CI: Show all compiler warnings and treat as error#1362
Merged
FFroehlich merged 8 commits intodevelopfrom Dec 11, 2020
Merged
Conversation
dweindl
changed the title
Codecov Report
@@ Coverage Diff @@
## develop #1362 +/- ##
===========================================
+ Coverage 78.79% 78.80% +0.01%
===========================================
Files 63 63
Lines 9928 9933 +5
===========================================
+ Hits 7823 7828 +5
Misses 2105 2105
Flags with carried forward coverage won't be shown. Click here to find out more.
|
|
SonarCloud Quality Gate failed. |
Merged
FFroehlich
added a commit
that referenced
this pull request
Dec 15, 2020
* Fix: Don't require code context for call stack (fixes #1347) (#1348) * Fix Intel compiler warnings (#1349) 'type qualifier on return type is meaningless' Closes #1346 * Avoid segfault in CVODES CVAdataStore (#1351) Does not fix the root cause of occassional segfaults, but turns them into exceptions / integration failues. * CI: Move windows tests from TravisCI to GitHub Actions (#1354) Closes #1350 Removes obsolete .travis.yml * Fix cxxcode import for SymPy 1.6 (#1356) * Piecewise to heaviside (#1352) * parse piecewise into heaviside functions * Add Events as model quantity, parse Heavisides slightly differently * bugfix * rename symbols of root to h and switch order of functions to make sure h is known when dxdotdx_explicit is generated, to have the header file of h included * rename root symbols to HeavisideFunction_ to have things more indicative * tell AMICI about root, stau, and deltasx functions * heavisides without sensitivities should be working * need to change generation of stau to generration via inverse function theorem * compute stau via inverse function theorem * added functionality for deltasx, but segfaulting * bugfixing * remove debug output * get indentations right * Update python/amici/ode_export.py Co-authored-by: Fabian Fröhlich <fabian@schaluck.com> * Update python/amici/ode_export.py Co-authored-by: Fabian Fröhlich <fabian@schaluck.com> * Update python/amici/ode_export.py Co-authored-by: Fabian Fröhlich <fabian@schaluck.com> * Update python/amici/ode_export.py Co-authored-by: Fabian Fröhlich <fabian@schaluck.com> * Update python/amici/ode_export.py Co-authored-by: Fabian Fröhlich <fabian@schaluck.com> * Update python/amici/sbml_import.py Co-authored-by: Fabian Fröhlich <fabian@schaluck.com> * add a test for trajectories * fix sroot and test * cosmetic * add analytical expressions for sensitivities * add test for a complex condition * add test for many conditions * fix test * improve documentation * rename tests and refactor test for iterated piecewise, to check SBML piecewise logic a bit further * cleanup for code review * further cleanup * quarter way done with parsing heavisides into piecewise * fix logic parsing * monkeypatch sympy printer * enable more tests * implement denesting of piecewise * fix SBML nonsense * fix boolean triggers * simplify logic checks * fix code smells * add events to variable prototypes * cleanup * report details for skipped tests durin GHA run * better skip printing * resubstitution of non-optimized RHS into stau * add sensitivity tests * refactor tests * remove skipping display code * update test stats * Update python/amici/ode_export.py * Apply suggestions from code review Co-authored-by: Daniel Weindl <dweindl@users.noreply.github.com> * document and simplify _collect_heaviside_roots * address review comments * reduce complexity * misplaced docstrings Co-authored-by: Fabian Fröhlich <fabian@schaluck.com> Co-authored-by: dilpath <dilan.private+github@outlook.com> Co-authored-by: Daniel Weindl <dweindl@users.noreply.github.com> * restore support for species references (#1358) * restore support for species references * fixup and improve error message * extend support for sbml functions (#1357) * add more function mappings * fixup min/max * fix rem * add Mod to unsupported functions * more trigonometric functions * more functions, fix xref * fix xref with init assignment * extend unsupported functions * fix plus with empty arguments, update statistics * update test stats * fix stats * Refactor: introduce import_utils.py (#1361) * Refactor: introduce import_utils.py To collect format-independent functions for model import. * add additional file to SBML Testsuite path check * Include new module in doc Co-authored-by: Fabian Fröhlich <fabian@schaluck.com> * CI: Show all compiler warnings and treat as error (#1362) * CI: Show all compiler errors and treat as error Closes #1167 * Fix unused arguments * Fix deprecated-copy * Fix NVector (non-)const mess * Fix CMake deprecation warning * Fix doxygen * Fix some typos * Simplify / reduce number of const_casts * Add support for different noise models for PySB import (#1360) * Add support for different noise models for PySB import .. as already the case for SBML import. Closes #1176 * Respect noise model selection for PySB-PEtab import (#1339) * doc, import * Respect observable transformation for PySB-PEtab import (Fixes #1339) * Set ODEModel._has_quadratic_nllh Co-authored-by: Fabian Fröhlich <fabian@schaluck.com> * version bump * fix some code smells to trigger GHA builds again? * update docker to 20.04 * pin breathe Co-authored-by: Daniel Weindl <dweindl@users.noreply.github.com> Co-authored-by: Lorenzo Contento <lcontento@users.noreply.github.com> Co-authored-by: Paul Stapor <paul.stapor@helmholtz-muenchen.de> Co-authored-by: dilpath <dilan.private+github@outlook.com>
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
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
2 participants
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.
Closes #1167
... and pass
NVectors as pointers to const where possible (as opposed to unintended const pointers to non-const before).