Updating changelog before release.

CHANGELOG.md

@@ -21,6 +21,19 @@ needed. This is equivalent to summarizing all activity on a feature branch versu
 
 ## Unreleased
 
+## v0.3.0
+
+### Added
+* fluorescent_probes_csv_2_md - script for creating the knowledge-base fluorescent_probes markdown page from the fluorescent_probes.csv.
+
+### Changed
+* reagent_resources_csv_2_md_url - In addition to the reagent_resources.csv we now use a template file into which the table is written. Allows us to modify the descriptive text without modifying code. Additionally, the table is sorted on the "Target Name / Protein Biomarker" column.
+* update_index_md_stats - Change the computed statistics to:
+  1. number_of_contributors - count both original contributors and folks that replicated the work.
+  1. number_of_validated_reagents - count rows in the reagent_resources.csv.
+  1. number_of_fluorescent_probes - count number of unique entries in conjugate column of the reagent_resources.csv (ignoring NA, Unconjugated, Biotin, HRP, UT014, UT015, UT016, UT019).
+  1. number_of_tissues - count unique combinations of Target_Species-Target_Tissue-Tissue_State.
+
 ## v0.2.0
 
 ### Added

src/ibex_imaging_knowledge_base_utilities/fluorescent_probes_csv_2_md.py

@@ -19,25 +19,21 @@
 import pandas as pd
 import argparse
 import sys
-import pathlib
-from .argparse_types import file_path
-import json
+from .argparse_types import file_path, dir_path
+
 
 """
 This script converts the IBEX knowledge-base fluorescent_probes.csv file to markdown.
 
 This script is automatically run when modifications to the fluorescent_probes.csv file is merged
 into the main branch of the ibex_knowledge_base repository (see .github/workflows/data2md.yml).
 
-Assumption: The fluorescent_probes.csv file is valid. It conforms to the expected format (empty entries denoted 
+Assumption: The fluorescent_probes.csv file is valid. It conforms to the expected format (empty entries denoted
 by the string "NA").
 """
 
-def fluorescent_probe_csv_to_md(
-    template_file_path,
-    csv_file_path,
-    output_dir
-):
+
+def fluorescent_probe_csv_to_md(template_file_path, csv_file_path, output_dir):
     """
     Convert the IBEX knowledge-base fluorescent probe csv file to markdown. Output is written to a
     file named fluorescent_probes.md in the output directory. The template_file_path file is expected
@@ -50,16 +46,14 @@ def fluorescent_probe_csv_to_md(
     with open(template_file_path, "r") as fp:
         input_md_str = fp.read()
     with open(output_dir / "fluorescent_probes.md", "w") as fp:
-        fp.write(
-            input_md_str.format(probe_table=df.to_markdown(index=False))
-        )
+        fp.write(input_md_str.format(probe_table=df.to_markdown(index=False)))
 
 
 def main(argv=None):
     if argv is None:  # script was invoked from commandline
         argv = sys.argv[1:]
     parser = argparse.ArgumentParser(
-        description="Convert knowledge-base fluorescent probes file from csv to md and sort according to excitation and emission."
+        description="Convert knowledge-base fluorescent probes file from csv to md and sort according to excitation and emission."  # noqa E501
     )
     parser.add_argument(
         "md_template_file",
@@ -80,7 +74,7 @@ def main(argv=None):
         return fluorescent_probe_csv_to_md(
             template_file_path=args.md_template_file,
             csv_file_path=args.csv_file,
-            output_dir=args.output_dir
+            output_dir=args.output_dir,
         )
     except Exception as e:
         print(

tests/test_scripts.py

@@ -5,7 +5,9 @@
 from ibex_imaging_knowledge_base_utilities.reagent_resources_csv_2_md_url import (
     csv_to_md_with_url,
 )
-from ibex_imaging_knowledge_base_utilities.fluorescent_probes_csv_2_md import fluorescent_probe_csv_to_md
+from ibex_imaging_knowledge_base_utilities.fluorescent_probes_csv_2_md import (
+    fluorescent_probe_csv_to_md,
+)
 
 from ibex_imaging_knowledge_base_utilities.bib2md import bibfile2md
 from ibex_imaging_knowledge_base_utilities.update_index_md_stats import (
@@ -35,7 +37,7 @@ def files_md5(self, file_path_list):
 
 class TestCSV2MD(BaseTest):
     @pytest.mark.parametrize(
-        "md_template_file_name, csv_file_name, supporting_material_root_dir, vendor_to_website_json_file_path, result_md5hash",
+        "md_template_file_name, csv_file_name, supporting_material_root_dir, vendor_to_website_json_file_path, result_md5hash",  # noqa E501
         [
             (
                 "reagent_resources.md.in",
@@ -66,6 +68,7 @@ def test_csv_2_md_with_url(
             == result_md5hash
         )
 
+
 class TestFluorescentProbesCSV2MD(BaseTest):
     @pytest.mark.parametrize(
         "md_template_file_name, csv_file_name, result_md5hash",
@@ -78,21 +81,15 @@ class TestFluorescentProbesCSV2MD(BaseTest):
         ],
     )
     def test_fluorescent_probe_csv_to_md(
-        self,
-        md_template_file_name,
-        csv_file_name,
-        result_md5hash,
-        tmp_path
+        self, md_template_file_name, csv_file_name, result_md5hash, tmp_path
     ):
         fluorescent_probe_csv_to_md(
-            template_file_path = self.data_path / md_template_file_name,
-            csv_file_path = self.data_path / csv_file_name,
-            output_dir = tmp_path
-        )
-        assert (
-            self.files_md5([tmp_path / "fluorescent_probes.md"])
-            == result_md5hash
+            template_file_path=self.data_path / md_template_file_name,
+            csv_file_path=self.data_path / csv_file_name,
+            output_dir=tmp_path,
         )
+        assert self.files_md5([tmp_path / "fluorescent_probes.md"]) == result_md5hash
+
 
 class TestBib2MD(BaseTest):
     @pytest.mark.parametrize(