From 99231970b658e2123859d28f694dfcccd8851655 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Yannik=20Sch=C3=A4lte?=
 <31767307+yannikschaelte@users.noreply.github.com>
Date: Fri, 12 Mar 2021 14:45:53 +0100
Subject: [PATCH] Fix pydocstyle was not called; update swig (#120)

* update swig

* add pydocstyle, min versions of flake8

* fix pydocstyle
---
 .github/workflows/install_deps.sh |  4 ++--
 tests/__init__.py                 |  1 +
 tox.ini                           | 36 +++++++++++++++----------------
 yaml2sbml/YamlModel.py            |  4 ++++
 yaml2sbml/version.py              |  2 ++
 yaml2sbml/yaml2sbml.py            |  1 -
 6 files changed, 27 insertions(+), 21 deletions(-)

diff --git a/.github/workflows/install_deps.sh b/.github/workflows/install_deps.sh
index c475457..60bcc4f 100755
--- a/.github/workflows/install_deps.sh
+++ b/.github/workflows/install_deps.sh
@@ -3,7 +3,7 @@
 # Install tox
 pip install tox
 
-# Update aptitude
+# Update apt package lists
 sudo apt-get update
 
 # iterate over optional dependencies
@@ -12,7 +12,7 @@ for par in "$@"; do
     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/tests/__init__.py b/tests/__init__.py
index e69de29..232940a 100644
--- a/tests/__init__.py
+++ b/tests/__init__.py
@@ -0,0 +1 @@
+"""yaml2sbml tests."""
diff --git a/tox.ini b/tox.ini
index 127a7c8..0541ab1 100644
--- a/tox.ini
+++ b/tox.ini
@@ -20,10 +20,10 @@ envlist =
 [testenv]
 # Dependencies
 deps =
-    coverage
-    pytest
-    pytest-cov
-    pytest-console-scripts
+    coverage >= 5.5
+    pytest >= 6.2.2
+    pytest-cov >= 2.11.1
+    pytest-console-scripts >= 1.1.0
 
 # Sub-environments
 #  inherit settings defined in the base
@@ -32,8 +32,7 @@ deps =
 # No installation of yaml2sbml required
 skip_install = true
 deps =
-    pygments
-    pyroma
+    pyroma >= 3.1
 commands = pyroma --min=10 .
 description =
     Run pyroma to check the package friendliness
@@ -41,20 +40,21 @@ description =
 [testenv:flake8]
 skip_install = true
 deps =
-    flake8
-    flake8-bandit
-    flake8-bugbear
-    flake8-colors
-    flake8-commas
-    flake8-comprehensions
-    flake8-print
-    flake8-use-fstring
-    pep8-naming
-    pydocstyle
+    flake8 >= 3.8.3
+    flake8-bandit >= 2.1.2
+    flake8-bugbear >= 20.1.4
+    flake8-colors >= 0.1.6
+    flake8-commas >= 2.0.0
+    flake8-comprehensions >= 3.2.3
+    flake8-print >= 3.1.4
+    flake8-use-fstring >= 1.1
+    pep8-naming >= 0.11.1
+    pydocstyle >= 5.1.1
 commands =
     flake8 yaml2sbml tests setup.py
+    pydocstyle yaml2sbml tests setup.py
 description =
-    Run flake8 with various plugins
+    Run flake8 with various plugins, and pydocstyle
 
 [testenv:unittests]
 commands =
@@ -67,7 +67,7 @@ description =
 
 [testenv:notebooks]
 deps =
-    nbmake
+    nbmake >= 0.4
 # Extras required from yaml2sbml
 extras = examples
 commands =
diff --git a/yaml2sbml/YamlModel.py b/yaml2sbml/YamlModel.py
index 37fa606..f68630b 100644
--- a/yaml2sbml/YamlModel.py
+++ b/yaml2sbml/YamlModel.py
@@ -181,16 +181,20 @@ def _get_reduced_model_dict(self) -> dict:
 
     # functionalities regarding the time
     def is_set_time(self):
+        """Check whether there is a time variable."""
         return 'variable' in self._yaml_model['time'].keys()
 
     def set_time(self,
                  time_variable: str):
+        """Set time variable."""
         self._yaml_model['time'] = {'variable': time_variable}
 
     def delete_time(self):
+        """Delete time variable."""
         self._yaml_model['time'] = {}
 
     def get_time(self):
+        """Get time variable."""
         if self.is_set_time():
             return self._yaml_model['time']['variable']
         else:
diff --git a/yaml2sbml/version.py b/yaml2sbml/version.py
index fc79d63..0f1ea38 100644
--- a/yaml2sbml/version.py
+++ b/yaml2sbml/version.py
@@ -1 +1,3 @@
+"""yaml2sbml version."""
+
 __version__ = '0.2.1'
diff --git a/yaml2sbml/yaml2sbml.py b/yaml2sbml/yaml2sbml.py
index 90c7467..1e007c1 100644
--- a/yaml2sbml/yaml2sbml.py
+++ b/yaml2sbml/yaml2sbml.py
@@ -224,7 +224,6 @@ def _create_time(model: sbml.Model, time_var: str):
         model: the SBML model to which the species will be added.
         time_var: str, the time variable
     """
-
     if time_var == 'time':
         return