Merge remote-tracking branch 'origin/stable-0.8'

Author: basnijholt

adaptive/learner/balancing_learner.py

@@ -291,8 +291,11 @@ def plot_function(*args):
 
         dm = hv.DynamicMap(plot_function, kdims=list(d.keys()))
         dm = dm.redim.values(**d)
+        dm.cache_size = 1
 
         if dynamic:
+            # XXX: change when https://github.com/pyviz/holoviews/issues/3637
+            # is fixed.
             return dm.map(lambda obj: obj.opts(framewise=True), hv.Element)
         else:
             # XXX: change when https://github.com/ioam/holoviews/issues/3085

adaptive/learner/learner1D.py

@@ -590,12 +590,11 @@ def plot(self):
             Plot of the evaluated data.
         """
         hv = ensure_holoviews()
-        if not self.data:
-            p = hv.Scatter([]) * hv.Path([])
-        elif not self.vdim > 1:
-            p = hv.Scatter(self.data) * hv.Path([])
+
+        xs, ys = zip(*sorted(self.data.items())) if self.data else ([], [])
+        if self.vdim == 1:
+            p = hv.Path([]) * hv.Scatter((xs, ys))
         else:
-            xs, ys = zip(*sorted(self.data.items()))
             p = hv.Path((xs, ys)) * hv.Scatter([])
 
         # Plot with 5% empty margins such that the boundary points are visible

adaptive/notebook_integration.py

@@ -96,7 +96,7 @@ def live_plot(runner, *, plotter=None, update_interval=2, name=None, normalize=T
 
     Parameters
     ----------
-    runner : `Runner`
+    runner : `~adaptive.Runner`
     plotter : function
         A function that takes the learner as a argument and returns a
         holoviews object. By default ``learner.plot()`` will be called.
@@ -136,6 +136,7 @@ def plot_generator():
 
     streams = [hv.streams.Stream.define("Next")()]
     dm = hv.DynamicMap(plot_generator(), streams=streams)
+    dm.cache_size = 1
 
     if normalize:
         # XXX: change when https://github.com/pyviz/holoviews/issues/3637

adaptive/runner.py

@@ -558,12 +558,12 @@ def cancel(self):
         """
         self.task.cancel()
 
-    def live_plot(self, *, plotter=None, update_interval=2, name=None):
+    def live_plot(self, *, plotter=None, update_interval=2, name=None, normalize=True):
         """Live plotting of the learner's data.
 
         Parameters
         ----------
-        runner : `Runner`
+        runner : `~adaptive.Runner`
         plotter : function
             A function that takes the learner as a argument and returns a
             holoviews object. By default ``learner.plot()`` will be called.
@@ -573,6 +573,8 @@ def live_plot(self, *, plotter=None, update_interval=2, name=None):
             Name for the `live_plot` task in `adaptive.active_plotting_tasks`.
             By default the name is None and if another task with the same name
             already exists that other `live_plot` is canceled.
+        normalize : bool
+            Normalize (scale to fit) the frame upon each update.
 
         Returns
         -------

adaptive/utils.py

@@ -7,6 +7,8 @@
 from contextlib import contextmanager
 from itertools import product
 
+from atomicwrites import AtomicWriter
+
 
 def named_product(**items):
     names = items.keys()
@@ -44,9 +46,13 @@ def save(fname, data, compress=True):
     dirname = os.path.dirname(fname)
     if dirname:
         os.makedirs(dirname, exist_ok=True)
-    _open = gzip.open if compress else open
-    with _open(fname, "wb") as f:
-        pickle.dump(data, f, protocol=pickle.HIGHEST_PROTOCOL)
+
+    blob = pickle.dumps(data, protocol=pickle.HIGHEST_PROTOCOL)
+    if compress:
+        blob = gzip.compress(blob)
+
+    with AtomicWriter(fname, "wb", overwrite=True).open() as f:
+        f.write(blob)
 
 
 def load(fname, compress=True):

docs/environment.yml

@@ -13,6 +13,7 @@ dependencies:
   - plotly=3.9.0
   - ipywidgets=7.4.2
   # - jupyter_sphinx=0.2.1
+  - atomicwrites=1.3.0
   - pip:
     - git+https://github.com/jbweston/jupyter-sphinx.git@feature/disable-stderr  # XXX: removed when merged in
     - sphinx_fontawesome==0.0.6

environment.yml

@@ -16,3 +16,4 @@ dependencies:
   - ipywidgets
   - scikit-optimize
   - plotly
+  - atomicwrites

setup.py

@@ -24,7 +24,12 @@ def get_version_and_cmdclass(package_name):
 version, cmdclass = get_version_and_cmdclass("adaptive")
 
 
-install_requires = ["scipy", "sortedcollections >= 1.1", "sortedcontainers >= 2.0"]
+install_requires = [
+    "scipy",
+    "sortedcollections >= 1.1",
+    "sortedcontainers >= 2.0",
+    "atomicwrites",
+]
 
 extras_require = {
     "notebook": [