Merging in old changes

.gitignore

@@ -71,4 +71,4 @@ venv/
 # Files
 /Data
 /docs/build
-
+.pytest_cache

README.md

@@ -63,16 +63,16 @@ For more examples of how to use artemis, read the [Artemis Documentation](http:/
 To use artemis from within your project, use the following to install Artemis and its dependencies: (You probably want to do this in a virtualenv with the latest version of pip - run `virtualenv venv; source venv/bin/activate; pip install --upgrade pip;` to make one and enter it).
 
 
-**Option 1: Simple install:**
+**Option 1: Simple install (stable) :**
 
 ```
 pip install artemis-ml
 ```
 
-**Option 2: Install as source.**
+**Option 2: Install as source (master branch, do this if you want latest updates or you want to contribute to Artemis).**
 
 ```
-pip install -e git+http://github.com/QUVA-Lab/artemis.git#egg=artemis 
+pip install -e git+https://github.com/petered/artemis.git#egg=artemis-ml
 ```
 This will install it in `(virtual env or system python root)/src/artemis`.  You can edit the code and submit pull requests to our git repo.  To install with the optional [remote plotting](https://github.com/QUVA-Lab/artemis/blob/master/artemis/remote/README.md) mode enabled, add the `[remote_plotting]` option, as in: `pip install -e git+http://github.com/QUVA-Lab/artemis.git#egg=artemis[remote_plotting]`
 

artemis/experiments/decorators.py

@@ -44,7 +44,7 @@ class ExperimentFunction(object):
     This is the most general decorator.  You can use this to add details on the experiment.
     """
 
-    def __init__(self, show = show_record, compare = compare_experiment_records, display_function=None, comparison_function=None, one_liner_function=sensible_str, is_root=False):
+    def __init__(self, show = None, compare = compare_experiment_records, display_function=None, comparison_function=None, one_liner_function=None, result_parser = None, is_root=False, name=None):
         """
         :param show:  A function that is called when you "show" an experiment record in the UI.  It takes an experiment
             record as an argument.
@@ -55,16 +55,17 @@ def __init__(self, show = show_record, compare = compare_experiment_records, dis
             You can use call this via the UI with the compare_experiment_results command.
         :param one_liner_function: A function that takes your results and returns a 1 line string summarizing them.
         :param is_root: True to make this a root experiment - so that it is not listed to be run itself.
+        :param name: Custom name (if None, experiment will be named after decorated function)
         """
         self.show = show
         self.compare = compare
 
         if display_function is not None:
-            assert show is show_record, "You can't set both display function and show.  (display_function is deprecated)"
+            assert show is None, "You can't set both display function and show.  (display_function is deprecated)"
             show = lambda rec: display_function(rec.get_result())
 
         if comparison_function is not None:
-            assert compare is compare_experiment_records, "You can't set both display function and show.  (display_function is deprecated)"
+            assert compare is None, "You can't set both display function and show.  (display_function is deprecated)"
 
             def compare(records):
                 record_experiment_ids_uniquified = uniquify_duplicates(rec.get_experiment_id() for rec in records)
@@ -74,15 +75,23 @@ def compare(records):
         self.compare = compare
         self.is_root = is_root
         self.one_liner_function = one_liner_function
+        self.result_parser = result_parser
+        self.name = name
 
     def __call__(self, f):
+        """
+        :param Callable f: The function you decorated
+        :return Experiment: An Experiment object (It still behaves as the original function when you call it, but now
+            has additional methods attached to it associated with the experiment).
+        """
         f.is_base_experiment = True
         ex = Experiment(
-            name=f.__name__,
+            name=f.__name__ if self.name is None else self.name,
             function=f,
             show=self.show,
             compare = self.compare,
             one_liner_function=self.one_liner_function,
-            is_root=self.is_root
+            is_root=self.is_root,
+            result_parser=self.result_parser,
         )
         return ex

artemis/experiments/experiment_record.py

@@ -13,6 +13,7 @@
 from contextlib import contextmanager
 from getpass import getuser
 from pickle import PicklingError
+import itertools
 
 from datetime import datetime, timedelta
 from uuid import getnode
@@ -23,7 +24,7 @@
 from artemis.general.display import CaptureStdOut
 from artemis.general.functional import get_partial_chain, get_defined_and_undefined_args
 from artemis.general.hashing import compute_fixed_hash
-from artemis.general.should_be_builtins import nested
+from artemis.general.should_be_builtins import nested, natural_keys
 from artemis.general.test_mode import is_test_mode
 from artemis.general.test_mode import set_test_mode
 from artemis._version import __version__ as ARTEMIS_VERSION
@@ -240,6 +241,7 @@ def get_figure_locs(self, include_directory=True):
         :return: A list of string file paths.
         """
         locs = [f for f in os.listdir(self._experiment_directory) if f.startswith('fig-')]
+        locs = sorted(locs, key=natural_keys)
         if include_directory:
             return [os.path.join(self._experiment_directory, f) for f in locs]
         else:
@@ -289,7 +291,7 @@ def get_experiment(self):
         """
         Load the experiment associated with this record.
         Note that this will raise an ExperimentNotFoundError if the experiment has not been imported.
-        :return: An Experiment object
+        :return Experiment: An Experiment object
         """
         from artemis.experiments.experiments import load_experiment
         return load_experiment(self.get_experiment_id())
@@ -310,7 +312,10 @@ def get_runtime(self):
         """
         :return datetime.timedelta: A timedelta object
         """
-        return timedelta(seconds=self.info.get_field(ExpInfoFields.RUNTIME))
+        try:
+            return timedelta(seconds=self.info.get_field(ExpInfoFields.RUNTIME))
+        except KeyError:  # Which will happen if the experiment is still running or was killed without due process
+            return None
 
     def get_dir(self):
         """
@@ -506,6 +511,7 @@ def get_current_record_id():
 def get_current_record_dir(default_if_none = True):
     """
     The directory in which the results of the current experiment are recorded.
+    :param default_if_none: True to put records in the "default" dir if no experiment is running.
     """
     if _CURRENT_EXPERIMENT_RECORD is None and default_if_none:
         return get_artemis_data_path('experiments/default/', make_local_dir=True)
@@ -657,7 +663,19 @@ def clear_experiment_records(ids):
         ExperimentRecord(exp_path).delete()
 
 
-def save_figure_in_record(name, fig=None, default_ext='.pkl'):
+_figure_ixs = {}
+
+
+def _get_next_figure_name(name_pattern, directory):
+    start_ix = _figure_ixs[directory] if directory in _figure_ixs else 0
+    for ix in itertools.count(start_ix):
+        full_path = os.path.join(directory, name_pattern).format(ix)
+        if not os.path.exists(full_path):
+            _figure_ixs[directory] = ix+1
+            return full_path
+
+
+def save_figure_in_record(name=None, fig=None, default_ext='.pkl'):
     '''
     Saves the given figure in the experiment directory. If no figure is passed, plt.gcf() is saved instead.
     :param name: The name of the figure to be saved
@@ -667,11 +685,17 @@ def save_figure_in_record(name, fig=None, default_ext='.pkl'):
     '''
     import matplotlib.pyplot as plt
     from artemis.plotting.saving_plots import save_figure
+
     if fig is None:
         fig = plt.gcf()
-    save_path = os.path.join(get_current_record_dir(), name)
-    save_figure(fig, path=save_path, default_ext=default_ext)
-    return save_path
+
+    current_dir = get_current_record_dir()
+    if name is None:
+        path = _get_next_figure_name(name_pattern='fig-{}.pkl', directory=current_dir)
+    else:
+        path = os.path.join(current_dir, name)
+    save_figure(fig, path=path, default_ext=default_ext)
+    return path
 
 
 def get_serialized_args(argdict):