PEtab-multilanguage proof of concept for PySB-PEtab #1800
Merged
Conversation
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Codecov Report
Additional details and impacted files@@ Coverage Diff @@
## develop #1800 +/- ##
===========================================
+ Coverage 76.11% 76.29% +0.18%
===========================================
Files 80 81 +1
Lines 14840 15959 +1119
===========================================
+ Hits 11295 12176 +881
- Misses 3545 3783 +238
Flags with carried forward coverage won't be shown. Click here to find out more.
|
dweindl
force-pushed
the
petab_abstract_model
branch
from
b24f413 to
4116235
Compare
dweindl
force-pushed
the
petab_abstract_model
branch
from
2d5b6ad to
91dbfc7
Compare
dweindl
commented
Jun 27, 2022
|
Kudos, SonarCloud Quality Gate passed! |
dweindl
changed the title
dweindl
commented
May 10, 2023
Comment on lines
+33
to
+35
| pytest-cov cmake_build_extension numpy | ||
| pip install git+https://github.com/FFroehlich/pysb@fix_pattern_matching # pin to PR for SPM with compartments | ||
| pip install --verbose -e ${AMICI_PATH}/python/sdist[petab,test,vis] --no-build-isolation |
Member
Author
There was a problem hiding this comment.
Suggested change
| pytest-cov cmake_build_extension numpy | |
| pip install git+https://github.com/FFroehlich/pysb@fix_pattern_matching # pin to PR for SPM with compartments | |
| pip install --verbose -e ${AMICI_PATH}/python/sdist[petab,test,vis] --no-build-isolation | |
| pytest-cov cmake_build_extension numpy | |
| pip install --verbose -e ${AMICI_PATH}/python/sdist[petab,test,pysb,vis] --no-build-isolation |
before merge
FFroehlich
approved these changes
May 18, 2023
documentation/rtd_requirements.txt
Outdated
| @@ -1,4 +1,5 @@ | |||
| # NOTE: relative paths are expected to be relative to the repository root | |||
| #git+https://github.com/PEtab-dev/libpetab-python@develop#egg=petab | |||
Member
There was a problem hiding this comment.
Suggested change
| #git+https://github.com/PEtab-dev/libpetab-python@develop#egg=petab | |
| petab>=0.2.1 |
Member
Author
There was a problem hiding this comment.
The current requirement is handled via setup.cfg. Will remove.
github-merge-queue
bot
removed this pull request from the merge queue due to failed status checks
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
This implements a proof of concept for the PEtab multi-language proposal.
Handles PySB-PEtab problems using the recent PEtab model abstraction (PEtab-dev/libpetab-python#145).
Removes the (need for the) current
PysbPetabProblemand allows for importing PEtab problems through a single interface.Runs the tentative PEtab version 2 test cases from PEtab-dev/petab_test_suite#53.
Blocked by pysb/pysb#570
Blocked by PEtab-dev/libpetab-python#203