Merge pull request #122 from yaml2sbml-dev/develop

Version 0.2.2
yaml2sbml-dev · Mar 21, 2021 · 6f42ee5 · 6f42ee5
2 parents 8f3bd49 + d680fdc
commit 6f42ee5
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diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -1,13 +1,26 @@
 name: CI
 
-on: [pull_request]
+# trigger
+on:
+  pull_request:
+  push:
+    branches:
+    - master
 
 jobs:
   base:
-    runs-on: ubuntu-latest
     strategy:
       matrix:
+        os: [ubuntu-latest, macos-latest, windows-latest]
+        include:
+        - os: ubuntu-latest
+          path: ~/.cache/pip
+        - os: macos-latest
+          path: ~/Library/Caches/pip
+        - os: windows-latest
+          path: ~\AppData\Local\pip\Cache
         python-version: [3.6, 3.9]
+    runs-on: ${{ matrix.os }}
 
     steps:
     - name: Check out repository
@@ -19,10 +32,10 @@ jobs:
         python-version: ${{ matrix.python-version }}
 
     - name: Cache
-      uses: actions/cache@v1
+      uses: actions/cache@v2
       with:
-        path: ~/.cache/pip
-        key: ${{ runner.os }}-${{ matrix.python-version }}-ci-base
+        path: ${{ matrix.path }}
+        key: ci-base-${{ runner.os }}-${{ matrix.python-version }}
 
     - name: Install tox
       run: pip install tox
@@ -55,17 +68,14 @@ jobs:
       uses: actions/cache@v1
       with:
         path: ~/.cache/pip
-        key: ${{ runner.os }}-${{ matrix.python-version }}-ci-notebooks
+        key: ci-notebooks-${{ runner.os }}-${{ matrix.python-version }}
 
-    - name: Install apt dependencies
-      run: |
-        .github/workflows/install_deps.sh amici
-
-    - name: Install tox
-      run: pip install tox
+    - name: Install dependencies
+      run: .github/workflows/install_deps.sh amici
 
     - name: Test notebooks
       run: tox -e notebooks
+      timeout-minutes: 60
 
   doc:
     runs-on: ubuntu-latest
@@ -86,14 +96,10 @@ jobs:
       uses: actions/cache@v1
       with:
         path: ~/.cache/pip
-        key: ${{ runner.os }}-${{ matrix.python-version }}-ci-doc
-
-    - name: Install apt dependencies
-      run: |
-        .github/workflows/install_deps.sh doc
+        key: ci-doc-${{ runner.os }}-${{ matrix.python-version }}
 
-    - name: Install tox
-      run: pip install tox
+    - name: Install dependencies
+      run: .github/workflows/install_deps.sh doc
 
     - name: Test documentation build
       run: tox -e doc

diff --git a/.github/workflows/install_deps.sh b/.github/workflows/install_deps.sh
@@ -1,12 +1,18 @@
 #!/bin/sh
 
+# Install tox
+pip install tox
+
+# Update apt package lists
+sudo apt-get update
+
 # iterate over optional dependencies
 for par in "$@"; do
   case $par in
     amici)
       # for amici
       sudo apt-get install \
-        swig3.0 libatlas-base-dev libhdf5-serial-dev
+        swig libatlas-base-dev libhdf5-serial-dev
     ;;
 
     doc)

diff --git a/.gitignore b/.gitignore
@@ -1,4 +1,4 @@
-__pycache__/
+**/__pycache__/
 *.egg-info/
 
 # PyCharm
@@ -12,44 +12,44 @@ yaml2sbml/tests/test_yaml2sbml/sbml_test.xml
 
 ### Files generated when running the notebooks (AMICI + PEtab files)
 
-## Lotka Volterra Python
-./doc/examples/Lotka_Volterra/Lotka_Volterra_python/amici_models
-./doc/examples/Lotka_Volterra/Lotka_Volterra_python/amici_models/*
+**/amici_models/
+**/AMICI_models/
 
-./doc/examples/Lotka_Volterra/Lotka_Volterra_python/Lotka_Volterra_AMICI
-./doc/examples/Lotka_Volterra/Lotka_Volterra_python/Lotka_Volterra_AMICI/*
+## FSP examples
 
-./doc/examples/Lotka_Volterra/Lotka_Volterra_python/Lotka_Volterra_basic.xml
+/doc/examples/Finite_State_Projection/gene_expression.xml
 
-./doc/examples/Lotka_Volterra/Lotka_Volterra_python/Lotka_Volterra_PEtab/*
-!./doc/examples/Lotka_Volterra/Lotka_Volterra_python/Lotka_Volterra_PEtab/measurement_table.tsv
+## Format Features
 
-## Lotka Volterra CLI
-./doc/examples/Lotka_Volterra/Lotka_Volterra_CLI/Lotka_Volterra_PEtab/*
-./doc/examples/Lotka_Volterra/Lotka_Volterra_CLI/Lotka_Volterra_PEtab.yml
-./doc/examples/Lotka_Volterra/Lotka_Volterra_CLI/Lotka_Volterra_PEtab/*.xml
+/doc/examples/Format_Features/functions_in_rhs.xml
+/doc/examples/Format_Features/step_function.xml
+/doc/examples/Format_Features/time_dependent_rhs.xml
 
-## Lotka Volterra Model Editor
-./doc/examples/Lotka_Volterra/Lotka_Volterra_Model_Editor/*.yaml
-./doc/examples/Lotka_Volterra/Lotka_Volterra_Model_Editor/*.xml
-./doc/examples/Lotka_Volterra/Lotka_Volterra_Model_Editor/Lotka_Volterra_PEtab
+## Lotka Volterra
 
-## Sorensen example
-./doc/examples/Sorensen/*.xml
-./doc/examples/Sorensen/amici_models
+/doc/examples/Lotka_Volterra/Lotka_Volterra_CLI/Lotka_Volterra_PEtab.yml
+/doc/examples/Lotka_Volterra/Lotka_Volterra_CLI/Lotka_Volterra_PEtab/
+/doc/examples/Lotka_Volterra/Lotka_Volterra_CLI/Lotka_Volterra_basic.xml
 
-## FSP examples
-./doc/examples/Finite_State_Projection/amici_models
-./doc/examples/Finite_State_Projection/*.xml
+/doc/examples/Lotka_Volterra/Lotka_Volterra_Model_Editor/Lotka_Volterra_PEtab.yaml
+/doc/examples/Lotka_Volterra/Lotka_Volterra_Model_Editor/Lotka_Volterra_PEtab/
+/doc/examples/Lotka_Volterra/Lotka_Volterra_Model_Editor/Lotka_Volterra_basic.xml
+/doc/examples/Lotka_Volterra/Lotka_Volterra_Model_Editor/Lotka_Volterra_basic.yaml
 
-## Format Features
+/doc/examples/Lotka_Volterra/Lotka_Volterra_python/Lotka_Volterra_AMICI/
+/doc/examples/Lotka_Volterra/Lotka_Volterra_python/Lotka_Volterra_PEtab/Lotka_Volterra_with_observables.xml
+/doc/examples/Lotka_Volterra/Lotka_Volterra_python/Lotka_Volterra_PEtab/experimental_conditions_Lotka_Volterra_with_observables.tsv
+/doc/examples/Lotka_Volterra/Lotka_Volterra_python/Lotka_Volterra_PEtab/observables_Lotka_Volterra_with_observables.tsv
+/doc/examples/Lotka_Volterra/Lotka_Volterra_python/Lotka_Volterra_PEtab/parameters_Lotka_Volterra_with_observables.tsv
+/doc/examples/Lotka_Volterra/Lotka_Volterra_python/Lotka_Volterra_PEtab/problem.yml
+/doc/examples/Lotka_Volterra/Lotka_Volterra_python/Lotka_Volterra_basic.xml
 
-./doc/examples/Format_Features/__pycache__
-./doc/examples/Format_Features/AMICI_models
+## Sorensen
 
-./doc/examples/Format_Features/*.xml
+/doc/examples/Sorensen/Fig71_Sorensen1985.xml
 
 ### JupyterNotebooks ###
+
 # gitignore template for Jupyter Notebooks
 # website: http://jupyter.org/
 
@@ -91,21 +91,9 @@ Network Trash Folder
 Temporary Items
 .apdisk
 
-# Gradle and Maven with auto-import
-# When using Gradle or Maven with auto-import, you should exclude module files,
-# since they will be recreated, and may cause churn.  Uncomment if using
-# auto-import.
-# .idea/artifacts
-# .idea/compiler.xml
-# .idea/jarRepositories.xml
-# .idea/modules.xml
-# .idea/*.iml
-# .idea/modules
-# *.iml
-# *.ipr
-
-# CMake
-cmake-build-*/
+# Build
+/build/
+/dist/
 
 # File-based project format
 *.iws

diff --git a/README.md b/README.md
@@ -4,6 +4,7 @@
 [![codecov](https://codecov.io/gh/yaml2sbml-dev/yaml2sbml/branch/master/graph/badge.svg)](https://codecov.io/gh/yaml2sbml-dev/yaml2sbml)
 [![Documentation Status](https://readthedocs.org/projects/yaml2sbml/badge/?version=latest)](https://yaml2sbml.readthedocs.io/en/latest/?badge=latest)
 [![Codacy Badge](https://app.codacy.com/project/badge/Grade/632acdc8d4ef4f50bf69892b8862fd24)](https://www.codacy.com/gh/yaml2sbml-dev/yaml2sbml/dashboard?utm_source=github.com&amp;utm_medium=referral&amp;utm_content=yaml2sbml-dev/yaml2sbml&amp;utm_campaign=Badge_Grade)
+[![PyPI](https://badge.fury.io/py/yaml2sbml.svg)](https://badge.fury.io/py/yaml2sbml)
 
 ## Table of contents
 
@@ -22,7 +23,7 @@
 
 `yaml2sbml` is a small package in Python to convert an ODE model specified in a YAML file into 
 [**SBML**](http://www.sbml.org/) for ODE simulation and into 
-[**PEtab**](https://github.com/martamatos/yaml2sbml) for parameter fitting. `yaml2sbml` offers:
+[**PEtab**](https://github.com/PEtab-dev/PEtab/) for parameter fitting. `yaml2sbml` offers:
 
 
 * a translator of ODE models specified in YAML into SBML/PEtab via a Python and a command-line interface;

diff --git a/doc/examples/Finite_State_Projection/Finite_State_Projection.ipynb b/doc/examples/Finite_State_Projection/Finite_State_Projection.ipynb
@@ -79,7 +79,9 @@
     "    \n",
     "    model.add_ode(state_id = f\"x_{r}_{p}\", \n",
     "                  right_hand_side=rhs,\n",
-    "                  initial_value=poisson.pmf(r, lambda_r)*poisson.pmf(p, lambda_p))\n",
+    "                  #convert from np.float to float\n",
+    "                  initial_value=float(poisson.pmf(r, lambda_r)*poisson.pmf(p, lambda_p))\n",
+    "                 )\n",
     "\n",
     "model.write_to_sbml('gene_expression.xml', overwrite=True)"
    ]

diff --git a/doc/examples/Lotka_Volterra/Lotka_Volterra_python/Lotka_Volterra.ipynb b/doc/examples/Lotka_Volterra/Lotka_Volterra_python/Lotka_Volterra.ipynb
diff --git a/doc/examples/Sorensen/yaml2sbml_Sorensen.ipynb b/doc/examples/Sorensen/yaml2sbml_Sorensen.ipynb
@@ -190,6 +190,9 @@
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
    "version": "3.7.1"
+  },
+  "execution": {
+   "timeout": 3600
   }
  },
  "nbformat": 4,

diff --git a/doc/format_specification.rst b/doc/format_specification.rst
@@ -67,7 +67,7 @@ odes
 
 Define **ODEs** (and states). An ODE consists of a `stateId` (string), a `rightHandSide` (string, encoding a mathematical expression), and an `initial value`. Initial values can be either numerical values or parameter Ids.
 
-For a more detailed description of the parsing of mathematical expressions ( for  `rightHandSide`) we refer to the [corresponding section](#parsing-of-mathematical-equations) of this documentation.
+For a more detailed description of the parsing of mathematical expressions ( for  `rightHandSide`) we refer to the :ref:`corresponding section<Parsing of mathematical equations>` of this documentation.
 
 
 
@@ -130,7 +130,7 @@ observables \[optional\]
 Define **observables**. Observables are not part of the SBML standard. If the SBML is generated via the `yaml2sbml.yaml2sbml` command and the `observables_as_assignments` flag is set to `True`, observables are represented as assignments to parameters of the form observable_<observable_id>.
 If the SBML is created via `yaml2sbml.yaml2petab`, observables are represented in the PEtab observables table. The entries are written to the corresponding columns of the PEtab observable table. According to the PEtab standard, an observable table can take the following entries:  `observableId, observableName, observableFormula, observableTransformation, noiseFormula, noiseDistribution`.
 
-For a detailed discussion see the `corresponding part of the PEtab documentation <https://github.com/PEtab-dev/PEtab/blob/master/doc/documentation_data_format.rst#observables-table>`_.
+For a detailed discussion see the corresponding part of the PEtab documentation <https://github.com/PEtab-dev/PEtab/blob/master/doc/documentation_data_format.rst#observables-table>`_.
 
 
 
@@ -157,7 +157,7 @@ The "trivial condition table" (if only one setup exists) is generated by:
         - conditionId: condition1
 
 
-For a detailed discussion see the `corresponding part of the PEtab documentation <https://github.com/PEtab-dev/PEtab/blob/master/doc/documentation_data_format.rst#condition-table>`_.
+For a detailed discussion see the corresponding part of the `PEtab documentation <https://github.com/PEtab-dev/PEtab/blob/master/doc/documentation_data_format.rst#condition-table>`_.
 
 
 

diff --git a/doc/index.rst b/doc/index.rst
@@ -13,14 +13,16 @@ yaml2sbml
 .. image:: https://app.codacy.com/project/badge/Grade/632acdc8d4ef4f50bf69892b8862fd24
    :target: https://www.codacy.com/gh/yaml2sbml-dev/yaml2sbml/dashboard?utm_source=github.com&amp;utm_medium=referral&amp;utm_content=yaml2sbml-dev/yaml2sbml&amp;utm_campaign=Badge_Grade
    :alt: Code quality
+.. image:: https://badge.fury.io/py/yaml2sbml.svg
+   :target: https://badge.fury.io/py/yaml2sbml
+   :alt: PyPI
 
 :Release: |version|
 :Source code: https://github.com/yaml2sbml-dev/yaml2sbml
 
 .. image:: logo/logo_yaml2sbml_long.png
    :alt: yaml2sbml logo
    :align: center
-   :scale: 30 %
 
 **yaml2sbml** allows the user to convert a system of ODEs specified in a YAML_
 file to SBML_.
@@ -44,6 +46,8 @@ converted to PEtab_.
 
    release_notes
    license
+   log
+   logo
    contact
 
 .. toctree::

diff --git a/doc/logo.rst b/doc/logo.rst
@@ -0,0 +1,15 @@
+Logo
+====
+
+.. image:: logo/logo_yaml2sbml_long.png
+   :alt: yaml2sbml logo
+   :align: center
+
+yaml2sbml's logo can be found in multiple variants in the
+`doc/logo <https://github.com/yaml2sbml-dev/yaml2sbml/tree/main/doc/logo>`_
+folder, in svg and png format.
+It is made available under a Creative Commons CC0 1.0 Universal (CC0 1.0)
+license, with the terms given in `doc/logo/LICENSE.md <https://github.com/yaml2sbml-dev/yaml2sbml/blob/master/doc/logo/LICENSE.md>`_.
+We encourage to use it e.g. in presentations and posters.
+
+We thank Elba Raimúndez for her contributions to the logo design.