Merge branch 'develop' into pybamm-team#3879-aarch64-broken-docker-im…

…ages
arjxn-py · Mar 18, 2024 · dc7f4c9 · dc7f4c9
2 parents 97c48ac + 39cff38
commit dc7f4c9
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Showing 4 changed files with 32 additions and 81 deletions.
diff --git a/.github/workflows/test_on_push.yml b/.github/workflows/test_on_push.yml
@@ -279,7 +279,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       fail-fast: false
-    name: Doctests (ubuntu-latest / Python 3.12)
+    name: Doctests (ubuntu-latest / Python 3.11)
 
     steps:
       - name: Check out PyBaMM repository
@@ -301,20 +301,20 @@ jobs:
           sudo dot -c
           sudo apt-get install texlive-latex-extra dvipng
 
-      - name: Set up Python 3.12
+      - name: Set up Python 3.11
         id: setup-python
         uses: actions/setup-python@v5
         with:
-          python-version: 3.12
+          python-version: 3.11
           cache: 'pip'
 
       - name: Install nox
         run: python -m pip install nox
 
-      - name: Install docs dependencies and run doctests for GNU/Linux with Python 3.12
+      - name: Install docs dependencies and run doctests for GNU/Linux with Python 3.11
         run: python -m nox -s doctests
 
-      - name: Check if the documentation can be built for GNU/Linux with Python 3.12
+      - name: Check if the documentation can be built for GNU/Linux with Python 3.11
         run: python -m nox -s docs
 
   # Runs only on Ubuntu with Python 3.12

diff --git a/noxfile.py b/noxfile.py
@@ -5,6 +5,7 @@
 
 
 # Options to modify nox behaviour
+nox.options.default_venv_backend = "virtualenv"
 nox.options.reuse_existing_virtualenvs = True
 if sys.platform != "win32":
     nox.options.sessions = ["pre-commit", "pybamm-requires", "unit"]
@@ -61,10 +62,6 @@ def run_coverage(session):
     """Run the coverage tests and generate an XML report."""
     set_environment_variables(PYBAMM_ENV, session=session)
     session.install("coverage", silent=False)
-    # Temporary fix for Python 3.12 CI. TODO: remove after
-    # https://bitbucket.org/pybtex-devs/pybtex/issues/169/replace-pkg_resources-with
-    # is fixed
-    session.install("setuptools", silent=False)
     if sys.platform != "win32":
         if sys.version_info > (3, 12):
             session.install("-e", ".[all,dev,jax]", silent=False)
@@ -93,10 +90,6 @@ def run_coverage(session):
 def run_integration(session):
     """Run the integration tests."""
     set_environment_variables(PYBAMM_ENV, session=session)
-    # Temporary fix for Python 3.12 CI. TODO: remove after
-    # https://bitbucket.org/pybtex-devs/pybtex/issues/169/replace-pkg_resources-with
-    # is fixed
-    session.install("setuptools", silent=False)
     if sys.platform != "win32":
         if sys.version_info > (3, 12):
             session.install("-e", ".[all,dev,jax]", silent=False)
@@ -122,10 +115,6 @@ def run_integration(session):
 @nox.session(name="doctests")
 def run_doctests(session):
     """Run the doctests and generate the output(s) in the docs/build/ directory."""
-    # Temporary fix for Python 3.12 CI. TODO: remove after
-    # https://bitbucket.org/pybtex-devs/pybtex/issues/169/replace-pkg_resources-with
-    # is fixed
-    session.install("setuptools", silent=False)
     session.install("-e", ".[all,docs]", silent=False)
     session.run("python", "run-tests.py", "--doctest")
 
@@ -134,10 +123,6 @@ def run_doctests(session):
 def run_unit(session):
     """Run the unit tests."""
     set_environment_variables(PYBAMM_ENV, session=session)
-    # Temporary fix for Python 3.12 CI. TODO: remove after
-    # https://bitbucket.org/pybtex-devs/pybtex/issues/169/replace-pkg_resources-with
-    # is fixed
-    session.install("setuptools", silent=False)
     if sys.platform != "win32":
         if sys.version_info > (3, 12):
             session.install("-e", ".[all,dev,jax]", silent=False)
@@ -164,10 +149,6 @@ def run_unit(session):
 def run_examples(session):
     """Run the examples tests for Jupyter notebooks."""
     set_environment_variables(PYBAMM_ENV, session=session)
-    # Temporary fix for Python 3.12 CI. TODO: remove after
-    # https://bitbucket.org/pybtex-devs/pybtex/issues/169/replace-pkg_resources-with
-    # is fixed
-    session.install("setuptools", silent=False)
     session.install("-e", ".[all,dev]", silent=False)
     notebooks_to_test = session.posargs if session.posargs else []
     session.run("pytest", "--nbmake", *notebooks_to_test, external=True)
@@ -253,10 +234,6 @@ def set_dev(session):
 def run_tests(session):
     """Run the unit tests and integration tests sequentially."""
     set_environment_variables(PYBAMM_ENV, session=session)
-    # Temporary fix for Python 3.12 CI. TODO: remove after
-    # https://bitbucket.org/pybtex-devs/pybtex/issues/169/replace-pkg_resources-with
-    # is fixed
-    session.install("setuptools", silent=False)
     if sys.platform != "win32":
         if sys.version_info > (3, 12):
             session.install("-e", ".[all,dev,jax]", silent=False)
@@ -284,10 +261,6 @@ def build_docs(session):
     """Build the documentation and load it in a browser tab, rebuilding on changes."""
     envbindir = session.bin
     session.install("-e", ".[all,docs]", silent=False)
-    # Temporary fix for Python 3.12 CI. TODO: remove after
-    # https://bitbucket.org/pybtex-devs/pybtex/issues/169/replace-pkg_resources-with
-    # is fixed
-    session.install("setuptools", silent=False)
     session.chdir("docs")
     # Local development
     if session.interactive:

diff --git a/pybamm/citations.py b/pybamm/citations.py
@@ -38,14 +38,8 @@ def __init__(self):
         # Dict mapping citation tags for use when registering citations
         self._citation_tags = dict()
 
-        # store citation error
-        self._citation_err_msg = None
-
-        try:
-            self.read_citations()
-            self._reset()
-        except Exception as e:  # pragma: no cover
-            self._citation_err_msg = e
+        self.read_citations()
+        self._reset()
 
     def _reset(self):
         """Reset citations to default only (only for testing purposes)"""
@@ -122,23 +116,22 @@ def register(self, key):
             - The citation key for an entry in `pybamm/CITATIONS.bib` or
             - A BibTeX formatted citation
         """
-        if self._citation_err_msg is None:
-            # 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 for verbose output, but
-                # don't if they already exist in _citation_tags dict
-                if key not in self._citation_tags:
-                    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
-            else:
-                # If citation is unknown, parse it later with pybtex
-                self._unknown_citations.add(key)
-                return
+        # 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 for verbose output, but
+            # don't if they already exist in _citation_tags dict
+            if key not in self._citation_tags:
+                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
+        else:
+            # If citation is unknown, parse it later with pybtex
+            self._unknown_citations.add(key)
+            return
 
     def _parse_citation(self, key):
         """
@@ -254,25 +247,15 @@ def print(self, filename=None, output_format="text", verbose=False):
 
 def print_citations(filename=None, output_format="text", 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/. "
-            "Please manually cite all the references."
-            "\nError encountered -\n"
-            f"{citations._citation_err_msg}"
-        )
-    else:
-        if verbose:  # pragma: no cover
-            if filename is not None:  # pragma: no cover
-                raise Exception(
-                    "Verbose output is available only for the terminal and not for printing to files",
-                )
-            else:
-                citations.print(filename, output_format, verbose=True)
+    if verbose:  # pragma: no cover
+        if filename is not None:  # pragma: no cover
+            raise Exception(
+                "Verbose output is available only for the terminal and not for printing to files",
+            )
         else:
-            pybamm.citations.print(filename, output_format)
+            citations.print(filename, output_format, verbose=True)
+    else:
+        pybamm.citations.print(filename, output_format)
 
 
 citations = Citations()
diff --git a/tests/unit/test_citations.py b/tests/unit/test_citations.py
@@ -70,11 +70,6 @@ def test_print_citations(self):
         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"):
-            pybamm.print_citations()
-        pybamm.citations._citation_err_msg = None
-
         # Test that unknown citation raises warning message on printing
         pybamm.citations._reset()
         pybamm.citations.register("not a citation")