Merge pull request #132 from TRI-AMDD/development

v1.0.1

.github/workflows/mpet-code-style.yml

@@ -9,13 +9,13 @@ jobs:
 
     steps:
       - name: Set up python
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
-          python-version: 3.9
+          python-version: 3.12
           architecture: x64
 
       - name: Checkout MPET
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
         with:
           fetch-depth: 1
           path: mpet

.github/workflows/mpet-regression-test-sourceforge-daetools.yml

@@ -1,4 +1,4 @@
-name: MPET regression test with daetools 2.2.0 from sourceforge on python 3.10
+name: MPET regression test with daetools from sourceforge
 
 on: [push, workflow_dispatch]
 
@@ -9,35 +9,20 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ["3.10"]
+        python-version: ["3.10", "3.11", "3.12"]
     defaults:
       run:
         shell: bash -l {0}
     steps:
 
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
       with:
         fetch-depth: 1
         path: mpet
 
-    - uses: conda-incubator/setup-miniconda@v2
+    - uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
-        mamba-version: "*"
-        channels: conda-forge,defaults
-        activate-environment: mpet-env
-
-    - name: Install dependencies for daetools
-      run: |
-        mamba install numpy scipy matplotlib pyqt lxml pandas h5py openpyxl
-
-
-    - name: Install daetools from sourceforge
-      run: |
-        curl -L 'https://master.dl.sourceforge.net/project/daetools/daetools/2.2.0/daetools-2.2.0-gnu_linux-x86_64.zip' -o dae.zip
-        unzip dae.zip
-        cd daetools*
-        python setup.py install
 
     - name: Install additional dependencies using mpet's setup.py
       run: |

.github/workflows/mpet-regression-test.yml

@@ -9,18 +9,18 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ["3.8","3.9","3.10","3.11"]
+        python-version: ["3.8","3.9"]
     defaults:
       run:
         shell: bash -l {0}
     steps:
 
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
       with:
         fetch-depth: 1
         path: mpet
 
-    - uses: conda-incubator/setup-miniconda@v2
+    - uses: conda-incubator/setup-miniconda@v3
       with:
         python-version: ${{ matrix.python-version }}
         mamba-version: "*"

.gitignore

@@ -46,6 +46,4 @@ docs/_build
 docs/apidocs
 
 # ignore python biuld files
-build/
-# ignore daetools
-daetools*
+build/

CHANGELOG.md

@@ -5,6 +5,15 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
 
+## [1.0.1] - 2024-09-19
+### Added
+- daetools is now installed by setup.py on Windows and Linux, no need to download it separately.
+
+### Fixed
+- Github actions updates
+- Regression test all active Python versions
+
+
 ## [1.0.0] - 2024-04-11
 ### Added
 - Ability to simulate complex battery cycling protocols with 'profileType = CCCVCPcycle'.

dockerfiles/daetools-2.3.0/Dockerfile

@@ -0,0 +1,8 @@
+FROM python:3.12-bookworm
+
+#Install necessary packages for daetools
+RUN apt-get update && \
+    apt-get install --yes libgl1-mesa-glx libgfortran5
+
+#Download and install daetools
+RUN pip install https://sourceforge.net/projects/daetools/files/daetools/2.3.0/daetools-2.3.0-gnu_linux-x86_64.zip

docs/install.rst

@@ -4,59 +4,14 @@ Installation
 Prerequisites
 ----------------------------
 
-
   * Python 3.6 to 3.12
   * numpy, scipy, matplotlib, pyqt5, h5py, configparser, schema
   * daetools
 
-MPET on Windows
------------------------------
-
-MPET on Windows can be installed directly.
-
-The python version can be chosen with (ana)conda, for
-example:
-
-
-.. code-block:: bash
-
-  conda create -n mpet python=3.X pip
-  conda activate mpet
-
-Then install daetools via PyPi
-
-
-.. code-block:: bash
-
-  conda activate mpet
-  pip install daetools
-
-
-Then either clone the MPET repository if you want to work on the source code, or
-install the mpet package through PyPi (see steps below)
-
-
-MPET on Linux
------------------------------
-
-The easiest way to install MPET on Linux is via conda
-
-Install the daetools dependency via conda (in a new environment called mpet)
-
-
-.. code-block:: bash
-
-  conda create -n mpet -c conda-forge daetools
-  conda activate mpet
-
-Then either clone the MPET repository if you want to work on the source code, or
-install the mpet package through PyPi (see steps below)
-
-
 Install via PyPi
 -----------------------------
 
-MPET is available on PyPi, the Python Packaging Index and can be installed with :
+MPET is available on PyPi, the Python Packaging Index, and can be installed with:
 
 ``pip install mpet``
 
@@ -69,6 +24,15 @@ You can also download the source code and install the latest version
  * Enter the mpet directory : ``cd mpet``
  * install MPET using pip ``pip install -e .``
 
+MPET on Linux
+-----------------------------
+
+Running MPET on Linux requires a few additional libraries, which are dependencies for daetools:
+
+.. code-block:: bash
+
+  apt-get install libgl1-mesa-glx libgfortran5
+
 Test your installation
 ---------------------------
  To test your installation make sure to install MPET following :

mpet/version.py

@@ -1 +1 @@
-__version__ = '1.0.0'
+__version__ = '1.0.1'

requirements.txt

@@ -0,0 +1,12 @@
+numpy
+scipy
+matplotlib
+pyQt5
+h5py
+configparser
+schema
+setuptools; python_version >= "3.12"
+daetools @ https://sourceforge.net/projects/daetools/files/daetools/2.3.0/daetools-2.3.0-gnu_linux-x86_64.zip ; python_version >= "3.10" and python_version <= "3.12" and sys_platform == "linux"
+daetools @ https://sourceforge.net/projects/daetools/files/daetools/2.3.0/daetools-2.3.0-win64.zip ; python_version >= "3.10" and python_version <= "3.12" and sys_platform == "win32"
+daetools @ https://sourceforge.net/projects/daetools/files/Old-releases/daetools-old/1.9.0/daetools-1.9.0-gnu_linux-x86_64.tar.gz ; python_version >= "3.5" and python_version <= "3.7" and sys_platform == "linux"
+daetools @ https://sourceforge.net/projects/daetools/files/Old-releases/daetools-old/1.9.0/daetools-1.9.0-win64.zip ; python_version >= "3.5" and python_version <= "3.7" and sys_platform == "win32"

setup.py

@@ -25,7 +25,7 @@
         'mpet.electrode.reactions',
         'mpet.electrolyte','mpet.config'
     ],
-    install_requires=['numpy','scipy','matplotlib','pyQt5', 'h5py', 'configparser', 'schema'],
+    install_requires=open('requirements.txt').readlines(),
     extras_require={'test':['pytest','coverage', 'coveralls', 'flake8'],
                     'doc':['sphinx','sphinx_rtd_theme'],
                     'dashboard': ['dash', 'dash_bootstrap_components'],