Merge pull request #1 from sequana/update_wrapper_ext

Finalise package

README.rst

@@ -2,8 +2,8 @@ Sequana Sphinxext
 ##################
 
 
-.. image:: https://badge.fury.io/py/sequana_sphinxext.svg
-    :target: https://pypi.python.org/pypi/sequana_sphinxext
+.. image:: https://badge.fury.io/py/sequana-sphinxext.svg
+    :target: https://pypi.python.org/pypi/sequana-sphinxext
 
 .. image:: https://github.com/sequana/sequana_sphinxext/actions/workflows/main.yml/badge.svg?branch=master
     :target: https://github.com/sequana/sequana_sphinext/actions/workflows/main.yml
@@ -17,7 +17,8 @@ Sequana Sphinxext
 
 
 :Python version:  3.7.3, 3.8 ,3.9
-:Issues: `On github <https://github.com/sequana/sequana/issues>`_
+:Status: Production
+:Issues: Please fill issues `On github <https://github.com/sequana/sequana/issues>`_
 :How to cite: Citations are important for us to carry on developments.
     For Sequana library (including the pipelines), please use
 
@@ -28,3 +29,26 @@ Sequana Sphinxext
 The sequana_sphinxext  package is used exclusively to provide Sphinx extensions for the Sequana
 project. **Sequana** includes a set of pipelines related to NGS (new generation sequencing) including quality control, variant calling, coverage, taxonomy, transcriptomics. **Please see the** `documentation <http://sequana.readthedocs.org>`_ for an up-to-date status.
 
+We have three sphinx extension to be added in your Sphinx configuration files in the extensions list:
+
+    extensions += [
+        "sequana_sphinxext.snakemakerule",
+        "sequana_sphinxext.pipeline",
+        "sequana_sphinxext.wrapper"]
+
+You can then include a wrapper from  `sequana wrappers <https://github.com/sequana/sequana-wrappers>` using e.g.::
+
+    .. sequana_wrapper:: fastqc
+
+or a rule from Sequana::
+
+    .. snakemakerule:: fastq_sampling
+
+or a pipeline from sequana::
+
+    .. sequana_pipeline:: demultiplex
+
+
+
+
+

sequana_sphinxext/pipeline.py

@@ -36,25 +36,25 @@ def get_rule_doc(name):
 
     try:
         data = urllib.request.urlopen(url).read().decode("utf8")
-    except HTTPError:
+    except HTTPError:  # pragma: no cover
         return f"Could not access to {url}"
 
     try:
         from sequana_pipetools import Module
 
         m = Module(f"pipeline:{name}")
         version = m.version
-    except ValueError:
+    except ValueError:  # pragma: no cover
         version = "Not installed locally."
-    except ImportError:
+    except ImportError:  # pragma: no cover
         version = "?"
 
     docstring = "**current version**:{}\n\n{}".format(version, data)
 
     return docstring
 
 
-class snakemake_base(Body, Element):
+class snakemake_base(Body, Element):  # pragma: no cover
     def dont_traverse(self, *args, **kwargs):
         return []
 
@@ -91,17 +91,17 @@ def visit_perform(self, node):
             res = core.publish_parts(node.rule_docstring, writer=w)["html_body"]
             self.body.append('<div class="">' + res + "</div>")
             node.children = []
-        except Exception as err:
+        except Exception as err:  # pragma: no cover
             print(err)
             self.body.append('<div class=""> no docstring </div>')
 
     def depart_perform(self, node):
         node.children = []
 
-    def visit_ignore(self, node):
+    def visit_ignore(self, node):  # pragma: no cover
         node.children = []
 
-    def depart_ignore(self, node):
+    def depart_ignore(self, node):  # pragma: no cover
         node.children = []
 
     app.add_node(

sequana_sphinxext/snakemakerule.py

@@ -37,7 +37,7 @@ def get_rule_doc(name):
         rule = Module(name)
         filename = rule.path + "/%s.rules" % name
         data = open(filename, "r").read()
-    except ImportError:
+    except ImportError:  # pragma no cover
         url = "https://raw.githubusercontent.com/sequana/sequana/master/sequana/rules/"
         if name.count("/") == 0:
             url = f"{url}/{name}/{name}.rules"
@@ -88,12 +88,12 @@ def get_rule_doc(name):
     return docstring
 
 
-class snakemake_base(Body, Element):
+class snakemake_base(Body, Element):  # pragma: no cover
     def dont_traverse(self, *args, **kwargs):
         return []
 
 
-class snakemake_rule(snakemake_base):
+class snakemake_rule(snakemake_base):  # pragma: no cover
     pass
 
 
@@ -141,10 +141,10 @@ def visit_perform(self, node):
     def depart_perform(self, node):
         node.children = []
 
-    def depart_ignore(self, node):
+    def depart_ignore(self, node):  # pragma: no cover
         node.children = []
 
-    def visit_ignore(self, node):
+    def visit_ignore(self, node):  # pragma: no cover
         node.children = []
 
     app.add_node(

sequana_sphinxext/wrapper.py

@@ -26,7 +26,6 @@
 from docutils.nodes import Body, Element
 
 
-# from sphinx.locale import _
 from sphinx.util.docutils import SphinxDirective
 
 
@@ -42,20 +41,18 @@ def get_rule_doc(name):
     data = r.content.decode()
     rulename_tag = "rule %s" % name
 
-    if "404: Not Found" in data:
+    if "404: Not Found" in data:  # pragma no cover
         print(f"URL not found: {url}")
-        return (
-            title
-            + f"**docstring for {name} wrapper not yet available (no README.md found)**"
-        )
+        return title + f"**docstring for {name} wrapper not yet available (no README.md found)**"
 
     def get_section(data, section):
 
         if section in ["Example", "Configuration"]:
             code = f"\n**{section}**\n::\n\n"
+        elif section in ["References", "Reference"]:
+            code = f"\n**{section}**\n\n"
         else:
             code = ""
-
         found = False
         for line in data.split("\n"):
             # while requested section is not found, we parse the data
@@ -77,20 +74,21 @@ def get_section(data, section):
     example_code = get_section(data, "Example")
     docstring = get_section(data, "Documentation")
     config = get_section(data, "Configuration")
-
-    rst = docstring + example_code + config
+    ref = get_section(data, "References")
 
     url = f"https://github.com/sequana/sequana-wrappers/blob/main/wrappers/{name}/README.md"
-    rst += f"\n`Extra information on the wrapper page itself. <{url}>`_"
+    rst = f"The `{name} <{url}>`_ wrapper "
+    rst += docstring + example_code + config + ref
+    rst += f"\n\n....\n\nFound a bug or have an issue ? Please report here https://github.com/sequana/sequana-wrappers/issues"
     return rst
 
 
-class snakemake_base(Body, Element):
+class snakemake_base(Body, Element):  # pragma: no cover
     def dont_traverse(self, *args, **kwargs):
         return []
 
 
-class sequana_wrapper(snakemake_base):
+class sequana_wrapper(snakemake_base):  # pragma: no cover
     pass
 
 
@@ -99,7 +97,7 @@ def run(content, node_class, state, content_offset):
     name = content[0]
     try:
         node.rule_docstring = get_rule_doc(name)
-    except Exception:
+    except Exception:  # pragma: no cover
         node.rule_docstring = f"Could not read or interpret documentation for {name}"
     state.nested_parse(content, content_offset, node)
     return [node]
@@ -131,17 +129,17 @@ def visit_perform(self, node):
             res = core.publish_parts(node.rule_docstring, writer=w)["html_body"]
             self.body.append('<div class="sequana_wrapper">' + res + "</div><br>")
             node.children = []
-        except Exception as err:
+        except Exception as err:  # pragma: no cover
             print(err)
-            self.body.append('<div class="sequana_wrapper"> no docstring </div>')
+            self.body.append('<div class="sequana_wrapper"> no valid docstring </div>')
 
     def depart_perform(self, node):
         node.children = []
 
-    def depart_ignore(self, node):
+    def depart_ignore(self, node):  # pragma: no cover
         node.children = []
 
-    def visit_ignore(self, node):
+    def visit_ignore(self, node):  # pragma: no cover
         node.children = []
 
     app.add_node(

setup.py

@@ -1,8 +1,8 @@
 from setuptools import setup, find_packages
 
 
-_MAJOR = 0
-_MINOR = 2
+_MAJOR = 1
+_MINOR = 0
 _MICRO = 0
 version = f"{_MAJOR}.{_MINOR}.{_MICRO}"
 release = f"{_MAJOR}.{_MINOR}"
@@ -13,7 +13,7 @@
     "version": version,
     "license": "new BSD",
     "url": "http://github.com/sequana/sequana_sphinxext",
-    "description": "A set of standalone application and pipelines dedicated to NGS (new generation sequencing) analysis",
+    "description": "A set of sphinx extension for Sequana pipelines, wrappers and rules",
     "platforms": ["Linux", "Unix", "MacOsX", "Windows"],
     "keywords": ["NGS", "snakemake"],
     "classifiers": [

tests/test_sphinxext.py

@@ -48,7 +48,7 @@ def test_sequana_pipeline():
 
 def test_doc():
     res = snakemakerule.get_rule_doc("dag")
-    res = snakemakerule.get_rule_doc("fastqc_dynamic")
+    res = snakemakerule.get_rule_doc("fastqc")
 
     try:
         res = snakemakerule.get_rule_doc("dummy")