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grass.script.db: Close opened file in db_connection #201

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grass.script.db: Close opened file in db_connection #201

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261769d
grass.script.db: Close opened file in db_connection
echoix Aug 24, 2024
1ca0c19
t.unregister: Use a context manager for opening files (SIM115)
echoix Aug 24, 2024
7a98608
t.remove: Use a context manager for opening files (SIM115)
echoix Aug 24, 2024
7963689
t.rast.what: Use a context manager for opening files (SIM115)
echoix Aug 24, 2024
a31c297
grass.temporal.aggregation: Use a context manager for opening files (…
echoix Aug 24, 2024
bb2e999
Apply suggestions from code review
echoix Aug 26, 2024
f7a60ec
Update t.rast.what.py
echoix Aug 26, 2024
7c2df57
Merge branch 'main' into fix-resourcewarning-1
echoix Sep 7, 2024
53e28d7
Merge remote-tracking branch 'origin/main' into fix-resourcewarning-1
echoix Sep 18, 2024
6a751c9
Merge branch 'main' into fix-resourcewarning-1
echoix Oct 17, 2024
71bc611
Move line out of context manager
echoix Oct 17, 2024
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5 changes: 2 additions & 3 deletions python/grass/script/db.py
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Original file line number Diff line number Diff line change
Expand Up @@ -127,9 +127,8 @@ def db_connection(force=False, env=None):
:return: parsed output of db.connect
""" # noqa: E501
try:
nuldev = open(os.devnull, "w")
conn = parse_command("db.connect", flags="g", stderr=nuldev, env=env)
nuldev.close()
with open(os.devnull, "w") as nuldev:
conn = parse_command("db.connect", flags="g", stderr=nuldev, env=env)
except CalledModuleError:
conn = None

Expand Down
19 changes: 8 additions & 11 deletions python/grass/temporal/aggregation.py
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Original file line number Diff line number Diff line change
Expand Up @@ -168,13 +168,11 @@ def aggregate_raster_maps(

# Create the r.series input file
filename = gs.tempfile(True)
file = open(filename, "w")
with open(filename, "w") as out_file:
for name in inputs:
string = "%s\n" % (name)
out_file.write(string)

for name in inputs:
string = "%s\n" % (name)
file.write(string)

file.close()
# Run r.series
try:
if len(inputs) > 1000:
Expand Down Expand Up @@ -365,11 +363,10 @@ def aggregate_by_topology(
if len(aggregation_list) > 1:
# Create the r.series input file
filename = gs.tempfile(True)
file = open(filename, "w")
for name in aggregation_list:
string = "%s\n" % (name)
file.write(string)
file.close()
with open(filename, "w") as out_file:
for name in aggregation_list:
string = "%s\n" % (name)
out_file.write(string)

mod = copy.deepcopy(r_series)
mod(file=filename, output=output_name)
Expand Down
286 changes: 137 additions & 149 deletions temporal/t.rast.what/t.rast.what.py
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Original file line number Diff line number Diff line change
Expand Up @@ -373,78 +373,72 @@ def one_point_per_row_output(
output is of type: x,y,start,end,value
"""
# open the output file for writing
out_file = open(output, "w") if output != "-" else sys.stdout

if write_header is True:
out_str = ""
if vcat:
out_str += "cat{sep}"
if site_input:
out_str += "x{sep}y{sep}site{sep}start{sep}end{sep}value\n"
else:
out_str += "x{sep}y{sep}start{sep}end{sep}value\n"
out_file.write(out_str.format(sep=separator))

for count in range(len(output_files)):
file_name = output_files[count]
gs.verbose(_("Transforming r.what output file %s" % (file_name)))
map_list = output_time_list[count]
in_file = open(file_name, "r")
for line in in_file:
line = line.split(separator)
with open(output, "w") if output != "-" else sys.stdout as out_file:
if write_header is True:
out_str = ""
if vcat:
cat = line[0]
x = line[1]
y = line[2]
values = line[4:]
if site_input:
site = line[3]
values = line[5:]

out_str += "cat{sep}"
if site_input:
out_str += "x{sep}y{sep}site{sep}start{sep}end{sep}value\n"
else:
x = line[0]
y = line[1]
if site_input:
site = line[2]
values = line[3:]
out_str += "x{sep}y{sep}start{sep}end{sep}value\n"
out_file.write(out_str.format(sep=separator))

for count in range(len(output_files)):
file_name = output_files[count]
gs.verbose(_("Transforming r.what output file %s" % (file_name)))
map_list = output_time_list[count]
with open(file_name) as in_file:
for line in in_file:
line = line.split(separator)
if vcat:
cat = line[0]
x = line[1]
y = line[2]
values = line[4:]
if site_input:
site = line[3]
values = line[5:]

for i in range(len(values)):
start, end = map_list[i].get_temporal_extent_as_tuple()
if vcat:
cat_str = "{ca}{sep}".format(ca=cat, sep=separator)
else:
cat_str = ""
if site_input:
coor_string = (
"%(x)10.10f%(sep)s%(y)10.10f%(sep)s%(site_name)s%(sep)s"
% (
else:
x = line[0]
y = line[1]
if site_input:
site = line[2]
values = line[3:]

for i in range(len(values)):
start, end = map_list[i].get_temporal_extent_as_tuple()
if vcat:
cat_str = "{ca}{sep}".format(ca=cat, sep=separator)
else:
cat_str = ""
if site_input:
coor_string = (
"%(x)10.10f%(sep)s%(y)10.10f%(sep)s%(site_name)s%(sep)s"
% (
{
"x": float(x),
"y": float(y),
"site_name": str(site),
"sep": separator,
}
)
)
else:
coor_string = "%(x)10.10f%(sep)s%(y)10.10f%(sep)s" % (
{"x": float(x), "y": float(y), "sep": separator}
)
time_string = "%(start)s%(sep)s%(end)s%(sep)s%(val)s\n" % (
{
"x": float(x),
"y": float(y),
"site_name": str(site),
"start": str(start),
"end": str(end),
"val": (values[i].strip()),
"sep": separator,
}
)
)
else:
coor_string = "%(x)10.10f%(sep)s%(y)10.10f%(sep)s" % (
{"x": float(x), "y": float(y), "sep": separator}
)
time_string = "%(start)s%(sep)s%(end)s%(sep)s%(val)s\n" % (
{
"start": str(start),
"end": str(end),
"val": (values[i].strip()),
"sep": separator,
}
)

out_file.write(cat_str + coor_string + time_string)

in_file.close()

if out_file is not sys.stdout:
out_file.close()
out_file.write(cat_str + coor_string + time_string)


############################################################################
Expand All @@ -460,84 +454,82 @@ def one_point_per_col_output(
Each row represents a single raster map, hence a single time stamp
"""
# open the output file for writing
out_file = open(output, "w") if output != "-" else sys.stdout

first = True
for count in range(len(output_files)):
file_name = output_files[count]
gs.verbose(_("Transforming r.what output file %s" % (file_name)))
map_list = output_time_list[count]
in_file = open(file_name, "r")
lines = in_file.readlines()
with open(output, "w") if output != "-" else sys.stdout as out_file:
for count in range(len(output_files)):
file_name = output_files[count]
gs.verbose(_("Transforming r.what output file %s" % (file_name)))
map_list = output_time_list[count]
with open(file_name) as in_file:
lines = in_file.readlines()

matrix = []
for line in lines:
matrix.append(line.split(separator))
matrix = []
for line in lines:
matrix.append(line.split(separator))

num_cols = len(matrix[0])

if first is True:
if write_header is True:
out_str = "start%(sep)send" % ({"sep": separator})
num_cols = len(matrix[0])

# Define different separator for coordinates and sites
if separator == ",":
coor_sep = ";"
else:
coor_sep = ","
if first is True:
if write_header is True:
out_str = "start%(sep)send" % ({"sep": separator})

for row in matrix:
if vcat:
cat = row[0]
x = row[1]
y = row[2]
out_str += (
"{sep}{cat}{csep}{x:10.10f}{csep}"
"{y:10.10f}".format(
cat=cat,
x=float(x),
y=float(y),
sep=separator,
csep=coor_sep,
)
)
if site_input:
site = row[3]
out_str += "{sep}{site}".format(sep=coor_sep, site=site)
# Define different separator for coordinates and sites
if separator == ",":
coor_sep = ";"
else:
x = row[0]
y = row[1]
out_str += "{sep}{x:10.10f}{csep}{y:10.10f}".format(
x=float(x), y=float(y), sep=separator, csep=coor_sep
)
if site_input:
site = row[2]
out_str += "{sep}{site}".format(sep=coor_sep, site=site)
coor_sep = ","

for row in matrix:
if vcat:
cat = row[0]
x = row[1]
y = row[2]
out_str += (
"{sep}{cat}{csep}{x:10.10f}{csep}"
"{y:10.10f}".format(
cat=cat,
x=float(x),
y=float(y),
sep=separator,
csep=coor_sep,
)
)
if site_input:
site = row[3]
out_str += "{sep}{site}".format(sep=coor_sep, site=site)
else:
x = row[0]
y = row[1]
out_str += "{sep}{x:10.10f}{csep}{y:10.10f}".format(
x=float(x), y=float(y), sep=separator, csep=coor_sep
)
if site_input:
site = row[2]
out_str += "{sep}{site}".format(sep=coor_sep, site=site)

out_file.write(out_str + "\n")
out_file.write(out_str + "\n")

first = False
first = False

if vcat:
ncol = 4
else:
ncol = 3
for col in range(num_cols - ncol):
start, end = output_time_list[count][col].get_temporal_extent_as_tuple()
time_string = "%(start)s%(sep)s%(end)s" % (
{"start": str(start), "end": str(end), "sep": separator}
)
out_file.write(time_string)
for row in range(len(matrix)):
value = matrix[row][col + ncol]
out_file.write(
"%(sep)s%(value)s" % ({"sep": separator, "value": value.strip()})
if vcat:
ncol = 4
else:
ncol = 3
for col in range(num_cols - ncol):
start, end = output_time_list[count][col].get_temporal_extent_as_tuple()
time_string = "%(start)s%(sep)s%(end)s" % (
{"start": str(start), "end": str(end), "sep": separator}
)
out_file.write("\n")
out_file.write(time_string)
for row in range(len(matrix)):
value = matrix[row][col + ncol]
out_file.write(
"%(sep)s%(value)s"
% ({"sep": separator, "value": value.strip()})
)
out_file.write("\n")

in_file.close()
if out_file is not sys.stdout:
out_file.close()


echoix marked this conversation as resolved.
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############################################################################
Expand All @@ -554,7 +546,6 @@ def one_point_per_timerow_output(
3730731.49590371|5642483.51236521|6|8|7|7
3581249.04638104|5634411.97526282|5|8|7|7
""" # noqa: E501
out_file = open(output, "w") if output != "-" else sys.stdout

matrix = []
header = ""
Expand All @@ -564,7 +555,6 @@ def one_point_per_timerow_output(
file_name = output_files[count]
gs.verbose("Transforming r.what output file %s" % (file_name))
map_list = output_time_list[count]
in_file = open(file_name, "r")

if write_header:
if first is True:
Expand All @@ -583,7 +573,8 @@ def one_point_per_timerow_output(
)
header += time_string

lines = in_file.readlines()
with open(file_name) as in_file:
lines = in_file.readlines()

for i in range(len(lines)):
cols = lines[i].split(separator)
Expand All @@ -603,26 +594,23 @@ def one_point_per_timerow_output(

first = False

in_file.close()

if write_header:
out_file.write(header + "\n")
with open(output, "w") if output != "-" else sys.stdout as out_file:
if write_header:
out_file.write(header + "\n")

gs.verbose(_("Writing the output file <%s>" % (output)))
for row in matrix:
first = True
for col in row:
value = col.strip()
gs.verbose(_("Writing the output file <%s>" % (output)))
for row in matrix:
first = True
for col in row:
value = col.strip()

if first is False:
out_file.write("%s" % (separator))
out_file.write(value)
if first is False:
out_file.write("%s" % (separator))
out_file.write(value)

first = False
first = False

out_file.write("\n")
if out_file is not sys.stdout:
out_file.close()
out_file.write("\n")


############################################################################
Expand Down
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