readthedocs: show readme

doc/Makefile

@@ -17,5 +17,4 @@ help:
 # Catch-all target: route all unknown targets to Sphinx using the new
 # "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
 %: Makefile
-	python md2rst.py
 	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)

doc/_static/custom.css

@@ -0,0 +1,4 @@
+/* Enlarge to max-width 900px (default: 800px) */
+.wy-nav-content {
+   max-width: 900px !important;
+}

doc/conf.py

@@ -23,6 +23,11 @@
 # The full version, including alpha/beta/rc tags
 release = 'latest'
 
+# -- Custom pre-build --------------------------------------------------------
+
+import subprocess
+
+subprocess.run(['python', 'md2rst.py'])
 
 # -- General configuration ---------------------------------------------------
 
@@ -35,7 +40,7 @@
     'recommonmark',
     'sphinx.ext.autosummary',
     'sphinx_markdown_tables',
-    'nbsphinx'
+    'nbsphinx',
 ]
 
 # Add any paths that contain templates here, relative to this directory.
@@ -73,7 +78,8 @@
 # a list of builtin themes.
 #
 html_theme = 'sphinx_rtd_theme'
-
+def setup(app):
+    app.add_stylesheet('custom.css')
 # Add any paths that contain custom static files (such as style sheets) here,
 # relative to this directory. They are copied after the builtin static files,
 # so a file named "default.css" will overwrite the builtin "default.css".

doc/md2rst.py

@@ -23,7 +23,13 @@ def absolute_links(txt):
     return txt
 
 
-txt = absolute_links(read("../README.md"))
-txt = m2r.convert(txt)
-with open("_static/README.rst", 'w') as f:
-    f.write(txt)
+def md2rst(source: str, target: str):
+    txt = absolute_links(read(source))
+    txt = m2r.convert(txt)
+    with open(target, 'w') as f:
+        f.write(txt)
+
+
+if __name__ == '__main__':
+    # parse readme
+    md2rst('../README.md', '_static/README.rst')

tests/test_conditions.py

@@ -3,6 +3,7 @@
 import pandas as pd
 import tempfile
 import pytest
+import os
 
 import petab
 from petab import conditions
@@ -44,6 +45,8 @@ def test_get_condition_df():
     with pytest.raises(KeyError):
         petab.get_condition_df(file_name)
 
+    os.remove(file_name)
+
     # with ids
     condition_df = pd.DataFrame(data={
         CONDITION_ID: ['condition1', 'condition2'],
@@ -58,6 +61,8 @@ def test_get_condition_df():
     df = petab.get_condition_df(file_name).replace(np.nan, '')
     assert (df == condition_df.set_index(CONDITION_ID)).all().all()
 
+    os.remove(file_name)
+
     # test other arguments
     assert (petab.get_condition_df(condition_df) == condition_df).all().all()
     assert petab.get_condition_df(None) is None

tests/test_petab.py

@@ -397,7 +397,7 @@ def test_concat_measurements():
 
 def test_get_obervable_ids(petab_problem):  # pylint: disable=W0621
     """Test if observable ids functions returns correct value."""
-    assert set(petab_problem.get_observable_ids()) == set(['observable_1'])
+    assert set(petab_problem.get_observable_ids()) == {'observable_1'}
 
 
 def test_parameter_properties(petab_problem):  # pylint: disable=W0621