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Rename load_file_list_of_signatures to load_pathlist_from_file #1423

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merged 8 commits into from
Apr 2, 2021
Merged

Rename load_file_list_of_signatures to load_pathlist_from_file #1423

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81b3290
Add ORCID to checklist
keyabarve Mar 23, 2021
c38309e
Changes made to ORCID checklist
keyabarve Mar 26, 2021
a23abae
Made a small change to ORCID checklist
keyabarve Mar 26, 2021
def0971
Merge branch 'latest' of https://github.com/dib-lab/sourmash into ORC…
keyabarve Mar 29, 2021
be6cc44
Markdown issue fixed.
keyabarve Mar 29, 2021
fb5e231
Rename all instances of load_file_list_of_signatures
keyabarve Mar 30, 2021
ae30a1c
Merge branch 'latest' of https://github.com/dib-lab/sourmash into Ren…
keyabarve Apr 1, 2021
b97be02
Merge branch 'latest' into RenameIssue1369
ctb Apr 1, 2021
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4 changes: 2 additions & 2 deletions src/sourmash/command_sketch.py
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Original file line number Diff line number Diff line change
Expand Up @@ -154,9 +154,9 @@ def __call__(self):

def _add_from_file_to_filenames(args):
"Add filenames from --from-file to args.filenames"
from .sourmash_args import load_file_list_of_signatures
from .sourmash_args import load_pathlist_from_file
if args.from_file:
file_list = load_file_list_of_signatures(args.from_file)
file_list = load_pathlist_from_file(args.from_file)
args.filenames.extend(file_list)


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6 changes: 3 additions & 3 deletions src/sourmash/commands.py
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Original file line number Diff line number Diff line change
Expand Up @@ -33,7 +33,7 @@ def compare(args):

inp_files = list(args.signatures)
if args.from_file:
more_files = sourmash_args.load_file_list_of_signatures(args.from_file)
more_files = sourmash_args.load_pathlist_from_file(args.from_file)
inp_files.extend(more_files)

progress = sourmash_args.SignatureLoadingProgress()
Expand Down Expand Up @@ -353,7 +353,7 @@ def index(args):

inp_files = list(args.signatures)
if args.from_file:
more_files = sourmash_args.load_file_list_of_signatures(args.from_file)
more_files = sourmash_args.load_pathlist_from_file(args.from_file)
inp_files.extend(more_files)

if not inp_files:
Expand Down Expand Up @@ -725,7 +725,7 @@ def multigather(args):
args.db = [item for sublist in args.db for item in sublist]
inp_files = [item for sublist in args.query for item in sublist]
if args.query_from_file:
more_files = sourmash_args.load_file_list_of_signatures(args.query_from_file)
more_files = sourmash_args.load_pathlist_from_file(args.query_from_file)
inp_files.extend(more_files)

# need a query to get ksize, moltype for db loading
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2 changes: 1 addition & 1 deletion src/sourmash/lca/command_classify.py
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Expand Up @@ -101,7 +101,7 @@ def classify(args):
notify('finding query signatures...')
inp_files = list(args.query)
if args.query_from_file:
more_files = sourmash_args.load_file_list_of_signatures(args.query_from_file)
more_files = sourmash_args.load_pathlist_from_file(args.query_from_file)
inp_files.extend(more_files)

if not check_files_exist(*inp_files):
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2 changes: 1 addition & 1 deletion src/sourmash/lca/command_index.py
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Expand Up @@ -168,7 +168,7 @@ def index(args):

inp_files = list(args.signatures)
if args.from_file:
more_files = sourmash_args.load_file_list_of_signatures(args.from_file)
more_files = sourmash_args.load_pathlist_from_file(args.from_file)
inp_files.extend(more_files)

# track duplicates
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2 changes: 1 addition & 1 deletion src/sourmash/lca/command_summarize.py
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Original file line number Diff line number Diff line change
Expand Up @@ -181,7 +181,7 @@ def summarize_main(args):
inp_files = args.query

if args.query_from_file:
more_files = sourmash_args.load_file_list_of_signatures(args.query_from_file)
more_files = sourmash_args.load_pathlist_from_file(args.query_from_file)
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please create a new issue for testing --query-from-file for sourmash lca summarize - thanks!

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(because our current tests don't execute this, apparently!)

inp_files.extend(more_files)

if not inp_files:
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4 changes: 2 additions & 2 deletions src/sourmash/sourmash_args.py
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Expand Up @@ -385,7 +385,7 @@ def _load_database(filename, traverse_yield_all, *, cache_size=None):
idx_list = []
src_list = []

file_list = load_file_list_of_signatures(filename)
file_list = load_pathlist_from_file(filename)
for fname in file_list:
idx = load_file_as_index(fname)
src = fname
Expand Down Expand Up @@ -485,7 +485,7 @@ def load_file_as_signatures(filename, select_moltype=None, ksize=None,
return loader


def load_file_list_of_signatures(filename):
def load_pathlist_from_file(filename):
"Load a list-of-files text file."
try:
with open(filename, 'rt') as fp:
Expand Down