Dev: Incremental update #29
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@@ Coverage Diff @@
## master #29 +/- ##
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+ Coverage 70.06% 70.79% +0.73%
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Files 44 45 +1
Lines 3311 3339 +28
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+ Hits 2320 2364 +44
+ Misses 991 975 -16
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psalvy
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Jun 7, 2019
* Dev: Incremental update (#29) * MNT: Pypi details * MNT: Adding veriable creation logs * FIX: typo * FIX: Issue #28, incorrect variable referencing * TST: adding tests for some of the analysis functions * FIX: more fixes from #28 * FIX: fixed transport reaction function * TST: Better tests, with a smaller model for I/O * TST/FIX: relative<- absolute paths for small_model resources * FIX: typo in paths to small_model resources for tests * VER: Bump v0.9.0-b2 * FIX: Update subclasses dynamically for the dict serialization.
psalvy
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Jan 21, 2020
* Dev: Incremental update (#29) * MNT: Pypi details * MNT: Adding veriable creation logs * FIX: typo * FIX: Issue #28, incorrect variable referencing * TST: adding tests for some of the analysis functions * FIX: more fixes from #28 * FIX: fixed transport reaction function * TST: Better tests, with a smaller model for I/O * TST/FIX: relative<- absolute paths for small_model resources * FIX: typo in paths to small_model resources for tests * VER: Bump v0.9.0-b2 * VER: bump to v0.9.1 * Update LICENSE.txt * Fixing a couple of minor bugs and added new variable class (#35) Thank you @remidhum * FIX: fixed the apply_directionality function solution.raw dataframe index does not contain the fwd and bwd use variables. * ENH: added new binary variable class This class is usefull to deal with inactive reactions in a model. * ENH: deal with models without an objective function Objective function is set to Zero (symbol("0") does not work!) if there is no defined objective function * OOPS: change proper function ... * FIX: fixed the failing test As suggested, I added a check to determine what object type is passed. * MNT: solution object type testing improved * feat: TOO SLOW eQuilibrator integration * refactor: make use of new changes on equilibrator_api (https://gitlab.com/elad.noor/equilibrator-api/merge_requests/13) * chore: equilibrator_api as extra dependency * fix: make thermo_data optional * chore: test equilibrator_api integration * chore: set equilibrator_api as extra dependency * refactor: back to previous init to impose thermo_data argument * refactor: build thermo data from equilibrator as external function * fix: install equilibrator as package Co-Authored-By: Moritz E. Beber <midnighter@posteo.net> * FIX: correct typo on error attribute * refactor: load equilibrator on import of file * REFACTOR: move print to logger warning * FIX: set lower bound version on equilibrator_cache compatibility * FIX: remove f-string syntax * FIX: test equilibrator compatibility only for >= py3.6 * FIX: try to overcome py3.5 problems * REFACTOR: ignore equilibrator test collection on py<3.6 * FIX: collect tests properly * DOCS: add script as tutorial for equilibrator integration * refactor: move equilibrator test to another module * REFACTOR: encapsulate equilibrator testing * "REFACTOR: REVERT encapsulate equilibrator testing, it doesn't work" This reverts commit edc240d. * "REFACTOR: REVERT move equilibrator test to another module" This reverts commit 2f256de. * Update test_equilibrator.py * Update conftest.py * fix: require Py>=3.6 when for equilibrator extra * fix: import on function * fix: remove conftest, proper coverage * FIX: move pytfa import to function * DOCS: warn about python version for equilibrator integration * REFACTOR: remove GLPK solver enforcement * fix: avoid side effects on tmodel * FIX: change equilibrator-cache version * TEST: change extra dependency management before_install * FIX: typo * FIX: add equilibrator_api to build * fix: change travis pytest command to properly account for coverage * FIX: typo * FIX: separate coverage from pytest * FIX: call codecov * FIX: give coverage a try * FIX: correct coverage install and calls * Revert "FIX: correct coverage install and calls" This reverts commit c1dfe77. * Revert "FIX: give coverage a try" This reverts commit eda6365. * Revert "FIX: call codecov" This reverts commit 38399e3. * Revert "FIX: separate coverage from pytest" This reverts commit 43ba69b. * Revert "FIX: typo" This reverts commit f10f1f8. * Revert "fix: change travis pytest command to properly account for coverage" This reverts commit 2b7b257. * FIX: collect equilibrator tests at the end * FIX: try with edit mode * TEST: change file name Co-authored-by: realLCSB <31034133+realLCSB@users.noreply.github.com> Co-authored-by: Pierre Salvy <psalvy@users.noreply.github.com> Co-authored-by: RémiDhum <rdhumeaux@gmail.com> Co-authored-by: Moritz E. Beber <midnighter@posteo.net>
psalvy
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Mar 4, 2021
Bypassing Travis because failing on GLPK not sympy anymore. See PR #49 * Dev: Incremental update (#29) * MNT: Pypi details * MNT: Adding veriable creation logs * FIX: typo * FIX: Issue #28, incorrect variable referencing * TST: adding tests for some of the analysis functions * FIX: more fixes from #28 * FIX: fixed transport reaction function * TST: Better tests, with a smaller model for I/O * TST/FIX: relative<- absolute paths for small_model resources * FIX: typo in paths to small_model resources for tests * VER: Bump v0.9.0-b2 * VER: bump to v0.9.1 * Update LICENSE.txt * Fixing a couple of minor bugs and added new variable class (#35) Thank you @remidhum * FIX: fixed the apply_directionality function solution.raw dataframe index does not contain the fwd and bwd use variables. * ENH: added new binary variable class This class is usefull to deal with inactive reactions in a model. * ENH: deal with models without an objective function Objective function is set to Zero (symbol("0") does not work!) if there is no defined objective function * OOPS: change proper function ... * FIX: fixed the failing test As suggested, I added a check to determine what object type is passed. * MNT: solution object type testing improved * LIC: Create CLAI * Name correction (#41) Thank you for this correction :) Since I copied this from Google scholar, maybe check that they got your name right! Cheers, Pierre * Allow saving of imported mat files as json (#42) * Allow saving of imported mat files as json When importing .mat models, the membranePot type is numpy's int16. The change makes it a standard int so that it can be saved as json. * convert to float * VER: Bump to 0.9.2 * MNT: removing warnings from deprecated usage of logger.warn * FIX: metabolite thermo data was not recovered upon serialization * FIX: Equilibrator update + reqs for building Dockerfile * FIX: newer pypi version * FIX: actual newer pypi version * Update README.rst * Update utils.py * Zero import Co-authored-by: realLCSB <31034133+realLCSB@users.noreply.github.com> Co-authored-by: Pierre Salvy <psalvy@users.noreply.github.com> Co-authored-by: Pierre Salvy <pierre.salvy@epfl.ch> Co-authored-by: RémiDhum <rdhumeaux@gmail.com> Co-authored-by: Daniel F Hernandez <dan.fhg@gmail.com>
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solution.x_dict(see KeyError and potential solution in sampling tutorial #28)