Update changelog.

jmrohwer · jmrohwer · commit f9b56f546ef0 · 2024-05-09T22:24:07.000+02:00
diff --git a/CHANGES.md b/CHANGES.md
@@ -1,15 +1,100 @@
 # PySCeS changes (per GitHub release)
 
+## PySCeS release 1.2.1 (May 2024)
+
+We are pleased to announce the release of the Python Simulator for Cellular Systems:
+PySCeS (https://pysces.github.io/) version 1.2.1. This is a bugfix release.
+
+### Fixes
+
+- Fixed a bug in model evaluation where a model has events and assignment rules, and the
+  assignment rule contains a variable name and a parameter with the variable a
+  substring match of the parameter (e.g. `E1` and `E1tot`). Previously, this led to
+  garbage code during string replacements.
+- Cleaned up various error messages.
+
+## PySCeS release 1.2.0 (Feb 2024)
+
+We are pleased to announce the release of the Python Simulator for Cellular Systems:
+PySCeS (https://pysces.github.io/) version 1.2.0. This is the first release in the 1.2
+series and contains some new features and various bug fixes.
+
+### New features
+
+There have been major changes in the build system for PySCeS. This release
+implements [meson-python](https://meson-python.readthedocs.io/),
+a [PEP 517](https://peps.python.org/pep-0517/) compliant Python build backend that
+is suitable for building C and Fortran extension modules by implementing
+the [meson build system](https://mesonbuild.com/). There is no more `setup.py` and
+project build options and metadata are now in `pyproject.toml`.
+
+The main **motivation** for this has been support for Python 3.12, which deprecated
+the use of `distutils`, and consequently `numpy` dropped `numpy.distutils`. The
+previous build system had relied on `numpy.distutils` for building Fortran extension
+modules, which would no longer work on Python 3.12. In the mean time, `scipy`, `numpy`,
+as well as a number of other packages in the scientific Python ecosystem have moved
+their build systems to `meson-python`. This version thus brings PySCeS in line with
+the other packages.
+
+In addition, **binary wheels for macOS on Apple silicon** (*arm64*) are provided
+for the first time (Python 3.11 and 3.12).
+
+### What has changed?
+
+- From a regular user perspective, not much. Installation is still via `pip` or `conda`.
+
+- From a developer perspective: there is no longer a `setup.py`. Metadata has been
+  migrated to `pyproject.toml`. Build settings are spread between `pyproject.toml` and
+  various `meson.build` files. The build is straightforward using one of:
+  ```bash
+  $ pip wheel -w dist .
+  $ python -m build .
+  ```
+  as long as the relevant compiler toolchain is installed (gcc and gfortran on Linux and
+  macOS, RTools on Windows). Installation can be done with
+  ```bash
+  $ pip install .
+           or
+  $ pip install --no-build-isolation -e .          (for an editable install)
+  ```
+  Refer to [INSTALL.md](https://github.com/PySCeS/pysces/blob/main/INSTALL.md).
+
+- `Numpy` version >=1.26 is required for the build, as older versions of `f2py` (which
+  is distributed with `numpy`) are not compatible. At runtime, any `numpy` version >
+  =1.23 is supported, older versions don't work due to ABI incompatibility.
+- Binaries (wheels) are distributed for Python versions 3.9-3.12. Python 3.8 support is
+  dropped as the latest `numpy` and `scipy` versions also no longer support it.
+- Documentation has been updated to reflect these changes.
+
+### Bug fixes
+
+- Fixed a bug with assignment rule evaluation when one species was an exact substring of
+  another species.
+- Use vectorised functions `numpy.log`, `numpy.log10`, `numpy.exp` instead of
+  their `math.*` counterparts to support their application to arrays in e.g. assignment
+  rules.
+- Removed a bunch of deprecated `scipy.*` functions that have moved to the `numpy.*`
+  namespace.
+- Cleaned up unused imports.
+
 ## PySCeS release 1.1.1 (Jul 2023)
 
-We are pleased to announce the release of the Python Simulator for Cellular Systems: 
-PySCeS (https://pysces.github.io/) version 1.1.1. This is the first release in the 1.1 
+We are pleased to announce the release of the Python Simulator for Cellular Systems:
+PySCeS (https://pysces.github.io/) version 1.1.1. This is the first release in the 1.1
 series and contains some new features and various bug fixes.
 
 ### New features
 
-- When used in a notebook environment, the `ipympl` backend for matplotlib is now enabled if installed. This allows use in JupyterLab (as opposed to classic notebook). If `ipympl` is not installed, fallback is to the standard `nbAgg`, which is part of matplotlib.
-- Simulation results (`mod.sim` object) can now be returned as a pandas DataFrame if pandas is installed, otherwise a numpy recarray is returned as before. This option is configurable with `custom_datatype = pandas` in the user and system configuration files (see https://pyscesdocs.readthedocs.io/en/latest/userguide_doc.html#configuration), and can be enabled or disabled per session or per model:
+- When used in a notebook environment, the `ipympl` backend for matplotlib is now
+  enabled if installed. This allows use in JupyterLab (as opposed to classic notebook).
+  If `ipympl` is not installed, fallback is to the standard `nbAgg`, which is part of
+  matplotlib.
+- Simulation results (`mod.sim` object) can now be returned as a pandas DataFrame if
+  pandas is installed, otherwise a numpy recarray is returned as before. This option is
+  configurable with `custom_datatype = pandas` in the user and system configuration
+  files (
+  see https://pyscesdocs.readthedocs.io/en/latest/userguide_doc.html#configuration), and
+  can be enabled or disabled per session or per model:
   ```python
   pysces.enablePandas()
   pysces.enablePandas(False)
@@ -19,170 +104,141 @@ series and contains some new features and various bug fixes.
 
 ### Bug fixes
 
-- Fixed a bug in simulations with `RateRules` using Assimulo, where a wrong solver variable was being assigned internally.
+- Fixed a bug in simulations with `RateRules` using Assimulo, where a wrong solver
+  variable was being assigned internally.
 - Fixed SBML export when assignment rules were evaluating reaction rates.
-- Enabled assignment rules (forcing functions) to track parameter changes when using CVODE. This is needed in case events change parameters during the course of the simulation.
-
-README: https://github.com/PySCeS/pysces/blob/master/README.md
-
-DOCUMENTATION: https://pyscesdocs.readthedocs.io/en/latest/
+- Enabled assignment rules (forcing functions) to track parameter changes when using
+  CVODE. This is needed in case events change parameters during the course of the
+  simulation.
 
 ## PySCeS release 1.1.0 (Apr 2023)
 
-We are pleased to announce a new minor release (version 1.1.0) of the Python 
-Simulator for Cellular Systems: PySCeS (https://pysces.github.io/). This is the 
+We are pleased to announce a new minor release (version 1.1.0) of the Python
+Simulator for Cellular Systems: PySCeS (https://pysces.github.io/). This is the
 first release in the 1.1 series.
 
 ### What's new?
 
-The most significant new feature in Version 1.1 is a major upgrade in the way 
-**PySCeS handles events in simulations**. The definition of events follows the 
-framework described in the SBML Level 3 Version 2 specification, thus making the 
-event handling SBML-compliant. Specifically, event **persistence** (for events with 
-a delay) is now handled correctly, and simultaneous events can be executed 
+The most significant new feature in Version 1.1 is a major upgrade in the way
+**PySCeS handles events in simulations**. The definition of events follows the
+framework described in the SBML Level 3 Version 2 specification, thus making the
+event handling SBML-compliant. Specifically, event **persistence** (for events with
+a delay) is now handled correctly, and simultaneous events can be executed
 according to their assigned **priorities**.
 
 The new **event specification** in the PySCeS input file reads:
+
 ```
 Event: <name>, <trigger>, <optional_kwargs> { <assignments> }
 ```
 
-To achieve this, three new optional keyword arguments have been added as a 
-comma-separated list to the event specification. The general syntax for these 
+To achieve this, three new optional keyword arguments have been added as a
+comma-separated list to the event specification. The general syntax for these
 arguments is `<attribute>=<value>`. The keywords are:
 
-- *delay* (float): specifies a delay between when the trigger is fired (and the 
-  assignments are evaluated) and the eventual assignment to the model. If this 
+- *delay* (float): specifies a delay between when the trigger is fired (and the
+  assignments are evaluated) and the eventual assignment to the model. If this
   keyword is not specified, a value of `0.0` is assumed.
-- *priority* (integer or None): specifies a priority for events that trigger at the 
-  same simulation time. Events with a higher priority are executed before those 
-  with a lower priority, while events without a priority (`None`) are executed in 
-  random positions in the sequence. If this keyword is not specified, a value of 
+- *priority* (integer or None): specifies a priority for events that trigger at the
+  same simulation time. Events with a higher priority are executed before those
+  with a lower priority, while events without a priority (`None`) are executed in
+  random positions in the sequence. If this keyword is not specified, a value of
   `None` is assumed.
-- *persistent* (boolean): is only relevant to events with a delay, where the 
-  situation may occur that the trigger condition no longer holds by the time the 
-  delay in the simulation has passed. The persistent attribute specifies how to 
-  deal with this situation: if `True`, the event executes nevertheless; if `False`, 
-  the event does not execute if the trigger condition is no longer valid. If the 
+- *persistent* (boolean): is only relevant to events with a delay, where the
+  situation may occur that the trigger condition no longer holds by the time the
+  delay in the simulation has passed. The persistent attribute specifies how to
+  deal with this situation: if `True`, the event executes nevertheless; if `False`,
+  the event does not execute if the trigger condition is no longer valid. If the
   keyword is not specified, a default of `True` is assumed.
 
-The following event illustrates the use of a delay of ten time units with a 
+The following event illustrates the use of a delay of ten time units with a
 non-persistent trigger and a priority of 3:
+
 ```
 Event: event2, geq(_TIME_, 15.0), delay=10.0, persistent=False, priority=3 {
 V3 = V3*vfact2
 }
 ```
+
 The legacy event syntax is still supported.
 
 ### Other changes
 
-- A new setting has been added to the settings dictionary of the `PysMod` class 
+- A new setting has been added to the settings dictionary of the `PysMod` class
   with the following default:    
   `mod.__settings__["cvode_access_solver"] = True`    
-  This specifies if the Assimulo solver object is available from within the 
-  `PysMod` instance to make low-level changes to the integration algorithm. The 
-  current default emulates previous behaviour, but the setting can be changed to 
-  `False`, which facilitates serialization of the `PysMod` class in e.g. parallel 
-  computations. Previously, the attached Assimulo solver object would prevent 
+  This specifies if the Assimulo solver object is available from within the
+  `PysMod` instance to make low-level changes to the integration algorithm. The
+  current default emulates previous behaviour, but the setting can be changed to
+  `False`, which facilitates serialization of the `PysMod` class in e.g. parallel
+  computations. Previously, the attached Assimulo solver object would prevent
   serialization. Thanks @c-barry
 - Documentation has been updated to reflect the changes to the event syntax.
-- Various bug fixes, including dealing with deprecations for Numpy 1.24.x 
+- Various bug fixes, including dealing with deprecations for Numpy 1.24.x
   compatibility.
 
-README: https://github.com/PySCeS/pysces/blob/master/README.md
-
-DOCUMENTATION: https://pyscesdocs.readthedocs.io/en/latest/
-
-© Brett Olivier and Johann Rohwer, April 2023.
-
-
 ## PySCeS release 1.0.3 (Sep 2022)
 
-We are pleased to announce the release of the Python Simulator for Cellular 
-Systems: PySCeS (https://pysces.github.io/) version 1.0.3. This is the third 
+We are pleased to announce the release of the Python Simulator for Cellular
+Systems: PySCeS (https://pysces.github.io/) version 1.0.3. This is the third
 release in the 1.0 series.
 
 ### What's new?
-- The build-system has been adapted to make use of `scikit-build`. This gets rid of 
-the `distutils` and `numpy.distutils` dependencies, which are deprecated and will 
-be removed with the release of Python 3.12.
+
+- The build-system has been adapted to make use of `scikit-build`. This gets rid of
+  the `distutils` and `numpy.distutils` dependencies, which are deprecated and will
+  be removed with the release of Python 3.12.
 
 ### Bug Fixes:
+
 - Fixed CVODE defaults and set default tolerances to more sane levels
 - Fixed string replacement in parsing and construction of `PieceWise` functions
 
-README: https://github.com/PySCeS/pysces/blob/master/README.md
-
-DOCUMENTATION: https://pyscesdocs.readthedocs.io/en/latest/
-
-&copy; Brett Olivier and Johann Rohwer, September 2022.
-
-
 ## PySCeS release 1.0.2 (May 2022)
 
-We are pleased to announce the release of the Python Simulator for Cellular Systems: 
-PySCeS (https://pysces.github.io/) version 1.0.2. 
+We are pleased to announce the release of the Python Simulator for Cellular Systems:
+PySCeS (https://pysces.github.io/) version 1.0.2.
 This is the second bug-fix release in the 1.0 series.
 
 ### Fixes:
 
 - Fixed a number of bugs with `RateRule` execution with CVODE
-- Reintroduced the functionality to track additional items such as Assignment Rules 
+- Reintroduced the functionality to track additional items such as Assignment Rules
   during a simulation with CVODE
-- The Assimulo `CVODE` implementation has been updated, and legacy PySUNDIALS CVODE 
+- The Assimulo `CVODE` implementation has been updated, and legacy PySUNDIALS CVODE
   code removed
-- The `RateRule` and `AssignmentRule` implementations have been checked against the 
+- The `RateRule` and `AssignmentRule` implementations have been checked against the
   SBML Test Suite
 
-README: https://github.com/PySCeS/pysces/blob/master/README.md
-
-DOCUMENTATION: https://pyscesdocs.readthedocs.io/en/latest/
-
-&copy; Brett Olivier and Johann Rohwer, May 2022.
-
 ## PySCeS release 1.0.1 (Feb 2022)
 
-We are pleased to announce the release of the Python Simulator for Cellular Systems: 
-PySCeS (https://pysces.github.io/) version 1.0.1. This is the first bug-fix release 
+We are pleased to announce the release of the Python Simulator for Cellular Systems:
+PySCeS (https://pysces.github.io/) version 1.0.1. This is the first bug-fix release
 in the 1.0 series.
 
 ### Fixes:
 
 - Fixed references to numpy/scipy
 - Fixed a bug in `mod.Simulate(userinit=1)` with CVODE
-- Fixed bug where the maximal number of steps in LSODA would not be honoured from the 
+- Fixed bug where the maximal number of steps in LSODA would not be honoured from the
   `mod.__settings__["lsoda_mxstep"]` dictionary entry
 - General cleanup of license files, version files, and the way requirements are handled
 
-README: https://github.com/PySCeS/pysces/blob/master/README.md
-
-DOCUMENTATION: https://pyscesdocs.readthedocs.io/en/latest/
-
-&copy; Brett Olivier and Johann Rohwer, February 2022.
-
 ## PySCeS release 1.0.0 (Sep 2021)
 
-We are pleased to announce the release of the Python Simulator for Cellular 
+We are pleased to announce the release of the Python Simulator for Cellular
 Systems: PySCeS (https://pysces.github.io/) version 1.0.0.
 
 **What's new in this release:**
 
-- Re-introduced support for CVODE as integrator under Python 3 (via Assimulo), 
+- Re-introduced support for CVODE as integrator under Python 3 (via Assimulo),
   which brings back support of events in models
 - Improved import and export of SBML
 - Automatic installation of optional dependencies with `pip install "pysces
   [optional_dep]"`
 - Extensive update of documentation
 - Numerous bug fixes
 
-**README:** https://github.com/PySCeS/pysces/blob/master/README.md
-
-**DOCUMENTATION:** https://pyscesdocs.readthedocs.io/en/latest/
-
-&copy; Brett Olivier and Johann Rohwer, September 2021.
-
-
 ## PySCeS release 0.9.8 (May 2020)
 
 We are pleased to announce the release of the Python Simulator for Cellular Systems:
@@ -191,7 +247,7 @@ PySCeS (http://pysces.sourceforge.net) version 0.9.8
 **What's new in this release:**
 
 * The main change from a user perspective is that the default model directory and output
-  directory on Windows have moved to `%USERPROFILE%\Pysces` and subfolders 
+  directory on Windows have moved to `%USERPROFILE%\Pysces` and subfolders
   (e.g. `C:\Users\<username>\Pysces`). These folders are created by default on a fresh
   install. The previous default location was `C:\Pysces`. This change brings the Windows
   version in line with the Linux and macOS versions, and moreover allows multiple users
@@ -273,7 +329,7 @@ cycles), bugfixes (assignment rules) and updates (SED-ML and COMBINE archive exp
 ## PySCeS releases 2004 - 2016
 
 These releases are available for download
-from [SourceForge] (https://sourceforge.net/projects/pysces/files/pysces)
+from [SourceForge](https://sourceforge.net/projects/pysces/files/pysces)
 
-© Brett G. Olivier & Johann M. Rohwer, August 2021
+© Brett G. Olivier & Johann M. Rohwer, 2004-2024
 
