opencobra/cobrapy-0.26.2.zip
opencobra-cobrapy-2839337
.editorconfig
327 Bytes
.github
CODE_OF_CONDUCT.md
5.6 kB
CONTRIBUTING.rst
8.0 kB
ISSUE_TEMPLATE
01-bug-report.md
1.0 kB
02-question.md
512 Bytes
03-feature-request.md
997 Bytes
config.yml
622 Bytes
PULL_REQUEST_TEMPLATE.md
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SUPPORT.rst
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workflows
biosimulators_dispatch.yml
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lint.yml
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main.yml
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safety.yml
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.gitignore
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.readthedocs.yaml
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INSTALL.rst
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LICENSE
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MANIFEST.in
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README.rst
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benchmarks
cobra-cameo-merge-benchmarks-before-merge.ipynb
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cobra-cameo-merge-benchmarks.ipynb
8.7 kB
geometric_fba.ipynb
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objective_benchmark.ipynb
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parallel_fva.ipynb
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single_gene_deletion_linear_room.ipynb
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single_gene_deletion_room.ipynb
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documentation_builder
.gitignore
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Makefile
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building_model.ipynb
20.5 kB
conf.py
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configuration.ipynb
10.9 kB
consistency.ipynb
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constraints_objectives.ipynb
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deletions.ipynb
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dfba.ipynb
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faq.ipynb
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gapfilling.ipynb
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getting_started.ipynb
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index.rst
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io.ipynb
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loopless.ipynb
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make.bat
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media.ipynb
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phenotype_phase_plane.ipynb
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plot_helper.py
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requirements.txt
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sampling.ipynb
19.4 kB
simulating.ipynb
43.6 kB
solvers.ipynb
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pyproject.toml
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release-notes
0.10.0.md
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0.10.1.md
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0.11.0.md
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0.11.1.md
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0.11.2.md
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0.11.3.md
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0.12.0.md
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0.12.1.md
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0.13.0.md
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0.13.1.md
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0.13.2.md
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0.13.3.md
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0.13.4.md
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0.14.0.md
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0.14.1.md
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0.14.2.md
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0.15.0.md
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0.15.1.md
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0.15.2.md
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0.15.3.md
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0.15.4.md
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0.16.0.md
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0.17.0.md
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0.17.1.md
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0.18.0.md
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0.18.1.md
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0.19.0.md
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0.20.0.md
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0.21.0.md
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0.22.0.md
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0.22.1.md
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0.23.0.md
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0.24.0.md
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0.25.0.md
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0.26.0.md
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0.26.1.md
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0.26.2.md
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0.6.0.md
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0.6.1.md
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0.6.2.md
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0.7.0.md
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0.8.0.md
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0.8.1.md
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0.8.2.md
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0.9.0.md
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0.9.1.md
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next-release.md
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scripts
compare-benchmark.py
1.4 kB
deploy_website.sh
629 Bytes
publish_release.py
3.5 kB
setup.cfg
2.6 kB
setup.py
454 Bytes
src
cobra
__init__.py
393 Bytes
core
__init__.py
417 Bytes
configuration.py
8.8 kB
dictlist.py
17.6 kB
formula.py
5.7 kB
gene.py
25.3 kB
group.py
4.8 kB
metabolite.py
11.5 kB
model.py
55.5 kB
object.py
3.3 kB
reaction.py
56.2 kB
singleton.py
398 Bytes
solution.py
6.3 kB
species.py
2.8 kB
data
__init__.py
0 Bytes
iJO1366.xml.gz
395.5 kB
mini.json
41.6 kB
mini.mat
55.0 kB
mini.yml
25.9 kB
mini_cobra.xml
102.7 kB
salmonella.xml.gz
574.2 kB
textbook.xml.gz
18.2 kB
exceptions.py
1.1 kB
flux_analysis
__init__.py
635 Bytes
deletion.py
20.3 kB
fastcc.py
5.9 kB
gapfilling.py
15.7 kB
geometric.py
4.8 kB
helpers.py
1.0 kB
loopless.py
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moma.py
5.9 kB
parsimonious.py
4.9 kB
phenotype_phase_plane.py
13.1 kB
reaction.py
9.9 kB
room.py
5.4 kB
variability.py
15.0 kB
io
__init__.py
509 Bytes
dict.py
11.4 kB
json.py
3.8 kB
mat.py
35.8 kB
sbml.py
72.1 kB
schema_v1.json
3.2 kB
web
__init__.py
250 Bytes
abstract_model_repository.py
2.0 kB
bigg_models_repository.py
2.0 kB
biomodels_repository.py
2.8 kB
cobrapy_repository.py
1.4 kB
load.py
5.7 kB
yaml.py
4.2 kB
manipulation
__init__.py
304 Bytes
annotate.py
1.1 kB
delete.py
8.6 kB
modify.py
5.3 kB
validate.py
1.7 kB
medium
__init__.py
168 Bytes
annotations.py
2.2 kB
boundary_types.py
6.2 kB
minimal_medium.py
9.7 kB
sampling
__init__.py
165 Bytes
achr.py
6.0 kB
core.py
3.6 kB
hr_sampler.py
20.5 kB
optgp.py
8.9 kB
sampling.py
3.4 kB
summary
__init__.py
165 Bytes
metabolite_summary.py
14.1 kB
model_summary.py
16.0 kB
reaction_summary.py
7.9 kB
summary.py
4.8 kB
util
__init__.py
164 Bytes
array.py
8.5 kB
context.py
2.8 kB
process_pool.py
3.6 kB
solver.py
21.8 kB
util.py
1.3 kB
tests
conftest.py
5.1 kB
data
AntCore.mat
2.9 kB
Ec_iAF1260_flux1.mat
490.1 kB
JSON_with_inf_bounds.json
2.9 kB
annotation.xml
15.1 kB
cardiac_mit_glcuptake_atpmax.mat
5.7 kB
compartments.mat
10.8 kB
e_coli_core.xml
494.6 kB
example_notes.xml
10.5 kB
fbc_ex1.xml
10.7 kB
fbc_ex2.xml
10.1 kB
iJO1366.pickle
3.5 MB
invalid0.xml
3.0 kB
invalid1.xml
2.5 kB
invalid2.xml
4.1 kB
invalid_annotation_format.json
413 Bytes
mini.pickle
35.2 kB
mini_cobra.xml
102.7 kB
mini_fbc1.xml
29.4 kB
mini_fbc2.xml
102.7 kB
mini_fbc2.xml.bz2
5.3 kB
mini_fbc2.xml.gz
6.4 kB
mini_history.xml
104.3 kB
mini_wrong_key_caps.mat
54.9 kB
raven.mat
2.5 kB
raven.pickle
10.5 kB
salmonella.media
4.7 kB
salmonella.pickle
2.9 MB
textbook_fva.json
3.2 kB
textbook_pfba_fva.json
3.2 kB
textbook_solution.pickle
7.5 kB
update_pickles.py
4.4 kB
valid_annotation_format.json
341 Bytes
valid_annotation_output.xml
2.5 kB
validation.xml
516 Bytes
test_core
conftest.py
831 Bytes
test_configuration.py
1.6 kB
test_core_reaction.py
40.1 kB
test_dictlist.py
13.4 kB
test_formula.py
731 Bytes
test_gene.py
309 Bytes
test_gpr.py
14.8 kB
test_group.py
1.2 kB
test_metabolite.py
1.8 kB
test_model.py
43.3 kB
test_solution.py
555 Bytes
test_flux_analysis
conftest.py
3.9 kB
test_deletion.py
13.7 kB
test_fastcc.py
3.3 kB
test_gapfilling.py
3.3 kB
test_geometric.py
2.2 kB
test_helpers.py
792 Bytes
test_loopless.py
3.0 kB
test_moma.py
2.3 kB
test_parsimonious.py
2.2 kB
test_phenotype_phase_plane.py
1.5 kB
test_reaction.py
902 Bytes
test_room.py
1.7 kB
test_variability.py
6.3 kB
test_io
conftest.py
4.9 kB
test_annotation.py
4.2 kB
test_annotation_format.py
1.3 kB
test_io_order.py
4.1 kB
test_json.py
3.4 kB
test_mat.py
11.9 kB
test_notes.py
1.5 kB
test_pickle.py
1.1 kB
test_sbml.py
24.0 kB
test_web
test_load.py
4.2 kB
test_yaml.py
1.1 kB
test_manipulation
test_annotate.py
800 Bytes
test_delete.py
12.1 kB
test_modify.py
4.2 kB
test_validate.py
1.1 kB
test_medium
test_boundary_types.py
3.6 kB
test_minimal_medium.py
4.7 kB
test_sampling
conftest.py
505 Bytes
test_achr.py
1.4 kB
test_optgp.py
2.1 kB
test_sampling.py
4.2 kB
test_summary
test_metabolite_summary.py
4.0 kB
test_model_summary.py
3.7 kB
test_reaction_summary.py
3.5 kB
test_util
test_array.py
1.3 kB
test_context.py
1.3 kB
test_process_pool.py
4.3 kB
test_solver.py
7.8 kB
test_util.py
1.6 kB
tox.ini
2.5 kB