Release 0.19.0 #2164

dweindl · 2023-08-24T05:50:25Z

waiting for Update reference list #2147
waiting for CMake: fix scope for -DHAS_BOOST_CHRONO #2163
waiting for Fix lib/ vs lib64/ issue with SUNDIALS config #2165

Adds support for SBML's `rateOf(.)` for most not-so-exotic cases. We currently can't check for functions with `<csymbol encoding="text" definitionURL="http://www.sbml.org/sbml/symbols/rateOf">`, and only check for functions named `rateOf`. This should be safe as long as we use the `SBMLFunctionDefinitionConverter` before. Tested in the following SBML semantic test suite cases: 01248,01249,01250,01251,01252,01253,01254,01255,01256,01257,01258,01259,01260,01261,01262,01263,01264,01265,01266,01267,01268,01269,01270,01293,01294,01295,01296,01297,01298,01299,01321,01322,01400,01401,01402,01403,01405,01406,01408,01409,01455,01456,01457,01458,01459,01460,01461,01462,01463,01482,01483,01525,01526,01527,01528,01529,01540,01541,01542,01543 Closes #769

Required for tellurium (via roadrunner)

Fixes `Jupyter command \`jupyter-nbconvert\` not found.`

* add SteadyStateComputationMode * fix namig * add steadystate_computation_mode_ to model * fix steadystate_sensitivity_mode default * fix * correct processPreEquilibration comment * correct x_ss and sx_ss description * clangformat * Update model settings * enum * serialization * .. * update docstrings in test_preequilibration * add SteadyStateComputationMode test * test that results with different steady-state computation modes are close * add compatibility check for SteadyStateComputationMode * split assertions and use numpy.testing.assert_allclose * change 'assert np.isclose' to 'assert_allclose' in all test_preequilibration tests * fix default values in test_swig_interface * nbconvert * fix example_errors notebook * nbconvert * -- --------- Co-authored-by: Daniel Weindl <dweindl@users.noreply.github.com> Co-authored-by: Daniel Weindl <daniel.weindl@helmholtz-muenchen.de>

Allows selecting parameters whose values are to be hard-coded (#1192). So far, restricted to parameters that aren't targets of rule or initial assignments. This can be extended later: lifting those restrictions on parameters, allow hard-coding Species with constant=True, ...

…ed off (#2137)

* More output * newtonOnly

Should avoid most `mxstep steps taken before reaching tout` failures (e.g. https://github.com/AMICI-dev/AMICI/actions/runs/5453350972/jobs/9922075162)

Closes #2040

* Wrapper for importing antimony models, this will allow for more concise test cases in the future * Remove tellurium dependency, use libantimony directly (so we don't need ncurses and other deps) * Add antimony example

…ters that are initial assignment targets (#2145) I.e. given the current way of processing initial assignments, events have to be processed first. Otherwise model compilation fails with `use of undeclared identifier`, because the respective parameter was replaced by its initial assignment value.

Add AMICI_TRY_ENABLE_HDF5 environment variable to disable trying to build with HDF5 support if HDF5 is found. Related to #2144

`/LIBPATH` doesn't seem to be compatible with ninja. See #2151.

Remove unused includes. Leftovers from the early beginnings, it seems ... In particular, don't use unistd.h for Windows-compatibility #2151

…assignments (#2156) Currently it is incorrectly assumed that the initial value of an event-assigned parameter is (convertible to) a float. Therefore, SBML import fails if the initial assignment contains a symbolic expression that can't be floatified. Fixes #2149.

* Use NEW version for any policy introduced up until 3.27. (Closes #2158) * Error on CMake dev warnings on GHA

We are unnecessarily building the complex / complex long versions of KLU. This PR removes them to speed up AMICI installation. We are still building both the int32_t and int64_t version of SuiteSparse, which leaves room for further optimization...

codecov · 2023-08-24T06:22:40Z

Codecov Report

Merging #2164 (8c80329) into master (a12d173) will increase coverage by 22.25%.
The diff coverage is 95.68%.

❗ Current head 8c80329 differs from pull request most recent head 0bf6216. Consider uploading reports for the commit 0bf6216 to get more accurate results

Additional details and impacted files

@@             Coverage Diff             @@
##           master    #2164       +/-   ##
===========================================
+ Coverage   54.38%   76.64%   +22.25%     
===========================================
  Files          33       82       +49     
  Lines        5518    14939     +9421     
===========================================
+ Hits         3001    11450     +8449     
- Misses       2517     3489      +972

Flag	Coverage Δ
cpp	`73.51% <80.95%> (?)`
petab	`54.23% <58.94%> (-0.16%)`	⬇️
python	`77.29% <97.89%> (?)`
sbmlsuite	`∅ <ø> (∅)`

Flags with carried forward coverage won't be shown. Click here to find out more.

Files Changed	Coverage Δ
include/amici/model.h	`61.11% <ø> (ø)`
include/amici/rdata.h	`95.23% <ø> (ø)`
src/rdata.cpp	`94.23% <ø> (ø)`
src/hdf5.cpp	`89.68% <33.33%> (ø)`
src/steadystateproblem.cpp	`86.34% <81.81%> (ø)`
python/sdist/amici/antimony_import.py	`94.11% <94.11%> (ø)`
include/amici/misc.h	`64.00% <100.00%> (ø)`
python/sdist/amici/de_export.py	`91.74% <100.00%> (+12.11%)`	⬆️
python/sdist/amici/import_utils.py	`87.95% <100.00%> (+33.73%)`	⬆️
python/sdist/amici/petab_util.py	`89.65% <100.00%> (ø)`
... and 3 more

... and 54 files with indirect coverage changes

Previously, the sundials cmake configuration wasn't found on systems that use lib64/ instead of lib/ Closes #2143

Closes #2040

* CMake: fix scope for -DHAS_BOOST_CHRONO (private -> public) Fixes the issue of potentially mixing boost and non-boost versions of CpuTimer. * CpuTimer unit test * simplify CpuTimer * document issues with compile definitions from dependencies * Add `amici.CpuTimer.uses_thread_clock` to check at runtime whether we are using `thread_clock`

Combine code for sparse model functions and their index files, i.e. generate only a single file instead of 3 individual files for content, rowvals, and colptrs, respectively. Advantage: Faster import of smaller models and fewer files. For a toy model, this reduced the build steps from 44 to 28, and reduced build time by >20% on my computer. Disadvantage: None found, so I don't think it worth adding an option for (not) combining those files. For larger models, there shouldn't be any impact. The extra time for compiling the index arrays should be negligible compared to computing the contents. Related to #2119 Here a test for a large model (N=1): | File | Size | Compilation time (s) | |--------------|--------:|---------------------:| | dwdx | 22.4MiB | 3413.64 | | dwdx_colptrs | 2.0KiB | 2.79 | | dwdx_rowvals | 65.6KiB | 2.66 | | *combined* | | 3416.79 | I'd consider this time increase negligible.

dweindl · 2023-08-25T07:55:04Z

Valgrind failures come from a libsbml issue. Not going to add a suppression, as it was fixed upstream already, just waiting for the next release.

socket-security · 2023-08-25T08:05:42Z

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* CI: Update sonar-scanner * Fix: `The property 'sonar.login' is deprecated and will be removed in the future. Please use the 'sonar.token' property instead when passing a token.` * Remove sonar cache config and GHA cache action By now, cache is stored on the server by default see https://docs.sonarcloud.io/advanced-setup/languages/c-c-objective-c/#analysis-cache * Sonar token to secrets

sonarqubecloud · 2023-08-25T20:51:51Z

SonarCloud Quality Gate failed.

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dweindl and others added 20 commits June 26, 2023 15:12

GHA: libncurses5

29dce6e

Required for tellurium (via roadrunner)

GHA: libncurses5

6dc927d

Fix nbconvert installation check

33550fb

Fixes `Jupyter command \`jupyter-nbconvert\` not found.`

black

b8edbcd

prevent the second run of newton's method in case simulation was turn…

e7b0643

…ed off (#2137)

Fix steadystate sensitivity mode for performance test (#2135)

a42ede2

* More output * newtonOnly

Increase maxSteps for ExampleSplinesSwameye2003.ipynb (#2136)

9f9a6ab

Should avoid most `mxstep steps taken before reaching tout` failures (e.g. https://github.com/AMICI-dev/AMICI/actions/runs/5453350972/jobs/9922075162)

Doc: Update reference list (#2138)

3d7bbc4

Closes #2040

Simplify / document antimony import (#2142)

7e0832a

* Wrapper for importing antimony models, this will allow for more concise test cases in the future * Remove tellurium dependency, use libantimony directly (so we don't need ncurses and other deps) * Add antimony example

Add AMICI_TRY_ENABLE_HDF5 env var (#2148)

3cccbb5

Add AMICI_TRY_ENABLE_HDF5 environment variable to disable trying to build with HDF5 support if HDF5 is found. Related to #2144

Doc: update sbml2amici (#2139)

bbf3295

Doc: Update Windows installation instructions (#2153)

515a68a

`/LIBPATH` doesn't seem to be compatible with ninja. See #2151.

Cleanup includes in hdf5.cpp (#2154)

3cd3494

Remove unused includes. Leftovers from the early beginnings, it seems ... In particular, don't use unistd.h for Windows-compatibility #2151

Set CMake policies for cmake 3.27 (#2162)

6090e21

* Use NEW version for any policy introduced up until 3.27. (Closes #2158) * Error on CMake dev warnings on GHA

dweindl force-pushed the release_0.19.0 branch from 39d929f to 06d1851 Compare August 24, 2023 05:51

dweindl added 2 commits August 24, 2023 13:21

Fix lib/ vs lib64/ issue with SUNDIALS config (#2165)

260b4f6

Previously, the sundials cmake configuration wasn't found on systems that use lib64/ instead of lib/ Closes #2143

Update reference list (#2147)

16aad6f

Closes #2040

dweindl force-pushed the release_0.19.0 branch 2 times, most recently from 262c6a8 to 3ba4ad9 Compare August 24, 2023 16:29

dweindl added 2 commits August 25, 2023 09:42

dweindl force-pushed the release_0.19.0 branch from 3ba4ad9 to 2b3d3dd Compare August 25, 2023 07:52

dweindl marked this pull request as ready for review August 25, 2023 07:53

dweindl requested a review from a team as a code owner August 25, 2023 07:53

dweindl mentioned this pull request Aug 25, 2023

CI: Update to jdk 17 to meet changed sonarcloud requirements #2166

Closed

dweindl force-pushed the release_0.19.0 branch from 2b3d3dd to 0e18eac Compare August 25, 2023 13:44

Release notes / v0.19.0

0bf6216

dweindl force-pushed the release_0.19.0 branch from 0e18eac to 0bf6216 Compare August 25, 2023 17:38

dweindl merged commit 7d161a6 into master Aug 26, 2023

dweindl deleted the release_0.19.0 branch August 26, 2023 06:02

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Release 0.19.0 #2164

Release 0.19.0 #2164

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Release 0.19.0 #2164

Release 0.19.0 #2164

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