From 646691b4b7c9147b96ff2c24e68ffeed7e8c4249 Mon Sep 17 00:00:00 2001
From: yuanx749 <yuanx749@gmail.com>
Date: Mon, 13 Nov 2023 00:34:02 +0800
Subject: [PATCH] Use Markdown link to target in notebook

- was blocked by myst-nb
- upgrade docs dependencies
---
 .github/workflows/sphinx.yml |  8 ++++----
 docs/examples/examples.ipynb |  4 ++--
 docs/make.bat                | 35 +++++++++++++++++++++++++++++++++++
 pycdhit/__init__.py          |  2 +-
 pyproject.toml               | 10 +++++-----
 5 files changed, 47 insertions(+), 12 deletions(-)
 create mode 100644 docs/make.bat

diff --git a/.github/workflows/sphinx.yml b/.github/workflows/sphinx.yml
index e51a196..7840e28 100644
--- a/.github/workflows/sphinx.yml
+++ b/.github/workflows/sphinx.yml
@@ -8,10 +8,10 @@ jobs:
   build:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
       - uses: actions/setup-python@v4
         with:
-          python-version: '3.8'
+          python-version: '3.10'
           cache: 'pip'
           cache-dependency-path: pyproject.toml
       - name: Install dependencies
@@ -22,7 +22,7 @@ jobs:
         run: make html
         working-directory: docs
       - name: Upload artifacts
-        uses: actions/upload-pages-artifact@v1
+        uses: actions/upload-pages-artifact@v2
         with:
           path: docs/_build/html/
 
@@ -38,4 +38,4 @@ jobs:
     steps:
       - name: Deploy to GitHub Pages
         id: deployment
-        uses: actions/deploy-pages@v1
+        uses: actions/deploy-pages@v2
diff --git a/docs/examples/examples.ipynb b/docs/examples/examples.ipynb
index fcf322d..b2e1b23 100644
--- a/docs/examples/examples.ipynb
+++ b/docs/examples/examples.ipynb
@@ -24,7 +24,7 @@
    "metadata": {},
    "source": [
     "## Higher level interface\n",
-    "Work on `DataFrame` using classes."
+    "Work on [DataFrame](#pandas.DataFrame) using classes."
    ]
   },
   {
@@ -41,7 +41,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "Read a fasta file as a `DataFrame` containing some amino acid sequences."
+    "Read a fasta file as a [DataFrame](#pandas.DataFrame) containing some amino acid sequences."
    ]
   },
   {
diff --git a/docs/make.bat b/docs/make.bat
new file mode 100644
index 0000000..32bb245
--- /dev/null
+++ b/docs/make.bat
@@ -0,0 +1,35 @@
+@ECHO OFF
+
+pushd %~dp0
+
+REM Command file for Sphinx documentation
+
+if "%SPHINXBUILD%" == "" (
+	set SPHINXBUILD=sphinx-build
+)
+set SOURCEDIR=.
+set BUILDDIR=_build
+
+%SPHINXBUILD% >NUL 2>NUL
+if errorlevel 9009 (
+	echo.
+	echo.The 'sphinx-build' command was not found. Make sure you have Sphinx
+	echo.installed, then set the SPHINXBUILD environment variable to point
+	echo.to the full path of the 'sphinx-build' executable. Alternatively you
+	echo.may add the Sphinx directory to PATH.
+	echo.
+	echo.If you don't have Sphinx installed, grab it from
+	echo.https://www.sphinx-doc.org/
+	exit /b 1
+)
+
+if "%1" == "" goto help
+
+%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+goto end
+
+:help
+%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+
+:end
+popd
diff --git a/pycdhit/__init__.py b/pycdhit/__init__.py
index 952b676..27fe23f 100644
--- a/pycdhit/__init__.py
+++ b/pycdhit/__init__.py
@@ -4,7 +4,7 @@
 from ._commands import *  # noqa: F403
 from ._io import *  # noqa: F403
 
-VERSION = "0.5.0"
+VERSION = "0.5.1"
 
 __all__ = [  # noqa: F405
     "CommandBase",
diff --git a/pyproject.toml b/pyproject.toml
index fe15fb3..250e68c 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -32,11 +32,11 @@ dev = [
     "pytest-cov>=4.0.0",
 ]
 doc = [
-    "sphinx==5.3.0",
-    "furo==2022.12.7",
-    "myst-nb==0.17.1",
-    "myst-parser==0.18.1",
-    "sphinx-copybutton==0.5.1",
+    "sphinx==7.2.6",
+    "furo==2023.9.10",
+    "myst-nb==1.0.0",
+    "myst-parser==2.0.0",
+    "sphinx-copybutton==0.5.2",
     "notebook>=6.5.4",
 ]