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Added an Analyser class #631

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merged 248 commits into from
Sep 30, 2020
Merged

Added an Analyser class #631

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168d016
Analyser: skeleton for our analyser class and test.
agarny Jun 16, 2020
efa318b
Analyser: added a test for an empty model.
agarny Jun 16, 2020
a27df70
Make ClangFormat happy.
agarny Jun 16, 2020
d183e7e
Some minor cleaning up.
agarny Jun 16, 2020
b8868ae
Analyser: test for an initialised VOI.
agarny Jun 16, 2020
6a4499c
Merge branch 'develop' into issue499.
agarny Jun 16, 2020
e0248f4
Merge branch 'develop' into issue499.
agarny Jun 19, 2020
5ff80f8
Some minor cleaning up.
agarny Jun 21, 2020
a64d1ac
Analyser: make sure that a model is valid before processing it.
agarny Jun 21, 2020
c2409b1
Analyser: make our `emptyModel` pass.
agarny Jun 21, 2020
d64ccb9
Analyser: moved all/most of the analysis code from the Generator clas…
agarny Jun 22, 2020
3e91cae
Make ClangFormat happy.
agarny Jun 22, 2020
0f3bb44
Debug: have `printAst()` now use of our new `AnalyserEquationAst` class.
agarny Jun 22, 2020
77b057e
Generator: removed the `emptyModel()` and `initializedVariableOfInteg…
agarny Jun 22, 2020
fa749da
Analyser: moved some Generator tests that are actually analysis tests.
agarny Jun 22, 2020
b018d1b
Some minor cleaning up.
agarny Jun 22, 2020
e66a48e
Analyser: added an `AnalyserModel` class.
agarny Jun 22, 2020
f2fbb8b
Some minor cleaning up.
agarny Jun 23, 2020
5fc50a6
Some minor cleaning up.
agarny Jun 23, 2020
1e1e25c
Some minor cleaning up.
agarny Jun 23, 2020
d036575
Some minor cleaning up.
agarny Jun 23, 2020
8db6248
Generator: don't use internal data.
agarny Jun 23, 2020
31af8f6
Some minor cleaning up.
agarny Jun 23, 2020
9386de0
Analyser variable: provide index value.
agarny Jun 23, 2020
a94c37a
Generator: don't use internal data.
agarny Jun 23, 2020
1fc4578
Some minor cleaning up.
agarny Jun 23, 2020
5d24b9f
Some minor cleaning up.
agarny Jun 23, 2020
2e1976e
Generator: created and use the GeneratorEquation class.
agarny Jun 24, 2020
62100d6
Debug: removed `printAst()`.
agarny Jun 24, 2020
13962c6
Some minor cleaning up.
agarny Jun 24, 2020
82658ca
Analyser: skeleton of the `AnalyserEquation` class.
agarny Jun 24, 2020
a5e4e04
Analyser: removed the `create()` method from the `AnalyserModel` and …
agarny Jun 24, 2020
36023ab
Some minor cleaning up.
agarny Jun 24, 2020
294a449
Analyser: converting `AnalyserEquationAst` to an API class.
agarny Jun 24, 2020
3185f3e
Some minor cleaning up.
agarny Jun 24, 2020
67f9fc8
Analyser: implemented the `AnalyserEquation` class.
agarny Jun 24, 2020
a27ad7d
Debug: put back `printAst()`.
agarny Jun 25, 2020
7e3803d
Generator: removed the analysis code from it.
agarny Jun 25, 2020
103deb8
Generator: added a test for coverage purposes.
agarny Jun 25, 2020
05ee73e
Some minor cleaning up.
agarny Jun 25, 2020
8e910ea
Generator: reworked the code a bit for coverage purposes.
agarny Jun 25, 2020
627bd4a
Some minor cleaning up.
agarny Jun 25, 2020
2878994
Analyser: some coverage tests.
agarny Jun 25, 2020
66807c0
Some minor cleaning up.
agarny Jun 25, 2020
09f5726
Generator: removed an old Python GeneratorVariable test.
agarny Jun 25, 2020
8852221
SWIG: updated some interfaces and created some new ones.
agarny Jun 25, 2020
9a8d391
Merge branch 'develop' into issue499.
agarny Jun 25, 2020
9cfd681
Python bindings: updated our __init__.py file.
agarny Jun 25, 2020
f3f46a2
Some minor cleaning up.
agarny Jun 25, 2020
c4b58c5
Some minor cleaning up.
agarny Jun 26, 2020
326f4df
Some minor cleaning up.
agarny Jun 26, 2020
e95ff4b
Some minor cleaning up.
agarny Jun 26, 2020
2628fe6
SWIG: cleaned up / added some interfaces.
agarny Jun 26, 2020
64cebfb
Merge branch 'develop' into issue499.
agarny Jun 29, 2020
9301f21
Some minor cleaning up.
agarny Jun 29, 2020
c361093
Analyser: added a couple of methods to go from an AnalyserVariable to…
agarny Jun 29, 2020
9b6bc20
Make GCC coverage happy.
agarny Jun 29, 2020
25edc9b
Make memcheck happy.
agarny Jun 29, 2020
d0ac8fa
Disable most tests.
agarny Jun 29, 2020
582d128
test
agarny Jun 29, 2020
8de3c09
test
agarny Jun 29, 2020
52699eb
test
agarny Jun 29, 2020
5e34092
test
agarny Jun 29, 2020
6adf4a3
test
agarny Jun 29, 2020
3f06986
Analyser: create a proper shared pointer.
agarny Jun 29, 2020
b0583d2
Some minor cleaning up.
agarny Jun 29, 2020
304c2c0
Merge branch 'issue499' into temp.
agarny Jun 29, 2020
41f83cb
test
agarny Jun 29, 2020
f584131
test
agarny Jun 29, 2020
714b5fd
test
agarny Jun 30, 2020
dd61307
Some minor cleaning up.
agarny Jun 30, 2020
785c0c9
Analyser: create a proper shared pointer.
agarny Jun 30, 2020
a6b6994
Analyser: make our consistent.
agarny Jun 30, 2020
0d92e92
Analyser: replaced static create() methods with private populate() ones.
agarny Jun 30, 2020
30b8d27
Analyser: replaced static create() methods with private populate() ones.
agarny Jun 30, 2020
7e2d89d
Merge branch 'issue499' into temp.
agarny Jun 30, 2020
27bc41a
Some minor cleaning up.
agarny Jun 30, 2020
8defb31
Oops, had committed some code that disabled some tests!
agarny Jun 30, 2020
65f934f
Some minor cleaning up.
agarny Jun 30, 2020
e9687ab
Revert "Oops, had committed some code that disabled some tests!"
agarny Jun 30, 2020
35c799f
Some minor cleaning up.
agarny Jun 30, 2020
2fb32ce
Analyser: make memcheck happy by avoiding circular referencing.
agarny Jun 30, 2020
06e91ff
Re-enable all of our tests.
agarny Jun 30, 2020
1d8a7bd
Merge branch 'develop' into issue499.
agarny Jun 30, 2020
71e5d13
Merge branch 'temp' into issue499.
agarny Jun 30, 2020
2d82138
Python: slight reworking of the generator profile test.
agarny Jun 30, 2020
c1c9e21
Some minor cleaning up.
agarny Jul 1, 2020
33edfa6
Analyser: added a Python test for the AnalyserEquationAst class.
agarny Jul 1, 2020
fd849b2
Analyser: added a Python test for testing the Analyser's inheritance.
agarny Jul 1, 2020
fde13a9
Some minor cleaning up.
agarny Jul 1, 2020
6f3a1ff
Analyser: added a comment to the test_process_model Python test.
agarny Jul 1, 2020
86f7324
Interfaces: some minor cleaning up for the Analyser and Generator cla…
agarny Jul 1, 2020
b696f26
Merge branch 'develop' into issue499.
agarny Jul 1, 2020
17707a8
Analyser: renamed a couple of functions for consistency with the rest…
agarny Jul 2, 2020
4125353
Analyser: renamed a couple of functions for consistency with the rest…
agarny Jul 2, 2020
a6c0aac
Fixed a typo.
agarny Jul 2, 2020
51fb4ad
Use British English.
agarny Jul 2, 2020
0d22590
Fixed a typo.
agarny Jul 2, 2020
dc6c820
Analyser: minor reworking of code.
agarny Jul 2, 2020
db958d8
Analyser: fixed the documentation.
agarny Jul 2, 2020
3bfe97e
AnalyserEquation: fixed the documentation.
agarny Jul 2, 2020
1983a4c
AnalyserEquationAst: fixed the documentation.
agarny Jul 2, 2020
681209c
Replaced "lower" with "less" across our documentation.
agarny Jul 2, 2020
e2600fb
Use "[less|greater] than or equal to".
agarny Jul 2, 2020
4762f45
Double quote function/operator names.
agarny Jul 2, 2020
cbe514c
Issue: properly order causes.
agarny Jul 2, 2020
c253986
Utilities: updated the documentation for `isSameOrEquivalentVariable()`.
agarny Jul 2, 2020
395a18e
Analyser: don't set the cause of an issue.
agarny Jul 2, 2020
577e1af
Generator: don't make it a logger anymore.
agarny Jul 2, 2020
f8278f0
Generator: don't make it a logger anymore.
agarny Jul 2, 2020
0e5bad4
SWIG: sorted out our types.
agarny Jul 2, 2020
27e86f0
SWIG: fixed the Prefix enum.
agarny Jul 2, 2020
5027d33
SWIG: added the check for the Issue::Level enum.
agarny Jul 2, 2020
80cffc0
SWIG: removed the check for Generator::ModelType since it doesn't exi…
agarny Jul 2, 2020
c9f1e4b
SWIG: added checks for AnalyserEquationAst::Type, AnalyserModel::Type…
agarny Jul 2, 2020
1a79518
Some minor cleaning up.
agarny Jul 3, 2020
f922c9a
SWIG: removed checks for AnalyserModel::Type and AnalyserVariable::Type.
agarny Jul 3, 2020
bf8780c
SWIG: use `$type` rather than the type itself.
agarny Jul 3, 2020
f9f8c88
Merge branch 'develop' into issue499.
agarny Jul 5, 2020
7f08c87
Use British spelling.
agarny Jul 5, 2020
ff355d8
Removed some debug code.
agarny Jul 6, 2020
e741b7c
Some minor cleaning up.
agarny Jul 7, 2020
b6296cc
Analyser: don't make the AnalyserEquationAst class a friend of the Ge…
agarny Jul 7, 2020
e18203e
Some minor cleaning up in our Analyser tests.
agarny Jul 7, 2020
0b6baf7
Analyser: remove model information from error messages.
agarny Jul 7, 2020
df4f564
Merge branch 'issue313' into issue499.
agarny Jul 9, 2020
fb3cda2
Analyser/Generator: made use of `auto` as much as possible.
agarny Jul 9, 2020
e7070d5
Some minor cleaning up.
agarny Jul 9, 2020
79b2215
Some minor cleaning up.
agarny Jul 10, 2020
bdb1144
Some minor cleaning up.
agarny Jul 10, 2020
2bf01bf
AnalyserEquationAst: track its corresponding AnalyserVariablePtr, not…
agarny Jul 10, 2020
17702c6
Some minor cleaning up.
agarny Jul 10, 2020
40eb8fe
Revert "AnalyserEquationAst: track its corresponding AnalyserVariable…
agarny Jul 10, 2020
77adf3b
Merge branch 'issue655' into issue499.
agarny Jul 13, 2020
f1ded05
AnalyserEquationAst: removed a method that we don't use anymore.
agarny Jul 13, 2020
3194f49
Merge branch 'issue313' into issue499.
agarny Jul 13, 2020
733e7c0
Some minor cleaning up.
agarny Jul 13, 2020
2df5024
Merge branch 'issue313' into issue499.
agarny Jul 13, 2020
6b0b7e9
Merge branch 'issue313' into issue499.
agarny Jul 14, 2020
c78a14c
Analyser: added a meaningful cause to the issues generated by the ana…
agarny Jul 14, 2020
5455625
Analyser: renamed `processModel()` to `analyseModel()`.
agarny Jul 15, 2020
6188519
Merge branch 'develop' into issue499
nickerso Jul 15, 2020
bc7f939
Merge branch 'develop' into issue499.
agarny Jul 16, 2020
acfb589
Generator: made some implementation methods constant.
agarny Jul 17, 2020
6826fcb
Merge branch 'issue665' into issue499.
agarny Jul 20, 2020
1cf9251
Merge branch 'issue665' into issue499.
agarny Jul 20, 2020
b3f9c03
Merge branch 'develop' into issue499.
agarny Jul 22, 2020
4ecbc18
Merge branch 'develop' into issue499.
agarny Jul 22, 2020
d083583
Merge branch 'develop' into issue499.
agarny Jul 23, 2020
d4e40d8
Merge branch 'develop' into issue499.
agarny Jul 28, 2020
2be8f89
Merge branch 'issue672' into issue499.
agarny Jul 28, 2020
0de2436
Merge branch 'issue672' into issue499.
agarny Jul 29, 2020
54bc8cf
Merge branch 'develop' into issue499.
agarny Jul 29, 2020
7b80a4e
Merge branch 'develop' into issue499.
agarny Jul 29, 2020
d783066
Analyser: various reworking/improvements of/to the code.
agarny Jul 30, 2020
c36b577
AnalyserEquation: fixed a memory leak.
agarny Jul 31, 2020
dfec864
Some minor cleaning up.
agarny Aug 1, 2020
d178b98
GeneratorProfile: updated the documentation.
agarny Aug 2, 2020
7f8a383
Analyser tests: check that the issues are errors.
agarny Aug 2, 2020
0ad65b2
Generator tests: look for errors, not just issues.
agarny Aug 2, 2020
4c6f971
Generator tests: slight update to our coverage test.
agarny Aug 2, 2020
1f70832
Merge branch 'develop' into issue499
kerimoyle Aug 5, 2020
e93d316
Generator: ensure that we get 100% coverage in our sha1() method.
agarny Aug 5, 2020
ffeb8d1
Merge branch 'develop' into issue499.
agarny Aug 11, 2020
7555d9e
Analyser: explain a bit more what the Analyser class is all about.
agarny Aug 12, 2020
3935a41
Generator: replaced occurrences of `the "exponential" constant` with …
agarny Aug 12, 2020
8b9cf1e
Analyser/Generator: replaced occurrences of `equivalence` with `equal…
agarny Aug 12, 2020
96e53b0
Analyser/Generator: replaced occurrences of `nonequivalence` with `no…
agarny Aug 12, 2020
5de8f11
Analyser/Generator: replaced occurrences of `xor` with `exclusive or`.
agarny Aug 12, 2020
f1d0e48
Fixed a small typo.
agarny Aug 12, 2020
0b8c03c
Merge branch 'develop' into issue499.
agarny Aug 13, 2020
7537550
Merge branch 'develop' into issue499.
agarny Aug 13, 2020
418adee
FIx type in analyser.h.
hsorby Aug 13, 2020
7b7020a
Merge branch 'develop' into issue499.
agarny Aug 19, 2020
234fd90
Some minor cleaning up.
agarny Aug 19, 2020
51cadb5
Merge branch 'develop' into issue499
agarny Aug 19, 2020
5ff9965
Merge branch 'develop' into issue499.
agarny Aug 20, 2020
b36380f
Analyser: slight improvement to our generation of issues.
agarny Aug 24, 2020
b39767d
Analyser: removed some unneeded code.
agarny Aug 27, 2020
8f4d590
Fixed a typo.
agarny Aug 27, 2020
8f965cf
Only #undef something if it was previously #define'd.
agarny Aug 27, 2020
7c9f32a
Make ClangFormat happy.
agarny Aug 27, 2020
ab0b64f
Analyser: renamed `compareVariablesByName` to `compareVariablesByComp…
agarny Aug 27, 2020
c3f598e
Analyser test: check that an issue references a variable with the exp…
agarny Aug 27, 2020
e38a5c0
GeneratorProfile: clarified the description of some methods.
agarny Aug 27, 2020
40a3682
Analyser/generator: provided some documentation for our enums.
agarny Aug 27, 2020
cf5cc4e
Update analyser.h
hsorby Aug 27, 2020
0eccc52
Generator: added a `model()` and `setModel()` method.
agarny Aug 28, 2020
982a609
Generator: updated our Python test.
agarny Aug 28, 2020
05af6ea
Some minor cleaning up.
agarny Aug 28, 2020
84b6c61
Analyser/Generator: use weak pointers where appropriate.
agarny Aug 31, 2020
0be267a
Make gcc happy.
agarny Aug 31, 2020
ef0e76d
Analyser/Generator: simplified our use of weak pointers.
agarny Sep 1, 2020
d73811f
Make both gcc and MSVC happy.
agarny Sep 1, 2020
0e77fb9
Analyser: improved a comment.
agarny Sep 1, 2020
e353c92
Analyser: updated some comments.
agarny Sep 1, 2020
d98dac4
Analyser: grammatically improved a comment.
agarny Sep 1, 2020
5253dcf
Analyser/Generator: slight improvement to our documentation for the `…
agarny Sep 1, 2020
9f8363a
Generator: slight improvement to the documentation for the `interface…
agarny Sep 1, 2020
3ef129d
AnalyserModel: clarified the API documentation.
agarny Sep 1, 2020
6e4a27a
AnalyserModel: clarified and added some API documentation.
agarny Sep 1, 2020
7818039
AnalyserModel interface: removed a duplicate.
agarny Sep 1, 2020
7db0034
AnalyserModel interface: fixed copy/paste gone wrong.
agarny Sep 1, 2020
e923d0a
Analyser: account for the fact that a math string may consist of seve…
agarny Sep 2, 2020
9d23a36
Merge branch 'develop' into issue499.
agarny Sep 3, 2020
feffc7f
Merge branch 'develop' into issue499.
agarny Sep 7, 2020
83b4049
Generator test: fixed a typo.
agarny Sep 9, 2020
4c641c3
Analyser: slight improvement to the documentation.
agarny Sep 16, 2020
0f277e0
Analyser: [co]sine, not [co]sinus.
agarny Sep 16, 2020
99112c8
Analyser: fixed a typo in the documentation.
agarny Sep 16, 2020
029a447
Analyser: fixed a small problem in the documentation.
agarny Sep 16, 2020
3c803c4
Generator: natural, not Napierian logarithm.
agarny Sep 16, 2020
240a547
Analyser: fixed a typo in the documentation.
agarny Sep 16, 2020
3008b3b
Analyser: properly handle the analysis of a null model.
agarny Sep 16, 2020
aa84f65
Merge branch 'develop' into issue499.
agarny Sep 16, 2020
5b01f53
Merge branch 'develop' into issue499
agarny Sep 16, 2020
f3b3161
Some minor cleaning up.
agarny Sep 16, 2020
abc7e61
Python: follow PEP8.
agarny Sep 17, 2020
ee940e1
Generator: fixed interfaces following commit aa84f653.
agarny Sep 17, 2020
4f855e3
Generator Python test: some minor cleaning up.
agarny Sep 17, 2020
f67dffb
Merge branch 'issue499' of https://github.com/agarny/libcellml into i…
agarny Sep 17, 2020
43bcde3
Generator: fixed interfaces following commit aa84f653.
agarny Sep 17, 2020
d1cfd35
Tests: some minor cleaning up.
agarny Sep 17, 2020
1195243
Generator: fixed Python tests following commit aa84f653.
agarny Sep 17, 2020
ddbea51
Some minor cleaning up.
agarny Sep 17, 2020
1960a52
Analyser/Generator: updated our interfaces to get Python coverage.
agarny Sep 17, 2020
e5528a6
Analyser/Generator: ensure 100% Python coverage.
agarny Sep 18, 2020
582887b
Analyser: improvement to our Python coverage test.
agarny Sep 18, 2020
9c5ddf5
Analyser: make our bindings aware of our use of std::vector.
agarny Sep 18, 2020
4c9583c
SWIG: bump up our requirements.
agarny Sep 18, 2020
f129dc0
SWIG: bump up our requirements.
agarny Sep 18, 2020
f583a0a
Generator profile Python test: some minor cleaning up.
agarny Sep 21, 2020
4fb3309
Analyser/generator: cleaned up the docstrings for our interfaces.
agarny Sep 21, 2020
6986509
Generator interface: some minor cleaning up.
agarny Sep 21, 2020
04d9f90
Some minor cleaning up.
agarny Sep 24, 2020
49714ac
Analyser: updated the documentation for `Analyser::model()`.
agarny Sep 25, 2020
9bc7021
AnalyserEquationAst: slight update to our documentation.
agarny Sep 25, 2020
489939a
Utilities: added the `replace()` method that used to be in our `Gener…
agarny Sep 25, 2020
ac7d660
GeneratorProfile Python tests: using Pythonic method names.
agarny Sep 25, 2020
03490c6
Merge branch 'develop' into issue499.
agarny Sep 29, 2020
57a75fe
Merge branch 'develop' into issue499
nickerso Sep 29, 2020
aa444bd
Tests: removed the ids from the sine approximations CellML files.
agarny Sep 29, 2020
7c78b3e
Merge branch 'develop' into issue499
agarny Sep 29, 2020
8d68394
Merge branch 'develop' into issue499.
agarny Sep 29, 2020
66027ba
AnalyserEquationAst: fixed the documentation for `DEGREE`.
agarny Sep 29, 2020
34851a0
AnalyserModel: slight update to the isValid() documentation.
agarny Sep 29, 2020
851ebb7
AnalyserModel: slight update to our the voi() documentation.
agarny Sep 29, 2020
3503425
AnalyserVariable: slight update to the Type documentation.
agarny Sep 29, 2020
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2 changes: 1 addition & 1 deletion cmake/environmentchecks.cmake
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -51,7 +51,7 @@ endif()

find_package(Doxygen)
find_package(Sphinx)
find_package(SWIG 3.0.3)
find_package(SWIG 4)

set(_ORIGINAL_CMAKE_REQUIRED_FLAGS ${CMAKE_REQUIRED_FLAGS})

Expand Down
10 changes: 10 additions & 0 deletions src/CMakeLists.txt
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Original file line number Diff line number Diff line change
Expand Up @@ -45,6 +45,11 @@ configure_file(
)

set(SOURCE_FILES
${CMAKE_CURRENT_SOURCE_DIR}/analyser.cpp
${CMAKE_CURRENT_SOURCE_DIR}/analyserequation.cpp
${CMAKE_CURRENT_SOURCE_DIR}/analyserequationast.cpp
${CMAKE_CURRENT_SOURCE_DIR}/analysermodel.cpp
${CMAKE_CURRENT_SOURCE_DIR}/analyservariable.cpp
${CMAKE_CURRENT_SOURCE_DIR}/component.cpp
${CMAKE_CURRENT_SOURCE_DIR}/componententity.cpp
${CMAKE_CURRENT_SOURCE_DIR}/entity.cpp
Expand Down Expand Up @@ -72,6 +77,11 @@ set(SOURCE_FILES
)

set(GIT_API_HEADER_FILES
${CMAKE_CURRENT_SOURCE_DIR}/api/libcellml/analyser.h
${CMAKE_CURRENT_SOURCE_DIR}/api/libcellml/analyserequation.h
${CMAKE_CURRENT_SOURCE_DIR}/api/libcellml/analyserequationast.h
${CMAKE_CURRENT_SOURCE_DIR}/api/libcellml/analysermodel.h
${CMAKE_CURRENT_SOURCE_DIR}/api/libcellml/analyservariable.h
${CMAKE_CURRENT_SOURCE_DIR}/api/libcellml/component.h
${CMAKE_CURRENT_SOURCE_DIR}/api/libcellml/componententity.h
${CMAKE_CURRENT_SOURCE_DIR}/api/libcellml/entity.h
Expand Down
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