fixed bug in conn, updated test/examples/* to use dynamic pathing (#817)

* fixed bug in conn, updated test/examples/* to use dynamic pathing

* update CHANGES.md

CHANGES.md

@@ -6,6 +6,8 @@
 
 - cfg.connRandomSecFromList and cfg.distributeSynsUniformly can now be overriden in individual conn rule
 
+- Updated tests.examples.utils to allow for dynamic pathing
+
 **Bug fixes**
 
 - Better handling of exceptions in `importCellParams()` (incl. issue 782)

netpyne/network/conn.py

@@ -511,7 +511,7 @@ def probConn(self, preCellsTags, postCellsTags, connParam):
     if sim.cfg.verbose:
         print('Generating set of probabilistic connections (rule: %s) ...' % (connParam['label']))
     if sim.rank == 0 and not sim.cfg.verbose: pbar = tqdm(total=len(postCellsTags.items()), ascii=True,
-                                  desc='  ' + connParam['label'], position=0, leave=True,
+                                  desc='  ' + str(connParam['label']), position=0, leave=True,
                                   bar_format= '{l_bar}{bar}| Creating synaptic connections for {n_fmt}/{total_fmt} postsynaptic cells on node %i (probabilistic connectivity)' % sim.rank)
 
     allRands = self.generateRandsPrePost(preCellsTags, postCellsTags)

tests/examples/test_HHTut.py

@@ -4,9 +4,10 @@
 if '-nogui' not in sys.argv:
     sys.argv.append('-nogui')
 
-from .utils import pkg_setup
+from .utils import pkg_setup, NETPYNE_DIR
 
-@pytest.mark.package_data(['examples/HHTut/', None])
+package_dir = NETPYNE_DIR + '/examples/HHTut/'
+@pytest.mark.package_data([package_dir, None])
 class TestHHTut():
     def test_run(self, pkg_setup):
         import src.init

tests/examples/test_HybridTut.py

@@ -5,9 +5,11 @@
 if '-nogui' not in sys.argv:
     sys.argv.append('-nogui')
 
-from .utils import pkg_setup
+from .utils import pkg_setup, NETPYNE_DIR
 
-@pytest.mark.package_data(['examples/HybridTut/', 'mod'])
+package_dir = NETPYNE_DIR + '/examples/HybridTut/'
+
+@pytest.mark.package_data([package_dir, 'mod'])
 class TestHybridTut:
     def test_run(self, pkg_setup):
         import src.init

tests/examples/test_LFPrecording.py

@@ -5,10 +5,10 @@
 if '-nogui' not in sys.argv:
     sys.argv.append('-nogui')
 
-from .utils import pkg_setup
+from .utils import pkg_setup, NETPYNE_DIR
 
-
-@pytest.mark.package_data(['examples/LFPrecording/', 'mod'])
+package_dir = NETPYNE_DIR + '/examples/LFPrecording/'
+@pytest.mark.package_data([package_dir, 'mod'])
 class TestLFPrecording:
     def test_cell_lfp(self, pkg_setup):
         import src.cell.init

tests/examples/test_M1.py

@@ -5,10 +5,10 @@
 if '-nogui' not in sys.argv:
     sys.argv.append('-nogui')
 
-from .utils import pkg_setup
+from .utils import pkg_setup, NETPYNE_DIR
 
-
-@pytest.mark.package_data(['examples/M1/', 'mod'])
+package_dir = NETPYNE_DIR + '/examples/M1/'
+@pytest.mark.package_data([package_dir, 'mod'])
 class TestM1:
     def test_run(self, pkg_setup):
         import src.init

tests/examples/test_NeuroMLImport.py

@@ -5,10 +5,10 @@
 if '-nogui' not in sys.argv:
     sys.argv.append('-nogui')
 
-from .utils import pkg_setup
+from .utils import pkg_setup, NETPYNE_DIR
 
-
-@pytest.mark.package_data(['examples/NeuroMLImport/', '.'])
+package_dir = NETPYNE_DIR + '/examples/NeuroMLImport/'
+@pytest.mark.package_data([package_dir, '.'])
 class TestPTcell:
     def test_init(self, pkg_setup):
         import SimpleNet_import

tests/examples/test_PTcell.py

@@ -5,10 +5,10 @@
 if '-nogui' not in sys.argv:
     sys.argv.append('-nogui')
 
-from .utils import pkg_setup
+from .utils import pkg_setup, NETPYNE_DIR
 
-
-@pytest.mark.package_data(['examples/PTcell/', 'mod'])
+package_dir = NETPYNE_DIR + '/examples/PTcell/'
+@pytest.mark.package_data([package_dir, 'mod'])
 class TestPTcell:
     def test_init(self, pkg_setup):
         import src.init

tests/examples/test_batchCell.py

@@ -8,10 +8,10 @@
 if "-nogui" not in sys.argv:
     sys.argv.append("-nogui")
 
-from .utils import pkg_setup
+from .utils import pkg_setup, NETPYNE_DIR
 
-
-@pytest.mark.package_data(["examples/batchCell/", "mod"])
+package_dir = NETPYNE_DIR + "/examples/batchCell/"
+@pytest.mark.package_data([package_dir, "mod"])
 class TestBatchCell:
     def batch_run(self, pkg_setup):
         """run a reduced version of the batchCell example"""

tests/examples/test_evolCell.py

@@ -9,10 +9,10 @@
 if "-nogui" not in sys.argv:
     sys.argv.append("-nogui")
 
-from .utils import pkg_setup
+from .utils import pkg_setup, NETPYNE_DIR
 
-
-@pytest.mark.package_data(["examples/evolCell/", "mod"])
+package_dir = NETPYNE_DIR + "/examples/evolCell/"
+@pytest.mark.package_data([package_dir, "mod"])
 class TestEvolCell:
     def evol_run(self, pkg_setup):
         """run a reduced version of the evolCell example"""

tests/examples/test_rxd_buffering.py

@@ -3,9 +3,10 @@
 if '-nogui' not in sys.argv:
     sys.argv.append('-nogui')
 
-from .utils import pkg_setup
+from .utils import pkg_setup, NETPYNE_DIR
 
-@pytest.mark.package_data(['examples/rxd_buffering/', None])
+package_dir = NETPYNE_DIR + '/examples/rxd_buffering/'
+@pytest.mark.package_data([package_dir, None])
 class Test_rxd_buffering():
     def test_buffering(self, pkg_setup):
         import src.init

tests/examples/test_rxd_net.py

@@ -5,10 +5,10 @@
 if '-nogui' not in sys.argv:
     sys.argv.append('-nogui')
 
-from .utils import pkg_setup
+from .utils import pkg_setup, NETPYNE_DIR
 
-
-@pytest.mark.package_data(['examples/rxd_net/', 'mod'])
+package_dir = NETPYNE_DIR + '/examples/rxd_net/'
+@pytest.mark.package_data([package_dir, 'mod'])
 class TestRxdNet:
     def test_init(self, pkg_setup):
         import src.init

tests/examples/test_saving.py

@@ -5,10 +5,10 @@
     sys.argv.append('-nogui')
 
 
-from .utils import pkg_setup
+from .utils import pkg_setup, NETPYNE_DIR
 
-
-@pytest.mark.package_data(['examples/saving', None])
+package_dir = NETPYNE_DIR + '/examples/saving/'
+@pytest.mark.package_data([package_dir, None])
 class Test_saving():
     def test_init(self, pkg_setup):
         import src.init

tests/examples/utils.py

@@ -1,7 +1,10 @@
 import os
 import pytest
 import sys
+import inspect
+import netpyne
 
+NETPYNE_DIR = '/' + os.path.join(*inspect.getfile(netpyne).split('/')[:-2])
 def compile_neuron_mod_dir(pkg_dir):
     try:
         print('Compiling {}'.format(pkg_dir))
@@ -14,7 +17,6 @@ def compile_neuron_mod_dir(pkg_dir):
         print(err)
         return
 
-
 @pytest.fixture
 def pkg_setup(request):
     mark = request.node.get_closest_marker("package_data")