Merge branch 'fix/trimming'

NEWS.md

@@ -5,6 +5,12 @@ This includes a list of major changes for each minor version starting from 0.10.
 For information on how to use `q2-micom` please refer to
 [the tutorial](https://micom-dev.github.io/q2-micom).
 
+#### 0.13.1
+
+Fixes the broken prefix trimming.
+
+Now also reports the matched relative abundance in verbose build output.
+
 ### 0.13.0
 
 Fixes issues with the new model databases due to automatic stripping of taxonomic rank

q2_micom/_build.py

@@ -46,13 +46,29 @@ def build_spec(
     micom_taxonomy = pd.merge(model_files, tax, on=ranks)
     micom_taxonomy = micom_taxonomy[micom_taxonomy.relative > cutoff]
     del micom_taxonomy["file"]
-    stats = micom_taxonomy.sample_id.value_counts().describe()
+    n_stats = micom_taxonomy.sample_id.value_counts().describe()
+    ab_stats = micom_taxonomy.groupby("sample_id").relative.sum().describe() * 100.0
     print("Merged with the database using ranks: %s" % ", ".join(ranks))
-    if stats.count == 1.0:
-        stats["std"] = 0.0
+    if n_stats.count() == 1:
+        n_stats["std"] = 0.0
+        ab_stats["std"] = 0.0
     print(
         "Each community model contains %d-%d taxa (average %d+-%d)."
-        % (stats["min"], stats["max"], round(stats["mean"]), round(stats["std"]))
+        % (
+            n_stats["min"],
+            n_stats["max"],
+            round(n_stats["mean"]),
+            round(n_stats["std"]),
+        )
+    )
+    print(
+        "Community models cover %.2f%%-%.2f%% of the total abundance (average %.2f%%+-%.2f%%)."
+        % (
+            ab_stats["min"],
+            ab_stats["max"],
+            round(ab_stats["mean"]),
+            round(ab_stats["std"]),
+        )
     )
     return micom_taxonomy
 

setup.cfg

@@ -12,7 +12,7 @@ long_description = file: README.md
 long_description_content_type = text/markdown
 license = Apache License 2.0
 url = https://github.com/micom-dev/q2-micom
-classifiers = 
+classifiers =
 	Development Status :: 4 - Beta
 	Intended Audience :: Science/Research
 	Topic :: Scientific/Engineering :: Bio-Informatics
@@ -22,7 +22,7 @@ classifiers =
 	Programming Language :: Python :: 3.9
 	Programming Language :: Python :: 3.10
 	Programming Language :: Python :: 3.11
-keywords = 
+keywords =
 	microbiome
 	modeling
 	metabolism
@@ -32,25 +32,25 @@ keywords =
 zip_safe = False
 packages = find:
 python_requires = >=3.6
-install_requires = 
+install_requires =
 	cobra>=0.18.1
-	micom>=0.33.0
+	micom>=0.33.1
 	jinja2>=2.10.3
 	qiime2>=2021.2
 	rich>=6.0
 	pandas>=1.0
-tests_require = 
+tests_require =
 	coverage
 	pytest
 	pytest-cov
 	flake8
 
 [options.package_data]
-q2_micom = 
+q2_micom =
 	citations.bib
 
 [options.entry_points]
-qiime2.plugins = 
+qiime2.plugins =
 	q2-micom = q2_micom.plugin_setup:plugin
 
 [bumpversion:file:setup.py]
@@ -62,7 +62,7 @@ search = __version__ = "{current_version}"
 replace = __version__ = "{new_version}"
 
 [tool:pytest]
-filterwarnings = 
+filterwarnings =
 	ignore::DeprecationWarning
 	ignore::FutureWarning
 
@@ -75,15 +75,15 @@ branch = True
 omit = q2_micom/tests/*
 
 [coverage:report]
-exclude_lines = 
+exclude_lines =
 	pragma: no cover
-	
+
 	def __repr__
 	if self\.debug
-	
+
 	raise AssertionError
 	raise NotImplementedError
-	
+
 	if 0:
 	if __name__ == .__main__.:
 ignore_errors = True