update sphinx comparison

docs/conf.py

@@ -49,6 +49,7 @@
 
 linkcheck_anchors = False
 linkcheck_retries = 5
+linkcheck_report_timeouts_as_broken = False
 linkcheck_ignore = [
     'http://localhost:8080/ga4gh/wes/v1', 'https://support.orcid.org/hc/en-us/articles/360006894754-Edit-works',
     'https://dx.doi.org/10.12688/f1000research.10137.1', 'https://dockstore.org/api/',

docs/docker_instructions.md

@@ -6,7 +6,7 @@ The Docker CLI is a command-line tool with a whole library of commands for inter
 
 
 ### Part A - Running Containers
-In this section you will try running a basic container called whalesay. Refer to the [part A readings](#part-a-readings) if you need a refresher on the content taught in the training.
+In this section you will try running a basic container called whalesay. Refer to part A below if you need a refresher on the content taught in the training.
 
 Run whalesay with the following command:
 ```shell
@@ -36,7 +36,7 @@ docker run docker/whalesay cowsay "hello"
 Now try getting the whale to say "Hello [your name]!".
 
 ### Part B - Exploring Containers
-We will now try running a container with [Samtools](https://www.htslib.org/) installed to convert a SAM file to a BAM file. Refer to the [part B readings](#part-b-readings) if you need a refresher on the content taught in the training.
+We will now try running a container with [Samtools](https://www.htslib.org/) installed to convert a SAM file to a BAM file. Refer to the part b below if you need a refresher on the content taught in the training.
 
 #### Sharing data between host and container
 Here we will map the `/root/bcc2020-training/data` on the host machine to `/data` on the container. Then we will confirm that the files in `/root/bcc2020-training/data` are available on the container.

requirements.in

@@ -0,0 +1,5 @@
+sphinx==7.4.7
+glossarpy==0.1.2
+sphinxcontrib-discourse @ git+https://github.com/pdavide/sphinxcontrib-discourse@02453dff2c56b14987cf662cfd8cddb3b31b0dd7
+myst-parser==3.0.0
+sphinx-rtd-theme==2.0.0

requirements.txt

@@ -1,32 +1,80 @@
+#
+# This file is autogenerated by pip-compile with Python 3.10
+# by the following command:
+#
+#    pip-compile
+#
 alabaster==0.7.16
-attrs==21.4.0
-Babel==2.14.0
+    # via sphinx
+babel==2.14.0
+    # via sphinx
 certifi==2024.7.4
+    # via requests
 charset-normalizer==3.3.2
-docutils==0.17.1
+    # via requests
+docutils==0.20.1
+    # via
+    #   myst-parser
+    #   sphinx
+    #   sphinx-rtd-theme
 glossarpy==0.1.2
+    # via -r requirements.in
 idna==3.7
+    # via requests
 imagesize==1.4.1
-importlib-metadata==7.0.1
-Jinja2==3.1.4
-markdown-it-py==2.2.0
-MarkupSafe==2.1.3
-mdit-py-plugins==0.3.5
+    # via sphinx
+jinja2==3.1.4
+    # via
+    #   myst-parser
+    #   sphinx
+markdown-it-py==3.0.0
+    # via
+    #   mdit-py-plugins
+    #   myst-parser
+markupsafe==2.1.3
+    # via jinja2
+mdit-py-plugins==0.4.1
+    # via myst-parser
 mdurl==0.1.2
-myst-parser==0.16.1
+    # via markdown-it-py
+myst-parser==3.0.0
+    # via -r requirements.in
 packaging==23.2
-Pygments==2.17.2
-PyYAML==6.0.1
+    # via sphinx
+pygments==2.17.2
+    # via sphinx
+pyyaml==6.0.2
+    # via myst-parser
 requests==2.32.3
+    # via sphinx
 snowballstemmer==2.2.0
-Sphinx==4.4.0
-sphinx-rtd-theme==1.0.0
+    # via sphinx
+sphinx==7.4.7
+    # via
+    #   -r requirements.in
+    #   myst-parser
+    #   sphinx-rtd-theme
+    #   sphinxcontrib-discourse
+    #   sphinxcontrib-jquery
+sphinx-rtd-theme==2.0.0
+    # via -r requirements.in
 sphinxcontrib-applehelp==1.0.4
+    # via sphinx
 sphinxcontrib-devhelp==1.0.2
+    # via sphinx
 sphinxcontrib-discourse @ git+https://github.com/pdavide/sphinxcontrib-discourse@02453dff2c56b14987cf662cfd8cddb3b31b0dd7
+    # via -r requirements.in
 sphinxcontrib-htmlhelp==2.0.1
+    # via sphinx
+sphinxcontrib-jquery==4.1
+    # via sphinx-rtd-theme
 sphinxcontrib-jsmath==1.0.1
+    # via sphinx
 sphinxcontrib-qthelp==1.0.3
-sphinxcontrib-serializinghtml==1.1.5
+    # via sphinx
+sphinxcontrib-serializinghtml==2.0.0
+    # via sphinx
+tomli==2.0.1
+    # via sphinx
 urllib3==2.2.2
-zipp==3.19.1
+    # via requests