Version 1.0.0 with citation.

Author: csachs

.github/workflows/python-package.yml

@@ -22,4 +22,10 @@ jobs:
       - uses: actions/upload-artifact@v2
         with:
           name: cellsium-package
-          path: dist/*
+          path: dist/*
+      - name: Publish distribution to PyPI
+        if: startsWith(github.ref, 'refs/tags')
+        uses: pypa/gh-action-pypi-publish@v1.5.1
+        with:
+          user: __token__
+          password: ${{ secrets.PYPI_API_TOKEN }}

CITATION.cff

@@ -0,0 +1,63 @@
+cff-version: 1.2.0
+message: "If you use this software, please cite it as below."
+authors:
+  - family-names: Sachs
+    given-names: Christian Carsten
+    orcid: https://orcid.org/0000-0001-8848-5775
+
+  - family-names: Ruzaeva
+    given-names: Karina
+    orcid: https://orcid.org/0000-0003-3610-0989
+
+  - family-names: Seiffarth
+    given-names: Johannes
+    orcid: https://orcid.org/0000-0002-2087-9847
+
+  - family-names: Wiechert
+    given-names: Wolfgang
+    orcid: https://orcid.org/0000-0001-8501-0694
+
+  - family-names: Berkels
+    given-names: Benjamin
+    orcid: https://orcid.org/0000-0002-6969-187X
+
+  - family-names: Nöh
+    given-names: Katharina
+    orcid: https://orcid.org/0000-0002-5407-2275
+version: 1.0.0
+title: "CellSium"
+doi: 10.5281/zenodo.6193033
+
+preferred-citation:
+  title: "CellSium: versatile cell simulator for microcolony ground truth generation"
+  type: article
+  journal: Bioinformatics Advances
+  month: 8
+  year: 2022
+  doi: 10.1093/bioadv/vbac053
+  volume: 2
+  issue: 1
+  authors:
+    - family-names: Sachs
+      given-names: Christian Carsten
+      orcid: https://orcid.org/0000-0001-8848-5775
+  
+    - family-names: Ruzaeva
+      given-names: Karina
+      orcid: https://orcid.org/0000-0003-3610-0989
+  
+    - family-names: Seiffarth
+      given-names: Johannes
+      orcid: https://orcid.org/0000-0002-2087-9847
+  
+    - family-names: Wiechert
+      given-names: Wolfgang
+      orcid: https://orcid.org/0000-0001-8501-0694
+  
+    - family-names: Berkels
+      given-names: Benjamin
+      orcid: https://orcid.org/0000-0002-6969-187X
+  
+    - family-names: Nöh
+      given-names: Katharina
+      orcid: https://orcid.org/0000-0002-5407-2275

README.rst

@@ -37,7 +37,13 @@ CellSium is a cell simulator developed for the primary application of generating
 Publication
 ###########
 
-The publication is currently in preparation. If you use CellSium within scientific research, we ask you to cite our publication.
+If you use CellSium within scientific research, we ask you to cite our publication:
+
+    Sachs CC, Ruzaeva K, Seiffarth J, Wiechert W, Berkels B, Nöh K (2022)
+    CellSium: versatile cell simulator for microcolony ground truth generation
+    Bioinformatics Advances, Volume 2, Issue 1, 2022, vbac053, doi: 10.1093/bioadv/vbac053
+
+It is available on the *Bioinformatics Advances* homepage at `DOI: 10.1093/bioadv/vbac053 <https://doi.org/10.1093/bioadv/vbac053>`.
 
 Documentation
 #############
@@ -76,7 +82,7 @@ Usage
 
 Once installed, run CellSium via :code:`python -m cellsium`, specifying the desired entrypoint and options, such as outputs.
 CellSium is built modular, various output modules can be activated simultaneously. To get an overview of the available options,
-use the :code:`--help` switch. Furthermore, the main mode of setting tunable paramters are so called *tunables*, which can
+use the :code:`--help` switch. Furthermore, the main mode of setting tunable parameters are so called *tunables*, which can
 be set from the command line using the :code:`-t` switches. A list of tunables can be shown using the :code:`--tunables-show` argument.
 
 .. code-block:: bash

cellsium/__init__.py

@@ -2,12 +2,16 @@
 
 __project__ = 'CellSium'
 
-__version__ = '1.0.0rc1'
+__version__ = '1.0.0'
 
 __author__ = 'Christian C. Sachs'
 
 __copyright__ = '2021, Christian C. Sachs, Forschungszentrum Jülich GmbH'
 
-__citation__ = ''
+__citation__ = '''
+Sachs CC, Ruzaeva K, Seiffarth J, Wiechert W, Berkels B, Nöh K (2022)
+CellSium: versatile cell simulator for microcolony ground truth generation
+Bioinformatics Advances, Volume 2, Issue 1, 2022, vbac053, doi: 10.1093/bioadv/vbac053
+'''
 
 __banner__ = ''

docs/examples.rst

@@ -25,7 +25,7 @@ For example, the following command will random cell images, and output three dat
         --Output GenericMaskOutput \
         -p
 
-Note how the main mode of configuration of CellSium are *tunables*, these tunable paramters are set using the :code:`-t` argument, followed by :code:`Name=value`. The tunables are explained in the documentation, and can be listed via :code:`--tunables-show` as well.
+Note how the main mode of configuration of CellSium are *tunables*, these tunable parameters are set using the :code:`-t` argument, followed by :code:`Name=value`. The tunables are explained in the documentation, and can be listed via :code:`--tunables-show` as well.
 
 In this example, the output of 64 images of 512x512 size are requested, setting the pixel calibration to 0.0905158 µm per pixel. :code:`ChipmunkPlacementRadius` configures the physical placement and yields denser colonies. The name of the output files/directories is specified using :code:`-o`.
 

recipe/meta.yaml

@@ -1,5 +1,5 @@
 {% set name = "cellsium" %}
-{% set version = "0.0.1.dev1" %}
+{% set version = "1.0.0" %}
 {% set sha256 = "" %}
 
 package: