Merge pull request #172 from matthiaskoenig/develop

Latest changes develop

Author: matthiaskoenig

.github/ISSUE_TEMPLATE/01-bug-report.md

@@ -37,7 +37,7 @@ Create a [minimal, complete, verifiable example](https://stackoverflow.com/help/
 <!-- Run the following code and paste the output between the ``` tickmarks below
 inside the details block.
 
-python -c "import sbmlsim;sbmlsim.show_versions()"
+depinfo sbmlsim
 
 -->
 

.github/workflows/main.yml

@@ -1,26 +1,15 @@
 name: CI-CD
 
-on:
-  push:
-    branches:
-    - master
-    - develop
-    tags:
-      - '[0-9]+.[0-9]+.[0-9]+'
-      - '[0-9]+.[0-9]+.[0-9]+a[0-9]+'
-  pull_request:
-    branches:
-    - master
-    - develop
+on: [push]
 
 jobs:
-  test:
+  tests:
     runs-on: ${{ matrix.os }}
     strategy:
       fail-fast: false
       matrix:
         os: [ubuntu-latest]  # [ubuntu-latest, macos-latest, windows-latest]
-        python-version: [3.7, 3.8]
+        python-version: [3.8, 3.9]
 
     steps:
     - uses: actions/checkout@v2
@@ -40,14 +29,13 @@ jobs:
       run: bash <(curl -s https://codecov.io/bash)
 
   release:
-    needs: test
+    needs: tests
     if: startsWith(github.ref, 'refs/tags')
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
         os: [ubuntu-latest]
-        python-version: [3.7]
-
+        python-version: [3.9]
     steps:
     - uses: actions/checkout@v2
     - name: Set up Python ${{ matrix.python-version }}
@@ -81,3 +69,11 @@ jobs:
         body_path: "release-notes/${{ steps.tag.outputs.version }}.md"
         draft: false
         prerelease: false
+    - name: Send release tweet
+      uses: ethomson/send-tweet-action@v1
+      with:
+        status: "New ${{ github.event.repository.name }} release ${{ steps.tag.outputs.version }}! https://github.com/matthiaskoenig/sbmlsim/releases/tag/${{ steps.tag.outputs.version }} #python #SBML #release"
+        consumer-key: ${{ secrets.TWITTER_CONSUMER_API_KEY }}
+        consumer-secret: ${{ secrets.TWITTER_CONSUMER_API_SECRET }}
+        access-token: ${{ secrets.TWITTER_ACCESS_TOKEN }}
+        access-token-secret: ${{ secrets.TWITTER_ACCESS_TOKEN_SECRET }}

.gitignore

@@ -1,4 +1,10 @@
+.vscode
+workspace.code-workspace
+
 .idea
+.vscode
+workspace.code-workspace
+
 dist
 build
 sbmlsim.egg-info
@@ -12,6 +18,7 @@ coverage.xml
 *.pyc
 *~
 __pycache__
+src/sbmlsim/comparison/results/amici/
 
 # cached model state
 *.xml.dat
@@ -22,8 +29,20 @@ __pycache__
 
 # documentation
 docs_builder/_build/
-
+src/sbmlsim/examples/experiments/covid/results/
 src/sbmlsim/examples/experiments/glucose/results/DoseResponseExperiment/DoseResponseExperiment_fig1.svg
 src/sbmlsim/examples/experiments/repressilator/RepressilatorExperiment/RepressilatorExperiment_task_tc.h5
 src/sbmlsim/examples/experiments/midazolam/results/
 src/sbmlsim/examples/experiments/midazolam/results_fit/
+
+# sedml
+src/sbmlsim/combine/examples/results/
+src/sbmlsim/examples/experiments/repressilator/results/
+src/sbmlsim/examples/experiments/covid/results/
+src/sbmlsim/examples/experiments/covid/omex/results/
+src/sbmlsim/examples/experiments/midazolam/results/
+
+src/sbmlsim/combine/results
+src/sbmlsim/combine/examples/l1v4/sbmlsim/
+
+src/sbmlsim/comparison/amicitesting/icg_sd/

.readthedocs.yml

@@ -18,7 +18,7 @@ formats: []
 
 # Optionally set the version of Python and requirements required to build your docs
 python:
-  version: 3.7
+  version: 3.8
   install:
     - requirements: docs_builder/requirements-docs.txt
     - method: pip

.zenodo.json

@@ -0,0 +1,31 @@
+{
+  "upload_type": "software",
+  "title": "sbmlsim: SBML simulation made easy",
+  "creators": [
+    {
+      "orcid": "0000-0003-1725-179X",
+      "affiliation": "Humboldt-University Berlin, Institute for Theoretical Biology, Berlin",
+      "name": "König, Matthias"
+    }
+  ],
+  "description": "<p><code>sbmlsim</code> is a collection of python utilities to simplify simulations with <a href=\"http://www.sbml.org\">SBML</a> models implemented on top of <code><a href=\"http://libroadrunner.org/\">roadrunner</a></code> and other libraries with source code available from <a href=\"https://github.com/matthiaskoenig/sbmlsim\">https://github.com/matthiaskoenig/sbmlsim</a></p>\n<p>Features include among others<ul><li>simulation experiments</li><li>simulation reports</a></li><li>parameter fitting</li></ul></p>\n<p>The documentation is available on <a href=\"https://sbmlsim.readthedocs.io\">https://sbmlsim.readthedocs.io</a></p>\n<p>If you have any questions or issues please <a href=\"https://github.com/matthiaskoenig/sbmlsim/issues\">open an issue</a></p>\n<h2>Funding</h2><p>Matthias König is supported by the Federal Ministry of Education and Research (BMBF, Germany) within the research network Systems Medicine of the Liver (<strong>LiSyM</strong>, grant number 031L0054) and by the German Research Foundation (DFG) within the Research Unit Programme FOR 5151 <strong><a href=\"https://qualiperf.de\">QuaLiPerF</a></strong> (Quantifying Liver Perfusion-Function Relationship in Complex Resection - A Systems Medicine Approach)\" by grant number 436883643 and by grant number 465194077 (Priority Programme SPP 2311, Subproject SimLivA). Matthias König has received funds from the EOSCsecretariat.eu which has received funding from the European Union's Horizon Programme call H2020-INFRAEOSC-05-2018-2019, grant Agreement number 831644.</p>",
+  "access_right": "open",
+  "license": "LGPL-3.0",
+  "keywords": [
+    "modeling",
+    "standardization",
+    "SBML",
+    "SED-ML",
+    "COMBINE"
+  ],
+  "communities": [
+    {
+      "identifier": "eoscsecretariat"
+    }
+  ],
+  "grants": [
+    {
+      "id": "831644"
+    }
+  ]
+}

README.rst

@@ -1,3 +1,8 @@
+.. image:: https://github.com/matthiaskoenig/sbmlsim/raw/develop/docs/images/favicon/sbmlsim-100x100-300dpi.png
+   :align: left
+   :alt: pymetadata logo
+
+
 sbmlsim: SBML simulation made easy
 ==================================
 
@@ -34,7 +39,7 @@ sbmlsim: SBML simulation made easy
    :alt: Black
 
 
-sbmlsim is a collection of python utilities to simulate to simplify simulations with
+sbmlsim is a collection of python utilities to simplify simulations with
 `SBML <http://www.sbml.org>`__ models implemented on top of
 `roadrunner <http://libroadrunner.org/>`__. Source code is available from
 `https://github.com/matthiaskoenig/sbmlsim <https://github.com/matthiaskoenig/sbmlsim>`__.
@@ -84,7 +89,13 @@ PARTICULAR PURPOSE. See the GNU General Public License for more details.
 Funding
 =======
 Matthias König is supported by the Federal Ministry of Education and Research (BMBF, Germany)
-within the research network Systems Medicine of the Liver (**LiSyM**, grant number 031L0054).
+within the research network Systems Medicine of the Liver (**LiSyM**, grant number 031L0054) 
+and by the German Research Foundation (DFG) within the Research Unit Programme FOR 5151 
+"`QuaLiPerF <https://qualiperf.de>`__ (Quantifying Liver Perfusion-Function Relationship in Complex Resection - 
+A Systems Medicine Approach)" by grant number 436883643 and by grant number 
+465194077 (Priority Programme SPP 2311, Subproject SimLivA). Matthias König has received funding from the EOSCsecretariat.eu which has received funding 
+from the European Union's Horizon Programme call H2020-INFRAEOSC-05-2018-2019, grant Agreement number 831644.
+
 
 Installation
 ============
@@ -116,4 +127,4 @@ To install for development use::
 
     pip install -e .[development]
     
-© 2019-2020 Matthias König
+© 2019-2022 Matthias König

RELEASE.md

@@ -1,15 +1,10 @@
 # Release information
 
-## update documentation
-* make necessary updates to notebooks
-* build documentation `cd docs_builder` and `./make_docs.sh 2>&1 | tee ./make_docs.log`
 
 ## make release
-* sort imports (`isort src/sbmlsim`)
-* code formating (`black src/sbmlsim`)
-* make sure all tests run (`tox`)
+* make sure all tests run (`tox -p`)
 * update release notes in `release-notes`
-* bump version (`bumpversion patch` or `bumpversion` minor)
+* bump version (`bumpversion patch` or `bumpversion minor` or `bumpversion major`)
 * `git push --tags` (triggers release)
 * add release-notes for next version
 

docs/images/favicon/about.txt

@@ -0,0 +1,6 @@
+This favicon was generated using the following graphics from Twitter Twemoji:
+
+- Graphics Title: 1f9ee.svg
+- Graphics Author: Copyright 2020 Twitter, Inc and other contributors (https://github.com/twitter/twemoji)
+- Graphics Source: https://github.com/twitter/twemoji/blob/master/assets/svg/1f9ee.svg
+- Graphics License: CC-BY 4.0 (https://creativecommons.org/licenses/by/4.0/)