Using bibtexparser instead of pybtex for bibtex.

pybamm/citations.py

@@ -4,14 +4,12 @@
 # https://firedrakeproject.org/citing.html
 #
 import pybamm
-import os
 import warnings
+import os
 from sys import _getframe
-from pybamm.util import import_optional_dependency
 
 
 class Citations:
-
     """Entry point to citations management.
     This object may be used to record BibTeX citation information and then register that
     a particular citation is relevant for a particular simulation.
@@ -74,24 +72,25 @@ def read_citations(self):
         """Reads the citations in `pybamm.CITATIONS.bib`. Other works can be cited
         by passing a BibTeX citation to :meth:`register`.
         """
-        parse_file = import_optional_dependency("pybtex.database", "parse_file")
         citations_file = os.path.join(pybamm.root_dir(), "pybamm", "CITATIONS.bib")
-        bib_data = parse_file(citations_file, bib_format="bibtex")
-        for key, entry in bib_data.entries.items():
-            self._add_citation(key, entry)
+        parse_file = import_optional_dependency("bibtexparser", "parse_file")
+        bib_data = parse_file(citations_file)
+        entries = bib_data.entries
+        for entry in entries:
+            self._add_citation(entry.key, entry)
 
     def _add_citation(self, key, entry):
         """Adds `entry` to `self._all_citations` under `key`, warning the user if a
         previous entry is overwritten
         """
 
-        Entry = import_optional_dependency("pybtex.database", "Entry")
         # Check input types are correct
+        Entry = import_optional_dependency("bibtexparser.model", "Entry")
         if not isinstance(key, str) or not isinstance(entry, Entry):
             raise TypeError()
 
         # Warn if overwriting a previous citation
-        new_citation = entry.to_string("bibtex")
+        new_citation = entry
         if key in self._all_citations and new_citation != self._all_citations[key]:
             warnings.warn(f"Replacing citation for {key}")
 
@@ -151,23 +150,22 @@ def _parse_citation(self, key):
         key: str
             A BibTeX formatted citation
         """
-        PybtexError = import_optional_dependency("pybtex.scanner", "PybtexError")
-        parse_string = import_optional_dependency("pybtex.database", "parse_string")
+
+        # Parse string as a bibtex citation, and check that a citation was found
         try:
-            # Parse string as a bibtex citation, and check that a citation was found
-            bib_data = parse_string(key, bib_format="bibtex")
+            parse_string = import_optional_dependency("bibtexparser", "parse_string")
+            bib_data = parse_string(key)
             if not bib_data.entries:
-                raise PybtexError("no entries found")
+                raise Exception("no entries found")
 
             # Add and register all citations
-            for key, entry in bib_data.entries.items():
+            for entry in bib_data.entries:
                 # Add to _all_citations dictionary
-                self._add_citation(key, entry)
+                self._add_citation(entry.key, entry)
                 # Add to _papers_to_cite set
-                self._papers_to_cite.add(key)
+                self._papers_to_cite.add(entry.key)
                 return
-        except PybtexError:
-            # Unable to parse / unknown key
+        except Exception:
             raise KeyError(f"Not a bibtex citation or known citation: {key}")
 
     def _tag_citations(self):
@@ -179,10 +177,10 @@ def _tag_citations(self):
             for key, entry in self._citation_tags.items():
                 print(f"{key} was cited due to the use of {entry}")
 
-    def print(self, filename=None, output_format="text", verbose=False):
+    def print(self, filename=None, verbose=False):
         """Print all citations that were used for running simulations. The verbose
         option is provided to print tags for citations in the output such that it can
-        can be seen where the citations were registered due to the use of PyBaMM models
+        be seen where the citations were registered due to the use of PyBaMM models
         and solvers in the code.
 
         .. note::
@@ -217,9 +215,6 @@ def print(self, filename=None, output_format="text", verbose=False):
             Marquis2019 was cited due to the use of SPM
 
         """
-        # Parse citations that were not known keys at registration, but do not
-        # fail if they cannot be parsed
-        pybtex = import_optional_dependency("pybtex")
         try:
             for key in self._unknown_citations:
                 self._parse_citation(key)
@@ -231,37 +226,43 @@ def print(self, filename=None, output_format="text", verbose=False):
             # delete the invalid citation from the set
             self._unknown_citations.remove(key)
 
-        if output_format == "text":
-            citations = pybtex.format_from_strings(
-                self._cited, style="plain", output_backend="plaintext"
-            )
-        elif output_format == "bibtex":
-            citations = "\n".join(self._cited)
-        else:
-            raise pybamm.OptionError(
-                f"Output format {output_format} not recognised."
-                "It should be 'text' or 'bibtex'."
-            )
+        citations = self._cited
 
         if filename is None:
-            print(citations)
+            for entry in citations:
+                print(self._string_formatting(entry))
             if verbose:
                 self._tag_citations()  # pragma: no cover
         else:
             with open(filename, "w") as f:
-                f.write(citations)
+                for entry in citations:
+                    f.write(self._string_formatting(entry))
+
+    def _string_formatting(self, entry):
+        bibtexparser = import_optional_dependency("bibtexparser")
+        if not isinstance(entry, bibtexparser.model.Entry):
+            raise TypeError(
+                "Input for string formatting must be an instance of bibtexparser.model.Entry"
+            )
+        txt_format = " "
+        for key, value in entry.items():
+            if key != "ID" and key != "ENTRYTYPE":
+                txt_format = txt_format + " " + str(value)
+        return f" {txt_format} \n"
+
+    @property
+    def citation_err_msg(self):
+        return self._citation_err_msg
 
 
-def print_citations(filename=None, output_format="text", verbose=False):
+def print_citations(filename=None, verbose=False):
     """See :meth:`Citations.print`"""
     if citations._citation_err_msg is not None:
         raise ImportError(
-            f"Citations could not be registered. If you are on Google Colab - "
-            "pybtex does not work with Google Colab due to a known bug - "
-            "https://bitbucket.org/pybtex-devs/pybtex/issues/148/. "
+            f"Citations could not be registered."
             "Please manually cite all the references."
             "\nError encountered -\n"
-            f"{citations._citation_err_msg}"
+            f"{citations.citation_err_msg}"
         )
     else:
         if verbose:  # pragma: no cover
@@ -270,9 +271,9 @@ def print_citations(filename=None, output_format="text", verbose=False):
                     "Verbose output is available only for the terminal and not for printing to files",
                 )
             else:
-                citations.print(filename, output_format, verbose=True)
+                citations.print(filename, verbose=True)
         else:
-            pybamm.citations.print(filename, output_format)
+            citations.print(filename)
 
 
 citations = Citations()

pyproject.toml

@@ -86,7 +86,7 @@ plot = [
 ]
 # For the Citations class
 cite = [
-    "pybtex>=0.24.0",
+     "bibtexparser>=2.0.0b5",
 ]
 # Battery Parameter eXchange format
 bpx = [

tests/unit/test_citations.py

@@ -7,7 +7,7 @@
 import unittest
 import contextlib
 import warnings
-from pybtex.database import Entry
+from bibtexparser.model import Entry
 from tempfile import NamedTemporaryFile
 
 
@@ -47,15 +47,9 @@ def test_citations(self):
     def test_print_citations(self):
         pybamm.citations._reset()
 
-        # Text Style
-        with temporary_filename() as filename:
-            pybamm.print_citations(filename, "text")
-            with open(filename) as f:
-                self.assertTrue(len(f.readlines()) > 0)
-
         # Bibtext Style
         with temporary_filename() as filename:
-            pybamm.print_citations(filename, "bibtex")
+            pybamm.print_citations(filename)
             with open(filename) as f:
                 self.assertTrue(len(f.readlines()) > 0)
 
@@ -64,11 +58,11 @@ def test_print_citations(self):
         with contextlib.redirect_stdout(f):
             pybamm.print_citations()
         self.assertTrue(
-            "Python Battery Mathematical Modelling (PyBaMM)." in f.getvalue()
+            "   {Python Battery Mathematical Modelling (PyBaMM)}" in f.getvalue()
         )
 
-        with self.assertRaisesRegex(pybamm.OptionError, "'text' or 'bibtex'"):
-            pybamm.print_citations("test_citations.txt", "bad format")
+        # with self.assertRaisesRegex(pybamm.OptionError, "'text' or 'bibtex'"):
+        #     pybamm.print_citations("test_citations.txt", "bad format")
 
         pybamm.citations._citation_err_msg = "Error"
         with self.assertRaisesRegex(ImportError, "Error"):
@@ -111,7 +105,7 @@ def test_input_validation(self):
         """Test type validation of ``_add_citation``"""
         pybamm.citations.register(1)
 
-        with self.assertRaises(TypeError):
+        with self.assertRaises(KeyError):
             pybamm.citations._parse_citation(1)
 
         with self.assertRaises(TypeError):
@@ -120,6 +114,11 @@ def test_input_validation(self):
         with self.assertRaises(TypeError):
             pybamm.citations._add_citation(1001, Entry("misc"))
 
+    def test_string_formatting(self):
+        """Test type validation of ``_string_formatting``"""
+        with self.assertRaisesRegex(TypeError, "Input for string formatting"):
+            pybamm.citations._string_formatting("NotAnEntry")
+
     def test_andersson_2019(self):
         citations = pybamm.citations
         citations._reset()

tests/unit/test_util.py

@@ -101,10 +101,10 @@ def test_git_commit_info(self):
 
     def test_import_optional_dependency(self):
         with self.assertRaisesRegex(
-            ModuleNotFoundError, "Optional dependency pybtex is not available."
+            ModuleNotFoundError, "Optional dependency bibtexparser is not available."
         ):
-            pybtex = sys.modules["pybtex"]
-            sys.modules["pybtex"] = None
+            bibtexparser = sys.modules["bibtexparser"]
+            sys.modules["bibtexparser"] = None
             pybamm.print_citations()
         with self.assertRaisesRegex(
             ModuleNotFoundError, "Optional dependency anytree is not available."
@@ -118,8 +118,8 @@ def test_import_optional_dependency(self):
                 sym = pybamm.div(c * pybamm.grad(c)) + (c / d + c - d) ** 5
                 sym.visualise(test_name)
 
-        sys.modules["pybtex"] = pybtex
-        pybamm.util.import_optional_dependency("pybtex")
+        sys.modules["bibtexparser"] = bibtexparser
+        pybamm.util.import_optional_dependency("bibtexparser")
         pybamm.print_citations()