Update requirements.txt

requirements.txt

@@ -8,33 +8,19 @@ albucore==0.0.11
 albumentations==1.1.0
 annotated-types==0.7.0
 antlr4-python3-runtime==4.9.3
-anyio @ file:///croot/anyio_1706220167567/work
-argon2-cffi @ file:///opt/conda/conda-bld/argon2-cffi_1645000214183/work
-argon2-cffi-bindings @ file:///tmp/build/80754af9/argon2-cffi-bindings_1644553347904/work
-asttokens @ file:///home/conda/feedstock_root/build_artifacts/asttokens_1698341106958/work
-async-lru @ file:///croot/async-lru_1699554519285/work
 async-timeout==4.0.3
-attrs @ file:///croot/attrs_1695717823297/work
-Babel @ file:///croot/babel_1671781930836/work
 backcall==0.2.0
 backoff==2.2.1
-beautifulsoup4 @ file:///croot/beautifulsoup4-split_1718029820055/work
-bleach @ file:///opt/conda/conda-bld/bleach_1641577558959/work
 blinker==1.8.2
-Brotli @ file:///croot/brotli-split_1714483155106/work
 cachetools==5.5.0
 cairocffi==1.7.1
 CairoSVG==2.7.1
-certifi @ file:///croot/certifi_1738623731865/work/certifi
-cffi @ file:///croot/cffi_1714483155441/work
 chardet==5.2.0
-charset-normalizer @ file:///croot/charset-normalizer_1721748349566/work
 chemrxnextractor @ git+https://github.com/CrystalEye42/ChemRxnExtractor.git@0f9529dbe3656e4ef5ea96c5b5ba990f7481700b
 ci-info==0.3.0
 click==8.1.7
 cmake==4.0.0
 coloredlogs==15.0.1
-comm @ file:///home/conda/feedstock_root/build_artifacts/comm_1710320294760/work
 ConfigArgParse==1.7
 configobj==5.0.8
 configparser==7.1.0
@@ -43,10 +29,7 @@ cryptography==43.0.1
 cssselect2==0.7.0
 cycler==0.12.1
 dataclasses-json==0.6.7
-debugpy @ file:///croot/debugpy_1690905042057/work
-decorator @ file:///home/conda/feedstock_root/build_artifacts/decorator_1641555617451/work
 deepdiff==8.0.1
-defusedxml @ file:///tmp/build/80754af9/defusedxml_1615228127516/work
 Deprecated==1.2.14
 dirtyjson==1.0.8
 distro==1.9.0
@@ -54,17 +37,11 @@ easyocr==1.7.1
 effdet==0.2.1
 einops==0.8.1
 emoji==2.12.1
-entrypoints @ file:///home/conda/feedstock_root/build_artifacts/entrypoints_1643888246732/work
 et-xmlfile==1.1.0
 etelemetry==0.3.1
 eval_type_backport==0.2.0
-exceptiongroup @ file:///home/conda/feedstock_root/build_artifacts/exceptiongroup_1720869315914/work
-executing @ file:///home/conda/feedstock_root/build_artifacts/executing_1725214404607/work
-fastapi==0.115.4
-fastjsonschema @ file:///opt/conda/conda-bld/python-fastjsonschema_1661371079312/work
 fastprogress==1.0.3
 ffmpy==0.4.0
-filelock @ file:///croot/filelock_1700591183607/work
 filetype==1.2.0
 fitz==0.0.1.dev2
 Flask==3.0.3
@@ -75,7 +52,7 @@ frozenlist==1.4.1
 fsspec==2024.9.0
 GeneralAgent==0.3.25
 gensim==4.3.3
-gmpy2 @ file:///croot/gmpy2_1738085463648/work
+gmpy2
 google-api-core==2.19.2
 google-auth==2.34.0
 google-cloud-vision==3.7.4
@@ -86,38 +63,19 @@ gradio_client==1.4.2
 greenlet==3.1.0
 grpcio==1.66.1
 grpcio-status==1.66.1
-h11 @ file:///croot/h11_1706652277403/work
-httpcore @ file:///croot/httpcore_1706728464539/work
 httplib2==0.22.0
-httpx @ file:///croot/httpx_1723474802858/work
 huggingface-hub==0.30.2
 humanfriendly==10.0
-idna @ file:///croot/idna_1714398848350/work
 imageio==2.35.1
 iopath==0.1.10
-ipykernel @ file:///home/conda/feedstock_root/build_artifacts/ipykernel_1719845459717/work
 ipython==8.12.2
 isodate==0.6.1
 itsdangerous==2.2.0
-jedi @ file:///home/conda/feedstock_root/build_artifacts/jedi_1696326070614/work
-Jinja2 @ file:///croot/jinja2_1716993405101/work
 jiter==0.5.0
 joblib==1.4.2
-json5 @ file:///tmp/build/80754af9/json5_1624432770122/work
 jsonpatch==1.33
 jsonpath-python==1.0.6
 jsonpointer==3.0.0
-jsonschema @ file:///croot/jsonschema_1699041609003/work
-jsonschema-specifications @ file:///croot/jsonschema-specifications_1699032386549/work
-jupyter-events @ file:///croot/jupyter_events_1718738097486/work
-jupyter-lsp @ file:///croot/jupyter-lsp-meta_1699978238815/work
-jupyter_client @ file:///croot/jupyter_client_1699455897726/work
-jupyter_core @ file:///home/conda/feedstock_root/build_artifacts/jupyter_core_1710257277185/work
-jupyter_server @ file:///croot/jupyter_server_1718827083372/work
-jupyter_server_terminals @ file:///croot/jupyter_server_terminals_1686870725608/work
-jupyterlab @ file:///croot/jupyterlab_1725895214311/work
-jupyterlab-pygments @ file:///tmp/build/80754af9/jupyterlab_pygments_1601490720602/work
-jupyterlab_server @ file:///croot/jupyterlab_server_1725865349919/work
 kiwisolver==1.4.7
 langchain==0.3.0
 langchain-community==0.3.0
@@ -148,31 +106,17 @@ looseversion==1.3.0
 lxml==5.3.0
 Markdown==3.7
 markdown-it-py==3.0.0
-MarkupSafe @ file:///croot/markupsafe_1704205993651/work
 marshmallow==3.22.0
 matplotlib==3.9.2
-matplotlib-inline @ file:///home/conda/feedstock_root/build_artifacts/matplotlib-inline_1713250518406/work
 mdurl==0.1.2
--e git+https://github.com/aspuru-guzik-group/MERMaid/@4a4a455ff69e976cf8de5b9d9db38651c4714d6f#egg=MERMaid
-mistune @ file:///opt/conda/conda-bld/mistune_1661496219659/work
 mkl-service==2.4.0
-mkl_fft @ file:///io/mkl313/mkl_fft_1730824109137/work
-mkl_random @ file:///io/mkl313/mkl_random_1730823916628/work
-MolScribe @ git+https://github.com/CrystalEye42/MolScribe.git@250f683f52f5050eb624870ccfd04bccbcaa27e1
-mpmath @ file:///croot/mpmath_1690848262763/work
 multidict==6.0.5
 mypy-extensions==1.0.0
-nbclient @ file:///croot/nbclient_1698934205032/work
-nbconvert @ file:///croot/nbconvert_1699022732553/work
-nbformat @ file:///croot/nbformat_1694616755618/work
-nest_asyncio @ file:///home/conda/feedstock_root/build_artifacts/nest-asyncio_1705850609492/work
 networkx==3.3
 nibabel==5.2.1
 ninja==1.11.1.1
 nipype==1.8.6
 nltk==3.9.1
-notebook @ file:///croot/notebook_1725954770513/work
-notebook_shim @ file:///croot/notebook-shim_1699455894279/work
 numpy==1.26.4
 olefile==0.47
 omegaconf==2.3.0
@@ -185,43 +129,30 @@ OpenNMT-py==2.2.0
 openpyxl==3.1.5
 orderly-set==5.2.2
 orjson==3.10.7
-overrides @ file:///croot/overrides_1699371140756/work
-packaging @ file:///home/conda/feedstock_root/build_artifacts/packaging_1718189413536/work
 pandas==2.2.2
-pandocfilters @ file:///opt/conda/conda-bld/pandocfilters_1643405455980/work
-parso @ file:///home/conda/feedstock_root/build_artifacts/parso_1712320355065/work
 pathlib==1.0.1
 pdf2image==1.17.0
 pdfminer.six==20231228
 pdfplumber==0.11.4
 pdftotext==2.2.2
-pexpect @ file:///home/conda/feedstock_root/build_artifacts/pexpect_1706113125309/work
 pi_heif==0.18.0
-pickleshare @ file:///home/conda/feedstock_root/build_artifacts/pickleshare_1602536217715/work
 pikepdf==9.2.1
 pillow==10.4.0
-platformdirs @ file:///home/conda/feedstock_root/build_artifacts/platformdirs_1715777629804/work
 portalocker==2.10.1
-prometheus-client @ file:///tmp/abs_d3zeliano1/croots/recipe/prometheus_client_1659455100375/work
-prompt_toolkit @ file:///home/conda/feedstock_root/build_artifacts/prompt-toolkit_1718047967974/work
 proto-plus==1.24.0
 protobuf==5.28.0
 prov==2.0.1
-psutil @ file:///opt/conda/conda-bld/psutil_1656431268089/work
-ptyprocess @ file:///home/conda/feedstock_root/build_artifacts/ptyprocess_1609419310487/work/dist/ptyprocess-0.7.0-py2.py3-none-any.whl
 PubChemPy==1.0.4
-pure_eval @ file:///home/conda/feedstock_root/build_artifacts/pure_eval_1721585709575/work
 pyasn1==0.6.1
 pyasn1_modules==0.4.1
 pyclipper==1.3.0.post5
 pycocotools==2.0.8
-pycparser @ file:///tmp/build/80754af9/pycparser_1636541352034/work
+pycparser
 pydantic==2.9.0
 pydantic-settings==2.5.2
 pydantic_core==2.23.2
 pydot==3.0.1
 pydub==0.25.1
-Pygments @ file:///home/conda/feedstock_root/build_artifacts/pygments_1714846767233/work
 PyMuPDF==1.25.5
 pymupdf4llm==0.0.21
 PyMuPDFb==1.24.10
@@ -231,34 +162,22 @@ pyparsing==3.1.4
 pypdf==4.3.1
 PyPDF2==3.0.1
 pypdfium2==4.30.0
-PySocks @ file:///home/builder/ci_310/pysocks_1640793678128/work
 python-bidi==0.6.0
-python-dateutil @ file:///home/conda/feedstock_root/build_artifacts/python-dateutil_1709299778482/work
 python-docx==1.1.2
 python-dotenv==1.0.1
 python-iso639==2024.4.27
-python-json-logger @ file:///croot/python-json-logger_1683823803357/work
 python-magic==0.4.27
 python-multipart==0.0.12
 python-oxmsg==0.0.1
-python-pptx==1.0.2
-pytz @ file:///croot/pytz_1713974312559/work
 pyxnat==1.6.2
-PyYAML @ file:///croot/pyyaml_1698096049011/work
-pyzmq @ file:///croot/pyzmq_1705605076900/work
 qudida==0.0.4
 rapidfuzz==3.9.7
 rdflib==6.3.2
 rdkit==2024.3.5
 rdkit-pypi==2022.9.5
-referencing @ file:///croot/referencing_1699012038513/work
 regex==2024.7.24
-requests @ file:///croot/requests_1721410876868/work
 requests-toolbelt==1.0.0
-rfc3339-validator @ file:///croot/rfc3339-validator_1683077044675/work
-rfc3986-validator @ file:///croot/rfc3986-validator_1683058983515/work
 rich==13.9.4
-rpds-py @ file:///croot/rpds-py_1698945930462/work
 rsa==4.9
 ruff==0.7.3
 safehttpx==0.1.1
@@ -267,19 +186,14 @@ scikit-image==0.24.0
 scikit-learn==1.5.1
 scipy==1.13.1
 semantic-version==2.10.0
-Send2Trash @ file:///croot/send2trash_1699371139552/work
 sentencepiece==0.2.0
 seqeval==1.2.2
 shapely==2.0.6
 shellingham==1.5.4
 simplejson==3.19.3
-six @ file:///home/conda/feedstock_root/build_artifacts/six_1620240208055/work
 smart-open==7.0.4
 SmilesPE==0.0.3
-sniffio @ file:///croot/sniffio_1705431295498/work
-soupsieve @ file:///croot/soupsieve_1696347547217/work
 SQLAlchemy==2.0.34
-stack-data @ file:///home/conda/feedstock_root/build_artifacts/stack_data_1669632077133/work
 starlette==0.41.2
 striprtf==0.0.26
 sympy==1.13.2
@@ -287,42 +201,33 @@ tabulate==0.9.0
 tenacity==8.5.0
 tensorboard==2.17.1
 tensorboard-data-server==0.7.2
-terminado @ file:///croot/terminado_1671751832461/work
 tesseract==0.1.3
 threadpoolctl==3.5.0
 tifffile==2024.8.30
 tiktoken==0.7.0
 timm==0.4.12
-tinycss2 @ file:///croot/tinycss2_1668168815555/work
 tinydb==4.8.0
 tokenizers==0.21.1
-tomli @ file:///opt/conda/conda-bld/tomli_1657175507142/work
 tomlkit==0.12.0
 torch==2.2.0
 torchaudio
 torchtext
 torchvision
-tornado @ file:///croot/tornado_1718740109488/work
 tqdm==4.66.5
-traitlets @ file:///home/conda/feedstock_root/build_artifacts/traitlets_1713535121073/work
 traits==6.3.2
 transformers==4.47.0
 triton==2.3.0
 typer==0.13.0
 typing-inspect==0.9.0
-typing_extensions @ file:///croot/typing_extensions_1715268824938/work
 tzdata==2024.1
 unstructured==0.15.12
 unstructured-client==0.25.8
 unstructured-inference==0.7.36
 unstructured.pytesseract==0.3.13
-urllib3 @ file:///croot/urllib3_1718912636303/work
 uvicorn==0.30.6
 valgrind==0.0.0
 waitress==3.0.0
-wcwidth @ file:///home/conda/feedstock_root/build_artifacts/wcwidth_1704731205417/work
 webencodings==0.5.1
-websocket-client @ file:///croot/websocket-client_1715878298792/work
 websockets==12.0
 Werkzeug==3.0.4
 wrapt==1.16.0