Remove dispatcher plot dependencies and upgrade bokeh

.github/styles/vocab.txt

@@ -1,4 +1,3 @@
-cdci
 oda
 api
 Tramacere

LICENSE.rst

@@ -1,4 +1,4 @@
-cdci_data_analysis is distributed under the terms of The MIT License (MIT), reproduced below.
+oda_api is distributed under the terms of The MIT License (MIT), reproduced below.
 
 MIT License
 

README.md

@@ -7,7 +7,7 @@ oda_api
 [![Documentation Status](https://readthedocs.org/projects/oda-api/badge/?version=latest)](https://oda-api.readthedocs.io/en/latest/?badge=latest)
 
 
-![Upload Python Package](https://github.com/cdcihub/oda_api/workflows/Upload%20Python%20Package/badge.svg)
+![Upload Python Package](https://github.com/oda-hub/oda_api/workflows/Upload%20Python%20Package/badge.svg)
 ![Prose Linting](https://github.com/volodymyrss/integral-isgri-rate-meaning/workflows/Prose%20Linting/badge.svg)
 ![Executing Notebook](https://github.com/volodymyrss/integral-isgri-rate-meaning/workflows/Executing%20Notebook/badge.svg)
 [![Python package](https://github.com/oda-hub/oda_api/actions/workflows/python-package.yml/badge.svg)](https://github.com/oda-hub/oda_api/actions/workflows/python-package.yml)

doc/requirements.txt

@@ -18,4 +18,5 @@ pyjwt==2.4.0
 astroquery==0.4.4
 
 rdflib
+bokeh
 puremagic

doc/source/index.rst

@@ -5,9 +5,9 @@
 
 ODA API documentation
 ===================================
-API for cdci_data_analysis
+API for Multi Messenger Online Data Analysis (MMODA)
 
-:Authors: `Andrea Tramacere <[email protected]>, Carlo Ferrigno <[email protected]>`_
+:Authors: `Andrea Tramacere <[email protected]>, Carlo Ferrigno <[email protected]>, Gabriele Barni <[email protected]>`_
 
 Documentation
 -------------

doc/source/user_guide/tutorial_main.rst

@@ -27,17 +27,17 @@ The following tutorial covers a large fraction of the code features. The example
 
    Progress reporting for long running tasks <ProgressReporter.ipynb>
 
-   Examples of workflows <https://github.com/cdcihub/oda_api_benchmark>
+   Examples of workflows <https://github.com/oda-hub/oda_api_benchmark>
 
 
 
 .. image:: https://img.shields.io/badge/run%20quick%20start%20-binder-579ACA.svg?logo=data:image/png;base64,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
-   :target: https://mybinder.org/v2/gh/cdcihub/oda_api/master
+   :target: https://mybinder.org/v2/gh/oda-hub/oda_api/master
 
 
 
 
 
 
 .. image:: https://img.shields.io/badge/run%20examples-binder-579ACA.svg?logo=data:image/png;base64,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
-   :target: https://mybinder.org/v2/gh/cdcihub/oda_api_benchmark/master
+   :target: https://mybinder.org/v2/gh/oda-hub/oda_api_benchmark/master

oda_api/plot_tools.py

@@ -30,6 +30,22 @@
 import time as _time
 import astropy.wcs as wcs
 
+from bokeh.layouts import row, gridplot
+#column,
+from bokeh.models import HoverTool
+#                          (CustomJS,
+#                           Toggle, 
+#                           RangeSlider,
+#                           HoverTool,
+#                           ColorBar,
+#                           LinearColorMapper,
+#                           LabelSet,
+#                           ColumnDataSource,
+#                           LogColorMapper)
+from bokeh.embed import components
+from bokeh.plotting import figure
+#from bokeh.palettes import Plasma256
+
 # NOTE GW, optional
 try:
     import ligo.skymap.plot
@@ -711,7 +727,7 @@
         return True
 
     def get_html_image(self, source_name, systematic_fraction, color='blue'):
-        import cdci_data_analysis.analysis.plot_tools
+
         x, dx, y, dy, e_min, e_max = self.get_lc(source_name, systematic_fraction)
         mask = numpy.logical_not(numpy.isnan(y))
 
@@ -724,17 +740,17 @@
         else:
             xlabel = 'Time [IJD]'
 
-        sp = cdci_data_analysis.analysis.plot_tools.ScatterPlot(w=800, h=600,
-                                                                x_label=xlabel,
-                                                                y_label='Rate (%.0f - %.0f keV)' % (e_min, e_max),
-                                                                title=source_name)
+        sp = ScatterPlot(w=800, h=600,
+                        x_label=xlabel,
+                        y_label='Rate (%.0f - %.0f keV)' % (e_min, e_max),
+                        title=source_name)
 
         sp.add_errorbar(x, y, yerr=dy, xerr=dx, color=color)
         html_dict = sp.get_html_draw()
 
         html_str = html_dict['div'] + '\n'
-        html_str += '<script src="https://cdn.bokeh.org/bokeh/release/bokeh-2.4.2.min.js"></script>\n' + \
-                    '<script src="https://cdn.bokeh.org/bokeh/release/bokeh-widgets-2.4.2.min.js"></script>\n'
+        html_str += '<script src="https://cdn.bokeh.org/bokeh/release/bokeh-3.5.1.min.js"></script>\n' + \
+                    '<script src="https://cdn.bokeh.org/bokeh/release/bokeh-widgets-3.5.1.min.js"></script>\n'
         html_str += html_dict['script']
 
         return html_str
@@ -794,8 +810,7 @@
             plt.show()
 
     def get_html_image(self, in_source_name, systematic_fraction, x_range=None, y_range=None, color='blue'):
-        import cdci_data_analysis.analysis.plot_tools
-
+
         x, dx, y, dy = self.get_values(in_source_name, systematic_fraction)
 
         if len(x) == 0:
@@ -807,14 +822,14 @@
         if y_range is None:
             y_range = [numpy.max([1e-4, (y-dy)[x < x_range[1]].min()]), (y+dy).max()]
 
-        sp = cdci_data_analysis.analysis.plot_tools.ScatterPlot(w=800, h=600,
-                                                                x_label="Energy [keV]",
-                                                                y_label='Counts/s/keV',
-                                                                x_axis_type='log',
-                                                                y_axis_type='log',
-                                                                x_range=x_range,
-                                                                y_range=y_range,
-                                                                title=in_source_name)
+        sp = ScatterPlot(w=800, h=600,
+                        x_label="Energy [keV]",
+                        y_label='Counts/s/keV',
+                        x_axis_type='log',
+                        y_axis_type='log',
+                        x_range=x_range,
+                        y_range=y_range,
+                        title=in_source_name)
         if len(x) == 0:
             return ''
         sp.add_errorbar(x, y, yerr=dy, xerr=dx, color=color)
@@ -1071,3 +1086,102 @@
     # TODO can an implementation of this method provided?
     def write_fits(self):
         raise NotImplementedError
+
+
+class ScatterPlot(object):
+
+    def __init__(self,w,h,x_label=None,y_label=None,x_range=None,y_range=None,title=None,y_axis_type='linear',x_axis_type='linear'):
+        hover = HoverTool(tooltips=[("x", "$x"), ("y", "$y")])
+
+        self.fig = figure(title=title, width=w, height=h,x_range=x_range,y_range=y_range,
+                          y_axis_type=y_axis_type,
+                          x_axis_type=x_axis_type,
+                     tools=[hover, 'pan,box_zoom,box_select,wheel_zoom,reset,save,crosshair']
+                     )
+
+        if x_label is not None:
+            self.fig.xaxis.axis_label = x_label
+
+        if y_label is not None:
+            self.fig.yaxis.axis_label = y_label
+
+    def add_errorbar(self, x, y, xerr=None, yerr=None, color='red',
+                 point_kwargs={}, error_kwargs={}):
+
+        self.fig.circle(x, y, color=color, **point_kwargs)
+
+        if xerr is not None:
+            x_err_x = []
+            x_err_y = []
+            for px, py, err in zip(x, y, xerr):
+                x_err_x.append((px - err, px + err))
+                x_err_y.append((py, py))
+            self.fig.multi_line(x_err_x, x_err_y, color=color, **error_kwargs)
+
+        if yerr is not None:
+            y_err_x = []
+            y_err_y = []
+            for px, py, err in zip(x, y, yerr):
+                y_err_x.append((px, px))
+                y_err_y.append((py - err, py + err))
+            self.fig.multi_line(y_err_x, y_err_y, color=color, **error_kwargs)
+
+
+
+    def add_step_line(self, x, y, legend=None):
+        if legend:
+            self.fig.step(x, y, legend_label=legend, mode="center")
+        else:
+            self.fig.step(x, y, mode="center")
+
+    def add_line(self, x, y, legend=None, color='red'):
+        if legend:
+            self.fig.line(x, y, legend_label=legend, line_color=color)
+        else:
+            self.fig.line(x, y, line_color=color)
+
+    def get_html_draw(self):
+
+
+
+        layout = row(
+            self.fig
+        )
+        #curdoc().add_root(layout)
+
+
+        #show(layout)
+
+        script, div = components(layout)
+
+        #print ('script',script)
+        #print ('div',div)
+
+        html_dict = {}
+        html_dict['script'] = script
+        html_dict['div'] = div
+        return html_dict
+
+
+class GridPlot(object):
+
+    def __init__(self,f1,f2,w=None,h=None):
+
+        self.f1=f1
+        self.f2=f2
+
+    def get_html_draw(self,w=None,h=None):
+        #l = layout([self.f1.fig],[self.f2.fig])
+
+
+        grid = gridplot([self.f1.fig,self.f2.fig],ncols=1,plot_width=w, plot_height=h)
+        #curdoc().add_root(grid)
+        #show(grid)
+        #output_file("test.html")
+        script, div = components(grid)
+
+        html_dict={}
+        html_dict['script']=script
+        html_dict['div'] = div
+        return html_dict
+

requirements.txt

@@ -5,9 +5,12 @@ json_tricks
 matplotlib
 numpy
 jsonschema
+pyjwt
 astroquery
--e git+https://github.com/oda-hub/dispatcher-app.git#egg=cdci_data_analysis[test]
-simplejson
-sentry_sdk
+scipy
 rdflib
+black
+bokeh
+-e git+https://github.com/oda-hub/dispatcher-app.git#egg=cdci_data_analysis[test]
+# This needs to be editable to allow setting the necessary variables. 
 puremagic

requirements_docker.txt

@@ -1,2 +1,2 @@
--e git://github.com/andreatramacere/oda_api.git#egg=oda_api
+-e git://github.com/oda-hub/oda_api.git#egg=oda_api
 matplotlib

tests/conftest.py

@@ -44,7 +44,6 @@ def pytest_collection_modifyitems(config, items):
                     item.add_marker(pytest.mark.skip(reason=f"--run-only-{option} prevents this test from running"))
 
 
-
 @pytest.fixture
 def dispatcher_api(dispatcher_live_fixture):
     import oda_api