Update requirements.txt and notebooks readme

notebooks/analysis/README.md

@@ -6,7 +6,7 @@ Code for data analysis and figure generation for ["Mapping MAVE data for use in
 * [`mapping_analysis.ipynb`](mapping_analysis.ipynb): This notebook computes reference sequence concordance across the generated VRS mapping pairs. The notebook also computes the number of unique pre-mapped and post-mapped variants.
 * [`mavedb_scoreset_breakdown.ipynb`](mavedb_scoreset_breakdown.ipynb): This notebook generates the summary statistics that are described in the manuscript.
 
-**Note that these notebooks may not be using the most recent release of the `dcd_mapping` library** -- they are intended to reflect the state of the code at the time of artifact generation, without any features that have been added since. The included `requirements.txt` file should produce an environment matching this expectation.
+**Note that these notebooks may not be using the most recent ['release'](https://github.com/ave-dcd/dcd_mapping/tree/0.1.3) of the `dcd_mapping` library** -- they are intended to reflect the state of the code at the time of artifact generation, without any features that have been added since. The included `requirements.txt` file should produce an environment matching this expectation.
 
 ## Environment
 

requirements.txt

@@ -0,0 +1,144 @@
+agct==0.1.0.dev1
+aiofiles==23.2.1
+annotated-types==0.6.0
+anyio==4.3.0
+appdirs==1.4.4
+appnope==0.1.4
+asttokens==2.4.1
+async-timeout==4.0.3
+asyncpg==0.29.0
+attrs==23.2.0
+beautifulsoup4==4.12.3
+biocommons==0.0.0
+biocommons.seqrepo==0.6.9
+biopython==1.83
+bioservices==1.11.2
+bioutils==0.5.8.post1
+boto3==1.34.69
+botocore==1.34.69
+bs4==0.0.2
+canonicaljson==2.0.0
+cattrs==24.1.2
+cdot==0.2.26
+certifi==2024.2.2
+cfgv==3.4.0
+charset-normalizer==3.3.2
+click==8.1.7
+colorama==0.4.6
+coloredlogs==15.0.1
+colorlog==6.8.2
+comm==0.2.2
+configparser==6.0.1
+contourpy==1.3.0
+cool_seq_tool==0.6.0
+coverage==7.6.1
+cycler==0.12.1
+-e git+https://github.com/ave-dcd/dcd_mapping.git@9a87efae7192ba88ae01a1a233f1bdc528c47d5f#egg=dcd_mapping
+debugpy==1.8.1
+decorator==5.1.1
+distlib==0.3.8
+easydev==0.13.2
+eutils==0.6.0
+executing==2.0.1
+fastapi==0.110.0
+filelock==3.16.1
+fonttools==4.54.1
+fqfa==1.3.1
+ga4gh.vrs==2.0.0a10
+gene-normalizer==0.4.1
+gevent==24.2.1
+greenlet==3.1.1
+grequests==0.7.0
+h11==0.14.0
+hgvs==1.5.4
+httpcore==1.0.6
+httpx==0.26.0
+humanfriendly==10.0
+identify==2.6.1
+idna==3.6
+idutils==1.2.1
+importlib_metadata==7.1.0
+iniconfig==2.0.0
+intervaltree==3.1.0
+ipykernel==6.29.3
+ipython==8.22.2
+isbnlib==3.10.14
+jedi==0.19.1
+jmespath==1.0.1
+jupyter_client==8.6.1
+jupyter_core==5.7.2
+kiwisolver==1.4.7
+lazy==1.6
+line_profiler==4.1.3
+lxml==5.3.0
+matplotlib==3.9.2
+matplotlib-inline==0.1.6
+mavedb==2024.1.0
+mavehgvs==0.6.1
+nest-asyncio==1.6.0
+nodeenv==1.9.1
+numpy==1.26.4
+packaging==24.0
+pandas==1.4.4
+Parsley==1.3
+parso==0.8.3
+pexpect==4.9.0
+pillow==10.4.0
+platformdirs==4.2.0
+pluggy==1.5.0
+polars==1.8.2
+pre-commit==3.8.0
+prompt-toolkit==3.0.43
+psutil==5.9.8
+psycopg==3.1.18
+psycopg-binary==3.1.18
+psycopg2==2.9.9
+ptyprocess==0.7.0
+pure-eval==0.2.2
+pydantic==2.9.2
+pydantic_core==2.23.4
+Pygments==2.17.2
+pyhumps==3.8.0
+pyparsing==3.1.4
+pysam==0.22.0
+pytest==8.3.3
+pytest-asyncio==0.24.0
+pytest-cov==5.0.0
+pytest-mock==3.14.0
+python-dateutil==2.9.0.post0
+python-dotenv==0.20.0
+pytz==2024.1
+PyYAML==6.0.1
+pyzmq==25.1.2
+requests==2.31.0
+requests-cache==1.2.1
+requests-mock==1.12.1
+ruff==0.5.0
+s3transfer==0.10.1
+six==1.16.0
+sniffio==1.3.1
+sortedcontainers==2.4.0
+soupsieve==2.5
+SQLAlchemy==2.0.35
+sqlparse==0.4.4
+stack-data==0.6.3
+starlette==0.36.3
+suds-community==1.2.0
+tabulate==0.9.0
+tornado==6.4
+tqdm==4.66.2
+traitlets==5.14.2
+typing_extensions==4.10.0
+tzdata==2024.1
+url-normalize==1.4.3
+urllib3==1.26.18
+uvicorn==0.29.0
+virtualenv==20.26.6
+wags_tails==0.1.3
+wcwidth==0.2.13
+wrapt==1.16.0
+xmltodict==0.14.0
+yoyo-migrations==8.2.0
+zipp==3.18.1
+zope.event==5.0
+zope.interface==7.0.3