From 1f3e73361553bce1e7656338eb8e556cc3d0f68e Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Felix=20K=C3=B6hler?=
 <27728103+Ceyron@users.noreply.github.com>
Date: Fri, 18 Oct 2024 10:57:06 +0200
Subject: [PATCH 1/5] Add warning

---
 README.md | 1 +
 1 file changed, 1 insertion(+)

diff --git a/README.md b/README.md
index 3f5832c..599d703 100644
--- a/README.md
+++ b/README.md
@@ -1,3 +1,4 @@
+ ⚠️ ⚠️ ⚠️ This is a pre-release version of the package to test the PyPI workflow. Proper release **with breaking API changes** will be by end of October. ⚠️ ⚠️ ⚠️
 
 <h1 align="center">
   <img src="docs/imgs/exponax_logo.png" width="200">

From a9a772a3f2f2d7991b71a28429d1b8a756835f47 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Felix=20K=C3=B6hler?=
 <27728103+Ceyron@users.noreply.github.com>
Date: Fri, 18 Oct 2024 11:00:54 +0200
Subject: [PATCH 2/5] Add Test workflow

---
 .github/workflows/test.yml | 33 +++++++++++++++++++++++++++++++++
 tests/requirements.txt     |  2 ++
 2 files changed, 35 insertions(+)
 create mode 100644 .github/workflows/test.yml
 create mode 100644 tests/requirements.txt

diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
new file mode 100644
index 0000000..38457ee
--- /dev/null
+++ b/.github/workflows/test.yml
@@ -0,0 +1,33 @@
+name: Run tests
+
+on: [push, pull_request]
+
+permissions:
+  contents: read
+
+jobs:
+  run-test:
+    strategy:
+      matrix:
+        python-version: [ "3.10", "3.11", "3.12" ]
+        os: [ ubuntu-latest ]
+      fail-fast: false
+    runs-on: ${{ matrix.os }}
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v4
+
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          python -m pip install -r ./tests/requirements.txt
+
+      - name: Test with pytest
+        run: |
+          python -m pip install .
+          python -m pytest tests/
\ No newline at end of file
diff --git a/tests/requirements.txt b/tests/requirements.txt
new file mode 100644
index 0000000..df05b4d
--- /dev/null
+++ b/tests/requirements.txt
@@ -0,0 +1,2 @@
+jaxlib
+pytest

From 3cb90d30f2039fb70d619b23648d10f67e17d909 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Felix=20K=C3=B6hler?=
 <27728103+Ceyron@users.noreply.github.com>
Date: Fri, 18 Oct 2024 11:03:53 +0200
Subject: [PATCH 3/5] Rework readme

---
 README.md | 38 ++++++++++++++++++--------------------
 1 file changed, 18 insertions(+), 20 deletions(-)

diff --git a/README.md b/README.md
index 599d703..92ecd80 100644
--- a/README.md
+++ b/README.md
@@ -1,12 +1,5 @@
  ⚠️ ⚠️ ⚠️ This is a pre-release version of the package to test the PyPI workflow. Proper release **with breaking API changes** will be by end of October. ⚠️ ⚠️ ⚠️
 
-<h1 align="center">
-  <img src="docs/imgs/exponax_logo.png" width="200">
-  <br>
-    Exponax
-  <br>
-</h1>
-
 <h4 align="center">Efficient Differentiable PDE solvers built on top of <a href="https://github.com/google/jax" target="_blank">JAX</a> & <a href="https://github.com/patrick-kidger/equinox" target="_blank">Equinox</a>.</h4>
 
 <p align="center">
@@ -16,7 +9,7 @@
   <a href="#documentation">Documentation</a> •
   <a href="#background">Background</a> •
   <a href="#related">Related</a> •
-  <a href="#license">License</a>
+    <a href="#acknowledgements">Acknowledgements</a>
 </p>
 
 <p align="center">
@@ -26,10 +19,10 @@
 ## Installation
 
 ```bash
-pip install git+ssh://git@github.com/Ceyron/exponax@main
+pip install exponax
 ```
 
-Requires Python 3.10+ and JAX 0.4.13+ (and Equinox & Matplotlib). 👉 [JAX install guide](https://jax.readthedocs.io/en/latest/installation.html).
+Requires Python 3.10+ and JAX 0.4.13+. 👉 [JAX install guide](https://jax.readthedocs.io/en/latest/installation.html).
 
 ## Quickstart
 
@@ -91,13 +84,7 @@ For a next step, check out the [simple_advection_example_1d.ipynb](examples/simp
 
 ## Documentation
 
-The following Jupyter notebooks showcase the usage of the package:
-
-1. [Simple Advection Example in 1d](docs/examples/simple_advection_example_1d.ipynb)
-2. ...
-
-The documentation is still in progress. For now, the best way to get started is
-to look at the examples and the docstrings in the code.
+Documentation is available at [fkoehler.site/exponax](https://fkoehler.site/exponax/).
 
 ## Background
 
@@ -169,12 +156,23 @@ This package also took much inspiration from the
 integral method of [2] and how to handle (de)aliasing.
 
 
-## License
+## Acknowledgements
+
+### Citation
+
+This package was developed as part of the `APEBench paper` (accepted at Neurips 2024), we will soon add the citation here.
+
+### Funding
+
+The main author (Felix Koehler) is a PhD student in the group of [Prof. Thuerey at TUM](https://ge.in.tum.de/) and his research is funded by the [Munich Center for Machine Learning](https://mcml.ai/).
+
+### License
 
-MIT, see [here](LICENSE.txt)
+MIT, see [here](https://github.com/Ceyron/exponax/blob/main/LICENSE.txt)
 
 ---
 
 > [fkoehler.site](https://fkoehler.site/) &nbsp;&middot;&nbsp;
 > GitHub [@ceyron](https://github.com/ceyron) &nbsp;&middot;&nbsp;
-> X [@felix_m_koehler](https://twitter.com/felix_m_koehler)
+> X [@felix_m_koehler](https://twitter.com/felix_m_koehler) &nbsp;&middot;&nbsp;
+> LinkedIn [Felix Köhler](www.linkedin.com/in/felix-koehler)

From 824154b37b18408b6111f1f0d1001b9f5d8f47c6 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Felix=20K=C3=B6hler?=
 <27728103+Ceyron@users.noreply.github.com>
Date: Fri, 18 Oct 2024 11:05:45 +0200
Subject: [PATCH 4/5] Ignore 3D visualization tests for now

---
 tests/test_viz.py | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/tests/test_viz.py b/tests/test_viz.py
index 045ac57..0440727 100644
--- a/tests/test_viz.py
+++ b/tests/test_viz.py
@@ -28,8 +28,8 @@ def test_plot_state_2d():
     plt.close(fig)
 
 
-def test_plot_state_3d():
-    state = jax.random.normal(jax.random.PRNGKey(0), (1, 32, 32, 32))
+# def test_plot_state_3d():
+#     state = jax.random.normal(jax.random.PRNGKey(0), (1, 32, 32, 32))
 
-    fig = ex.viz.plot_state_3d(state)
-    plt.close(fig)
+#     fig = ex.viz.plot_state_3d(state)
+#     plt.close(fig)

From 8959079f16863ae9122be9a607da068208d8271c Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Felix=20K=C3=B6hler?=
 <27728103+Ceyron@users.noreply.github.com>
Date: Fri, 18 Oct 2024 11:07:27 +0200
Subject: [PATCH 5/5] Add PyPI publishing workflow

---
 .github/workflows/publish.yml | 71 +++++++++++++++++++++++++++++++++++
 1 file changed, 71 insertions(+)
 create mode 100644 .github/workflows/publish.yml

diff --git a/.github/workflows/publish.yml b/.github/workflows/publish.yml
new file mode 100644
index 0000000..f5a7e15
--- /dev/null
+++ b/.github/workflows/publish.yml
@@ -0,0 +1,71 @@
+name: Publish Python Package
+
+on:
+  release:
+    types: [created]
+
+permissions:
+  contents: read
+
+jobs:
+  test:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ["3.10", "3.11", "3.12"]
+    steps:
+    - uses: actions/checkout@v4
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v5
+      with:
+        python-version: ${{ matrix.python-version }}
+        cache: pip
+        cache-dependency-path: pyproject.toml
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        python -m pip install -r ./tests/requirements.txt
+
+    - name: Run tests
+      run: |
+        python -m pip install .
+        python -m pytest tests/
+  build:
+    runs-on: ubuntu-latest
+    needs: [test]
+    steps:
+    - uses: actions/checkout@v4
+    - name: Set up Python
+      uses: actions/setup-python@v5
+      with:
+        python-version: "3.12"
+        cache: pip
+        cache-dependency-path: pyproject.toml
+    - name: Install dependencies
+      run: |
+        pip install setuptools wheel build
+    - name: Build
+      run: |
+        python -m build
+    - name: Store the distribution packages
+      uses: actions/upload-artifact@v4
+      with:
+        name: python-packages
+        path: dist/
+  publish:
+    name: Publish to PyPI
+    runs-on: ubuntu-latest
+    if: startsWith(github.ref, 'refs/tags/')
+    needs: [build]
+    environment: release
+    permissions:
+      id-token: write
+    steps:
+    - name: Download distribution packages
+      uses: actions/download-artifact@v4
+      with:
+        name: python-packages
+        path: dist/
+    - name: Publish to PyPI
+      uses: pypa/gh-action-pypi-publish@release/v1
+