PySCeS · jmrohwer · Feb 13, 2024 · Dec 10, 2023 · Dec 10, 2023 · Dec 10, 2023
diff --git a/.github/workflows/build-conda.yml b/.github/workflows/build-conda.yml
@@ -11,26 +11,44 @@ jobs:
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-#        os: [ubuntu-latest, windows-2019, macos-12]
-        os: [ubuntu-latest]
+        os: [ubuntu-latest, windows-latest, macos-12]
     name: Build Anaconda packages on ${{ matrix.os }}
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
+
+      - name: (windows) Install rtools MinGW compilers
+        if: matrix.os == 'windows-latest'
+        run: |
+          choco install rtools -y --no-progress --force --version=4.0.0.20220206
+
+      - name: (windows) Add compiler path to PATH
+        if: matrix.os == 'windows-latest'
+        uses: myci-actions/export-env-var-powershell@1
+        with:
+          name: PATH
+          value: c:\rtools40\ucrt64\bin;c:\rtools40\usr\bin;$env:PATH
+
       - name: Setup conda
         uses: s-weigand/setup-conda@v1
         with:
-          update-conda: true
+          update-conda: false
           conda-channels: conda-forge
 
       - name: Prepare conda environment
         run: |
-          conda install mamba conda-build conda-verify anaconda-client
+          conda install mamba boa conda-verify anaconda-client
+          mamba update --all
           mkdir build_output
 
-      - name: Build packages
-        run: mamba build --no-anaconda-upload --output-folder ./build_output ./packaging/conda
+      - name: (unix) Build packages for ${{ matrix.os }}
+        if: matrix.os != 'windows-latest'
+        run: conda mambabuild --no-anaconda-upload --output-folder ./build_output ./packaging/conda-unix
 
+      - name: (windows) Build packages for ${{ matrix.os }}
+        if: matrix.os == 'windows-latest'
+        run: conda mambabuild --no-anaconda-upload --output-folder ./build_output ./packaging/conda-win
+
       - uses: actions/upload-artifact@v3
         with:
           name: build_outputs

diff --git a/.github/workflows/cibuildwheel.yml b/.github/workflows/cibuildwheel.yml
@@ -15,7 +15,7 @@ jobs:
         os: [ubuntu-latest, windows-latest, macos-12]
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - name: (windows) Install rtools MinGW compilers
         if: matrix.os == 'windows-latest'
@@ -43,7 +43,7 @@ jobs:
 
       - name: Build sdist
         run: |
-          pip install scikit-build build
+          pip install build
           python -m build -s .
 
       - uses: actions/upload-artifact@v3

diff --git a/ADDITIONAL_LICENCES.md b/ADDITIONAL_LICENCES.md
@@ -6,21 +6,22 @@ Licences for other software (or parts thereof) distributed with, or used by, PyS
 
 The NLEQ2 algorithm from ZIB which has its own licence and warranty and does not fall
 under the PySCeS GPL licence. ZIB has kindly given us permission to distribute NLEQ2
-with PySCeS provided its use falls within their terms of usage (/nleq2/nleq2_readme):
+with PySCeS provided its use falls within their terms of usage 
+(`pysces/nleq2/nleq2.f`):
 
 You may use or modify this code for your own non-commercial purposes for an unlimited
 time. In any case you should not deliver this code without a special permission of ZIB.
 In case you intend to use the code commercially, we oblige you to sign an according
 licence agreement with ZIB.
 
 If you are not using PySCeS for research or personal use you **must** disable NLEQ2 by
-setting `nleq2 = 0` in setup.py before installation. This is a plug-in solver and its
-removal does not otherwise influence PySCeS.
+setting `nleq2 = False` in `config.py` before installation. This is a plug-in solver 
+and its removal does not otherwise influence PySCeS.
 
 ## PLY
 
-David Beazley's PLY 3.3 (http://www.dabeaz.com/ply/). This package is included unchanged
-and consists of two files *lex.py* and *yacc.py* in the `pysces/lib` and `pysces/core2`
-modules.
+David Beazley's PLY 3.11 (http://www.dabeaz.com/ply/). This package is included 
+unchanged and consists of two files *lex.py* and *yacc.py* in the `pysces/lib` 
+and `pysces/core2` modules. PLY is distributed under a BSD licence.
 
-© Brett G. Olivier & Johann M. Rohwer, August 2021
+© Brett G. Olivier & Johann M. Rohwer, January 2024
diff --git a/CITATION.cff b/CITATION.cff
@@ -1,6 +1,6 @@
 # YAML 1.2
 ---
-cff-version: "1.1.2"
+cff-version: "1.2.0"
 message: "If you use this software, please cite it using the information provided in this metadata."
 authors:
   -
@@ -14,9 +14,9 @@ authors:
     affiliation: "Stellenbosch University"
     orcid: "https://orcid.org/0000-0001-6288-8904"
 title: "The Python Simulator for Cellular Systems: PySCeS"
-version: "1.1.2"
-repository-code: "https://github.com/PySCeS/pysces/tree/1.1.2"
-date-released: 2023-11-17
+version: "1.2.0"
+repository-code: "https://github.com/PySCeS/pysces/tree/1.2.0"
+date-released: 2023-12-14
 doi: "10.5281/zenodo.2600905"
 license: "BSD-3-Clause"
 url: https://pysces.github.io

diff --git a/CMakeLists.txt b/CMakeLists.txt
diff --git a/CONTRIBUTORS.md b/CONTRIBUTORS.md
@@ -22,4 +22,4 @@ organisations:
 * The South African National Bioinformatics Network (2003-2008)
 * The South African National Research Foundation (2000-2004)
 
-© Brett G. Olivier & Johann M. Rohwer, August 2021
+© Brett G. Olivier & Johann M. Rohwer, January 2024
diff --git a/DESCRIPTION.md b/DESCRIPTION.md
@@ -0,0 +1,18 @@
+# PySCeS - the Python Simulator for Cellular Systems
+
+PySCeS was originally developed by the Triple-J Group for Molecular 
+Cell Physiology at Stellenbosch University in order to try to model and understand the 
+complex processes and systems which make up the living cell. The project is 
+maintained by Brett Olivier (AIMMS, Vrije Universiteit Amsterdam) and Johann Rohwer 
+(Laboratory for Molecular Systems Biology, Stellenbosch University).
+
+PySCeS features, amongst other things:
+- A text-based model description language.
+- A structural analysis module.
+- Integrators for time simulation.
+- Non-linear solvers for steady-state analysis.
+- A module for performing Metabolic Control Analysis.
+- A bifurcation module for systems which exhibit multiple steady states.
+- A variety of extra utilities for parameter scans, data output and plotting.
+- A dynamic module loading framework.
+- Systems Biology Markup Language (SBML) import and export capability.
diff --git a/INSTALL.md b/INSTALL.md
@@ -1,7 +1,9 @@
 # Installing PySCeS
 
-Binary install packages for all three OSs and Python versions 3.6-3.9 are provided.
-Anaconda users can conveniently install PySCeS with:
+Binary install packages for all three OSs and recent Python versions are 
+provided. Anaconda packages are available for 64-bit Windows and Linux, as well as 
+macOS *x86_64* architecture. Apple Silicon (*arm64*) macOS users should install with 
+`pip` (see below). Anaconda users can conveniently install PySCeS with:
 
 ```bash
 $ conda install -c conda-forge -c pysces pysces
@@ -11,7 +13,9 @@ Any dependencies will be installed automatically, including the optional depende
 *Assimulo*, *ipyparallel* and *libSBML*. 
 
 Alternatively, you can use *pip* to
-install PySCeS from PyPI. Core dependencies will be installed automatically.
+install PySCeS from PyPI. Core dependencies will be installed automatically. Wheels 
+are available for 64-bit Windows and Linux, as well as macOS architectures *x86_64* and 
+*arm64* (starting from PySCeS version 1.2.0).
 
 ```bash
 $ pip install pysces
@@ -30,7 +34,7 @@ To install the optional dependences:
 >  very limited number of Python versions and operating systems on PyPI. 
 >  **This is not guaranteed to work!** If you require Assimulo, the conda
 >  install is by far the easier option as up-to-date binaries are supplied
->  for all OS and recent Python versions.
+>  for all OSs and recent Python versions.
 
 For more information on installing and configuring PySCeS please see the
 [PySCeS User Guide](https://github.com/PySCeS/pysces-documentation/blob/main/source/userguide_doc.rst#installing-and-configuring)
@@ -42,17 +46,25 @@ installation from source. This requires Fortran and C compilers.
 
 ### Windows build
 
-The fastest way to build your own copy of PySCeS is to use Anaconda Python.
+The fastest way to build your own copy of PySCeS is to use Anaconda for 
+installing Python and the required libraries. In addition, the *RTools* compiler 
+toolchain is required.
 
 * Download and install 
-  [Anaconda for Python 3](https://www.anaconda.com/products/individual#Downloads)
+  [Anaconda for Python 3](https://www.anaconda.com/download#Downloads)
 * Obtain [Git for Windows](https://git-scm.com/download/win)
+* Obtain the *RTools* compiler toolchain (**version 4.0.0.20220206**), either using
+  [Chocolatey](https://chocolatey.org/install) 
+  (`choco install rtools -y --version=4.0.0.20220206`) or by
+  [direct download](https://github.com/r-windows/rtools-installer/releases/download/2022-02-06/rtools40-x86_64.exe)
+  - Install in `C:\rtools40` (Chocolatey automatically installs to this path)
+  - Add `c:\rtools40\ucrt64\bin` and `c:\rtools40\usr\bin` to the system `PATH`
 * Create a PySCeS environment using conda and activate it:
 
 ```bash
-$ conda create -n pyscesdev -c conda-forge python=3.8 numpy scipy \ 
+$ conda create -n pyscesdev -c conda-forge python=3.11 numpy=1.26 scipy \ 
   matplotlib sympy packaging pip wheel ipython python-libsbml \
-  fortran-compiler assimulo scikit-build
+  assimulo meson meson-python ninja
 $ conda activate pyscesdev
 ```
 
@@ -63,11 +75,10 @@ $ conda activate pyscesdev
 (pyscesdev)$ cd pysces-src
 ```
 
-* Now you can build and install PySCeS into the pyscesdev environment
+* Now you can build and install PySCeS into the *pyscesdev* environment
 
 ```bash
-(pyscesdev)$ python setup.py build
-(pyscesdev)$ python setup.py install
+(pyscesdev)$ pip install --no-deps --no-build-isolation .
 ```
 
 ### Linux build
@@ -80,7 +91,7 @@ Clone the source from Github as described above, change into the source director
 run:
 
 ```bash
-$ python setup.py install
+$ pip install .
 ```
 
 ### macOS build
@@ -92,7 +103,7 @@ compilers may be installed via [Xcode](https://developer.apple.com/xcode). Clone
 source from Github as described above, change into the source directory and run:
 
 ```bash
-$ python setup.py install
+$ pip install .
 ```
 
-© Brett G. Olivier & Johann M. Rohwer, August 2021
+© Johann M. Rohwer & Brett G. Olivier, January 2024
diff --git a/LATEST.md b/LATEST.md
@@ -9,7 +9,7 @@ git clone [email protected]:PySCeS/pysces.git
 ```
 
 PySCeS binaries for release versions are available from PyPI and the Anaconda.org 
-for 64-bit Windows, Linux and macOS.
+repository for 64-bit Windows, Linux and macOS.
 
 **For PyPI:**
 
@@ -20,7 +20,7 @@ pip install pysces
 **For Anaconda:**
 
 ```
-conda install -c sbmlteam -c pysces pysces
+conda install -c conda-forge -c pysces pysces
 ```
 
-© Brett G. Olivier & Johann M. Rohwer, August 2021
+© Brett G. Olivier & Johann M. Rohwer, January 2024
diff --git a/LICENSE b/LICENSE
diff --git a/LICENCE.txt → LICENSE.txt b/LICENCE.txt → LICENSE.txt
@@ -1,6 +1,7 @@
 BSD 3-Clause License
 
-Copyright (c) 2004 - 2021, PySCeS: The Python Simulator for Cellular Systems, Brett G. Olivier, Johann M. Rohwer and Jan-Hendrik S. Hofmeyr
+Copyright (c) 2004 - 2024, PySCeS: The Python Simulator for Cellular Systems,
+Brett G. Olivier, Johann M. Rohwer and Jan-Hendrik S. Hofmeyr
 All rights reserved.
 
 Redistribution and use in source and binary forms, with or without modification,
@@ -13,9 +14,9 @@ are permitted provided that the following conditions are met:
   conditions and the following disclaimer in the documentation and/or other materials
   provided with the distribution.
 
-* Neither the name of the B.G. Olivier, J.M. Rohwer, J.-H.S. Hofmeyr nor the names of any
-  contributors may be used to endorse or promote products derived from this software
-  without specific prior written permission.
+* Neither the name of the copyright holders B.G. Olivier, J.M. Rohwer, and J.-H.S.
+  Hofmeyr, nor the names of any contributors, may be used to endorse or promote products
+  derived from this software without specific prior written permission.
 
 THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY
 EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF

diff --git a/MANIFEST.in b/MANIFEST.in
diff --git a/README.md b/README.md
@@ -52,7 +52,7 @@ PySCeS releases are available on [PyPI](https://pypi.org/project/pysces/#files),
 [Anaconda.org](https://anaconda.org/pysces/pysces) and 
 [Github](https://github.com/PySCeS/pysces)
 
-PySCeS binaries are available for Python 3.6+ on Windows, Linux and OSX and can be
+PySCeS binaries are available for Python 3.9+ on Windows, Linux and OSX and can be
 installed using
 
 **PyPI**

diff --git a/conda-environment.yml b/conda-environment.yml