MyST-Parser: WARNING reference target not found, even though reference exists

Describe the bug

context After upgrading MyST-Parser to the latest version, we’re seeing these warnings while building our docs with Sphinx:

/home/runner/work/tango/tango/docs/source/CONTRIBUTING.md:154: WARNING: 'myst' reference target not found: #writing-docstrings
/home/runner/work/tango/tango/docs/source/CONTRIBUTING.md:179: WARNING: 'myst' reference target not found: #making-a-pull-request

MyST-Parser is complaining about internal header links in this file, such as on this line, even though those links clearly exists.

expectation No warnings.

problem This is causing a problem in our docs build, since we treat warnings as errors. We could silence these specific warnings, but I’d rather not do that since it could cause us to miss true positives in the future.

Reproduce the bug

git clone https://github.com/allenai/tango.git
cd tango
git checkout dependabot/pip/myst-parser-0.17.0
pip install -e '.[dev,all]'
make docs

List your environment

Python 3.9

absl-py==0.15.0
-e git+ssh://git@github.com/allenai/tango.git@f46379b9fac6cb77a2a5f8ef34a1fb208203d587#egg=ai2_tango
aiohttp==3.7.4.post0
alabaster==0.7.12
appnope==0.1.2
async-timeout==3.0.1
attrs==21.2.0
Babel==2.9.1
backcall==0.2.0
base58==2.1.0
beautifulsoup4==4.10.0
black==21.12b0
bleach==4.1.0
boto3==1.18.47
botocore==1.21.47
cached-path==1.0.2
cachetools==4.2.2
certifi==2021.5.30
chardet==4.0.0
charset-normalizer==2.0.6
click==8.0.3
click-help-colors==0.9.1
codecov==2.1.12
colorama==0.4.4
configparser==5.0.2
coverage==5.5
datasets==1.18.1
decorator==5.1.0
deepspeed==0.5.5
dill==0.3.4
distlib==0.3.4
docker-pycreds==0.4.0
docopt==0.6.2
docutils==0.17.1
fairscale==0.4.5
filelock==3.4.0
flake8==3.9.2
flaky==3.7.0
Flask==2.0.2
fsspec==2021.9.0
furo==2022.1.2
future==0.18.2
gitdb==4.0.7
GitPython==3.1.24
glob2==0.7
google-api-core==2.0.1
google-auth==2.1.0
google-auth-oauthlib==0.4.6
google-cloud-core==2.0.0
google-cloud-storage==1.42.2
google-crc32c==1.2.0
google-resumable-media==2.0.3
googleapis-common-protos==1.53.0
GPUtil==1.4.0
greenlet==1.1.1
grip==4.5.2
grpcio==1.41.1
huggingface-hub==0.2.1
idna==3.2
imagesize==1.2.0
importlib-metadata==4.8.1
iniconfig==1.1.1
ipython==7.28.0
isort==5.10.1
itsdangerous==2.0.1
jedi==0.18.0
Jinja2==3.0.1
jmespath==0.10.0
joblib==1.1.0
jsonnet==0.17.0
keyring==23.2.1
livereload==2.6.3
m2r==0.2.1
Markdown==3.3.4
markdown-it-py==1.1.0
MarkupSafe==2.0.1
matplotlib-inline==0.1.3
mccabe==0.6.1
mdit-py-plugins==0.3.0
mistune==0.8.4
more-itertools==8.10.0
msgpack==0.5.6
multidict==5.1.0
multiprocess==0.70.12.2
mypy==0.931
mypy-extensions==0.4.3
myst-parser==0.17.0
neovim==0.2.6
ninja==1.10.2.2
nltk==3.6.7
numpy==1.21.2
oauthlib==3.1.1
overrides==6.1.0
packaging==21.0
pandas==1.3.3
parso==0.8.2
path-and-address==2.0.1
pathspec==0.9.0
pathtools==0.1.2
petname==2.6
pexpect==4.8.0
pickleshare==0.7.5
Pillow==9.0.0
pkginfo==1.7.1
platformdirs==2.3.0
pluggy==1.0.0
promise==2.3
prompt-toolkit==3.0.20
protobuf==3.18.0
psutil==5.8.0
ptyprocess==0.7.0
py==1.10.0
pyarrow==5.0.0
pyasn1==0.4.8
pyasn1-modules==0.2.8
pycodestyle==2.7.0
pyDeprecate==0.3.1
pydocstyle==6.1.1
pyflakes==2.3.1
Pygments==2.10.0
pyparsing==2.4.7
pytest==6.2.5
pytest-cov==2.12.1
pytest-sphinx==0.3.1
python-dateutil==2.8.2
pytorch-lightning==1.5.9
pytz==2021.1
PyYAML==5.4.1
readme-renderer==29.0
regex==2021.8.28
requests==2.26.0
requests-oauthlib==1.3.0
requests-toolbelt==0.9.1
rfc3986==1.5.0
rouge-score==0.0.4
rsa==4.7.2
s3transfer==0.5.0
sacremoses==0.0.46
sentencepiece==0.1.96
sentry-sdk==1.4.3
shortuuid==1.0.1
six==1.16.0
smmap==4.0.0
snowballstemmer==2.1.0
soupsieve==2.2.1
Sphinx==4.4.0
sphinx-autobuild==2021.3.14
sphinx-copybutton==0.5.0
sphinx-design==0.0.13
sphinxcontrib-applehelp==1.0.2
sphinxcontrib-devhelp==1.0.2
sphinxcontrib-htmlhelp==2.0.0
sphinxcontrib-jsmath==1.0.1
sphinxcontrib-qthelp==1.0.3
sphinxcontrib-serializinghtml==1.1.5
sqlitedict==1.7.0
subprocess32==3.5.4
tensorboard==2.7.0
tensorboard-data-server==0.6.1
tensorboard-plugin-wit==1.8.0
tensorboardX==1.8
termcolor==1.1.0
tokenizers==0.10.3
toml==0.10.2
tomli==1.2.1
torch==1.10.1
torchaudio==0.10.1
torchmetrics==0.6.0
torchvision==0.11.2
tornado==6.1
tqdm==4.62.3
traitlets==5.1.0
transformers==4.15.0
twine==3.4.2
types-PyYAML==6.0.0
types-setuptools==57.4.2
typing-extensions==3.10.0.2
typing-utils==0.1.0
urllib3==1.26.7
virtualenv==20.13.0
wandb==0.12.4
wcwidth==0.2.5
webencodings==0.5.1
Werkzeug==2.0.2
xxhash==2.0.2
yarl==1.6.3
yaspin==2.1.0
zipp==3.5.0