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Refactor/tests #1191

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merged 70 commits into from
Apr 29, 2022
Merged

Refactor/tests #1191

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75cadac
moved tests to src directory
Mar 22, 2022
5856f8b
tests no longer use __init__.py
Mar 22, 2022
2c2a347
turned compare_models to a function fixture
Mar 22, 2022
bd19003
update conftest.py to Python 3.6
Mar 22, 2022
fe49b8e
fixed minor typing error
Mar 23, 2022
3d92c9a
updated release notes for next-release.md
Mar 23, 2022
b708d3f
moved tests to src directory
Mar 22, 2022
d491139
moved to tests from src/tests
Mar 29, 2022
93756ea
working on test_all()
Mar 29, 2022
5de2c05
test_all() will work
Mar 29, 2022
4507941
test_io directory files will work. test_io/conftest.py had errors
Mar 29, 2022
4c9aec2
inital attempt at loading from cobrapy, via cobrapy_repository.py
Mar 29, 2022
7c68c00
some tidying of imports
Mar 29, 2022
28ffd6c
allow load_model to load locally
Mar 30, 2022
812a696
modified all examples in .py file comments
Mar 30, 2022
d2e0a17
some formatting
Mar 30, 2022
27d1c31
fixed some errors, fixed setup.cfg, tox.ini
Mar 30, 2022
916d8b1
constraints_objectives.ipynb source
Apr 5, 2022
4320e1a
constraints_objectives.ipynb outputs
Apr 5, 2022
2289a27
constraints_objectives.ipynb code
Apr 5, 2022
6ef029c
constraints_objectives.ipynb outputs
Apr 5, 2022
0ac4550
cobra-cameo-merge-benchmarks-before-merge.ipynb code
Apr 5, 2022
73b7c80
cobra-cameo-merge-benchmarks-before-merge.ipynb outputs
Apr 5, 2022
76980d4
deletions.ipynb code
Apr 5, 2022
b1ba5d3
deletions.ipynb outputs
Apr 5, 2022
a2736b1
configuration.ipynb code
Apr 5, 2022
0cd0bc8
configuration.ipynb outputs
Apr 5, 2022
d5c4e8e
add local salmonella models that doesn't have buckets of warnings
Apr 5, 2022
6fe789d
gapfilling.ipynb code
Apr 5, 2022
10a7de2
gapfilling.ipynb outputs
Apr 5, 2022
1b8a7a5
Trying to make windows work
Apr 20, 2022
b759ebb
cobra-cameo-merge-benchmarks.ipynb code
Apr 20, 2022
ab3ed7d
cobra-cameo-merge-benchmarks.ipynb outputs
Apr 20, 2022
054c218
geometric_fba.ipynb corrected.
Apr 26, 2022
3a0ca3f
parallel_fva.ipynb code
Apr 26, 2022
ffa1264
parallel_fva.ipynb output
Apr 26, 2022
2dfb29e
single_gene_deletion_linear_room.ipynb changes
Apr 26, 2022
967fd7d
single_gene_deletion_room.ipynb changes
Apr 26, 2022
1baa1d1
faq.ipynb fixed as much as I could fix it
Apr 26, 2022
ee3d4b6
dfba.ipynb code
Apr 26, 2022
68fa1b4
dfba.ipynb outpu
Apr 26, 2022
52450e2
getting_started.ipynb code
Apr 26, 2022
0c19c29
getting_started.ipynb markdown and output
Apr 26, 2022
b61dc4e
getting_started.ipynb minor error
Apr 26, 2022
ea62f09
io.ipynb code
Apr 26, 2022
eafa9cc
io.ipynb output
Apr 26, 2022
636816a
loopless.ipynb code
Apr 26, 2022
ebd0ee2
loopless.ipynb output
Apr 26, 2022
5c5a3cf
media.ipynb code
Apr 26, 2022
a47f87f
media.ipynb output
Apr 26, 2022
a10b684
phenotype_phase_plane.ipynb code
Apr 26, 2022
eb054b7
phenotype_phase_plane.ipynb output
Apr 26, 2022
fc8f5c5
pymatbridge.ipynb code
Apr 26, 2022
be13970
sampling.ipynb code
Apr 26, 2022
6e998d8
sampling.ipynb output
Apr 26, 2022
b98e281
solvers.ipynb code
Apr 26, 2022
f8e9b2d
simulating.ipynb code
Apr 26, 2022
07092c9
simulating.ipynb output
Apr 26, 2022
f7e768a
fixed faq.ipynb and removed irrelevant section
Apr 28, 2022
64b6bec
fixed according to comments
Apr 28, 2022
77c7b21
changes in io from tests/data to src/cobra/data
Apr 28, 2022
5ee579f
io.ipynb should work now
Apr 28, 2022
e4268ab
fixed py.path instead of py.test
Apr 28, 2022
f72b78f
delet pymatbridge.ipynb
Apr 28, 2022
f931815
fixed more merge problems
Apr 28, 2022
b4bc3a6
fixed changes in compare_models
Apr 28, 2022
8a8b2cd
Apply suggestions from code review - mostly path
akaviaLab Apr 29, 2022
868bfe1
deleted iOJ1366.pickle
Apr 29, 2022
a4bc963
isort black and flake8
Apr 29, 2022
e13e8df
removed test_all and pytest_addoption which seem irrelevant
Apr 29, 2022
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195 changes: 97 additions & 98 deletions benchmarks/cobra-cameo-merge-benchmarks-before-merge.ipynb
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391 changes: 137 additions & 254 deletions benchmarks/cobra-cameo-merge-benchmarks.ipynb
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46 changes: 23 additions & 23 deletions benchmarks/geometric_fba.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -22,26 +22,9 @@
"cell_type": "code",
"execution_count": 3,
"metadata": {},
"outputs": [
{
"name": "stderr",
"output_type": "stream",
"text": [
"DEBUG:optlang.util:Gurobi python bindings found at /home/moritz/.virtualenvs/cobra/lib/python3.5/site-packages/gurobipy\n",
"DEBUG:optlang.util:GLPK python bindings found at /home/moritz/.virtualenvs/cobra/lib/python3.5/site-packages/swiglpk\n",
"DEBUG:optlang.util:Mosek python bindings not available.\n",
"DEBUG:optlang.util:CPLEX python bindings found at /home/moritz/.virtualenvs/cobra/lib/python3.5/site-packages/cplex\n",
"DEBUG:optlang.util:Scipy solver not available\n",
"DEBUG:pip._internal.utils.misc:lzma module is not available\n",
"DEBUG:pip._internal.vcs:Registered VCS backend: git\n",
"DEBUG:pip._internal.vcs:Registered VCS backend: hg\n",
"DEBUG:pip._internal.vcs:Registered VCS backend: svn\n",
"DEBUG:pip._internal.vcs:Registered VCS backend: bzr\n"
]
}
],
"outputs": [],
"source": [
"from cobra.test import create_test_model"
"from cobra.io import load_model"
]
},
{
Expand All @@ -57,9 +40,26 @@
"cell_type": "code",
"execution_count": 5,
"metadata": {},
"outputs": [],
"outputs": [
{
"name": "stderr",
"output_type": "stream",
"text": [
"INFO:cobra.core.model:The current solver interface glpk doesn't support setting the optimality tolerance.\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Scaling...\n",
" A: min|aij| = 1.000e+00 max|aij| = 1.000e+00 ratio = 1.000e+00\n",
"Problem data seem to be well scaled\n"
]
}
],
"source": [
"model = create_test_model(\"textbook\")"
"model = load_model(\"textbook\")"
]
},
{
Expand Down Expand Up @@ -459,7 +459,7 @@
],
"metadata": {
"kernelspec": {
"display_name": "Python 3",
"display_name": "Python 3 (ipykernel)",
"language": "python",
"name": "python3"
},
Expand All @@ -473,7 +473,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.5.5"
"version": "3.7.1"
}
},
"nbformat": 4,
Expand Down
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