Merge pull request #1398 from amath-idm/fix-readthedocs

Fix readthedocs

.readthedocs.yml

@@ -1,37 +1,28 @@
-# .readthedocs.yml
+# .readthedocs.yaml
 # Read the Docs configuration file
 # See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
 
 # Required
 version: 2
 
+# Set the version of Python and other tools you might need
+build:
+  os: ubuntu-20.04
+  tools:
+    python: "3.9"
+
 # Build documentation in the docs/ directory with Sphinx
 sphinx:
-  configuration: docs/conf.py
-  fail_on_warning: true
-
-# Build documentation with MkDocs
-#mkdocs:
-#  configuration: mkdocs.yml
+   configuration: docs/conf.py
 
-# Optionally build your docs in additional formats such as PDF
+# If using Sphinx, optionally build your docs in additional formats such as PDF
 formats:
-  - htmlzip
-  - pdf
+   - pdf
 
-# Optionally set the version of Python and requirements required to build your docs
+# Optionally declare the Python requirements required to build your docs
 python:
-  version: 3.8
   install:
     - requirements: docs/requirements.txt
     - method: pip
       path: .
-  system_packages: true
-
-# Optionally rank topics in search results, between -10 (lower) and 10 (higher).
-# 0 is normal rank, not no rank
-
-search:
-  ranking:
-    index.html: 3
-    modules.html: 2
+  system_packages: true

covasim/analysis.py

@@ -1106,7 +1106,7 @@ def reconcile_inputs(self):
             self.inds.data[key] = []
             self.date_matches[key] = []
             count = -1
-            for d, datum in self.data[key].iteritems():
+            for d, datum in self.data[key].items():
                 count += 1
                 if np.isfinite(datum):
                     if d in self.sim_dates:

covasim/settings.py

@@ -65,7 +65,7 @@ class Options(sc.objdict):
         - font:           the font family/face used for the plots
         - fontsize:       the font size used for the plots
         - interactive:    convenience method to set show, close, and backend
-        - jupyter:        defaults for Jupyter (change backend and figure close/return)
+        - jupyter:        defaults for Jupyter (change backend and figure return)
         - show:           whether to show figures
         - close:          whether to close the figures
         - backend:        which Matplotlib backend to use
@@ -241,16 +241,15 @@ def set(self, key=None, value=None, use=False, **kwargs):
                 jupyter = 'retina' # Default option for True
             if 'returnfig' not in kwargs:
                 kwargs['returnfig'] = False # We almost never want to return figs from Jupyter, since then they appear twice
-            if 'show' not in kwargs:
-                kwargs['show'] = False
             try: 
-                if jupyter == 'retina': # This makes plots much nicer, but isn't available on all systems
-                    import matplotlib_inline
-                    matplotlib_inline.backend_inline.set_matplotlib_formats('retina')
-                elif jupyter in ['widget', 'interactive']: # Or use interactive
-                    from IPython import get_ipython
-                    magic = get_ipython().magic
-                    magic('%matplotlib widget')
+                if not os.environ.get('SPHINX_BUILD'): # Custom check implemented in conf.py to skip this if we're inside Sphinx
+                    if jupyter == 'retina': # This makes plots much nicer, but isn't available on all systems
+                        import matplotlib_inline
+                        matplotlib_inline.backend_inline.set_matplotlib_formats('retina')
+                    elif jupyter in ['widget', 'interactive']: # Or use interactive
+                        from IPython import get_ipython
+                        magic = get_ipython().magic
+                        magic('%matplotlib widget')
             except:
                 pass
 

docs/conf.py

@@ -20,7 +20,6 @@
 
 # Set environment
 os.environ['SPHINX_BUILD'] = 'True' # This is used so cv.options.set('jupyter') doesn't reset the Matplotlib renderer
-os.environ['COVASIM_WARNINGS'] = 'error' # Don't let warnings pass in the tutorials
 on_rtd = os.environ.get('READTHEDOCS') == 'True'
 
 if sys.platform in ["linux", "darwin"]:

docs/tutorials/tut_plotting.ipynb

@@ -213,7 +213,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "sim.plot(style='seaborn-whitegrid')"
+    "sim.plot(style='ggplot')"
    ]
   },
   {
@@ -236,7 +236,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "(Note: Covasim comes bundled with two fonts, Mulish (sans-serif, the default) and Rosario (serif).)"
+    "(Note: Covasim comes bundled with two fonts, [Mulish](https://github.com/googlefonts/mulish) (sans-serif, the default) and [Rosario](https://fonts.adobe.com/fonts/rosario) (serif).)"
    ]
   },
   {