Add pylint to CI; add PR preview deployments

.github/workflows/test.yml

@@ -20,3 +20,6 @@ jobs:
 
       - name: Run tests
         run: pytest tests/ -v
+
+      - name: Lint
+        run: pylint assemblytics/ --fail-under=9.0

README.md

@@ -141,6 +141,9 @@ This runs `python3 -m build --wheel` and copies the result into `public/`. If yo
 To re-run the pipeline on each input and diff its variant calls against the matching example output:
 
 ```bash
+pip3 uninstall assemblytics        # remove whatever's installed
+pip3 install -e .                  # install editable from current directory
+
 # E. coli (uses a smaller unique anchor length since it's a small genome)
 assemblytics -d input_examples/ecoli.delta.gz -o /tmp/assemblytics_test/ecoli -l 1000
 diff <(tail -n +2 /tmp/assemblytics_test/ecoli/assemblytics_structural_variants.bed | sort) \

assemblytics/dot_prep.py

@@ -93,7 +93,7 @@ def index_for_dot(reference_lengths, fields_by_query, output_prefix, max_overvie
 
 		# orientation:
 		flip = sum_reverse > sum_forward
-		flip_by_query[query_name] = "-" if (flip == True) else "+"
+		flip_by_query[query_name] = "-" if flip else "+"
 
 
 		for tag in ordered_tags:
@@ -103,7 +103,7 @@ def index_for_dot(reference_lengths, fields_by_query, output_prefix, max_overvie
 
 			for fields in lines:
 				if fields[8] == tag:
-					if flip == True:
+					if flip:
 						fields[2] = int(fields[5]) - int(fields[2])
 						fields[3] = int(fields[5]) - int(fields[3])
 
@@ -138,7 +138,7 @@ def index_for_dot(reference_lengths, fields_by_query, output_prefix, max_overvie
 	f_out_index.write("#query\n")
 	f_out_index.write("query,query_length,orientation,bytePosition_unique,bytePosition_repetitive,bytePosition_end,unique_matching_refs,matching_refs\n")
 	# relative_ref_position_by_query is sorted by rel_pos
-	for query,rel_pos in relative_ref_position_by_query:
+	for query,_ in relative_ref_position_by_query:
 		f_out_index.write("%s,%d,%s,%d,%d,%d,%s,%s\n" % (query, query_lengths[query], flip_by_query[query], query_byte_positions[(query,"unique")], query_byte_positions[(query,"repetitive")] - query_byte_positions[(query,"unique")], query_byte_positions[(query,"end")] - query_byte_positions[(query,"repetitive")], "~".join(unique_references_by_query[query]), "~".join(all_references_by_query[query])))
 
 	f_out_index.write("#overview\n")

assemblytics/dotplot.py

@@ -5,7 +5,6 @@
 import matplotlib
 matplotlib.use('Agg')
 import matplotlib.pyplot as plt
-import numpy as np
 import os
 
 def run(output_dir):

assemblytics/nchart.py

@@ -5,7 +5,6 @@
 import matplotlib
 matplotlib.use('Agg')
 import matplotlib.pyplot as plt
-import numpy as np
 import os
 
 def bp_format(num):

assemblytics/uniq_anchor.py

@@ -30,11 +30,9 @@ def run(args):
     try:
         f = gzip.open(filename, 'rt')
         header1 = f.readline().strip()
-        # Detected gzipped delta file.
-    except:
+    except Exception:  # noqa: BLE001 — fallback for uncompressed delta
         f = open(filename, 'r')
         header1 = f.readline().strip()
-        # Detected uncompressed delta file.
 
     # Skip the second line
     f.readline()
@@ -97,11 +95,9 @@ def run(args):
     try:
         f = gzip.open(filename, 'rt')
         header1 = f.readline()
-        # Detected gzipped delta file.
-    except:
+    except Exception:  # noqa: BLE001 — fallback for uncompressed delta
         f = open(filename, 'r')
         header1 = f.readline()
-        # Detected uncompressed delta file.
 
     fout.write(header1)
     fout.write(f.readline())
@@ -112,6 +108,7 @@ def run(args):
     list_of_alignments_to_keep = []
     alignment_counter = {}
     keep_printing = False
+    query = ""
 
     # For coords:
     current_query_name = ""
@@ -152,7 +149,7 @@ def run(args):
             for index in list_of_alignments_to_keep:
                 if line.strip() == header_lines_by_query[query][index]:
                     header_needed = True
-            if header_needed == True:
+            if header_needed:
                 fout.write(line) # if we have any alignments under this header, print the header
             alignment_counter[query] = alignment_counter.get(query,0)
 
@@ -204,7 +201,7 @@ def run(args):
                 )
                 alignment_counter[query] = alignment_counter[query] + 1
 
-            elif keep_printing == True:
+            elif keep_printing:
                 fout.write(line)
 
     fcoords_out_tab.close()

pyproject.toml

@@ -31,10 +31,38 @@ Repository = "https://github.com/MariaNattestad/assemblytics"
 assemblytics = "assemblytics.cli:main"
 
 [project.optional-dependencies]
-dev = ["pytest"]
+dev = ["pytest", "pylint"]
 
 [tool.setuptools]
 packages = ["assemblytics"]
 
 [tool.pytest.ini_options]
 testpaths = ["tests"]
+
+[tool.pylint.format]
+max-line-length = 250
+
+[tool.pylint."messages control"]
+disable = [
+    "missing-module-docstring",
+    "missing-function-docstring",
+    "missing-class-docstring",
+    "trailing-whitespace",
+    "wrong-import-order",
+    "wrong-import-position",
+    "import-outside-toplevel",
+    "too-many-locals",
+    "too-many-branches",
+    "too-many-statements",
+    "too-many-positional-arguments",
+    "too-many-arguments",
+    "consider-using-f-string",
+    "consider-using-with",
+    "consider-using-dict-items",
+    "unspecified-encoding",
+    "duplicate-code",
+    "bad-indentation",
+    "redefined-outer-name",
+    "chained-comparison",
+    "broad-exception-caught",
+]