improvements to log chart (#83)

* moved log chart to api submodule, added support for bokeh and altair, added log_table

* fixed formatting errors

* added log_html and reinstated the old xgboost_monitor file with a deprecation warning

neptunecontrib/api/__init__.py

@@ -13,3 +13,35 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 #
+
+from neptunecontrib.api.chart import log_chart
+from neptunecontrib.api.html import log_html
+from neptunecontrib.api.table import log_table
+from neptunecontrib.api.utils import (
+    concat_experiments_on_channel,
+    extract_project_progress_info,
+    get_channel_columns,
+    get_parameter_columns,
+    get_property_columns,
+    get_system_columns,
+    strip_prefices,
+    pickle_and_log_artifact,
+    get_pickled_artifact,
+    get_filepaths
+)
+
+__all__ = [
+    'log_table',
+    'log_html',
+    'log_chart',
+    'concat_experiments_on_channel',
+    'extract_project_progress_info',
+    'get_channel_columns',
+    'get_parameter_columns',
+    'get_property_columns',
+    'get_system_columns',
+    'strip_prefices',
+    'pickle_and_log_artifact',
+    'get_pickled_artifact',
+    'get_filepaths'
+]

neptunecontrib/api/chart.py

@@ -0,0 +1,202 @@
+#
+# Copyright (c) 2020, Neptune Labs Sp. z o.o.
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+#
+
+import neptune
+
+__all__ = [
+    'log_chart',
+]
+
+
+def log_chart(name, chart, experiment=None):
+    """Logs charts from matplotlib, plotly, bokeh, and altair to neptune.
+
+    Plotly, Bokeh, and Altair charts are converted to interactive HTML objects and then uploaded to Neptune
+    as an artifact with path charts/{name}.html.
+
+    Matplotlib figures are converted optionally. If plotly is installed, matplotlib figures are converted
+    to plotly figures and then converted to interactive HTML and uploaded to Neptune as an artifact with
+    path charts/{name}.html. If plotly is not installed, matplotlib figures are converted to PNG images
+    and uploaded to Neptune as an artifact with path charts/{name}.png
+
+    Args:
+        name (:obj:`str`):
+            | Name of the chart (without extension) that will be used as a part of artifact's destination.
+        chart (:obj:`matplotlib` or :obj:`plotly` Figure):
+            | Figure from `matplotlib` or `plotly`. If you want to use global figure from `matplotlib`, you
+              can also pass reference to `matplotlib.pyplot` module.
+        experiment (:obj:`neptune.experiments.Experiment`, optional, default is ``None``):
+            | For advanced users only. Pass Neptune
+              `Experiment <https://docs.neptune.ai/neptune-client/docs/experiment.html#neptune.experiments.Experiment>`_
+              object if you want to control to which experiment data is logged.
+            | If ``None``, log to currently active, and most recent experiment.
+
+    Examples:
+        Start an experiment::
+
+            import neptune
+
+            neptune.init(api_token='ANONYMOUS',
+                         project_qualified_name='shared/showroom')
+            neptune.create_experiment(name='experiment_with_charts')
+
+        Create matplotlib figure and log it to Neptune::
+
+            import matplotlib.pyplot as plt
+
+            fig = plt.figure()
+            x = [21,22,23,4,5,6,77,8,9,10,31,32,33,34,35,36,37,18,49,50,100]
+            plt.hist(x, bins=5)
+            plt.show()
+
+            from neptunecontrib.logging.chart import log_chart
+
+            log_chart('matplotlib_figure', fig)
+
+        Create Plotly chart and log it to Neptune::
+
+            import plotly.express as px
+
+            df = px.data.tips()
+            fig = px.histogram(df, x="total_bill", y="tip", color="sex", marginal="rug",
+                               hover_data=df.columns)
+            fig.show()
+
+            from neptunecontrib.logging.chart import log_chart
+
+            log_chart('plotly_figure', fig)
+
+        Create Altair chart and log it to Neptune::
+
+            import altair as alt
+            from vega_datasets import data
+
+            source = data.cars()
+
+            chart = alt.Chart(source).mark_circle(size=60).encode(
+                            x='Horsepower',
+                            y='Miles_per_Gallon',
+                            color='Origin',
+                            tooltip=['Name', 'Origin', 'Horsepower', 'Miles_per_Gallon']
+            ).interactive()
+
+            from neptunecontrib.logging.chart import log_chart
+
+            log_chart('altair_chart', chart)
+
+        Create Bokeh figure and log it to Neptune::
+
+            from bokeh.plotting import figure
+
+            p = figure(plot_width=400, plot_height=400)
+
+            # add a circle renderer with a size, color, and alpha
+            p.circle([1, 2, 3, 4, 5], [6, 7, 2, 4, 5], size=20, color="navy", alpha=0.5)
+
+            from neptunecontrib.logging.chart import log_chart
+
+            log_chart('bokeh_figure', p)
+
+        Check out how the logged charts look in Neptune:
+        https://ui.neptune.ai/o/shared/org/showroom/e/SHOW-973/artifacts?path=charts%2F&file=bokeh_figure.html
+     """
+    _exp = experiment if experiment else neptune
+
+    if is_matplotlib_pyplot(chart) or is_matplotlib_figure(chart):
+        if is_matplotlib_pyplot(chart):
+            chart = chart.gcf()
+
+        try:
+            from plotly import tools
+            chart = tools.mpl_to_plotly(chart)
+
+            _exp.log_artifact(export_plotly_figure(chart), "charts/" + name + '.html')
+        except ImportError:
+            _exp.log_artifact(export_matplotlib_figure(chart), "charts/" + name + '.png')
+
+    elif is_plotly_figure(chart):
+        _exp.log_artifact(export_plotly_figure(chart), "charts/" + name + '.html')
+
+    elif is_bokeh_figure(chart):
+        _exp.log_artifact(export_bokeh_figure(chart), "charts/" + name + '.html')
+
+    elif is_altair_chart(chart):
+        _exp.log_artifact(export_altair_chart(chart), "charts/" + name + '.html')
+
+    else:
+        raise ValueError("Currently supported are matplotlib, plotly, altair, and bokeh figures")
+
+
+def is_matplotlib_pyplot(chart):
+    return hasattr(chart, '__name__') and chart.__name__.startswith('matplotlib.')
+
+
+def is_matplotlib_figure(chart):
+    return chart.__class__.__module__.startswith('matplotlib.') and chart.__class__.__name__ == 'Figure'
+
+
+def is_plotly_figure(chart):
+    return chart.__class__.__module__.startswith('plotly.') and chart.__class__.__name__ == 'Figure'
+
+
+def is_altair_chart(chart):
+    return chart.__class__.__module__.startswith('altair.') and 'Chart' in chart.__class__.__name__
+
+
+def is_bokeh_figure(chart):
+    return chart.__class__.__module__.startswith('bokeh.') and chart.__class__.__name__ == 'Figure'
+
+
+def export_plotly_figure(chart):
+    from io import StringIO
+
+    buffer = StringIO()
+    chart.write_html(buffer)
+    buffer.seek(0)
+
+    return buffer
+
+
+def export_matplotlib_figure(chart):
+    from io import BytesIO
+
+    buffer = BytesIO()
+    chart.savefig(buffer, format='png')
+    buffer.seek(0)
+
+    return buffer
+
+
+def export_altair_chart(chart):
+    from io import StringIO
+
+    buffer = StringIO()
+    chart.save(buffer, format='html')
+    buffer.seek(0)
+
+    return buffer
+
+
+def export_bokeh_figure(chart):
+    from io import StringIO
+    from bokeh.resources import CDN
+    from bokeh.embed import file_html
+
+    html = file_html(chart, CDN)
+    buffer = StringIO(html)
+    buffer.seek(0)
+
+    return buffer

neptunecontrib/api/html.py

@@ -0,0 +1,74 @@
+#
+# Copyright (c) 2020, Neptune Labs Sp. z o.o.
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+#
+
+import neptune
+
+__all__ = [
+    'log_html',
+]
+
+
+def log_html(name, html, experiment=None):
+    """Logs html to neptune.
+
+    HTML is logged to Neptune as an artifact with path html/{name}.html
+
+    Args:
+        name (:obj:`str`):
+            | Name of the chart (without extension) that will be used as a part of artifact's destination.
+        html_body (:obj:`str`):
+            | HTML string that is logged and rendered as HTML.
+        experiment (:obj:`neptune.experiments.Experiment`, optional, default is ``None``):
+            | For advanced users only. Pass Neptune
+              `Experiment <https://docs.neptune.ai/neptune-client/docs/experiment.html#neptune.experiments.Experiment>`_
+              object if you want to control to which experiment data is logged.
+            | If ``None``, log to currently active, and most recent experiment.
+
+    Examples:
+        Start an experiment::
+
+            import neptune
+
+            neptune.init(api_token='ANONYMOUS',
+                         project_qualified_name='shared/showroom')
+            neptune.create_experiment(name='experiment_with_html')
+
+        Create an HTML string::
+
+            html = "<button type='button',style='background-color:#005879; width:300px; height:200px; font-size:30px'> \
+                 <a style='color: #ccc', href='https://docs.neptune.ai'> Take me back to the docs!!<a> </button>"
+
+        Log it to Neptune::
+
+             from neptunecontrib.api import log_html
+
+             log_html('go_to_docs_button', html)
+
+        Check out how the logged table looks in Neptune:
+        https://ui.neptune.ai/o/shared/org/showroom/e/SHOW-988/artifacts?path=html%2F&file=button_example.html
+    """
+
+    _exp = experiment if experiment else neptune
+
+    _exp.log_artifact(export_html(html), "htmls/" + name + '.html')
+
+
+def export_html(html):
+    from io import StringIO
+    buffer = StringIO(html)
+    buffer.seek(0)
+
+    return buffer

neptunecontrib/api/table.py

@@ -0,0 +1,74 @@
+#
+# Copyright (c) 2020, Neptune Labs Sp. z o.o.
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+#
+
+import neptune
+
+__all__ = [
+    'log_table',
+]
+
+def log_table(name, table, experiment=None):
+    """Logs pandas dataframe to neptune.
+
+    Pandas dataframe is converted to an HTML table and logged to Neptune as an artifact with path tables/{name}.html
+
+    Args:
+        name (:obj:`str`):
+            | Name of the chart (without extension) that will be used as a part of artifact's destination.
+        table (:obj:`pandas.Dataframe`):
+            | DataFrame table
+        experiment (:obj:`neptune.experiments.Experiment`, optional, default is ``None``):
+            | For advanced users only. Pass Neptune
+              `Experiment <https://docs.neptune.ai/neptune-client/docs/experiment.html#neptune.experiments.Experiment>`_
+              object if you want to control to which experiment data is logged.
+            | If ``None``, log to currently active, and most recent experiment.
+
+    Examples:
+        Start an experiment::
+
+            import neptune
+
+            neptune.init(api_token='ANONYMOUS',
+                         project_qualified_name='shared/showroom')
+            neptune.create_experiment(name='experiment_with_tables')
+
+        Create or load dataframe::
+
+            import pandas as pd
+
+            iris_df = pd.read_csv('https://raw.githubusercontent.com/mwaskom/seaborn-data/master/iris.csv', nrows=100)
+
+        Log it to Neptune::
+
+             from neptunecontrib.api import log_table
+
+             log_table('pandas_df', iris_df)
+
+        Check out how the logged table looks in Neptune:
+        https://ui.neptune.ai/o/shared/org/showroom/e/SHOW-977/artifacts?path=tables%2F&file=pandas_df.html
+     """
+    _exp = experiment if experiment else neptune
+
+    _exp.log_artifact(export_pandas_dataframe(table), "tables/" + name + '.html')
+
+
+def export_pandas_dataframe(table):
+    from io import StringIO
+
+    buffer = StringIO(table.to_html())
+    buffer.seek(0)
+
+    return buffer