Toepfer-Lab · JanNiklasWeder · Jul 27, 2026 · Jul 27, 2026
diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
@@ -1,7 +1,10 @@
-name: Test
+name: Test, build and publish Cobra2D to PyPI
 on:
   workflow_dispatch:
 
+  schedule:
+    - cron: "0 5 * * 1"
+
   pull_request:
     types: [ opened, synchronize, reopened, closed ]
     branches:
@@ -23,12 +26,11 @@ jobs:
           run: python -m tox -e format
 
   types:
-    needs: [lint-format]
+    needs: [ lint-format ]
     runs-on: ubuntu-latest
     strategy:
       matrix:
         python: [ '3.9', '3.10', '3.11', '3.12', '3.13' ]
-
     steps:
       - uses: actions/checkout@v4
       - uses: actions/setup-python@v5
@@ -40,7 +42,7 @@ jobs:
         run: python -m tox -e types
 
   test-dev:
-    needs: [lint-format, types]
+    needs: [ lint-format, types ]
     runs-on: ubuntu-latest
     steps:
         - uses: actions/checkout@v4
@@ -52,38 +54,68 @@ jobs:
         - name: Run dev env test
           run: python -m tox -e py310-req
 
+  build:
+    needs: [ types ]
+    runs-on: ubuntu-latest
+    outputs:
+      file-path: ${{ steps.path.outputs.file-path }}
+    steps:
+      - uses: actions/checkout@v4
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: '3.13'
+          cache: 'pip'
+      - name: Install dependencies
+        run: python -m pip install --upgrade pip build
+      - name: Build package
+        run: python -m build
+      - name: Get wheel file name
+        id: path
+        run: echo "file-path=$(cd dist && find . -type f -iname 'cobra2d-*.whl')" >> "$GITHUB_OUTPUT"
+      - name: Archive package as artifact
+        uses: actions/upload-artifact@v4
+        with:
+          name: cobra2d-dist
+          path: dist
+
   test:
-    needs: [test-dev]
+    needs: [ build ]
     strategy:
       matrix:
         os: [ ubuntu-latest ]
         python-version: [ '3.9', '3.10', '3.11', '3.12', '3.13' ]
-    runs-on: ${{ matrix.os}}
-
+    runs-on: ${{ matrix.os }}
     steps:
       - 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
+      - name: Download built package
+        uses: actions/download-artifact@v4
+        with:
+          name: cobra2d-dist
+      - name: Install tox
         run: python -m pip install tox tox-uv
+      - name: Set up test suite (install the built wheel)
+        run: python -m tox -e py --notest --installpkg ${{ needs.build.outputs.file-path }}
       - name: Run tests
-        run: tox -e py
+        run: python -m tox -e py --skip-pkg-install
 
   create-tag:
-    needs: [test]
+    needs: [ test, test-dev ]
     runs-on: ubuntu-latest
+    if: github.event.pull_request.merged == true
     steps:
       - uses: actions/checkout@v4
-      - run: |
-          output=$(python setup.py --version)
-          echo "version=$output" >> "$GITHUB_OUTPUT"
+      - name: Get version
         id: version
-
+        run: |
+          version=$(grep -Po '(?<=^__version__ = ")[^"]+' src/cobra2d/__init__.py)
+          echo "version=$version" >> "$GITHUB_OUTPUT"
       - name: Create tag
-        if: github.event.pull_request.merged == true
-        uses: actions/github-script@v5
+        uses: actions/github-script@v7
         with:
           script: |
             github.rest.git.createRef({
@@ -93,30 +125,31 @@ jobs:
               sha: context.sha
             })
 
-  build-publish:
-    needs: [ lint-format, types, test ]
-    name: Build and publish the package to TestPyPI
+  publish-to-pypi:
+    needs: [ test, test-dev ]
+    name: Publish Cobra2D 📦 to PyPI
     if: github.event.pull_request.merged == true && github.event_name != 'schedule'
     runs-on: ubuntu-latest
-
+    environment:
+      name: pypi
+      url: https://pypi.org/p/cobra2d
+    permissions:
+      id-token: write
     steps:
-      - uses: actions/checkout@v4
+      - name: Download built package
+        uses: actions/download-artifact@v4
+        with:
+          name: cobra2d-dist
+          path: dist
       - name: Set up Python
         uses: actions/setup-python@v5
         with:
-          python-version: '3.10'
-
-      - name: Install dependencies
-        run: |
-          python -m pip install --upgrade pip
-          python -m pip install build twine
-      - name: Build package
-        run: python -m build
+          python-version: '3.13'
+      - name: Install twine
+        run: python -m pip install --upgrade pip twine
       - name: Check the package
         run: twine check dist/*
-      - name: Publish to PyPI
-        env:
-          TWINE_USERNAME: ${{ secrets.PYPI_USERNAME }}
-          TWINE_PASSWORD: ${{ secrets.PYPI_PASSWORD }}
-        run:
-          twine upload --non-interactive dist/*
+      - name: Publish distribution 📦 to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1
+        with:
+          skip-existing: true
diff --git a/README.md b/README.md
@@ -1,14 +1,16 @@
-![Generic badge](<https://img.shields.io/badge/python-3.9%20%7C%203.10%20%7C%203.11%20%7C%203.12%20%7C%203.13-blue>)
-![Tests](https://github.com/Toepfer-Lab/model_duplication/actions/workflows/test.yml/badge.svg)
-![GitHub last commit](https://img.shields.io/github/last-commit/Toepfer-Lab/model_duplication)
-![GitHub pull requests](https://img.shields.io/github/issues-pr/Toepfer-Lab/model_duplication)
+# Cobra2D
+
+![Python versions](https://img.shields.io/badge/python-3.9%20%7C%203.10%20%7C%203.11%20%7C%203.12%20%7C%203.13-blue)
+![Tests](https://github.com/Toepfer-Lab/Cobra2D/actions/workflows/test.yml/badge.svg)
+![GitHub last commit](https://img.shields.io/github/last-commit/Toepfer-Lab/Cobra2D)
+![GitHub pull requests](https://img.shields.io/github/issues-pr/Toepfer-Lab/Cobra2D)
 
 Cobra2D is a Python package that extends COBRApy to automatically reconstruct time-resolved and/or multi-subsystem metabolic models. It generates context-specific submodels, adds linker and/or transfer reactions to connect them, and scales reactions to account for the lengths of the respective time intervals and the sizes of the subsystems. Cobra2D also provides a time interval- and subsystem size-aware weighted pFBA function.
 
-### General process:
+### General process
 
 * Define time intervals (phases) and subsystems (e.g. cell types, tissues or organs)
-* Contextualizing sub-models
+* Contextualize submodels
   * Adjusting compartment sizes
   * Adjusting time intervals
   * Defining linker reactions (auxiliary reactions that connect phases and allow storage metabolites to be transferred across consecutive phases)
@@ -19,32 +21,52 @@ Cobra2D is a Python package that extends COBRApy to automatically reconstruct ti
 For this process, this package provides functionalities to not only simplify this process, but also to easily save and
 share the defined settings with other people.
 
-### Use cases for this package
+### Quick start
+
+Define the spatial submodels and time slots, connect phases, and apply the resulting constraints to a COBRApy model:
+
+```python
+from cobra2d import Constraints
+from cobra.io import load_model
+
+model = load_model("textbook")
+
+constraints = Constraints()
+constraints.add_sub_models(["leaf", "root"], [2, 1])
+constraints.add_time_slots(n_ranges=2, time=12)
+constraints.add_linker_series("atp_c")
+constraints.add_transfer_series("glc__D_e", ["leaf", "root"])
+
+resolved_model = constraints.apply_to_model(model)
+```
+
+Constraints can also be saved as XML and shared:
+
+```python
+constraints.save_as_xml("constraints.xml")
+restored = Constraints.load_from_xml("constraints.xml")
+```
 
-There are two ways to use this package: functions implemented in Python can be used to define phases and constraints directly, or an XML file can be created and read in to generate a new model.
+See the [constraints notebook](docs/source/examples/Constraints.ipynb) for a complete introduction and [linkage and phases](docs/source/examples/LinkageAndPhases.ipynb) for more advanced model construction.
 
 ### Examples
 
-Examples of package usage can be found in the examples folder, including scripts that demonstrate the core functions and a sample XML file showing how parameters are stored. 
+The documentation includes notebooks for [constraints](docs/source/examples/Constraints.ipynb), [linkage and phases](docs/source/examples/LinkageAndPhases.ipynb), and [visualization](docs/source/examples/Visualization/cytoscape.ipynb). A sample XML configuration is available at [docs/source/examples/data/conf.xml](docs/source/examples/data/conf.xml).
 
 ### Visualization
 
 The package also provides the possibility to obtain an overview of the created settings via an animated or static graphic.
 
-<object data="../../assets/media/ConInteractive.gif" type="image/gif">
-      <object data="https://github.com/Toepfer-Lab/model_duplication/blob/c42dfdac52524a93323e78e1f3d996aef5e01714/assets/media/ConInteractive.gif" type="image/gif">
-        <img src="./assets/media/ConInteractive.gif" alt="ConInteractive.gif">
-      </object>
-</object>
+![Interactive Cytoscape visualization of Cobra2D constraints](assets/media/ConInteractive.gif)
 
 ### Installation
 
 After cloning the repository, the package can be installed in the current Python environment using pip. In a terminal, this can be done with the following commands: 
 
 ```
-git clone https://github.com/Toepfer-Lab/model_duplication
+git clone https://github.com/Toepfer-Lab/Cobra2D.git
 
-cd model_duplication
+cd Cobra2D
 
 pip install .
 ```

diff --git a/docs/source/example.rst b/docs/source/example.rst
@@ -6,5 +6,6 @@ Examples
 
     examples/Constraints
     examples/LinkageAndPhases
-    examples/Visualization/cytoscape.ipynb
-
+    examples/Visualization/classic
+    examples/Visualization/cytoscape
+    examples/converter
diff --git a/docs/source/index.rst b/docs/source/index.rst
@@ -8,12 +8,13 @@ Cobra2D
     :glob:
     :maxdepth: 2
 
-    README <self>
+    Getting started <self>
     Structural design <structure>
     Linker and transfer reactions <transport>
     Visualisation <visualization>
     Naming convention <convention>
     Examples <example>
+    API reference <api>
 
 Indices and tables
 ==================

diff --git a/docs/source/visualization.rst b/docs/source/visualization.rst
@@ -38,7 +38,9 @@ The visualization can be created with the following command.
 .. figure:: ../../assets/media/GraphViz.png
    :scale: 50 %
    :alt: Example of visualization using GraphViz
-    Example of visualization with GraphViz where ATP is transported to the following time period respectively.
+
+   Example of a GraphViz visualization in which ATP is transported to each
+   following time period.
 
 Cytoscape visualizes the same as GraphViz but in an interactive environment. Thus, much more information is available
 than is available when using Graphviz. However, this information is not all displayed at the same time,
@@ -62,7 +64,9 @@ Below is a brief example of this visualization.
 .. figure:: ../../assets/media/ConInteractive.gif
    :scale: 50 %
    :alt: Example of visualization using Cytoscape
-    Example of visualization with Cytoscape where ATP is transported to the following time period respectively.
+
+   Example of an interactive Cytoscape visualization in which ATP is
+   transported to each following time period.
 
 
 Metexplore
@@ -83,4 +87,6 @@ The pathways are sorted alphabetically and the metabolites are sorted based on t
 .. figure:: ../../assets/media/MetExploreVizInterface.png
    :scale: 50 %
    :alt: Example of the MetExploreViz interface
-    Example of the interface used to select groups and hide metabolites before visualizing a COBRApy model with MetExploreViz.
+
+   Interface for selecting groups and hiding metabolites before visualizing a
+   COBRApy model with MetExploreViz.