diff --git a/.travis.yml b/.travis.yml
index a604df641f8a7689cf4b4ef7e4004fb03c674e23..0d555b54df85c8fe42c1a3de0772d34002860cdc 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -132,7 +132,7 @@ install:
if [[ "$WITH_PYTHON" == "true" ]]; then
curl https://bootstrap.pypa.io/get-pip.py -o get-pip.py
python$PY get-pip.py
- pip --version
+ pip$PY --version
fi
- if [[ ( "$WITH_PYTHON" == "true" ) && ( "$TRAVIS_OS_NAME" == "osx" ) ]]; then pip$PY install numpy; fi
- |
diff --git a/ci/codecov/build.Dockerfile b/ci/codecov/build.Dockerfile
index 1cb095e3e1c544bfc44c04ac0f8e6ef8582397da..23f9e621b0d2966ce67efdab1652152ffa348728 100644
--- a/ci/codecov/build.Dockerfile
+++ b/ci/codecov/build.Dockerfile
@@ -11,12 +11,12 @@ ENV MPICH_VERSION ${MPICH_VERSION}
# Install basic tools
RUN apt-get update -qq && apt-get install -qq -y --no-install-recommends \
build-essential lcov \
- python \
+ python3 \
git tar wget curl && \
rm -rf /var/lib/apt/lists/*
# Install cmake
-RUN wget -qO- "https://cmake.org/files/v3.17/cmake-3.17.0-Linux-x86_64.tar.gz" | tar --strip-components=1 -xz -C /usr/local
+RUN wget -qO- "https://github.com/Kitware/CMake/releases/download/v3.12.4/cmake-3.12.4-Linux-x86_64.tar.gz" | tar --strip-components=1 -xz -C /usr/local
# Install MPICH ABI compatible with Cray's lib on Piz Daint
RUN wget -q https://www.mpich.org/static/downloads/${MPICH_VERSION}/mpich-${MPICH_VERSION}.tar.gz && \
@@ -27,7 +27,7 @@ RUN wget -q https://www.mpich.org/static/downloads/${MPICH_VERSION}/mpich-${MPIC
rm -rf mpich-${MPICH_VERSION}.tar.gz mpich-${MPICH_VERSION}
# Install bundle tooling for creating small Docker images
-RUN wget -q https://github.com/haampie/libtree/releases/download/v1.1.3/libtree_x86_64.tar.gz && \
+RUN wget -q https://github.com/haampie/libtree/releases/download/v1.2.0/libtree_x86_64.tar.gz && \
tar -xzf libtree_x86_64.tar.gz && \
rm libtree_x86_64.tar.gz && \
ln -s /root/libtree/libtree /usr/local/bin/libtree
\ No newline at end of file
diff --git a/ci/release/build.Dockerfile b/ci/release/build.Dockerfile
index 67ba8be8aa21edc61f52bdbd9659f2675714be1e..4c17a820e44a2e5fc5d9d66d0fd0f6fe2e8b8888 100644
--- a/ci/release/build.Dockerfile
+++ b/ci/release/build.Dockerfile
@@ -11,12 +11,12 @@ ENV MPICH_VERSION ${MPICH_VERSION}
# Install basic tools
RUN apt-get update -qq && apt-get install -qq -y --no-install-recommends \
build-essential \
- python \
+ python3 \
git tar wget curl && \
rm -rf /var/lib/apt/lists/*
# Install cmake
-RUN wget -qO- "https://cmake.org/files/v3.17/cmake-3.17.0-Linux-x86_64.tar.gz" | tar --strip-components=1 -xz -C /usr/local
+RUN wget -qO- "https://github.com/Kitware/CMake/releases/download/v3.12.4/cmake-3.12.4-Linux-x86_64.tar.gz" | tar --strip-components=1 -xz -C /usr/local
# Install MPICH ABI compatible with Cray's lib on Piz Daint
RUN wget -q https://www.mpich.org/static/downloads/${MPICH_VERSION}/mpich-${MPICH_VERSION}.tar.gz && \
@@ -27,7 +27,7 @@ RUN wget -q https://www.mpich.org/static/downloads/${MPICH_VERSION}/mpich-${MPIC
rm -rf mpich-${MPICH_VERSION}.tar.gz mpich-${MPICH_VERSION}
# Install bundle tooling for creating small Docker images
-RUN wget -q https://github.com/haampie/libtree/releases/download/v1.1.3/libtree_x86_64.tar.gz && \
+RUN wget -q https://github.com/haampie/libtree/releases/download/v1.2.0/libtree_x86_64.tar.gz && \
tar -xzf libtree_x86_64.tar.gz && \
rm libtree_x86_64.tar.gz && \
- ln -s /root/libtree/libtree /usr/local/bin/libtree
\ No newline at end of file
+ ln -s /root/libtree/libtree /usr/local/bin/libtree
diff --git a/example/lfp/plot-lfp.py b/example/lfp/plot-lfp.py
index 14ddde3eacd33da10de67a8879498c2d21eb6001..bbbeff05be3109880c5859f073407fe5cfe01ba8 100755
--- a/example/lfp/plot-lfp.py
+++ b/example/lfp/plot-lfp.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/env python3
import argparse
import matplotlib.pyplot as plt
diff --git a/scripts/compare_spike_trains.py b/scripts/compare_spike_trains.py
index 597ce1b9100b94763026bd60eaddc910a2abb2c9..c2bbb4088d18b7f13689a359de3bf4efb18a1501 100644
--- a/scripts/compare_spike_trains.py
+++ b/scripts/compare_spike_trains.py
@@ -1,10 +1,11 @@
-#!/usr/bin/env python
+#!/usr/bin/env python3
import os
import sys
import collections
+from itertools import zip_longest
def usage(default_delta):
- print ("""
+ print("""
compare two input spike time files on equality with a delta of max_delta
order of the spikes is not important. GID should always be equal
Display the first 50 differences encountered.
@@ -36,9 +37,9 @@ def parse_file(path):
gid = int(split_items[0].strip())
time = float(split_items[1].strip())
except:
- print "Could not parse a line in the file!!!! \n"
- print " line: " , line_idx, ": ", stripped_line
- print path
+ print("Could not parse a line in the file!!!! \n")
+ print(" line: " , line_idx, ": ", stripped_line)
+ print(path)
exit(1) #failure
@@ -59,20 +60,20 @@ def compare(path1, data1, path2, data2, delta):
"""
combined_data = collections.defaultdict(lambda : [[],[]])
- for gid, spike_data in data1.items():
+ for gid, spike_data in list(data1.items()):
combined_data[gid][0].extend(spike_data)
- for gid, spike_data in data2.items():
+ for gid, spike_data in list(data2.items()):
combined_data[gid][1].extend(spike_data)
different_spikes = []
- for gid, (data_1, data_2)in combined_data.items():
+ for gid, (data_1, data_2)in list(combined_data.items()):
gid_list1 = data_1
gid_list2 = data_2
if len(gid_list1) != len(gid_list2):
- for idx, (time1, time2) in enumerate(map(None, gid_list1, gid_list2)):
+ for idx, (time1, time2) in enumerate(zip_longest(gid_list1, gid_list2)):
# We have to loop all spikes, check here if we have missing spikes
# and treat those different
if time1 == None or time2 == None:
@@ -93,18 +94,18 @@ def compare(path1, data1, path2, data2, delta):
different_spikes.append((gid, time1, time2))
if len(different_spikes) != 0:
- print "Found difference in spike times, displaying first 50 \n"
- print "key == (line_nr, spike_time, content line parsed)\n"
- print "difference #, gid : target output != simulation output"
+ print("Found difference in spike times, displaying first 50 \n")
+ print("key == (line_nr, spike_time, content line parsed)\n")
+ print("difference #, gid : target output != simulation output")
for idx, (gid, time1, time2) in enumerate(different_spikes):
if idx == 50:
break
dif_str = "difference #{0}, {3}: {1} != {2}".format(idx, time1, time2, gid)
- print dif_str
+ print(dif_str)
- print "\n\n"
+ print("\n\n")
# Also output to file (could be done in previous loop, but seperation
diff --git a/scripts/print_backtrace b/scripts/print_backtrace
index bca8a5bc6fb4dee1bf8e336ab23f5c2807105f84..ecba7600ef2cb5ce245dbdb39692d7a3d7c964d0 100755
--- a/scripts/print_backtrace
+++ b/scripts/print_backtrace
@@ -1,4 +1,4 @@
-#!/usr/bin/env python2
+#!/usr/bin/env python3
#coding: utf-8
import argparse
@@ -54,7 +54,7 @@ def parse_backtrace(source):
tokens = line.split()
trace.append({'location':tokens[0], 'function':tokens[1]})
else:
- print "error: unable to open back trace file ", source
+ print("error: unable to open back trace file ", source)
return trace
@@ -75,7 +75,7 @@ args = parse_clargs()
# check that a valid executable was provided
executable = args.executable
if not os.path.isfile(executable):
- print "error:", executable, "is not a valid executable"
+ print("error:", executable, "is not a valid executable")
else:
for frame in parse_backtrace(args.input):
location = get_function_name(frame['location'], executable)
@@ -84,6 +84,6 @@ else:
fname = c.yellow + location['filename'] + c.end
line = c.cyan + location['line'] + c.end
if args.brief:
- print fname + ':' + line
+ print(fname + ':' + line)
else:
- print fname + ':' + line, '\n ', name
+ print(fname + ':' + line, '\n ', name)
diff --git a/scripts/tsplot b/scripts/tsplot
index 3207dcb9590977227a0e5007759ac0a7aae74968..c64e7b18160bf78f90b25099e91fde6a042a2a0d 100755
--- a/scripts/tsplot
+++ b/scripts/tsplot
@@ -1,8 +1,6 @@
-#!/usr/bin/env python
+#!/usr/bin/env python3
#coding: utf-8
-from __future__ import print_function
-
import argparse
import json
import numpy as np
@@ -84,7 +82,7 @@ def parse_clargs():
return P.parse_args(argsbis)
def isstring(s):
- return isinstance(s,str) or isinstance(s,unicode)
+ return isinstance(s,str)
def take(n, s):
return islice((i for i in s), 0, n)
@@ -225,7 +223,7 @@ def read_json_timeseries(j, axis='time', select=[]):
return ""
i = 1
- for key in jdata.keys():
+ for key in list(jdata.keys()):
if key==axis: continue
meta = j.copy()
@@ -278,7 +276,7 @@ class PlotData:
return labels
n = len(labels)
- keyset = reduce(lambda k, s: k.union(s.meta.keys()), self.series, set())
+ keyset = reduce(lambda k, s: k.union(list(s.meta.keys())), self.series, set())
keyi = iter(keyset)
try:
while len(set(labels)) != n:
@@ -293,7 +291,7 @@ class PlotData:
for i in range(n):
prefix = '' if k=='name' else k+'='
if vs[i] is not None:
- labels[i] += u', '+k+u'='+unicode(formatter(vs[i]))
+ labels[i] += ', '+k+'='+str(formatter(vs[i]))
except StopIteration:
pass
@@ -310,7 +308,7 @@ def gather_ts_plots(tss, groupby):
for ts in tss:
key = tuple([ts.meta.get(g) for g in groupby])
if key is () or None in key or key not in group_lookup:
- pretty_key=', '.join([unicode(k)+u'='+unicode(v) for k,v in zip(groupby, key) if v is not None])
+ pretty_key=', '.join([str(k)+'='+str(v) for k,v in zip(groupby, key) if v is not None])
pd = PlotData(pretty_key)
pd.series = [ts]
plot_groups.append(pd)
diff --git a/validation/ref/neuron/ball_and_3stick.py b/validation/ref/neuron/ball_and_3stick.py
index 473fbda9e33aa113fd27fde638fdf2da466a6e30..a14ae07392bab81140eecd46096bdb242c1733db 100644
--- a/validation/ref/neuron/ball_and_3stick.py
+++ b/validation/ref/neuron/ball_and_3stick.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/env python3
#coding: utf-8
import json
diff --git a/validation/ref/neuron/ball_and_squiggle.py b/validation/ref/neuron/ball_and_squiggle.py
index 9fcc5b49c5affdb5600437a500f50d8c0f20fb6d..b69bc2ece2726070bd551a4c8537bd130a833367 100644
--- a/validation/ref/neuron/ball_and_squiggle.py
+++ b/validation/ref/neuron/ball_and_squiggle.py
@@ -1,15 +1,10 @@
-#!/usr/bin/env python
+#!/usr/bin/env python3
#coding: utf-8
import json
import math
import nrn_validation as V
-try:
- from builtins import range
-except ImportError:
- from __builtin__ import range
-
V.override_defaults_from_args()
# dendrite geometry: 100 µm long, varying diameter.
diff --git a/validation/ref/neuron/ball_and_stick.py b/validation/ref/neuron/ball_and_stick.py
index 52378e64e9f3163aa30332acfc50b3cee66e6faf..93cc097eb07c05b13e00108e68534bcccb5762ac 100644
--- a/validation/ref/neuron/ball_and_stick.py
+++ b/validation/ref/neuron/ball_and_stick.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/env python3
#coding: utf-8
import json
diff --git a/validation/ref/neuron/ball_and_taper.py b/validation/ref/neuron/ball_and_taper.py
index 13961c0e62b57bc1bc9c8ba901e8f1b7e11c60d6..7c351021220dd8609a533cc1bdd863daeba2aba7 100644
--- a/validation/ref/neuron/ball_and_taper.py
+++ b/validation/ref/neuron/ball_and_taper.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/env python3
#coding: utf-8
import json
diff --git a/validation/ref/neuron/nrn_validation.py b/validation/ref/neuron/nrn_validation.py
index a924937474c3c7988a87569746da21fa35d01dea..5370a077b072ec9ee766abddc468f0a8c10bda90 100644
--- a/validation/ref/neuron/nrn_validation.py
+++ b/validation/ref/neuron/nrn_validation.py
@@ -1,7 +1,6 @@
-#!/usr/bin/env python
+#!/usr/bin/env python3
#coding: utf-8
-import json
import sys
import os
import re
@@ -9,11 +8,6 @@ import numpy as np
import neuron
from neuron import h
-try:
- from builtins import range
-except ImportError:
- from __builtin__ import range
-
# This is super annoying: without neuron.gui, need
# to explicit load 'standard' hoc routines like 'run',
# but this is chatty on stdout, which means we get
@@ -55,7 +49,7 @@ default_model_parameters = {
def override_defaults_from_args(args=sys.argv):
global default_model_parameters
- keys = default_model_parameters.keys()
+ keys = list(default_model_parameters.keys())
r = re.compile('('+'|'.join(keys)+')=(.*)')
for m in [r.match(a) for a in args]:
if m:
@@ -77,7 +71,7 @@ class VModel:
self.netcons = []
def set_ncomp(self, n):
- for s in self.sections.values():
+ for s in list(self.sections.values()):
s.nseg = int(n)
def add_iclamp(self, t0, dt, i, to=None, pos=1):
diff --git a/validation/ref/neuron/simple_exp2_synapse.py b/validation/ref/neuron/simple_exp2_synapse.py
index c2314e7619cde5fcfbef583437237546ee3ff043..bbaaa0688cf603d6ba8d7ec27b520ff6b508cdf2 100644
--- a/validation/ref/neuron/simple_exp2_synapse.py
+++ b/validation/ref/neuron/simple_exp2_synapse.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/env python3
#coding: utf-8
import json
diff --git a/validation/ref/neuron/simple_exp_synapse.py b/validation/ref/neuron/simple_exp_synapse.py
index 587317faaa785491caa640ae5069f9202bacb968..e83a7051dc14a2a0df484fa592a91a4271049af5 100644
--- a/validation/ref/neuron/simple_exp_synapse.py
+++ b/validation/ref/neuron/simple_exp_synapse.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/env python3
#coding: utf-8
import json
diff --git a/validation/ref/neuron/soma.py b/validation/ref/neuron/soma.py
index 393d898cf20fcac084125e89392182b87dc424f3..372f420732ab294f3cfebacbc1ffae3042a78b5d 100644
--- a/validation/ref/neuron/soma.py
+++ b/validation/ref/neuron/soma.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/env python3
#coding: utf-8
import json