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libsbml based SBML parser #685

Merged
merged 171 commits into from
Mar 18, 2019
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31c2343
Test cases implemented
matthiaskoenig Mar 22, 2018
ce9d59e
genes parsed
matthiaskoenig Mar 22, 2018
b0c6a23
objectives and flux bounds reader
matthiaskoenig Mar 22, 2018
17f4e2d
annotations parsed
matthiaskoenig Mar 22, 2018
d1f5728
first work on GPAs
matthiaskoenig Mar 22, 2018
112bf52
small changes
matthiaskoenig Mar 22, 2018
da34ea2
starting writing sbml
matthiaskoenig Mar 23, 2018
f447695
writing annotations
matthiaskoenig Mar 23, 2018
daa5913
writing bounds
matthiaskoenig Mar 23, 2018
bd09944
write objective functions
matthiaskoenig Mar 23, 2018
40bb738
validation
matthiaskoenig Mar 23, 2018
ef55d12
minor changes
matthiaskoenig Mar 23, 2018
03e8154
parsing of cobra format
matthiaskoenig Mar 23, 2018
b402044
fixing sboterms
matthiaskoenig Mar 23, 2018
eb0f83d
minor changes
matthiaskoenig Mar 23, 2018
b97214c
handling legacy fbc, and consistency checks
matthiaskoenig Mar 25, 2018
15b9131
id replacements
matthiaskoenig Mar 25, 2018
9810b21
fixed reading/writing GPRs
matthiaskoenig Mar 25, 2018
84d651f
fixed annotation parsing
matthiaskoenig Mar 25, 2018
d259607
fixed annotation issue
matthiaskoenig Mar 25, 2018
a829122
fixed COBRA formula bug, all test passing
matthiaskoenig Mar 25, 2018
2095e09
fixed package version bug
matthiaskoenig Mar 25, 2018
e3331cf
working on optimizations
matthiaskoenig Mar 25, 2018
efd4266
minor optimizations
matthiaskoenig Mar 25, 2018
38b3ca8
latest changes
matthiaskoenig Jun 13, 2018
27f108a
fixing no objective issue
matthiaskoenig Jul 30, 2018
8af8d58
fixing no active flux objective
matthiaskoenig Jul 30, 2018
86b134d
updated devel
matthiaskoenig Feb 27, 2019
193b349
fixed failing tests due to changed solution structure
matthiaskoenig Feb 27, 2019
b2bf382
working on documentation and pep8
matthiaskoenig Feb 27, 2019
f7f7726
documentation and pep8 fixes
matthiaskoenig Feb 27, 2019
420c9aa
chore: merge Greg's groups feature
Midnighter Feb 27, 2019
3d88bfd
fix: update method name
Midnighter Feb 27, 2019
4087b84
chore: update model files
Midnighter Feb 27, 2019
f87d236
fixing pep8 issues
matthiaskoenig Feb 27, 2019
e64fc03
Merge remote-tracking branch 'origin/feat-libsbml' into libsbml
matthiaskoenig Feb 27, 2019
6d95ad1
fixing pep8 issues
matthiaskoenig Feb 27, 2019
6a1f442
latest changes
matthiaskoenig Feb 27, 2019
1f1fb0e
fixme comments added
matthiaskoenig Feb 28, 2019
5f996c5
reading SBML meta information
matthiaskoenig Feb 28, 2019
3545772
simplified handling of annotations and notes
matthiaskoenig Feb 28, 2019
fd986c0
support for filehandles
matthiaskoenig Feb 28, 2019
e3b8967
updated handling of notes and meta information
matthiaskoenig Feb 28, 2019
5a0e7f9
parsing legacy notes dictionary
matthiaskoenig Feb 28, 2019
d2fd12c
reading legacy GENE_ASSOCIATION
matthiaskoenig Feb 28, 2019
085fc5f
fix incorrect warnings
matthiaskoenig Feb 28, 2019
5aaf740
fixed py27 tests
matthiaskoenig Feb 28, 2019
72037bf
fixed pep8 issues
matthiaskoenig Feb 28, 2019
345d8f2
replacing old sbml readers and writers
matthiaskoenig Mar 1, 2019
f9dc1c3
working on annotation fixes
matthiaskoenig Mar 1, 2019
c254c71
fixed pep8 issues
matthiaskoenig Mar 1, 2019
ed35ad5
reading of groups information, buxfixes and typos
matthiaskoenig Mar 1, 2019
e4413c5
groups added to model
matthiaskoenig Mar 1, 2019
5d45093
writing groups to SBML
matthiaskoenig Mar 1, 2019
3ce011d
https bugfix for identifiers.org
matthiaskoenig Mar 1, 2019
c8132c4
proper handling of qualifiers on sbml export
matthiaskoenig Mar 1, 2019
24416da
typo fix
matthiaskoenig Mar 1, 2019
d88eee6
Merge branch 'devel' into libsbml
matthiaskoenig Mar 1, 2019
38e29ac
fixing attribute access for Windows
matthiaskoenig Mar 1, 2019
4f08728
additional fix for windows attribute access
matthiaskoenig Mar 1, 2019
6cd5830
changing matrix for faster test failure
matthiaskoenig Mar 1, 2019
20a2214
more windows attribute fixes
matthiaskoenig Mar 1, 2019
ed97685
reverting appveyor order
matthiaskoenig Mar 1, 2019
4b07922
gitignore in local exclude
matthiaskoenig Mar 5, 2019
6c088bd
writing to file handles, referencing issues
matthiaskoenig Mar 5, 2019
05a6c53
updated fixmes and referencing of underlying issues
matthiaskoenig Mar 5, 2019
cbacd03
updating bounds to config.Configuration bounds
matthiaskoenig Mar 5, 2019
7a32d56
replaced single letter variables, documentation
matthiaskoenig Mar 5, 2019
77c95ea
refactoring top level functions
matthiaskoenig Mar 5, 2019
45bdc43
updated exception handling and error messages
matthiaskoenig Mar 5, 2019
7f97c87
renaming variable names and pep8 fixes
matthiaskoenig Mar 5, 2019
b51a2dd
renamed namespaces
matthiaskoenig Mar 5, 2019
92c1cd7
using config.bounds consistently
matthiaskoenig Mar 5, 2019
96f214e
Fixing ModelHistory bug & adding tests for filehandles
matthiaskoenig Mar 5, 2019
ef9b07d
tests for SBML groups added
matthiaskoenig Mar 5, 2019
89776e9
testing validation and smaller fixes
matthiaskoenig Mar 5, 2019
2994615
handling maximal path length on windows
matthiaskoenig Mar 5, 2019
a064fb1
Fix #811, Fix #663, Fix #804, correct handling of boundaryCondition=True
matthiaskoenig Mar 6, 2019
b5dd9c5
merged devel
matthiaskoenig Mar 11, 2019
3bc38a3
using tmp_path fixture
matthiaskoenig Mar 11, 2019
c56ab01
more pep8 nonsense, linelimit back to 79 in devel
matthiaskoenig Mar 12, 2019
79404dd
fixing order of imports for isort
matthiaskoenig Mar 12, 2019
0dd3526
fixing imports for isort
matthiaskoenig Mar 12, 2019
2e7b690
Test cases implemented
matthiaskoenig Mar 22, 2018
63750d4
genes parsed
matthiaskoenig Mar 22, 2018
0eb0976
objectives and flux bounds reader
matthiaskoenig Mar 22, 2018
a153ee4
annotations parsed
matthiaskoenig Mar 22, 2018
6cec2d5
first work on GPAs
matthiaskoenig Mar 22, 2018
1d0941a
small changes
matthiaskoenig Mar 22, 2018
b95e2c2
starting writing sbml
matthiaskoenig Mar 23, 2018
1b9ed5a
writing annotations
matthiaskoenig Mar 23, 2018
67212c9
writing bounds
matthiaskoenig Mar 23, 2018
0d76d52
write objective functions
matthiaskoenig Mar 23, 2018
e885c69
validation
matthiaskoenig Mar 23, 2018
72eff44
minor changes
matthiaskoenig Mar 23, 2018
451a296
parsing of cobra format
matthiaskoenig Mar 23, 2018
4099e82
fixing sboterms
matthiaskoenig Mar 23, 2018
4046d4e
minor changes
matthiaskoenig Mar 23, 2018
3a38f0e
handling legacy fbc, and consistency checks
matthiaskoenig Mar 25, 2018
7aa3ae8
id replacements
matthiaskoenig Mar 25, 2018
fcaedee
fixed reading/writing GPRs
matthiaskoenig Mar 25, 2018
51231e0
fixed annotation parsing
matthiaskoenig Mar 25, 2018
2df3efd
fixed annotation issue
matthiaskoenig Mar 25, 2018
a6e6141
fixed COBRA formula bug, all test passing
matthiaskoenig Mar 25, 2018
5bc0ee6
fixed package version bug
matthiaskoenig Mar 25, 2018
f4a975d
working on optimizations
matthiaskoenig Mar 25, 2018
2548cc3
minor optimizations
matthiaskoenig Mar 25, 2018
c4e57a1
latest changes
matthiaskoenig Jun 13, 2018
5b74129
fixing no objective issue
matthiaskoenig Jul 30, 2018
6cf95f9
fixing no active flux objective
matthiaskoenig Jul 30, 2018
b0b2a13
fixed failing tests due to changed solution structure
matthiaskoenig Feb 27, 2019
b87e670
working on documentation and pep8
matthiaskoenig Feb 27, 2019
f024da4
documentation and pep8 fixes
matthiaskoenig Feb 27, 2019
c68a1a4
chore: merge Greg's groups feature
Midnighter Feb 27, 2019
a8db73e
fix: update method name
Midnighter Feb 27, 2019
b15b715
chore: update model files
Midnighter Feb 27, 2019
d56e834
fixing pep8 issues
matthiaskoenig Feb 27, 2019
56af0bf
fixing pep8 issues
matthiaskoenig Feb 27, 2019
9578cd1
latest changes
matthiaskoenig Feb 27, 2019
1f13f37
fixme comments added
matthiaskoenig Feb 28, 2019
dfe468d
reading SBML meta information
matthiaskoenig Feb 28, 2019
0dc3a48
simplified handling of annotations and notes
matthiaskoenig Feb 28, 2019
5e929dc
support for filehandles
matthiaskoenig Feb 28, 2019
2574865
updated handling of notes and meta information
matthiaskoenig Feb 28, 2019
78f7b01
parsing legacy notes dictionary
matthiaskoenig Feb 28, 2019
bbeca17
reading legacy GENE_ASSOCIATION
matthiaskoenig Feb 28, 2019
867154f
fix incorrect warnings
matthiaskoenig Feb 28, 2019
f341c32
fixed py27 tests
matthiaskoenig Feb 28, 2019
26593ca
fixed pep8 issues
matthiaskoenig Feb 28, 2019
4747354
replacing old sbml readers and writers
matthiaskoenig Mar 1, 2019
41945c7
working on annotation fixes
matthiaskoenig Mar 1, 2019
8f20769
fixed pep8 issues
matthiaskoenig Mar 1, 2019
d00ea65
reading of groups information, buxfixes and typos
matthiaskoenig Mar 1, 2019
0c7d203
groups added to model
matthiaskoenig Mar 1, 2019
59e89a2
writing groups to SBML
matthiaskoenig Mar 1, 2019
fd3f3c3
https bugfix for identifiers.org
matthiaskoenig Mar 1, 2019
016ab49
proper handling of qualifiers on sbml export
matthiaskoenig Mar 1, 2019
c5bb107
typo fix
matthiaskoenig Mar 1, 2019
7a9df39
fixing attribute access for Windows
matthiaskoenig Mar 1, 2019
22a1474
additional fix for windows attribute access
matthiaskoenig Mar 1, 2019
d0925b3
changing matrix for faster test failure
matthiaskoenig Mar 1, 2019
ee6ec1a
more windows attribute fixes
matthiaskoenig Mar 1, 2019
d813829
reverting appveyor order
matthiaskoenig Mar 1, 2019
8ee55ba
gitignore in local exclude
matthiaskoenig Mar 5, 2019
fa15a68
writing to file handles, referencing issues
matthiaskoenig Mar 5, 2019
7c0fc13
updated fixmes and referencing of underlying issues
matthiaskoenig Mar 5, 2019
d0473b8
updating bounds to config.Configuration bounds
matthiaskoenig Mar 5, 2019
6511942
replaced single letter variables, documentation
matthiaskoenig Mar 5, 2019
b1e6b2b
refactoring top level functions
matthiaskoenig Mar 5, 2019
72aec05
updated exception handling and error messages
matthiaskoenig Mar 5, 2019
895281c
renaming variable names and pep8 fixes
matthiaskoenig Mar 5, 2019
5f145ce
renamed namespaces
matthiaskoenig Mar 5, 2019
e496da5
using config.bounds consistently
matthiaskoenig Mar 5, 2019
02a0060
Fixing ModelHistory bug & adding tests for filehandles
matthiaskoenig Mar 5, 2019
7597c96
tests for SBML groups added
matthiaskoenig Mar 5, 2019
23d8e83
testing validation and smaller fixes
matthiaskoenig Mar 5, 2019
08b6396
handling maximal path length on windows
matthiaskoenig Mar 5, 2019
cdf27b7
Fix #811, Fix #663, Fix #804, correct handling of boundaryCondition=True
matthiaskoenig Mar 6, 2019
d3d8033
using tmp_path fixture
matthiaskoenig Mar 11, 2019
39ddfeb
more pep8 nonsense, linelimit back to 79 in devel
matthiaskoenig Mar 12, 2019
3e93b62
fixing order of imports for isort
matthiaskoenig Mar 12, 2019
f986187
fixing imports for isort
matthiaskoenig Mar 12, 2019
02efdd0
rebased against devel
matthiaskoenig Mar 12, 2019
983a7cd
fixing unnecessary newline
matthiaskoenig Mar 12, 2019
0efc282
changes for isort
matthiaskoenig Mar 12, 2019
8f42291
more isort nonsense
matthiaskoenig Mar 12, 2019
4b5a275
more isort nonsense
matthiaskoenig Mar 12, 2019
f8c8616
some testing lxml
matthiaskoenig Mar 13, 2019
97b2972
major speedup groups parsing via hashmaps
matthiaskoenig Mar 13, 2019
327b987
bugfix of missing bounds in fbc, and better missing bounds reporting
matthiaskoenig Mar 15, 2019
24c2b9a
bugfix for sbo checks
matthiaskoenig Mar 15, 2019
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starting writing sbml
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matthiaskoenig committed Mar 23, 2018
commit da34ea220ceef74b19eff412a891eb348a518005
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