&gt;`_">`Jupyter notebooks &lt;https://github.com/yinchi/histopath-bim-des/tree/main/notebooks&gt;`_</a></li>
+<li class="toctree-l1"><a class="reference external" href="https://github.com/yinchi/histopath-bim-des/tree/main/notebooks">Jupyter notebooks</a></li>
 </ul>
 <p class="caption" role="heading"><span class="caption-text">API reference:</span></p>
 <ul>
diff --git a/docs/html/_modules/histopath_bim_des/process/p60_labelling.html b/docs/html/_modules/histopath_bim_des/process/p60_labelling.html
index c5590c6..3e04579 100644
--- a/docs/html/_modules/histopath_bim_des/process/p60_labelling.html
+++ b/docs/html/_modules/histopath_bim_des/process/p60_labelling.html
@@ -46,7 +46,7 @@
 <li class="toctree-l1"><a class="reference internal" href="../../../config.html">Model Configuration</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../../../simulation.html">Simulation and KPI extraction</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../../../processes.html">Histopathology processes</a></li>
-<li class="toctree-l1"><a class="reference external" href="`Jupyter notebooks &lt;https://github.com/yinchi/histopath-bim-des/tree/main/notebooks&gt;`_">`Jupyter notebooks &lt;https://github.com/yinchi/histopath-bim-des/tree/main/notebooks&gt;`_</a></li>
+<li class="toctree-l1"><a class="reference external" href="https://github.com/yinchi/histopath-bim-des/tree/main/notebooks">Jupyter notebooks</a></li>
 </ul>
 <p class="caption" role="heading"><span class="caption-text">API reference:</span></p>
 <ul>
diff --git a/docs/html/_modules/histopath_bim_des/process/p70_scanning.html b/docs/html/_modules/histopath_bim_des/process/p70_scanning.html
index ae5735e..2c7ee1f 100644
--- a/docs/html/_modules/histopath_bim_des/process/p70_scanning.html
+++ b/docs/html/_modules/histopath_bim_des/process/p70_scanning.html
@@ -46,7 +46,7 @@
 <li class="toctree-l1"><a class="reference internal" href="../../../config.html">Model Configuration</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../../../simulation.html">Simulation and KPI extraction</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../../../processes.html">Histopathology processes</a></li>
-<li class="toctree-l1"><a class="reference external" href="`Jupyter notebooks &lt;https://github.com/yinchi/histopath-bim-des/tree/main/notebooks&gt;`_">`Jupyter notebooks &lt;https://github.com/yinchi/histopath-bim-des/tree/main/notebooks&gt;`_</a></li>
+<li class="toctree-l1"><a class="reference external" href="https://github.com/yinchi/histopath-bim-des/tree/main/notebooks">Jupyter notebooks</a></li>
 </ul>
 <p class="caption" role="heading"><span class="caption-text">API reference:</span></p>
 <ul>
diff --git a/docs/html/_modules/histopath_bim_des/process/p80_qc.html b/docs/html/_modules/histopath_bim_des/process/p80_qc.html
index 4e52d14..c0334b7 100644
--- a/docs/html/_modules/histopath_bim_des/process/p80_qc.html
+++ b/docs/html/_modules/histopath_bim_des/process/p80_qc.html
@@ -46,7 +46,7 @@
 <li class="toctree-l1"><a class="reference internal" href="../../../config.html">Model Configuration</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../../../simulation.html">Simulation and KPI extraction</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../../../processes.html">Histopathology processes</a></li>
-<li class="toctree-l1"><a class="reference external" href="`Jupyter notebooks &lt;https://github.com/yinchi/histopath-bim-des/tree/main/notebooks&gt;`_">`Jupyter notebooks &lt;https://github.com/yinchi/histopath-bim-des/tree/main/notebooks&gt;`_</a></li>
+<li class="toctree-l1"><a class="reference external" href="https://github.com/yinchi/histopath-bim-des/tree/main/notebooks">Jupyter notebooks</a></li>
 </ul>
 <p class="caption" role="heading"><span class="caption-text">API reference:</span></p>
 <ul>
diff --git a/docs/html/_modules/histopath_bim_des/process/p90_reporting.html b/docs/html/_modules/histopath_bim_des/process/p90_reporting.html
index 88bd83e..b0f537f 100644
--- a/docs/html/_modules/histopath_bim_des/process/p90_reporting.html
+++ b/docs/html/_modules/histopath_bim_des/process/p90_reporting.html
@@ -46,7 +46,7 @@
 <li class="toctree-l1"><a class="reference internal" href="../../../config.html">Model Configuration</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../../../simulation.html">Simulation and KPI extraction</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../../../processes.html">Histopathology processes</a></li>
-<li class="toctree-l1"><a class="reference external" href="`Jupyter notebooks &lt;https://github.com/yinchi/histopath-bim-des/tree/main/notebooks&gt;`_">`Jupyter notebooks &lt;https://github.com/yinchi/histopath-bim-des/tree/main/notebooks&gt;`_</a></li>
+<li class="toctree-l1"><a class="reference external" href="https://github.com/yinchi/histopath-bim-des/tree/main/notebooks">Jupyter notebooks</a></li>
 </ul>
 <p class="caption" role="heading"><span class="caption-text">API reference:</span></p>
 <ul>
diff --git a/docs/html/_modules/histopath_bim_des/specimens.html b/docs/html/_modules/histopath_bim_des/specimens.html
index 5f362a8..13e3542 100644
--- a/docs/html/_modules/histopath_bim_des/specimens.html
+++ b/docs/html/_modules/histopath_bim_des/specimens.html
@@ -46,7 +46,7 @@
 <li class="toctree-l1"><a class="reference internal" href="../../config.html">Model Configuration</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../../simulation.html">Simulation and KPI extraction</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../../processes.html">Histopathology processes</a></li>
-<li class="toctree-l1"><a class="reference external" href="`Jupyter notebooks &lt;https://github.com/yinchi/histopath-bim-des/tree/main/notebooks&gt;`_">`Jupyter notebooks &lt;https://github.com/yinchi/histopath-bim-des/tree/main/notebooks&gt;`_</a></li>
+<li class="toctree-l1"><a class="reference external" href="https://github.com/yinchi/histopath-bim-des/tree/main/notebooks">Jupyter notebooks</a></li>
 </ul>
 <p class="caption" role="heading"><span class="caption-text">API reference:</span></p>
 <ul>
diff --git a/docs/html/_modules/index.html b/docs/html/_modules/index.html
index f0b62c9..68df053 100644
--- a/docs/html/_modules/index.html
+++ b/docs/html/_modules/index.html
@@ -46,7 +46,7 @@
 <li class="toctree-l1"><a class="reference internal" href="../config.html">Model Configuration</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../simulation.html">Simulation and KPI extraction</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../processes.html">Histopathology processes</a></li>
-<li class="toctree-l1"><a class="reference external" href="`Jupyter notebooks &lt;https://github.com/yinchi/histopath-bim-des/tree/main/notebooks&gt;`_">`Jupyter notebooks &lt;https://github.com/yinchi/histopath-bim-des/tree/main/notebooks&gt;`_</a></li>
+<li class="toctree-l1"><a class="reference external" href="https://github.com/yinchi/histopath-bim-des/tree/main/notebooks">Jupyter notebooks</a></li>
 </ul>
 <p class="caption" role="heading"><span class="caption-text">API reference:</span></p>
 <ul>
diff --git a/docs/html/_sources/index.rst.txt b/docs/html/_sources/index.rst.txt
index 3cb377b..738517a 100644
--- a/docs/html/_sources/index.rst.txt
+++ b/docs/html/_sources/index.rst.txt
@@ -25,7 +25,7 @@ Examples can be found in the ``notebooks/`` directory of this project.
    config
    simulation
    processes
-   `Jupyter notebooks <https://github.com/yinchi/histopath-bim-des/tree/main/notebooks>`_
+   Jupyter notebooks <https://github.com/yinchi/histopath-bim-des/tree/main/notebooks>
 
 .. toctree::
    :maxdepth: 2
diff --git a/docs/html/apidoc/histopath_bim_des.bim.html b/docs/html/apidoc/histopath_bim_des.bim.html
index a56769e..7daa771 100644
--- a/docs/html/apidoc/histopath_bim_des.bim.html
+++ b/docs/html/apidoc/histopath_bim_des.bim.html
@@ -49,7 +49,7 @@
 <li class="toctree-l1"><a class="reference internal" href="../config.html">Model Configuration</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../simulation.html">Simulation and KPI extraction</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../processes.html">Histopathology processes</a></li>
-<li class="toctree-l1"><a class="reference external" href="`Jupyter notebooks &lt;https://github.com/yinchi/histopath-bim-des/tree/main/notebooks&gt;`_">`Jupyter notebooks &lt;https://github.com/yinchi/histopath-bim-des/tree/main/notebooks&gt;`_</a></li>
+<li class="toctree-l1"><a class="reference external" href="https://github.com/yinchi/histopath-bim-des/tree/main/notebooks">Jupyter notebooks</a></li>
 </ul>
 <p class="caption" role="heading"><span class="caption-text">API reference:</span></p>
 <ul class="current">
diff --git a/docs/html/apidoc/histopath_bim_des.config.arrivals.html b/docs/html/apidoc/histopath_bim_des.config.arrivals.html
index 10af604..7851f61 100644
--- a/docs/html/apidoc/histopath_bim_des.config.arrivals.html
+++ b/docs/html/apidoc/histopath_bim_des.config.arrivals.html
@@ -49,7 +49,7 @@
 <li class="toctree-l1"><a class="reference internal" href="../config.html">Model Configuration</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../simulation.html">Simulation and KPI extraction</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../processes.html">Histopathology processes</a></li>
-<li class="toctree-l1"><a class="reference external" href="`Jupyter notebooks &lt;https://github.com/yinchi/histopath-bim-des/tree/main/notebooks&gt;`_">`Jupyter notebooks &lt;https://github.com/yinchi/histopath-bim-des/tree/main/notebooks&gt;`_</a></li>
+<li class="toctree-l1"><a class="reference external" href="https://github.com/yinchi/histopath-bim-des/tree/main/notebooks">Jupyter notebooks</a></li>
 </ul>
 <p class="caption" role="heading"><span class="caption-text">API reference:</span></p>
 <ul class="current">
diff --git a/docs/html/apidoc/histopath_bim_des.config.batching.html b/docs/html/apidoc/histopath_bim_des.config.batching.html
index fbc3f92..e73670d 100644
--- a/docs/html/apidoc/histopath_bim_des.config.batching.html
+++ b/docs/html/apidoc/histopath_bim_des.config.batching.html
@@ -49,7 +49,7 @@
 <li class="toctree-l1"><a class="reference internal" href="../config.html">Model Configuration</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../simulation.html">Simulation and KPI extraction</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../processes.html">Histopathology processes</a></li>
-<li class="toctree-l1"><a class="reference external" href="`Jupyter notebooks &lt;https://github.com/yinchi/histopath-bim-des/tree/main/notebooks&gt;`_">`Jupyter notebooks &lt;https://github.com/yinchi/histopath-bim-des/tree/main/notebooks&gt;`_</a></li>
+<li class="toctree-l1"><a class="reference external" href="https://github.com/yinchi/histopath-bim-des/tree/main/notebooks">Jupyter notebooks</a></li>
 </ul>
 <p class="caption" role="heading"><span class="caption-text">API reference:</span></p>
 <ul class="current">
diff --git a/docs/html/apidoc/histopath_bim_des.config.config.html b/docs/html/apidoc/histopath_bim_des.config.config.html
index 3e50095..49edc2e 100644
--- a/docs/html/apidoc/histopath_bim_des.config.config.html
+++ b/docs/html/apidoc/histopath_bim_des.config.config.html
@@ -49,7 +49,7 @@
 <li class="toctree-l1"><a class="reference internal" href="../config.html">Model Configuration</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../simulation.html">Simulation and KPI extraction</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../processes.html">Histopathology processes</a></li>
-<li class="toctree-l1"><a class="reference external" href="`Jupyter notebooks &lt;https://github.com/yinchi/histopath-bim-des/tree/main/notebooks&gt;`_">`Jupyter notebooks &lt;https://github.com/yinchi/histopath-bim-des/tree/main/notebooks&gt;`_</a></li>
+<li class="toctree-l1"><a class="reference external" href="https://github.com/yinchi/histopath-bim-des/tree/main/notebooks">Jupyter notebooks</a></li>
 </ul>
 <p class="caption" role="heading"><span class="caption-text">API reference:</span></p>
 <ul class="current">
diff --git a/docs/html/apidoc/histopath_bim_des.config.distributions.html b/docs/html/apidoc/histopath_bim_des.config.distributions.html
index 4a82733..173dfa3 100644
--- a/docs/html/apidoc/histopath_bim_des.config.distributions.html
+++ b/docs/html/apidoc/histopath_bim_des.config.distributions.html
@@ -49,7 +49,7 @@
 <li class="toctree-l1"><a class="reference internal" href="../config.html">Model Configuration</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../simulation.html">Simulation and KPI extraction</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../processes.html">Histopathology processes</a></li>
-<li class="toctree-l1"><a class="reference external" href="`Jupyter notebooks &lt;https://github.com/yinchi/histopath-bim-des/tree/main/notebooks&gt;`_">`Jupyter notebooks &lt;https://github.com/yinchi/histopath-bim-des/tree/main/notebooks&gt;`_</a></li>
+<li class="toctree-l1"><a class="reference external" href="https://github.com/yinchi/histopath-bim-des/tree/main/notebooks">Jupyter notebooks</a></li>
 </ul>
 <p class="caption" role="heading"><span class="caption-text">API reference:</span></p>
 <ul class="current">
diff --git a/docs/html/apidoc/histopath_bim_des.config.global_vars.html b/docs/html/apidoc/histopath_bim_des.config.global_vars.html
index 6d5392b..b82ff7b 100644
--- a/docs/html/apidoc/histopath_bim_des.config.global_vars.html
+++ b/docs/html/apidoc/histopath_bim_des.config.global_vars.html
@@ -49,7 +49,7 @@
 <li class="toctree-l1"><a class="reference internal" href="../config.html">Model Configuration</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../simulation.html">Simulation and KPI extraction</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../processes.html">Histopathology processes</a></li>
-<li class="toctree-l1"><a class="reference external" href="`Jupyter notebooks &lt;https://github.com/yinchi/histopath-bim-des/tree/main/notebooks&gt;`_">`Jupyter notebooks &lt;https://github.com/yinchi/histopath-bim-des/tree/main/notebooks&gt;`_</a></li>
+<li class="toctree-l1"><a class="reference external" href="https://github.com/yinchi/histopath-bim-des/tree/main/notebooks">Jupyter notebooks</a></li>
 </ul>
 <p class="caption" role="heading"><span class="caption-text">API reference:</span></p>
 <ul class="current">
diff --git a/docs/html/apidoc/histopath_bim_des.config.html b/docs/html/apidoc/histopath_bim_des.config.html
index b08fb9f..2c98432 100644
--- a/docs/html/apidoc/histopath_bim_des.config.html
+++ b/docs/html/apidoc/histopath_bim_des.config.html
@@ -49,7 +49,7 @@
 <li class="toctree-l1"><a class="reference internal" href="../config.html">Model Configuration</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../simulation.html">Simulation and KPI extraction</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../processes.html">Histopathology processes</a></li>
-<li class="toctree-l1"><a class="reference external" href="`Jupyter notebooks &lt;https://github.com/yinchi/histopath-bim-des/tree/main/notebooks&gt;`_">`Jupyter notebooks &lt;https://github.com/yinchi/histopath-bim-des/tree/main/notebooks&gt;`_</a></li>
+<li class="toctree-l1"><a class="reference external" href="https://github.com/yinchi/histopath-bim-des/tree/main/notebooks">Jupyter notebooks</a></li>
 </ul>
 <p class="caption" role="heading"><span class="caption-text">API reference:</span></p>
 <ul class="current">
diff --git a/docs/html/apidoc/histopath_bim_des.config.resources.html b/docs/html/apidoc/histopath_bim_des.config.resources.html
index 302c293..c4cb4bb 100644
--- a/docs/html/apidoc/histopath_bim_des.config.resources.html
+++ b/docs/html/apidoc/histopath_bim_des.config.resources.html
@@ -49,7 +49,7 @@
 <li class="toctree-l1"><a class="reference internal" href="../config.html">Model Configuration</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../simulation.html">Simulation and KPI extraction</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../processes.html">Histopathology processes</a></li>
-<li class="toctree-l1"><a class="reference external" href="`Jupyter notebooks &lt;https://github.com/yinchi/histopath-bim-des/tree/main/notebooks&gt;`_">`Jupyter notebooks &lt;https://github.com/yinchi/histopath-bim-des/tree/main/notebooks&gt;`_</a></li>
+<li class="toctree-l1"><a class="reference external" href="https://github.com/yinchi/histopath-bim-des/tree/main/notebooks">Jupyter notebooks</a></li>
 </ul>
 <p class="caption" role="heading"><span class="caption-text">API reference:</span></p>
 <ul class="current">
diff --git a/docs/html/apidoc/histopath_bim_des.config.runners.html b/docs/html/apidoc/histopath_bim_des.config.runners.html
index 28723c3..c0b64d7 100644
--- a/docs/html/apidoc/histopath_bim_des.config.runners.html
+++ b/docs/html/apidoc/histopath_bim_des.config.runners.html
@@ -49,7 +49,7 @@
 <li class="toctree-l1"><a class="reference internal" href="../config.html">Model Configuration</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../simulation.html">Simulation and KPI extraction</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../processes.html">Histopathology processes</a></li>
-<li class="toctree-l1"><a class="reference external" href="`Jupyter notebooks &lt;https://github.com/yinchi/histopath-bim-des/tree/main/notebooks&gt;`_">`Jupyter notebooks &lt;https://github.com/yinchi/histopath-bim-des/tree/main/notebooks&gt;`_</a></li>
+<li class="toctree-l1"><a class="reference external" href="https://github.com/yinchi/histopath-bim-des/tree/main/notebooks">Jupyter notebooks</a></li>
 </ul>
 <p class="caption" role="heading"><span class="caption-text">API reference:</span></p>
 <ul class="current">
diff --git a/docs/html/apidoc/histopath_bim_des.config.tasks.html b/docs/html/apidoc/histopath_bim_des.config.tasks.html
index be2936d..4be3123 100644
--- a/docs/html/apidoc/histopath_bim_des.config.tasks.html
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diff --git a/docs/html/apidoc/histopath_bim_des.distribution.html b/docs/html/apidoc/histopath_bim_des.distribution.html
index a92f177..9d7e13f 100644
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diff --git a/docs/html/apidoc/histopath_bim_des.excel.html b/docs/html/apidoc/histopath_bim_des.excel.html
index 323aeb5..13f79f9 100644
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diff --git a/docs/html/apidoc/histopath_bim_des.html b/docs/html/apidoc/histopath_bim_des.html
index 8cb84c1..6c8b457 100644
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diff --git a/docs/html/apidoc/histopath_bim_des.model.html b/docs/html/apidoc/histopath_bim_des.model.html
index e6e8db9..2b18aac 100644
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diff --git a/docs/html/apidoc/histopath_bim_des.process.core.html b/docs/html/apidoc/histopath_bim_des.process.core.html
index a7c4fbb..901595b 100644
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diff --git a/docs/html/apidoc/histopath_bim_des.process.html b/docs/html/apidoc/histopath_bim_des.process.html
index eb09b11..fdd820e 100644
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diff --git a/docs/html/apidoc/histopath_bim_des.process.p10_reception.html b/docs/html/apidoc/histopath_bim_des.process.p10_reception.html
index 1a151a8..ea34a67 100644
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diff --git a/docs/html/apidoc/histopath_bim_des.process.p20_cutup.html b/docs/html/apidoc/histopath_bim_des.process.p20_cutup.html
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diff --git a/docs/html/apidoc/histopath_bim_des.process.p30_processing.html b/docs/html/apidoc/histopath_bim_des.process.p30_processing.html
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diff --git a/docs/html/apidoc/histopath_bim_des.process.p40_microtomy.html b/docs/html/apidoc/histopath_bim_des.process.p40_microtomy.html
index d5ad2fd..392aafc 100644
--- a/docs/html/apidoc/histopath_bim_des.process.p40_microtomy.html
+++ b/docs/html/apidoc/histopath_bim_des.process.p40_microtomy.html
@@ -49,7 +49,7 @@
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diff --git a/docs/html/apidoc/histopath_bim_des.process.p50_staining.html b/docs/html/apidoc/histopath_bim_des.process.p50_staining.html
index b8814f1..c9003cc 100644
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@@ -49,7 +49,7 @@
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diff --git a/docs/html/apidoc/histopath_bim_des.process.p60_labelling.html b/docs/html/apidoc/histopath_bim_des.process.p60_labelling.html
index b8d9ef6..ba5abba 100644
--- a/docs/html/apidoc/histopath_bim_des.process.p60_labelling.html
+++ b/docs/html/apidoc/histopath_bim_des.process.p60_labelling.html
@@ -49,7 +49,7 @@
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+<li class="toctree-l1"><a class="reference external" href="https://github.com/yinchi/histopath-bim-des/tree/main/notebooks">Jupyter notebooks</a></li>
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diff --git a/docs/html/apidoc/histopath_bim_des.process.p70_scanning.html b/docs/html/apidoc/histopath_bim_des.process.p70_scanning.html
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--- a/docs/html/apidoc/histopath_bim_des.process.p70_scanning.html
+++ b/docs/html/apidoc/histopath_bim_des.process.p70_scanning.html
@@ -49,7 +49,7 @@
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+<li class="toctree-l1"><a class="reference external" href="https://github.com/yinchi/histopath-bim-des/tree/main/notebooks">Jupyter notebooks</a></li>
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diff --git a/docs/html/apidoc/histopath_bim_des.process.p80_qc.html b/docs/html/apidoc/histopath_bim_des.process.p80_qc.html
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--- a/docs/html/apidoc/histopath_bim_des.process.p80_qc.html
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+<li class="toctree-l1"><a class="reference external" href="https://github.com/yinchi/histopath-bim-des/tree/main/notebooks">Jupyter notebooks</a></li>
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diff --git a/docs/html/apidoc/histopath_bim_des.process.p90_reporting.html b/docs/html/apidoc/histopath_bim_des.process.p90_reporting.html
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--- a/docs/html/apidoc/histopath_bim_des.process.p90_reporting.html
+++ b/docs/html/apidoc/histopath_bim_des.process.p90_reporting.html
@@ -49,7 +49,7 @@
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+<li class="toctree-l1"><a class="reference external" href="https://github.com/yinchi/histopath-bim-des/tree/main/notebooks">Jupyter notebooks</a></li>
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diff --git a/docs/html/apidoc/histopath_bim_des.specimens.html b/docs/html/apidoc/histopath_bim_des.specimens.html
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--- a/docs/html/apidoc/histopath_bim_des.specimens.html
+++ b/docs/html/apidoc/histopath_bim_des.specimens.html
@@ -49,7 +49,7 @@
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+<li class="toctree-l1"><a class="reference external" href="https://github.com/yinchi/histopath-bim-des/tree/main/notebooks">Jupyter notebooks</a></li>
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diff --git a/docs/html/apidoc/histopath_bim_des.util.html b/docs/html/apidoc/histopath_bim_des.util.html
index de42beb..213d75a 100644
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@@ -48,7 +48,7 @@
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diff --git a/docs/html/apidoc/modules.html b/docs/html/apidoc/modules.html
index 474403d..1fd276d 100644
--- a/docs/html/apidoc/modules.html
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 <p class="caption" role="heading"><span class="caption-text">API reference:</span></p>
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false]], "processing_microtomy (histopath_bim_des.model.runnertimes attribute)": [[13, "histopath_bim_des.model.RunnerTimes.processing_microtomy", false]], "processing_regular (histopath_bim_des.config.batching.batchsizes attribute)": [[4, "histopath_bim_des.config.batching.BatchSizes.processing_regular", false]], "processing_room_staff (histopath_bim_des.config.resources.resourcesinfo attribute)": [[8, "histopath_bim_des.config.resources.ResourcesInfo.processing_room_staff", false]], "processing_room_staff (histopath_bim_des.model.resources attribute)": [[13, "histopath_bim_des.model.Resources.processing_room_staff", false]], "processing_small_surgicals (histopath_bim_des.config.tasks.taskdurationsinfo attribute)": [[10, "histopath_bim_des.config.tasks.TaskDurationsInfo.processing_small_surgicals", false]], "processing_small_surgicals (histopath_bim_des.model.taskdurations attribute)": [[13, "histopath_bim_des.model.TaskDurations.processing_small_surgicals", false]], "processing_smalls() (in module histopath_bim_des.process.p30_processing)": [[18, "histopath_bim_des.process.p30_processing.processing_smalls", false]], "processing_start() (in module histopath_bim_des.process.p30_processing)": [[18, "histopath_bim_des.process.p30_processing.processing_start", false]], "processing_urgent (histopath_bim_des.config.tasks.taskdurationsinfo attribute)": [[10, "histopath_bim_des.config.tasks.TaskDurationsInfo.processing_urgent", false]], "processing_urgent (histopath_bim_des.model.taskdurations attribute)": [[13, "histopath_bim_des.model.TaskDurations.processing_urgent", false]], "processing_urgents() (in module histopath_bim_des.process.p30_processing)": [[18, "histopath_bim_des.process.p30_processing.processing_urgents", false]], "qc (histopath_bim_des.config.runners.processdoormap attribute)": [[9, "histopath_bim_des.config.runners.ProcessDoorMap.qc", false]], "qc() (in module histopath_bim_des.process.p80_qc)": [[23, "histopath_bim_des.process.p80_qc.qc", false]], "qc_staff (histopath_bim_des.config.resources.resourcesinfo attribute)": [[8, "histopath_bim_des.config.resources.ResourcesInfo.qc_staff", false]], "qc_staff (histopath_bim_des.model.resources attribute)": [[13, "histopath_bim_des.model.Resources.qc_staff", false]], "rates (histopath_bim_des.config.arrivals.arrivalschedule attribute)": [[3, "histopath_bim_des.config.arrivals.ArrivalSchedule.rates", false]], "receive_and_sort (histopath_bim_des.config.tasks.taskdurationsinfo attribute)": [[10, "histopath_bim_des.config.tasks.TaskDurationsInfo.receive_and_sort", false]], "receive_and_sort (histopath_bim_des.model.taskdurations attribute)": [[13, "histopath_bim_des.model.TaskDurations.receive_and_sort", false]], "reception (histopath_bim_des.config.runners.processdoormap attribute)": [[9, "histopath_bim_des.config.runners.ProcessDoorMap.reception", false]], "reception_cutup (histopath_bim_des.config.runners.runnertimesconfig attribute)": [[9, "histopath_bim_des.config.runners.RunnerTimesConfig.reception_cutup", false]], "reception_cutup (histopath_bim_des.model.runnertimes attribute)": [[13, "histopath_bim_des.model.RunnerTimes.reception_cutup", false]], "register_process() (in module histopath_bim_des.process.core)": [[15, "histopath_bim_des.process.core.register_process", false]], "register_processes() (in module histopath_bim_des.process.p10_reception)": [[16, "histopath_bim_des.process.p10_reception.register_processes", false]], "register_processes() (in module histopath_bim_des.process.p20_cutup)": [[17, "histopath_bim_des.process.p20_cutup.register_processes", false]], "register_processes() (in module histopath_bim_des.process.p30_processing)": [[18, "histopath_bim_des.process.p30_processing.register_processes", false]], "register_processes() (in module histopath_bim_des.process.p40_microtomy)": [[19, "histopath_bim_des.process.p40_microtomy.register_processes", false]], "register_processes() (in module histopath_bim_des.process.p50_staining)": [[20, "histopath_bim_des.process.p50_staining.register_processes", false]], "register_processes() (in module histopath_bim_des.process.p60_labelling)": [[21, "histopath_bim_des.process.p60_labelling.register_processes", false]], "register_processes() (in module histopath_bim_des.process.p70_scanning)": [[22, "histopath_bim_des.process.p70_scanning.register_processes", false]], "register_processes() (in module histopath_bim_des.process.p80_qc)": [[23, "histopath_bim_des.process.p80_qc.register_processes", false]], "register_processes() (in module histopath_bim_des.process.p90_reporting)": [[24, "histopath_bim_des.process.p90_reporting.register_processes", false]], "remove_table_filters() (in module histopath_bim_des.excel)": [[12, "histopath_bim_des.excel.remove_table_filters", false]], "report() (in module histopath_bim_des.process.p90_reporting)": [[24, "histopath_bim_des.process.p90_reporting.report", false]], "resource (histopath_bim_des.process.core.resourcescheduler attribute)": [[15, "histopath_bim_des.process.core.ResourceScheduler.resource", false]], "resource_allocation_interval_hours (in module histopath_bim_des.util)": [[26, "histopath_bim_des.util.RESOURCE_ALLOCATION_INTERVAL_HOURS", false]], "resourceinfo (class in histopath_bim_des.config.resources)": [[8, "histopath_bim_des.config.resources.ResourceInfo", false]], "resources (class in histopath_bim_des.model)": [[13, "histopath_bim_des.model.Resources", false]], "resources (histopath_bim_des.config.config.config attribute)": [[5, "histopath_bim_des.config.config.Config.resources", false]], "resources (histopath_bim_des.model.model attribute)": [[13, "histopath_bim_des.model.Model.resources", false]], "resourceschedule (class in histopath_bim_des.config.resources)": [[8, "histopath_bim_des.config.resources.ResourceSchedule", false]], "resourcescheduler (class in histopath_bim_des.process.core)": [[15, "histopath_bim_des.process.core.ResourceScheduler", false]], "resourcesinfo (class in histopath_bim_des.config.resources)": [[8, "histopath_bim_des.config.resources.ResourcesInfo", false]], "retur (histopath_bim_des.process.core.runnerdurations attribute)": [[15, "histopath_bim_des.process.core.RunnerDurations.retur", false]], "routine (histopath_bim_des.specimens.priority attribute)": [[25, "histopath_bim_des.specimens.Priority.ROUTINE", false]], "run() (histopath_bim_des.model.model method)": [[13, "histopath_bim_des.model.Model.run", false]], "runner (histopath_bim_des.process.core.deliveryprocess attribute)": [[15, "histopath_bim_des.process.core.DeliveryProcess.runner", false]], "runner_speed (histopath_bim_des.config.runners.runnerconfig attribute)": [[9, "histopath_bim_des.config.runners.RunnerConfig.runner_speed", false]], "runner_times (histopath_bim_des.config.config.config attribute)": [[5, "histopath_bim_des.config.config.Config.runner_times", false]], "runner_times() (in module histopath_bim_des.bim)": [[1, "histopath_bim_des.bim.runner_times", false]], "runnerconfig (class in histopath_bim_des.config.runners)": [[9, "histopath_bim_des.config.runners.RunnerConfig", false]], "runnerdurations (class in histopath_bim_des.process.core)": [[15, "histopath_bim_des.process.core.RunnerDurations", false]], "runnerextradurations (class in histopath_bim_des.config.runners)": [[9, "histopath_bim_des.config.runners.RunnerExtraDurations", false]], "runnertimes (class in histopath_bim_des.model)": [[13, "histopath_bim_des.model.RunnerTimes", false]], "runnertimesconfig (class in histopath_bim_des.config.runners)": [[9, "histopath_bim_des.config.runners.RunnerTimesConfig", false]], "sample() (histopath_bim_des.distribution.intpert method)": [[11, "histopath_bim_des.distribution.IntPERT.sample", false]], "sample() (histopath_bim_des.distribution.inttri method)": [[11, "histopath_bim_des.distribution.IntTri.sample", false]], "sample() (histopath_bim_des.distribution.pert method)": [[11, "histopath_bim_des.distribution.PERT.sample", false]], "scanning (histopath_bim_des.config.runners.processdoormap attribute)": [[9, "histopath_bim_des.config.runners.ProcessDoorMap.scanning", false]], "scanning_generic() (in module histopath_bim_des.process.p70_scanning)": [[22, "histopath_bim_des.process.p70_scanning.scanning_generic", false]], "scanning_machine_megas (histopath_bim_des.config.resources.resourcesinfo attribute)": [[8, "histopath_bim_des.config.resources.ResourcesInfo.scanning_machine_megas", false]], "scanning_machine_megas (histopath_bim_des.model.resources attribute)": [[13, "histopath_bim_des.model.Resources.scanning_machine_megas", false]], "scanning_machine_regular (histopath_bim_des.config.resources.resourcesinfo attribute)": [[8, "histopath_bim_des.config.resources.ResourcesInfo.scanning_machine_regular", false]], "scanning_machine_regular (histopath_bim_des.model.resources attribute)": [[13, "histopath_bim_des.model.Resources.scanning_machine_regular", false]], "scanning_megas (histopath_bim_des.config.tasks.taskdurationsinfo attribute)": [[10, "histopath_bim_des.config.tasks.TaskDurationsInfo.scanning_megas", false]], "scanning_megas (histopath_bim_des.model.taskdurations attribute)": [[13, "histopath_bim_des.model.TaskDurations.scanning_megas", false]], "scanning_megas() (in module histopath_bim_des.process.p70_scanning)": [[22, "histopath_bim_des.process.p70_scanning.scanning_megas", false]], "scanning_qc (histopath_bim_des.config.runners.runnertimesconfig attribute)": [[9, "histopath_bim_des.config.runners.RunnerTimesConfig.scanning_qc", false]], "scanning_qc (histopath_bim_des.model.runnertimes attribute)": [[13, "histopath_bim_des.model.RunnerTimes.scanning_qc", false]], "scanning_regular (histopath_bim_des.config.tasks.taskdurationsinfo attribute)": [[10, "histopath_bim_des.config.tasks.TaskDurationsInfo.scanning_regular", false]], "scanning_regular 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"setup() (histopath_bim_des.model.model method)": [[13, "histopath_bim_des.model.Model.setup", false]], "setup() (histopath_bim_des.process.core.arrivalgenerator method)": [[15, "histopath_bim_des.process.core.ArrivalGenerator.setup", false]], "setup() (histopath_bim_des.process.core.baseprocess method)": [[15, "histopath_bim_des.process.core.BaseProcess.setup", false]], "setup() (histopath_bim_des.process.core.batchingprocess method)": [[15, "histopath_bim_des.process.core.BatchingProcess.setup", false]], "setup() (histopath_bim_des.process.core.collationprocess method)": [[15, "histopath_bim_des.process.core.CollationProcess.setup", false]], "setup() (histopath_bim_des.process.core.deliveryprocess method)": [[15, "histopath_bim_des.process.core.DeliveryProcess.setup", false]], "setup() (histopath_bim_des.process.core.process method)": [[15, "histopath_bim_des.process.core.Process.setup", false]], "setup() (histopath_bim_des.process.core.resourcescheduler method)": [[15, "histopath_bim_des.process.core.ResourceScheduler.setup", false]], "setup() (histopath_bim_des.specimens.batch method)": [[25, "histopath_bim_des.specimens.Batch.setup", false]], "setup() (histopath_bim_des.specimens.block method)": [[25, "histopath_bim_des.specimens.Block.setup", false]], "setup() (histopath_bim_des.specimens.slide method)": [[25, "histopath_bim_des.specimens.Slide.setup", false]], "setup() (histopath_bim_des.specimens.specimen method)": [[25, "histopath_bim_des.specimens.Specimen.setup", false]], "shapelymodel (class in histopath_bim_des.bim)": [[1, "histopath_bim_des.bim.ShapelyModel", false]], "shortest_path() (histopath_bim_des.bim.shapelymodel method)": [[1, "histopath_bim_des.bim.ShapelyModel.shortest_path", false]], "sim_hours (histopath_bim_des.config.config.config attribute)": [[5, "histopath_bim_des.config.config.Config.sim_hours", false]], "sim_length (histopath_bim_des.model.model attribute)": [[13, "histopath_bim_des.model.Model.sim_length", false]], "slide (class in histopath_bim_des.specimens)": [[25, "histopath_bim_des.specimens.Slide", false]], "specimen (class in histopath_bim_des.specimens)": [[25, "histopath_bim_des.specimens.Specimen", false]], "specimen_data (histopath_bim_des.model.model attribute)": [[13, "histopath_bim_des.model.Model.specimen_data", false]], "staining (histopath_bim_des.config.runners.processdoormap attribute)": [[9, "histopath_bim_des.config.runners.ProcessDoorMap.staining", false]], "staining_labelling (histopath_bim_des.config.runners.runnertimesconfig attribute)": [[9, "histopath_bim_des.config.runners.RunnerTimesConfig.staining_labelling", false]], "staining_labelling (histopath_bim_des.model.runnertimes attribute)": [[13, "histopath_bim_des.model.RunnerTimes.staining_labelling", false]], "staining_machine (histopath_bim_des.config.resources.resourcesinfo attribute)": [[8, "histopath_bim_des.config.resources.ResourcesInfo.staining_machine", false]], "staining_machine 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"histopath_bim_des.config.tasks.TaskDurationsInfo.staining_regular", false]], "staining_regular (histopath_bim_des.model.taskdurations attribute)": [[13, "histopath_bim_des.model.TaskDurations.staining_regular", false]], "staining_regular() (in module histopath_bim_des.process.p50_staining)": [[20, "histopath_bim_des.process.p50_staining.staining_regular", false]], "staining_staff (histopath_bim_des.config.resources.resourcesinfo attribute)": [[8, "histopath_bim_des.config.resources.ResourcesInfo.staining_staff", false]], "staining_staff (histopath_bim_des.model.resources attribute)": [[13, "histopath_bim_des.model.Resources.staining_staff", false]], "staining_start() (in module histopath_bim_des.process.p50_staining)": [[20, "histopath_bim_des.process.p50_staining.staining_start", false]], "task_durations (histopath_bim_des.config.config.config attribute)": [[5, "histopath_bim_des.config.config.Config.task_durations", false]], "task_durations (histopath_bim_des.model.model attribute)": [[13, "histopath_bim_des.model.Model.task_durations", false]], "taskdurations (class in histopath_bim_des.model)": [[13, "histopath_bim_des.model.TaskDurations", false]], "taskdurationsinfo (class in histopath_bim_des.config.tasks)": [[10, "histopath_bim_des.config.tasks.TaskDurationsInfo", false]], "time_unit (histopath_bim_des.config.distributions.distributioninfo attribute)": [[6, "histopath_bim_des.config.distributions.DistributionInfo.time_unit", false]], "timestamp() (histopath_bim_des.specimens.specimen method)": [[25, "histopath_bim_des.specimens.Specimen.timestamp", false]], "to_shapely() (histopath_bim_des.bim.bimmodel method)": [[1, "histopath_bim_des.bim.BimModel.to_shapely", false]], "total (histopath_bim_des.model.wips attribute)": [[13, "histopath_bim_des.model.Wips.total", false]], "tri (class in histopath_bim_des.distribution)": [[11, "histopath_bim_des.distribution.Tri", false]], "tri (histopath_bim_des.distribution.inttri attribute)": [[11, "histopath_bim_des.distribution.IntTri.tri", false]], "type (histopath_bim_des.config.distributions.distributioninfo attribute)": [[6, "histopath_bim_des.config.distributions.DistributionInfo.type", false]], "type (histopath_bim_des.config.distributions.intdistributioninfo attribute)": [[6, "histopath_bim_des.config.distributions.IntDistributionInfo.type", false]], "type (histopath_bim_des.config.resources.resourceinfo attribute)": [[8, "histopath_bim_des.config.resources.ResourceInfo.type", false]], "unload (histopath_bim_des.process.core.runnerdurations attribute)": [[15, "histopath_bim_des.process.core.RunnerDurations.unload", false]], "unload_bone_station (histopath_bim_des.config.tasks.taskdurationsinfo attribute)": [[10, "histopath_bim_des.config.tasks.TaskDurationsInfo.unload_bone_station", false]], "unload_bone_station (histopath_bim_des.model.taskdurations attribute)": [[13, "histopath_bim_des.model.TaskDurations.unload_bone_station", false]], "unload_coverslip_machine_regular (histopath_bim_des.config.tasks.taskdurationsinfo attribute)": [[10, "histopath_bim_des.config.tasks.TaskDurationsInfo.unload_coverslip_machine_regular", false]], "unload_coverslip_machine_regular (histopath_bim_des.model.taskdurations attribute)": [[13, "histopath_bim_des.model.TaskDurations.unload_coverslip_machine_regular", false]], "unload_from_decalc_oven (histopath_bim_des.config.tasks.taskdurationsinfo attribute)": [[10, "histopath_bim_des.config.tasks.TaskDurationsInfo.unload_from_decalc_oven", false]], "unload_from_decalc_oven (histopath_bim_des.model.taskdurations attribute)": [[13, "histopath_bim_des.model.TaskDurations.unload_from_decalc_oven", false]], "unload_processing_machine (histopath_bim_des.config.tasks.taskdurationsinfo attribute)": [[10, "histopath_bim_des.config.tasks.TaskDurationsInfo.unload_processing_machine", false]], "unload_processing_machine (histopath_bim_des.model.taskdurations attribute)": [[13, "histopath_bim_des.model.TaskDurations.unload_processing_machine", false]], "unload_scanning_machine_megas (histopath_bim_des.config.tasks.taskdurationsinfo attribute)": [[10, "histopath_bim_des.config.tasks.TaskDurationsInfo.unload_scanning_machine_megas", false]], "unload_scanning_machine_megas (histopath_bim_des.model.taskdurations attribute)": [[13, "histopath_bim_des.model.TaskDurations.unload_scanning_machine_megas", false]], "unload_scanning_machine_regular (histopath_bim_des.config.tasks.taskdurationsinfo attribute)": [[10, "histopath_bim_des.config.tasks.TaskDurationsInfo.unload_scanning_machine_regular", false]], "unload_scanning_machine_regular (histopath_bim_des.model.taskdurations attribute)": [[13, "histopath_bim_des.model.TaskDurations.unload_scanning_machine_regular", false]], "unload_staining_machine_megas (histopath_bim_des.config.tasks.taskdurationsinfo attribute)": [[10, "histopath_bim_des.config.tasks.TaskDurationsInfo.unload_staining_machine_megas", false]], 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29, "you": 13, "your": 31}, "titles": ["histopath_bim_des package", "histopath_bim_des.bim module", "histopath_bim_des.config package", "histopath_bim_des.config.arrivals module", "histopath_bim_des.config.batching module", "histopath_bim_des.config.config module", "histopath_bim_des.config.distributions module", "histopath_bim_des.config.global_vars module", "histopath_bim_des.config.resources module", "histopath_bim_des.config.runners module", "histopath_bim_des.config.tasks module", "histopath_bim_des.distribution module", "histopath_bim_des.excel module", "histopath_bim_des.model module", "histopath_bim_des.process package", "histopath_bim_des.process.core module", "histopath_bim_des.process.p10_reception module", "histopath_bim_des.process.p20_cutup module", "histopath_bim_des.process.p30_processing module", "histopath_bim_des.process.p40_microtomy module", "histopath_bim_des.process.p50_staining module", "histopath_bim_des.process.p60_labelling module", 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\ No newline at end of file
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attribute)": [[7, "histopath_bim_des.config.global_vars.Globals.prob_internal", false]], "prob_internal (histopath_bim_des.model.globals attribute)": [[13, "histopath_bim_des.model.Globals.prob_internal", false]], "prob_invest_easy (histopath_bim_des.config.global_vars.globals attribute)": [[7, "histopath_bim_des.config.global_vars.Globals.prob_invest_easy", false]], "prob_invest_easy (histopath_bim_des.model.globals attribute)": [[13, "histopath_bim_des.model.Globals.prob_invest_easy", false]], "prob_invest_external (histopath_bim_des.config.global_vars.globals attribute)": [[7, "histopath_bim_des.config.global_vars.Globals.prob_invest_external", false]], "prob_invest_external (histopath_bim_des.model.globals attribute)": [[13, "histopath_bim_des.model.Globals.prob_invest_external", false]], "prob_invest_hard (histopath_bim_des.config.global_vars.globals attribute)": [[7, "histopath_bim_des.config.global_vars.Globals.prob_invest_hard", false]], "prob_invest_hard (histopath_bim_des.model.globals attribute)": [[13, "histopath_bim_des.model.Globals.prob_invest_hard", false]], "prob_large_cutup (histopath_bim_des.config.global_vars.globals attribute)": [[7, "histopath_bim_des.config.global_vars.Globals.prob_large_cutup", false]], "prob_large_cutup (histopath_bim_des.model.globals attribute)": [[13, "histopath_bim_des.model.Globals.prob_large_cutup", false]], "prob_large_cutup_urgent (histopath_bim_des.config.global_vars.globals attribute)": [[7, "histopath_bim_des.config.global_vars.Globals.prob_large_cutup_urgent", false]], "prob_large_cutup_urgent (histopath_bim_des.model.globals attribute)": [[13, "histopath_bim_des.model.Globals.prob_large_cutup_urgent", false]], "prob_mega_blocks (histopath_bim_des.config.global_vars.globals attribute)": [[7, "histopath_bim_des.config.global_vars.Globals.prob_mega_blocks", false]], "prob_mega_blocks (histopath_bim_des.model.globals attribute)": [[13, "histopath_bim_des.model.Globals.prob_mega_blocks", false]], "prob_microtomy_levels (histopath_bim_des.config.global_vars.globals attribute)": [[7, "histopath_bim_des.config.global_vars.Globals.prob_microtomy_levels", false]], "prob_microtomy_levels (histopath_bim_des.model.globals attribute)": [[13, "histopath_bim_des.model.Globals.prob_microtomy_levels", false]], "prob_pool_cutup (histopath_bim_des.config.global_vars.globals attribute)": [[7, "histopath_bim_des.config.global_vars.Globals.prob_pool_cutup", false]], "prob_pool_cutup (histopath_bim_des.model.globals attribute)": [[13, "histopath_bim_des.model.Globals.prob_pool_cutup", false]], "prob_pool_cutup_urgent (histopath_bim_des.config.global_vars.globals attribute)": [[7, "histopath_bim_des.config.global_vars.Globals.prob_pool_cutup_urgent", false]], "prob_pool_cutup_urgent (histopath_bim_des.model.globals attribute)": [[13, "histopath_bim_des.model.Globals.prob_pool_cutup_urgent", false]], "prob_prebook (histopath_bim_des.config.global_vars.globals attribute)": [[7, "histopath_bim_des.config.global_vars.Globals.prob_prebook", false]], "prob_prebook (histopath_bim_des.model.globals attribute)": [[13, "histopath_bim_des.model.Globals.prob_prebook", false]], "prob_priority_cancer (histopath_bim_des.config.global_vars.globals attribute)": [[7, "histopath_bim_des.config.global_vars.Globals.prob_priority_cancer", false]], "prob_priority_cancer (histopath_bim_des.model.globals attribute)": [[13, "histopath_bim_des.model.Globals.prob_priority_cancer", false]], "prob_priority_non_cancer (histopath_bim_des.config.global_vars.globals attribute)": [[7, "histopath_bim_des.config.global_vars.Globals.prob_priority_non_cancer", false]], "prob_priority_non_cancer (histopath_bim_des.model.globals attribute)": [[13, "histopath_bim_des.model.Globals.prob_priority_non_cancer", false]], "prob_urgent_cancer (histopath_bim_des.config.global_vars.globals attribute)": [[7, "histopath_bim_des.config.global_vars.Globals.prob_urgent_cancer", false]], "prob_urgent_cancer (histopath_bim_des.model.globals attribute)": [[13, "histopath_bim_des.model.Globals.prob_urgent_cancer", false]], "prob_urgent_non_cancer (histopath_bim_des.config.global_vars.globals attribute)": [[7, "histopath_bim_des.config.global_vars.Globals.prob_urgent_non_cancer", false]], "prob_urgent_non_cancer (histopath_bim_des.model.globals attribute)": [[13, "histopath_bim_des.model.Globals.prob_urgent_non_cancer", false]], "process (class in histopath_bim_des.process.core)": [[15, "histopath_bim_des.process.core.Process", false]], "process() (histopath_bim_des.process.core.arrivalgenerator method)": [[15, "histopath_bim_des.process.core.ArrivalGenerator.process", false]], "process() (histopath_bim_des.process.core.baseprocess method)": [[15, "histopath_bim_des.process.core.BaseProcess.process", false]], "process() (histopath_bim_des.process.core.batchingprocess method)": [[15, "histopath_bim_des.process.core.BatchingProcess.process", false]], "process() (histopath_bim_des.process.core.collationprocess method)": [[15, "histopath_bim_des.process.core.CollationProcess.process", false]], "process() (histopath_bim_des.process.core.deliveryprocess method)": [[15, "histopath_bim_des.process.core.DeliveryProcess.process", false]], "process() (histopath_bim_des.process.core.process method)": [[15, "histopath_bim_des.process.core.Process.process", false]], "process() (histopath_bim_des.process.core.resourcescheduler method)": [[15, "histopath_bim_des.process.core.ResourceScheduler.process", false]], "process() (histopath_bim_des.specimens.specimen method)": [[25, "histopath_bim_des.specimens.Specimen.process", false]], "processdoormap (class in histopath_bim_des.config.runners)": [[9, "histopath_bim_des.config.runners.ProcessDoorMap", false]], "processes (histopath_bim_des.model.model attribute)": [[13, "histopath_bim_des.model.Model.processes", false]], "processing (histopath_bim_des.config.runners.processdoormap attribute)": [[9, "histopath_bim_des.config.runners.ProcessDoorMap.processing", false]], "processing_assign_queue() (in module histopath_bim_des.process.p30_processing)": [[18, "histopath_bim_des.process.p30_processing.processing_assign_queue", false]], "processing_generic() (in module histopath_bim_des.process.p30_processing)": [[18, "histopath_bim_des.process.p30_processing.processing_generic", false]], "processing_large_surgicals (histopath_bim_des.config.tasks.taskdurationsinfo attribute)": [[10, "histopath_bim_des.config.tasks.TaskDurationsInfo.processing_large_surgicals", false]], "processing_large_surgicals (histopath_bim_des.model.taskdurations attribute)": [[13, "histopath_bim_des.model.TaskDurations.processing_large_surgicals", false]], "processing_larges() (in module histopath_bim_des.process.p30_processing)": [[18, "histopath_bim_des.process.p30_processing.processing_larges", false]], "processing_machine (histopath_bim_des.config.resources.resourcesinfo attribute)": [[8, "histopath_bim_des.config.resources.ResourcesInfo.processing_machine", false]], "processing_machine (histopath_bim_des.model.resources attribute)": [[13, "histopath_bim_des.model.Resources.processing_machine", false]], "processing_megas (histopath_bim_des.config.batching.batchsizes attribute)": [[4, "histopath_bim_des.config.batching.BatchSizes.processing_megas", false]], "processing_megas (histopath_bim_des.config.tasks.taskdurationsinfo attribute)": [[10, "histopath_bim_des.config.tasks.TaskDurationsInfo.processing_megas", false]], "processing_megas (histopath_bim_des.model.taskdurations attribute)": [[13, "histopath_bim_des.model.TaskDurations.processing_megas", false]], "processing_megas() (in module histopath_bim_des.process.p30_processing)": [[18, "histopath_bim_des.process.p30_processing.processing_megas", false]], "processing_microtomy (histopath_bim_des.config.runners.runnertimesconfig attribute)": [[9, "histopath_bim_des.config.runners.RunnerTimesConfig.processing_microtomy", false]], "processing_microtomy (histopath_bim_des.model.runnertimes attribute)": [[13, "histopath_bim_des.model.RunnerTimes.processing_microtomy", false]], "processing_regular (histopath_bim_des.config.batching.batchsizes attribute)": [[4, "histopath_bim_des.config.batching.BatchSizes.processing_regular", false]], "processing_room_staff (histopath_bim_des.config.resources.resourcesinfo attribute)": [[8, "histopath_bim_des.config.resources.ResourcesInfo.processing_room_staff", false]], "processing_room_staff (histopath_bim_des.model.resources attribute)": [[13, "histopath_bim_des.model.Resources.processing_room_staff", false]], "processing_small_surgicals (histopath_bim_des.config.tasks.taskdurationsinfo attribute)": [[10, "histopath_bim_des.config.tasks.TaskDurationsInfo.processing_small_surgicals", false]], "processing_small_surgicals (histopath_bim_des.model.taskdurations attribute)": [[13, "histopath_bim_des.model.TaskDurations.processing_small_surgicals", false]], "processing_smalls() (in module histopath_bim_des.process.p30_processing)": [[18, "histopath_bim_des.process.p30_processing.processing_smalls", false]], "processing_start() (in module histopath_bim_des.process.p30_processing)": [[18, "histopath_bim_des.process.p30_processing.processing_start", false]], "processing_urgent (histopath_bim_des.config.tasks.taskdurationsinfo attribute)": [[10, "histopath_bim_des.config.tasks.TaskDurationsInfo.processing_urgent", false]], "processing_urgent (histopath_bim_des.model.taskdurations attribute)": [[13, "histopath_bim_des.model.TaskDurations.processing_urgent", false]], "processing_urgents() (in module histopath_bim_des.process.p30_processing)": [[18, "histopath_bim_des.process.p30_processing.processing_urgents", false]], "qc (histopath_bim_des.config.runners.processdoormap attribute)": [[9, "histopath_bim_des.config.runners.ProcessDoorMap.qc", false]], "qc() (in module histopath_bim_des.process.p80_qc)": [[23, "histopath_bim_des.process.p80_qc.qc", false]], "qc_staff (histopath_bim_des.config.resources.resourcesinfo attribute)": [[8, "histopath_bim_des.config.resources.ResourcesInfo.qc_staff", false]], "qc_staff (histopath_bim_des.model.resources attribute)": [[13, "histopath_bim_des.model.Resources.qc_staff", false]], "rates (histopath_bim_des.config.arrivals.arrivalschedule attribute)": [[3, "histopath_bim_des.config.arrivals.ArrivalSchedule.rates", false]], "receive_and_sort (histopath_bim_des.config.tasks.taskdurationsinfo attribute)": [[10, "histopath_bim_des.config.tasks.TaskDurationsInfo.receive_and_sort", false]], "receive_and_sort (histopath_bim_des.model.taskdurations attribute)": [[13, "histopath_bim_des.model.TaskDurations.receive_and_sort", false]], "reception (histopath_bim_des.config.runners.processdoormap attribute)": [[9, "histopath_bim_des.config.runners.ProcessDoorMap.reception", false]], "reception_cutup (histopath_bim_des.config.runners.runnertimesconfig attribute)": [[9, "histopath_bim_des.config.runners.RunnerTimesConfig.reception_cutup", false]], "reception_cutup (histopath_bim_des.model.runnertimes attribute)": [[13, "histopath_bim_des.model.RunnerTimes.reception_cutup", false]], "register_process() (in module histopath_bim_des.process.core)": [[15, "histopath_bim_des.process.core.register_process", false]], "register_processes() (in module histopath_bim_des.process.p10_reception)": [[16, "histopath_bim_des.process.p10_reception.register_processes", false]], "register_processes() (in module histopath_bim_des.process.p20_cutup)": [[17, "histopath_bim_des.process.p20_cutup.register_processes", false]], "register_processes() (in module histopath_bim_des.process.p30_processing)": [[18, "histopath_bim_des.process.p30_processing.register_processes", false]], "register_processes() (in module histopath_bim_des.process.p40_microtomy)": [[19, "histopath_bim_des.process.p40_microtomy.register_processes", false]], "register_processes() (in module histopath_bim_des.process.p50_staining)": [[20, "histopath_bim_des.process.p50_staining.register_processes", false]], "register_processes() (in module histopath_bim_des.process.p60_labelling)": [[21, "histopath_bim_des.process.p60_labelling.register_processes", false]], "register_processes() (in module histopath_bim_des.process.p70_scanning)": [[22, "histopath_bim_des.process.p70_scanning.register_processes", false]], "register_processes() (in module histopath_bim_des.process.p80_qc)": [[23, "histopath_bim_des.process.p80_qc.register_processes", false]], "register_processes() (in module histopath_bim_des.process.p90_reporting)": [[24, "histopath_bim_des.process.p90_reporting.register_processes", false]], "remove_table_filters() (in module histopath_bim_des.excel)": [[12, "histopath_bim_des.excel.remove_table_filters", false]], "report() (in module histopath_bim_des.process.p90_reporting)": [[24, "histopath_bim_des.process.p90_reporting.report", false]], "resource (histopath_bim_des.process.core.resourcescheduler attribute)": [[15, "histopath_bim_des.process.core.ResourceScheduler.resource", false]], "resource_allocation_interval_hours (in module histopath_bim_des.util)": [[26, "histopath_bim_des.util.RESOURCE_ALLOCATION_INTERVAL_HOURS", false]], "resourceinfo (class in histopath_bim_des.config.resources)": [[8, "histopath_bim_des.config.resources.ResourceInfo", false]], "resources (class in histopath_bim_des.model)": [[13, "histopath_bim_des.model.Resources", false]], "resources (histopath_bim_des.config.config.config attribute)": [[5, "histopath_bim_des.config.config.Config.resources", false]], "resources (histopath_bim_des.model.model attribute)": [[13, "histopath_bim_des.model.Model.resources", false]], "resourceschedule (class in histopath_bim_des.config.resources)": [[8, "histopath_bim_des.config.resources.ResourceSchedule", false]], "resourcescheduler (class in histopath_bim_des.process.core)": [[15, "histopath_bim_des.process.core.ResourceScheduler", false]], "resourcesinfo (class in histopath_bim_des.config.resources)": [[8, "histopath_bim_des.config.resources.ResourcesInfo", false]], "retur (histopath_bim_des.process.core.runnerdurations attribute)": [[15, "histopath_bim_des.process.core.RunnerDurations.retur", false]], "routine (histopath_bim_des.specimens.priority attribute)": [[25, "histopath_bim_des.specimens.Priority.ROUTINE", false]], "run() (histopath_bim_des.model.model method)": [[13, "histopath_bim_des.model.Model.run", false]], "runner (histopath_bim_des.process.core.deliveryprocess attribute)": [[15, "histopath_bim_des.process.core.DeliveryProcess.runner", false]], "runner_speed (histopath_bim_des.config.runners.runnerconfig attribute)": [[9, "histopath_bim_des.config.runners.RunnerConfig.runner_speed", false]], "runner_times (histopath_bim_des.config.config.config attribute)": [[5, "histopath_bim_des.config.config.Config.runner_times", false]], "runner_times() (in module histopath_bim_des.bim)": [[1, "histopath_bim_des.bim.runner_times", false]], "runnerconfig (class in histopath_bim_des.config.runners)": [[9, "histopath_bim_des.config.runners.RunnerConfig", false]], "runnerdurations (class in histopath_bim_des.process.core)": [[15, "histopath_bim_des.process.core.RunnerDurations", false]], "runnerextradurations (class in histopath_bim_des.config.runners)": [[9, "histopath_bim_des.config.runners.RunnerExtraDurations", false]], "runnertimes (class in histopath_bim_des.model)": [[13, "histopath_bim_des.model.RunnerTimes", false]], "runnertimesconfig (class in histopath_bim_des.config.runners)": [[9, "histopath_bim_des.config.runners.RunnerTimesConfig", false]], "sample() (histopath_bim_des.distribution.intpert method)": [[11, "histopath_bim_des.distribution.IntPERT.sample", false]], "sample() (histopath_bim_des.distribution.inttri method)": [[11, "histopath_bim_des.distribution.IntTri.sample", false]], "sample() (histopath_bim_des.distribution.pert method)": [[11, "histopath_bim_des.distribution.PERT.sample", false]], "scanning (histopath_bim_des.config.runners.processdoormap attribute)": [[9, "histopath_bim_des.config.runners.ProcessDoorMap.scanning", false]], "scanning_generic() (in module histopath_bim_des.process.p70_scanning)": [[22, "histopath_bim_des.process.p70_scanning.scanning_generic", false]], "scanning_machine_megas (histopath_bim_des.config.resources.resourcesinfo attribute)": [[8, "histopath_bim_des.config.resources.ResourcesInfo.scanning_machine_megas", false]], "scanning_machine_megas (histopath_bim_des.model.resources attribute)": [[13, "histopath_bim_des.model.Resources.scanning_machine_megas", false]], "scanning_machine_regular (histopath_bim_des.config.resources.resourcesinfo attribute)": [[8, "histopath_bim_des.config.resources.ResourcesInfo.scanning_machine_regular", false]], "scanning_machine_regular (histopath_bim_des.model.resources attribute)": [[13, "histopath_bim_des.model.Resources.scanning_machine_regular", false]], "scanning_megas (histopath_bim_des.config.tasks.taskdurationsinfo attribute)": [[10, "histopath_bim_des.config.tasks.TaskDurationsInfo.scanning_megas", false]], "scanning_megas (histopath_bim_des.model.taskdurations attribute)": [[13, "histopath_bim_des.model.TaskDurations.scanning_megas", false]], "scanning_megas() (in module histopath_bim_des.process.p70_scanning)": [[22, "histopath_bim_des.process.p70_scanning.scanning_megas", false]], "scanning_qc (histopath_bim_des.config.runners.runnertimesconfig attribute)": [[9, "histopath_bim_des.config.runners.RunnerTimesConfig.scanning_qc", false]], "scanning_qc (histopath_bim_des.model.runnertimes attribute)": [[13, "histopath_bim_des.model.RunnerTimes.scanning_qc", false]], "scanning_regular (histopath_bim_des.config.tasks.taskdurationsinfo attribute)": [[10, "histopath_bim_des.config.tasks.TaskDurationsInfo.scanning_regular", false]], "scanning_regular (histopath_bim_des.model.taskdurations attribute)": [[13, "histopath_bim_des.model.TaskDurations.scanning_regular", false]], "scanning_regular() (in module histopath_bim_des.process.p70_scanning)": [[22, "histopath_bim_des.process.p70_scanning.scanning_regular", false]], "scanning_staff (histopath_bim_des.config.resources.resourcesinfo attribute)": [[8, "histopath_bim_des.config.resources.ResourcesInfo.scanning_staff", false]], "scanning_staff (histopath_bim_des.model.resources attribute)": [[13, "histopath_bim_des.model.Resources.scanning_staff", false]], "scanning_start() (in module histopath_bim_des.process.p70_scanning)": [[22, "histopath_bim_des.process.p70_scanning.scanning_start", false]], "schedule (histopath_bim_des.config.resources.resourceinfo attribute)": [[8, "histopath_bim_des.config.resources.ResourceInfo.schedule", false]], "schedule (histopath_bim_des.process.core.resourcescheduler attribute)": [[15, "histopath_bim_des.process.core.ResourceScheduler.schedule", false]], "setup() (histopath_bim_des.model.model method)": [[13, "histopath_bim_des.model.Model.setup", false]], "setup() (histopath_bim_des.process.core.arrivalgenerator method)": [[15, "histopath_bim_des.process.core.ArrivalGenerator.setup", false]], "setup() (histopath_bim_des.process.core.baseprocess method)": [[15, "histopath_bim_des.process.core.BaseProcess.setup", false]], "setup() (histopath_bim_des.process.core.batchingprocess method)": [[15, "histopath_bim_des.process.core.BatchingProcess.setup", false]], "setup() (histopath_bim_des.process.core.collationprocess method)": [[15, "histopath_bim_des.process.core.CollationProcess.setup", false]], "setup() (histopath_bim_des.process.core.deliveryprocess method)": [[15, "histopath_bim_des.process.core.DeliveryProcess.setup", false]], "setup() (histopath_bim_des.process.core.process method)": [[15, "histopath_bim_des.process.core.Process.setup", false]], "setup() (histopath_bim_des.process.core.resourcescheduler method)": [[15, "histopath_bim_des.process.core.ResourceScheduler.setup", false]], "setup() (histopath_bim_des.specimens.batch method)": [[25, "histopath_bim_des.specimens.Batch.setup", false]], "setup() (histopath_bim_des.specimens.block method)": [[25, "histopath_bim_des.specimens.Block.setup", false]], "setup() (histopath_bim_des.specimens.slide method)": [[25, "histopath_bim_des.specimens.Slide.setup", false]], "setup() (histopath_bim_des.specimens.specimen method)": [[25, "histopath_bim_des.specimens.Specimen.setup", false]], "shapelymodel (class in histopath_bim_des.bim)": [[1, "histopath_bim_des.bim.ShapelyModel", false]], "shortest_path() (histopath_bim_des.bim.shapelymodel method)": [[1, "histopath_bim_des.bim.ShapelyModel.shortest_path", false]], "sim_hours (histopath_bim_des.config.config.config attribute)": [[5, "histopath_bim_des.config.config.Config.sim_hours", false]], "sim_length (histopath_bim_des.model.model attribute)": [[13, "histopath_bim_des.model.Model.sim_length", false]], "slide (class in histopath_bim_des.specimens)": [[25, "histopath_bim_des.specimens.Slide", false]], "specimen (class in histopath_bim_des.specimens)": [[25, "histopath_bim_des.specimens.Specimen", false]], "specimen_data (histopath_bim_des.model.model attribute)": [[13, "histopath_bim_des.model.Model.specimen_data", false]], "staining (histopath_bim_des.config.runners.processdoormap attribute)": [[9, "histopath_bim_des.config.runners.ProcessDoorMap.staining", false]], "staining_labelling (histopath_bim_des.config.runners.runnertimesconfig attribute)": [[9, "histopath_bim_des.config.runners.RunnerTimesConfig.staining_labelling", false]], "staining_labelling (histopath_bim_des.model.runnertimes attribute)": [[13, "histopath_bim_des.model.RunnerTimes.staining_labelling", false]], "staining_machine (histopath_bim_des.config.resources.resourcesinfo attribute)": [[8, "histopath_bim_des.config.resources.ResourcesInfo.staining_machine", false]], "staining_machine 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"histopath_bim_des.bim module", "histopath_bim_des.config package", "histopath_bim_des.config.arrivals module", "histopath_bim_des.config.batching module", "histopath_bim_des.config.config module", "histopath_bim_des.config.distributions module", "histopath_bim_des.config.global_vars module", "histopath_bim_des.config.resources module", "histopath_bim_des.config.runners module", "histopath_bim_des.config.tasks module", "histopath_bim_des.distribution module", "histopath_bim_des.excel module", "histopath_bim_des.model module", "histopath_bim_des.process package", "histopath_bim_des.process.core module", "histopath_bim_des.process.p10_reception module", "histopath_bim_des.process.p20_cutup module", "histopath_bim_des.process.p30_processing module", "histopath_bim_des.process.p40_microtomy module", "histopath_bim_des.process.p50_staining module", "histopath_bim_des.process.p60_labelling module", "histopath_bim_des.process.p70_scanning module", "histopath_bim_des.process.p80_qc module", "histopath_bim_des.process.p90_reporting module", "histopath_bim_des.specimens module", "histopath_bim_des.util module", "histopath_bim_des", "Model Configuration", "BIM-DES integration demo", "Histopathology processes", "Simulation and KPI extraction"], "titleterms": {"api": 29, "arriv": 3, "batch": 4, "bim": [1, 29], "config": [2, 3, 4, 5, 6, 7, 8, 9, 10], "configur": 28, "content": [0, 2, 14, 29], "core": 15, "de": 29, "demo": 29, "distribut": [6, 11], "excel": 12, "extract": 31, "gener": 28, "global_var": 7, "histopath_bim_d": [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27], "histopathologi": 30, "indic": 29, "integr": 29, "kpi": 31, "model": [13, 28], "modul": [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26], "p10_recept": 16, "p20_cutup": 17, "p30_process": 18, "p40_microtomi": 19, "p50_stain": 20, "p60_label": 21, "p70_scan": 22, "p80_qc": 23, "p90_report": 24, "packag": [0, 2, 14], "process": [14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 30], "refer": 29, "resourc": 8, "runner": [9, 28], "simul": 31, "specimen": 25, "submodul": [0, 2, 14], "subpackag": 0, "tabl": 29, "task": 10, "time": 28, "util": 26}})
\ No newline at end of file
diff --git a/docs/html/simulation.html b/docs/html/simulation.html
index 8dceb71..c6ed4aa 100644
--- a/docs/html/simulation.html
+++ b/docs/html/simulation.html
@@ -49,7 +49,7 @@
 <li class="toctree-l1"><a class="reference internal" href="config.html">Model Configuration</a></li>
 <li class="toctree-l1 current"><a class="current reference internal" href="#">Simulation and KPI extraction</a></li>
 <li class="toctree-l1"><a class="reference internal" href="processes.html">Histopathology processes</a></li>
-<li class="toctree-l1"><a class="reference external" href="`Jupyter notebooks &lt;https://github.com/yinchi/histopath-bim-des/tree/main/notebooks&gt;`_">`Jupyter notebooks &lt;https://github.com/yinchi/histopath-bim-des/tree/main/notebooks&gt;`_</a></li>
+<li class="toctree-l1"><a class="reference external" href="https://github.com/yinchi/histopath-bim-des/tree/main/notebooks">Jupyter notebooks</a></li>
 </ul>
 <p class="caption" role="heading"><span class="caption-text">API reference:</span></p>
 <ul>