Fix argument order in distribution.unflatten()

CHANGELOG.md

@@ -35,6 +35,10 @@ _Next version_
 ### Fixes
 - Fixed `convert.be2le_state_by_state()` and `convert.le2be_state_by_state()`;
   previously the columns were not permuted
+- Fixed `distribution.unflatten()`, which passed its arguments to
+  `repertoire_shape()` in the wrong order (`(purview, N)` instead of
+  `(range(N), purview)`) and raised `TypeError: argument of type 'int' is not
+  iterable` on every call.
 
 1.2.0
 -----

benchmarks/benchmarks/compute.py

@@ -1,3 +1,4 @@
+# -*- coding: utf-8 -*-
 import copy
 import timeit
 
@@ -9,28 +10,28 @@
 
 class BenchmarkConstellation:
 
-    params = [["parallel", "sequential"], ["basic", "rule154", "fig16"]]
-    param_names = ["mode", "network"]
+    params = [['parallel', 'sequential'], ['basic', 'rule154', 'fig16']]
+    param_names = ['mode', 'network']
     number = 1
     repeat = 1
 
     def setup(self, mode, network):
-        if network == "basic":
+        if network == 'basic':
             self.subsys = examples.basic_subsystem()
-        elif network == "rule154":
+        elif network == 'rule154':
             network = examples.rule154_network()
             state = (1,) * 5
             self.subsys = Subsystem(network, state, network.node_indices)
-        elif network == "fig16":
+        elif network == 'fig16':
             network = examples.fig16()
             state = (0,) * 7
             self.subsys = Subsystem(network, state, network.node_indices)
         else:
             raise ValueError(network)
 
-        if mode == "parallel":
+        if mode == 'parallel':
             config.PARALLEL_CONCEPT_EVALUATION = True
-        elif mode == "sequential":
+        elif mode == 'sequential':
             config.PARALLEL_CONCEPT_EVALUATION = False
         else:
             raise ValueError(mode)
@@ -44,11 +45,11 @@ def time_constellation(self, mode, network):
 class BenchmarkMainComplex:
 
     params = [
-        ["parallel", "sequential"],
-        ["basic", "rule154", "fig16"],
-        ["local", "redis"],
+        ['parallel', 'sequential'],
+        ['basic', 'rule154', 'fig16'],
+        ['local', 'redis'],
     ]
-    param_names = ["mode", "network", "cache"]
+    param_names = ['mode', 'network', 'cache']
 
     # Use `default_timer` (clock time) instead of process time because
     # parallel execution spawns separate processes which are not counted
@@ -63,13 +64,13 @@ class BenchmarkMainComplex:
 
     def setup(self, mode, network, cache):
 
-        if network == "basic":
+        if network == 'basic':
             self.network = examples.basic_network()
             self.state = (0, 1, 1)
-        elif network == "rule154":
+        elif network == 'rule154':
             self.network = examples.rule154_network()
             self.state = (0, 1, 0, 1, 1)
-        elif network == "fig16":
+        elif network == 'fig16':
             self.network = examples.fig16()
             self.state = (1, 0, 0, 1, 1, 1, 0)
         else:
@@ -79,17 +80,17 @@ def setup(self, mode, network, cache):
         self.default_config = copy.copy(config.__dict__)
 
         # Execution mode
-        if mode == "parallel":
+        if mode == 'parallel':
             config.PARALLEL_CUT_EVALUATION = True
-        elif mode == "sequential":
+        elif mode == 'sequential':
             config.PARALLEL_CUT_EVALUATION = False
         else:
             raise ValueError(mode)
 
         # Cache mode
-        if cache == "local":
+        if cache == 'local':
             config.REDIS_CACHE = False
-        elif cache == "redis":
+        elif cache == 'redis':
             config.REDIS_CACHE = True
             if _cache.RedisConn().ping() is False:
                 # No server running

benchmarks/benchmarks/emd.py

@@ -1,3 +1,4 @@
+# -*- coding: utf-8 -*-
 
 import os
 

benchmarks/benchmarks/subsystem.py

@@ -1,3 +1,4 @@
+# -*- coding: utf-8 -*-
 import copy
 
 from pyphi import Subsystem, compute, config, examples

benchmarks/benchmarks/tpm.py

@@ -14,8 +14,8 @@
 
 class SimulateTPM:
     def setup(self):
-        test_data = Path(__file__).resolve().parent / "../../test/data"
-        self.tpm = np.load(test_data / "ising_tpm.npy")
+        test_data = Path(__file__).resolve().parent / '../../test/data'
+        self.tpm = np.load(test_data / 'ising_tpm.npy')
 
         seed_sequence = np.random.SeedSequence(ENTROPY)
         self.rng = np.random.default_rng(seed_sequence)

benchmarks/benchmarks/utils.py

@@ -1,3 +1,4 @@
+# -*- coding: utf-8 -*-
 import numpy as np
 
 from pyphi import utils

benchmarks/time_emd.py

@@ -1,3 +1,4 @@
+# -*- coding: utf-8 -*-
 import random
 import timeit
 from collections import defaultdict
@@ -337,10 +338,10 @@ def statement():
 
 def print_results(emd, time):
     """Report the results of timing an EMD computation"""
-    print("%s  %.2fs" % (emd, time))
+    print('%s  %.2fs' % (emd, time))
 
 
-if __name__ == "__main__":
+if __name__ == '__main__':
 
     # Dict of repertoires organized by purview size
     repertoires = defaultdict(list)
@@ -349,12 +350,12 @@ def report():
         """Time and print results"""
 
         print()
-        print("The reported times are the minimum of %d repetitions" % REPEAT)
-        print("Each timing is %d executions" % NUMBER)
+        print('The reported times are the minimum of %d repetitions' % REPEAT)
+        print('Each timing is %d executions' % NUMBER)
         print()
         print(
-            "Set set n = 0 for the `utils.purview_size(d1) > n` check \n"
-            "in `cause_emd` to see accurate timings for all purview sizes.")
+            'Set set n = 0 for the `utils.purview_size(d1) > n` check \n'
+            'in `cause_emd` to see accurate timings for all purview sizes.')
         print()
 
         # There are at least `k` data points for each purview size
@@ -365,16 +366,16 @@ def report():
             data = random.sample(repertoires[purview_size], k)
             num_repertoires = len(repertoires[purview_size])
 
-            print("%s-node purviews (timing %d/%d repertoires)" % (
+            print('%s-node purviews (timing %d/%d repertoires)' % (
                 purview_size, k, num_repertoires))
 
             num_independent = len([d for d in repertoires[purview_size]
                                    if pyphi.utils.independent(d[0])])
 
-            print("%d%% independent" % (
+            print('%d%% independent' % (
                 num_independent / num_repertoires * 100))
 
-            print("----------------------------------------------")
+            print('----------------------------------------------')
 
             t = time_emd('hamming', data)
             print_results('hamming', t)

conftest.py

@@ -12,48 +12,48 @@
 from pyphi.conf import config
 from pyphi.deferred.ray import ray, NO_RAY
 
-log = logging.getLogger("pyphi.test")
+log = logging.getLogger('pyphi.test')
 
-collect_ignore = ["setup.py", ".pythonrc.py"]
+collect_ignore = ['setup.py', '.pythonrc.py']
 # Also ignore everything that git ignores.
-with open(Path(__file__).parent / ".gitignore", mode="rt") as f:
-    collect_ignore += list(filter(None, f.read().split("\n")))
+with open(Path(__file__).parent / '.gitignore', mode='rt') as f:
+    collect_ignore += list(filter(None, f.read().split('\n')))
 
 
-IIT_3_CONFIG = "pyphi_config_3.0.yml"
+IIT_3_CONFIG = 'pyphi_config_3.0.yml'
 
 # Run slow tests separately with command-line option, filter tests
 # ================================================================
 
 
 def pytest_addoption(parser):
     parser.addoption(
-        "--filter", action="store", help="only run tests with the given mark"
+        '--filter', action='store', help='only run tests with the given mark'
     )
-    parser.addoption("--outdated", action="store_true", help="run outdated tests")
-    parser.addoption("--slow", action="store_true", help="run slow tests")
-    parser.addoption("--veryslow", action="store_true", help="run very slow tests")
+    parser.addoption('--outdated', action='store_true', help='run outdated tests')
+    parser.addoption('--slow', action='store_true', help='run slow tests')
+    parser.addoption('--veryslow', action='store_true', help='run very slow tests')
 
 
 def pytest_runtest_setup(item):
-    filt = item.config.getoption("--filter")
+    filt = item.config.getoption('--filter')
     if filt:
         if filt not in item.keywords:
             pytest.skip("only running tests with the '{}' mark".format(filt))
     else:
-        if "outdated" in item.keywords and not item.config.getoption("--outdated"):
-            pytest.skip("need --outdated option to run")
-        if "slow" in item.keywords and not item.config.getoption("--slow"):
-            pytest.skip("need --slow option to run")
-        if "veryslow" in item.keywords and not item.config.getoption("--veryslow"):
-            pytest.skip("need --veryslow option to run")
+        if 'outdated' in item.keywords and not item.config.getoption('--outdated'):
+            pytest.skip('need --outdated option to run')
+        if 'slow' in item.keywords and not item.config.getoption('--slow'):
+            pytest.skip('need --slow option to run')
+        if 'veryslow' in item.keywords and not item.config.getoption('--veryslow'):
+            pytest.skip('need --veryslow option to run')
 
 
 # PyPhi configuration management
 # ================================================================
 
 
-@pytest.fixture(scope="function")
+@pytest.fixture(scope='function')
 def restore_config_afterwards():
     """Reset PyPhi configuration after a test.
 
@@ -63,7 +63,7 @@ def restore_config_afterwards():
         yield
 
 
-@pytest.fixture(scope="session", autouse=True)
+@pytest.fixture(scope='session', autouse=True)
 def disable_progress_bars():
     """Disable progress bars during tests.
 
@@ -74,10 +74,10 @@ def disable_progress_bars():
         yield
 
 
-@pytest.fixture(scope="function")
+@pytest.fixture(scope='function')
 def use_iit_3_config():
     """Use the IIT-3 configuration for all tests."""
-    with open(IIT_3_CONFIG, mode="rt") as f:
+    with open(IIT_3_CONFIG, mode='rt') as f:
         iit3_config = yaml.load(f, Loader=yaml.SafeLoader)
     with pyphi.config.override(**iit3_config):
         yield
@@ -87,7 +87,7 @@ def use_iit_3_config():
 # ================================================================
 
 
-@pytest.fixture(scope="session", autouse=True)
+@pytest.fixture(scope='session', autouse=True)
 def protect_caches(request):
     """Temporarily backup, then restore, the user's Redis caches
     before and after the testing session.
@@ -96,7 +96,7 @@ def protect_caches(request):
     """
     # Initialize a test Redis connection
     original_redis_conn = redis.conn
-    redis.conn = redis.init(config.REDIS_CONFIG["test_db"])
+    redis.conn = redis.init(config.REDIS_CONFIG['test_db'])
     yield
     # Restore the cache after the last test has run
     redis.conn = original_redis_conn
@@ -109,21 +109,21 @@ def _flush_redis_cache():
 
 
 # TODO: flush Redis cache
-@pytest.fixture(scope="function", autouse=True)
+@pytest.fixture(scope='function', autouse=True)
 def flushcache(request):
     """Flush the currently enabled cache.
 
     This is called before every test case.
     """
-    log.info("Flushing caches...")
+    log.info('Flushing caches...')
     _flush_redis_cache()
 
 
 # Ray
 # ================================================================
 
 
-@pytest.fixture(scope="module")
+@pytest.fixture(scope='module')
 def ray_context():
     context = ray.init(num_cpus=3)
     yield context

docs/_themes/LICENSE

@@ -1,9 +1,9 @@
-Modifications: 
+Modifications:
 
 Copyright (c) 2010 Kenneth Reitz.
 
 
-Original Project: 
+Original Project:
 
 Copyright (c) 2010 by Armin Ronacher.
 

docs/_themes/README.rst

@@ -22,4 +22,3 @@ The following themes exist:
 
 **kr_small**
 	small one-page theme.  Intended to be used by very small addon libraries.
-