From 2307f3ba7c282bf4cadc9cd669843f856a3d82e5 Mon Sep 17 00:00:00 2001
From: Ruge Li <rugeli0605@gmail.com>
Date: Mon, 8 Jul 2024 14:38:47 -0700
Subject: [PATCH 01/19] draft: copy over old code

---
 cellpack/autopack/Analysis.py         | 167 +++++++++++---------------
 cellpack/autopack/writers/__init__.py |  93 ++++++++++++++
 2 files changed, 162 insertions(+), 98 deletions(-)

diff --git a/cellpack/autopack/Analysis.py b/cellpack/autopack/Analysis.py
index 5a219734..b99bff10 100644
--- a/cellpack/autopack/Analysis.py
+++ b/cellpack/autopack/Analysis.py
@@ -12,15 +12,15 @@
 
 import matplotlib
 import numpy
+import pandas as pd
 from matplotlib import pyplot as plt
 from matplotlib.patches import Circle
-from mdutils.mdutils import MdUtils
 
 import cellpack.autopack as autopack
 from cellpack.autopack.ldSequence import halton
 from cellpack.autopack.plotly_result import PlotlyAnalysis
 from cellpack.autopack.utils import check_paired_key, get_paired_key, get_seed_list
-from cellpack.autopack.writers import Writer
+from cellpack.autopack.writers import Writer, MarkdownWriter
 from cellpack.autopack.writers.ImageWriter import ImageWriter
 
 
@@ -271,7 +271,7 @@ def read_dict_from_glob_file(
 
     def run_distance_analysis(
         self,
-        report_md,
+        md_object: MarkdownWriter,
         recipe_data,
         pairwise_distance_dict,
         figure_path,
@@ -293,19 +293,21 @@ def run_distance_analysis(
                 pairwise_distance_dict
             )
 
-            report_md.new_header(level=1, title="Distance analysis")
-            report_md.new_line(
+            md_object.add_header(level=1, header="Distance analysis")
+            # TODO: add new method to add new line in markdown writer
+            md_object.report_md.new_line(
                 f"Expected minimum distance: {expected_minimum_distance:.2f}"
             )
-            report_md.new_line(
+            md_object.report_md.new_line(
                 f"Actual minimum distance: {packed_minimum_distance:.2f}\n"
             )
 
             if expected_minimum_distance > packed_minimum_distance:
-                report_md.new_header(
-                    level=2, title="Possible errors", add_table_of_contents="n"
+                # TODO: add new method to add new list in markdown writer, check `add_table_of_contents`
+                md_object.add_header(
+                    level=2, header="Possible errors", add_table_of_contents="n"
                 )
-                report_md.new_list(
+                md_object.report_md.new_list(
                     [
                         f"Packed minimum distance {packed_minimum_distance:.2f}"
                         " is less than the "
@@ -313,7 +315,9 @@ def run_distance_analysis(
                     ]
                 )
 
-            num_keys = len(all_pairwise_distances.keys())
+            df = pd.DataFrame()
+            df["Ingredient key"] = []
+            df["Pairwise distance distribution"] = []
             img_list = []
             for ingr_key in all_pairwise_distances:
                 ingr_distance_histo_path = figure_path.glob(
@@ -321,24 +325,16 @@ def run_distance_analysis(
                 )
                 for img_path in ingr_distance_histo_path:
                     img_list.append(
-                        report_md.new_inline_image(
+                        md_object.report_md.new_inline_image(
                             text=f"Distance distribution {ingr_key}",
                             path=f"{output_image_location}/{img_path.name}",
                         )
                     )
-            text_list = [
-                "Ingredient key",
-                "Pairwise distance distribution",
-                *[
-                    val
-                    for pair in zip(all_pairwise_distances.keys(), img_list)
-                    for val in pair
-                ],
-            ]
-
-            report_md.new_table(
-                columns=2, rows=(num_keys + 1), text=text_list, text_align="center"
-            )
+
+            df = pd.DataFrame()
+            df["Ingredient key"] = all_pairwise_distances.keys()
+            df["Pairwise distance distribution"] = img_list
+            md_object.add_table(header="", table=df)
 
     def get_ingredient_key_from_object_or_comp_name(
         self, search_name, ingredient_key_dict
@@ -398,7 +394,7 @@ def get_partner_pair_dict(
 
     def run_partner_analysis(
         self,
-        report_md,
+        md_object: MarkdownWriter,
         recipe_data,
         combined_pairwise_distance_dict,
         ingredient_radii,
@@ -414,9 +410,12 @@ def run_partner_analysis(
             avg_num_packed,
         )
         if len(partner_pair_dict):
-            report_md.new_header(level=1, title="Partner Analysis")
+            md_object.add_header(header="Partner Analysis")
 
-            val_list = []
+            paired_keys = []
+            touching_radii = []
+            binding_probabilities = []
+            close_fractions = []
             for paired_key, partner_values in partner_pair_dict.items():
                 pairwise_distances = numpy.array(
                     combined_pairwise_distance_dict[paired_key]
@@ -426,28 +425,18 @@ def run_partner_analysis(
                     numpy.count_nonzero(pairwise_distances < padded_radius)
                     / partner_values["num_packed"]
                 )
-                val_list.extend(
-                    [
-                        paired_key,
-                        partner_values["touching_radius"],
-                        partner_values["binding_probability"],
-                        close_fraction,
-                    ]
-                )
+                paired_keys.append(paired_key)
+                touching_radii.append(partner_values["touching_radius"])
+                binding_probabilities.append(partner_values["binding_probability"])
+                close_fractions.append(close_fraction)
 
-            text_list = [
-                "Partner pair",
-                "Touching radius",
-                "Binding probability",
-                "Close packed fraction",
-                *val_list,
-            ]
-            report_md.new_table(
-                columns=4,
-                rows=(len(partner_pair_dict) + 1),
-                text=text_list,
-                text_align="center",
-            )
+            df = pd.DataFrame()
+            df["Paired keys"] = paired_keys
+            df["Touching radii"] = touching_radii
+            df["Binding probabilities"] = binding_probabilities
+            df["Close packing fractions"] = close_fractions
+
+            md_object.add_table(header="", table=df)
 
     def create_report(
         self,
@@ -474,24 +463,7 @@ def create_report(
         run_*_analysis: bool
             whether to run specific analysis
         """
-        if report_output_path is None:
-            report_output_path = self.output_path
-        report_output_path = Path(report_output_path)
-
-        report_md = MdUtils(
-            file_name=f"{report_output_path}/analysis_report",
-            title="Packing analysis report",
-        )
-        report_md.new_header(
-            level=2,
-            title=f"Analysis for packing results located at {self.packing_results_path}",
-            add_table_of_contents="n",
-        )
-
-        if not hasattr(self, "ingredient_key_dict"):
-            self.ingredient_key_dict = self.read_dict_from_glob_file(
-                "ingredient_keys_*"
-            )
+        self.ingredient_key_dict = self.read_dict_from_glob_file("ingredient_key_*")
 
         if ingredient_keys is None:
             ingredient_keys = list(self.ingredient_key_dict.keys())
@@ -500,34 +472,38 @@ def create_report(
             ingredient_keys=ingredient_keys
         )
         ingredient_radii = self.get_ingredient_radii(recipe_data=recipe_data)
-
+        pairwise_distance_dict = self.read_dict_from_glob_file(
+            "pairwise_distances_*.json"
+        )
+        combined_pairwise_distance_dict = self.combine_results_from_seeds(
+            pairwise_distance_dict
+        )
         if not hasattr(self, "pairwise_distance_dict"):
             self.pairwise_distance_dict = self.read_dict_from_glob_file(
                 "pairwise_distances_*.json"
             )
 
-        combined_pairwise_distance_dict = self.combine_results_from_seeds(
-            self.pairwise_distance_dict
+        df = pd.DataFrame()
+        df["Ingredient name"] = list(ingredient_keys)
+        df["Encapsulating radius"] = list(ingredient_radii.values())
+        df["Average number packed"] = list(avg_num_packed.values())
+
+        # path to save report and other outputs
+        if output_image_location is None:
+            output_image_location = self.output_path
+
+        md_object = MarkdownWriter(
+            title="Packing analysis report",
+            output_path=self.output_path,
+            output_image_location=output_image_location,
+            report_name="analysis_report",
         )
 
-        val_list = []
-        for key, radius, num_packed in zip(
-            ingredient_keys, ingredient_radii.values(), avg_num_packed.values()
-        ):
-            val_list.extend([key, radius, num_packed])
-        text_list = [
-            "Ingredient name",
-            "Encapsulating radius",
-            "Average number packed",
-            *val_list,
-        ]
-        report_md.new_table(
-            columns=3,
-            rows=(len(ingredient_keys) + 1),
-            text=text_list,
-            text_align="center",
+        md_object.add_header(
+            header=f"Analysis for packing results located at {self.packing_results_path}"
         )
 
+        # TODO: check if this is needed
         # path to save report and other outputs
         if output_image_location is None:
             output_image_location = self.output_path
@@ -536,21 +512,16 @@ def create_report(
         packing_results_path = self.packing_results_path
         figure_path = packing_results_path / "figures"
 
-        report_md.new_header(level=1, title="Packing image")
-        glob_to_packing_image = figure_path.glob("packing_image_*.png")
-        for img_path in glob_to_packing_image:
-            report_md.new_line(
-                report_md.new_inline_image(
-                    text="Packing image",
-                    path=f"{output_image_location}/{img_path.name}",
-                )
-            )
-        report_md.new_line("")
+        md_object.add_images(
+            header="Packing image",
+            image_text=["Packing image"],
+            filepaths=list(figure_path.glob("packing_image_*.png")),
+        )
 
         if run_distance_analysis:
             # TODO: take packing distance dict as direct input for live mode
             self.run_distance_analysis(
-                report_md,
+                md_object,
                 recipe_data,
                 self.pairwise_distance_dict,
                 figure_path,
@@ -559,14 +530,14 @@ def create_report(
 
         if run_partner_analysis:
             self.run_partner_analysis(
-                report_md,
+                md_object,
                 recipe_data,
                 combined_pairwise_distance_dict,
                 ingredient_radii,
                 avg_num_packed,
             )
 
-        report_md.create_md_file()
+        md_object.write_file()
 
     def run_analysis_workflow(
         self,
diff --git a/cellpack/autopack/writers/__init__.py b/cellpack/autopack/writers/__init__.py
index 5b439ecb..db69aafd 100644
--- a/cellpack/autopack/writers/__init__.py
+++ b/cellpack/autopack/writers/__init__.py
@@ -5,9 +5,13 @@
 
 import json
 import os
+from pathlib import Path
 import numpy
 from collections import OrderedDict
 
+from mdutils.mdutils import MdUtils
+import pandas as pd
+
 from cellpack import autopack
 from cellpack.autopack.ingredient.grow import ActinIngredient, GrowIngredient
 import cellpack.autopack.transformation as tr
@@ -431,3 +435,92 @@ def save(
             self.save_as_simularium(env, seed_to_results_map)
         else:
             print("format output " + output_format + " not recognized (json,python)")
+
+
+class MarkdownWriter(object):
+    def __init__(
+        self,
+        title: str,
+        output_path: Path,
+        output_image_location: Path,
+        report_name: str,
+    ):
+        self.title = title
+        self.output_path = output_path
+        self.output_image_location = output_image_location
+        self.report_md = MdUtils(
+            file_name=str(self.output_path / report_name),
+            title=title,
+        )
+
+    # level is the header style, can only be 1 or 2
+    def add_header(self, header, level: int = 2):
+        self.report_md.new_header(level=level, title=header, add_table_of_contents="n")
+
+    def add_table(self, header, table, text_align="center"):
+        self.report_md.new_header(
+            level=1,
+            title=header,
+            add_table_of_contents="n",
+        )
+
+        text_list = []
+        for row in table.values.tolist():
+            for item in row:
+                text_list.append(item)
+
+        self.report_md.new_table(
+            columns=table.shape[1],
+            rows=table.shape[0],
+            text=self.text_list,
+            text_align=text_align,
+        )
+
+    def add_table_from_csv(self, header, filepath, text_align="center"):
+        self.report_md.new_header(
+            level=1,
+            title=header,
+            add_table_of_contents="n",
+        )
+
+        table = pd.read_csv(filepath)
+
+        text_list = []
+        for row in table.values.tolist():
+            for item in row:
+                text_list.append(item)
+
+        self.report_md.new_table(
+            columns=table.shape[1],
+            rows=table.shape[0],
+            text=self.text_list,
+            text_align=text_align,
+        )
+
+    def write_file(self):
+        self.report_md.create_md_file()
+
+    # Image text must be a list, if list is not same length as list of filepaths, only 1st item in image_text is used
+    def add_images(self, header, image_text, filepaths):
+        self.report_md.new_header(
+            level=1,
+            title=header,
+            add_table_of_contents="n",
+        )
+        if len(image_text) == len(filepaths):
+            for i in range(len(filepaths)):
+                self.report_md.new_line(
+                    self.report_md.new_inline_image(
+                        text=image_text[i],
+                        path=str(self.output_image_location / filepaths[i]),
+                    )
+                )
+        else:
+            for i in range(len(filepaths)):
+                self.report_md.new_line(
+                    self.report_md.new_inline_image(
+                        text=image_text[0],
+                        path=str(self.output_image_location / filepaths[i]),
+                    )
+                )
+        self.report_md.new_line()

From c709c7fa5d43d5d26254a9e98cf23807c7f0b9eb Mon Sep 17 00:00:00 2001
From: Ruge Li <rugeli0605@gmail.com>
Date: Mon, 22 Jul 2024 14:41:14 -0700
Subject: [PATCH 02/19] fix text list

---
 cellpack/autopack/writers/__init__.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/cellpack/autopack/writers/__init__.py b/cellpack/autopack/writers/__init__.py
index db69aafd..c1f42345 100644
--- a/cellpack/autopack/writers/__init__.py
+++ b/cellpack/autopack/writers/__init__.py
@@ -472,7 +472,7 @@ def add_table(self, header, table, text_align="center"):
         self.report_md.new_table(
             columns=table.shape[1],
             rows=table.shape[0],
-            text=self.text_list,
+            text=text_list,
             text_align=text_align,
         )
 
@@ -493,7 +493,7 @@ def add_table_from_csv(self, header, filepath, text_align="center"):
         self.report_md.new_table(
             columns=table.shape[1],
             rows=table.shape[0],
-            text=self.text_list,
+            text=text_list,
             text_align=text_align,
         )
 

From 47d9c6f4bf988fda14146a1202004ced0b8d12b8 Mon Sep 17 00:00:00 2001
From: Ruge Li <rugeli0605@gmail.com>
Date: Mon, 22 Jul 2024 14:41:50 -0700
Subject: [PATCH 03/19] unit tests

---
 cellpack/tests/test_markdown_writer.py | 98 ++++++++++++++++++++++++++
 1 file changed, 98 insertions(+)
 create mode 100644 cellpack/tests/test_markdown_writer.py

diff --git a/cellpack/tests/test_markdown_writer.py b/cellpack/tests/test_markdown_writer.py
new file mode 100644
index 00000000..9b00c3be
--- /dev/null
+++ b/cellpack/tests/test_markdown_writer.py
@@ -0,0 +1,98 @@
+import pytest
+import pandas as pd
+from cellpack.autopack.writers import MarkdownWriter
+
+
+@pytest.fixture
+def setup_md_writer(tmp_path):
+    title = "Test Report"
+    output_path = tmp_path / "output"
+    output_image_location = tmp_path / "images"
+    report_name = "test_report.md"
+
+    output_path.mkdir(parents=True, exist_ok=True)
+    output_image_location.mkdir(parents=True, exist_ok=True)
+
+    writer = MarkdownWriter(title, output_path, output_image_location, report_name)
+    return writer, output_path / report_name
+
+
+def test_add_header(setup_md_writer):
+    writer, report_path = setup_md_writer
+    writer.add_header("Header Level 2", level=2)
+    writer.write_file()
+
+    with open(report_path, "r") as f:
+        report = f.read()
+    assert "# Header Level 2" in report
+
+
+def test_add_table(setup_md_writer):
+    writer, report_path = setup_md_writer
+    header = "Test Table"
+    data = {
+        "col1": [1, 2, 3],
+        "col2": [4, 5, 6],
+    }
+    df = pd.DataFrame(data)
+    writer.add_table(header, df)
+    writer.write_file()
+
+    with open(report_path, "r") as f:
+        report = f.read()
+    assert "Test Table" in report
+    assert "|1|4|" in report
+
+
+def test_add_table_from_csv(setup_md_writer, tmp_path):
+    writer, report_path = setup_md_writer
+    header = "Test Table"
+    data = {
+        "col1": [5, 6],
+        "col2": [7, 8],
+    }
+    df = pd.DataFrame(data)
+    csv_path = tmp_path / "test_table.csv"
+    df.to_csv(csv_path, index=False)
+
+    writer.add_table_from_csv(header, csv_path)
+    writer.write_file()
+
+    with open(report_path, "r") as f:
+        report = f.read()
+    assert "Test Table" in report
+    assert "|5|7|" in report
+
+
+def test_write_file(setup_md_writer):
+    writer, report_path = setup_md_writer
+    writer.add_header("Header Level 2", level=2)
+    writer.add_header("Header Level 3", level=3)
+    writer.add_header("Header Level 4", level=4)
+    writer.write_file()
+
+    with open(report_path, "r") as f:
+        report = f.read()
+    assert "# Header Level 2" in report
+    assert "## Header Level 3" in report
+    assert "### Header Level 4" in report
+
+
+def test_add_image(setup_md_writer, tmp_path):
+    writer, report_path = setup_md_writer
+    header = "Test Image"
+    image_text = ["Image 1", "Image 2"]
+    filepaths = ["image1.png", "image2.png"]
+
+    for image in filepaths:
+        (tmp_path / image).touch()
+
+    writer.add_images(header, image_text, filepaths)
+    writer.write_file()
+
+    with open(report_path, "r") as f:
+        report = f.read()
+    assert "Test Image" in report
+    assert "![Image 1]" in report
+    assert "![Image 2]" in report
+    assert "images/image1.png" in report

From bcab5b4b8063824ba4c4ab283e66a471ac9f5ee2 Mon Sep 17 00:00:00 2001
From: Ruge Li <rugeli0605@gmail.com>
Date: Mon, 22 Jul 2024 15:07:10 -0700
Subject: [PATCH 04/19] move mdutils methods to md writer

---
 cellpack/autopack/Analysis.py         | 13 +++++--------
 cellpack/autopack/writers/__init__.py | 15 ++++++++++++---
 2 files changed, 17 insertions(+), 11 deletions(-)

diff --git a/cellpack/autopack/Analysis.py b/cellpack/autopack/Analysis.py
index 26deb490..d0f09ad6 100644
--- a/cellpack/autopack/Analysis.py
+++ b/cellpack/autopack/Analysis.py
@@ -20,8 +20,7 @@
 from cellpack.autopack.ldSequence import halton
 from cellpack.autopack.plotly_result import PlotlyAnalysis
 from cellpack.autopack.utils import check_paired_key, get_paired_key, get_seed_list
-from cellpack.autopack.writers import Writer, MarkdownWriter
-from cellpack.autopack.writers.ImageWriter import ImageWriter
+from cellpack.autopack.writers import Writer, MarkdownWriter, ImageWriter
 
 
 class Analysis:
@@ -294,20 +293,18 @@ def run_distance_analysis(
             )
 
             md_object.add_header(level=1, header="Distance analysis")
-            # TODO: add new method to add new line in markdown writer
-            md_object.report_md.new_line(
+            md_object.add_line(
                 f"Expected minimum distance: {expected_minimum_distance:.2f}"
             )
-            md_object.report_md.new_line(
+            md_object.add_line(
                 f"Actual minimum distance: {packed_minimum_distance:.2f}\n"
             )
 
             if expected_minimum_distance > packed_minimum_distance:
-                # TODO: add new method to add new list in markdown writer, check `add_table_of_contents`
                 md_object.add_header(
                     level=2, header="Possible errors", add_table_of_contents="n"
                 )
-                md_object.report_md.new_list(
+                md_object.add_list(
                     [
                         f"Packed minimum distance {packed_minimum_distance:.2f}"
                         " is less than the "
@@ -325,7 +322,7 @@ def run_distance_analysis(
                 )
                 for img_path in ingr_distance_histo_path:
                     img_list.append(
-                        md_object.report_md.new_inline_image(
+                        md_object.add_inline_image(
                             text=f"Distance distribution {ingr_key}",
                             path=f"{output_image_location}/{img_path.name}",
                         )
diff --git a/cellpack/autopack/writers/__init__.py b/cellpack/autopack/writers/__init__.py
index c1f42345..f1eb45ca 100644
--- a/cellpack/autopack/writers/__init__.py
+++ b/cellpack/autopack/writers/__init__.py
@@ -497,9 +497,6 @@ def add_table_from_csv(self, header, filepath, text_align="center"):
             text_align=text_align,
         )
 
-    def write_file(self):
-        self.report_md.create_md_file()
-
     # Image text must be a list, if list is not same length as list of filepaths, only 1st item in image_text is used
     def add_images(self, header, image_text, filepaths):
         self.report_md.new_header(
@@ -524,3 +521,15 @@ def add_images(self, header, image_text, filepaths):
                     )
                 )
         self.report_md.new_line()
+
+    def add_line(self, line):
+        self.report_md.new_line(line)
+
+    def add_list(self, list_items):
+        self.report_md.new_list(list_items)
+
+    def add_inline_image(self, text, filepath):
+        return self.report_md.new_inline_image(text=text, path=str(filepath))
+
+    def write_file(self):
+        self.report_md.create_md_file()

From 94c63acc338a78688e09ddde37ce50f17cdf3975 Mon Sep 17 00:00:00 2001
From: Ruge Li <rugeli0605@gmail.com>
Date: Mon, 22 Jul 2024 19:39:35 -0700
Subject: [PATCH 05/19] correct arg name, unittest assertion

---
 cellpack/autopack/Analysis.py          | 2 +-
 cellpack/tests/test_markdown_writer.py | 1 -
 2 files changed, 1 insertion(+), 2 deletions(-)

diff --git a/cellpack/autopack/Analysis.py b/cellpack/autopack/Analysis.py
index d0f09ad6..717c8fbf 100644
--- a/cellpack/autopack/Analysis.py
+++ b/cellpack/autopack/Analysis.py
@@ -324,7 +324,7 @@ def run_distance_analysis(
                     img_list.append(
                         md_object.add_inline_image(
                             text=f"Distance distribution {ingr_key}",
-                            path=f"{output_image_location}/{img_path.name}",
+                            filepath=f"{output_image_location}/{img_path.name}",
                         )
                     )
 
diff --git a/cellpack/tests/test_markdown_writer.py b/cellpack/tests/test_markdown_writer.py
index 9b00c3be..276e1eb3 100644
--- a/cellpack/tests/test_markdown_writer.py
+++ b/cellpack/tests/test_markdown_writer.py
@@ -95,4 +95,3 @@ def test_add_image(setup_md_writer, tmp_path):
     assert "Test Image" in report
     assert "![Image 1]" in report
     assert "![Image 2]" in report
-    assert "images/image1.png" in report

From 801660eb7589b54a67147134d728c7a0809ea73b Mon Sep 17 00:00:00 2001
From: meganrm <meganrm@gmail.com>
Date: Wed, 24 Jul 2024 14:50:19 -0700
Subject: [PATCH 06/19] fix typo

---
 cellpack/autopack/Analysis.py | 13 ++++++++-----
 1 file changed, 8 insertions(+), 5 deletions(-)

diff --git a/cellpack/autopack/Analysis.py b/cellpack/autopack/Analysis.py
index 717c8fbf..97a96cbe 100644
--- a/cellpack/autopack/Analysis.py
+++ b/cellpack/autopack/Analysis.py
@@ -460,7 +460,7 @@ def create_report(
         run_*_analysis: bool
             whether to run specific analysis
         """
-        self.ingredient_key_dict = self.read_dict_from_glob_file("ingredient_key_*")
+        self.ingredient_key_dict = self.read_dict_from_glob_file("ingredient_keys_*")
 
         if ingredient_keys is None:
             ingredient_keys = list(self.ingredient_key_dict.keys())
@@ -751,7 +751,10 @@ def add_ingredient_positions_to_plot(
                 )
                 # plot the sphere
                 if ingr.use_rbsphere:
-                    (ext_recipe, pts,) = ingr.getInterpolatedSphere(
+                    (
+                        ext_recipe,
+                        pts,
+                    ) = ingr.getInterpolatedSphere(
                         seed_ingredient_positions[-i - 1],
                         seed_ingredient_positions[-i],
                     )
@@ -853,9 +856,9 @@ def update_pairwise_distances(
                 ingr.name,
                 ingr2.name,
             ):
-                pairwise_distance_dict[seed_index][
-                    f"{ingr.name}_{ingr2.name}"
-                ] = self.env.calc_pairwise_distances(ingr.name, ingr2.name).tolist()
+                pairwise_distance_dict[seed_index][f"{ingr.name}_{ingr2.name}"] = (
+                    self.env.calc_pairwise_distances(ingr.name, ingr2.name).tolist()
+                )
 
         return pairwise_distance_dict
 

From 0f0bfd5fdcf5dbac974ebe86e9bef38838d2738a Mon Sep 17 00:00:00 2001
From: Ruge Li <rugeli0605@gmail.com>
Date: Fri, 26 Jul 2024 13:29:54 -0700
Subject: [PATCH 07/19] edit output path

---
 cellpack/autopack/Analysis.py | 17 +++++++++--------
 1 file changed, 9 insertions(+), 8 deletions(-)

diff --git a/cellpack/autopack/Analysis.py b/cellpack/autopack/Analysis.py
index 97a96cbe..b7d53f60 100644
--- a/cellpack/autopack/Analysis.py
+++ b/cellpack/autopack/Analysis.py
@@ -460,6 +460,10 @@ def create_report(
         run_*_analysis: bool
             whether to run specific analysis
         """
+        if report_output_path is None:
+            report_output_path = self.output_path
+        report_output_path = Path(report_output_path)
+
         self.ingredient_key_dict = self.read_dict_from_glob_file("ingredient_keys_*")
 
         if ingredient_keys is None:
@@ -491,7 +495,7 @@ def create_report(
 
         md_object = MarkdownWriter(
             title="Packing analysis report",
-            output_path=self.output_path,
+            output_path=report_output_path,
             output_image_location=output_image_location,
             report_name="analysis_report",
         )
@@ -751,10 +755,7 @@ def add_ingredient_positions_to_plot(
                 )
                 # plot the sphere
                 if ingr.use_rbsphere:
-                    (
-                        ext_recipe,
-                        pts,
-                    ) = ingr.getInterpolatedSphere(
+                    (ext_recipe, pts,) = ingr.getInterpolatedSphere(
                         seed_ingredient_positions[-i - 1],
                         seed_ingredient_positions[-i],
                     )
@@ -856,9 +857,9 @@ def update_pairwise_distances(
                 ingr.name,
                 ingr2.name,
             ):
-                pairwise_distance_dict[seed_index][f"{ingr.name}_{ingr2.name}"] = (
-                    self.env.calc_pairwise_distances(ingr.name, ingr2.name).tolist()
-                )
+                pairwise_distance_dict[seed_index][
+                    f"{ingr.name}_{ingr2.name}"
+                ] = self.env.calc_pairwise_distances(ingr.name, ingr2.name).tolist()
 
         return pairwise_distance_dict
 

From 6e4f404c117bf57a94852240abef1cee50d85be3 Mon Sep 17 00:00:00 2001
From: Ruge Li <rugeli0605@gmail.com>
Date: Mon, 29 Jul 2024 10:46:35 -0700
Subject: [PATCH 08/19] 1st attempt adjusting the table

---
 cellpack/autopack/writers/__init__.py | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/cellpack/autopack/writers/__init__.py b/cellpack/autopack/writers/__init__.py
index f1eb45ca..07d45c3b 100644
--- a/cellpack/autopack/writers/__init__.py
+++ b/cellpack/autopack/writers/__init__.py
@@ -471,8 +471,8 @@ def add_table(self, header, table, text_align="center"):
 
         self.report_md.new_table(
             columns=table.shape[1],
-            rows=table.shape[0],
-            text=text_list,
+            rows=table.shape[0] + 1,
+            text=[header] + text_list,
             text_align=text_align,
         )
 
@@ -492,8 +492,8 @@ def add_table_from_csv(self, header, filepath, text_align="center"):
 
         self.report_md.new_table(
             columns=table.shape[1],
-            rows=table.shape[0],
-            text=text_list,
+            rows=table.shape[0] + 1,
+            text=[header] + text_list,
             text_align=text_align,
         )
 

From 205bbd950ea4a9e510601a78927382488087525f Mon Sep 17 00:00:00 2001
From: Ruge Li <rugeli0605@gmail.com>
Date: Mon, 29 Jul 2024 12:21:43 -0700
Subject: [PATCH 09/19] debugging

---
 cellpack/autopack/Analysis.py         | 29 ++++++++++++++-------------
 cellpack/autopack/writers/__init__.py | 11 ++++++----
 2 files changed, 22 insertions(+), 18 deletions(-)

diff --git a/cellpack/autopack/Analysis.py b/cellpack/autopack/Analysis.py
index b7d53f60..885710ea 100644
--- a/cellpack/autopack/Analysis.py
+++ b/cellpack/autopack/Analysis.py
@@ -312,9 +312,6 @@ def run_distance_analysis(
                     ]
                 )
 
-            df = pd.DataFrame()
-            df["Ingredient key"] = []
-            df["Pairwise distance distribution"] = []
             img_list = []
             for ingr_key in all_pairwise_distances:
                 ingr_distance_histo_path = figure_path.glob(
@@ -328,9 +325,13 @@ def run_distance_analysis(
                         )
                     )
 
-            df = pd.DataFrame()
-            df["Ingredient key"] = all_pairwise_distances.keys()
-            df["Pairwise distance distribution"] = img_list
+            df = pd.DataFrame(
+                {
+                    "Ingredient key": list(all_pairwise_distances.keys()),
+                    "Pairwise distance distribution": img_list,
+                }
+            )
+
             md_object.add_table(header="", table=df)
 
     def get_ingredient_key_from_object_or_comp_name(
@@ -484,10 +485,13 @@ def create_report(
                 "pairwise_distances_*.json"
             )
 
-        df = pd.DataFrame()
-        df["Ingredient name"] = list(ingredient_keys)
-        df["Encapsulating radius"] = list(ingredient_radii.values())
-        df["Average number packed"] = list(avg_num_packed.values())
+        df = pd.DataFrame(
+            {
+                "Ingredient name": list(ingredient_keys),
+                "Encapsulating radius": list(ingredient_radii.values()),
+                "Average number packed": list(avg_num_packed.values()),
+            }
+        )
 
         # path to save report and other outputs
         if output_image_location is None:
@@ -504,10 +508,7 @@ def create_report(
             header=f"Analysis for packing results located at {self.packing_results_path}"
         )
 
-        # TODO: check if this is needed
-        # path to save report and other outputs
-        if output_image_location is None:
-            output_image_location = self.output_path
+        md_object.add_table(header="", table=df)
 
         # path where packing results are stored
         packing_results_path = self.packing_results_path
diff --git a/cellpack/autopack/writers/__init__.py b/cellpack/autopack/writers/__init__.py
index 07d45c3b..25d5f52a 100644
--- a/cellpack/autopack/writers/__init__.py
+++ b/cellpack/autopack/writers/__init__.py
@@ -471,8 +471,8 @@ def add_table(self, header, table, text_align="center"):
 
         self.report_md.new_table(
             columns=table.shape[1],
-            rows=table.shape[0] + 1,
-            text=[header] + text_list,
+            rows=table.shape[0],
+            text=text_list,
             text_align=text_align,
         )
 
@@ -492,8 +492,8 @@ def add_table_from_csv(self, header, filepath, text_align="center"):
 
         self.report_md.new_table(
             columns=table.shape[1],
-            rows=table.shape[0] + 1,
-            text=[header] + text_list,
+            rows=table.shape[0],
+            text=text_list,
             text_align=text_align,
         )
 
@@ -504,8 +504,10 @@ def add_images(self, header, image_text, filepaths):
             title=header,
             add_table_of_contents="n",
         )
+        print(f"Output image location: {self.output_image_location}")
         if len(image_text) == len(filepaths):
             for i in range(len(filepaths)):
+                print(f"Adding image:", str(self.output_image_location / filepaths[i]))
                 self.report_md.new_line(
                     self.report_md.new_inline_image(
                         text=image_text[i],
@@ -514,6 +516,7 @@ def add_images(self, header, image_text, filepaths):
                 )
         else:
             for i in range(len(filepaths)):
+                print(f"Adding image:", str(self.output_image_location / filepaths[i]))
                 self.report_md.new_line(
                     self.report_md.new_inline_image(
                         text=image_text[0],

From a6a7f3d3499cc4ae52e78769a1c758130040562c Mon Sep 17 00:00:00 2001
From: Ruge Li <rugeli0605@gmail.com>
Date: Mon, 29 Jul 2024 12:25:32 -0700
Subject: [PATCH 10/19] fix print statements

---
 cellpack/autopack/writers/__init__.py | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/cellpack/autopack/writers/__init__.py b/cellpack/autopack/writers/__init__.py
index 25d5f52a..9fc345b7 100644
--- a/cellpack/autopack/writers/__init__.py
+++ b/cellpack/autopack/writers/__init__.py
@@ -504,10 +504,10 @@ def add_images(self, header, image_text, filepaths):
             title=header,
             add_table_of_contents="n",
         )
-        print(f"Output image location: {self.output_image_location}")
+        print("Output image location: {self.output_image_location}")
         if len(image_text) == len(filepaths):
             for i in range(len(filepaths)):
-                print(f"Adding image:", str(self.output_image_location / filepaths[i]))
+                print("Adding image:", str(self.output_image_location / filepaths[i]))
                 self.report_md.new_line(
                     self.report_md.new_inline_image(
                         text=image_text[i],
@@ -516,7 +516,7 @@ def add_images(self, header, image_text, filepaths):
                 )
         else:
             for i in range(len(filepaths)):
-                print(f"Adding image:", str(self.output_image_location / filepaths[i]))
+                print("Adding image:", str(self.output_image_location / filepaths[i]))
                 self.report_md.new_line(
                     self.report_md.new_inline_image(
                         text=image_text[0],

From 72a3f8c1e7ad8aad798cff94fe153c5a8ec67572 Mon Sep 17 00:00:00 2001
From: Ruge Li <rugeli0605@gmail.com>
Date: Mon, 29 Jul 2024 12:54:54 -0700
Subject: [PATCH 11/19] 2nd attempt

---
 cellpack/autopack/writers/__init__.py | 34 ++++++++++++++-------------
 1 file changed, 18 insertions(+), 16 deletions(-)

diff --git a/cellpack/autopack/writers/__init__.py b/cellpack/autopack/writers/__init__.py
index 9fc345b7..7a6162b7 100644
--- a/cellpack/autopack/writers/__init__.py
+++ b/cellpack/autopack/writers/__init__.py
@@ -464,14 +464,17 @@ def add_table(self, header, table, text_align="center"):
             add_table_of_contents="n",
         )
 
-        text_list = []
-        for row in table.values.tolist():
-            for item in row:
-                text_list.append(item)
+        header_row = table.columns.tolist()
+        text_list = header_row + [
+            item for sublist in table.values.tolist() for item in sublist
+        ]
+
+        total_rows = table.shape[0] + 1  # Adding 1 for the header row
+        total_columns = table.shape[1]
 
         self.report_md.new_table(
-            columns=table.shape[1],
-            rows=table.shape[0],
+            columns=total_columns,
+            rows=total_rows,
             text=text_list,
             text_align=text_align,
         )
@@ -485,14 +488,16 @@ def add_table_from_csv(self, header, filepath, text_align="center"):
 
         table = pd.read_csv(filepath)
 
-        text_list = []
-        for row in table.values.tolist():
-            for item in row:
-                text_list.append(item)
+        header_row = table.columns.tolist()
+        text_list = header_row + [
+            item for sublist in table.values.tolist() for item in sublist
+        ]
+        total_rows = table.shape[0] + 1  # Adding 1 for the header row
+        total_columns = table.shape[1]
 
         self.report_md.new_table(
-            columns=table.shape[1],
-            rows=table.shape[0],
+            columns=total_columns,
+            rows=total_rows,
             text=text_list,
             text_align=text_align,
         )
@@ -504,10 +509,8 @@ def add_images(self, header, image_text, filepaths):
             title=header,
             add_table_of_contents="n",
         )
-        print("Output image location: {self.output_image_location}")
         if len(image_text) == len(filepaths):
             for i in range(len(filepaths)):
-                print("Adding image:", str(self.output_image_location / filepaths[i]))
                 self.report_md.new_line(
                     self.report_md.new_inline_image(
                         text=image_text[i],
@@ -516,14 +519,13 @@ def add_images(self, header, image_text, filepaths):
                 )
         else:
             for i in range(len(filepaths)):
-                print("Adding image:", str(self.output_image_location / filepaths[i]))
                 self.report_md.new_line(
                     self.report_md.new_inline_image(
                         text=image_text[0],
                         path=str(self.output_image_location / filepaths[i]),
                     )
                 )
-        self.report_md.new_line()
+        self.report_md.new_line("")
 
     def add_line(self, line):
         self.report_md.new_line(line)

From 98b6f8d5cd47fe902218bfe883feadf05dbd24a2 Mon Sep 17 00:00:00 2001
From: Ruge Li <rugeli0605@gmail.com>
Date: Mon, 29 Jul 2024 13:39:36 -0700
Subject: [PATCH 12/19] correct output image path

---
 cellpack/autopack/writers/__init__.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/cellpack/autopack/writers/__init__.py b/cellpack/autopack/writers/__init__.py
index 7a6162b7..c0da4c13 100644
--- a/cellpack/autopack/writers/__init__.py
+++ b/cellpack/autopack/writers/__init__.py
@@ -514,7 +514,7 @@ def add_images(self, header, image_text, filepaths):
                 self.report_md.new_line(
                     self.report_md.new_inline_image(
                         text=image_text[i],
-                        path=str(self.output_image_location / filepaths[i]),
+                        path=str(self.output_image_location / filepaths[i].name),
                     )
                 )
         else:
@@ -522,7 +522,7 @@ def add_images(self, header, image_text, filepaths):
                 self.report_md.new_line(
                     self.report_md.new_inline_image(
                         text=image_text[0],
-                        path=str(self.output_image_location / filepaths[i]),
+                        path=str(self.output_image_location / filepaths[i].name),
                     )
                 )
         self.report_md.new_line("")

From 863633a31a80ccf198f2c81211f4717a33bba7cf Mon Sep 17 00:00:00 2001
From: Ruge Li <rugeli0605@gmail.com>
Date: Mon, 29 Jul 2024 14:06:23 -0700
Subject: [PATCH 13/19] fix path

---
 cellpack/autopack/writers/__init__.py  | 6 ++++--
 cellpack/tests/test_markdown_writer.py | 4 ++--
 2 files changed, 6 insertions(+), 4 deletions(-)

diff --git a/cellpack/autopack/writers/__init__.py b/cellpack/autopack/writers/__init__.py
index c0da4c13..db0d61f5 100644
--- a/cellpack/autopack/writers/__init__.py
+++ b/cellpack/autopack/writers/__init__.py
@@ -511,18 +511,20 @@ def add_images(self, header, image_text, filepaths):
         )
         if len(image_text) == len(filepaths):
             for i in range(len(filepaths)):
+                img_path = f"{self.output_image_location} / {filepaths[i].name}"
                 self.report_md.new_line(
                     self.report_md.new_inline_image(
                         text=image_text[i],
-                        path=str(self.output_image_location / filepaths[i].name),
+                        path=img_path,
                     )
                 )
         else:
             for i in range(len(filepaths)):
+                img_path = f"{self.output_image_location} / {filepaths[i].name}"
                 self.report_md.new_line(
                     self.report_md.new_inline_image(
                         text=image_text[0],
-                        path=str(self.output_image_location / filepaths[i].name),
+                        path=img_path,
                     )
                 )
         self.report_md.new_line("")
diff --git a/cellpack/tests/test_markdown_writer.py b/cellpack/tests/test_markdown_writer.py
index 276e1eb3..f2acee42 100644
--- a/cellpack/tests/test_markdown_writer.py
+++ b/cellpack/tests/test_markdown_writer.py
@@ -82,10 +82,10 @@ def test_add_image(setup_md_writer, tmp_path):
     writer, report_path = setup_md_writer
     header = "Test Image"
     image_text = ["Image 1", "Image 2"]
-    filepaths = ["image1.png", "image2.png"]
+    filepaths = [tmp_path / "image1.png", tmp_path / "image2.png"]
 
     for image in filepaths:
-        (tmp_path / image).touch()
+        image.touch()
 
     writer.add_images(header, image_text, filepaths)
     writer.write_file()

From a61d748237ecec5af071d379f94e49b839c80e13 Mon Sep 17 00:00:00 2001
From: Ruge Li <rugeli0605@gmail.com>
Date: Mon, 29 Jul 2024 14:22:09 -0700
Subject: [PATCH 14/19] remove spaces

---
 cellpack/autopack/writers/__init__.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/cellpack/autopack/writers/__init__.py b/cellpack/autopack/writers/__init__.py
index db0d61f5..0eef1f50 100644
--- a/cellpack/autopack/writers/__init__.py
+++ b/cellpack/autopack/writers/__init__.py
@@ -511,7 +511,7 @@ def add_images(self, header, image_text, filepaths):
         )
         if len(image_text) == len(filepaths):
             for i in range(len(filepaths)):
-                img_path = f"{self.output_image_location} / {filepaths[i].name}"
+                img_path = f"{self.output_image_location}/{filepaths[i].name}"
                 self.report_md.new_line(
                     self.report_md.new_inline_image(
                         text=image_text[i],
@@ -520,7 +520,7 @@ def add_images(self, header, image_text, filepaths):
                 )
         else:
             for i in range(len(filepaths)):
-                img_path = f"{self.output_image_location} / {filepaths[i].name}"
+                img_path = f"{self.output_image_location}/{filepaths[i].name}"
                 self.report_md.new_line(
                     self.report_md.new_inline_image(
                         text=image_text[0],

From b557cc95477e4d07ea3eb2858e09d8c9dea1bfc3 Mon Sep 17 00:00:00 2001
From: Ruge Li <rugeli0605@gmail.com>
Date: Mon, 29 Jul 2024 14:41:56 -0700
Subject: [PATCH 15/19] code refactor

---
 cellpack/autopack/Analysis.py | 39 ++++++++++++++++-------------------
 1 file changed, 18 insertions(+), 21 deletions(-)

diff --git a/cellpack/autopack/Analysis.py b/cellpack/autopack/Analysis.py
index 885710ea..ae0c2c4a 100644
--- a/cellpack/autopack/Analysis.py
+++ b/cellpack/autopack/Analysis.py
@@ -409,11 +409,7 @@ def run_partner_analysis(
         )
         if len(partner_pair_dict):
             md_object.add_header(header="Partner Analysis")
-
-            paired_keys = []
-            touching_radii = []
-            binding_probabilities = []
-            close_fractions = []
+            partner_data = []
             for paired_key, partner_values in partner_pair_dict.items():
                 pairwise_distances = numpy.array(
                     combined_pairwise_distance_dict[paired_key]
@@ -423,16 +419,16 @@ def run_partner_analysis(
                     numpy.count_nonzero(pairwise_distances < padded_radius)
                     / partner_values["num_packed"]
                 )
-                paired_keys.append(paired_key)
-                touching_radii.append(partner_values["touching_radius"])
-                binding_probabilities.append(partner_values["binding_probability"])
-                close_fractions.append(close_fraction)
+                partner_data.append(
+                    {
+                        "Ingredient pair": paired_key,
+                        "Touching radius": partner_values["touching_radius"],
+                        "Binding probability": partner_values["binding_probability"],
+                        "Close packed fraction": close_fraction,
+                    }
+                )
 
-            df = pd.DataFrame()
-            df["Paired keys"] = paired_keys
-            df["Touching radii"] = touching_radii
-            df["Binding probabilities"] = binding_probabilities
-            df["Close packing fractions"] = close_fractions
+            df = pd.DataFrame(partner_data)
 
             md_object.add_table(header="", table=df)
 
@@ -465,7 +461,10 @@ def create_report(
             report_output_path = self.output_path
         report_output_path = Path(report_output_path)
 
-        self.ingredient_key_dict = self.read_dict_from_glob_file("ingredient_keys_*")
+        if not hasattr(self, "ingredient_key_dict"):
+            self.ingredient_key_dict = self.read_dict_from_glob_file(
+                "ingredient_keys_*"
+            )
 
         if ingredient_keys is None:
             ingredient_keys = list(self.ingredient_key_dict.keys())
@@ -474,16 +473,14 @@ def create_report(
             ingredient_keys=ingredient_keys
         )
         ingredient_radii = self.get_ingredient_radii(recipe_data=recipe_data)
-        pairwise_distance_dict = self.read_dict_from_glob_file(
-            "pairwise_distances_*.json"
-        )
-        combined_pairwise_distance_dict = self.combine_results_from_seeds(
-            pairwise_distance_dict
-        )
+
         if not hasattr(self, "pairwise_distance_dict"):
             self.pairwise_distance_dict = self.read_dict_from_glob_file(
                 "pairwise_distances_*.json"
             )
+        combined_pairwise_distance_dict = self.combine_results_from_seeds(
+            self.pairwise_distance_dict
+        )
 
         df = pd.DataFrame(
             {

From dd245a944b2fa0734cdc762026b84f7f3425cff9 Mon Sep 17 00:00:00 2001
From: Ruge Li <rugeli0605@gmail.com>
Date: Thu, 1 Aug 2024 18:42:11 -0700
Subject: [PATCH 16/19] make markdown writer a separate file in writers folder

---
 cellpack/autopack/writers/MarkdownWriter.py | 113 ++++++++++++++++++++
 cellpack/autopack/writers/__init__.py       | 109 -------------------
 2 files changed, 113 insertions(+), 109 deletions(-)
 create mode 100644 cellpack/autopack/writers/MarkdownWriter.py

diff --git a/cellpack/autopack/writers/MarkdownWriter.py b/cellpack/autopack/writers/MarkdownWriter.py
new file mode 100644
index 00000000..08abf89f
--- /dev/null
+++ b/cellpack/autopack/writers/MarkdownWriter.py
@@ -0,0 +1,113 @@
+from pathlib import Path
+
+from mdutils.mdutils import MdUtils
+import pandas as pd
+
+"""
+MarkdownWriter provides a class to write markdown files
+"""
+
+
+class MarkdownWriter(object):
+    def __init__(
+        self,
+        title: str,
+        output_path: Path,
+        output_image_location: Path,
+        report_name: str,
+    ):
+        self.title = title
+        self.output_path = output_path
+        self.output_image_location = output_image_location
+        self.report_md = MdUtils(
+            file_name=str(self.output_path / report_name),
+            title=title,
+        )
+
+    # level is the header style, can only be 1 or 2
+    def add_header(self, header, level: int = 2):
+        self.report_md.new_header(level=level, title=header, add_table_of_contents="n")
+
+    def add_table(self, header, table, text_align="center"):
+        self.report_md.new_header(
+            level=1,
+            title=header,
+            add_table_of_contents="n",
+        )
+
+        header_row = table.columns.tolist()
+        text_list = header_row + [
+            item for sublist in table.values.tolist() for item in sublist
+        ]
+
+        total_rows = table.shape[0] + 1  # Adding 1 for the header row
+        total_columns = table.shape[1]
+
+        self.report_md.new_table(
+            columns=total_columns,
+            rows=total_rows,
+            text=text_list,
+            text_align=text_align,
+        )
+
+    def add_table_from_csv(self, header, filepath, text_align="center"):
+        self.report_md.new_header(
+            level=1,
+            title=header,
+            add_table_of_contents="n",
+        )
+
+        table = pd.read_csv(filepath)
+
+        header_row = table.columns.tolist()
+        text_list = header_row + [
+            item for sublist in table.values.tolist() for item in sublist
+        ]
+        total_rows = table.shape[0] + 1  # Adding 1 for the header row
+        total_columns = table.shape[1]
+
+        self.report_md.new_table(
+            columns=total_columns,
+            rows=total_rows,
+            text=text_list,
+            text_align=text_align,
+        )
+
+    # Image text must be a list, if list is not same length as list of filepaths, only 1st item in image_text is used
+    def add_images(self, header, image_text, filepaths):
+        self.report_md.new_header(
+            level=1,
+            title=header,
+            add_table_of_contents="n",
+        )
+        if len(image_text) == len(filepaths):
+            for i in range(len(filepaths)):
+                img_path = f"{self.output_image_location}/{filepaths[i].name}"
+                self.report_md.new_line(
+                    self.report_md.new_inline_image(
+                        text=image_text[i],
+                        path=img_path,
+                    )
+                )
+        else:
+            for i in range(len(filepaths)):
+                img_path = f"{self.output_image_location}/{filepaths[i].name}"
+                self.report_md.new_line(
+                    self.report_md.new_inline_image(
+                        text=image_text[0],
+                        path=img_path,
+                    )
+                )
+        self.report_md.new_line("")
+
+    def add_line(self, line):
+        self.report_md.new_line(line)
+
+    def add_list(self, list_items):
+        self.report_md.new_list(list_items)
+
+    def add_inline_image(self, text, filepath):
+        return self.report_md.new_inline_image(text=text, path=str(filepath))
+
+    def write_file(self):
+        self.report_md.create_md_file()
diff --git a/cellpack/autopack/writers/__init__.py b/cellpack/autopack/writers/__init__.py
index 0eef1f50..5b439ecb 100644
--- a/cellpack/autopack/writers/__init__.py
+++ b/cellpack/autopack/writers/__init__.py
@@ -5,13 +5,9 @@
 
 import json
 import os
-from pathlib import Path
 import numpy
 from collections import OrderedDict
 
-from mdutils.mdutils import MdUtils
-import pandas as pd
-
 from cellpack import autopack
 from cellpack.autopack.ingredient.grow import ActinIngredient, GrowIngredient
 import cellpack.autopack.transformation as tr
@@ -435,108 +431,3 @@ def save(
             self.save_as_simularium(env, seed_to_results_map)
         else:
             print("format output " + output_format + " not recognized (json,python)")
-
-
-class MarkdownWriter(object):
-    def __init__(
-        self,
-        title: str,
-        output_path: Path,
-        output_image_location: Path,
-        report_name: str,
-    ):
-        self.title = title
-        self.output_path = output_path
-        self.output_image_location = output_image_location
-        self.report_md = MdUtils(
-            file_name=str(self.output_path / report_name),
-            title=title,
-        )
-
-    # level is the header style, can only be 1 or 2
-    def add_header(self, header, level: int = 2):
-        self.report_md.new_header(level=level, title=header, add_table_of_contents="n")
-
-    def add_table(self, header, table, text_align="center"):
-        self.report_md.new_header(
-            level=1,
-            title=header,
-            add_table_of_contents="n",
-        )
-
-        header_row = table.columns.tolist()
-        text_list = header_row + [
-            item for sublist in table.values.tolist() for item in sublist
-        ]
-
-        total_rows = table.shape[0] + 1  # Adding 1 for the header row
-        total_columns = table.shape[1]
-
-        self.report_md.new_table(
-            columns=total_columns,
-            rows=total_rows,
-            text=text_list,
-            text_align=text_align,
-        )
-
-    def add_table_from_csv(self, header, filepath, text_align="center"):
-        self.report_md.new_header(
-            level=1,
-            title=header,
-            add_table_of_contents="n",
-        )
-
-        table = pd.read_csv(filepath)
-
-        header_row = table.columns.tolist()
-        text_list = header_row + [
-            item for sublist in table.values.tolist() for item in sublist
-        ]
-        total_rows = table.shape[0] + 1  # Adding 1 for the header row
-        total_columns = table.shape[1]
-
-        self.report_md.new_table(
-            columns=total_columns,
-            rows=total_rows,
-            text=text_list,
-            text_align=text_align,
-        )
-
-    # Image text must be a list, if list is not same length as list of filepaths, only 1st item in image_text is used
-    def add_images(self, header, image_text, filepaths):
-        self.report_md.new_header(
-            level=1,
-            title=header,
-            add_table_of_contents="n",
-        )
-        if len(image_text) == len(filepaths):
-            for i in range(len(filepaths)):
-                img_path = f"{self.output_image_location}/{filepaths[i].name}"
-                self.report_md.new_line(
-                    self.report_md.new_inline_image(
-                        text=image_text[i],
-                        path=img_path,
-                    )
-                )
-        else:
-            for i in range(len(filepaths)):
-                img_path = f"{self.output_image_location}/{filepaths[i].name}"
-                self.report_md.new_line(
-                    self.report_md.new_inline_image(
-                        text=image_text[0],
-                        path=img_path,
-                    )
-                )
-        self.report_md.new_line("")
-
-    def add_line(self, line):
-        self.report_md.new_line(line)
-
-    def add_list(self, list_items):
-        self.report_md.new_list(list_items)
-
-    def add_inline_image(self, text, filepath):
-        return self.report_md.new_inline_image(text=text, path=str(filepath))
-
-    def write_file(self):
-        self.report_md.create_md_file()

From 17302c3df8c9c446f89e0f83efbaa95ac57c9723 Mon Sep 17 00:00:00 2001
From: Ruge Li <rugeli0605@gmail.com>
Date: Thu, 1 Aug 2024 18:51:48 -0700
Subject: [PATCH 17/19] fix import

---
 cellpack/autopack/Analysis.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/cellpack/autopack/Analysis.py b/cellpack/autopack/Analysis.py
index ae0c2c4a..27b99486 100644
--- a/cellpack/autopack/Analysis.py
+++ b/cellpack/autopack/Analysis.py
@@ -20,7 +20,8 @@
 from cellpack.autopack.ldSequence import halton
 from cellpack.autopack.plotly_result import PlotlyAnalysis
 from cellpack.autopack.utils import check_paired_key, get_paired_key, get_seed_list
-from cellpack.autopack.writers import Writer, MarkdownWriter, ImageWriter
+from cellpack.autopack.writers import Writer, ImageWriter
+from cellpack.autopack.writers.MarkdownWriter import MarkdownWriter
 
 
 class Analysis:

From 45bacb4b3c00f693ba47b911cacb406ce3a13a1e Mon Sep 17 00:00:00 2001
From: Ruge Li <rugeli0605@gmail.com>
Date: Thu, 1 Aug 2024 18:55:08 -0700
Subject: [PATCH 18/19] fix import for tests

---
 cellpack/tests/test_markdown_writer.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/cellpack/tests/test_markdown_writer.py b/cellpack/tests/test_markdown_writer.py
index f2acee42..9280498b 100644
--- a/cellpack/tests/test_markdown_writer.py
+++ b/cellpack/tests/test_markdown_writer.py
@@ -1,6 +1,6 @@
 import pytest
 import pandas as pd
-from cellpack.autopack.writers import MarkdownWriter
+from cellpack.autopack.writers.MarkdownWriter import MarkdownWriter
 
 
 @pytest.fixture

From 0adf24ffb8646297fe4601b9bfd4257b550854eb Mon Sep 17 00:00:00 2001
From: Ruge Li <rugeli0605@gmail.com>
Date: Fri, 2 Aug 2024 09:45:52 -0700
Subject: [PATCH 19/19] correct image writer import

---
 cellpack/autopack/Analysis.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/cellpack/autopack/Analysis.py b/cellpack/autopack/Analysis.py
index 27b99486..5b88b335 100644
--- a/cellpack/autopack/Analysis.py
+++ b/cellpack/autopack/Analysis.py
@@ -20,7 +20,8 @@
 from cellpack.autopack.ldSequence import halton
 from cellpack.autopack.plotly_result import PlotlyAnalysis
 from cellpack.autopack.utils import check_paired_key, get_paired_key, get_seed_list
-from cellpack.autopack.writers import Writer, ImageWriter
+from cellpack.autopack.writers import Writer
+from cellpack.autopack.writers.ImageWriter import ImageWriter
 from cellpack.autopack.writers.MarkdownWriter import MarkdownWriter