Fix/sacred observer (#57)

* updated git_info discovery to be that of sacred
* update base_dir discovery to be that of sacred
* updated resource tracking to be more sacred-like with a list of `resources` property and `filename: md5` pairs in properties

docs/conf.py

@@ -49,7 +49,7 @@
 # The short X.Y version
 version = '0.13'
 # The full version, including alpha/beta/rc tags
-release = '0.13.2'
+release = '0.13.3'
 
 # -- General configuration ---------------------------------------------------
 

docs/index.rst

@@ -57,6 +57,7 @@ And the best thing is you can extend it yourself or... tell us to do it for you
    monitoring.fastai <user_guide/monitoring/fastai>
    monitoring.metrics <user_guide/monitoring/metrics>
    monitoring.fairness <user_guide/monitoring/fairness>
+   monitoring.sacred <user_guide/monitoring/sacred>
    monitoring.skopt <user_guide/monitoring/skopt>
    monitoring.utils <user_guide/monitoring/utils>
    sync.with_json <user_guide/sync/with_json>

docs/user_guide/monitoring/sacred.rst

@@ -0,0 +1,6 @@
+Sacred
+===========
+
+.. automodule:: neptunecontrib.monitoring.sacred
+    :members:
+    :show-inheritance:

neptunecontrib/monitoring/sacred.py

@@ -15,7 +15,6 @@
 #
 
 import collections
-import os
 
 import neptune
 from sacred.dependencies import get_digest
@@ -74,26 +73,28 @@ def run(C, gamma, _run):
         Go to the app and see the experiment. For example, https://ui.neptune.ml/jakub-czakon/examples/e/EX-263
     """
 
-    def __init__(self, project_name, api_token=None, base_dir='.', source_extensions=None):
+    def __init__(self, project_name, api_token=None, source_extensions=None):
         neptune.init(project_qualified_name=project_name, api_token=api_token)
+
         self.resources = {}
-        self.base_dir = base_dir
+
         if source_extensions:
             self.source_extensions = source_extensions
         else:
-            self.source_extensions = ['.py', '.R', '.cpp', '.yaml', '.yml']
+            self.source_extensions = ['**/*.py', '**/*.yaml', '**/*.yml']
 
     def started_event(self, ex_info, command, host_info, start_time, config, meta_info, _id):
 
         neptune.create_experiment(name=ex_info['name'],
                                   params=_flatten_dict(config),
-                                  upload_source_files=_get_filepaths(dirpath=self.base_dir,
-                                                                     extensions=self.source_extensions),
+                                  upload_source_files=self.source_extensions,
                                   properties={'mainfile': ex_info['mainfile'],
                                               'dependencies': str(ex_info['dependencies']),
                                               'sacred_id': str(_id),
                                               **_str_dict_values(host_info),
-                                              **_str_dict_values(_flatten_dict(meta_info))})
+                                              **_str_dict_values(_flatten_dict(meta_info)),
+                                              **_str_dict_values(_flatten_dict(ex_info))},
+                                  git_info=neptune.utils.get_git_info(ex_info['base_dir']))
 
     def completed_event(self, stop_time, result):
         if result:
@@ -111,38 +112,19 @@ def artifact_event(self, name, filename, metadata=None, content_type=None):
 
     def resource_event(self, filename):
         if filename not in self.resources:
-            new_prefix = self._create_new_prefix()
-            self.resources[filename] = new_prefix
             md5 = get_digest(filename)
+            self.resources[filename] = md5
 
-            neptune.set_property('{}data_path'.format(new_prefix), filename)
-            neptune.set_property('{}data_version'.format(new_prefix), md5)
+        neptune.set_property('resources', str(list(self.resources.keys())))
+        neptune.set_property(filename, self.resources[filename])
 
     def log_metrics(self, metrics_by_name, info):
         for metric_name, metric_ptr in metrics_by_name.items():
             for step, value in zip(metric_ptr["steps"], metric_ptr["values"]):
                 neptune.log_metric(metric_name, x=step, y=value)
 
-    def _create_new_prefix(self):
-        existing_prefixes = self.resources.values()
-        if existing_prefixes:
-            prefix_ids = [int(prefix.replace('resource', '')) for prefix in existing_prefixes]
-            new_prefix = 'resource{}'.format(max(prefix_ids) + 1)
-        else:
-            new_prefix = 'resource0'
-        return new_prefix
-
-
-def _get_filepaths(dirpath, extensions):
-    files = []
-    for r, _, f in os.walk(dirpath):
-        for file in f:
-            if any(file.endswith(ext) for ext in extensions):
-                files.append(os.path.join(r, file))
-    return files
-
 
-def _flatten_dict(d, parent_key='', sep='_'):
+def _flatten_dict(d, parent_key='', sep=' '):
     items = []
     for k, v in d.items():
         new_key = parent_key + sep + k if parent_key else k

pylintrc

@@ -41,7 +41,7 @@ load-plugins=pylintfileheader
 # W0511 Allow TODO/FIXME comments.
 # W0703 Allow too broad except clause (Exception).
 # I0011 Do not show Locally disabled warnings in report
-disable=R,C0103,C0111,W0401,W0511,W0614,W0703,I0011,W0613,E0401,C0411
+disable=R,C0103,C0111,W0401,W0511,W0614,W0703,I0011,W0613,E0401,C0411,E0611
 
 # Enable the message, report, category or checker with the given id(s). You can
 # either give multiple identifier separated by comma (,) or put this option

setup.py

@@ -20,7 +20,7 @@ def main():
 
     setup(
         name='neptune-contrib',
-        version='0.13.2',
+        version='0.13.3',
         description='Neptune Python library contributions',
         author='neptune.ml',
         author_email='[email protected]',

test_requirements.txt

@@ -1,7 +1,7 @@
 neptune-client
 mock==2.0.0
 pylint==1.9.4
-pytest==4.1.0
+pytest==5.2.0
 pytest-cov==2.6.1
 pytest-xdist==1.25.0
 tox==3.6.1