Merge pull request #485 from Epistimio/release-v0.1.10rc

Release v0.1.10rc

.github/workflows/build.yml

@@ -8,6 +8,9 @@ on:
       - master
       - develop
   release:
+    types:
+      [published]
+  workflow_dispatch:
 
 jobs:
   pretest:

README.rst

@@ -102,25 +102,29 @@ If you use Oríon for published work, please cite our work using the following b
 
 .. code-block:: bibtex
 
-   @software{xavier_bouthillier_2019_3478593,
+   @software{xavier_bouthillier_2020_4265424,
      author       = {Xavier Bouthillier and
                      Christos Tsirigotis and
                      François Corneau-Tremblay and
+                     Thomas Schweizer and
                      Pierre Delaunay and
+                     Mirko Bronzi and
+                     Lin Dong and
                      Reyhane Askari and
                      Dendi Suhubdy and
+                     Hadrien Bertrand and
                      Michael Noukhovitch and
-                     Dmitriy Serdyuk and
                      Arnaud Bergeron and
+                     Dmitriy Serdyuk and
                      Peter Henderson and
                      Pascal Lamblin and
-                     Mirko Bronzi and
                      Christopher Beckham},
-     title        = {Oríon - Asynchronous Distributed Hyperparameter Optimization},
-     month        = oct,
-     year         = 2019,
+     title        = {{Epistimio/orion: Plotting API and Database
+                      commands}},
+     month        = nov,
+     year         = 2020,
      publisher    = {Zenodo},
-     version      = {v0.1.8},
+     version      = {v0.1.9},
      doi          = {10.5281/zenodo.3478592},
      url          = {https://doi.org/10.5281/zenodo.3478592}
    }

ROADMAP.md

@@ -2,15 +2,16 @@
 Last update February 25th, 2020
 
 ## Next releases - Short-Term
-### v0.1.9
+### v0.1.10
+
+#### Quick release for bug fixes
+
+### v0.1.11
+
 #### Default database backend
 PickledDB will become the default database backend instead of MongoDB. This initiative reduces
 initial configuration, allowing users to get started faster.
 
-#### Deleting experiments
-Adding a new (very requested) feature enabling the deletion of experiments from the CLI or python 
-API.
-
 ### v0.2
 #### Journal Protocol Plugins
 Offering:

codecov.yml

@@ -1,21 +1,7 @@
-codecov:
-  branch: master
-  bot: null
-
 coverage:
   precision: 2
   round: down
-  range: "60...100"
-
-  notify:
-    slack:
-      default:
-        url: "https://hooks.slack.com/services/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"
-        threshold: null
-        only_pulls: false
-        branches: master
-        flags: null
-        paths: null
+  range: "70...100"
 
   status:
     project:
@@ -27,25 +13,16 @@ coverage:
       core:
         # change this to more strict number and some allowance threshold later
         target: auto
-        threshold: null
         branches: null
-        paths: src/orion
+        paths:
+          - "src"
 
     patch:
       default:
-        target: auto
         branches: null
 
     changes:
       default:
         branches: null
 
-  ignore:
-    - tests/*
-  fixes:
-    - .tox
-
-comment:
-  layout: "header, diff, changes, sunburst, uncovered, tree"
-  branches: null
-  behavior: default
+comment: false

conda/meta.yaml

@@ -30,6 +30,7 @@ requirements:
     - pandas
     - falcon
     - gunicorn
+    - scikit-learn
 
 test:
   import:

docs/src/user/config.rst

@@ -532,7 +532,8 @@ non_monitored_arguments
 :Description:
     Ignore these commandline arguments when looking for differences in user's commandline call.
     Environment variable and commandline only supports one argument. Use global config or local
-    config to pass a list of arguments to ignore.
+    config to pass a list of arguments to ignore. When defined with environment variables,
+    use ':' to delimit multiple arguments (ex: 'three:different:arguments').
 
 
 
@@ -572,13 +573,13 @@ code_change_type
 :Default: break
 :Env var: ORION_EVC_CODE_CHANGE
 :Description:
-    One of ``break``, ``unsure`` or ``noeffet``. Defines how trials should be filtered in Experiment
-    Version Control tree if there is a change in the user's code repository. If the effect of the
-    change is ``unsure``, the child experiment will access the trials of the parent but not the
-    other way around. This is to ensure parent experiment does not get corrupted with possibly
-    incompatible results. The child cannot access the trials from parent if ``code_change_type`` is
-    ``break``. The parent cannot access trials from child if ``code_change_type`` is ``unsure`` or
-    ``break``.
+    One of ``break``, ``unsure`` or ``noeffect``. Defines how trials should be filtered in
+    Experiment Version Control tree if there is a change in the user's code repository. If the
+    effect of the change is ``unsure``, the child experiment will access the trials of the parent
+    but not the other way around. This is to ensure parent experiment does not get corrupted with
+    possibly incompatible results. The child cannot access the trials from parent if
+    ``code_change_type`` is ``break``. The parent cannot access trials from child if
+    ``code_change_type`` is ``unsure`` or ``break``.
 
 
 
@@ -591,13 +592,13 @@ cli_change_type
 :Default: break
 :Env var: ORION_EVC_CMDLINE_CHANGE
 :Description:
-    One of ``break``, ``unsure`` or ``noeffet``. Defines how trials should be filtered in Experiment
-    Version Control tree if there is a change in the user's commandline call. If the effect of the
-    change is ``unsure``, the child experiment will access the trials of the parent but not the
-    other way around. This is to ensure parent experiment does not get corrupted with possibly
-    incompatible results. The child cannot access the trials from parent if ``cli_change_type`` is
-    ``break``. The parent cannot access trials from child if ``cli_change_type`` is ``unsure`` or
-    ``break``.
+    One of ``break``, ``unsure`` or ``noeffect``. Defines how trials should be filtered in
+    Experiment Version Control tree if there is a change in the user's commandline call. If the
+    effect of the change is ``unsure``, the child experiment will access the trials of the parent
+    but not the other way around. This is to ensure parent experiment does not get corrupted with
+    possibly incompatible results. The child cannot access the trials from parent if
+    ``cli_change_type`` is ``break``. The parent cannot access trials from child if
+    ``cli_change_type`` is ``unsure`` or ``break``.
 
 
 
@@ -610,9 +611,10 @@ config_change_type
 :Default: break
 :Env var: ORION_EVC_CONFIG_CHANGE
 :Description:
-    One of ``break``, ``unsure`` or ``noeffet``. Defines how trials should be filtered in Experiment
-    Version Control tree if there is a change in the user's script. If the effect of the change is
-    ``unsure``, the child experiment will access the trials of the parent but not the other way
-    around. This is to ensure parent experiment does not get corrupted with possibly incompatible
-    results. The child cannot access the trials from parent if ``config_change_type`` is ``break``.
-    The parent cannot access trials from child if ``config_change_type`` is ``unsure`` or ``break``.
+    One of ``break``, ``unsure`` or ``noeffect``. Defines how trials should be filtered in
+    Experiment Version Control tree if there is a change in the user's script. If the effect of the
+    change is ``unsure``, the child experiment will access the trials of the parent but not the
+    other way around. This is to ensure parent experiment does not get corrupted with possibly
+    incompatible results. The child cannot access the trials from parent if ``config_change_type``
+    is ``break``.  The parent cannot access trials from child if ``config_change_type`` is
+    ``unsure`` or ``break``.

docs/src/user/storage.rst

@@ -180,12 +180,21 @@ Here is a short example to fetch trials or insert a new one.
    # To fetch all trials from an experiment
    trials = experiment.fetch_trials()
 
+   # To fetch trials in a form on panda dataframe
+   df = experiment.to_pandas()
+
    # Insert a new trial in storage
    experiment.insert(dict(x=0.5))
 
    # Insert a new trial and reserve to execute
    trial = experiment.insert(dict(x=0.6), reserve=True)
 
+:hidden:`to_pandas`
+----------------------
+
+.. automethod:: orion.client.experiment.ExperimentClient.to_pandas
+   :noindex:
+
 :hidden:`fetch_trials`
 ----------------------
 

docs/src/user/web_api.rst

@@ -244,6 +244,36 @@ Plots
 The plot resource permits the generation and retrieval of `Plotly <https://plotly.com/>`_ plots to
 visualize your experiments and their results.
 
+.. http:get:: /plots/lpi/:experiment
+
+   Return a lpi plot for the specified experiment.
+
+   **Example response**
+
+   .. sourcecode:: http
+
+      HTTP/1.1 200 OK
+      Content-Type: text/javascript
+
+   The JSON output is generated automatically according to the `Plotly.js schema reference <https://plotly.com/python/reference/index/>`_.
+
+   :statuscode 404: When the specified experiment doesn't exist in the database.
+
+.. http:get:: /plots/parallel_coordinates/:experiment
+
+   Return a parallel coordinates plot for the specified experiment.
+
+   **Example response**
+
+   .. sourcecode:: http
+
+      HTTP/1.1 200 OK
+      Content-Type: text/javascript
+
+   The JSON output is generated automatically according to the `Plotly.js schema reference <https://plotly.com/python/reference/index/>`_.
+
+   :statuscode 404: When the specified experiment doesn't exist in the database.
+
 .. http:get:: /plots/regret/:experiment
 
    Return a regret plot for the specified experiment.
@@ -259,6 +289,7 @@ visualize your experiments and their results.
 
    :statuscode 404: When the specified experiment doesn't exist in the database.
 
+
 Errors
 ------
 Oríon uses `conventional HTTP response codes <https://en.wikipedia.org/wiki/List_of_HTTP_status_codes>`_

setup.py

@@ -58,7 +58,8 @@
             ]
         },
     install_requires=['PyYAML', 'pymongo>=3', 'numpy', 'scipy', 'gitpython', 'filelock',
-                      'tabulate', 'AppDirs', 'plotly', 'pandas', 'gunicorn', 'falcon'],
+                      'tabulate', 'AppDirs', 'plotly', 'pandas', 'gunicorn', 'falcon',
+                      'scikit-learn'],
     tests_require=tests_require,
     setup_requires=['setuptools', 'appdirs', 'pytest-runner'],
     extras_require=dict(test=tests_require),