Amici

Features:
* Add expression IDs and names to generated models (1374)

Fixes:
* Raise minimum sympy version to 1.7.1 (Closes 1367)
* Fix species assignment rules in reactions (1372)
* Fix id vector for DAEs (1376)

Docs:
* Update how-to-cite (1378)

Python
* Restore support for species references (1358)
* Add support for noise models in pysb (1360)
* Proper handling of discontinuities in the ODE rhs (1352)
* Fix directly calling AMICI from snakemake (1348 )
* Extend mathml function support, particularly for numerical arguments (1357)
* Restore support for sympy 1.6 (1356)

C++
* Fix some compiler related warnings (1349, 1362 )
* Fix a rare segfault for adjoint sensitivities (1351)

CI
* Move windows tests to GHA (1354)
* Pin breathe to 4.24.1

Docker
* Update ubuntu to 20.04

Bugfix release that restores compatibility with sympy 1.7

Python
* General improvements to SBML import (1312, 1316, 1315, 1322 , 1324 1333, 1329)
* Small bugfixes and improvements (1321 )
* Improve derivative computation for instances of `power` (1320 )

C++
* Fix FIM and residual computation for models with parameter dependent sigma. (1338)
* Disable chi2/residual/FIM computation for non-gaussian objective functions. (1338)
* Bugfix for integration failure during adjoint solve (1327)

Doc
* Update references (1331, 1336)

CI
* Update OpenBLAS for windows (1334)

Python
* Fix pysb-petab support (1288)
* Fix ExpData constructor overloading (1299)
* Fix support for positivity enforcement (1306)
* **Refactor SBML import, adds support for parameter rate rules and initial assignments** (1284, 1296, 1304)
* Improve model generation for models with many parameters (1300)
* Add support for PEtab based synthetic data generation (1283)

C++
* Make HDF5 an optional dependency (1285)

Doc
* General Improvements to Documentation (1289, 1291, 1292, 1293, 1294, 1286, 1277, 1281)

CI
* Add python 3.9 support test (1282)
* Allow manual triggering of GitHub actions (1287)
* Remove appveyor config (1295)
* Update GHA env and path management (1302)

Python
* Improve and extend available objective functions (1235)
* Fix processing of compartment definitions (1223)
* Fix replacement of reserved symbols (1265)
* Use Hierarchical Derivatives for Expressions (1224, 1246)
* Fix duplicate running of swig (1216)
* Overload python interface functions for amici.{Model,Solver,ExpData} and amici.{Model,Solver,ExpData}Ptr (1271)

C++
* Fix and extend use of sparse matrix operations (1230, 1240, 1244, 1247, 1271)
* **Fix application of maximal number of steps**, MaxNumStep parameter now limit total number of steps, not number of steps between output times. (1267)

Doc
* Move all Documentation to RTD (1229, 1241)
* General Improvements to Documentation (1225, 1227, 1219, 1228, 1232, 1233, 1234, 1237, 1238, 1239, 1243, 1253, 1255, 1262)

CI
* Better check for doc building (1226)
* Add more gradient checks (1213)
* Update GHA to Ubuntu 20.04 (1268)