Remove Björn's local machine paths from repository files (#385)

* Initial plan

* Remove Björn's local machine paths from repository files

Co-authored-by: manulera <22526102+manulera@users.noreply.github.com>

* Update genbankfixer.py

.../ to ... / in docstring

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: manulera <22526102+manulera@users.noreply.github.com>
Co-authored-by: Björn Johansson <bjorn_johansson@bio.uminho.pt>

Author: 3 people

src/pydna/__init__.py

@@ -335,12 +335,12 @@ class _PydnaDeprecationWarning(_PydnaWarning):
 #         [main]
 #         loglevel=30
 #         email=myemail@example.org
-#         data_dir=/home/bjorn/.local/share/pydna
-#         log_dir=/home/bjorn/.cache/pydna/log
-#         ape=tclsh /home/bjorn/.ApE/AppMain.tcl
+#         data_dir=/home/user/.local/share/pydna
+#         log_dir=/home/user/.cache/pydna/log
+#         ape=tclsh /path/to/ape/AppMain.tcl
 #         cached_funcs=Genbank_nucleotide
-#         primers=/home/bjorn/Dropbox/wikidata/PRIMERS.txt
-#         enzymes=/home/bjorn/Dropbox/wikidata/RestrictionEnzymes.txt
+#         primers=/path/to/primers/PRIMERS.txt
+#         enzymes=/path/to/enzymes/RestrictionEnzymes.txt
 
 #     The email address is set to someone@example.com by default. If you change
 #     this to you own address, the :func:`pydna.genbank.genbank` function can be

src/pydna/genbankfixer.py

@@ -535,19 +535,19 @@ def gbtext_clean(gbtext):
     ... //'''
     >>> from pydna.readers import read
     >>> read(s)  # doctest: +SKIP
-    /home/bjorn/anaconda3/envs/bjorn36/lib/python3.6/site-packages/Bio/GenBank/Scanner.py:1388: BiopythonParserWarning: Malformed LOCUS line found - is this correct?
+    ... /site-packages/Bio/GenBank/Scanner.py:1388: BiopythonParserWarning: Malformed LOCUS line found - is this correct?
     :'LOCUS       New_DNA      3 bp    DNA   CIRCULAR SYN        19-JUN-2013\\n'
       "correct?\\n:%r" % line, BiopythonParserWarning)
     Traceback (most recent call last):
-      File "/home/bjorn/python_packages/pydna/pydna/readers.py", line 48, in read
+      File "... /pydna/readers.py", line 48, in read
         results = results.pop()
     IndexError: pop from empty list
     <BLANKLINE>
     During handling of the above exception, another exception occurred:
     <BLANKLINE>
     Traceback (most recent call last):
       File "<stdin>", line 1, in <module>
-      File "/home/bjorn/python_packages/pydna/pydna/readers.py", line 50, in read
+      File "... /pydna/readers.py", line 50, in read
         raise ValueError("No sequences found in data:\\n({})".format(data[:79]))
     ValueError: No sequences found in data:
     (LOCUS       New_DNA      3 bp    DNA   CIRCULAR SYN        19-JUN-2013