github.com/GeomScale/dingo commits | Ecosyste.ms: OpenCollective

Merge pull request #88 from vfisikop/fix/dingo_with_lpsolve

Build volestipy with lpsolve

3af76645125902fab442fae30df10299533149c8 authored 12 months ago

Merge branch 'develop' into fix/dingo_with_lpsolve

3589f8c0e18c9fd34cf368bd39ee0b83f29e2e4e authored 12 months ago

Merge pull request #87 from vfisikop/fix/remove_volesti4dingo_branch

Update dingo to use volesti develop instead of volesti4dingo branch

4ce6da31f2ea796deb2a4152e1f3cbe47cb85ffd authored 12 months ago

Update dingo to use volesti develop instead of volesti4dingo branch

38b7ffb2defa95dbc00f432a8fde76ce85f662bd authored 12 months ago

Build volestipy with lpsolve

43938d9ebebf12c439beaceaacff3e2f823f2d92 authored 12 months ago

Update dingo to use volesti develop instead of volesti4dingo branch

382abab03d36b4ed0a7763d07fbacd9a0b71a4cf authored 12 months ago

support of medium modification and cobra model loading (#76)

* remove commented line

* address issues #74 and #75

* import Dict type

* test for boun...

e7a96d9cdfa0aece53ec8befca064b6b3c0ab0eb authored about 1 year ago

Create redundant_facet_removal_backup.py (#81)

* Create redundant_facet_removal_backup.py

* Update redundant_facet_removal_backup.py

* Cr...

aaae4ae63f432da45eb0f4363a92767ba537a074 authored over 1 year ago

Expose HMC walks with Gaussian and exponential distributions (#73)

* Exposed HMC walk with Gaussian and exponential distribution with specified parameters

* Min...

a1724b07217248d51e4b3e799a82c039b667c91e authored over 1 year ago

Exposed two HMC walks with exponential and Gaussian sampling from Volesti (#68)

* Exposed two HMC exact walks with exponential and Gaussian sampling from Volesti

* Modified ...

5c6a4f5613bcfa927f891168e63b7aee12bae510 authored over 1 year ago

Fix bug in retrieving samples (#70)

* fix bug in retrieving samples

* resolve PR reviews

---------

Co-authored-by: Apostolo...

f5440b697a597405b04221208d5644f53f95a2bd authored over 1 year ago

Fix typo in README.md (#69)

c71b3c69ee800231e3ed43f159c215a5b87598ff authored over 1 year ago

fix magic command denoter; issue 60 (#63)

d9bdef9507849edd863763ca854d8d35ad3f0dc8 authored almost 2 years ago

Fix poetry version 1.3.2 in actions. (#62)

c32ce986cbcb12e47d8c432d3756644bf57ac8cf authored almost 2 years ago

update colab; fix #60 (#61)

1b6d598885f6eaf12ad21eaad5341bba707c5863 authored almost 2 years ago

Edits on copula illustration and export (#58)

* export and edits on copula function

* edit camera on copula

* kaleido dependency added
...

3104cbd214fa7200a7763da6f446445ec2160147 authored almost 2 years ago

Bump future from 0.18.2 to 0.18.3 (#56)

Bumps [future](https://github.com/PythonCharmers/python-future) from 0.18.2 to 0.18.3.
- [Relea...

12785fbcc0c43d851c55f3d961e4413c167d71da authored about 2 years ago

Update README.md

31e283bc0fcbaee25952ff1d9e54ee41af99dc99 authored about 2 years ago

Move the documentation to readme (#54)

* move the documentation to readme

* fix readme

* minor improvement in readme

* minor i...

3f98892ee7fe3bce9b5f437ed0a557e787c5716c authored about 2 years ago

Expose rounding methods (#53)

* expose rounding methods

* fix minor bug in function declaration

* remove unused comments...

c82849f92df90762bf37d8c0621392dd3b515872 authored about 2 years ago

Expose uniform random walks (#40)

* fix gen_samples breaking point

* add to polytope sampler the option to not use mmcs

* im...

aeef11141af844a1eb2074097a22214f4a99d53a authored about 2 years ago

implement copula illustration in dingo pipeline (#52)

* implement copula illustration in dingo pipeline

* add documentation comments in the new fun...

dc929d782ab3daa574da07bfc8fe907c6ffa691d authored about 2 years ago

Load models (#50)

* minor edits

* fix fba - fva

* fixed refs

* build model from sbml fil...

7e86be3f8aaf0046b178c6821b3cb718b0286551 authored about 2 years ago

Merge pull request #51 from vissarion/add_cobrapy

Add cobra package as a dependence.

2893dfa4e74e101f9df659a3c56002f8050898df authored about 2 years ago

Add cobra package.

b6bccc43725f24ee45b8c8cbf739a6dd146bcf4d authored about 2 years ago

Merge pull request #49 from hariszaf/dingo_tutorial

reorder Jupyter notebook sections and minor edits

1f1bbb7547c67c2e80fd8d3b6c82d15952bf8dbf authored about 2 years ago

reorder sections and minor edits

37e2952b573f130ba3766f663f44098f7fd71344 authored about 2 years ago

Merge pull request #48 from vissarion/fix/ci

Update poetry installation CI command

cdb5245d3f07c73bf75bf8bbf39895a5c9c0d4e1 authored about 2 years ago

Update poetry installation CI command from get-poetry.py to install.python-poetry.org

0bbc1e1a77b3de36250cde11d356b6afa13789e3 authored about 2 years ago

Move updated tutorial to tutorials folder and copyedit (#38)

* Move updated tutorial to tutorials folder

* Copyedit tutorial

* Delete reference to comm...

03d6e65a1278753bd879ea24f6512e7e8b95af93 authored over 2 years ago

Update mention of unit tests in main README (#39)

tests/unit_tests.py was deleted, so instead instruct the user to run the individual tests.

aba7913a0ec6841f02014bdacb6c98c4bbfb97a8 authored over 2 years ago

Make changes to code style (#37)

* Condense conditionals to boolean expression

* Delete overridden C++ bool import

* Use bi...

b7c3ffb14c06ecf7d8257c7972eb255508acfff1 authored over 2 years ago

Enable github actions for pull requests and activate more tests

41a89df84df5700ee9ddea87ea058be5a2188320 authored over 2 years ago

Copyedit main README + comments in volestipy.pyx (#36)

* Copyedit comments in volestipy.pyx

* Copyedit main README

24e1ac7c3c6857969b98d2e5764a95b052a55835 authored over 2 years ago

Update poetry dependencies

ec4228bb685bf079e99bf7516d17918860efc047 authored over 2 years ago

Fix typo in README (#35)

66e1cc7184776b8a2296dc21d83debd3eb2a552f authored over 2 years ago

add logo

fa5b5b38f14bbf247906b8ca235facb2dab89486 authored about 3 years ago

Add a boolean to control the preprocessing method (#31)

* add a boolean to control the preprocessing method

* add warning when slow mode in on

* c...

311375bd584b82ad24aea5e2d0870d316c69047d authored over 3 years ago

fix the bug in sample_from_polytope() (#29)

dcfe3973fcbec6867102274066b51ab2a6934940 authored over 3 years ago

Improve preprocessing (#27)

* implement a function to compute redundant facets

* update facet redundant removal

* use ...

085d41ce712e4b48df666d03cefb5bf750b22813 authored over 3 years ago

Fix compile errors (#28)

* fix break points

* fix bugs in bindings.cpp

* resolve the comments in PR's discussion

c476a7b5d46947f69070248e79734622706e64b4 authored over 3 years ago

Rename volume_approximation to volesti

c0128e0bd0ffc29af442d58d5f83dd64c5183b82 authored over 3 years ago

Set submodule volume_approximation to track volesti4dingo branch of volesti main repository

541a8c2d5468cede97c51e1fd5c595e8db766368 authored over 3 years ago

Fix/json biomass index value (#22)

* Add github actions

* fix unittests

* set black code style

* implement a knock out of ...

45c531826654e73af57000e77877a2c4b276cd90 authored over 3 years ago

update to the new commit in volesti

2815502aaf2285c0e677e5d842fc604c64fabfc3 authored over 3 years ago

update the commit of mmcs

7f10f42bc614b5c71039860b24ae6d768ac2d696 authored over 3 years ago

dingo tutorial notebook (#17)

* unknown

* Revert "Create CODE_OF_CONDUCT.md"

This reverts commit 23639fc2d40957d7fb20b46...

b5dfb9b2a1f1357b565f00886c8e46e6889344ca authored over 3 years ago

Update issue templates

a76b4be22f33feac86dff38746c7f2706afb2b67 authored over 3 years ago

Create CODE_OF_CONDUCT.md

23639fc2d40957d7fb20b464df7c6b3ed225ca2b authored over 3 years ago

Add github actions (#10)

a7e980e0ff5e89487cc173119caab6e816863b50 authored over 3 years ago

Merge pull request #13 from TolisChal/shut_down_reaction

Knock out a reaction flux

bc6fa3b49664063bb03994ca191108aad357bd3d authored over 3 years ago

Merge pull request #12 from TolisChal/black_style

Set Black code style

6953311b25dcb2ecd469dc45c70e39ba891ed1cb authored over 3 years ago

Merge pull request #11 from TolisChal/fix_unittests

Fix tests

cc119e9775d9ef0998ae6a2a8d25be5f961aab58 authored over 3 years ago

check if the reaction-index is integer

51a6a18b71cb9d9e35112a571509e0d7eb8f254a authored over 3 years ago

implement a knock out of a reaction flux

401b5d4dfe3db29f0bdedb7e7c6801081c6f6950 authored over 3 years ago

set black code style

50676dded93c6a4be18e6571df5018def4f7db7a authored over 3 years ago

fix unittests

a86add1706180e9bb2761f7fa87c586014f401b2 authored over 3 years ago

Improve Python code (#9)

* improve python interface and classes

* improvements in the python code

* update readme

97ac69719ca14ffec48def2ece52b0578c20ef0f authored over 3 years ago

Update boost download link (#8)

44511a0762f4e2809724aeb7844746314fa20cd6 authored over 3 years ago

fix broken links in the documentation

a7f0dbccaa814ea62e1f42e39d062e54be0dd7b3 authored almost 4 years ago

Restructure of Python code (#7)

* implement metabolic network and sampler classes

* implement new pipeline

* fix run-time ...

f7c8ad64f87972d337610fcdef18987545a093ad authored almost 4 years ago

Initialization of the default branch (#6)

* add volesti as submodule

* add external and rhino interface

* rename to misha

* renam...

b9c8b8702655674d835dc530c08dd828ef0b0475 authored almost 4 years ago

changw name in readme

a31d20ced2b6f018cca4a048b958b2256552971e authored almost 4 years ago

Create LICENSE

3c771e134ad020201b4aa12747d97b8a47b37958 authored almost 4 years ago

rename to misha

a81f6d4f0de3d6857fe30bdeb818f200920dbe45 authored almost 4 years ago

Initial commit

f678817dbcb18b55e4e6263d7c28e3ebdd8fa4ae authored almost 4 years ago