the graphs are stable, the system generates sorted node orders

Makefile

@@ -20,7 +20,7 @@ web:
 
 # Performs the testing.
 test:
-	(cd test && make test)
+	pytest
 
 # Runs a linter.
 lint:
@@ -38,12 +38,11 @@ fix:
 push:
 	git commit -am 'saving work' && git push
 
-VERSION ?= $(shell grep '__version__' src/genescape/__about__.py | sed "s/__version__ = \"\\(.*\\)\"/\1/" )
+VERSION ?= $(shell grep '__VERSION__' src/genescape/__about__.py | sed "s/__VERSION__ = \"\\(.*\\)\"/\1/" )
 
 NAME = GeneScape
 
 mac:
-
 	# Example of generating a tag file with the version
 	@echo "VERSION=${VERSION}"
 
@@ -63,7 +62,7 @@ clean:
 realclean: clean
 	rm -rf build dist
 
-build:
+build: test
 	rm -rf build dist
 	hatch build 
 	ls -lh dist

pyproject.toml

@@ -110,12 +110,15 @@ all = [
 ]
 
 [tool.black]
-target-version = ["py39"]
+target-version = [ 'py310' ]
 line-length = 120
 skip-string-normalization = true
+exclude = '''
+src/genescape/bottle\.py
+'''
 
 [tool.ruff]
-target-version = "py39"
+target-version = 'py310'
 line-length = 120
 exclude = [
     # This a vendored third-party library.
@@ -159,7 +162,7 @@ ignore = [
   "C901", "PLR0911", "PLR0912", "PLR0913", "PLR0915",
 
   # Pet peevees
-  "Q000", "C402",  "F401", "E401",  "T201",
+  "Q000", "C402",  "F401", "E401",  "T201", "E501", 
 ]
 unfixable = [
   # Don't touch unused imports

src/genescape/__about__.py

@@ -1 +1 @@
-__version__ = "0.7.2"
+__VERSION__ = "0.8.0"

src/genescape/__init__.py

@@ -1,2 +1 @@
-
-from genescape.__about__ import __version__
+from genescape.__about__ import __VERSION__

src/genescape/annot.py

@@ -1,22 +1,24 @@
 """
 Annotates a list of genes with functions based on the GO graph
 """
-import csv, io
+
+import csv
 import gzip
-import sys, json, re
+import io
+import json
+import re
+import sys
 from collections import Counter
 from itertools import *
 from pathlib import Path
-from genescape import utils, resources
+
+from genescape import resources, utils
 
 
 def run(data, index, pattern='', mincount=1, root=utils.NS_ALL, csvout=False):
 
     # Collect the run status into this list.
-    status = {
-        utils.CODE_FIELD: 0,
-        utils.INVALID_FIELD: []
-    }
+    status = {utils.CODE_FIELD: 0, utils.INVALID_FIELD: []}
 
     # Checking the input
     if not index:
@@ -46,7 +48,7 @@ def build():
     go = idx[utils.IDX_OBO]
 
     # The valid ids are the unqiue gene and protein ids.
-    valid_ids = set(sym2go) |set(go)
+    valid_ids = set(sym2go) | set(go)
 
     # Fetch GO functions for a given gene or protein id.
     def get_func(name):
@@ -73,7 +75,7 @@ def get_func(name):
     # The missing ids.
     if miss:
         status[utils.CODE_FIELD] = 1
-        status[utils.INVALID_FIELD] = (list(miss))
+        status[utils.INVALID_FIELD] = list(miss)
         utils.warn(f"{status}")
 
     # Get the elements for a go id.
@@ -119,7 +121,7 @@ def go2ns(goid):
         if root != utils.NS_ALL and root != root_code:
             continue
 
-        name = dict(zip(data_fields, [goid, root_code, cnt,func, funcs, cnt, n_size, label]))
+        name = dict(zip(data_fields, [goid, root_code, cnt, func, funcs, cnt, n_size, label], strict=False))
 
         res.append(name)
 

src/genescape/build.py

@@ -1,14 +1,18 @@
 #
 # Parse an OBO and produces a GZIPed JSON file
 #
-import gzip, os, sys
-import json
 import csv
+import gzip
+import json
+import os
+import sys
 from itertools import *
 from pathlib import Path
-from genescape import utils, resources
+
+from genescape import resources, utils
 from genescape.__about__ import __version__
 
+
 def parse_line(text, sep):
     text = text.strip()
     elem = text.split(sep)[1].strip().strip('"')
@@ -50,6 +54,7 @@ def parse_gaf(fname):
     stream = csv.reader(stream, delimiter="\t")
     return stream
 
+
 def make_index(obo, gaf, index, with_synonyms=False):
 
     if not os.path.isfile(obo):
@@ -99,8 +104,8 @@ def make_index(obo, gaf, index, with_synonyms=False):
 
     # Database metadata
     meta = dict(
-        version=__version__, date=utils.get_date(),
-        gaf=gaf.name, obo=obo.name, index=index.name, synonyms=with_synonyms)
+        version=__version__, date=utils.get_date(), gaf=gaf.name, obo=obo.name, index=index.name, synonyms=with_synonyms
+    )
 
     # The complete data
     data = {
@@ -132,13 +137,11 @@ def make_index(obo, gaf, index, with_synonyms=False):
     gaf = res.GAF_FILE
     ind = Path("genescape.json.gz")
 
-
     @utils.timer
     def test_make_index():
         retval = make_index(obo=obo, gaf=gaf, index=ind, with_synonyms=False)
         return retval
 
-
     @utils.timer
     def test_load_json():
         retval = resources.get_json(ind)
@@ -147,8 +150,5 @@ def test_load_json():
     vals = test_make_index()
     obj = test_load_json()
 
-    #data = obj[utils.IDX_SYM2GO]
-    #print (json.dumps(data, indent=4))
-
-
-
+    # data = obj[utils.IDX_SYM2GO]
+    # print (json.dumps(data, indent=4))

src/genescape/main.py

@@ -1,9 +1,10 @@
 import os
 import sys
 from pathlib import Path
+
 import click
 
-from genescape import utils, resources
+from genescape import resources, utils
 
 
 @click.group()
@@ -13,16 +14,29 @@ def cli():
     """
     pass
 
+
 ROOT_CHOICES = [utils.NS_BP, utils.NS_MF, utils.NS_CC, utils.NS_ALL]
 
 
 @cli.command()
 @click.argument("fname", default=None, required=False)
 @click.option("-o", "--out", "out", metavar="TEXT", default="genescape.pdf", help="output graph file")
-@click.option("-i", "--index", "index", metavar="FILE", help="OBO index file", )
+@click.option(
+    "-i",
+    "--index",
+    "index",
+    metavar="FILE",
+    help="OBO index file",
+)
 @click.option("-m", "--match", "match", metavar="REGEX", default='', help="Regular expression match on function")
 @click.option("-c", "--count", "count", metavar="INT", default=1, type=int, help="The minimal count for a GO term (1)")
-@click.option('-r', '--root', type=click.Choice(ROOT_CHOICES, case_sensitive=False), default=utils.NS_ALL, help='Select a category: BP, MF, CC, or ALL.')
+@click.option(
+    '-r',
+    '--root',
+    type=click.Choice(ROOT_CHOICES, case_sensitive=False),
+    default=utils.NS_ALL,
+    help='Select a category: BP, MF, CC, or ALL.',
+)
 @click.option("-t", "--test", "test", is_flag=True, help="run with demo data")
 @click.option("-v", "verbose", is_flag=True, help="verbose output")
 @click.help_option("-h", "--help")
@@ -64,7 +78,13 @@ def tree(fname, out=None, index=None, root=utils.NS_ALL, match=None, count=1, ve
 @click.option("-m", "--match", "match", metavar="REGEX", default='', help="Regular expression match on function")
 @click.option("-c", "--count", "count", metavar="INT", default=1, type=int, help="The minimal count for a GO term (1)")
 @click.option("-t", "--test", "test", is_flag=True, help="Run with test data")
-@click.option('-r', '--root', type=click.Choice(ROOT_CHOICES, case_sensitive=False), default=utils.NS_ALL, help='Select a category: BP, MF, CC, or ALL.')
+@click.option(
+    '-r',
+    '--root',
+    type=click.Choice(ROOT_CHOICES, case_sensitive=False),
+    default=utils.NS_ALL,
+    help='Select a category: BP, MF, CC, or ALL.',
+)
 @click.option("--csv", "csvout", is_flag=True, help="Produce CSV output instead of JSON")
 @click.option("-v", "verbose", is_flag=True, help="Verbose output.")
 @click.help_option("-h", "--help")
@@ -106,17 +126,18 @@ def annotate(fname, index=None, root=utils.NS_ALL, verbose=False, test=False, cs
     if not out:
         print(text)
     else:
-        with open(out, "wt") as fp:
+        with open(out, "w") as fp:
             fp.write(text)
 
+
 @cli.command()
 @click.option("-b", "--obo", "obo", help="Input OBO file (go-basic.obo)")
 @click.option("-g", "--gaf", "gaf", help="Input GAF file (goa_human.gaf.gz)")
 @click.option("-i", "--index", "index", default="genescape.json.gz", help="Output index file (genescape.json.gz)")
-@click.option("-s", "--synonms", "synon", is_flag=True,  help="Include synonyms in the index")
-@click.option("-d", "--dump", "dump", is_flag=True,  help="Print the index to stdout")
+@click.option("-s", "--synonms", "synon", is_flag=True, help="Include synonyms in the index")
+@click.option("-d", "--dump", "dump", is_flag=True, help="Print the index to stdout")
 @click.help_option("-h", "--help")
-def build(index=None, obo=None, gaf=None, synon=False, dump=False ):
+def build(index=None, obo=None, gaf=None, synon=False, dump=False):
     """
     Builds a JSON index file from an OBO file.
     """
@@ -135,26 +156,29 @@ def build(index=None, obo=None, gaf=None, synon=False, dump=False ):
     ind = Path(index)
 
     if dump:
+
         @utils.timer
         def load_index():
             retval = resources.get_json(ind)
             return retval
+
         obj = load_index()
         meta = obj[utils.IDX_META_DATA]
-        print (f"# {meta}")
+        print(f"# {meta}")
         sym2go = obj[utils.IDX_SYM2GO]
         for key, value in sym2go.items():
-            row = [ key] + value
+            row = [key] + value
             print("\t".join(row))
 
     else:
         # Run the build command.
         build.make_index(obo=obo, gaf=gaf, index=ind, with_synonyms=synon)
 
+
 @cli.command()
 @click.option("--devmode", "devmode", is_flag=True, help="run in development mode")
 @click.option("--reset", "reset", is_flag=True, help="reset the resources")
-@click.option("-i", "--index", "index",  help="Genescape index file")
+@click.option("-i", "--index", "index", help="Genescape index file")
 @click.option("-v", "verbose", is_flag=True, help="Verbose output.")
 @click.help_option("-h", "--help")
 def web(devmode=False, reset=False, verbose=False, index=None):