From 527b00076cd98e5e6e251b9cfb9c2fc99b0ef97c Mon Sep 17 00:00:00 2001
From: Ishaan Desai <ishaandesai@gmail.com>
Date: Tue, 19 Mar 2024 09:44:08 +0100
Subject: [PATCH 01/10] Add pyproject.toml

---
 pyproject.toml | 46 ++++++++++++++++++++++++++++++++++++++++++++++
 setup.py       | 34 ++--------------------------------
 2 files changed, 48 insertions(+), 32 deletions(-)
 create mode 100644 pyproject.toml

diff --git a/pyproject.toml b/pyproject.toml
new file mode 100644
index 00000000..352b4ae3
--- /dev/null
+++ b/pyproject.toml
@@ -0,0 +1,46 @@
+[build-system]
+requires = ["setuptools>=41", "wheel", "setuptools-git-versioning"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name="micro-manager-precice"
+dynamic = [ "version" ]
+dependencies = [
+    "lxml", "pydot", "xdot", "PyGObject"
+]
+requires-python = ">=3.8"
+authors = [
+    { name = "Ishaan Desai",  email="ishaan.desai@ipva.uni-stuttgart.de"}
+]
+maintainers = [
+    { name = "Ishaan Desai",  email="ishaan.desai@ipvs.uni-stuttgart.de"}
+]
+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]
+precice-config-visualizer = "preciceconfigvisualizer.cli:main"
+
+[project.gui-scripts]
+precice-config-visualizer-gui = "preciceconfigvisualizer.gui:main"
+
+[tool.setuptools]
+packages=["preciceconfigvisualizer"]
+
+[tool.setuptools-git-versioning]
+enabled = true
diff --git a/setup.py b/setup.py
index 90de2a93..60684932 100644
--- a/setup.py
+++ b/setup.py
@@ -1,33 +1,3 @@
-import os
-from setuptools import setup, find_packages
+from setuptools import setup
 
-# from https://stackoverflow.com/a/9079062
-import sys
-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='v0.3.0',
-    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='ishaan.desai@uni-stuttgart.de',
-    license='LGPL-3.0',
-    packages=find_packages(
-        exclude=['examples']),
-    install_requires=[
-        'pyprecice>=3.0.0.0',
-        'numpy>=1.13.3',
-        'mpi4py'],
-    test_suite='tests',
-    zip_safe=False)
+setup()

From 9058a88a3feac629158c04fcc4572294a6eddbe6 Mon Sep 17 00:00:00 2001
From: Ishaan Desai <ishaandesai@gmail.com>
Date: Tue, 19 Mar 2024 13:40:38 +0100
Subject: [PATCH 02/10] Further changes to the pyproject.toml

---
 pyproject.toml | 14 ++++----------
 1 file changed, 4 insertions(+), 10 deletions(-)

diff --git a/pyproject.toml b/pyproject.toml
index 352b4ae3..069cd50a 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,12 +1,12 @@
 [build-system]
-requires = ["setuptools>=41", "wheel", "setuptools-git-versioning"]
+requires = ["setuptools>=61", "wheel", "setuptools-git-versioning"]
 build-backend = "setuptools.build_meta"
 
 [project]
 name="micro-manager-precice"
 dynamic = [ "version" ]
 dependencies = [
-    "lxml", "pydot", "xdot", "PyGObject"
+    "pyprecice>=3.0.0.0", "numpy", "mpi4py"
 ]
 requires-python = ">=3.8"
 authors = [
@@ -24,7 +24,7 @@ classifiers=[
 "License :: OSI Approved :: GNU General Public License v3 (GPLv3)",
 "Programming Language :: Python :: 3 :: Only",
 "Programming Language :: Python :: 3.8",
-Topic :: Scientific/Engineering
+"Topic :: Scientific/Engineering",
 ]
 
 [project.urls]
@@ -33,14 +33,8 @@ 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]
-precice-config-visualizer = "preciceconfigvisualizer.cli:main"
-
-[project.gui-scripts]
-precice-config-visualizer-gui = "preciceconfigvisualizer.gui:main"
-
 [tool.setuptools]
-packages=["preciceconfigvisualizer"]
+packages=["micro_manager"]
 
 [tool.setuptools-git-versioning]
 enabled = true

From 2b43cde907ed6bb13e5d8912d629ea2b871bcd45 Mon Sep 17 00:00:00 2001
From: Ishaan Desai <ishaandesai@gmail.com>
Date: Tue, 19 Mar 2024 15:05:59 +0100
Subject: [PATCH 03/10] Add adaptivity module explicitly to the pyproject.toml

---
 pyproject.toml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pyproject.toml b/pyproject.toml
index 069cd50a..a15db67b 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -34,7 +34,7 @@ Repository = "https://github.com/precice/micro-manager"
 "Bug Tracker" = "https://github.com/precice/micro-manager/issues"
 
 [tool.setuptools]
-packages=["micro_manager"]
+packages=["micro_manager", "micro_manager.adaptivity"]
 
 [tool.setuptools-git-versioning]
 enabled = true

From 5e0199ed1dd36be3697d7333eaece7c45fff06fb Mon Sep 17 00:00:00 2001
From: Ishaan Desai <ishaandesai@gmail.com>
Date: Fri, 3 May 2024 15:27:23 -0700
Subject: [PATCH 04/10] Adding package information to pyproject.toml

---
 pyproject.toml | 9 ++++++---
 1 file changed, 6 insertions(+), 3 deletions(-)

diff --git a/pyproject.toml b/pyproject.toml
index a15db67b..9da1df35 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,5 +1,5 @@
 [build-system]
-requires = ["setuptools>=61", "wheel", "setuptools-git-versioning"]
+requires = ["setuptools>=41", "wheel", "setuptools-git-versioning"]
 build-backend = "setuptools.build_meta"
 
 [project]
@@ -10,7 +10,7 @@ dependencies = [
 ]
 requires-python = ">=3.8"
 authors = [
-    { name = "Ishaan Desai",  email="ishaan.desai@ipva.uni-stuttgart.de"}
+    { name = "The preCICE Developers",  email="info@precice.org"}
 ]
 maintainers = [
     { name = "Ishaan Desai",  email="ishaan.desai@ipvs.uni-stuttgart.de"}
@@ -33,8 +33,11 @@ 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"]
+packages=["micro_manager"]
 
 [tool.setuptools-git-versioning]
 enabled = true

From cf7010f9e1da7246938651bdf18bf4bf5a3926f1 Mon Sep 17 00:00:00 2001
From: Ishaan Desai <ishaandesai@gmail.com>
Date: Fri, 3 May 2024 15:52:50 -0700
Subject: [PATCH 05/10] Reintroduce micro_manager.adaptivity to packaged in
 pyproject.toml

---
 pyproject.toml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pyproject.toml b/pyproject.toml
index 9da1df35..66fa3743 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -37,7 +37,7 @@ Repository = "https://github.com/precice/micro-manager"
 micro-manager-precice = "micro_manager.micro_manager:main"
 
 [tool.setuptools]
-packages=["micro_manager"]
+packages=["micro_manager", "micro_manager.adaptivity"]
 
 [tool.setuptools-git-versioning]
 enabled = true

From bdf32440ae0b99812e4c6dd0a75dacef73041247 Mon Sep 17 00:00:00 2001
From: Ishaan Desai <ishaandesai@gmail.com>
Date: Thu, 9 May 2024 13:43:23 -0700
Subject: [PATCH 06/10] Add scikit-learn as a dependency in pyproject.toml

---
 pyproject.toml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pyproject.toml b/pyproject.toml
index 66fa3743..f9aa9562 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -6,7 +6,7 @@ build-backend = "setuptools.build_meta"
 name="micro-manager-precice"
 dynamic = [ "version" ]
 dependencies = [
-    "pyprecice>=3.0.0.0", "numpy", "mpi4py"
+    "pyprecice>=3.0.0.0", "numpy", "mpi4py", "scikit-learn"
 ]
 requires-python = ">=3.8"
 authors = [

From 06883c441defce3b980a56f93588dae5efd6cff3 Mon Sep 17 00:00:00 2001
From: Ishaan Desai <ishaandesai@gmail.com>
Date: Mon, 13 May 2024 15:25:55 +0200
Subject: [PATCH 07/10] Change package name to micro_manager_precice

---
 CHANGELOG.md                     | 1 +
 pyproject.toml                   | 2 +-
 tests/unit/test_micro_manager.py | 2 +-
 3 files changed, 3 insertions(+), 2 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 1e4559ed..db9ba20e 100644
--- a/CHANGELOG.md
+++ b/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 switch to turn adaptivity on and off in configuration https://github.com/precice/micro-manager/pull/93
 
 ## v0.4.0
diff --git a/pyproject.toml b/pyproject.toml
index f9aa9562..d805eab7 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -34,7 +34,7 @@ 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"
+micro_manager_precice = "micro_manager.micro_manager:main"
 
 [tool.setuptools]
 packages=["micro_manager", "micro_manager.adaptivity"]
diff --git a/tests/unit/test_micro_manager.py b/tests/unit/test_micro_manager.py
index d5db7b7c..a46716c6 100644
--- a/tests/unit/test_micro_manager.py
+++ b/tests/unit/test_micro_manager.py
@@ -3,7 +3,7 @@
 
 import numpy as np
 
-import micro_manager
+import micro_manager_precice
 
 
 class MicroSimulation:

From e957a1904edc4cce2e6d161756ee69dc51272ad6 Mon Sep 17 00:00:00 2001
From: Ishaan Desai <ishaandesai@gmail.com>
Date: Mon, 13 May 2024 15:50:30 +0200
Subject: [PATCH 08/10] Go back to using micro_manager in the unit tests

---
 tests/unit/test_micro_manager.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tests/unit/test_micro_manager.py b/tests/unit/test_micro_manager.py
index a46716c6..d5db7b7c 100644
--- a/tests/unit/test_micro_manager.py
+++ b/tests/unit/test_micro_manager.py
@@ -3,7 +3,7 @@
 
 import numpy as np
 
-import micro_manager_precice
+import micro_manager
 
 
 class MicroSimulation:

From 93d864703bdf7a332b82d203fcc9740f202e5673 Mon Sep 17 00:00:00 2001
From: Ishaan Desai <ishaandesai@gmail.com>
Date: Mon, 13 May 2024 16:06:30 +0200
Subject: [PATCH 09/10] Upgrade pip before installing the Micro Manager in the
 unit tests CI

---
 .github/workflows/run-unit-tests.yml | 8 ++++++--
 1 file changed, 6 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/run-unit-tests.yml b/.github/workflows/run-unit-tests.yml
index a8fddd62..cbf151d9 100644
--- a/.github/workflows/run-unit-tests.yml
+++ b/.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
 

From 234262915a7d75f68035a18c72f54b64b48f4a0e Mon Sep 17 00:00:00 2001
From: Ishaan Desai <ishaandesai@gmail.com>
Date: Wed, 15 May 2024 22:47:07 +0200
Subject: [PATCH 10/10] Make executable name the same as the package name

---
 docs/running.md | 16 +++-------------
 pyproject.toml  |  2 +-
 2 files changed, 4 insertions(+), 14 deletions(-)

diff --git a/docs/running.md b/docs/running.md
index cf0e9dd3..4b5f0c8b 100644
--- a/docs/running.md
+++ b/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
 ```
diff --git a/pyproject.toml b/pyproject.toml
index d805eab7..f9aa9562 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -34,7 +34,7 @@ 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"
+micro-manager-precice = "micro_manager.micro_manager:main"
 
 [tool.setuptools]
 packages=["micro_manager", "micro_manager.adaptivity"]