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From: Andreas Tille <tille@debian.org>
Date: Fri, 6 Dec 2024 10:36:57 +0100
Subject: Fix Python3.12 string syntax
Bug-Debian: https://bugs.debian.org/1085366
Last-Update: 2024-12-06
Forwarded: https://github.com/AllenInstitute/bmtk/pull/406
---
bmtk/simulator/bionet/modules/comsol.py | 4 ++--
bmtk/simulator/filternet/lgnmodel/util_fns.py | 2 +-
bmtk/utils/io/cell_vars.py | 2 +-
bmtk/utils/sonata/config/sonata_config.py | 2 +-
4 files changed, 5 insertions(+), 5 deletions(-)
diff --git a/bmtk/simulator/bionet/modules/comsol.py b/bmtk/simulator/bionet/modules/comsol.py
index 6e152e8..f8f6793 100644
--- a/bmtk/simulator/bionet/modules/comsol.py
+++ b/bmtk/simulator/bionet/modules/comsol.py
@@ -174,9 +174,9 @@ class ComsolMod(SimulatorMod):
"""
# Extract column headers and data from comsol_file
- headers = pd.read_csv(comsol_file, sep="\s{3,}", header=None, skiprows=8, nrows=1, engine='python')
+ headers = pd.read_csv(comsol_file, sep=r"\s{3,}", header=None, skiprows=8, nrows=1, engine='python')
headers = headers.to_numpy()[0]
- data = pd.read_csv(comsol_file, sep="\s+", header=None, skiprows=9)
+ data = pd.read_csv(comsol_file, sep=r"\s+", header=None, skiprows=9)
# Convert V to mV if necessary
if headers[3][3] == 'V':
diff --git a/bmtk/simulator/filternet/lgnmodel/util_fns.py b/bmtk/simulator/filternet/lgnmodel/util_fns.py
index c66025c..9a8801d 100644
--- a/bmtk/simulator/filternet/lgnmodel/util_fns.py
+++ b/bmtk/simulator/filternet/lgnmodel/util_fns.py
@@ -48,7 +48,7 @@ def create_ff_mov(frame_rate, tst, tend, xrng, yrng):
##################################################
def create_grating_movie_list(gr_dir_name):
gr_fnames = os.listdir(gr_dir_name)
- gr_fnames_ord = sorted(gr_fnames, key=lambda x: (int(re.sub('\D', '', x)), x))
+ gr_fnames_ord = sorted(gr_fnames, key=lambda x: (int(re.sub(r'\D', '', x)), x))
gr_mov_list = []
for fname in gr_fnames_ord[:5]:
diff --git a/bmtk/utils/io/cell_vars.py b/bmtk/utils/io/cell_vars.py
index 76c04b0..30c6452 100644
--- a/bmtk/utils/io/cell_vars.py
+++ b/bmtk/utils/io/cell_vars.py
@@ -16,7 +16,7 @@ class CellVarRecorder(object):
_io = io
class DataTable(object):
- """A small struct to keep track of different \*/data (and buffer) tables"""
+ """A small struct to keep track of different data (and buffer) tables"""
def __init__(self, var_name):
self.var_name = var_name
# If buffering data, buffer_block will be an in-memory array and will write to data_block during when
diff --git a/bmtk/utils/sonata/config/sonata_config.py b/bmtk/utils/sonata/config/sonata_config.py
index 91906fa..f695ebe 100644
--- a/bmtk/utils/sonata/config/sonata_config.py
+++ b/bmtk/utils/sonata/config/sonata_config.py
@@ -397,7 +397,7 @@ class ConfigParser(object):
:return: json rvalue with resolved variables. Won't resolve variables that don't exist in manifest.
"""
ret_val = json_str
- variables = [m for m in re.finditer('\$\{?[\w]+\}?', json_str)]
+ variables = [m for m in re.finditer(r'\$\{?[\w]+\}?', json_str)]
for var in variables:
var_key = var.group()
# change $VAR or ${VAR} --> VAR
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