update sourmash and snakemake dependencies

charcoal/Snakefile

@@ -4,7 +4,7 @@
 # --configfile must be specified on command line.
 #
 # CTB TODO: bring CLI improvements from grist over (@toplevel, etc.)
-import csv, sys, os, json
+import csv, sys, os, json, urllib
 from snakemake.workflow import srcdir
 from charcoal.utils import CSV_DictHelper
 

charcoal/compare_taxonomy.py

@@ -11,7 +11,8 @@
 
 import sourmash
 from sourmash.lca.command_index import load_taxonomy_assignments
-from sourmash.lca import LCA_Database, LineagePair
+from sourmash.lca import LCA_Database
+from sourmash.tax.tax_utils import LineagePair
 
 from . import utils
 from .lineage_db import LineageDB
@@ -124,16 +125,9 @@ def get_genome_taxonomy(matches_filename, database_list,
                         genome_sig_filename, provided_lineage,
                         tax_assign, match_rank, min_f_ident, min_f_major):
     # load the matches from prefetch as a picklist
-    picklist = sourmash.picklist.SignaturePicklist('prefetch')
-    try:
-        picklist.load(matches_filename, picklist.column_name)
-    except ValueError:
-        with open(matches_filename, 'rt') as fp:
-            contents = fp.read()
-            if not len(contents): # empty is ok.
-                picklist = None
-            else:
-                raise
+    picklist = sourmash.picklist.SignaturePicklist('prefetch',
+                                                   pickfile=matches_filename)
+    picklist.load(allow_empty=True)
 
     # load all of the matches in the database, as found by prefetch;
     # select on them; and then aggregate into MultiIndex.

charcoal/conf/env-reporting.yml

@@ -4,13 +4,13 @@ channels:
     - bioconda
     - defaults
 dependencies:
-    - python>=3.8
+    - python>=3.10
     - papermill>=2.1.2,<3
     - notebook>=6,<7
     - matplotlib=3.5.2
     - plotly>=4.9.0,<5
     - ipykernel
-    - sourmash>=4.4.3,<5
+    - sourmash>=4.8.4,<5
     - pip
     - pip:
       - git+https://github.com/dib-lab/charcoal.git

charcoal/conf/env-sourmash.yml

@@ -4,11 +4,10 @@ channels:
     - bioconda
     - defaults
 dependencies:
-    - python>=3.7,<3.10
     - pytest>6,<7
     - pytest-dependency>=0.5.1
     - pyyaml>5.3,<6
-    - sourmash>=4.4.3,<5
+    - sourmash>=4.8.4,<5
     - pip
     - pip:
       - git+https://github.com/dib-lab/charcoal.git

charcoal/contigs_list_contaminants.py

@@ -83,8 +83,9 @@ def main(args):
     genome_sig = sourmash.load_one_signature(args.genome_sig)
 
     # load the matches from prefetch as a picklist
-    picklist = sourmash.picklist.SignaturePicklist('prefetch')
-    picklist.load(args.matches_csv, picklist.column_name)
+    picklist = sourmash.picklist.SignaturePicklist('prefetch',
+                                                   pickfile=args.matches_csv)
+    picklist.load()
 
     # load all of the matches in the database, as found by prefetch;
     # select on them; and then aggregate into MultiIndex.

charcoal/contigs_search_taxonomy.py

@@ -32,16 +32,9 @@ def main(args):
     genome_sig = sourmash.load_one_signature(args.genome_sig)
 
     # load the matches from prefetch as a picklist
-    picklist = sourmash.picklist.SignaturePicklist('prefetch')
-    try:
-        picklist.load(args.matches_csv, picklist.column_name)
-    except ValueError:
-        with open(args.matches_csv, 'rt') as fp:
-            contents = fp.read()
-            if not len(contents): # empty is ok.
-                picklist = None
-            else:
-                raise
+    picklist = sourmash.picklist.SignaturePicklist('prefetch',
+                                                   pickfile=args.matches_csv)
+    picklist.load(allow_empty=True)
 
     # load all of the matches in the database, as found by prefetch;
     # select on them; and then aggregate into MultiIndex.

charcoal/figs/sourmash_sankey.py

@@ -1,6 +1,7 @@
 from charcoal import utils
 import sourmash
-from sourmash.lca import taxlist, LineagePair
+from sourmash.lca import taxlist
+from sourmash.tax.tax_utils import LineagePair
 import collections
 
 import plotly.graph_objects as go

charcoal/just_taxonomy.py

@@ -13,7 +13,8 @@
 
 import sourmash
 from sourmash.lca.command_index import load_taxonomy_assignments
-from sourmash.lca import LCA_Database, LineagePair
+from sourmash.lca import LCA_Database
+from sourmash.tax.tax_utils import LineagePair
 
 from . import utils
 from . import lineage_db

charcoal/lineage_db.py

@@ -16,7 +16,7 @@
 import functools
 import pytest
 
-from sourmash.lca import LineagePair
+from sourmash.tax.tax_utils import LineagePair
 
 
 def cached_property(fun):
@@ -85,7 +85,7 @@ def __repr__(self):
     @classmethod
     def load(cls, db_name):
         "Load LCA_Database from a JSON file."
-        from .lca_utils import taxlist, LineagePair
+        from .lca_utils import taxlist
 
         xopen = open
         if db_name.endswith('.gz'):

charcoal/utils.py

@@ -6,7 +6,8 @@
 import csv
 
 import sourmash
-from sourmash.lca import lca_utils, LineagePair, taxlist, display_lineage
+from sourmash.lca import lca_utils, taxlist, display_lineage
+from sourmash.tax.tax_utils import LineagePair
 from sourmash.lca.lca_utils import (is_lineage_match, pop_to_rank,
                                     make_lineage)
 

environment.yml

@@ -4,10 +4,10 @@ channels:
     - bioconda
     - defaults
 dependencies:
-    - python>=3.8,<3.10
-    - snakemake-minimal=6.5.1
+    - python>=3.10
+    - snakemake-minimal==7.32.4
     - screed
     - click>=7,<8
     - pip
     - mamba
-    - sourmash=4.4.3
+    - sourmash==4.8.4

setup.py

@@ -30,8 +30,8 @@
     },
     include_package_data=True,
     package_data = { "charcoal": ["Snakefile", "*.yml", "*.ipynb"] },
-    setup_requires = [ "setuptools>=38.6.0",
+    setup_requires = [ "setuptools>=68.2.2",
                        'setuptools_scm', 'setuptools_scm_git_archive' ],
     use_scm_version = {"write_to": "charcoal/version.py"},
-    install_requires = ['snakemake==6.4.1', 'click>=7,<8']
+    install_requires = ['snakemake==7.32.4', 'click>=7,<8']
 )

tests/test_decontam.py

@@ -11,7 +11,8 @@
 
 import sourmash
 from sourmash.lca import LCA_Database
-from sourmash.lca import LineagePair, taxlist
+from sourmash.lca import taxlist
+from sourmash.tax.tax_utils import LineagePair
 from sourmash.lca.command_index import load_taxonomy_assignments