From 9643c71e4869b89e72bbcd1459e6bc872c00835a Mon Sep 17 00:00:00 2001
From: Christophe Demko <chdemko@gmail.com>
Date: Thu, 18 Jan 2024 12:51:35 +0100
Subject: [PATCH 1/6] Update pandoc version

---
 .github/workflows/python-package.yml | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/.github/workflows/python-package.yml b/.github/workflows/python-package.yml
index 010c092..804822c 100644
--- a/.github/workflows/python-package.yml
+++ b/.github/workflows/python-package.yml
@@ -16,7 +16,7 @@ jobs:
       matrix:
         python-version: ['3.9', '3.10', '3.11', '3.12']
         poetry-version: [1.7.1]
-        pandoc-version: [3.1.9]
+        pandoc-version: [3.1.11.1]
     steps:
     - uses: actions/checkout@v4
     - name: Set up Python ${{ matrix.python-version }}
@@ -42,7 +42,7 @@ jobs:
       matrix:
         python-version: ['3.12']
         poetry-version: [1.2.2, 1.3.2, 1.4.2, 1.5.1, 1.6.1, 1.7.1]
-        pandoc-version: [3.1.9]
+        pandoc-version: [3.1.11.1]
     steps:
     - uses: actions/checkout@v4
     - name: Set up Python ${{ matrix.python-version }}
@@ -68,7 +68,7 @@ jobs:
       matrix:
         python-version: ['3.12']
         poetry-version: [1.7.1]
-        pandoc-version: [2.14.2, '2.15', 2.16.2, 2.17.1.1, '2.18', 2.19.2, 3.0.1, 3.1.9]
+        pandoc-version: [2.14.2, '2.15', 2.16.2, 2.17.1.1, '2.18', 2.19.2, 3.0.1, 3.1.11.1]
     steps:
     - uses: actions/checkout@v4
     - name: Set up Python ${{ matrix.python-version }}
@@ -122,8 +122,8 @@ jobs:
         poetry-version: 1.7.1
     - name: Install dependencies
       run: |
-        wget https://github.com/jgm/pandoc/releases/download/3.1.9/pandoc-3.1.9-1-amd64.deb
-        sudo dpkg -i ./pandoc-3.1.9-1-amd64.deb
+        wget https://github.com/jgm/pandoc/releases/download/3.1.11.1/pandoc-3.1.11.1-1-amd64.deb
+        sudo dpkg -i ./pandoc-3.1.11.1-1-amd64.deb
         poetry install
     - name: Test
       env:

From c44aaf731a51eac8d85bce622723ec61a5fc477c Mon Sep 17 00:00:00 2001
From: Christophe Demko <chdemko@gmail.com>
Date: Sun, 21 Jan 2024 11:31:09 +0100
Subject: [PATCH 2/6] Update project

---
 poetry.lock | 112 ++++++++++++++++++++++++++++------------------------
 1 file changed, 61 insertions(+), 51 deletions(-)

diff --git a/poetry.lock b/poetry.lock
index 66ebb6e..83fac8d 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -983,61 +983,71 @@ testing = ["coverage", "pytest", "pytest-cov", "pytest-regressions"]
 
 [[package]]
 name = "markupsafe"
-version = "2.1.3"
+version = "2.1.4"
 description = "Safely add untrusted strings to HTML/XML markup."
 optional = false
 python-versions = ">=3.7"
 files = [
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+    {file = "MarkupSafe-2.1.4-cp37-cp37m-win_amd64.whl", hash = "sha256:d6e427c7378c7f1b2bef6a344c925b8b63623d3321c09a237b7cc0e77dd98ceb"},
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+    {file = "MarkupSafe-2.1.4-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:23984d1bdae01bee794267424af55eef4dfc038dc5d1272860669b2aa025c9e3"},
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+    {file = "MarkupSafe-2.1.4-cp39-cp39-macosx_10_9_universal2.whl", hash = "sha256:765f036a3d00395a326df2835d8f86b637dbaf9832f90f5d196c3b8a7a5080cb"},
+    {file = "MarkupSafe-2.1.4-cp39-cp39-macosx_10_9_x86_64.whl", hash = "sha256:21e7af8091007bf4bebf4521184f4880a6acab8df0df52ef9e513d8e5db23411"},
+    {file = "MarkupSafe-2.1.4-cp39-cp39-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:d5c31fe855c77cad679b302aabc42d724ed87c043b1432d457f4976add1c2c3e"},
+    {file = "MarkupSafe-2.1.4-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:7653fa39578957bc42e5ebc15cf4361d9e0ee4b702d7d5ec96cdac860953c5b4"},
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+    {file = "MarkupSafe-2.1.4-cp39-cp39-musllinux_1_1_aarch64.whl", hash = "sha256:fe8512ed897d5daf089e5bd010c3dc03bb1bdae00b35588c49b98268d4a01e00"},
+    {file = "MarkupSafe-2.1.4-cp39-cp39-musllinux_1_1_i686.whl", hash = "sha256:36d7626a8cca4d34216875aee5a1d3d654bb3dac201c1c003d182283e3205949"},
+    {file = "MarkupSafe-2.1.4-cp39-cp39-musllinux_1_1_x86_64.whl", hash = "sha256:b6f14a9cd50c3cb100eb94b3273131c80d102e19bb20253ac7bd7336118a673a"},
+    {file = "MarkupSafe-2.1.4-cp39-cp39-win32.whl", hash = "sha256:c8f253a84dbd2c63c19590fa86a032ef3d8cc18923b8049d91bcdeeb2581fbf6"},
+    {file = "MarkupSafe-2.1.4-cp39-cp39-win_amd64.whl", hash = "sha256:8b570a1537367b52396e53325769608f2a687ec9a4363647af1cded8928af959"},
+    {file = "MarkupSafe-2.1.4.tar.gz", hash = "sha256:3aae9af4cac263007fd6309c64c6ab4506dd2b79382d9d19a1994f9240b8db4f"},
 ]
 
 [[package]]

From 6db32a5afeb9c313cc00c303f0d9b38e3e9af80c Mon Sep 17 00:00:00 2001
From: Christophe Demko <chdemko@gmail.com>
Date: Sun, 21 Jan 2024 13:30:24 +0100
Subject: [PATCH 3/6] Normalize files

---
 .github/workflows/python-publish.yml | 8 +++-----
 1 file changed, 3 insertions(+), 5 deletions(-)

diff --git a/.github/workflows/python-publish.yml b/.github/workflows/python-publish.yml
index 9d68754..c7c77d6 100644
--- a/.github/workflows/python-publish.yml
+++ b/.github/workflows/python-publish.yml
@@ -9,9 +9,7 @@ on:
 
 jobs:
   deploy:
-
     runs-on: ubuntu-latest
-
     steps:
     - uses: actions/checkout@v4
       with:
@@ -24,13 +22,13 @@ jobs:
       uses: abatilo/actions-poetry@v2
       with:
         poetry-version: 1.7.1
+    - name: Set up poetry-dynamic-versioning
+      run: |
+        poetry self add "poetry-dynamic-versioning[plugin]"        
     - name: Install dependencies
       run: |
         poetry install
         poetry run pip install twine
-    - name: Set up poetry-dynamic-versioning
-      run: |
-        poetry self add "poetry-dynamic-versioning[plugin]"        
     - name: Build and publish
       env:
         TWINE_USERNAME: ${{ secrets.PYPI_USERNAME }}

From 364ac0dfb1ea3656037ed876decbcdfab20c5da6 Mon Sep 17 00:00:00 2001
From: Christophe Demko <chdemko@gmail.com>
Date: Sun, 21 Jan 2024 16:16:33 +0100
Subject: [PATCH 4/6] Update sphinx_rtd_theme

---
 .github/workflows/python-publish.yml |  2 +-
 poetry.lock                          | 22 +++++++++++-----------
 pyproject.toml                       |  2 +-
 3 files changed, 13 insertions(+), 13 deletions(-)

diff --git a/.github/workflows/python-publish.yml b/.github/workflows/python-publish.yml
index c7c77d6..a768d89 100644
--- a/.github/workflows/python-publish.yml
+++ b/.github/workflows/python-publish.yml
@@ -24,7 +24,7 @@ jobs:
         poetry-version: 1.7.1
     - name: Set up poetry-dynamic-versioning
       run: |
-        poetry self add "poetry-dynamic-versioning[plugin]"        
+        poetry self add "poetry-dynamic-versioning[plugin]"
     - name: Install dependencies
       run: |
         poetry install
diff --git a/poetry.lock b/poetry.lock
index 83fac8d..d34c1b9 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -434,13 +434,13 @@ stevedore = "*"
 
 [[package]]
 name = "docutils"
-version = "0.18.1"
+version = "0.20.1"
 description = "Docutils -- Python Documentation Utilities"
 optional = false
-python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*"
+python-versions = ">=3.7"
 files = [
-    {file = "docutils-0.18.1-py2.py3-none-any.whl", hash = "sha256:23010f129180089fbcd3bc08cfefccb3b890b0050e1ca00c867036e9d161b98c"},
-    {file = "docutils-0.18.1.tar.gz", hash = "sha256:679987caf361a7539d76e584cbeddc311e3aee937877c87346f31debc63e9d06"},
+    {file = "docutils-0.20.1-py3-none-any.whl", hash = "sha256:96f387a2c5562db4476f09f13bbab2192e764cac08ebbf3a34a95d9b1e4a59d6"},
+    {file = "docutils-0.20.1.tar.gz", hash = "sha256:f08a4e276c3a1583a86dce3e34aba3fe04d02bba2dd51ed16106244e8a923e3b"},
 ]
 
 [[package]]
@@ -1677,18 +1677,18 @@ test = ["cython (>=3.0)", "filelock", "html5lib", "pytest (>=4.6)", "setuptools
 
 [[package]]
 name = "sphinx-rtd-theme"
-version = "1.3.0"
+version = "2.0.0"
 description = "Read the Docs theme for Sphinx"
 optional = false
-python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,!=3.5.*,>=2.7"
+python-versions = ">=3.6"
 files = [
-    {file = "sphinx_rtd_theme-1.3.0-py2.py3-none-any.whl", hash = "sha256:46ddef89cc2416a81ecfbeaceab1881948c014b1b6e4450b815311a89fb977b0"},
-    {file = "sphinx_rtd_theme-1.3.0.tar.gz", hash = "sha256:590b030c7abb9cf038ec053b95e5380b5c70d61591eb0b552063fbe7c41f0931"},
+    {file = "sphinx_rtd_theme-2.0.0-py2.py3-none-any.whl", hash = "sha256:ec93d0856dc280cf3aee9a4c9807c60e027c7f7b461b77aeffed682e68f0e586"},
+    {file = "sphinx_rtd_theme-2.0.0.tar.gz", hash = "sha256:bd5d7b80622406762073a04ef8fadc5f9151261563d47027de09910ce03afe6b"},
 ]
 
 [package.dependencies]
-docutils = "<0.19"
-sphinx = ">=1.6,<8"
+docutils = "<0.21"
+sphinx = ">=5,<8"
 sphinxcontrib-jquery = ">=4,<5"
 
 [package.extras]
@@ -2041,4 +2041,4 @@ testing = ["big-O", "jaraco.functools", "jaraco.itertools", "more-itertools", "p
 [metadata]
 lock-version = "2.0"
 python-versions = "^3.9"
-content-hash = "425d3e17453df7073a8da12e6114de73464c3630b629090c795b92de51208516"
+content-hash = "fc6654e687730a6888ea6d05f3528797bbf2e9d771ea7f24283bd1f353f9627d"
diff --git a/pyproject.toml b/pyproject.toml
index 51ee7f1..af749dd 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -90,7 +90,7 @@ optional = true
 [tool.poetry.group.docs.dependencies]
 myst-parser = "^2.0"
 sphinx = "^7.2"
-sphinx_rtd_theme = "^1.3"
+sphinx_rtd_theme = "^2.0"
 
 [tool.poetry.scripts]
 pandoc-numbering = "pandoc_numbering:main"

From 7bf5fe99f95835072a0fd0043ea2bf7e615db2b9 Mon Sep 17 00:00:00 2001
From: Christophe Demko <chdemko@gmail.com>
Date: Sun, 21 Jan 2024 21:31:04 +0100
Subject: [PATCH 5/6] Finish poetry-dynamic-versioning

---
 README.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/README.md b/README.md
index 15f0850..e1cb4eb 100644
--- a/README.md
+++ b/README.md
@@ -42,7 +42,7 @@ $ pipx install pandoc-numbering
 To upgrade to the most recent release, use
 
 ~~~shell
-$ pipx install --upgrade pandoc-numbering
+$ pipx upgrade pandoc-numbering
 ~~~
 
 `pipx` is a script to install and run python applications in isolated environments from the Python Package Index, [PyPI]. It can be installed using instructions given [here](https://pipx.pypa.io/stable/).

From 0379af3f7d8d0befdb62f99bc6781aad67710d0a Mon Sep 17 00:00:00 2001
From: Christophe Demko <chdemko@gmail.com>
Date: Mon, 22 Jan 2024 11:35:19 +0100
Subject: [PATCH 6/6] Get pandoc-crossref compatibility

---
 pandoc_numbering.py            | 18 ++++++++++++++-
 tests/test_listings_meta.py    | 42 ++++++++++++++++++++++++++++++----
 tests/test_para.py             | 21 +++++++++++++++--
 tests/test_referencing.py      | 21 +++++++++++++++--
 tests/test_referencing_meta.py | 42 ++++++++++++++++++++++++++++++----
 5 files changed, 131 insertions(+), 13 deletions(-)

diff --git a/pandoc_numbering.py b/pandoc_numbering.py
index 7fef409..127335f 100644
--- a/pandoc_numbering.py
+++ b/pandoc_numbering.py
@@ -8,6 +8,7 @@
 import re
 import unicodedata
 from functools import partial
+from textwrap import dedent
 
 from panflute import (
     BlockQuote,
@@ -1520,7 +1521,22 @@ def finalize(doc):
             doc.metadata["header-includes"] = MetaList(doc.metadata["header-includes"])
 
         doc.metadata["header-includes"].append(
-            MetaInlines(RawInline(r"\usepackage{tocloft}", "tex"))
+            MetaInlines(
+                RawInline(
+                    dedent(
+                        r"""
+                        \makeatletter
+                        \@ifpackageloaded{subfig}{
+                            \usepackage[subfigure]{tocloft}
+                        }{
+                            \usepackage{tocloft}
+                        }
+                        \makeatother
+                        """
+                    ),
+                    "tex",
+                )
+            )
         )
         doc.metadata["header-includes"].append(
             MetaInlines(RawInline(r"\usepackage{etoolbox}", "tex"))
diff --git a/tests/test_listings_meta.py b/tests/test_listings_meta.py
index 8841bab..c3d5a2f 100644
--- a/tests/test_listings_meta.py
+++ b/tests/test_listings_meta.py
@@ -168,7 +168,16 @@ def test_listing_latex(self):
             r"""
 ---
 header-includes:
-- "`\\usepackage{tocloft}`{=tex}"
+- |
+  `
+  \makeatletter
+  \@ifpackageloaded{subfig}{
+      \usepackage[subfigure]{tocloft}
+  }{
+      \usepackage{tocloft}
+  }
+  \makeatother
+  `{=tex}
 - "`\\usepackage{etoolbox}`{=tex}"
 - "`\\newlistof{exercise}{exercise}{List of exercises}\\renewcommand{\\cftexercisetitlefont}{\\cfttoctitlefont}\\setlength{\\cftexercisenumwidth}{\\cftfignumwidth}\\setlength{\\cftexerciseindent}{\\cftfigindent}`{=tex}"
 - "`\\ifdef{\\mainmatter}{\\let\\oldmainmatter\\mainmatter\\renewcommand{\\mainmatter}[0]{\\listofexercise\\oldmainmatter}}{}`{=tex}"
@@ -178,7 +187,15 @@ def test_listing_latex(self):
       listing-title: List of exercises
 ---
 
-`\usepackage{tocloft}`{=tex}
+`
+\makeatletter
+\@ifpackageloaded{subfig}{
+    \usepackage[subfigure]{tocloft}
+}{
+    \usepackage{tocloft}
+}
+\makeatother
+`{=tex}
 
 `\usepackage{etoolbox}`{=tex}
 
@@ -260,7 +277,16 @@ def test_listing_latex_format(self):
             r"""
 ---
 header-includes:
-- "`\\usepackage{tocloft}`{=tex}"
+- |
+  `
+  \makeatletter
+  \@ifpackageloaded{subfig}{
+      \usepackage[subfigure]{tocloft}
+  }{
+      \usepackage{tocloft}
+  }
+  \makeatother
+  `{=tex}
 - "`\\usepackage{etoolbox}`{=tex}"
 - "`\\newlistof{exercise}{exercise}{List of exercises}\\renewcommand{\\cftexercisetitlefont}{\\cfttoctitlefont}\\setlength{\\cftexercisenumwidth}{\\cftfignumwidth}\\setlength{\\cftexerciseindent}{\\cftfigindent}`{=tex}"
 - "`\\ifdef{\\mainmatter}{\\let\\oldmainmatter\\mainmatter\\renewcommand{\\mainmatter}[0]{\\listofexercise\\oldmainmatter}}{}`{=tex}"
@@ -276,7 +302,15 @@ def test_listing_latex_format(self):
 toccolor: blue
 ---
 
-`\usepackage{tocloft}`{=tex}
+`
+\makeatletter
+\@ifpackageloaded{subfig}{
+    \usepackage[subfigure]{tocloft}
+}{
+    \usepackage{tocloft}
+}
+\makeatother
+`{=tex}
 
 `\usepackage{etoolbox}`{=tex}
 
diff --git a/tests/test_para.py b/tests/test_para.py
index e8b5020..1410a31 100644
--- a/tests/test_para.py
+++ b/tests/test_para.py
@@ -196,12 +196,29 @@ def test_numbering_latex(self):
             r"""
 ---
 header-includes:
-- "`\\usepackage{tocloft}`{=tex}"
+- |
+  `
+  \makeatletter
+  \@ifpackageloaded{subfig}{
+      \usepackage[subfigure]{tocloft}
+  }{
+      \usepackage{tocloft}
+  }
+  \makeatother
+  `{=tex}
 - "`\\usepackage{etoolbox}`{=tex}"
 - "`\\ifdef{\\mainmatter}{\\let\\oldmainmatter\\mainmatter\\renewcommand{\\mainmatter}[0]{\\oldmainmatter}}{}`{=tex}"
 ---
 
-`\usepackage{tocloft}`{=tex}
+`
+\makeatletter
+\@ifpackageloaded{subfig}{
+    \usepackage[subfigure]{tocloft}
+}{
+    \usepackage{tocloft}
+}
+\makeatother
+`{=tex}
 
 `\usepackage{etoolbox}`{=tex}
 
diff --git a/tests/test_referencing.py b/tests/test_referencing.py
index 26fd6b9..ab7a0f7 100644
--- a/tests/test_referencing.py
+++ b/tests/test_referencing.py
@@ -57,12 +57,29 @@ def test_referencing_latex(self):
             r"""
 ---
 header-includes:
-- "`\\usepackage{tocloft}`{=tex}"
+- |
+  `
+  \makeatletter
+  \@ifpackageloaded{subfig}{
+      \usepackage[subfigure]{tocloft}
+  }{
+      \usepackage{tocloft}
+  }
+  \makeatother
+  `{=tex}
 - "`\\usepackage{etoolbox}`{=tex}"
 - "`\\ifdef{\\mainmatter}{\\let\\oldmainmatter\\mainmatter\\renewcommand{\\mainmatter}[0]{\\oldmainmatter}}{}`{=tex}"
 ---
 
-`\usepackage{tocloft}`{=tex}
+`
+\makeatletter
+\@ifpackageloaded{subfig}{
+    \usepackage[subfigure]{tocloft}
+}{
+    \usepackage{tocloft}
+}
+\makeatother
+`{=tex}
 
 `\usepackage{etoolbox}`{=tex}
 
diff --git a/tests/test_referencing_meta.py b/tests/test_referencing_meta.py
index 7887f5f..dc809ef 100644
--- a/tests/test_referencing_meta.py
+++ b/tests/test_referencing_meta.py
@@ -82,7 +82,16 @@ def test_referencing_link_latex(self):
             r"""
 ---
 header-includes:
-- "`\\usepackage{tocloft}`{=tex}"
+- |
+  `
+  \makeatletter
+  \@ifpackageloaded{subfig}{
+      \usepackage[subfigure]{tocloft}
+  }{
+      \usepackage{tocloft}
+  }
+  \makeatother
+  `{=tex}
 - "`\\usepackage{etoolbox}`{=tex}"
 - "`\\ifdef{\\mainmatter}{\\let\\oldmainmatter\\mainmatter\\renewcommand{\\mainmatter}[0]{\\oldmainmatter}}{}`{=tex}"
 pandoc-numbering:
@@ -94,7 +103,15 @@ def test_referencing_link_latex(self):
       format-link-title: "**%D %d %T %t %g %s %n %p**"
 ---
 
-`\usepackage{tocloft}`{=tex}
+`
+\makeatletter
+\@ifpackageloaded{subfig}{
+    \usepackage[subfigure]{tocloft}
+}{
+    \usepackage{tocloft}
+}
+\makeatother
+`{=tex}
 
 `\usepackage{etoolbox}`{=tex}
 
@@ -192,7 +209,16 @@ def test_referencing_caption_latex(self):
             r"""
 ---
 header-includes:
-- "`\\usepackage{tocloft}`{=tex}"
+- |
+  `
+  \makeatletter
+  \@ifpackageloaded{subfig}{
+      \usepackage[subfigure]{tocloft}
+  }{
+      \usepackage{tocloft}
+  }
+  \makeatother
+  `{=tex}
 - "`\\usepackage{etoolbox}`{=tex}"
 - "`\\ifdef{\\mainmatter}{\\let\\oldmainmatter\\mainmatter\\renewcommand{\\mainmatter}[0]{\\oldmainmatter}}{}`{=tex}"
 pandoc-numbering:
@@ -204,7 +230,15 @@ def test_referencing_caption_latex(self):
       format-caption-title: "%D %d %T %t %g %s %n %c %p"
 ---
 
-`\usepackage{tocloft}`{=tex}
+`
+\makeatletter
+\@ifpackageloaded{subfig}{
+    \usepackage[subfigure]{tocloft}
+}{
+    \usepackage{tocloft}
+}
+\makeatother
+`{=tex}
 
 `\usepackage{etoolbox}`{=tex}