"
],
"metadata": {},
"output_type": "display_data",
"text": [
- "
"
+ ""
]
},
{
"javascript": [
- "jQuery('#progress-bar-ee6685c7-c46b-4d2e-9ba6-8bf82eaea0cb').val('85')"
+ "$('div#58e17efe-44ee-4c42-9797-f59c611f97d8').text(' 5%');"
],
"metadata": {},
"output_type": "display_data",
"text": [
- ""
+ ""
]
},
{
"javascript": [
- "jQuery('#progress-bar-ee6685c7-c46b-4d2e-9ba6-8bf82eaea0cb').val('90')"
+ "\n",
+ " var $myPB = $(\"div#db82843f-77c7-4c40-8d3f-b5299cb62e25\")\n",
+ " if ($myPB.hasClass('ui-progressbar')) {\n",
+ " $myPB.progressbar('value', 100);\n",
+ " } else {\n",
+ " $myPB.progressbar({value: 0, max: 2000});\n",
+ " }\n",
+ " "
],
"metadata": {},
"output_type": "display_data",
"text": [
- ""
+ ""
]
},
{
"javascript": [
- "jQuery('#progress-bar-ee6685c7-c46b-4d2e-9ba6-8bf82eaea0cb').val('95')"
+ "$('div#58e17efe-44ee-4c42-9797-f59c611f97d8').text(' 10%');"
],
"metadata": {},
"output_type": "display_data",
"text": [
- ""
+ ""
]
},
{
"javascript": [
- "jQuery('#progress-bar-ee6685c7-c46b-4d2e-9ba6-8bf82eaea0cb').val('100')"
+ "\n",
+ " var $myPB = $(\"div#db82843f-77c7-4c40-8d3f-b5299cb62e25\")\n",
+ " if ($myPB.hasClass('ui-progressbar')) {\n",
+ " $myPB.progressbar('value', 200);\n",
+ " } else {\n",
+ " $myPB.progressbar({value: 0, max: 2000});\n",
+ " }\n",
+ " "
],
"metadata": {},
"output_type": "display_data",
"text": [
- ""
- ]
- },
- {
- "html": [
- "Result:
- model: iJO1366
- heuristic: GA
- objective function: bpcy = (Ec_biomass_iJO1366_core_53p95M * EX_succ_LPAREN_e_RPAREN_) / EX_glc_LPAREN_e_RPAREN_
- simulation method: fba
- type: gene
"
- ],
- "metadata": {},
- "output_type": "pyout",
- "prompt_number": 5,
- "text": [
- ""
+ ""
]
}
- ],
- "prompt_number": 5
+ ]
},
{
"cell_type": "code",
diff --git a/examples/islands_model.py b/examples/islands_model.py
index 685b5cf96..3af5ee5f7 100644
--- a/examples/islands_model.py
+++ b/examples/islands_model.py
@@ -1,11 +1,11 @@
# Copyright 2014 Novo Nordisk Foundation Center for Biosustainability, DTU.
-
+#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
-
-# http://www.apache.org/licenses/LICENSE-2.0
-
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
diff --git a/requirements.txt b/requirements.txt
index eaeb8b9ff..347efff4e 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -1,4 +1,4 @@
-numpy>=1.8.1
+numpy>=1.9.1
pyzmq>=14.3.1
ipython>=2.1.0
scipy>=0.9.0
diff --git a/setup.py b/setup.py
index e7e70a3db..a4f6883e7 100644
--- a/setup.py
+++ b/setup.py
@@ -5,7 +5,7 @@
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
-# http://www.apache.org/licenses/LICENSE-2.0
+# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
diff --git a/tests/test_cobrapy_compatibility.py b/tests/test_cobrapy_compatibility.py
index cec424a0c..32afcf744 100644
--- a/tests/test_cobrapy_compatibility.py
+++ b/tests/test_cobrapy_compatibility.py
@@ -1,3 +1,17 @@
+# Copyright 2014 Novo Nordisk Foundation Center for Biosustainability, DTU.
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
import types
import nose
from cobra.test import create_test_model
diff --git a/tests/test_flux_analysis.py b/tests/test_flux_analysis.py
index 32c03c611..a1db407ee 100644
--- a/tests/test_flux_analysis.py
+++ b/tests/test_flux_analysis.py
@@ -1,9 +1,19 @@
-# Copyright (c) 2014 Novo Nordisk Foundation Center for Biosustainability, DTU.
-# See LICENSE for details.
-
-import unittest
+# Copyright 2014 Novo Nordisk Foundation Center for Biosustainability, DTU.
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
import os
+import unittest
from cameo.flux_analysis.simulation import fba, pfba, lmoma
from cameo.parallel import SequentialView, MultiprocessingView
diff --git a/tests/test_io.py b/tests/test_io.py
index e9b46d93a..6c9480ee4 100644
--- a/tests/test_io.py
+++ b/tests/test_io.py
@@ -1,9 +1,19 @@
-# Copyright (c) 2014 Novo Nordisk Foundation Center for Biosustainability, DTU.
-# See LICENSE for details.
-
-import unittest
+# Copyright 2014 Novo Nordisk Foundation Center for Biosustainability, DTU.
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
import os
+import unittest
import cobra
import optlang
diff --git a/tests/test_parallel.py b/tests/test_parallel.py
index 3b132869c..07d0bddb1 100644
--- a/tests/test_parallel.py
+++ b/tests/test_parallel.py
@@ -1,8 +1,19 @@
-# Copyright (c) 2014 Novo Nordisk Foundation Center for Biosustainability, DTU.
-# See LICENSE for details.
-import Queue
+# Copyright 2014 Novo Nordisk Foundation Center for Biosustainability, DTU.
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
import unittest
+import Queue
from cameo.parallel import SequentialView
import subprocess
from time import sleep
diff --git a/tests/test_solver_based_model.py b/tests/test_solver_based_model.py
index 6404d0f91..6e55191c3 100644
--- a/tests/test_solver_based_model.py
+++ b/tests/test_solver_based_model.py
@@ -1,10 +1,21 @@
-# Copyright (c) 2014 Novo Nordisk Foundation Center for Biosustainability, DTU.
-# See LICENSE for details.
-import copy
+# Copyright 2014 Novo Nordisk Foundation Center for Biosustainability, DTU.
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+import os
+import copy
import unittest
-import os
from cobra import Metabolite
from optlang import Objective
from cameo import load_model
diff --git a/tests/test_strain_design_heuristics.py b/tests/test_strain_design_heuristics.py
index 1a3ea32e0..2363f9d67 100644
--- a/tests/test_strain_design_heuristics.py
+++ b/tests/test_strain_design_heuristics.py
@@ -1,18 +1,18 @@
# Copyright 2014 Novo Nordisk Foundation Center for Biosustainability, DTU.
-
+#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
-
-# http://www.apache.org/licenses/LICENSE-2.0
-
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.
+
import os
-from cameo.util import RandomGenerator as Random
import unittest
import inspyred
import pickle
@@ -20,6 +20,7 @@
from pandas.util.testing import assert_frame_equal
from cameo import load_model, fba, config
+from cameo.util import RandomGenerator as Random
from cameo.strain_design.heuristic import HeuristicOptimization, ReactionKnockoutOptimization, set_distance_function
from cameo.strain_design.heuristic.archivers import SolutionTuple, BestSolutionArchiver
from cameo.strain_design.heuristic.decoders import ReactionKnockoutDecoder, KnockoutDecoder, GeneKnockoutDecoder
diff --git a/tests/test_util.py b/tests/test_util.py
index debe43b57..db36806d0 100644
--- a/tests/test_util.py
+++ b/tests/test_util.py
@@ -1,5 +1,16 @@
-# Copyright (c) 2014 Novo Nordisk Foundation Center for Biosustainability, DTU.
-# See LICENSE for details.
+# Copyright 2014 Novo Nordisk Foundation Center for Biosustainability, DTU.
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
import unittest
from functools import partial