Fix tests and update documentation

Author: cokelaer

README.rst

@@ -20,6 +20,10 @@ BIOSERVICES: access to biological web services programmatically
 .. image:: https://static.pepy.tech/personalized-badge/bioservices?period=month&units=international_system&left_color=black&right_color=orange&left_text=Downloads
     :target: https://pepy.tech/project/bioservices
 
+.. image:: https://anaconda.org/conda-forge/bioservices/badges/version.svg   
+    :target: https://anaconda.org/conda-forge/bioservices
+
+
 |Codacy-Grade|
 
 

doc/all_relations.png

@@ -5,7 +5,6 @@ References to BioServices on the Web
 * Galaxy: See the Log Archive at `Galaxy log archive <http://wiki.galaxyproject.org/Community/Log/2013/UsingBioServicesWithGalaxy>`_
 * EBI: See `EBI programming web services <http://www.ebi.ac.uk/Tools/webservices/tutorials/06_programming/python>`_
 * WikiPathways: `references <http://wikipathways.tumblr.com/search/bioservices>`_
-* GeneProf: `example python <https://www.geneprof.org/GeneProf/webapi.jsp#example-python>`_
 * http://www.scoop.it/t/bioinformatique
 * http://bioinfo-fr.net/bioservices-module-python
 *  http://devbio.eu/?p=resources&presel=bioinfo

doc/external_references.rst

@@ -0,0 +1,33 @@
+import __main__
+__main__.pymol_argv = [ 'pymol', '-qc'] # Quiet and no GUI
+
+import os
+if os.path.isfile("bioservices_pdb.png"):
+    os.remove("bioservices_pdb.png")
+
+# BioServices 1: obtain the PDB ID from a given uniprot ID (P43403 i.e. ZAP70)
+from bioservices import *
+print("Retrieving PDB ID")
+u = UniProt(verbose=False)
+res = u.mapping(fr="UniProtKB_AC-ID", to="PDB", query="P43403")
+pdb_id = res['results']['P43403'][0]   # e.g, "1FBV"
+
+# BioServices 2: Download the PDB file from the PDB Web Service
+print("Fetching PDB file")
+p = pdbe.PDBe()
+res = p.get_files(pdb_id)
+
+# General: save the fetched file in a temporary file
+import tempfile
+fh = tempfile.NamedTemporaryFile()
+fh.write(res)
+sname = fh.name
+
+# THIS IS NOT BIOSERVICES ANYMORE but PYMOL 
+import pymol
+pymol.finish_launching()
+pymol.cmd.load(sname)
+pymol.cmd.png("bioservices_pdb.png", width="15cm", height="15cm", dpi=140)
+#pymol.cmd.png("my_image.png")
+# Get out!
+pymol.cmd.quit()

doc/geneprof_tutorial.rst

@@ -29,7 +29,7 @@ Services
 ArrayExpress
 ===================
 
-.. .. automodule:: bioservices.arrayexpress
+.. automodule:: bioservices.arrayexpress
     :members:
     :undoc-members:
     :synopsis:
@@ -130,10 +130,6 @@ GeneProf
 Currently removed from the main API from version 1.6.0 onwards. You can still get
 the code in earlier version or in the github repository in the attic/ directory
 
-.. .. automodule:: bioservices.geneprof
-    :members:
-    :undoc-members:
-    :synopsis:
 
 QuickGO
 ================

doc/pymol_app.py

@@ -21,4 +21,3 @@ welcomed.
     compound_tutorial.rst
     convertor_tutorial.rst
     biomart.rst
-    geneprof_tutorial.rst

doc/references.rst

@@ -694,15 +694,19 @@ def get_organism(self, query=None, limit=20, offset=0, filters=None):
         params = {"limit": limit, "offset": offset, "filters": filters}
         return self._get_this_service("organism", query, params=params)
 
+    """
+    # subservices removed apparatently (march 2023) hence the commented code
+
     def search_protein_class(self, query, limit=20, offset=0):
         params = {"limit": limit, "offset": offset}
         return self._search("protein_class", query, params=params)
 
     def get_protein_class(self, query=None, limit=20, offset=0, filters=None):
-        """Protein family classification of TargetComponents"""
+        "Protein family classification of TargetComponents"
         params = {"limit": limit, "offset": offset, "filters": filters}
         return self._get_this_service("protein_class", query, params=params)
 
+    """
     def get_substructure(self, structure, limit=20, offset=0, filters=None):
         """Molecule substructure search
 
@@ -906,10 +910,10 @@ def get_image(self, query, dimensions=500, format="png", save=True, view=True, e
         .. todo:: ignorecoords option
         """
         # NOTE: not async requests here.
-        self.devtools.check_range(dimensions, 1, 500)
-        self.devtools.check_param_in_list(engine, ["rdkit", "indigo"])
-        self.devtools.check_param_in_list(format, ["png", "svg"])
-        queries = self.devtools.to_list(query)
+        self.services.devtools.check_range(dimensions, 1, 500)
+        self.services.devtools.check_param_in_list(engine, ["rdkit", "indigo"])
+        self.services.devtools.check_param_in_list(format, ["png", "svg"])
+        queries = self.services.devtools.to_list(query)
 
         res = {"filenames": [], "images": [], "chemblids": []}
         for query in queries: