Merge branch 'master' of git+ssh://scm.gforge.inria.fr/gitroot/biocham/biocham

Makefile

@@ -61,6 +61,9 @@ biocham_tests: swipl-biocham $(MODULES) $(TEST_MODULES) Makefile
 		--goal="call_cleanup((run_tests, halt(0)), halt(1))" \
 		-c $(MODULES) $(TEST_MODULES)
 
+jupyter: biocham
+	jupyter kernelspec install --user --name=biocham biocham_kernel
+
 clean:
 	- make -C modules/graphviz clean
 	- make -C modules/sbml clean

biocham_kernel/__main__.py

+if __name__ == '__main__':
+    from ipykernel.kernelapp import IPKernelApp
+    from .kernel import BiochamKernel
+    IPKernelApp.launch_instance(kernel_class=BiochamKernel)

biocham_kernel/kernel.json

+{
+   "argv": ["python3", "-m", "biocham_kernel", "-f", "{connection_file}"],
+   "display_name": "Biocham"
+}

biocham_kernel/kernel.py

+from subprocess import check_output
+
+from ipykernel.kernelbase import Kernel
+from pexpect import replwrap
+
+
+class BiochamKernel(Kernel):
+    implementation = 'Biocham'
+    implementation_version = '0.1.0'
+    language = 'biocham'
+    language_info = {
+        'name': 'biocham',
+        'mimetype': 'text/plain',
+        'file_extension': '.bc',
+    }
+    banner = check_output(['biocham4', '--version']).decode('utf-8')
+    language_version = banner.split()[1]
+
+    def __init__(self, **kwargs):
+        Kernel.__init__(self, **kwargs)
+        self._start_biocham()
+
+
+    def _start_biocham(self):
+        self.biocham = replwrap.REPLWrapper( 'biocham4 --jupyter', 'biocham: ', None)
+
+
+    def do_execute(self, code, silent, store_history=True,
+                   user_expressions=None, allow_stdin=False):
+        output = self.biocham.run_command(code)
+
+        if not silent:
+            stream_content = {'name': 'stdout', 'text': output}
+            self.send_response(self.iopub_socket, 'stream', stream_content)
+
+        return {'status': 'ok',
+                # The base class increments the execution count
+                'execution_count': self.execution_count,
+                'payload': [],
+                'user_expressions': {},
+                }
+
+    # TODO: do_complete

commandline.pl

@@ -60,6 +60,17 @@ option('', '--generate-doc', Arg, Arg) :-
   generate_doc,
   quit.
 
+option('', '--version', Arg, Arg) :-
+   quit.
+
+option('', '--jupyter', Arg, Arg) :-
+  set_counter(plot_png, 0),
+  set_counter(graph_svg, 0),
+  set_plot_driver(gnu_plot_png),
+  set_image_viewer_driver(img_tag),
+  set_draw_graph_driver(graph_svg).
+
+
 add_files(Files) :-
   \+ (
     member(File, Files),