Python Black Formatting (#492)

* Apply black formatting

* Add black.yml workflow for checking Python formatting

.github/workflows/black.yml

@@ -0,0 +1,13 @@
+name: Lint
+
+on: [push, pull_request]
+
+jobs:
+  lint:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - uses: psf/black@stable
+        with:
+          src: "./src/python"
+          options: "--check --verbose"

src/python/sourmash_plugin_branchwater/prettyprint.py

@@ -1,16 +1,17 @@
 import csv
 
+
 def pretty_print_manysearch(manysearch_csv):
     "Pretty-print the manysearch output."
-    with open(manysearch_csv, newline='') as fp:
+    with open(manysearch_csv, newline="") as fp:
         r = csv.DictReader(fp)
         rows = list(r)
 
-    rows.sort(key=lambda row: row['query_name']) # sort by metagenome, for now
+    rows.sort(key=lambda row: row["query_name"])  # sort by metagenome, for now
 
     first = True
     for row in rows:
-        has_abundance = 'average_abund' in row
+        has_abundance = "average_abund" in row
 
         #
         # display!
@@ -23,21 +24,25 @@ def pretty_print_manysearch(manysearch_csv):
             print("--------          -------- ---------   -------   ---------------")
             first = False
 
-        f_genome_found = float(row['containment'])
+        f_genome_found = float(row["containment"])
         pct_genome = f"{f_genome_found*100:.1f}"
 
         if has_abundance:
-            n_weighted_found = int(row['n_weighted_found'])
-            total_weighted_hashes = int(row['total_weighted_hashes'])
-            f_metag_weighted = n_weighted_found / total_weighted_hashes # results_d['f_match_weighted']
+            n_weighted_found = int(row["n_weighted_found"])
+            total_weighted_hashes = int(row["total_weighted_hashes"])
+            f_metag_weighted = (
+                n_weighted_found / total_weighted_hashes
+            )  # results_d['f_match_weighted']
             pct_metag = f"{f_metag_weighted*100:.1f}%"
 
-            avg_abund = float(row['average_abund'])
+            avg_abund = float(row["average_abund"])
             avg_abund = f"{avg_abund:.1f}"
         else:
             avg_abund = "N/A"
             pct_metag = "N/A"
 
-        query_name = row['query_name'][:17]
-        metag_name = row['match_name'][:17]
-        print(f'{query_name:<17} {pct_genome:>6}%  {avg_abund:>6}     {pct_metag:>6}     {metag_name}')
+        query_name = row["query_name"][:17]
+        metag_name = row["match_name"][:17]
+        print(
+            f"{query_name:<17} {pct_genome:>6}%  {avg_abund:>6}     {pct_metag:>6}     {metag_name}"
+        )

src/python/tests/__init__.py

@@ -1,2 +1,3 @@
 from sourmash_plugin_branchwater import sourmash_plugin_branchwater
+
 sourmash_plugin_branchwater.set_global_thread_pool(4)

src/python/tests/conftest.py

@@ -2,6 +2,7 @@
 
 from .sourmash_tst_utils import TempDirectory, RunnerContext
 
+
 @pytest.fixture
 def runtmp():
     with TempDirectory() as location:
@@ -12,26 +13,32 @@ def runtmp():
 def toggle_internal_storage(request):
     return request.param
 
+
 @pytest.fixture(params=[True, False])
 def zip_query(request):
     return request.param
 
+
 @pytest.fixture(params=[True, False])
 def zip_db(request):
     return request.param
 
+
 @pytest.fixture(params=[True, False])
 def zip_against(request):
     return request.param
 
+
 @pytest.fixture(params=[True, False])
 def indexed(request):
     return request.param
 
+
 @pytest.fixture(params=[True, False])
 def indexed_query(request):
     return request.param
 
+
 @pytest.fixture(params=[True, False])
 def indexed_against(request):
     return request.param

src/python/tests/sourmash_tst_utils.py

@@ -16,31 +16,49 @@
 
 def get_test_data(filename):
     thisdir = os.path.dirname(__file__)
-    return os.path.join(thisdir, 'test-data', filename)
+    return os.path.join(thisdir, "test-data", filename)
 
 
 def make_file_list(filename, paths):
-    with open(filename, 'wt') as fp:
+    with open(filename, "wt") as fp:
         fp.write("\n".join(paths))
         fp.write("\n")
 
 
 def zip_siglist(runtmp, siglist, db):
-    runtmp.sourmash('sig', 'cat', siglist,
-                    '-o', db)
+    runtmp.sourmash("sig", "cat", siglist, "-o", db)
     return db
 
 
-def index_siglist(runtmp, siglist, db, *, ksize=31, scaled=1000, moltype='DNA',
-                  toggle_internal_storage='--internal-storage'):
+def index_siglist(
+    runtmp,
+    siglist,
+    db,
+    *,
+    ksize=31,
+    scaled=1000,
+    moltype="DNA",
+    toggle_internal_storage="--internal-storage",
+):
     # build index
-    runtmp.sourmash('scripts', 'index', siglist,
-                    '-o', db, '-k', str(ksize), '--scaled', str(scaled),
-                    '--moltype', moltype, toggle_internal_storage)
+    runtmp.sourmash(
+        "scripts",
+        "index",
+        siglist,
+        "-o",
+        db,
+        "-k",
+        str(ksize),
+        "--scaled",
+        str(scaled),
+        "--moltype",
+        moltype,
+        toggle_internal_storage,
+    )
     return db
 
 
-def scriptpath(scriptname='sourmash'):
+def scriptpath(scriptname="sourmash"):
     """Return the path to the scripts, in both dev and install situations."""
     # note - it doesn't matter what the scriptname is here, as long as
     # it's some script present in this version of sourmash.
@@ -53,18 +71,18 @@ def scriptpath(scriptname='sourmash'):
     if os.path.exists(os.path.join(path, scriptname)):
         return path
 
-    for path in os.environ['PATH'].split(':'):
+    for path in os.environ["PATH"].split(":"):
         if os.path.exists(os.path.join(path, scriptname)):
             return path
 
 
 def _runscript(scriptname):
     """Find & run a script with exec (i.e. not via os.system or subprocess)."""
     namespace = {"__name__": "__main__"}
-    namespace['sys'] = globals()['sys']
+    namespace["sys"] = globals()["sys"]
 
     try:
-        pkg_resources.load_entry_point("sourmash", 'console_scripts', scriptname)()
+        pkg_resources.load_entry_point("sourmash", "console_scripts", scriptname)()
         return 0
     except pkg_resources.ResolutionError:
         pass
@@ -75,15 +93,15 @@ def _runscript(scriptname):
     if os.path.isfile(scriptfile):
         if os.path.isfile(scriptfile):
             exec(  # pylint: disable=exec-used
-                compile(open(scriptfile).read(), scriptfile, 'exec'),
-                namespace)
+                compile(open(scriptfile).read(), scriptfile, "exec"), namespace
+            )
             return 0
 
     return -1
 
 
-ScriptResults = collections.namedtuple('ScriptResults',
-                                       ['status', 'out', 'err'])
+ScriptResults = collections.namedtuple("ScriptResults", ["status", "out", "err"])
+
 
 def runscript(scriptname, args, **kwargs):
     """Run a Python script using exec().
@@ -99,17 +117,17 @@ def runscript(scriptname, args, **kwargs):
     sysargs.extend(args)
 
     cwd = os.getcwd()
-    in_directory = kwargs.get('in_directory', cwd)
-    fail_ok = kwargs.get('fail_ok', False)
+    in_directory = kwargs.get("in_directory", cwd)
+    fail_ok = kwargs.get("fail_ok", False)
 
     try:
         status = -1
         oldargs = sys.argv
         sys.argv = sysargs
 
         oldin = None
-        if 'stdin_data' in kwargs:
-            oldin, sys.stdin = sys.stdin, StringIO(kwargs['stdin_data'])
+        if "stdin_data" in kwargs:
+            oldin, sys.stdin = sys.stdin, StringIO(kwargs["stdin_data"])
 
         oldout, olderr = sys.stdout, sys.stderr
         sys.stdout = StringIO()
@@ -119,8 +137,8 @@ def runscript(scriptname, args, **kwargs):
         os.chdir(in_directory)
 
         try:
-            print('running:', scriptname, 'in:', in_directory, file=oldout)
-            print('arguments', sysargs, file=oldout)
+            print("running:", scriptname, "in:", in_directory, file=oldout)
+            print("arguments", sysargs, file=oldout)
 
             status = _runscript(scriptname)
         except SystemExit as err:
@@ -150,7 +168,7 @@ def runscript(scriptname, args, **kwargs):
 
 class TempDirectory(object):
     def __init__(self):
-        self.tempdir = tempfile.mkdtemp(prefix='sourmashtest_')
+        self.tempdir = tempfile.mkdtemp(prefix="sourmashtest_")
 
     def __enter__(self):
         return self.tempdir
@@ -168,7 +186,7 @@ def __exit__(self, exc_type, exc_value, traceback):
 class SourmashCommandFailed(Exception):
     def __init__(self, msg):
         Exception.__init__(self, msg)
-        self.message = msg 
+        self.message = msg
 
 
 class RunnerContext(object):
@@ -181,32 +199,34 @@ class RunnerContext(object):
 
     You can use the 'output' method to build filenames in my temp directory.
     """
+
     def __init__(self, location):
         self.location = location
         self.last_command = None
         self.last_result = None
 
     def run_sourmash(self, *args, **kwargs):
         "Run the sourmash script with the given arguments."
-        kwargs['fail_ok'] = True
-        if 'in_directory' not in kwargs:
-            kwargs['in_directory'] = self.location
+        kwargs["fail_ok"] = True
+        if "in_directory" not in kwargs:
+            kwargs["in_directory"] = self.location
 
-        cmdlist = ['sourmash']
-        cmdlist.extend(( str(x) for x in args))
+        cmdlist = ["sourmash"]
+        cmdlist.extend((str(x) for x in args))
         self.last_command = " ".join(cmdlist)
-        self.last_result = runscript('sourmash', args, **kwargs)
+        self.last_result = runscript("sourmash", args, **kwargs)
 
         if self.last_result.status:
             raise SourmashCommandFailed(self.last_result.err)
 
         return self.last_result
+
     sourmash = run_sourmash
 
     def run(self, scriptname, *args, **kwargs):
         "Run a script with the given arguments."
-        if 'in_directory' not in kwargs:
-            kwargs['in_directory'] = self.location
+        if "in_directory" not in kwargs:
+            kwargs["in_directory"] = self.location
         self.last_command = " ".join(args)
         self.last_result = runscript(scriptname, args, **kwargs)
         return self.last_result
@@ -224,11 +244,11 @@ def __str__(self):
                 if self.last_result.out:
                     s += "- stdout:\n---\n{}---\n".format(self.last_result.out)
                 else:
-                    s += '(no stdout)\n\n'
+                    s += "(no stdout)\n\n"
                 if self.last_result.err:
                     s += "- stderr:\n---\n{}---\n".format(self.last_result.err)
                 else:
-                    s += '(no stderr)\n'
+                    s += "(no stderr)\n"
 
         return s