From f311eb3e493f69766b5ec15f06d45ceeb4bbcbc1 Mon Sep 17 00:00:00 2001
From: gordonkoehn <gordon@koehn.net>
Date: Fri, 13 Oct 2023 11:55:11 +0200
Subject: [PATCH 01/19] add copied docs workflow

---
 .github/workflows/docs.yml | 39 ++++++++++++++++++++++++++++++++++++++
 1 file changed, 39 insertions(+)
 create mode 100644 .github/workflows/docs.yml

diff --git a/.github/workflows/docs.yml b/.github/workflows/docs.yml
new file mode 100644
index 00000000..063831e3
--- /dev/null
+++ b/.github/workflows/docs.yml
@@ -0,0 +1,39 @@
+# This pipeline builds the documentation.
+name: docs
+
+on:
+  push:
+    branches: [ main ]
+
+permissions:
+  contents: write
+
+jobs:
+  deploy:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+      - name: Set up Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: "3.9"
+          cache: "pip"
+      - name: Install Poetry
+        uses: snok/install-poetry@v1
+        with:
+          virtualenvs-create: true
+          virtualenvs-in-project: true
+          version: "1.3.2"
+      - name: Cache dependencies
+        id: cache-deps
+        uses: actions/cache@v2
+        with:
+          path: .venv
+          key: pydeps-${{ hashFiles('**/poetry.lock') }}
+      - name: Install the dependencies
+        run: poetry install --no-interaction --no-root --with dev
+        if: steps.cache-deps.outputs.cache-hit != 'true'
+      - name: Install the module
+        run: poetry install --with dev --no-interaction
+      - name: Generate the documentation
+        run: poetry run mkdocs gh-deploy --force

From d43488a5bc81a2dff12cb21d9a6d940c611a1011 Mon Sep 17 00:00:00 2001
From: gordonkoehn <gordon@koehn.net>
Date: Fri, 13 Oct 2023 13:41:23 +0200
Subject: [PATCH 02/19] add mkdoscs to poetry + steal config file

---
 mkdocs.yml     | 75 ++++++++++++++++++++++++++++++++++++++++++++++++++
 pyproject.toml |  1 +
 2 files changed, 76 insertions(+)
 create mode 100644 mkdocs.yml

diff --git a/mkdocs.yml b/mkdocs.yml
new file mode 100644
index 00000000..bc283c1d
--- /dev/null
+++ b/mkdocs.yml
@@ -0,0 +1,75 @@
+site_name: PYggdrasil
+theme:
+  name: material
+  features:
+    - navigation.tabs
+    - navigation.sections
+    - toc.integrate
+    - search.suggest
+    - search.highlight
+    - content.tabs.link
+    - content.code.annotation
+    - content.code.copy
+  language: en
+  palette:
+    - scheme: default
+      toggle:
+        icon: material/toggle-switch-off-outline 
+        name: Switch to dark mode
+      primary: teal
+      accent: purple 
+    - scheme: slate 
+      toggle:
+        icon: material/toggle-switch
+        name: Switch to light mode    
+      primary: teal
+      accent: lime
+
+repo_name: PYggdrasil
+repo_url: https://github.com/cbg-ethz/PYggdrasil
+
+plugins:
+  - search
+  - mkdocstrings:
+      default_handler: python
+      handlers:
+        python:
+          options:
+            show_source: false
+            show_root_heading: true
+
+nav:
+  - Home: index.md
+  - Contributing: contributing.md
+  - API: api/index.md
+
+watch:
+  - src/pyggdrasil
+
+extra:
+  social:
+    - icon: fontawesome/brands/github-alt
+      link: https://github.com/cbg-ethz/PYggdrasil
+
+markdown_extensions:
+  - pymdownx.highlight:
+      anchor_linenums: true
+  - pymdownx.inlinehilite
+  - pymdownx.snippets
+  - admonition
+  - pymdownx.arithmatex:
+      generic: true
+  - footnotes
+  - pymdownx.details
+  - pymdownx.superfences
+  - pymdownx.mark
+  - attr_list
+  - pymdownx.emoji:
+      emoji_index: !!python/name:materialx.emoji.twemoji
+      emoji_generator: !!python/name:materialx.emoji.to_svg
+
+
+extra_javascript:
+  - javascripts/mathjax.js
+  - https://polyfill.io/v3/polyfill.min.js?features=es6
+  - https://cdn.jsdelivr.net/npm/mathjax@3/es5/tex-mml-chtml.js
diff --git a/pyproject.toml b/pyproject.toml
index ef38dc2f..b6e7d72f 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -26,6 +26,7 @@ tqdm = "^4.65.0"
 networkx = "^3.0"
 arviz = "^0.16.1"
 seaborn = "^0.12.2"
+mkdocs = "^1.5.3"
 
 
 [tool.poetry.group.dev.dependencies]

From cd8ebb99068e8a2505c8a393981a06e3a922848d Mon Sep 17 00:00:00 2001
From: gordonkoehn <gordon@koehn.net>
Date: Fri, 13 Oct 2023 14:39:57 +0200
Subject: [PATCH 03/19] add correct project depend + update description

---
 pyproject.toml | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/pyproject.toml b/pyproject.toml
index b6e7d72f..2f84802e 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -26,7 +26,7 @@ tqdm = "^4.65.0"
 networkx = "^3.0"
 arviz = "^0.16.1"
 seaborn = "^0.12.2"
-mkdocs = "^1.5.3"
+
 
 
 [tool.poetry.group.dev.dependencies]
@@ -38,6 +38,10 @@ pytest-xdist = "^3.2.0"
 pre-commit = "^3.1.0"
 interrogate = "^1.5.0"
 pyright = "^1.1.309"
+mkdocs-material = "^9.1.6"
+mkdocstrings = {extras = ["python"], version = "^0.21.2"}
+mkdocs-gen-files = "^0.4.0"
+mkdocs-literate-nav = "^0.6.0"
 
 [tool.coverage.report]
 fail_under = 85.0

From 75d16b2d0721544f2c535e998c7b7f7a337ba72b Mon Sep 17 00:00:00 2001
From: gordonkoehn <gordon@koehn.net>
Date: Fri, 13 Oct 2023 14:43:56 +0200
Subject: [PATCH 04/19] add correct project depend + update description

---
 pyproject.toml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/pyproject.toml b/pyproject.toml
index 2f84802e..dab796e8 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,8 +1,8 @@
 [tool.poetry]
 name = "pyggdrasil"
 version = "0.1.0"
-description = ""
-authors = ["Computational Biology Group"]
+description = "Inference and analysis of mutation trees in Python with SCITE"
+authors = ["Gordon J. Köhn <gkoehn@student.ethz.ch>", "Paweł Czyż <pawelpiotr.czyz@ai.ethz.ch>",]
 readme = "README.md"
 packages = [{include = "pyggdrasil", from = "src"}]
 

From bc34f0509d8e0d2d60b0063cada21ad32aeb7693 Mon Sep 17 00:00:00 2001
From: gordonkoehn <gordon@koehn.net>
Date: Fri, 13 Oct 2023 15:05:49 +0200
Subject: [PATCH 05/19] remove problematic emoji usage

---
 mkdocs.yml | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

diff --git a/mkdocs.yml b/mkdocs.yml
index bc283c1d..b13e8cdd 100644
--- a/mkdocs.yml
+++ b/mkdocs.yml
@@ -64,9 +64,10 @@ markdown_extensions:
   - pymdownx.superfences
   - pymdownx.mark
   - attr_list
-  - pymdownx.emoji:
-      emoji_index: !!python/name:materialx.emoji.twemoji
-      emoji_generator: !!python/name:materialx.emoji.to_svg
+ # TODO (Gordon): cannot get this packages to be found my mkdocs 
+ # - pymdownx.emoji:
+ #     emoji_index: !!python/name:materialx.emoji.twemoji
+ #     emoji_generator: !!python/name:materialx.emoji.to_svg
 
 
 extra_javascript:

From 05e9ec8b84d87512e1ee844d66181b965060adc4 Mon Sep 17 00:00:00 2001
From: gordonkoehn <gordon@koehn.net>
Date: Fri, 13 Oct 2023 15:15:28 +0200
Subject: [PATCH 06/19] add soft link to readme

---
 docs/index.md | 1 +
 1 file changed, 1 insertion(+)
 create mode 100644 docs/index.md

diff --git a/docs/index.md b/docs/index.md
new file mode 100644
index 00000000..32d46ee8
--- /dev/null
+++ b/docs/index.md
@@ -0,0 +1 @@
+../README.md
\ No newline at end of file

From 152e3cd4cb1a1ec29102b245a68dd384a78ea879 Mon Sep 17 00:00:00 2001
From: gordonkoehn <gordon@koehn.net>
Date: Fri, 13 Oct 2023 15:22:48 +0200
Subject: [PATCH 07/19] add softlink

---
 docs/index.md | 0
 1 file changed, 0 insertions(+), 0 deletions(-)
 mode change 100644 => 120000 docs/index.md

diff --git a/docs/index.md b/docs/index.md
deleted file mode 100644
index 32d46ee8..00000000
--- a/docs/index.md
+++ /dev/null
@@ -1 +0,0 @@
-../README.md
\ No newline at end of file
diff --git a/docs/index.md b/docs/index.md
new file mode 120000
index 00000000..32d46ee8
--- /dev/null
+++ b/docs/index.md
@@ -0,0 +1 @@
+../README.md
\ No newline at end of file

From ead56b7b859dd727f62eec81ea3c4fc6207e331a Mon Sep 17 00:00:00 2001
From: gordonkoehn <gordon@koehn.net>
Date: Fri, 13 Oct 2023 15:41:21 +0200
Subject: [PATCH 08/19] add minimal example api

---
 docs/api/analyze.md | 3 +++
 docs/api/index.md   | 4 ++++
 2 files changed, 7 insertions(+)
 create mode 100644 docs/api/analyze.md
 create mode 100644 docs/api/index.md

diff --git a/docs/api/analyze.md b/docs/api/analyze.md
new file mode 100644
index 00000000..b324399c
--- /dev/null
+++ b/docs/api/analyze.md
@@ -0,0 +1,3 @@
+# Analyze
+
+::: pyggdrasil.analyze._rhat.rhats
diff --git a/docs/api/index.md b/docs/api/index.md
new file mode 100644
index 00000000..372a0a7e
--- /dev/null
+++ b/docs/api/index.md
@@ -0,0 +1,4 @@
+# API
+
+- [Analyze](analyze.md) provides analysis tools of tree samples and inference runs.
+

From 75fdb1a60c1b07e068d400f1d104b66cce0a2af8 Mon Sep 17 00:00:00 2001
From: gordonkoehn <gordon@koehn.net>
Date: Fri, 13 Oct 2023 15:54:20 +0200
Subject: [PATCH 09/19] update gitignore

---
 .gitignore          |  1 +
 docs/api/analyze.md | 10 ++++++++++
 2 files changed, 11 insertions(+)

diff --git a/.gitignore b/.gitignore
index 2ff6c3cc..94f6decf 100644
--- a/.gitignore
+++ b/.gitignore
@@ -12,6 +12,7 @@ poetry.lock
 # Notebooks are disallowed by default
 *.nb
 *.ipynb
+/notebooks
 
 # Environmental files
 .idea/
diff --git a/docs/api/analyze.md b/docs/api/analyze.md
index b324399c..aec5c92f 100644
--- a/docs/api/analyze.md
+++ b/docs/api/analyze.md
@@ -1,3 +1,13 @@
 # Analyze
 
 ::: pyggdrasil.analyze._rhat.rhats
+
+::: pyggdrasil.analyze._ess.ess
+
+::: pyggdrasil.analyze._metrics.Metrics
+
+::: pyggdrasil.analyze._utils.to_pure_mcmc_data
+
+::: pyggdrasil.analyze._calculation.check_run_for_tree
+
+::: pyggdrasil.analyze._calculation.analyze_mcmc_run
\ No newline at end of file

From 873bc033c0ea6076329a73b7c69beb8e590babfd Mon Sep 17 00:00:00 2001
From: gordonkoehn <gordon@koehn.net>
Date: Sat, 14 Oct 2023 13:30:30 +0200
Subject: [PATCH 10/19] enhance docs

---
 src/pyggdrasil/analyze/_metrics.py | 25 +++++++++++++++++++++++--
 1 file changed, 23 insertions(+), 2 deletions(-)

diff --git a/src/pyggdrasil/analyze/_metrics.py b/src/pyggdrasil/analyze/_metrics.py
index 9df47927..936c439b 100644
--- a/src/pyggdrasil/analyze/_metrics.py
+++ b/src/pyggdrasil/analyze/_metrics.py
@@ -7,11 +7,32 @@
 
 
 class Metrics:
-    """Metrics for comparing trees."""
+    """Metrics for comparing trees.
+
+    Attributes:
+        _METRICS: Dictionary of metrics.
+    """
 
     @staticmethod
     def get(metric: str) -> Callable[[TreeNode, TreeNode], float]:
-        """Return metric function."""
+        """Return metric function.
+
+        Args:
+            metric: Name of metric.
+
+        Returns:
+            - AD: Ancestor-Descendant Similarity;
+              pyggdrasil.distances.AncestorDescendantSimilarity().calculate,
+            - MP3: MP3 Similarity;
+              pyggdrasil.distances.MP3Similarity().calculate,
+            - TrueTree: True Tree Similarity;
+              pyggdrasil.compare_trees
+            - DL: Different Lineage Similarity;
+              pyggdrasil.distances.DifferentLineageSimilarity().calculate,
+            - MLTD: MLTD Similarity;
+              pyggdrasil.distances.MLTDSimilarity().calculate,
+
+        """
         return Metrics._METRICS[metric]
 
     _METRICS: Dict[str, Callable[[TreeNode, TreeNode], float]] = {  # type: ignore

From 2caed6647045bf7fefe2e15159472dfadc17b115 Mon Sep 17 00:00:00 2001
From: gordonkoehn <gordon@koehn.net>
Date: Sat, 14 Oct 2023 14:24:04 +0200
Subject: [PATCH 11/19] add remaining packages

---
 docs/api/analyze.md        | 12 ++++-----
 docs/api/distances.md      | 21 +++++++++++++++
 docs/api/index.md          | 12 +++++++++
 docs/api/interface.md      |  7 +++++
 docs/api/serialize.md      | 18 +++++++++++++
 docs/api/tree_inference.md | 52 ++++++++++++++++++++++++++++++++++++++
 docs/api/visualize.md      | 11 ++++++++
 7 files changed, 127 insertions(+), 6 deletions(-)
 create mode 100644 docs/api/distances.md
 create mode 100644 docs/api/interface.md
 create mode 100644 docs/api/serialize.md
 create mode 100644 docs/api/tree_inference.md
 create mode 100644 docs/api/visualize.md

diff --git a/docs/api/analyze.md b/docs/api/analyze.md
index aec5c92f..57d53c55 100644
--- a/docs/api/analyze.md
+++ b/docs/api/analyze.md
@@ -1,13 +1,13 @@
 # Analyze
 
-::: pyggdrasil.analyze._rhat.rhats
+::: pyggdrasil.analyze.rhats
 
-::: pyggdrasil.analyze._ess.ess
+::: pyggdrasil.analyze.ess
 
-::: pyggdrasil.analyze._metrics.Metrics
+::: pyggdrasil.analyze.Metrics
 
-::: pyggdrasil.analyze._utils.to_pure_mcmc_data
+::: pyggdrasil.analyze.to_pure_mcmc_data
 
-::: pyggdrasil.analyze._calculation.check_run_for_tree
+::: pyggdrasil.analyze.check_run_for_tree
 
-::: pyggdrasil.analyze._calculation.analyze_mcmc_run
\ No newline at end of file
+::: pyggdrasil.analyze.analyze_mcmc_run
\ No newline at end of file
diff --git a/docs/api/distances.md b/docs/api/distances.md
new file mode 100644
index 00000000..8e9f117e
--- /dev/null
+++ b/docs/api/distances.md
@@ -0,0 +1,21 @@
+# Distances
+
+::: pyggdrasil.distances.TreeDistance
+
+::: pyggdrasil.distances.TreeSimilarity
+
+::: pyggdrasil.distances.TreeSimilarityMeasure
+
+::: pyggdrasil.distances.calculate_distance_matrix
+
+::: pyggdrasil.distances.AncestorDescendantSimilarity
+
+::: pyggdrasil.distances.MP3Similarity
+
+::: pyggdrasil.distances.AncestorDescendantSimilarityInclRoot
+
+::: pyggdrasil.distances.DifferentLineageSimilarity
+
+::: pyggdrasil.distances.MLTDSimilarity
+
+
diff --git a/docs/api/index.md b/docs/api/index.md
index 372a0a7e..4633483a 100644
--- a/docs/api/index.md
+++ b/docs/api/index.md
@@ -1,4 +1,16 @@
 # API
 
 - [Analyze](analyze.md) provides analysis tools of tree samples and inference runs.
+- [Distances](distances.md) provides tree-tree distance and similarity measures.
+- [Interface](interface.md) provides dataclasses for processing MCMC data.
+- [Serialize](serialize.md) contains utilities for serialization and  deserialization of trees, MCMC rus and analysis.
+- [Tree Inference](tree_inference.md) implements the mutation tree infernce; scDNA mutation profiles synthesis.
+- [Visualize](visualize.md) implements visualization of trees and MCMC runs and diagostics theirof.
+
+This package handels trees with _Anytree_, see our adaption in the class _TreeNode_ below.  For the inference we convert trees to binary adjacency matrices see [Tree Inference](tree_inference.md), for reasons of performance.
+
+::: pyggdrasil.TreeNode
+
+::: pyggdrasil.compare_trees
+
 
diff --git a/docs/api/interface.md b/docs/api/interface.md
new file mode 100644
index 00000000..cafb00f3
--- /dev/null
+++ b/docs/api/interface.md
@@ -0,0 +1,7 @@
+# Interface
+
+::: pyggdrasil.interface.PureMcmcData
+
+
+
+
diff --git a/docs/api/serialize.md b/docs/api/serialize.md
new file mode 100644
index 00000000..14b2d7f9
--- /dev/null
+++ b/docs/api/serialize.md
@@ -0,0 +1,18 @@
+# Serialize
+
+::: pyggdrasil.serialize.serialize_tree_to_dict
+
+::: pyggdrasil.serialize.deserialize_tree_from_dict
+
+::: pyggdrasil.serialize.read_mcmc_samples
+
+::: pyggdrasil.serialize.save_mcmc_sample
+
+::: pyggdrasil.serialize.read_tree_node
+
+::: pyggdrasil.serialize.save_tree_node
+
+::: pyggdrasil.serialize.save_metric_result
+
+::: pyggdrasil.serialize.read_metric_result
+
diff --git a/docs/api/tree_inference.md b/docs/api/tree_inference.md
new file mode 100644
index 00000000..6572722d
--- /dev/null
+++ b/docs/api/tree_inference.md
@@ -0,0 +1,52 @@
+# Tree Inference
+
+::: pyggdrasil.tree_inference.CellAttachmentStrategy
+
+::: pyggdrasil.tree_inference.CellSimulationData
+
+::: pyggdrasil.tree_inference.CellSimulationId
+
+::: pyggdrasil.tree_inference.CellSimulationModel
+
+::: pyggdrasil.tree_inference.ErrorCombinations
+
+::: pyggdrasil.tree_inference.ErrorRates
+
+::: pyggdrasil.tree_inference.evolve_tree_mcmc
+
+::: pyggdrasil.tree_inference.evolve_tree_mcmc_all
+
+::: pyggdrasil.tree_inference.gen_sim_data
+
+::: pyggdrasil.tree_inference.get_descendants
+
+::: pyggdrasil.tree_inference.get_simulation_data
+
+::: pyggdrasil.tree_inference.huntress_tree_inference
+
+::: pyggdrasil.tree_inference.make_tree
+
+::: pyggdrasil.tree_inference.McmcConfig
+
+::: pyggdrasil.tree_inference.McmcConfigOptions
+
+::: pyggdrasil.tree_inference.McmcRunId
+
+::: pyggdrasil.tree_inference.mcmc_sampler
+
+::: pyggdrasil.tree_inference.MoveProbabilities
+
+::: pyggdrasil.tree_inference.MoveProbConfig
+
+::: pyggdrasil.tree_inference.MoveProbConfigOptions
+
+::: pyggdrasil.tree_inference.MutationDataId
+
+::: pyggdrasil.tree_inference.MutationMatrix
+
+::: pyggdrasil.tree_inference.Tree
+
+::: pyggdrasil.tree_inference.TreeId
+
+::: pyggdrasil.tree_inference.TreeType
+
diff --git a/docs/api/visualize.md b/docs/api/visualize.md
new file mode 100644
index 00000000..1d57527c
--- /dev/null
+++ b/docs/api/visualize.md
@@ -0,0 +1,11 @@
+# Visualize
+
+::: pyggdrasil.visualize.plot_tree
+::: pyggdrasil.visualize.save_metric_iteration
+::: pyggdrasil.visualize.save_log_p_iteration
+::: pyggdrasil.visualize.plot_tree_mcmc_sample
+::: pyggdrasil.visualize.plot_tree_no_print
+::: pyggdrasil.visualize.save_top_trees_plots
+::: pyggdrasil.visualize.save_rhat_iteration
+::: pyggdrasil.visualize.save_rhat_iteration_AD_DL
+::: pyggdrasil.visualize.save_ess_iteration_AD_DL
\ No newline at end of file

From 2ca228141dc416aa2331541232cfe353460342ad Mon Sep 17 00:00:00 2001
From: gordonkoehn <gordon@koehn.net>
Date: Mon, 16 Oct 2023 10:11:04 +0200
Subject: [PATCH 12/19] add contributing

---
 docs/api/contributing.md | 52 ++++++++++++++++++++++++++++++++++++++++
 mkdocs.yml               |  1 +
 2 files changed, 53 insertions(+)
 create mode 100644 docs/api/contributing.md

diff --git a/docs/api/contributing.md b/docs/api/contributing.md
new file mode 100644
index 00000000..46a50788
--- /dev/null
+++ b/docs/api/contributing.md
@@ -0,0 +1,52 @@
+# Contributing
+
+Thank you for your time to contribute to this project!
+Below we present some guidelines.
+
+## Reporting a bug
+
+If you find a bug, please [submit a new issue](https://github.com/cbg-ethz/PYggdrasil/issues).
+
+To be able to reproduce a bug, we will usually need the following information:
+
+  - Versions of Python packages used (in particular version of this library).
+  - A minimal code snippet allowing us to reproduce the bug.
+  - What is the desired behaviour in the reported case?
+  - What is the actual behaviour?
+
+
+## Submitting a pull request
+
+**Do:**
+
+  - Do use [Google Style Guide](https://google.github.io/styleguide/pyguide.html). We use [black](https://github.com/psf/black) for code formatting.
+  - Do write unit tests. We use [pytest](https://docs.pytest.org/).
+  - Do write docstrings. We use [Material for Mkdocs](https://squidfunk.github.io/mkdocs-material/) to generate the documentation.
+  - Do write high-level documentation as examples and tutorials, illustrating introduced features.
+  - Do consider submitting a *draft* pull request with a description of proposed changes.
+  - Do check the [Development section](#development).
+
+**Don't:**
+
+  - Don't include license information. This project is MIT licensed and by submitting your pull request you implicitly and irrevocably agree to use this.
+  - Don't implement too many ideas in a single pull request. Multiple features should be implemented in separate pull requests.
+
+
+## Development
+
+### Installation & dependencies
+To install the repository together with the dependencies run:
+```
+$ git clone git@github.com:cbg-ethz/PYggdrasil.git  # Clone the repository
+$ poetry add install -G dev                  # Install the dependencies
+$ poetry run pre-commit install              # Install pre-commit hooks
+$ poetry run pytest                          # Check if unit tests are passing
+```
+
+### Building documentation locally
+You can build the documentation on your machine using:
+```
+$ poetry run mkdocs serve
+```
+and opening the generated link using web browser.
+
diff --git a/mkdocs.yml b/mkdocs.yml
index b13e8cdd..6f084c5f 100644
--- a/mkdocs.yml
+++ b/mkdocs.yml
@@ -41,6 +41,7 @@ plugins:
 nav:
   - Home: index.md
   - Contributing: contributing.md
+  - Tutorial: tutorial/index.md
   - API: api/index.md
 
 watch:

From c12eecb93e692fde420eb484489bb42035d18172 Mon Sep 17 00:00:00 2001
From: gordonkoehn <gordon@koehn.net>
Date: Mon, 16 Oct 2023 10:21:49 +0200
Subject: [PATCH 13/19] refine contributing

---
 docs/api/contributing.md | 52 ----------------------------------------
 1 file changed, 52 deletions(-)
 delete mode 100644 docs/api/contributing.md

diff --git a/docs/api/contributing.md b/docs/api/contributing.md
deleted file mode 100644
index 46a50788..00000000
--- a/docs/api/contributing.md
+++ /dev/null
@@ -1,52 +0,0 @@
-# Contributing
-
-Thank you for your time to contribute to this project!
-Below we present some guidelines.
-
-## Reporting a bug
-
-If you find a bug, please [submit a new issue](https://github.com/cbg-ethz/PYggdrasil/issues).
-
-To be able to reproduce a bug, we will usually need the following information:
-
-  - Versions of Python packages used (in particular version of this library).
-  - A minimal code snippet allowing us to reproduce the bug.
-  - What is the desired behaviour in the reported case?
-  - What is the actual behaviour?
-
-
-## Submitting a pull request
-
-**Do:**
-
-  - Do use [Google Style Guide](https://google.github.io/styleguide/pyguide.html). We use [black](https://github.com/psf/black) for code formatting.
-  - Do write unit tests. We use [pytest](https://docs.pytest.org/).
-  - Do write docstrings. We use [Material for Mkdocs](https://squidfunk.github.io/mkdocs-material/) to generate the documentation.
-  - Do write high-level documentation as examples and tutorials, illustrating introduced features.
-  - Do consider submitting a *draft* pull request with a description of proposed changes.
-  - Do check the [Development section](#development).
-
-**Don't:**
-
-  - Don't include license information. This project is MIT licensed and by submitting your pull request you implicitly and irrevocably agree to use this.
-  - Don't implement too many ideas in a single pull request. Multiple features should be implemented in separate pull requests.
-
-
-## Development
-
-### Installation & dependencies
-To install the repository together with the dependencies run:
-```
-$ git clone git@github.com:cbg-ethz/PYggdrasil.git  # Clone the repository
-$ poetry add install -G dev                  # Install the dependencies
-$ poetry run pre-commit install              # Install pre-commit hooks
-$ poetry run pytest                          # Check if unit tests are passing
-```
-
-### Building documentation locally
-You can build the documentation on your machine using:
-```
-$ poetry run mkdocs serve
-```
-and opening the generated link using web browser.
-

From e75be7a254674d86ba818bf4653dd343d22d8130 Mon Sep 17 00:00:00 2001
From: gordonkoehn <gordon@koehn.net>
Date: Mon, 16 Oct 2023 11:47:48 +0200
Subject: [PATCH 14/19] enhance contributing

---
 docs/contributing.md | 93 ++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 93 insertions(+)
 create mode 100644 docs/contributing.md

diff --git a/docs/contributing.md b/docs/contributing.md
new file mode 100644
index 00000000..720debd7
--- /dev/null
+++ b/docs/contributing.md
@@ -0,0 +1,93 @@
+# Contributing
+
+Thank you for your time to contribute to this project!
+Below we present some guidelines.
+
+## Reporting a bug
+
+If you find a bug, please [submit a new issue](https://github.com/cbg-ethz/PYggdrasil/issues).
+
+To be able to reproduce a bug, we will usually need the following information:
+
+  - Versions of Python packages used (in particular version of this library).
+  - A minimal code snippet allowing us to reproduce the bug.
+  - What is the desired behaviour in the reported case?
+  - What is the actual behaviour?
+
+
+## Submitting a pull request
+
+**Do:**
+
+  - Do use [Google Style Guide](https://google.github.io/styleguide/pyguide.html). We use [black](https://github.com/psf/black) for code formatting.
+  - Do write unit tests. We use [pytest](https://docs.pytest.org/).
+  - Do write docstrings. We use [Material for Mkdocs](https://squidfunk.github.io/mkdocs-material/) to generate the documentation.
+  - Do write high-level documentation as examples and tutorials, illustrating introduced features.
+  - Do consider submitting a *draft* pull request with a description of proposed changes.
+  - Do check the [Development section](#development).
+
+**Don't:**
+
+  - Don't include license information. This project is MIT licensed and by submitting your pull request you implicitly and irrevocably agree to use this.
+  - Don't implement too many ideas in a single pull request. Multiple features should be implemented in separate pull requests.
+
+
+## Development
+
+### Workflow
+
+We use [Feature Branch Workflow](https://www.atlassian.com/git/tutorials/comparing-workflows/feature-branch-workflow),
+in which modifications of the code should happen via small pull requests.
+
+We recommend submitting small pull requests and starting with drafts outlining proposed changes.
+
+### Installation & dependencies
+To install the repository together with the dependencies run:
+```
+$ git clone git@github.com:cbg-ethz/PYggdrasil.git  # Clone the repository
+$ poetry install --with dev                         # Install the dependencies
+$ poetry run pre-commit install                     # Install pre-commit hooks
+$ poetry run pytest                                 # Check if unit tests are passing
+```
+
+
+### Testing & Checking
+
+Then, you will be able to run tests:
+```bash
+$ poetry run pytest
+```
+... or check the types:
+```bash
+$ poetry run pyright
+```
+
+### Existing code quality checks
+The code quality checks run during on GitHub can be seen in ``.github/workflows/test.yml``.
+
+We are using:
+  - [Ruff](https://github.com/charliermarsh/ruff) to lint the code.
+  - [Black](https://github.com/psf/black) to format the code.
+  - [Pyright](https://github.com/microsoft/pyright) to check the types.
+  - [Pytest](https://docs.pytest.org/) to run the unit tests.
+  - [Interrogate](https://interrogate.readthedocs.io/) to check the documentation.
+
+Alternatively, you may prefer to work with the right Python environment using:
+```bash
+$ poetry shell
+$ pytest
+```
+
+### Building documentation locally
+You can build the documentation on your machine using:
+```
+$ poetry run mkdocs serve
+```
+and opening the generated link using web browser.
+
+### Code organisation
+
+- The package code is in ``src/pyggdrasil/`` and is partitioned into subpackages.
+- The unit tests are in ``tests/`` and the structure of this directory should reflect the one of the package.
+- Experimental workflows are in ``workflows/``, with a description of how to set up the environment in ``workflows/README.md``
+

From 31b721b1ca32b4c31ed6c31c2eb56462e55e697e Mon Sep 17 00:00:00 2001
From: gordonkoehn <gordon@koehn.net>
Date: Mon, 16 Oct 2023 11:53:12 +0200
Subject: [PATCH 15/19] first test notebook with quarto

---
 docs/tutorial/index.md                        |   9 +
 docs/tutorial/mcmc_test.json                  | 100 +++++
 docs/tutorial/singleMCMC.md                   | 372 ++++++++++++++++++
 docs/tutorial/singleMCMC.qmd                  | 143 +++++++
 .../log-prob-iter-output-1.png                | Bin 0 -> 15399 bytes
 5 files changed, 624 insertions(+)
 create mode 100644 docs/tutorial/index.md
 create mode 100644 docs/tutorial/mcmc_test.json
 create mode 100644 docs/tutorial/singleMCMC.md
 create mode 100644 docs/tutorial/singleMCMC.qmd
 create mode 100644 docs/tutorial/singleMCMC_files/figure-commonmark/log-prob-iter-output-1.png

diff --git a/docs/tutorial/index.md b/docs/tutorial/index.md
new file mode 100644
index 00000000..3a06640d
--- /dev/null
+++ b/docs/tutorial/index.md
@@ -0,0 +1,9 @@
+# Tutorials
+
+We'd love to see you built upon PYggdrasil. Below we provide some tutorials to help you get started.
+
+## Functional Usage
+
+- [Single MCMC Run](singleMCMC.md) demonstrated how to run a single MCMC chain.
+
+## Experimental Workflows
\ No newline at end of file
diff --git a/docs/tutorial/mcmc_test.json b/docs/tutorial/mcmc_test.json
new file mode 100644
index 00000000..8e27da89
--- /dev/null
+++ b/docs/tutorial/mcmc_test.json
@@ -0,0 +1,100 @@
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+{"coords": {"from_node_k": {"dims": ["from_node_k"], "attrs": {}, "data": [0, 1, 2, 3, 4]}, "to_node_k": {"dims": ["to_node_k"], "attrs": {}, "data": [0, 1, 2, 3, 4]}}, "attrs": {}, "dims": {"from_node_k": 5, "to_node_k": 5}, "data_vars": {"iteration": {"dims": [], "attrs": {}, "data": 95}, "tree": {"dims": ["from_node_k", "to_node_k"], "attrs": {}, "data": [[0.0, 0.0, 0.0, 0.0, 0.0], [0.0, 0.0, 0.0, 0.0, 0.0], [0.0, 1.0, 0.0, 0.0, 0.0], [0.0, 0.0, 0.0, 0.0, 0.0], [1.0, 0.0, 1.0, 1.0, 0.0]]}, "log-probability": {"dims": [], "attrs": {}, "data": -468.29644775390625}}}
+{"coords": {"from_node_k": {"dims": ["from_node_k"], "attrs": {}, "data": [0, 1, 2, 3, 4]}, "to_node_k": {"dims": ["to_node_k"], "attrs": {}, "data": [0, 1, 2, 3, 4]}}, "attrs": {}, "dims": {"from_node_k": 5, "to_node_k": 5}, "data_vars": {"iteration": {"dims": [], "attrs": {}, "data": 96}, "tree": {"dims": ["from_node_k", "to_node_k"], "attrs": {}, "data": [[0.0, 0.0, 0.0, 0.0, 0.0], [0.0, 0.0, 0.0, 0.0, 0.0], [0.0, 1.0, 0.0, 0.0, 0.0], [0.0, 0.0, 0.0, 0.0, 0.0], [1.0, 0.0, 1.0, 1.0, 0.0]]}, "log-probability": {"dims": [], "attrs": {}, "data": -468.29644775390625}}}
+{"coords": {"from_node_k": {"dims": ["from_node_k"], "attrs": {}, "data": [0, 1, 2, 3, 4]}, "to_node_k": {"dims": ["to_node_k"], "attrs": {}, "data": [0, 1, 2, 3, 4]}}, "attrs": {}, "dims": {"from_node_k": 5, "to_node_k": 5}, "data_vars": {"iteration": {"dims": [], "attrs": {}, "data": 97}, "tree": {"dims": ["from_node_k", "to_node_k"], "attrs": {}, "data": [[0.0, 0.0, 0.0, 0.0, 0.0], [0.0, 0.0, 0.0, 0.0, 0.0], [0.0, 1.0, 0.0, 0.0, 0.0], [0.0, 0.0, 0.0, 0.0, 0.0], [1.0, 0.0, 1.0, 1.0, 0.0]]}, "log-probability": {"dims": [], "attrs": {}, "data": -468.29644775390625}}}
+{"coords": {"from_node_k": {"dims": ["from_node_k"], "attrs": {}, "data": [0, 1, 2, 3, 4]}, "to_node_k": {"dims": ["to_node_k"], "attrs": {}, "data": [0, 1, 2, 3, 4]}}, "attrs": {}, "dims": {"from_node_k": 5, "to_node_k": 5}, "data_vars": {"iteration": {"dims": [], "attrs": {}, "data": 98}, "tree": {"dims": ["from_node_k", "to_node_k"], "attrs": {}, "data": [[0.0, 0.0, 0.0, 0.0, 0.0], [0.0, 0.0, 0.0, 0.0, 0.0], [0.0, 1.0, 0.0, 0.0, 0.0], [0.0, 0.0, 0.0, 0.0, 0.0], [1.0, 0.0, 1.0, 1.0, 0.0]]}, "log-probability": {"dims": [], "attrs": {}, "data": -468.29644775390625}}}
+{"coords": {"from_node_k": {"dims": ["from_node_k"], "attrs": {}, "data": [0, 1, 2, 3, 4]}, "to_node_k": {"dims": ["to_node_k"], "attrs": {}, "data": [0, 1, 2, 3, 4]}}, "attrs": {}, "dims": {"from_node_k": 5, "to_node_k": 5}, "data_vars": {"iteration": {"dims": [], "attrs": {}, "data": 99}, "tree": {"dims": ["from_node_k", "to_node_k"], "attrs": {}, "data": [[0.0, 0.0, 0.0, 0.0, 0.0], [0.0, 0.0, 0.0, 0.0, 0.0], [0.0, 1.0, 0.0, 0.0, 0.0], [0.0, 0.0, 0.0, 0.0, 0.0], [1.0, 0.0, 1.0, 1.0, 0.0]]}, "log-probability": {"dims": [], "attrs": {}, "data": -468.29644775390625}}}
+{"coords": {"from_node_k": {"dims": ["from_node_k"], "attrs": {}, "data": [0, 1, 2, 3, 4]}, "to_node_k": {"dims": ["to_node_k"], "attrs": {}, "data": [0, 1, 2, 3, 4]}}, "attrs": {}, "dims": {"from_node_k": 5, "to_node_k": 5}, "data_vars": {"iteration": {"dims": [], "attrs": {}, "data": 100}, "tree": {"dims": ["from_node_k", "to_node_k"], "attrs": {}, "data": [[0.0, 0.0, 0.0, 0.0, 0.0], [0.0, 0.0, 0.0, 0.0, 0.0], [0.0, 1.0, 0.0, 0.0, 0.0], [0.0, 0.0, 0.0, 0.0, 0.0], [1.0, 0.0, 1.0, 1.0, 0.0]]}, "log-probability": {"dims": [], "attrs": {}, "data": -468.29644775390625}}}
diff --git a/docs/tutorial/singleMCMC.md b/docs/tutorial/singleMCMC.md
new file mode 100644
index 00000000..642024cc
--- /dev/null
+++ b/docs/tutorial/singleMCMC.md
@@ -0,0 +1,372 @@
+# Single MCMC Run
+
+This tutorial shows how to run a single MCMC chain of SCITE using
+PYggdrasil. - We will generate our own ground-truth mutation histroy and
+generate a noisy single-cell mutation profile from it. - We will then
+run a single MCMC chain to infer the mutation history from the noisy
+single-cell mutation profile. - Visualize the results. The trees and the
+evolution of the MCMC.
+
+## 0) Imports
+
+``` python
+## imports
+import pyggdrasil as yg
+import jax.numpy as jnp
+import jax.random as random
+from pathlib import Path
+import matplotlib.pyplot as plt
+
+# matplotlib inline
+%matplotlib inline 
+```
+
+## 1) Generate a ground-truth mutation history and a noisy single-cell mutation profile
+
+The below cell generates a random tree with 4 mutations, plus root. For
+debugging we may use the *print_topo* to plot its topology.
+
+``` python
+# make true tree
+tree_type = yg.tree_inference.TreeType.RANDOM
+mutations = 4
+nodes = mutations + 1
+tree_seed = 42
+true_tree = yg.tree_inference.make_tree(nodes, tree_type, tree_seed) 
+
+true_tree.print_topo()
+```
+
+    4
+    ├── 0
+    ├── 2
+    │   └── 1
+    └── 3
+
+## 2) Generate an initial tree to start the Markov Chain from
+
+We also choose a random tree here.
+
+``` python
+# make random starting tree
+tree_type = yg.tree_inference.TreeType.RANDOM
+tree_seed = 487
+starting_tree = yg.tree_inference.make_tree(nodes, tree_type, tree_seed)
+starting_tree.print_topo()
+```
+
+    4
+    ├── 1
+    └── 3
+        ├── 0
+        └── 2
+
+## 3) Generate a noisy single-cell mutation profile from the ground-truth tree
+
+``` python
+## generate some little nois data
+# Set up the simulation model
+csm = yg.tree_inference.CellSimulationModel(
+    n_cells=1000,
+    n_mutations=mutations,
+    fpr=0.01,
+    fnr=0.01,
+    na_rate=0.0,
+    observe_homozygous=False,
+    strategy=yg.tree_inference.CellAttachmentStrategy.UNIFORM_EXCLUDE_ROOT,
+)
+
+
+# Generate Data
+seed = 42
+rng = random.PRNGKey(seed)
+data = yg.tree_inference.gen_sim_data(
+    csm,
+    rng,
+    true_tree
+    )
+
+mut_mat = jnp.array(data['noisy_mutation_mat'])
+print(mut_mat)
+```
+
+    [[0 0 0 ... 0 0 1]
+     [1 0 0 ... 0 0 0]
+     [1 1 1 ... 0 0 0]
+     [0 0 0 ... 1 1 0]]
+
+## 4) Run the Markov Monte Carlo Chain
+
+The below cell runs a single MCMC chain. We initialize ti with the
+initial tree from before. We configure the move probabilities and error
+rates and run the MCMC chain for 100 iterations. The sampels are saved
+to disk and loaded back into memory as chains may be very long.
+
+``` python
+## Run MCMC
+# converting initial tree from TreeNode to Tree format
+init_tree_t = yg.tree_inference.Tree.tree_from_tree_node(starting_tree)
+
+## file handling
+# set up save location
+save_dir = Path("")
+# make directory if it doesn't exist
+save_dir.mkdir(parents=True, exist_ok=True)
+save_name = "mcmc_test"
+full_save_name = save_dir / f"{save_name}.json"
+# make file / empty it if it exists
+with open(full_save_name, "w") as f:
+    f.write("")
+
+# set the move probabilities and error rates
+move_probs = yg.tree_inference.MoveProbabilities()
+error_rates = yg.tree_inference.ErrorCombinations.IDEAL.value
+
+# run mcmc sampler
+yg.tree_inference.mcmc_sampler(
+    rng_key=rng,
+    data=mut_mat,
+    error_rates=(error_rates.fpr, error_rates.fnr),
+    move_probs=move_probs,
+    num_samples=100,
+    num_burn_in=0,
+    out_fp=full_save_name,
+    thinning=1,
+    init_tree=init_tree_t,
+)
+
+# load the data from disk
+mcmc_data = yg.serialize.read_mcmc_samples(save_dir / f"{save_name}.json")
+```
+
+    INFO:pyggdrasil.tree_inference._mcmc:Move Accepted
+    INFO:pyggdrasil.tree_inference._mcmc:Move Accepted
+    INFO:pyggdrasil.tree_inference._mcmc:Move Rejected
+    INFO:pyggdrasil.tree_inference._mcmc:Move Rejected
+    INFO:pyggdrasil.tree_inference._mcmc:Move Accepted
+    INFO:pyggdrasil.tree_inference._mcmc:Move Rejected
+    INFO:pyggdrasil.tree_inference._mcmc:Move Rejected
+    INFO:pyggdrasil.tree_inference._mcmc:Move Rejected
+    INFO:pyggdrasil.tree_inference._mcmc:Move Rejected
+    INFO:pyggdrasil.tree_inference._mcmc:Move Rejected
+    INFO:pyggdrasil.tree_inference._mcmc:Move Accepted
+    INFO:pyggdrasil.tree_inference._mcmc:Move Accepted
+    INFO:pyggdrasil.tree_inference._mcmc:Move Accepted
+    INFO:pyggdrasil.tree_inference._mcmc:Move Rejected
+    INFO:pyggdrasil.tree_inference._mcmc:Move Rejected
+    INFO:pyggdrasil.tree_inference._mcmc:Move Rejected
+    INFO:pyggdrasil.tree_inference._mcmc:Move Rejected
+    INFO:pyggdrasil.tree_inference._mcmc:Move Rejected
+    INFO:pyggdrasil.tree_inference._mcmc:Move Rejected
+    INFO:pyggdrasil.tree_inference._mcmc:Move Rejected
+    INFO:pyggdrasil.tree_inference._mcmc:Move Rejected
+    INFO:pyggdrasil.tree_inference._mcmc:Move Rejected
+    INFO:pyggdrasil.tree_inference._mcmc:Move Accepted
+    INFO:pyggdrasil.tree_inference._mcmc:Move Rejected
+    INFO:pyggdrasil.tree_inference._mcmc:Move Rejected
+    INFO:pyggdrasil.tree_inference._mcmc:Move Rejected
+    INFO:pyggdrasil.tree_inference._mcmc:Move Rejected
+    INFO:pyggdrasil.tree_inference._mcmc:Move Rejected
+    INFO:pyggdrasil.tree_inference._mcmc:Move Rejected
+    INFO:pyggdrasil.tree_inference._mcmc:Move Rejected
+    INFO:pyggdrasil.tree_inference._mcmc:Move Rejected
+    INFO:pyggdrasil.tree_inference._mcmc:Move Rejected
+    INFO:pyggdrasil.tree_inference._mcmc:Move Rejected
+    INFO:pyggdrasil.tree_inference._mcmc:Move Rejected
+    INFO:pyggdrasil.tree_inference._mcmc:Move Rejected
+    INFO:pyggdrasil.tree_inference._mcmc:Move Accepted
+    INFO:pyggdrasil.tree_inference._mcmc:Move Rejected
+    INFO:pyggdrasil.tree_inference._mcmc:Move Rejected
+    INFO:pyggdrasil.tree_inference._mcmc:Move Rejected
+    INFO:pyggdrasil.tree_inference._mcmc:Move Accepted
+    INFO:pyggdrasil.tree_inference._mcmc:Move Accepted
+    INFO:pyggdrasil.tree_inference._mcmc:Move Accepted
+    INFO:pyggdrasil.tree_inference._mcmc:Move Rejected
+    INFO:pyggdrasil.tree_inference._mcmc:Move Rejected
+    INFO:pyggdrasil.tree_inference._mcmc:Move Accepted
+    INFO:pyggdrasil.tree_inference._mcmc:Move Accepted
+    INFO:pyggdrasil.tree_inference._mcmc:Move Rejected
+    INFO:pyggdrasil.tree_inference._mcmc:Move Rejected
+    INFO:pyggdrasil.tree_inference._mcmc:Move Rejected
+    INFO:pyggdrasil.tree_inference._mcmc:Move Rejected
+    INFO:pyggdrasil.tree_inference._mcmc:Move Rejected
+    INFO:pyggdrasil.tree_inference._mcmc:Move Rejected
+    INFO:pyggdrasil.tree_inference._mcmc:Move Rejected
+    INFO:pyggdrasil.tree_inference._mcmc:Move Rejected
+    INFO:pyggdrasil.tree_inference._mcmc:Move Rejected
+    INFO:pyggdrasil.tree_inference._mcmc:Move Accepted
+    INFO:pyggdrasil.tree_inference._mcmc:Move Accepted
+    INFO:pyggdrasil.tree_inference._mcmc:Move Rejected
+    INFO:pyggdrasil.tree_inference._mcmc:Move Rejected
+    INFO:pyggdrasil.tree_inference._mcmc:Move Rejected
+    INFO:pyggdrasil.tree_inference._mcmc:Move Rejected
+    INFO:pyggdrasil.tree_inference._mcmc:Move Rejected
+    INFO:pyggdrasil.tree_inference._mcmc:Move Accepted
+    INFO:pyggdrasil.tree_inference._mcmc:Move Accepted
+    INFO:pyggdrasil.tree_inference._mcmc:Move Rejected
+    INFO:pyggdrasil.tree_inference._mcmc:Move Accepted
+    INFO:pyggdrasil.tree_inference._mcmc:Move Rejected
+    INFO:pyggdrasil.tree_inference._mcmc:Move Accepted
+    INFO:pyggdrasil.tree_inference._mcmc:Move Rejected
+    INFO:pyggdrasil.tree_inference._mcmc:Move Rejected
+    INFO:pyggdrasil.tree_inference._mcmc:Move Rejected
+    INFO:pyggdrasil.tree_inference._mcmc:Move Rejected
+    INFO:pyggdrasil.tree_inference._mcmc:Move Rejected
+    INFO:pyggdrasil.tree_inference._mcmc:Move Rejected
+    INFO:pyggdrasil.tree_inference._mcmc:Move Accepted
+    INFO:pyggdrasil.tree_inference._mcmc:Move Rejected
+    INFO:pyggdrasil.tree_inference._mcmc:Move Rejected
+    INFO:pyggdrasil.tree_inference._mcmc:Move Rejected
+    INFO:pyggdrasil.tree_inference._mcmc:Move Accepted
+    INFO:pyggdrasil.tree_inference._mcmc:Move Rejected
+    INFO:pyggdrasil.tree_inference._mcmc:Move Rejected
+    INFO:pyggdrasil.tree_inference._mcmc:Move Accepted
+    INFO:pyggdrasil.tree_inference._mcmc:Move Rejected
+    INFO:pyggdrasil.tree_inference._mcmc:Move Rejected
+    INFO:pyggdrasil.tree_inference._mcmc:Move Rejected
+    INFO:pyggdrasil.tree_inference._mcmc:Move Rejected
+    INFO:pyggdrasil.tree_inference._mcmc:Move Accepted
+    INFO:pyggdrasil.tree_inference._mcmc:Move Accepted
+    INFO:pyggdrasil.tree_inference._mcmc:Move Rejected
+    INFO:pyggdrasil.tree_inference._mcmc:Move Rejected
+    INFO:pyggdrasil.tree_inference._mcmc:Move Rejected
+    INFO:pyggdrasil.tree_inference._mcmc:Move Accepted
+    INFO:pyggdrasil.tree_inference._mcmc:Move Rejected
+    INFO:pyggdrasil.tree_inference._mcmc:Move Rejected
+    INFO:pyggdrasil.tree_inference._mcmc:Move Rejected
+    INFO:pyggdrasil.tree_inference._mcmc:Move Rejected
+    INFO:pyggdrasil.tree_inference._mcmc:Move Rejected
+    INFO:pyggdrasil.tree_inference._mcmc:Move Rejected
+    INFO:pyggdrasil.tree_inference._mcmc:Move Rejected
+    INFO:pyggdrasil.tree_inference._mcmc_sampler:Finished MCMC sampler.
+
+## 5) Visualize the results
+
+In the following we would like to plot the evolution of the MCMC chain
+and the trees that were sampled. First we convert the data from the
+serialized format to a *pureMCMCdata* format. This is a simple dataclass
+that contains the trees and the log probabilities of the trees.
+
+``` python
+# unpack the data - reads in the serialized trees to Tree objects
+# takes some time as tree objects are built and checked for validity
+mcmc_samples = yg.analyze.to_pure_mcmc_data(mcmc_data)
+```
+
+    DEBUG:pyggdrasil.analyze._utils:converting sample of index: 0
+    DEBUG:pyggdrasil.analyze._utils:converting sample of index: 1
+    DEBUG:pyggdrasil.analyze._utils:converting sample of index: 2
+    DEBUG:pyggdrasil.analyze._utils:converting sample of index: 3
+    DEBUG:pyggdrasil.analyze._utils:converting sample of index: 4
+    DEBUG:pyggdrasil.analyze._utils:converting sample of index: 5
+    DEBUG:pyggdrasil.analyze._utils:converting sample of index: 6
+    DEBUG:pyggdrasil.analyze._utils:converting sample of index: 7
+    DEBUG:pyggdrasil.analyze._utils:converting sample of index: 8
+    DEBUG:pyggdrasil.analyze._utils:converting sample of index: 9
+    DEBUG:pyggdrasil.analyze._utils:converting sample of index: 10
+    DEBUG:pyggdrasil.analyze._utils:converting sample of index: 11
+    DEBUG:pyggdrasil.analyze._utils:converting sample of index: 12
+    DEBUG:pyggdrasil.analyze._utils:converting sample of index: 13
+    DEBUG:pyggdrasil.analyze._utils:converting sample of index: 14
+    DEBUG:pyggdrasil.analyze._utils:converting sample of index: 15
+    DEBUG:pyggdrasil.analyze._utils:converting sample of index: 16
+    DEBUG:pyggdrasil.analyze._utils:converting sample of index: 17
+    DEBUG:pyggdrasil.analyze._utils:converting sample of index: 18
+    DEBUG:pyggdrasil.analyze._utils:converting sample of index: 19
+    DEBUG:pyggdrasil.analyze._utils:converting sample of index: 20
+    DEBUG:pyggdrasil.analyze._utils:converting sample of index: 21
+    DEBUG:pyggdrasil.analyze._utils:converting sample of index: 22
+    DEBUG:pyggdrasil.analyze._utils:converting sample of index: 23
+    DEBUG:pyggdrasil.analyze._utils:converting sample of index: 24
+    DEBUG:pyggdrasil.analyze._utils:converting sample of index: 25
+    DEBUG:pyggdrasil.analyze._utils:converting sample of index: 26
+    DEBUG:pyggdrasil.analyze._utils:converting sample of index: 27
+    DEBUG:pyggdrasil.analyze._utils:converting sample of index: 28
+    DEBUG:pyggdrasil.analyze._utils:converting sample of index: 29
+    DEBUG:pyggdrasil.analyze._utils:converting sample of index: 30
+    DEBUG:pyggdrasil.analyze._utils:converting sample of index: 31
+    DEBUG:pyggdrasil.analyze._utils:converting sample of index: 32
+    DEBUG:pyggdrasil.analyze._utils:converting sample of index: 33
+    DEBUG:pyggdrasil.analyze._utils:converting sample of index: 34
+    DEBUG:pyggdrasil.analyze._utils:converting sample of index: 35
+    DEBUG:pyggdrasil.analyze._utils:converting sample of index: 36
+    DEBUG:pyggdrasil.analyze._utils:converting sample of index: 37
+    DEBUG:pyggdrasil.analyze._utils:converting sample of index: 38
+    DEBUG:pyggdrasil.analyze._utils:converting sample of index: 39
+    DEBUG:pyggdrasil.analyze._utils:converting sample of index: 40
+    DEBUG:pyggdrasil.analyze._utils:converting sample of index: 41
+    DEBUG:pyggdrasil.analyze._utils:converting sample of index: 42
+    DEBUG:pyggdrasil.analyze._utils:converting sample of index: 43
+    DEBUG:pyggdrasil.analyze._utils:converting sample of index: 44
+    DEBUG:pyggdrasil.analyze._utils:converting sample of index: 45
+    DEBUG:pyggdrasil.analyze._utils:converting sample of index: 46
+    DEBUG:pyggdrasil.analyze._utils:converting sample of index: 47
+    DEBUG:pyggdrasil.analyze._utils:converting sample of index: 48
+    DEBUG:pyggdrasil.analyze._utils:converting sample of index: 49
+    DEBUG:pyggdrasil.analyze._utils:converting sample of index: 50
+    DEBUG:pyggdrasil.analyze._utils:converting sample of index: 51
+    DEBUG:pyggdrasil.analyze._utils:converting sample of index: 52
+    DEBUG:pyggdrasil.analyze._utils:converting sample of index: 53
+    DEBUG:pyggdrasil.analyze._utils:converting sample of index: 54
+    DEBUG:pyggdrasil.analyze._utils:converting sample of index: 55
+    DEBUG:pyggdrasil.analyze._utils:converting sample of index: 56
+    DEBUG:pyggdrasil.analyze._utils:converting sample of index: 57
+    DEBUG:pyggdrasil.analyze._utils:converting sample of index: 58
+    DEBUG:pyggdrasil.analyze._utils:converting sample of index: 59
+    DEBUG:pyggdrasil.analyze._utils:converting sample of index: 60
+    DEBUG:pyggdrasil.analyze._utils:converting sample of index: 61
+    DEBUG:pyggdrasil.analyze._utils:converting sample of index: 62
+    DEBUG:pyggdrasil.analyze._utils:converting sample of index: 63
+    DEBUG:pyggdrasil.analyze._utils:converting sample of index: 64
+    DEBUG:pyggdrasil.analyze._utils:converting sample of index: 65
+    DEBUG:pyggdrasil.analyze._utils:converting sample of index: 66
+    DEBUG:pyggdrasil.analyze._utils:converting sample of index: 67
+    DEBUG:pyggdrasil.analyze._utils:converting sample of index: 68
+    DEBUG:pyggdrasil.analyze._utils:converting sample of index: 69
+    DEBUG:pyggdrasil.analyze._utils:converting sample of index: 70
+    DEBUG:pyggdrasil.analyze._utils:converting sample of index: 71
+    DEBUG:pyggdrasil.analyze._utils:converting sample of index: 72
+    DEBUG:pyggdrasil.analyze._utils:converting sample of index: 73
+    DEBUG:pyggdrasil.analyze._utils:converting sample of index: 74
+    DEBUG:pyggdrasil.analyze._utils:converting sample of index: 75
+    DEBUG:pyggdrasil.analyze._utils:converting sample of index: 76
+    DEBUG:pyggdrasil.analyze._utils:converting sample of index: 77
+    DEBUG:pyggdrasil.analyze._utils:converting sample of index: 78
+    DEBUG:pyggdrasil.analyze._utils:converting sample of index: 79
+    DEBUG:pyggdrasil.analyze._utils:converting sample of index: 80
+    DEBUG:pyggdrasil.analyze._utils:converting sample of index: 81
+    DEBUG:pyggdrasil.analyze._utils:converting sample of index: 82
+    DEBUG:pyggdrasil.analyze._utils:converting sample of index: 83
+    DEBUG:pyggdrasil.analyze._utils:converting sample of index: 84
+    DEBUG:pyggdrasil.analyze._utils:converting sample of index: 85
+    DEBUG:pyggdrasil.analyze._utils:converting sample of index: 86
+    DEBUG:pyggdrasil.analyze._utils:converting sample of index: 87
+    DEBUG:pyggdrasil.analyze._utils:converting sample of index: 88
+    DEBUG:pyggdrasil.analyze._utils:converting sample of index: 89
+    DEBUG:pyggdrasil.analyze._utils:converting sample of index: 90
+    DEBUG:pyggdrasil.analyze._utils:converting sample of index: 91
+    DEBUG:pyggdrasil.analyze._utils:converting sample of index: 92
+    DEBUG:pyggdrasil.analyze._utils:converting sample of index: 93
+    DEBUG:pyggdrasil.analyze._utils:converting sample of index: 94
+    DEBUG:pyggdrasil.analyze._utils:converting sample of index: 95
+    DEBUG:pyggdrasil.analyze._utils:converting sample of index: 96
+    DEBUG:pyggdrasil.analyze._utils:converting sample of index: 97
+    DEBUG:pyggdrasil.analyze._utils:converting sample of index: 98
+    DEBUG:pyggdrasil.analyze._utils:converting sample of index: 99
+
+Now, we may plot it.
+
+``` python
+plt.plot(mcmc_samples.iterations, mcmc_samples.log_probabilities)
+plt.xlabel("Iteration")
+plt.ylabel("Log-probability")
+plt.grid()
+plt.show()
+```
+
+<img src="singleMCMC_files/figure-commonmark/log-prob-iter-output-1.png"
+id="log-prob-iter"
+alt="The evolution of the log-probability of the trees over the MCMC iterations." />
+
+This log-probability quickly improved for such a small tree - SCITE
+works.
diff --git a/docs/tutorial/singleMCMC.qmd b/docs/tutorial/singleMCMC.qmd
new file mode 100644
index 00000000..cc6be621
--- /dev/null
+++ b/docs/tutorial/singleMCMC.qmd
@@ -0,0 +1,143 @@
+---
+title: "Single MCMC Run"
+format: gfm
+jupyter: python3
+---
+
+This tutorial shows how to run a single MCMC chain of SCITE using PYggdrasil. 
+- We will generate our own ground-truth mutation histroy and generate a noisy single-cell mutation profile from it.
+- We will then run a single MCMC chain to infer the mutation history from the noisy single-cell mutation profile.
+- Visualize the results. The trees and the evolution of the MCMC.
+
+## 0) Imports
+```{python}
+## imports
+import pyggdrasil as yg
+import jax.numpy as jnp
+import jax.random as random
+from pathlib import Path
+import matplotlib.pyplot as plt
+
+# matplotlib inline
+%matplotlib inline 
+```
+
+## 1) Generate a ground-truth mutation history and a noisy single-cell mutation profile
+The below cell generates a random tree with 4 mutations, plus root. For debugging we may use the _print_topo_ to plot its topology.
+```{python}
+# make true tree
+tree_type = yg.tree_inference.TreeType.RANDOM
+mutations = 4
+nodes = mutations + 1
+tree_seed = 42
+true_tree = yg.tree_inference.make_tree(nodes, tree_type, tree_seed) 
+
+true_tree.print_topo()
+```
+
+## 2) Generate an initial tree to start the Markov Chain from
+We also choose a random tree here. 
+
+```{python}
+# make random starting tree
+tree_type = yg.tree_inference.TreeType.RANDOM
+tree_seed = 487
+starting_tree = yg.tree_inference.make_tree(nodes, tree_type, tree_seed)
+starting_tree.print_topo()
+```
+
+## 3) Generate a noisy single-cell mutation profile from the ground-truth tree
+
+```{python}
+## generate some little nois data
+# Set up the simulation model
+csm = yg.tree_inference.CellSimulationModel(
+    n_cells=1000,
+    n_mutations=mutations,
+    fpr=0.01,
+    fnr=0.01,
+    na_rate=0.0,
+    observe_homozygous=False,
+    strategy=yg.tree_inference.CellAttachmentStrategy.UNIFORM_EXCLUDE_ROOT,
+)
+
+
+# Generate Data
+seed = 42
+rng = random.PRNGKey(seed)
+data = yg.tree_inference.gen_sim_data(
+    csm,
+    rng,
+    true_tree
+    )
+
+mut_mat = jnp.array(data['noisy_mutation_mat'])
+print(mut_mat)
+```
+
+## 4) Run the Markov Monte Carlo Chain
+The below cell runs a single MCMC chain. We initialize ti with the initial tree from before.
+We configure the move probabilities and error rates and run the MCMC chain for 100 iterations.
+The sampels are saved to disk and loaded back into memory as chains may be very long.
+
+```{python}
+## Run MCMC
+# converting initial tree from TreeNode to Tree format
+init_tree_t = yg.tree_inference.Tree.tree_from_tree_node(starting_tree)
+
+## file handling
+# set up save location
+save_dir = Path("")
+# make directory if it doesn't exist
+save_dir.mkdir(parents=True, exist_ok=True)
+save_name = "mcmc_test"
+full_save_name = save_dir / f"{save_name}.json"
+# make file / empty it if it exists
+with open(full_save_name, "w") as f:
+    f.write("")
+
+# set the move probabilities and error rates
+move_probs = yg.tree_inference.MoveProbabilities()
+error_rates = yg.tree_inference.ErrorCombinations.IDEAL.value
+
+# run mcmc sampler
+yg.tree_inference.mcmc_sampler(
+    rng_key=rng,
+    data=mut_mat,
+    error_rates=(error_rates.fpr, error_rates.fnr),
+    move_probs=move_probs,
+    num_samples=100,
+    num_burn_in=0,
+    out_fp=full_save_name,
+    thinning=1,
+    init_tree=init_tree_t,
+)
+
+# load the data from disk
+mcmc_data = yg.serialize.read_mcmc_samples(save_dir / f"{save_name}.json")
+```
+
+## 5) Visualize the results
+In the following we would like to plot the evolution of the MCMC chain and the trees that were sampled.
+First we convert the data from the serialized format to a _pureMCMCdata_ format. This is a simple dataclass that contains the trees and the log probabilities of the trees.
+
+```{python}
+# unpack the data - reads in the serialized trees to Tree objects
+# takes some time as tree objects are built and checked for validity
+mcmc_samples = yg.analyze.to_pure_mcmc_data(mcmc_data)
+```
+
+Now, we may plot it.
+
+```{python}
+#| label: log-prob-iter
+#| fig-cap: "The evolution of the log-probability of the trees over the MCMC iterations."
+plt.plot(mcmc_samples.iterations, mcmc_samples.log_probabilities)
+plt.xlabel("Iteration")
+plt.ylabel("Log-probability")
+plt.grid()
+plt.show()
+```
+
+This log-probability quickly improved for such a small tree - SCITE works.
+
diff --git a/docs/tutorial/singleMCMC_files/figure-commonmark/log-prob-iter-output-1.png b/docs/tutorial/singleMCMC_files/figure-commonmark/log-prob-iter-output-1.png
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From 9bd4b5eb2b83f96ea77e3d2994f658a465f079b0 Mon Sep 17 00:00:00 2001
From: gordonkoehn <gordon@koehn.net>
Date: Mon, 16 Oct 2023 11:59:26 +0200
Subject: [PATCH 16/19] remove .json raw data

---
 .gitignore                   |   1 -
 docs/tutorial/mcmc_test.json | 100 -----------------------------------
 docs/tutorial/singleMCMC.md  |   2 +
 docs/tutorial/singleMCMC.qmd |   2 +
 4 files changed, 4 insertions(+), 101 deletions(-)
 delete mode 100644 docs/tutorial/mcmc_test.json

diff --git a/.gitignore b/.gitignore
index 94f6decf..2ff6c3cc 100644
--- a/.gitignore
+++ b/.gitignore
@@ -12,7 +12,6 @@ poetry.lock
 # Notebooks are disallowed by default
 *.nb
 *.ipynb
-/notebooks
 
 # Environmental files
 .idea/
diff --git a/docs/tutorial/mcmc_test.json b/docs/tutorial/mcmc_test.json
deleted file mode 100644
index 8e27da89..00000000
--- a/docs/tutorial/mcmc_test.json
+++ /dev/null
@@ -1,100 +0,0 @@
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-{"coords": {"from_node_k": {"dims": ["from_node_k"], "attrs": {}, "data": [0, 1, 2, 3, 4]}, "to_node_k": {"dims": ["to_node_k"], "attrs": {}, "data": [0, 1, 2, 3, 4]}}, "attrs": {}, "dims": {"from_node_k": 5, "to_node_k": 5}, "data_vars": {"iteration": {"dims": [], "attrs": {}, "data": 100}, "tree": {"dims": ["from_node_k", "to_node_k"], "attrs": {}, "data": [[0.0, 0.0, 0.0, 0.0, 0.0], [0.0, 0.0, 0.0, 0.0, 0.0], [0.0, 1.0, 0.0, 0.0, 0.0], [0.0, 0.0, 0.0, 0.0, 0.0], [1.0, 0.0, 1.0, 1.0, 0.0]]}, "log-probability": {"dims": [], "attrs": {}, "data": -468.29644775390625}}}
diff --git a/docs/tutorial/singleMCMC.md b/docs/tutorial/singleMCMC.md
index 642024cc..fac1ce42 100644
--- a/docs/tutorial/singleMCMC.md
+++ b/docs/tutorial/singleMCMC.md
@@ -137,6 +137,8 @@ yg.tree_inference.mcmc_sampler(
 
 # load the data from disk
 mcmc_data = yg.serialize.read_mcmc_samples(save_dir / f"{save_name}.json")
+#delete file
+(full_save_name).unlink()
 ```
 
     INFO:pyggdrasil.tree_inference._mcmc:Move Accepted
diff --git a/docs/tutorial/singleMCMC.qmd b/docs/tutorial/singleMCMC.qmd
index cc6be621..b51803a4 100644
--- a/docs/tutorial/singleMCMC.qmd
+++ b/docs/tutorial/singleMCMC.qmd
@@ -115,6 +115,8 @@ yg.tree_inference.mcmc_sampler(
 
 # load the data from disk
 mcmc_data = yg.serialize.read_mcmc_samples(save_dir / f"{save_name}.json")
+#delete file
+(full_save_name).unlink()
 ```
 
 ## 5) Visualize the results

From 203e7ef139517469a5aca86af3c62972dc87438f Mon Sep 17 00:00:00 2001
From: gordonkoehn <gordon@koehn.net>
Date: Mon, 16 Oct 2023 12:03:46 +0200
Subject: [PATCH 17/19] remove whitespace

---
 docs/api/analyze.md        |  5 -----
 docs/api/distances.md      |  8 --------
 docs/api/index.md          |  1 -
 docs/api/tree_inference.md | 24 ------------------------
 4 files changed, 38 deletions(-)

diff --git a/docs/api/analyze.md b/docs/api/analyze.md
index 57d53c55..20e5c492 100644
--- a/docs/api/analyze.md
+++ b/docs/api/analyze.md
@@ -1,13 +1,8 @@
 # Analyze
 
 ::: pyggdrasil.analyze.rhats
-
 ::: pyggdrasil.analyze.ess
-
 ::: pyggdrasil.analyze.Metrics
-
 ::: pyggdrasil.analyze.to_pure_mcmc_data
-
 ::: pyggdrasil.analyze.check_run_for_tree
-
 ::: pyggdrasil.analyze.analyze_mcmc_run
\ No newline at end of file
diff --git a/docs/api/distances.md b/docs/api/distances.md
index 8e9f117e..4116acbf 100644
--- a/docs/api/distances.md
+++ b/docs/api/distances.md
@@ -1,21 +1,13 @@
 # Distances
 
 ::: pyggdrasil.distances.TreeDistance
-
 ::: pyggdrasil.distances.TreeSimilarity
-
 ::: pyggdrasil.distances.TreeSimilarityMeasure
-
 ::: pyggdrasil.distances.calculate_distance_matrix
-
 ::: pyggdrasil.distances.AncestorDescendantSimilarity
-
 ::: pyggdrasil.distances.MP3Similarity
-
 ::: pyggdrasil.distances.AncestorDescendantSimilarityInclRoot
-
 ::: pyggdrasil.distances.DifferentLineageSimilarity
-
 ::: pyggdrasil.distances.MLTDSimilarity
 
 
diff --git a/docs/api/index.md b/docs/api/index.md
index 4633483a..6298e98a 100644
--- a/docs/api/index.md
+++ b/docs/api/index.md
@@ -10,7 +10,6 @@
 This package handels trees with _Anytree_, see our adaption in the class _TreeNode_ below.  For the inference we convert trees to binary adjacency matrices see [Tree Inference](tree_inference.md), for reasons of performance.
 
 ::: pyggdrasil.TreeNode
-
 ::: pyggdrasil.compare_trees
 
 
diff --git a/docs/api/tree_inference.md b/docs/api/tree_inference.md
index 6572722d..61eaf21e 100644
--- a/docs/api/tree_inference.md
+++ b/docs/api/tree_inference.md
@@ -1,52 +1,28 @@
 # Tree Inference
 
 ::: pyggdrasil.tree_inference.CellAttachmentStrategy
-
 ::: pyggdrasil.tree_inference.CellSimulationData
-
 ::: pyggdrasil.tree_inference.CellSimulationId
-
 ::: pyggdrasil.tree_inference.CellSimulationModel
-
 ::: pyggdrasil.tree_inference.ErrorCombinations
-
 ::: pyggdrasil.tree_inference.ErrorRates
-
 ::: pyggdrasil.tree_inference.evolve_tree_mcmc
-
 ::: pyggdrasil.tree_inference.evolve_tree_mcmc_all
-
 ::: pyggdrasil.tree_inference.gen_sim_data
-
 ::: pyggdrasil.tree_inference.get_descendants
-
 ::: pyggdrasil.tree_inference.get_simulation_data
-
 ::: pyggdrasil.tree_inference.huntress_tree_inference
-
 ::: pyggdrasil.tree_inference.make_tree
-
 ::: pyggdrasil.tree_inference.McmcConfig
-
 ::: pyggdrasil.tree_inference.McmcConfigOptions
-
 ::: pyggdrasil.tree_inference.McmcRunId
-
 ::: pyggdrasil.tree_inference.mcmc_sampler
-
 ::: pyggdrasil.tree_inference.MoveProbabilities
-
 ::: pyggdrasil.tree_inference.MoveProbConfig
-
 ::: pyggdrasil.tree_inference.MoveProbConfigOptions
-
 ::: pyggdrasil.tree_inference.MutationDataId
-
 ::: pyggdrasil.tree_inference.MutationMatrix
-
 ::: pyggdrasil.tree_inference.Tree
-
 ::: pyggdrasil.tree_inference.TreeId
-
 ::: pyggdrasil.tree_inference.TreeType
 

From 7f9aa4cef16b6082c2a37e18b2f1094c8ed2f24e Mon Sep 17 00:00:00 2001
From: gordonkoehn <gordon@koehn.net>
Date: Mon, 16 Oct 2023 12:05:56 +0200
Subject: [PATCH 18/19] remove whitespace

---
 docs/api/serialize.md | 7 -------
 1 file changed, 7 deletions(-)

diff --git a/docs/api/serialize.md b/docs/api/serialize.md
index 14b2d7f9..65a99c24 100644
--- a/docs/api/serialize.md
+++ b/docs/api/serialize.md
@@ -1,18 +1,11 @@
 # Serialize
 
 ::: pyggdrasil.serialize.serialize_tree_to_dict
-
 ::: pyggdrasil.serialize.deserialize_tree_from_dict
-
 ::: pyggdrasil.serialize.read_mcmc_samples
-
 ::: pyggdrasil.serialize.save_mcmc_sample
-
 ::: pyggdrasil.serialize.read_tree_node
-
 ::: pyggdrasil.serialize.save_tree_node
-
 ::: pyggdrasil.serialize.save_metric_result
-
 ::: pyggdrasil.serialize.read_metric_result
 

From fdc7ccdbda20d42414b068ab8fd88be177e99410 Mon Sep 17 00:00:00 2001
From: gordonkoehn <gordon@koehn.net>
Date: Mon, 16 Oct 2023 12:15:39 +0200
Subject: [PATCH 19/19] remove long outputs

---
 docs/tutorial/singleMCMC.md  | 204 +----------------------------------
 docs/tutorial/singleMCMC.qmd |   2 +
 2 files changed, 4 insertions(+), 202 deletions(-)

diff --git a/docs/tutorial/singleMCMC.md b/docs/tutorial/singleMCMC.md
index fac1ce42..ee70442a 100644
--- a/docs/tutorial/singleMCMC.md
+++ b/docs/tutorial/singleMCMC.md
@@ -90,6 +90,8 @@ mut_mat = jnp.array(data['noisy_mutation_mat'])
 print(mut_mat)
 ```
 
+    INFO:pyggdrasil.tree_inference._simulate:Generated cell-mutation data.
+
     [[0 0 0 ... 0 0 1]
      [1 0 0 ... 0 0 0]
      [1 1 1 ... 0 0 0]
@@ -141,107 +143,6 @@ mcmc_data = yg.serialize.read_mcmc_samples(save_dir / f"{save_name}.json")
 (full_save_name).unlink()
 ```
 
-    INFO:pyggdrasil.tree_inference._mcmc:Move Accepted
-    INFO:pyggdrasil.tree_inference._mcmc:Move Accepted
-    INFO:pyggdrasil.tree_inference._mcmc:Move Rejected
-    INFO:pyggdrasil.tree_inference._mcmc:Move Rejected
-    INFO:pyggdrasil.tree_inference._mcmc:Move Accepted
-    INFO:pyggdrasil.tree_inference._mcmc:Move Rejected
-    INFO:pyggdrasil.tree_inference._mcmc:Move Rejected
-    INFO:pyggdrasil.tree_inference._mcmc:Move Rejected
-    INFO:pyggdrasil.tree_inference._mcmc:Move Rejected
-    INFO:pyggdrasil.tree_inference._mcmc:Move Rejected
-    INFO:pyggdrasil.tree_inference._mcmc:Move Accepted
-    INFO:pyggdrasil.tree_inference._mcmc:Move Accepted
-    INFO:pyggdrasil.tree_inference._mcmc:Move Accepted
-    INFO:pyggdrasil.tree_inference._mcmc:Move Rejected
-    INFO:pyggdrasil.tree_inference._mcmc:Move Rejected
-    INFO:pyggdrasil.tree_inference._mcmc:Move Rejected
-    INFO:pyggdrasil.tree_inference._mcmc:Move Rejected
-    INFO:pyggdrasil.tree_inference._mcmc:Move Rejected
-    INFO:pyggdrasil.tree_inference._mcmc:Move Rejected
-    INFO:pyggdrasil.tree_inference._mcmc:Move Rejected
-    INFO:pyggdrasil.tree_inference._mcmc:Move Rejected
-    INFO:pyggdrasil.tree_inference._mcmc:Move Rejected
-    INFO:pyggdrasil.tree_inference._mcmc:Move Accepted
-    INFO:pyggdrasil.tree_inference._mcmc:Move Rejected
-    INFO:pyggdrasil.tree_inference._mcmc:Move Rejected
-    INFO:pyggdrasil.tree_inference._mcmc:Move Rejected
-    INFO:pyggdrasil.tree_inference._mcmc:Move Rejected
-    INFO:pyggdrasil.tree_inference._mcmc:Move Rejected
-    INFO:pyggdrasil.tree_inference._mcmc:Move Rejected
-    INFO:pyggdrasil.tree_inference._mcmc:Move Rejected
-    INFO:pyggdrasil.tree_inference._mcmc:Move Rejected
-    INFO:pyggdrasil.tree_inference._mcmc:Move Rejected
-    INFO:pyggdrasil.tree_inference._mcmc:Move Rejected
-    INFO:pyggdrasil.tree_inference._mcmc:Move Rejected
-    INFO:pyggdrasil.tree_inference._mcmc:Move Rejected
-    INFO:pyggdrasil.tree_inference._mcmc:Move Accepted
-    INFO:pyggdrasil.tree_inference._mcmc:Move Rejected
-    INFO:pyggdrasil.tree_inference._mcmc:Move Rejected
-    INFO:pyggdrasil.tree_inference._mcmc:Move Rejected
-    INFO:pyggdrasil.tree_inference._mcmc:Move Accepted
-    INFO:pyggdrasil.tree_inference._mcmc:Move Accepted
-    INFO:pyggdrasil.tree_inference._mcmc:Move Accepted
-    INFO:pyggdrasil.tree_inference._mcmc:Move Rejected
-    INFO:pyggdrasil.tree_inference._mcmc:Move Rejected
-    INFO:pyggdrasil.tree_inference._mcmc:Move Accepted
-    INFO:pyggdrasil.tree_inference._mcmc:Move Accepted
-    INFO:pyggdrasil.tree_inference._mcmc:Move Rejected
-    INFO:pyggdrasil.tree_inference._mcmc:Move Rejected
-    INFO:pyggdrasil.tree_inference._mcmc:Move Rejected
-    INFO:pyggdrasil.tree_inference._mcmc:Move Rejected
-    INFO:pyggdrasil.tree_inference._mcmc:Move Rejected
-    INFO:pyggdrasil.tree_inference._mcmc:Move Rejected
-    INFO:pyggdrasil.tree_inference._mcmc:Move Rejected
-    INFO:pyggdrasil.tree_inference._mcmc:Move Rejected
-    INFO:pyggdrasil.tree_inference._mcmc:Move Rejected
-    INFO:pyggdrasil.tree_inference._mcmc:Move Accepted
-    INFO:pyggdrasil.tree_inference._mcmc:Move Accepted
-    INFO:pyggdrasil.tree_inference._mcmc:Move Rejected
-    INFO:pyggdrasil.tree_inference._mcmc:Move Rejected
-    INFO:pyggdrasil.tree_inference._mcmc:Move Rejected
-    INFO:pyggdrasil.tree_inference._mcmc:Move Rejected
-    INFO:pyggdrasil.tree_inference._mcmc:Move Rejected
-    INFO:pyggdrasil.tree_inference._mcmc:Move Accepted
-    INFO:pyggdrasil.tree_inference._mcmc:Move Accepted
-    INFO:pyggdrasil.tree_inference._mcmc:Move Rejected
-    INFO:pyggdrasil.tree_inference._mcmc:Move Accepted
-    INFO:pyggdrasil.tree_inference._mcmc:Move Rejected
-    INFO:pyggdrasil.tree_inference._mcmc:Move Accepted
-    INFO:pyggdrasil.tree_inference._mcmc:Move Rejected
-    INFO:pyggdrasil.tree_inference._mcmc:Move Rejected
-    INFO:pyggdrasil.tree_inference._mcmc:Move Rejected
-    INFO:pyggdrasil.tree_inference._mcmc:Move Rejected
-    INFO:pyggdrasil.tree_inference._mcmc:Move Rejected
-    INFO:pyggdrasil.tree_inference._mcmc:Move Rejected
-    INFO:pyggdrasil.tree_inference._mcmc:Move Accepted
-    INFO:pyggdrasil.tree_inference._mcmc:Move Rejected
-    INFO:pyggdrasil.tree_inference._mcmc:Move Rejected
-    INFO:pyggdrasil.tree_inference._mcmc:Move Rejected
-    INFO:pyggdrasil.tree_inference._mcmc:Move Accepted
-    INFO:pyggdrasil.tree_inference._mcmc:Move Rejected
-    INFO:pyggdrasil.tree_inference._mcmc:Move Rejected
-    INFO:pyggdrasil.tree_inference._mcmc:Move Accepted
-    INFO:pyggdrasil.tree_inference._mcmc:Move Rejected
-    INFO:pyggdrasil.tree_inference._mcmc:Move Rejected
-    INFO:pyggdrasil.tree_inference._mcmc:Move Rejected
-    INFO:pyggdrasil.tree_inference._mcmc:Move Rejected
-    INFO:pyggdrasil.tree_inference._mcmc:Move Accepted
-    INFO:pyggdrasil.tree_inference._mcmc:Move Accepted
-    INFO:pyggdrasil.tree_inference._mcmc:Move Rejected
-    INFO:pyggdrasil.tree_inference._mcmc:Move Rejected
-    INFO:pyggdrasil.tree_inference._mcmc:Move Rejected
-    INFO:pyggdrasil.tree_inference._mcmc:Move Accepted
-    INFO:pyggdrasil.tree_inference._mcmc:Move Rejected
-    INFO:pyggdrasil.tree_inference._mcmc:Move Rejected
-    INFO:pyggdrasil.tree_inference._mcmc:Move Rejected
-    INFO:pyggdrasil.tree_inference._mcmc:Move Rejected
-    INFO:pyggdrasil.tree_inference._mcmc:Move Rejected
-    INFO:pyggdrasil.tree_inference._mcmc:Move Rejected
-    INFO:pyggdrasil.tree_inference._mcmc:Move Rejected
-    INFO:pyggdrasil.tree_inference._mcmc_sampler:Finished MCMC sampler.
-
 ## 5) Visualize the results
 
 In the following we would like to plot the evolution of the MCMC chain
@@ -255,107 +156,6 @@ that contains the trees and the log probabilities of the trees.
 mcmc_samples = yg.analyze.to_pure_mcmc_data(mcmc_data)
 ```
 
-    DEBUG:pyggdrasil.analyze._utils:converting sample of index: 0
-    DEBUG:pyggdrasil.analyze._utils:converting sample of index: 1
-    DEBUG:pyggdrasil.analyze._utils:converting sample of index: 2
-    DEBUG:pyggdrasil.analyze._utils:converting sample of index: 3
-    DEBUG:pyggdrasil.analyze._utils:converting sample of index: 4
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-    DEBUG:pyggdrasil.analyze._utils:converting sample of index: 11
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-    DEBUG:pyggdrasil.analyze._utils:converting sample of index: 91
-    DEBUG:pyggdrasil.analyze._utils:converting sample of index: 92
-    DEBUG:pyggdrasil.analyze._utils:converting sample of index: 93
-    DEBUG:pyggdrasil.analyze._utils:converting sample of index: 94
-    DEBUG:pyggdrasil.analyze._utils:converting sample of index: 95
-    DEBUG:pyggdrasil.analyze._utils:converting sample of index: 96
-    DEBUG:pyggdrasil.analyze._utils:converting sample of index: 97
-    DEBUG:pyggdrasil.analyze._utils:converting sample of index: 98
-    DEBUG:pyggdrasil.analyze._utils:converting sample of index: 99
-
 Now, we may plot it.
 
 ``` python
diff --git a/docs/tutorial/singleMCMC.qmd b/docs/tutorial/singleMCMC.qmd
index b51803a4..1f45dd9f 100644
--- a/docs/tutorial/singleMCMC.qmd
+++ b/docs/tutorial/singleMCMC.qmd
@@ -81,6 +81,7 @@ We configure the move probabilities and error rates and run the MCMC chain for 1
 The sampels are saved to disk and loaded back into memory as chains may be very long.
 
 ```{python}
+#| warning: false
 ## Run MCMC
 # converting initial tree from TreeNode to Tree format
 init_tree_t = yg.tree_inference.Tree.tree_from_tree_node(starting_tree)
@@ -124,6 +125,7 @@ In the following we would like to plot the evolution of the MCMC chain and the t
 First we convert the data from the serialized format to a _pureMCMCdata_ format. This is a simple dataclass that contains the trees and the log probabilities of the trees.
 
 ```{python}
+#| warning: false
 # unpack the data - reads in the serialized trees to Tree objects
 # takes some time as tree objects are built and checked for validity
 mcmc_samples = yg.analyze.to_pure_mcmc_data(mcmc_data)