Modernize the CI and Release workflows, and reformat with black

.github/workflows/CI.yaml

@@ -13,24 +13,30 @@ on:
     # Run by default Sunday morning at 3:30:
     #   Scheduled workflows run on the latest commit on the default or base branch.
     #   (from https://help.github.com/en/actions/reference/events-that-trigger-workflows#scheduled-events-schedule)
+    #
+    # GitHub disables a scheduled workflow after 60 days without a commit to the
+    # repository, and disabling it stops the push and pull_request triggers too.
+    # If the badge goes stale, re-enable it on the Actions tab; workflow_dispatch
+    # below gives a way to run it by hand.
     - cron: "30 3 * * 0"
+  workflow_dispatch:
 
 jobs:
   lint:
-    name: Lint ubuntu-latest Py3.8
+    name: Lint ubuntu-latest Py3.12
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@v1
+    - uses: actions/checkout@v4
     - name: Additional info about the build
       shell: bash
       run: |
         uname -a
         df -h
         ulimit -a
     # More info on options: https://github.com/conda-incubator/setup-miniconda
-    - uses: conda-incubator/setup-miniconda@v2
+    - uses: conda-incubator/setup-miniconda@v3
       with:
-        python-version: 3.8
+        python-version: "3.12"
         environment-file: devtools/conda-envs/test_env.yaml
         activate-environment: test
         auto-update-conda: false
@@ -45,8 +51,9 @@ jobs:
     - name: Run linters
       shell: bash -l {0}
       run: |
-        flake8 reference_handler
-        yapf --diff --recursive reference_handler
+        black --extend-exclude '_version.py' --check --diff \
+            reference_handler reference_handler/tests
+        flake8 --color never reference_handler reference_handler/tests
 
   test:
     name: Test ${{ matrix.os }} Py${{ matrix.python-version }}
@@ -55,16 +62,16 @@ jobs:
     strategy:
       matrix:
         os: [macOS-latest, ubuntu-latest]
-        python-version: [3.7, 3.8]
+        python-version: ["3.11", "3.12"]
     steps:
-    - uses: actions/checkout@v1
+    - uses: actions/checkout@v4
     - name: Additional info about the build
       shell: bash
       run: |
         uname -a
         df -h
         ulimit -a
-    - uses: conda-incubator/setup-miniconda@v2
+    - uses: conda-incubator/setup-miniconda@v3
       with:
         python-version: ${{ matrix.python-version }}
         environment-file: devtools/conda-envs/test_env.yaml
@@ -82,7 +89,7 @@ jobs:
       run: |
         pytest -v --cov=reference_handler --cov-report=xml --color=yes reference_handler/tests/
     - name: CodeCov
-      uses: codecov/codecov-action@v2
+      uses: codecov/codecov-action@v4
       with:
         file: ./coverage.xml
         flags: unittests

.github/workflows/Release.yaml

@@ -17,10 +17,10 @@ jobs:
     strategy:
       matrix:
         os: [ubuntu-latest]
-        python-version: [3.8]
+        python-version: ["3.12"]
 
     steps:
-    - uses: actions/checkout@v1
+    - uses: actions/checkout@v4
 
     - name: Additional info about the build
       shell: bash
@@ -30,7 +30,7 @@ jobs:
         ulimit -a
 
     # More info on options: https://github.com/conda-incubator/setup-miniconda
-    - uses: conda-incubator/setup-miniconda@v2
+    - uses: conda-incubator/setup-miniconda@v3
       with:
         python-version: ${{ matrix.python-version }}
         environment-file: devtools/conda-envs/test_env.yaml
@@ -56,8 +56,9 @@ jobs:
       shell: bash -l {0}
 
       run: |
-        flake8 reference_handler reference_handler/tests
-        yapf --diff --recursive reference_handler
+        black --extend-exclude '_version.py' --check --diff \
+            reference_handler reference_handler/tests
+        flake8 --color never reference_handler reference_handler/tests
 
   test:
     name: Test ${{ matrix.os }} Py${{ matrix.python-version }}
@@ -66,10 +67,10 @@ jobs:
     strategy:
       matrix:
         os: [macOS-latest, ubuntu-latest]
-        python-version: [3.7, 3.8]
+        python-version: ["3.11", "3.12"]
 
     steps:
-    - uses: actions/checkout@v1
+    - uses: actions/checkout@v4
 
     - name: Additional info about the build
       shell: bash
@@ -80,7 +81,7 @@ jobs:
 
 
     # More info on options: https://github.com/conda-incubator/setup-miniconda
-    - uses: conda-incubator/setup-miniconda@v2
+    - uses: conda-incubator/setup-miniconda@v3
       with:
         python-version: ${{ matrix.python-version }}
         environment-file: devtools/conda-envs/test_env.yaml
@@ -107,7 +108,7 @@ jobs:
         pytest -v --cov=reference_handler --cov-report=xml --color=yes reference_handler/tests/
 
     - name: CodeCov
-      uses: codecov/codecov-action@v2
+      uses: codecov/codecov-action@v4
       with:
         file: ./coverage.xml
         flags: unittests
@@ -119,27 +120,25 @@ jobs:
     if: github.event_name == 'release' && startsWith(github.ref, 'refs/tags')
     runs-on: ${{ matrix.os }}
     needs: [lint, test]
+
+    # Trusted publishing: PyPI checks this token against the publisher registered
+    # for the project, so there is no API token to store or rotate.
+    permissions:
+      id-token: write
+      contents: read
     strategy:
       matrix:
         os: [ubuntu-latest]
-        python-version: [3.8]
+        python-version: ["3.12"]
 
     steps:
-    - uses: actions/checkout@v1
+    - uses: actions/checkout@v4
 
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v1
+      uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
 
-    - name: Install package
-
-      # conda setup requires this special shell
-      shell: bash -l {0}
-      run: |
-        python -m pip install . --no-deps
-        conda list
-
     - name: Install pypa/build
       run: |
         python -m pip install build --user
@@ -149,14 +148,5 @@ jobs:
         python -m build --sdist --wheel --outdir dist/
         ls -l dist/
 
-    - name: Publish distribution 📦 to Test PyPI
-      uses: pypa/gh-action-pypi-publish@master
-      with:
-        password: ${{ secrets.test_pypi_password }}
-        repository_url: https://test.pypi.org/legacy/
-        skip_existing: true
-
     - name: Publish distribution 📦 to PyPI
-      uses: pypa/gh-action-pypi-publish@master
-      with:
-        password: ${{ secrets.pypi_password }}
+      uses: pypa/gh-action-pypi-publish@release/v1

devtools/conda-envs/test_env.yaml

@@ -1,11 +1,15 @@
 name: test
+
 channels:
+  - conda-forge
+
 dependencies:
     # Base depends
   - python
   - pip
 
     # Testing
+  - black
   - codecov
   - coverage
   - flake8
@@ -16,7 +20,4 @@ dependencies:
     # Pip-only installs
   - pip:
     - bibtexparser<2
-
-      # Testing
-    - yapf
 

reference_handler/__init__.py

@@ -12,6 +12,6 @@
 from ._version import get_versions
 
 versions = get_versions()
-__version__ = versions['version']
-__git_revision__ = versions['full-revisionid']
+__version__ = versions["version"]
+__git_revision__ = versions["full-revisionid"]
 del get_versions, versions

reference_handler/latex_utf8.py

@@ -70,54 +70,53 @@
 import typing
 import unicodedata
 
-alphabet = 'ABCDEFGHIJKLMNOPQRSTUVWXYZabcdefghijklmnopqrstuvwxyz'
+alphabet = "ABCDEFGHIJKLMNOPQRSTUVWXYZabcdefghijklmnopqrstuvwxyz"
 
 # LaTeX characters in accent macros of form \<char>{<letter>}, i.e. \"{u}
 accent = {
-    '"': '\N{Combining Diaeresis}',
-    "'": '\N{Combining Acute Accent}',
-    '.': '\N{Combining Dot Above}',
-    '=': '\N{Combining Macron}',
-    '^': '\N{Combining Circumflex Accent}',
-    '`': '\N{Combining Grave Accent}',
-    '|': '\N{Combining Vertical Line Above}',
-    '~': '\N{Combining Tilde}',
-    'b': '\N{Combining Macron Below}',
-    'c': '\N{Combining Cedilla}',
-    'C': '\N{Combining Double Grave Accent}',
-    'd': '\N{Combining Dot Below}',
-    'f': '\N{Combining Inverted Breve}',
-    'h': '\N{Combining Hook Above}',
-    'H': '\N{Combining Double Acute Accent}',
-    'k': '\N{Combining Ogonek}',
-    'r': '\N{Combining Ring Above}',
-    't': '\N{Combining Double Inverted Breve}',
-    'u': '\N{Combining Breve}',
-    'U': '\N{Combining Double Vertical Line Above}',
-    'v': '\N{Combining Caron}'
+    '"': "\N{COMBINING DIAERESIS}",
+    "'": "\N{COMBINING ACUTE ACCENT}",
+    ".": "\N{COMBINING DOT ABOVE}",
+    "=": "\N{COMBINING MACRON}",
+    "^": "\N{COMBINING CIRCUMFLEX ACCENT}",
+    "`": "\N{COMBINING GRAVE ACCENT}",
+    "|": "\N{COMBINING VERTICAL LINE ABOVE}",
+    "~": "\N{COMBINING TILDE}",
+    "b": "\N{COMBINING MACRON BELOW}",
+    "c": "\N{COMBINING CEDILLA}",
+    "C": "\N{COMBINING DOUBLE GRAVE ACCENT}",
+    "d": "\N{COMBINING DOT BELOW}",
+    "f": "\N{COMBINING INVERTED BREVE}",
+    "h": "\N{COMBINING HOOK ABOVE}",
+    "H": "\N{COMBINING DOUBLE ACUTE ACCENT}",
+    "k": "\N{COMBINING OGONEK}",
+    "r": "\N{COMBINING RING ABOVE}",
+    "t": "\N{COMBINING DOUBLE INVERTED BREVE}",
+    "u": "\N{COMBINING BREVE}",
+    "U": "\N{COMBINING DOUBLE VERTICAL LINE ABOVE}",
+    "v": "\N{COMBINING CARON}",
 }
 
 # The regexp to detect the LaTeX accent commands. The two added characters
 # are the dotless i and j.
-accent_re = re.compile(
-    r'\\([' + ''.join(accent.keys()) + r']){([a-zA-Z\u0131\u0237])}'
-)
+accent_re = re.compile(r"\\([" + "".join(accent.keys()) + r"]){([a-zA-Z\u0131\u0237])}")
 
 # Invert the accent dictionary for each letter in the alphabet to make
 # a dictionary of LaTeX encodings.
 encoding = {}
 for key, val in accent.items():
     for char in list(alphabet):
-        encoding[char + val] = '\\' + key + '{' + char + '}'
+        encoding[char + val] = "\\" + key + "{" + char + "}"
         # handle any precombined versions of the character
-        string = unicodedata.normalize('NFC', char + val)
+        string = unicodedata.normalize("NFC", char + val)
         if len(string) == 1:
             encoding[string] = encoding[char + val]
     for char in [
-        '\N{Latin Small Letter Dotless I}', '\N{Latin Small Letter Dotless J}'
+        "\N{LATIN SMALL LETTER DOTLESS I}",
+        "\N{LATIN SMALL LETTER DOTLESS J}",
     ]:
-        encoding[char + val] = r'\%s{%s}' % (key, char)
-        string = unicodedata.normalize('NFC', char + val)
+        encoding[char + val] = r"\%s{%s}" % (key, char)
+        string = unicodedata.normalize("NFC", char + val)
         # These characters have no precombined versions, but check anyway
         if len(string) == 1:
             encoding[string] = encoding[char + val]
@@ -137,20 +136,20 @@ def _decode_latex_accent(match: typing.Match) -> str:
 
 # LaTeX single character symbols
 symbol = {
-    'i': '\N{Latin Small Letter Dotless I}',
-    'j': '\N{Latin Small Letter Dotless J}',
-    'l': '\N{Latin Small Letter L With Stroke}',
-    'L': '\N{Latin Capital Letter L With Stroke}',
-    'o': '\N{Latin Small Letter O With Stroke}',
-    'O': '\N{Latin Capital Letter O With Stroke}'
+    "i": "\N{LATIN SMALL LETTER DOTLESS I}",
+    "j": "\N{LATIN SMALL LETTER DOTLESS J}",
+    "l": "\N{LATIN SMALL LETTER L WITH STROKE}",
+    "L": "\N{LATIN CAPITAL LETTER L WITH STROKE}",
+    "o": "\N{LATIN SMALL LETTER O WITH STROKE}",
+    "O": "\N{LATIN CAPITAL LETTER O WITH STROKE}",
 }
 
 # The regexp to detect the LaTeX commands for special characters
-symbol_re = re.compile(r'\\([' + ''.join(symbol.keys()) + '])')
+symbol_re = re.compile(r"\\([" + "".join(symbol.keys()) + "])")
 
 # Invert the symbol dictionary to make a dictionary of LaTeX encodings.
 for key, val in symbol.items():
-    encoding[val] = '\\' + key
+    encoding[val] = "\\" + key
 
 
 def _decode_latex_symbol(match: typing.Match) -> str:
@@ -166,10 +165,10 @@ def _decode_latex_symbol(match: typing.Match) -> str:
 
 
 # LaTeX dashes
-dash = {'--': '\N{EN Dash}', '---': '\N{EM Dash}'}
+dash = {"--": "\N{EN DASH}", "---": "\N{EM DASH}"}
 
 # The regexp to detect the LaTeX commands for dashes
-dash_re = re.compile(r'([^-]?)(-{2,3})([^-]?)')
+dash_re = re.compile(r"([^-]?)(-{2,3})([^-]?)")
 
 # Invert the dictionary tomake a dictionary of LaTeX encodings.
 for key, val in dash.items():
@@ -205,13 +204,11 @@ def decode_latex(text: str) -> str:
     """
 
     return brace_re.sub(
-        r'\1',
+        r"\1",
         accent_re.sub(
             _decode_latex_accent,
-            symbol_re.sub(
-                _decode_latex_symbol, dash_re.sub(_decode_latex_dash, text)
-            )
-        )
+            symbol_re.sub(_decode_latex_symbol, dash_re.sub(_decode_latex_dash, text)),
+        ),
     )
 
 
@@ -228,7 +225,7 @@ def encode_latex(text: str) -> str:
     """
 
     # Map the double character representations
-    text2 = ''
+    text2 = ""
     char1 = text[0]
     i = 1
     len_text = len(text)
@@ -250,7 +247,7 @@ def encode_latex(text: str) -> str:
         text2 += char1
 
     # Map the single characters representations
-    result = ''
+    result = ""
     for char in list(text2):
         if char in encoding:
             result += encoding[char]
@@ -260,7 +257,7 @@ def encode_latex(text: str) -> str:
     return result
 
 
-if __name__ == '__main__':  # pragma: no cover
+if __name__ == "__main__":  # pragma: no cover
     text = r"""
 (Vorlova_2015) Barbora Vorlov{\'{a}} and Dana Nachtigallov{\'{a}} and Jana
 Jir{\'{a}}skov{\'{a}}-Van{\'{\i}}{\v{c}}kov{\'{a}} and Haresh Ajani and Petr