From fb6075a30b2d26a369e0e8f64b0a78313eccb66c Mon Sep 17 00:00:00 2001
From: Pradyot Ranjan <99216956+pradyotRanjan@users.noreply.github.com>
Date: Wed, 17 Jan 2024 14:27:48 +0530
Subject: [PATCH 01/13] Using bibtexparser instead of pybtex

Signed-off-by: Pradyot Ranjan <99216956+pradyotRanjan@users.noreply.github.com>
---
 pybamm/citations.py | 128 +++++++++++++++-----------------------------
 1 file changed, 43 insertions(+), 85 deletions(-)

diff --git a/pybamm/citations.py b/pybamm/citations.py
index ca260c5cfd..c61f8ba6bf 100644
--- a/pybamm/citations.py
+++ b/pybamm/citations.py
@@ -1,29 +1,19 @@
-#
-# Bibliographical information for PyBaMM
-# Inspired by firedrake/PETSc citation workflow
-# https://firedrakeproject.org/citing.html
-#
 import pybamm
-import os
+from pybamm.util import have_optional_dependency
 import warnings
+import os
 from sys import _getframe
-from pybamm.util import have_optional_dependency
 
 
 class Citations:
-
-    """Entry point to citations management.
+    """
+    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.
 
     Citations listed in `pybamm/CITATIONS.bib` can be registered with their citation
     key. For all other works provide a BibTeX Citation to :meth:`register`.
 
-    Examples
-    --------
-    >>> pybamm.citations.register("Sulzer2021")
-    >>> pybamm.citations.register("@misc{Newton1687, title={Mathematical...}}")
-    >>> pybamm.print_citations("citations.txt")
     """
 
     def __init__(self):
@@ -73,29 +63,32 @@ 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 = have_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)
+        citations_file = citations_file = os.path.join(pybamm.root_dir(), "pybamm", "CITATIONS.bib")
+        parse_file = have_optional_dependency("bibtexparser", "parse_file")
+        bib_data = parse_file(citations_file)
+        entries = bib_data.entries
+        for entry in entries:
+            # print(entry.key)
+            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 = have_optional_dependency("pybtex.database", "Entry")
         # Check input types are correct
+        Entry = have_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}")
 
         # Add to database
         self._all_citations[key] = new_citation
+        # print(new_citation)
 
     def _add_citation_tag(self, key, entry):
         """Adds a tag for a citation key in the dict, which represents the name of the
@@ -150,23 +143,22 @@ def _parse_citation(self, key):
         key: str
             A BibTeX formatted citation
         """
-        PybtexError = have_optional_dependency("pybtex.scanner", "PybtexError")
-        parse_string = have_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 = have_optional_dependency("bibtexparser", "parse_string")
+            bib_data = parse_string(key)
             if not bib_data.entries:
-                raise PybtexError("no entries found")
+                print("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:
             raise KeyError(f"Not a bibtex citation or known citation: {key}")
 
     def _tag_citations(self):
@@ -178,47 +170,10 @@ 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):
-        """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
-        and solvers in the code.
-
-        .. note::
-            If a citation is registered manually, it will not be tagged.
-
-        .. warning::
-            This function will notify the user if a citation that has been previously
-            registered is invalid or cannot be parsed.
-
-        Parameters
-        ----------
-        filename : str, optional
-            Filename to which to print citations. If None, citations are printed
-            to the terminal.
-        verbose: bool, optional
-            If True, prints the citation tags for the citations that have been
-            registered. An example of the output is shown below.
+    def print(self, filename=None, verbose=False):
 
-        Examples
-        --------
-        .. code-block:: python
-
-            pybamm.lithium_ion.SPM()
-            pybamm.Citations.print(verbose=True) or pybamm.print_citations(verbose=True)
-
-        will append the following at the end of the list of citations:
-
-        .. code-block::
-
-            Citations registered:
-
-            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 = have_optional_dependency("pybtex")
         try:
             for key in self._unknown_citations:
                 self._parse_citation(key)
@@ -230,28 +185,31 @@ 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)
+            # print(citations)
+            for entry in citations:
+                self._string_formatting(entry)
             if verbose:
                 self._tag_citations()  # pragma: no cover
         else:
             with open(filename, "w") as f:
                 f.write(citations)
 
+    def _string_formatting(self, entry):
+        txt_format = ' '
+        for key, value in entry.items():
+            if key != "ID" and key != "ENTRYTYPE":
+                txt_format = txt_format + " " + str(value)
+        print(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(
@@ -260,7 +218,7 @@ def print_citations(filename=None, output_format="text", verbose=False):
             "https://bitbucket.org/pybtex-devs/pybtex/issues/148/. "
             "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
@@ -269,9 +227,9 @@ 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()

From 9e3d7ed128c59123adb830b4ca1fdaa16d275f4f Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Wed, 17 Jan 2024 09:02:51 +0000
Subject: [PATCH 02/13] style: pre-commit fixes

---
 pybamm/citations.py | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

diff --git a/pybamm/citations.py b/pybamm/citations.py
index c61f8ba6bf..2f93801cca 100644
--- a/pybamm/citations.py
+++ b/pybamm/citations.py
@@ -63,7 +63,9 @@ def read_citations(self):
         """Reads the citations in `pybamm.CITATIONS.bib`. Other works can be cited
         by passing a BibTeX citation to :meth:`register`.
         """
-        citations_file = citations_file = os.path.join(pybamm.root_dir(), "pybamm", "CITATIONS.bib")
+        citations_file = citations_file = os.path.join(
+            pybamm.root_dir(), "pybamm", "CITATIONS.bib"
+        )
         parse_file = have_optional_dependency("bibtexparser", "parse_file")
         bib_data = parse_file(citations_file)
         entries = bib_data.entries
@@ -171,7 +173,6 @@ def _tag_citations(self):
                 print(f"{key} was cited due to the use of {entry}")
 
     def print(self, filename=None, verbose=False):
-
         # Parse citations that were not known keys at registration, but do not
         # fail if they cannot be parsed
         try:
@@ -198,7 +199,7 @@ def print(self, filename=None, verbose=False):
                 f.write(citations)
 
     def _string_formatting(self, entry):
-        txt_format = ' '
+        txt_format = " "
         for key, value in entry.items():
             if key != "ID" and key != "ENTRYTYPE":
                 txt_format = txt_format + " " + str(value)

From 210bfc770fe5d12aef8c716dc8683ba36e7b5380 Mon Sep 17 00:00:00 2001
From: Pradyot Ranjan <99216956+pradyotRanjan@users.noreply.github.com>
Date: Wed, 17 Jan 2024 14:36:14 +0530
Subject: [PATCH 03/13] Adding back wrongly removed docstring

Signed-off-by: Pradyot Ranjan <99216956+pradyotRanjan@users.noreply.github.com>
---
 pybamm/citations.py | 50 +++++++++++++++++++++++++++++++++++++++++++--
 1 file changed, 48 insertions(+), 2 deletions(-)

diff --git a/pybamm/citations.py b/pybamm/citations.py
index c61f8ba6bf..c3c5fe21e5 100644
--- a/pybamm/citations.py
+++ b/pybamm/citations.py
@@ -1,3 +1,8 @@
+#
+# Bibliographical information for PyBaMM
+# Inspired by firedrake/PETSc citation workflow
+# https://firedrakeproject.org/citing.html
+#
 import pybamm
 from pybamm.util import have_optional_dependency
 import warnings
@@ -6,14 +11,18 @@
 
 
 class Citations:
-    """
-    Entry point to citations management.
+    """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.
 
     Citations listed in `pybamm/CITATIONS.bib` can be registered with their citation
     key. For all other works provide a BibTeX Citation to :meth:`register`.
 
+    Examples
+    --------
+    >>> pybamm.citations.register("Sulzer2021")
+    >>> pybamm.citations.register("@misc{Newton1687, title={Mathematical...}}")
+    >>> pybamm.print_citations("citations.txt")
     """
 
     def __init__(self):
@@ -171,6 +180,43 @@ def _tag_citations(self):
                 print(f"{key} was cited due to the use of {entry}")
 
     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
+         and solvers in the code.
+
+         .. note::
+             If a citation is registered manually, it will not be tagged.
+
+         .. warning::
+             This function will notify the user if a citation that has been previously
+             registered is invalid or cannot be parsed.
+
+         Parameters
+         ----------
+         filename : str, optional
+             Filename to which to print citations. If None, citations are printed
+             to the terminal.
+         verbose: bool, optional
+             If True, prints the citation tags for the citations that have been
+             registered. An example of the output is shown below.
+
+         Examples
+         --------
+         .. code-block:: python
+
+             pybamm.lithium_ion.SPM()
+             pybamm.Citations.print(verbose=True) or pybamm.print_citations(verbose=True)
+
+         will append the following at the end of the list of citations:
+
+         .. code-block::
+
+             Citations registered:
+
+             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

From b67b9c29d079e8dfebba2277ee84a912e83ad60e Mon Sep 17 00:00:00 2001
From: Pradyot Ranjan <99216956+pradyotRanjan@users.noreply.github.com>
Date: Wed, 17 Jan 2024 14:42:28 +0530
Subject: [PATCH 04/13] Adding back wrongly removed docstring

Signed-off-by: Pradyot Ranjan <99216956+pradyotRanjan@users.noreply.github.com>
---
 pybamm/citations.py | 54 ++++++++++++++++++++++++++++++++++++++++-----
 1 file changed, 48 insertions(+), 6 deletions(-)

diff --git a/pybamm/citations.py b/pybamm/citations.py
index 2f93801cca..56f9339329 100644
--- a/pybamm/citations.py
+++ b/pybamm/citations.py
@@ -1,3 +1,8 @@
+#
+# Bibliographical information for PyBaMM
+# Inspired by firedrake/PETSc citation workflow
+# https://firedrakeproject.org/citing.html
+#
 import pybamm
 from pybamm.util import have_optional_dependency
 import warnings
@@ -6,14 +11,18 @@
 
 
 class Citations:
-    """
-    Entry point to citations management.
+    """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.
 
     Citations listed in `pybamm/CITATIONS.bib` can be registered with their citation
     key. For all other works provide a BibTeX Citation to :meth:`register`.
 
+    Examples
+    --------
+    >>> pybamm.citations.register("Sulzer2021")
+    >>> pybamm.citations.register("@misc{Newton1687, title={Mathematical...}}")
+    >>> pybamm.print_citations("citations.txt")
     """
 
     def __init__(self):
@@ -70,7 +79,6 @@ def read_citations(self):
         bib_data = parse_file(citations_file)
         entries = bib_data.entries
         for entry in entries:
-            # print(entry.key)
             self._add_citation(entry.key, entry)
 
     def _add_citation(self, key, entry):
@@ -90,7 +98,6 @@ def _add_citation(self, key, entry):
 
         # Add to database
         self._all_citations[key] = new_citation
-        # print(new_citation)
 
     def _add_citation_tag(self, key, entry):
         """Adds a tag for a citation key in the dict, which represents the name of the
@@ -173,8 +180,43 @@ def _tag_citations(self):
                 print(f"{key} was cited due to the use of {entry}")
 
     def print(self, filename=None, verbose=False):
-        # Parse citations that were not known keys at registration, but do not
-        # fail if they cannot be parsed
+        """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
+        and solvers in the code.
+
+        .. note::
+            If a citation is registered manually, it will not be tagged.
+
+        .. warning::
+            This function will notify the user if a citation that has been previously
+            registered is invalid or cannot be parsed.
+
+        Parameters
+        ----------
+        filename : str, optional
+            Filename to which to print citations. If None, citations are printed
+            to the terminal.
+        verbose: bool, optional
+            If True, prints the citation tags for the citations that have been
+            registered. An example of the output is shown below.
+
+        Examples
+        --------
+        .. code-block:: python
+
+            pybamm.lithium_ion.SPM()
+            pybamm.Citations.print(verbose=True) or pybamm.print_citations(verbose=True)
+
+        will append the following at the end of the list of citations:
+
+        .. code-block::
+
+            Citations registered:
+
+            Marquis2019 was cited due to the use of SPM
+
+        """
         try:
             for key in self._unknown_citations:
                 self._parse_citation(key)

From 07306e3d8b44a7df3238687d501d359a49d26382 Mon Sep 17 00:00:00 2001
From: Pradyot Ranjan <99216956+pradyotRanjan@users.noreply.github.com>
Date: Tue, 23 Jan 2024 20:44:10 +0530
Subject: [PATCH 05/13] PassCing test cases

Signed-off-by: Pradyot Ranjan <99216956+pradyotRanjan@users.noreply.github.com>
---
 pybamm/citations.py          | 22 ++++++++++------------
 pyproject.toml               |  3 ++-
 tests/unit/test_citations.py | 17 ++++++-----------
 tests/unit/test_util.py      | 10 +++++-----
 4 files changed, 23 insertions(+), 29 deletions(-)

diff --git a/pybamm/citations.py b/pybamm/citations.py
index 56f9339329..5a42369f5e 100644
--- a/pybamm/citations.py
+++ b/pybamm/citations.py
@@ -9,7 +9,6 @@
 import os
 from sys import _getframe
 
-
 class Citations:
     """Entry point to citations management.
     This object may be used to record BibTeX citation information and then register that
@@ -72,7 +71,7 @@ def read_citations(self):
         """Reads the citations in `pybamm.CITATIONS.bib`. Other works can be cited
         by passing a BibTeX citation to :meth:`register`.
         """
-        citations_file = citations_file = os.path.join(
+        citations_file = os.path.join(
             pybamm.root_dir(), "pybamm", "CITATIONS.bib"
         )
         parse_file = have_optional_dependency("bibtexparser", "parse_file")
@@ -158,7 +157,7 @@ def _parse_citation(self, key):
             parse_string = have_optional_dependency("bibtexparser", "parse_string")
             bib_data = parse_string(key)
             if not bib_data.entries:
-                print("no entries found")
+                raise Exception("no entries found")
 
             # Add and register all citations
             for entry in bib_data.entries:
@@ -167,7 +166,7 @@ def _parse_citation(self, key):
                 # Add to _papers_to_cite set
                 self._papers_to_cite.add(entry.key)
                 return
-        except:
+        except Exception:
             raise KeyError(f"Not a bibtex citation or known citation: {key}")
 
     def _tag_citations(self):
@@ -182,7 +181,7 @@ def _tag_citations(self):
     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::
@@ -231,21 +230,22 @@ def print(self, filename=None, verbose=False):
         citations = self._cited
 
         if filename is None:
-            # print(citations)
             for entry in citations:
-                self._string_formatting(entry)
+                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):
         txt_format = " "
         for key, value in entry.items():
             if key != "ID" and key != "ENTRYTYPE":
                 txt_format = txt_format + " " + str(value)
-        print(f" {txt_format} \n")
+        return f" {txt_format} \n"
 
     @property
     def citation_err_msg(self):
@@ -256,9 +256,7 @@ 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}"
diff --git a/pyproject.toml b/pyproject.toml
index 69fb9bfc1e..c39114700f 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -80,7 +80,8 @@ plot = [
 ]
 # For the Citations class
 cite = [
-    "pybtex>=0.24.0",
+     "pybtex>=0.24.0",
+     "bibtexparser>=2.0.0b5",
 ]
 # To generate LaTeX strings
 latexify = [
diff --git a/tests/unit/test_citations.py b/tests/unit/test_citations.py
index d8c1de3718..12508581eb 100644
--- a/tests/unit/test_citations.py
+++ b/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 +47,10 @@ 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 +59,11 @@ 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 +106,7 @@ 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):
diff --git a/tests/unit/test_util.py b/tests/unit/test_util.py
index 730e4cc08d..d4839e95b3 100644
--- a/tests/unit/test_util.py
+++ b/tests/unit/test_util.py
@@ -92,9 +92,9 @@ def test_git_commit_info(self):
         self.assertEqual(git_commit_info[:2], "v2")
 
     def test_have_optional_dependency(self):
-        with self.assertRaisesRegex(ModuleNotFoundError, "Optional dependency pybtex is not available."):
-            pybtex = sys.modules['pybtex']
-            sys.modules['pybtex'] = None
+        with self.assertRaisesRegex(ModuleNotFoundError, "Optional dependency bibtexparser is not available."):
+            bibtexparser = sys.modules['bibtexparser']
+            sys.modules['bibtexparser'] = None
             pybamm.print_citations()
         with self.assertRaisesRegex(ModuleNotFoundError, "Optional dependency anytree is not available."):
             with TemporaryDirectory() as dir_name:
@@ -106,8 +106,8 @@ def test_have_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.have_optional_dependency("pybtex")
+        sys.modules['bibtexparser'] = bibtexparser
+        pybamm.util.have_optional_dependency("bibtexparser")
         pybamm.print_citations()
 
 

From 4c3ed062a174b235ba4876d82d83521439e304e4 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Tue, 23 Jan 2024 15:18:55 +0000
Subject: [PATCH 06/13] style: pre-commit fixes

---
 pybamm/citations.py          |  6 ++----
 tests/unit/test_citations.py |  1 -
 tests/unit/test_util.py      | 10 ++++++----
 3 files changed, 8 insertions(+), 9 deletions(-)

diff --git a/pybamm/citations.py b/pybamm/citations.py
index 5a42369f5e..c926449076 100644
--- a/pybamm/citations.py
+++ b/pybamm/citations.py
@@ -9,6 +9,7 @@
 import os
 from sys import _getframe
 
+
 class Citations:
     """Entry point to citations management.
     This object may be used to record BibTeX citation information and then register that
@@ -71,9 +72,7 @@ def read_citations(self):
         """Reads the citations in `pybamm.CITATIONS.bib`. Other works can be cited
         by passing a BibTeX citation to :meth:`register`.
         """
-        citations_file = os.path.join(
-            pybamm.root_dir(), "pybamm", "CITATIONS.bib"
-        )
+        citations_file = os.path.join(pybamm.root_dir(), "pybamm", "CITATIONS.bib")
         parse_file = have_optional_dependency("bibtexparser", "parse_file")
         bib_data = parse_file(citations_file)
         entries = bib_data.entries
@@ -239,7 +238,6 @@ def print(self, filename=None, verbose=False):
                 for entry in citations:
                     f.write(self._string_formatting(entry))
 
-
     def _string_formatting(self, entry):
         txt_format = " "
         for key, value in entry.items():
diff --git a/tests/unit/test_citations.py b/tests/unit/test_citations.py
index 12508581eb..7d38b600c5 100644
--- a/tests/unit/test_citations.py
+++ b/tests/unit/test_citations.py
@@ -47,7 +47,6 @@ def test_citations(self):
     def test_print_citations(self):
         pybamm.citations._reset()
 
-
         # Bibtext Style
         with temporary_filename() as filename:
             pybamm.print_citations(filename)
diff --git a/tests/unit/test_util.py b/tests/unit/test_util.py
index 713f0af86d..4d26939ad2 100644
--- a/tests/unit/test_util.py
+++ b/tests/unit/test_util.py
@@ -93,9 +93,11 @@ def test_git_commit_info(self):
         self.assertEqual(git_commit_info[:2], "v2")
 
     def test_have_optional_dependency(self):
-        with self.assertRaisesRegex(ModuleNotFoundError, "Optional dependency bibtexparser is not available."):
-            bibtexparser = sys.modules['bibtexparser']
-            sys.modules['bibtexparser'] = None
+        with self.assertRaisesRegex(
+            ModuleNotFoundError, "Optional dependency bibtexparser is not available."
+        ):
+            bibtexparser = sys.modules["bibtexparser"]
+            sys.modules["bibtexparser"] = None
             pybamm.print_citations()
         with self.assertRaisesRegex(
             ModuleNotFoundError, "Optional dependency anytree is not available."
@@ -109,7 +111,7 @@ def test_have_optional_dependency(self):
                 sym = pybamm.div(c * pybamm.grad(c)) + (c / d + c - d) ** 5
                 sym.visualise(test_name)
 
-        sys.modules['bibtexparser'] = bibtexparser
+        sys.modules["bibtexparser"] = bibtexparser
         pybamm.util.have_optional_dependency("bibtexparser")
         pybamm.print_citations()
 

From 5aa706b6dbe590804db89738cb2ef47b0283d835 Mon Sep 17 00:00:00 2001
From: Pradyot Ranjan <99216956+pradyotRanjan@users.noreply.github.com>
Date: Wed, 24 Jan 2024 10:14:59 +0530
Subject: [PATCH 07/13] Checking for bbtexparser optional dependency

Signed-off-by: Pradyot Ranjan <99216956+pradyotRanjan@users.noreply.github.com>
---
 pybamm/citations.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/pybamm/citations.py b/pybamm/citations.py
index 5a42369f5e..9d21b58193 100644
--- a/pybamm/citations.py
+++ b/pybamm/citations.py
@@ -216,6 +216,7 @@ def print(self, filename=None, verbose=False):
             Marquis2019 was cited due to the use of SPM
 
         """
+        bibtexparser = have_optional_dependency("bibtexparser")
         try:
             for key in self._unknown_citations:
                 self._parse_citation(key)

From d25cde0179f6a1648547e3fc78ca5ebfd7589648 Mon Sep 17 00:00:00 2001
From: Pradyot Ranjan <99216956+pradyotRanjan@users.noreply.github.com>
Date: Wed, 24 Jan 2024 14:41:50 +0530
Subject: [PATCH 08/13] Fixing pre-commit

Signed-off-by: Pradyot Ranjan <99216956+pradyotRanjan@users.noreply.github.com>
---
 pybamm/citations.py | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/pybamm/citations.py b/pybamm/citations.py
index daf121a89d..17b35d4a5f 100644
--- a/pybamm/citations.py
+++ b/pybamm/citations.py
@@ -215,7 +215,6 @@ def print(self, filename=None, verbose=False):
             Marquis2019 was cited due to the use of SPM
 
         """
-        bibtexparser = have_optional_dependency("bibtexparser")
         try:
             for key in self._unknown_citations:
                 self._parse_citation(key)
@@ -240,6 +239,9 @@ def print(self, filename=None, verbose=False):
                     f.write(self._string_formatting(entry))
 
     def _string_formatting(self, entry):
+        bibtexparser = have_optional_dependency("bibtexparser")
+        if not isinstance(entry, bibtexparser.model.Entry):
+            raise TypeError()
         txt_format = " "
         for key, value in entry.items():
             if key != "ID" and key != "ENTRYTYPE":

From fe5dc3b957967c239ce007e854094d87d405c75b Mon Sep 17 00:00:00 2001
From: Pradyot Ranjan <99216956+pradyotRanjan@users.noreply.github.com>
Date: Tue, 30 Jan 2024 00:06:41 +0530
Subject: [PATCH 09/13] Better error handeling

Signed-off-by: Pradyot Ranjan <99216956+pradyotRanjan@users.noreply.github.com>
---
 pybamm/citations.py          | 2 +-
 pyproject.toml               | 1 -
 tests/unit/test_citations.py | 5 +++++
 3 files changed, 6 insertions(+), 2 deletions(-)

diff --git a/pybamm/citations.py b/pybamm/citations.py
index 17b35d4a5f..d86a69121a 100644
--- a/pybamm/citations.py
+++ b/pybamm/citations.py
@@ -241,7 +241,7 @@ def print(self, filename=None, verbose=False):
     def _string_formatting(self, entry):
         bibtexparser = have_optional_dependency("bibtexparser")
         if not isinstance(entry, bibtexparser.model.Entry):
-            raise TypeError()
+            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":
diff --git a/pyproject.toml b/pyproject.toml
index 4be291d670..316b305ddb 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -84,7 +84,6 @@ plot = [
 ]
 # For the Citations class
 cite = [
-     "pybtex>=0.24.0",
      "bibtexparser>=2.0.0b5",
 ]
 # To generate LaTeX strings
diff --git a/tests/unit/test_citations.py b/tests/unit/test_citations.py
index 7d38b600c5..5bb5a5a425 100644
--- a/tests/unit/test_citations.py
+++ b/tests/unit/test_citations.py
@@ -114,6 +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("NotAEntry")
+
     def test_andersson_2019(self):
         citations = pybamm.citations
         citations._reset()

From f8dce396aa97d99014c954b0588cd7865afa4212 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Mon, 29 Jan 2024 18:37:37 +0000
Subject: [PATCH 10/13] style: pre-commit fixes

---
 pybamm/citations.py | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/pybamm/citations.py b/pybamm/citations.py
index d86a69121a..7792eab942 100644
--- a/pybamm/citations.py
+++ b/pybamm/citations.py
@@ -241,7 +241,9 @@ def print(self, filename=None, verbose=False):
     def _string_formatting(self, entry):
         bibtexparser = have_optional_dependency("bibtexparser")
         if not isinstance(entry, bibtexparser.model.Entry):
-            raise TypeError("Input for string formatting must be an instance of 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":

From a71ce1da1f8ee38475bb59614904d324d9f1d037 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Thu, 7 Mar 2024 05:58:38 +0000
Subject: [PATCH 11/13] style: pre-commit fixes

---
 pybamm/citations.py | 1 -
 1 file changed, 1 deletion(-)

diff --git a/pybamm/citations.py b/pybamm/citations.py
index a62c428c69..690ba5577e 100644
--- a/pybamm/citations.py
+++ b/pybamm/citations.py
@@ -7,7 +7,6 @@
 import warnings
 import os
 from sys import _getframe
-from pybamm.util import import_optional_dependency
 
 
 class Citations:

From 98121fcc0c855f3f27f71d67af42100be2efd5af Mon Sep 17 00:00:00 2001
From: Arjun Verma <arjunverma.oc@gmail.com>
Date: Thu, 7 Mar 2024 11:36:09 +0530
Subject: [PATCH 12/13] Apply suggestions from code review

Co-authored-by: Agriya Khetarpal <74401230+agriyakhetarpal@users.noreply.github.com>
---
 pybamm/citations.py          | 8 ++++----
 tests/unit/test_citations.py | 2 +-
 tests/unit/test_util.py      | 2 +-
 3 files changed, 6 insertions(+), 6 deletions(-)

diff --git a/pybamm/citations.py b/pybamm/citations.py
index 690ba5577e..8512f0f62a 100644
--- a/pybamm/citations.py
+++ b/pybamm/citations.py
@@ -73,7 +73,7 @@ def read_citations(self):
         by passing a BibTeX citation to :meth:`register`.
         """
         citations_file = os.path.join(pybamm.root_dir(), "pybamm", "CITATIONS.bib")
-        parse_file = have_optional_dependency("bibtexparser", "parse_file")
+        parse_file = import_optional_dependency("bibtexparser", "parse_file")
         bib_data = parse_file(citations_file)
         entries = bib_data.entries
         for entry in entries:
@@ -85,7 +85,7 @@ def _add_citation(self, key, entry):
         """
 
         # Check input types are correct
-        Entry = have_optional_dependency("bibtexparser.model", "Entry")
+        Entry = import_optional_dependency("bibtexparser.model", "Entry")
         if not isinstance(key, str) or not isinstance(entry, Entry):
             raise TypeError()
 
@@ -153,7 +153,7 @@ def _parse_citation(self, key):
 
         # Parse string as a bibtex citation, and check that a citation was found
         try:
-            parse_string = have_optional_dependency("bibtexparser", "parse_string")
+            parse_string = import_optional_dependency("bibtexparser", "parse_string")
             bib_data = parse_string(key)
             if not bib_data.entries:
                 raise Exception("no entries found")
@@ -239,7 +239,7 @@ def print(self, filename=None, verbose=False):
                     f.write(self._string_formatting(entry))
 
     def _string_formatting(self, entry):
-        bibtexparser = have_optional_dependency("bibtexparser")
+        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"
diff --git a/tests/unit/test_citations.py b/tests/unit/test_citations.py
index 5bb5a5a425..f18377681e 100644
--- a/tests/unit/test_citations.py
+++ b/tests/unit/test_citations.py
@@ -117,7 +117,7 @@ def test_input_validation(self):
     def test_string_formatting(self):
         """Test type validation of ``_string_formatting``"""
         with self.assertRaisesRegex(TypeError, "Input for string formatting"):
-            pybamm.citations._string_formatting("NotAEntry")
+            pybamm.citations._string_formatting("NotAnEntry")
 
     def test_andersson_2019(self):
         citations = pybamm.citations
diff --git a/tests/unit/test_util.py b/tests/unit/test_util.py
index f2c9deebac..5864e13416 100644
--- a/tests/unit/test_util.py
+++ b/tests/unit/test_util.py
@@ -119,7 +119,7 @@ def test_import_optional_dependency(self):
                 sym.visualise(test_name)
 
         sys.modules["bibtexparser"] = bibtexparser
-        pybamm.util.have_optional_dependency("bibtexparser")
+        pybamm.util.import_optional_dependency("bibtexparser")
         pybamm.print_citations()
 
 

From c43805db4c5cfc4d82dd33c54e36b2f8d87317c1 Mon Sep 17 00:00:00 2001
From: Arjun Verma <arjunverma.oc@gmail.com>
Date: Thu, 7 Mar 2024 11:38:01 +0530
Subject: [PATCH 13/13] Update pybamm/citations.py

---
 pybamm/citations.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/pybamm/citations.py b/pybamm/citations.py
index 8512f0f62a..cf7da3aad3 100644
--- a/pybamm/citations.py
+++ b/pybamm/citations.py
@@ -7,6 +7,7 @@
 import warnings
 import os
 from sys import _getframe
+from pybamm.util import import_optional_dependency
 
 
 class Citations: