make markdown writer a separate file in writers folder

mesoscope · Aug 2, 2024 · dd245a9 · dd245a9
1 parent b557cc9
commit dd245a9
Show file tree

Hide file tree

Showing 2 changed files with 113 additions and 109 deletions.
diff --git a/cellpack/autopack/writers/MarkdownWriter.py 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
@@ -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()