Merge branch 'develop' into micro-sim-init-data

.github/workflows/run-unit-tests.yml

@@ -16,11 +16,15 @@ jobs:
         with:
           path: micro-manager
 
-      - name: Install Micro Manager and uninstall pyprecice
-        working-directory: micro-manager
+      - name: Install dependencies
         run: |
           apt-get -qq update
           apt-get -qq install python3-dev python3-pip git python-is-python3 pkg-config
+          pip3 install --upgrade pip
+
+      - name: Install Micro Manager and uninstall pyprecice
+        working-directory: micro-manager
+        run: |
           pip3 install --user .
           pip3 uninstall -y pyprecice
 

CHANGELOG.md

@@ -2,6 +2,7 @@
 
 ## latest
 
+- Use `pyproject.toml` instead of `setup.py` to configure the build. Package name is now `micro_manager_precice` https://github.com/precice/micro-manager/pull/84
 - Add handling of crashing micro simulations https://github.com/precice/micro-manager/pull/85
 - Add switch to turn adaptivity on and off in configuration https://github.com/precice/micro-manager/pull/93
 

docs/running.md

@@ -8,21 +8,11 @@ summary: Run the Micro Manager from the terminal with a configuration file as in
 The Micro Manager is run directly from the terminal by providing the path to the configuration file as an input argument in the following way
 
 ```bash
-micro_manager micro-manager-config.json
+micro-manager-precice micro-manager-config.json
 ```
 
-Alternatively the Manager can also be run by creating a Python script which imports the Micro Manager package and calls its run function. For example a run script `run-micro-manager.py` would look like
-
-```python
-from micro_manager import MicroManager
-
-manager = MicroManager("micro-manager-config.json")
-
-manager.solve()
-```
-
-The Micro Manager can also be run in parallel, using the same script as stated above
+The Micro Manager can also be run in parallel
 
 ```bash
-mpirun -n <number-of-procs> python3 run-micro-manager.py
+mpiexec -n micro-manager-precice micro-manager-config.json
 ```

pyproject.toml

@@ -0,0 +1,43 @@
+[build-system]
+requires = ["setuptools>=41", "wheel", "setuptools-git-versioning"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name="micro-manager-precice"
+dynamic = [ "version" ]
+dependencies = [
+    "pyprecice>=3.0.0.0", "numpy", "mpi4py", "scikit-learn"
+]
+requires-python = ">=3.8"
+authors = [
+    { name = "The preCICE Developers",  email="[email protected]"}
+]
+maintainers = [
+    { name = "Ishaan Desai",  email="[email protected]"}
+]
+description="A tool which facilitates two-scale macro-micro coupled simulations using preCICE."
+readme = "README.md"
+license={ text = "GPLv3" }
+keywords = [ "preCICE", "multiscale", "coupling" ]
+classifiers=[
+"Development Status :: 4 - Beta",
+"License :: OSI Approved :: GNU General Public License v3 (GPLv3)",
+"Programming Language :: Python :: 3 :: Only",
+"Programming Language :: Python :: 3.8",
+"Topic :: Scientific/Engineering",
+]
+
+[project.urls]
+Homepage = "https://precice.org"
+Documentation = "https://precice.org/tooling-micro-manager-overview.html"
+Repository = "https://github.com/precice/micro-manager"
+"Bug Tracker" = "https://github.com/precice/micro-manager/issues"
+
+[project.scripts]
+micro-manager-precice = "micro_manager.micro_manager:main"
+
+[tool.setuptools]
+packages=["micro_manager", "micro_manager.adaptivity"]
+
+[tool.setuptools-git-versioning]
+enabled = true

setup.py

@@ -1,35 +1,3 @@
-import os
+from setuptools import setup
 
-# from https://stackoverflow.com/a/9079062
-import sys
-
-from setuptools import find_packages, setup
-
-if sys.version_info[0] < 3:
-    raise Exception(
-        "micromanager only supports Python3. Did you run $python setup.py <option>.? "
-        "Try running $python3 setup.py <option>."
-    )
-
-this_directory = os.path.abspath(os.path.dirname(__file__))
-with open(os.path.join(this_directory, "README.md"), encoding="utf-8") as f:
-    long_description = f.read()
-
-setup(
-    name="micro-manager-precice",
-    version="v0.4.0",
-    description="micro-manager-precice is a package which facilitates two-scale macro-micro coupled simulations using preCICE",
-    long_description=long_description,
-    long_description_content_type="text/markdown",
-    url="https://precice.org/tooling-micro-manager-overview.html",
-    entry_points={
-        "console_scripts": ["micro_manager=micro_manager.micro_manager:main"]
-    },
-    author="Ishaan Desai",
-    author_email="[email protected]",
-    license="LGPL-3.0",
-    packages=find_packages(exclude=["examples"]),
-    install_requires=["pyprecice>=3.0.0.0", "numpy>=1.13.3", "scikit-learn", "mpi4py"],
-    test_suite="tests",
-    zip_safe=False,
-)
+setup()