Fi pyproject dependencies

README.rst

@@ -197,6 +197,8 @@ Changelog
 ========= ====================================================================
 Version   Description
 ========= ====================================================================
+1.13.0    * Fix pyproject missing requirements
+          * Fix pkg_resources warning
 1.12.0    * migrating to pyproject
 1.11.2    * Update COG service to be more user-friendly and return all pages
             by default

pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "poetry.core.masonry.api"
 
 [tool.poetry]
 name = "bioservices"
-version = "1.12.0"
+version = "1.13.0"
 description = "Access to Biological Web Services from Python"
 authors = ["Thomas Cokelaer <[email protected]>"]
 license = "GPLv3"
@@ -43,9 +43,10 @@ Documentation =  "https://bioesrvices.readthedocs.io"
 
 [tool.poetry.dependencies]
 python = "^3.8"
+appdirs = "^1.4.4"
 click = "^8.1.7"
 easydev = "^0.12.1"
-matplotlib = "<3.8.2"
+matplotlib = "<4"
 tqdm = "^4.66.1"
 rich-click = "^1.7.2"
 beautifulsoup4 = "^4.12.3"
@@ -61,7 +62,7 @@ suds-community = "^1.1.2"
 
 
 [tool.poetry.group.dev.dependencies]
-pytest = "^7.4.4"
+pytest = "^8"
 pytest-cov = "^4.1.0"
 pytest-xdist = "^3.5.0"
 pytest-mock = "^3.12.0"

src/bioservices/__init__.py

@@ -1,15 +1,24 @@
-import pkg_resources
+
+from importlib import metadata
+
+
+def get_package_version(package_name):
+    try:
+        version = metadata.version(package_name)
+        return version
+    except metadata.PackageNotFoundError:
+        return f"{package_name} not found"
+
+
+version = get_package_version("bioservices")
+
 
 from easydev import CustomConfig
 from easydev.logging_tools import Logging
 
 
 logger = Logging("bioservices", "WARNING", text_color="green")
 
-try:
-    version = pkg_resources.require("bioservices")[0].version
-except:
-    version = "1.9.0"
 
 import colorlog
 

src/bioservices/eutils.py

@@ -19,12 +19,12 @@
 
 .. topic:: What is EUtils ?
 
-    :URL: http://www.ncbi.nlm.nih.gov/books/NBK25499/
-    :URL: http://www.ncbi.nlm.nih.gov/books/NBK25500/#chapter1.Demonstration_Programs
+:URL: http://www.ncbi.nlm.nih.gov/books/NBK25499/
+:URL: http://www.ncbi.nlm.nih.gov/books/NBK25500/#chapter1.Demonstration_Programs
 
-    .. highlights::
+.. highlights::
 
-        The Entrez Programming Utilities (E-utilities) are a set of eight server-side programs that provide a stable interface into the Entrez query and database system at the National Center for Biotechnology Information (NCBI). The E-utilities use a fixed URL syntax that translates a standard set of input parameters into the values necessary for various NCBI software components to search for and retrieve the requested data. The E-utilities are therefore the structured interface to the Entrez system, which currently includes 38 databases covering a variety of biomedical data, including nucleotide and protein sequences, gene records, three-dimensional molecular structures, and the biomedical literature.
+    The Entrez Programming Utilities (E-utilities) are a set of eight server-side programs that provide a stable interface into the Entrez query and database system at the National Center for Biotechnology Information (NCBI). The E-utilities use a fixed URL syntax that translates a standard set of input parameters into the values necessary for various NCBI software components to search for and retrieve the requested data. The E-utilities are therefore the structured interface to the Entrez system, which currently includes 38 databases covering a variety of biomedical data, including nucleotide and protein sequences, gene records, three-dimensional molecular structures, and the biomedical literature.
 
        -- from http://www.ncbi.nlm.nih.gov/books/NBK25497/, March 2013
 

src/bioservices/wikipathway.py

@@ -569,3 +569,10 @@ def showPathwayInBrowser(self, pathwayId):
         """
         url = self.getPathwayInfo(pathwayId)["url"]
         webbrowser.open(url)
+
+
+    def getXrefList(self, pathwayId, code):
+        url = f"getXrefList?pwId={pathwayId}&format=json&code={code}"
+        request = self.services.http_get(url)
+        return request['xrefs']
+