#2908 revert citations tag

Author: valentinsulzer

CHANGELOG.md

@@ -1,15 +1,21 @@
 # [Unreleased](https://github.com/pybamm-team/PyBaMM/)
 
+# [v23.4.1](https://github.com/pybamm-team/PyBaMM/tree/v23.4) - 2023-05-01
+
+## Bug fixes
+
+- Fixed a performance regression introduced by citation tags ([#2862](https://github.com/pybamm-team/PyBaMM/pull/2862)). Citations tags functionality is removed for now.
+
 # [v23.4](https://github.com/pybamm-team/PyBaMM/tree/v23.4) - 2023-04-30
 
-# Features
+## Features
 
 - Added verbose logging to `pybamm.print_citations()` and citation tags for the `pybamm.Citations` class so that users can now see where the citations were registered when running simulations ([#2862](https://github.com/pybamm-team/PyBaMM/pull/2862))
 - PyBaMM is now natively supported on Apple silicon chips (`M1/M2`) ([#2435](https://github.com/pybamm-team/PyBaMM/pull/2435))
 - PyBaMM is now supported on Python `3.10` and `3.11` ([#2435](https://github.com/pybamm-team/PyBaMM/pull/2435))
 - Updated to casadi 3.6, which required some changes to the casadi integrator. ([#2859](https://github.com/pybamm-team/PyBaMM/pull/2859))
 
-# Optimizations
+## Optimizations
 
 - Fixed deprecated `interp2d` method by switching to `xarray.DataArray` as the backend for `ProcessedVariable` ([#2907](https://github.com/pybamm-team/PyBaMM/pull/2907))
 
@@ -19,7 +25,7 @@
 - Fixed a bug in the discretisation of initial conditions of a scaled variable ([#2856](https://github.com/pybamm-team/PyBaMM/pull/2856))
 - Fixed keyerror on "all" when getting sensitivities from IDAKLU solver([#2883](https://github.com/pybamm-team/PyBaMM/pull/2883))
 
-# Breaking changes
+## Breaking changes
 
 - Made `Jupyter` a development only dependency. Now `Jupyter` would not be a required dependency for users while installing `PyBaMM`. ([#2846](https://github.com/pybamm-team/PyBaMM/pull/2846))
 

CITATION.cff

@@ -24,6 +24,6 @@ keywords:
   - "expression tree"
   - "python"
   - "symbolic differentiation"
-version: "23.4"
+version: "23.4.1"
 repository-code: "https://github.com/pybamm-team/PyBaMM"
 title: "Python Battery Mathematical Modelling (PyBaMM)"

docs/conf.py

@@ -26,7 +26,7 @@
 author = "The PyBaMM Team"
 
 # The short X.Y version
-version = "23.4"
+version = pybamm.__version__
 # The full version, including alpha/beta/rc tags
 release = version
 

docs/source/_static/versions.json

@@ -1 +1 @@
-[{"name": "latest", "version": "latest", "url": "https://pybamm.readthedocs.io/en/latest/"}, {"name": "stable", "version": "stable", "url": "https://pybamm.readthedocs.io/en/stable/"}, {"version": "v23.4", "url": "https://pybamm.readthedocs.io/en/v23.4/"}, {"version": "v23.3", "url": "https://pybamm.readthedocs.io/en/v23.3/"}, {"version": "v23.2", "url": "https://pybamm.readthedocs.io/en/v23.2/"}, {"version": "v23.1", "url": "https://pybamm.readthedocs.io/en/v23.1/"}, {"version": "v22.12", "url": "https://pybamm.readthedocs.io/en/v22.12/"}, {"version": "v22.11.1", "url": "https://pybamm.readthedocs.io/en/v22.11.1/"}, {"version": "v22.11", "url": "https://pybamm.readthedocs.io/en/v22.11/"}, {"version": "v22.10", "url": "https://pybamm.readthedocs.io/en/v22.10/"}, {"version": "v22.9", "url": "https://pybamm.readthedocs.io/en/v22.9/"}, {"version": "v22.8", "url": "https://pybamm.readthedocs.io/en/v22.8/"}, {"version": "v22.7", "url": "https://pybamm.readthedocs.io/en/v22.7/"}, {"version": "v22.6", "url": "https://pybamm.readthedocs.io/en/v22.6/"}, {"version": "v22.5", "url": "https://pybamm.readthedocs.io/en/v22.5/"}, {"version": "v22.4", "url": "https://pybamm.readthedocs.io/en/v22.4/"}, {"version": "v22.3", "url": "https://pybamm.readthedocs.io/en/v22.3/"}, {"version": "v22.2", "url": "https://pybamm.readthedocs.io/en/v22.3/"}, {"version": "v22.1", "url": "https://pybamm.readthedocs.io/en/v22.1/"}, {"version": "v21.12", "url": "https://pybamm.readthedocs.io/en/v21.12/"}, {"version": "v21.11", "url": "https://pybamm.readthedocs.io/en/v21.11/"}, {"version": "v21.10", "url": "https://pybamm.readthedocs.io/en/v21.10/"}, {"version": "v21.9", "url": "https://pybamm.readthedocs.io/en/v21.9/"}, {"version": "v21.08", "url": "https://pybamm.readthedocs.io/en/v21.08/"}, {"version": "v0.4.0", "url": "https://pybamm.readthedocs.io/en/v0.4.0/"}, {"version": "v0.3.0", "url": "https://pybamm.readthedocs.io/en/v0.3.0/"}, {"version": "v0.2.3", "url": "https://pybamm.readthedocs.io/en/v0.2.3/"}, {"version": "v0.2.2", "url": "https://pybamm.readthedocs.io/en/v0.2.2/"}, {"version": "v0.2.1", "url": "https://pybamm.readthedocs.io/en/v0.2.1/"}, {"version": "v0.2.0", "url": "https://pybamm.readthedocs.io/en/v0.2.0/"}, {"version": "v0.1.0", "url": "https://pybamm.readthedocs.io/en/v0.1.0/"}]
+[{"name": "latest", "version": "latest", "url": "https://pybamm.readthedocs.io/en/latest/"}, {"name": "stable", "version": "stable", "url": "https://pybamm.readthedocs.io/en/stable/"}, {"version": "v23.4.1", "url": "https://pybamm.readthedocs.io/en/v23.4.1/"}, {"version": "v23.4", "url": "https://pybamm.readthedocs.io/en/v23.4/"}, {"version": "v23.3", "url": "https://pybamm.readthedocs.io/en/v23.3/"}, {"version": "v23.2", "url": "https://pybamm.readthedocs.io/en/v23.2/"}, {"version": "v23.1", "url": "https://pybamm.readthedocs.io/en/v23.1/"}, {"version": "v22.12", "url": "https://pybamm.readthedocs.io/en/v22.12/"}, {"version": "v22.11.1", "url": "https://pybamm.readthedocs.io/en/v22.11.1/"}, {"version": "v22.11", "url": "https://pybamm.readthedocs.io/en/v22.11/"}, {"version": "v22.10", "url": "https://pybamm.readthedocs.io/en/v22.10/"}, {"version": "v22.9", "url": "https://pybamm.readthedocs.io/en/v22.9/"}, {"version": "v22.8", "url": "https://pybamm.readthedocs.io/en/v22.8/"}, {"version": "v22.7", "url": "https://pybamm.readthedocs.io/en/v22.7/"}, {"version": "v22.6", "url": "https://pybamm.readthedocs.io/en/v22.6/"}, {"version": "v22.5", "url": "https://pybamm.readthedocs.io/en/v22.5/"}, {"version": "v22.4", "url": "https://pybamm.readthedocs.io/en/v22.4/"}, {"version": "v22.3", "url": "https://pybamm.readthedocs.io/en/v22.3/"}, {"version": "v22.2", "url": "https://pybamm.readthedocs.io/en/v22.3/"}, {"version": "v22.1", "url": "https://pybamm.readthedocs.io/en/v22.1/"}, {"version": "v21.12", "url": "https://pybamm.readthedocs.io/en/v21.12/"}, {"version": "v21.11", "url": "https://pybamm.readthedocs.io/en/v21.11/"}, {"version": "v21.10", "url": "https://pybamm.readthedocs.io/en/v21.10/"}, {"version": "v21.9", "url": "https://pybamm.readthedocs.io/en/v21.9/"}, {"version": "v21.08", "url": "https://pybamm.readthedocs.io/en/v21.08/"}, {"version": "v0.4.0", "url": "https://pybamm.readthedocs.io/en/v0.4.0/"}, {"version": "v0.3.0", "url": "https://pybamm.readthedocs.io/en/v0.3.0/"}, {"version": "v0.2.3", "url": "https://pybamm.readthedocs.io/en/v0.2.3/"}, {"version": "v0.2.2", "url": "https://pybamm.readthedocs.io/en/v0.2.2/"}, {"version": "v0.2.1", "url": "https://pybamm.readthedocs.io/en/v0.2.1/"}, {"version": "v0.2.0", "url": "https://pybamm.readthedocs.io/en/v0.2.0/"}, {"version": "v0.1.0", "url": "https://pybamm.readthedocs.io/en/v0.1.0/"}]

pybamm/citations.py

@@ -7,7 +7,6 @@
 import os
 import warnings
 import pybtex
-from inspect import stack
 from pybtex.database import parse_file, parse_string, Entry
 from pybtex.scanner import PybtexError
 
@@ -36,9 +35,6 @@ def __init__(self):
         # Dict mapping citations keys to BibTex entries
         self._all_citations: dict[str, str] = dict()
 
-        # Dict mapping citation tags for use when registering citations
-        self._citation_tags = dict()
-
         # store citation error
         self._citation_err_msg = None
 
@@ -52,21 +48,10 @@ def _reset(self):
         """Reset citations to default only (only for testing purposes)"""
         # Initialize empty papers to cite
         self._papers_to_cite = set()
-        # Initialize empty citation tags
-        self._citation_tags = dict()
         # Register the PyBaMM paper and the numpy paper
         self.register("Sulzer2021")
         self.register("Harris2020")
 
-    def _caller_name():
-        """
-        Returns the qualified name of classes that call :meth:`register` internally.
-        This is used for tagging citations but only for verbose output
-        """
-        # Attributed to https://stackoverflow.com/a/17065634
-        caller_name = stack()[2][0].f_locals["self"].__class__.__qualname__
-        return caller_name
-
     def read_citations(self):
         """Reads the citations in `pybamm.CITATIONS.txt`. Other works can be cited
         by passing a BibTeX citation to :meth:`register`.
@@ -93,14 +78,6 @@ def _add_citation(self, key, entry):
         # Add to database
         self._all_citations[key] = new_citation
 
-    def _add_citation_tag(self, key, entry):
-        """Adds a tag for a citation key which represents the name of the class that
-        called :meth:`register`"""
-
-        # Add a citation tag to the citation_tags ordered dictionary with
-        # the key being the citation itself and the value being the name of the class
-        self._citation_tags[key] = entry
-
     @property
     def _cited(self):
         """Return a list of the BibTeX entries that have been cited"""
@@ -124,14 +101,6 @@ def register(self, key):
             # Check if citation is a known key
             if key in self._all_citations:
                 self._papers_to_cite.add(key)
-                # Add citation tags for the key
-                # This is used for verbose output
-                try:
-                    caller = Citations._caller_name()
-                    self._add_citation_tag(key, entry=caller)
-                # Don't add citation tags if the citation is registered manually
-                except KeyError:  # pragma: no cover
-                    pass
                 return
 
             # Try to parse the citation using pybtex
@@ -150,54 +119,14 @@ def register(self, key):
                 # Unable to parse / unknown key
                 raise KeyError(f"Not a bibtex citation or known citation: {key}")
 
-    def tag_citations(self):  # pragma: no cover
-        """Prints the citations tags for the citations that have been registered
-        (non-manually). This is used for verbose output when printing citations
-        such that it can be seen which citations were registered by PyBaMM classes.
-
-        To use, either call :meth:`tag_citations` after calling :meth:`register`
-        for all citations, or enable verbose output with :meth:`print_citations`
-        or :meth:`print`.
-
-        .. note::
-            If a citation is registered manually, it will not be tagged.
-
-        Examples
-        --------
-        .. code-block:: python
-            :linenos:
-
-            pybamm.citations.register("Doyle1993")
-            pybamm.citations.print() or pybamm.print_citations()
-
-        will print the following:
-
-        .. code-block::
-
-            Citations registered:
-            Sulzer2021 was cited due to the use of
-            pybamm.models.full_battery_models.lithium_ion.dfn
-
-        """
-        if self._citation_tags:
-            print("\n Citations registered: \n")
-            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 the citation tags for the citations that have
-        been registered non-manually. This is available only upon printing
-        to the terminal.
+    def print(self, filename=None, output_format="text"):
+        """Print all citations that were used for running simulations.
 
         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
+            Filename to which to print citations. If None, citations are printed to the
+            terminal.
         """
         if output_format == "text":
             citations = pybtex.format_from_strings(
@@ -213,14 +142,12 @@ def print(self, filename=None, output_format="text", verbose=False):
 
         if filename is None:
             print(citations)
-            if verbose:
-                self.tag_citations()  # pragma: no cover
         else:
             with open(filename, "w") as f:
                 f.write(citations)
 
 
-def print_citations(filename=None, output_format="text", verbose=False):
+def print_citations(filename=None, output_format="text"):
     """See :meth:`Citations.print`"""
     if citations._citation_err_msg is not None:
         raise ImportError(
@@ -232,13 +159,7 @@ def print_citations(filename=None, output_format="text", verbose=False):
             f"{citations._citation_err_msg}"
         )
     else:
-        if verbose:  # pragma: no cover
-            warnings.warn(
-                "Verbose output is not available for printing to files, only to the terminal"  # noqa: E501
-            )
-            pybamm.citations.print(filename, output_format, verbose=True)
-        else:
-            pybamm.citations.print(filename, output_format)
+        pybamm.citations.print(filename, output_format)
 
 
 citations = Citations()

pybamm/version.py

@@ -1 +1 @@
-__version__ = "23.4"
+__version__ = "23.4.1"

scripts/update_version.py

@@ -32,14 +32,6 @@ def update_version():
         file.seek(0)
         file.write(replace_version)
 
-    # docs/conf.py
-    with open(os.path.join(pybamm.root_dir(), "docs", "conf.py"), "r+") as file:
-        output = file.read()
-        replace_version = re.sub('(?<=version = ")(.+)(?=")', release_version, output)
-        file.truncate(0)
-        file.seek(0)
-        file.write(replace_version)
-
     # CITATION.cff
     with open(os.path.join(pybamm.root_dir(), "CITATION.cff"), "r+") as file:
         output = file.read()
@@ -64,7 +56,7 @@ def update_version():
         )  # noqa: E501
         file.truncate(0)
         file.seek(0)
-        file.write(json.dumps(json_data))
+        file.write(json.dumps(json_data, indent=4))
 
     # vcpkg.json
     with open(os.path.join(pybamm.root_dir(), "vcpkg.json"), "r+") as file: