diff --git a/.github/colab-preinstalled.txt b/.github/colab-preinstalled.txt index 79da44fe..b18f7195 100644 --- a/.github/colab-preinstalled.txt +++ b/.github/colab-preinstalled.txt @@ -1,6 +1,6 @@ # Google Colab's preinstalled package versions (Python 3.13 runtime). # Source: https://github.com/googlecolab/backend-info (pip-freeze.txt) -# Last refreshed: 2026-09-21 +# Last refreshed: 2026-10-05 # # This file is used as a uv-pip-compile --constraint when resolving each # notebook's install-cell lock. Matching Colab's versions means the notebook @@ -13,7 +13,7 @@ # falls back to ignoring constraints for that notebook — the lock will end # up with non-Colab versions and the user WILL need to restart. That's the absl-py==1.4.0 -accelerate==1.14.0 +accelerate==1.15.0 access==1.1.10.post3 affine==3.0.1 aiofiles==25.1.0 @@ -29,7 +29,7 @@ altair==5.5.0 annotated-doc==0.0.5 annotated-types==0.8.0 antlr4-python3-runtime==4.9.3 -anyio==4.14.2 +anyio==4.15.1 anywidget==0.9.21 apsw==3.53.4.0 argon2-cffi==25.1.0 @@ -38,7 +38,7 @@ array_record==0.8.3 arrow==1.4.0 arviz==0.22.0 astropy==7.2.2 -astropy-iers-data==0.2026.8.31.0.57.9 +astropy-iers-data==0.2026.9.28.0.59.37 astunparse==1.6.3 atpublic==5.1 attrs==26.1.0 @@ -51,13 +51,13 @@ backcall==0.2.0 beartype==0.22.9 beautifulsoup4==4.13.5 betterproto==2.0.0b7 -bigframes==2.48.0 +bigframes==2.49.0 bigquery-magics==0.14.0 bleach==6.4.0 blinker==1.9.0 blis==1.3.3 blobfile==3.3.0 -blosc2==4.12.0 +blosc2==4.14.1 bokeh==3.8.2 Bottleneck==1.4.2 bqplot==0.12.47 @@ -82,11 +82,12 @@ colorlover==0.3.0 community==1.0.0b1 confection==1.3.3 cons==0.4.7 -contourpy==1.3.3 -cramjam==2.12.1 -cryptography==50.0.1 +contourpy==1.4.0 +cpsat-logutils==1.0.0 +cramjam==2.13.0 +cryptography==50.0.2 cufflinks==0.17.3 -curl_cffi==0.16.2 +curl_cffi==0.16.3 cvxopt==1.3.2 cvxpy==1.6.7 cycler==0.12.1 @@ -104,8 +105,9 @@ defusedxml==0.7.1 deprecation==2.1.0 diffusers==0.40.0 dill==0.4.1 +distributed==2026.8.0 distro==1.9.0 -dlib==19.24.6 +dlib==20.0.1 dm-tree==0.1.10 docstring_parser==0.18.0 docutils==0.21.2 @@ -114,7 +116,7 @@ duckdb==1.3.2 earthengine-api==1.7.39 easydict==1.13 editdistance==0.8.1 -eerepr==0.1.2 +eerepr==0.1.3 einops==0.8.2 entrypoints==0.4 esda==2.9.0 @@ -122,22 +124,22 @@ et_xmlfile==2.0.0 etils==1.14.0 etuples==0.3.10 Farama-Notifications==0.0.6 -fastai==2.8.8 +fastai==2.8.12 fastapi==0.141.1 -fastcore==2.2.19 -fastdownload==0.0.7 +fastcore==2.2.32 +fastdownload==0.0.8 fastjsonschema==2.22.2 fastprogress==1.1.6 -fasttransform==0.0.2 -filelock==3.32.5 +fasttransform==0.0.5 +filelock==4.0.7 firebase-admin==6.9.0 Flask==3.1.3 flatbuffers==25.12.19 flax==0.11.2 folium==0.20.0 -fonttools==4.64.0 +fonttools==4.66.1 formulaic==1.2.2 -fqdn==1.5.1 +fqdn==1.6.0 frozendict==2.4.7 frozenlist==1.8.0 fsspec==2025.12.0 @@ -146,54 +148,51 @@ gast==0.7.0 gcsfs==2025.12.0 GDAL==3.8.4 gdown==5.2.2 -geemap==0.38.4 +geemap==0.38.8 geocoder==1.38.1 geographiclib==2.1 -geopandas==1.1.4 +geopandas==1.2.0 geopy==2.4.1 giddy==2.3.9 gin-config==0.5.0 glob2==0.7 google==3.0.0 google-adk==2.7.1 -google-ai-generativelanguage==0.6.15 google-api-core==2.30.3 -google-api-python-client==2.200.0 +google-api-python-client==2.201.0 google-auth==2.49.0 -google-auth-httplib2==0.4.2 -google-auth-oauthlib==1.4.1 -google-cloud-bigquery==3.44.0 +google-auth-httplib2==0.4.3 +google-auth-oauthlib==1.5.0 +google-cloud-bigquery==3.45.2 google-cloud-bigquery-connection==1.22.0 -google-cloud-bigquery-storage==2.39.0 -google-cloud-core==2.7.0 -google-cloud-dataproc==5.28.0 -google-cloud-datastore==2.25.0 -google-cloud-firestore==2.27.0 +google-cloud-bigquery-storage==2.41.0 +google-cloud-core==2.8.0 +google-cloud-dataproc==5.30.0 +google-cloud-datastore==2.26.1 +google-cloud-firestore==2.33.0 google-cloud-functions==1.24.0 google-cloud-language==2.21.0 google-cloud-monitoring==2.31.0 google-cloud-resource-manager==1.18.0 -google-cloud-spanner==3.68.0 -google-cloud-storage==3.13.1 -google-cloud-storage-control==1.12.0 +google-cloud-spanner==3.71.0 +google-cloud-storage==3.15.1 +google-cloud-storage-control==1.15.0 google-cloud-translate==3.27.0 -google-crc32c==1.8.0 +google-crc32c==1.9.0 google-genai==2.12.1 -google-generativeai==0.8.6 google-pasta==0.2.0 -google-resumable-media==2.10.2 -googleapis-common-protos==1.75.0 +google-resumable-media==2.11.0 +googleapis-common-protos==1.75.5 googledrivedownloader==1.1.0 -gradio==6.26.0 -gradio_client==2.6.1 +gradio==6.29.0 +gradio_client==2.7.1 grain==0.2.18 graphviz==0.21 -greenlet==3.5.5 groovy==0.1.2 -grpc-google-iam-v1==0.14.4 +grpc-google-iam-v1==0.14.5 grpc-interceptor==0.15.4 -grpcio==1.83.1 -grpcio-status==1.71.2 +grpcio==1.84.0 +grpcio-status==1.84.0 grpclib==0.4.9 gspread==6.2.1 gspread-dataframe==4.0.0 @@ -203,29 +202,29 @@ gymnasium==1.3.0 h11==0.16.0 h2==4.4.1 h5netcdf==1.8.1 -h5py==3.16.0 +h5py==3.14.0 hdbscan==0.8.44 hf-gradio==0.4.1 hf-xet==1.6.0 highspy==1.15.1 -holidays==0.103 +holidays==0.105 holoviews==1.23.2 hpack==4.2.0 html5lib==1.1 httpcore==1.0.9 -httpcore2==2.12.0 +httpcore2==2.13.1 httpimport==1.4.1 httplib2==0.32.0 httptools==0.8.0 httpx==0.28.1 -httpx2==2.12.0 -huggingface_hub==1.29.0 +httpx2==2.13.1 +huggingface_hub==1.33.0 humanize==4.16.0 hyperframe==6.1.0 hyperopt==0.3.0 ibis-framework==9.5.0 -idna==3.19 -ImageIO==2.37.4 +idna==3.20 +ImageIO==2.38.0 imageio-ffmpeg==0.6.0 imagesize==2.0.1 imbalanced-learn==0.14.2 @@ -257,7 +256,7 @@ jaxlib==0.11.1 jeepney==0.9.0 jieba==0.42.1 Jinja2==3.1.6 -jiter==0.16.0 +jiter==0.17.0 joblib==1.6.0 joserfc==1.7.5 jsonpatch==1.33 @@ -284,19 +283,19 @@ keras-nlp==0.26.0 keyring==25.7.0 keyrings.google-artifactregistry-auth==1.1.2 kiwisolver==1.5.1 -langchain==1.3.18 -langchain-core==1.6.1 +langchain==1.4.3 +langchain-core==1.6.6 langchain-protocol==0.0.19 -langgraph==1.2.11 +langgraph==1.2.12 langgraph-checkpoint==4.2.0 langgraph-prebuilt==1.1.0 -langgraph-sdk==0.4.4 -langsmith==0.12.1 +langgraph-sdk==0.4.5 +langsmith==0.14.2 lark==1.3.1 launchpadlib==1.11.0 lazr.restfulclient==0.14.6 lazr.uri==1.0.6 -lazy-loader==0.5 +lazy-loader==0.6 libclang==18.1.1 libpysal==4.14.1 librosa==0.11.0 @@ -305,10 +304,11 @@ linkify-it-py==2.2.0 llvmlite==0.44.0 locket==1.0.0 logical-unification==0.4.7 -lxml==6.1.2 +lxml==6.1.3 +lz4==4.4.5 Mako==1.3.2.dev0 mapclassify==2.10.0 -Markdown==3.10.3 +Markdown==3.11 markdown-it-py==4.2.0 MarkupSafe==3.0.3 matplotlib==3.10.0 @@ -324,20 +324,20 @@ mizani==0.13.5 mkl==2025.3.1 ml_dtypes==0.6.0 mlxtend==0.23.4 -mmh3==5.3.0 +mmh3==5.3.1 momepy==0.11.0 more-itertools==10.8.0 moviepy==1.0.3 mpmath==1.3.0 -msgpack==1.2.2 -multidict==6.7.1 +msgpack==1.2.3 +multidict==6.9.1 multipledispatch==1.0.0 multiprocess==0.70.19 multitasking==0.0.13 murmurhash==1.0.15 music21==9.9.2 namex==0.1.0 -narwhals==2.25.0 +narwhals==2.26.0 natsort==8.4.0 nbclassic==1.3.3 nbclient==0.10.4 @@ -345,7 +345,7 @@ nbconvert==7.17.1 nbformat==5.11.1 ndindex==1.10.1 nest-asyncio==1.6.0 -networkx==3.6.1 +networkx==3.7 nh3==0.3.7 nibabel==5.4.2 nltk==3.9.1 @@ -354,7 +354,7 @@ notebook_shim==0.2.4 numba==0.61.2 numexpr==2.14.2 numpy==2.1.3 -nvidia-nccl-cu13==2.31.2 +nvidia-nccl-cu13==2.32.3 oauth2client==4.1.3 oauthlib==3.3.1 omegaconf==2.3.1 @@ -371,8 +371,9 @@ opentelemetry-semantic-conventions==0.63b1 opt_einsum==3.4.0 optax==0.2.8 optree==0.20.0 -orbax-checkpoint==0.12.4 +orbax-checkpoint==0.12.6 orjson==3.12.0 +orloge==1.0.0 ormsgpack==1.12.2 osqp==1.1.3 packaging==26.3 @@ -382,19 +383,19 @@ pandas-gbq==0.30.0 pandas-stubs==2.2.3.250527 pandocfilters==1.5.1 panel==1.9.4 -panel-material-ui==0.14.2 -param==2.4.1 +panel-material-ui==0.16.0 +param==2.4.2 parso==0.8.7 parsy==2.2 partd==1.4.2 patsy==1.0.3 -peewee==4.4.0 -peft==0.20.0 +peewee==4.5.2 +peft==0.21.1 pexpect==4.9.0 pickleshare==0.7.5 pillow==11.3.0 pip==24.1.2 -platformdirs==4.11.7 +platformdirs==4.12.2 plotly==5.24.1 plotnine==0.14.5 pluggy==1.6.0 @@ -411,15 +412,15 @@ progressbar2==4.5.0 prometheus_client==0.26.0 promise==2.3 prompt_toolkit==3.0.53 -propcache==0.5.2 +propcache==0.5.4 prophet==1.4.0 -proto-plus==1.28.2 -protobuf==5.29.6 +proto-plus==1.29.0 +protobuf==6.33.6 psutil==5.9.5 -psycopg2==2.9.12 -psygnal==0.15.1 +psycopg2==2.9.13 +psygnal==0.16.1 ptyprocess==0.7.0 -PuLP==3.3.2 +PuLP==4.0.0 py-cpuinfo==9.0.0 py4j==0.10.9.9 pyarrow==23.0.1 @@ -438,20 +439,20 @@ PyDrive2==1.21.1 pydub==0.25.1 pyerfa==2.0.1.5 pygame==2.6.1 -pygit2==1.20.0 +pygit2==1.20.1 Pygments==2.21.0 PyGObject==3.48.2 pyiceberg==0.12.0 -PyJWT==2.13.0 +PyJWT==2.15.1 pymc==5.28.5 pynndescent==0.6.0 pyogrio==0.13.0 pyomo==6.10.1 PyOpenGL==3.1.10 pyOpenSSL==26.4.0 -pyparsing==3.3.2 +pyparsing==3.3.3 pyperclip==1.11.0 -pyproj==3.7.2 +pyproj==3.8.0 pyroaring==1.1.0 pysal==25.7 pyshp==3.1.6 @@ -463,20 +464,20 @@ python-apt==0.0.0 python-box==7.4.1 python-dateutil==2.9.0.post0 python-dotenv==1.2.3 -python-fasthtml==0.14.12 +python-fasthtml==0.14.13 python-json-logger==4.2.0 python-louvain==0.16 python-multipart==0.0.32 -python-slugify==8.0.4 +python-slugify==9.1.2 python-snappy==0.7.3 python-utils==4.0.1 pytz==2025.2 pyviz_comms==3.0.6 -PyWavelets==1.9.0 +PyWavelets==1.10.0 PyYAML==6.0.3 pyzmq==26.2.1 -quantecon==0.11.4 -rasterio==1.5.1 +quantecon==0.12.0 +rasterio==1.5.2 rasterstats==0.21.0 ratelim==0.1.6 referencing==0.37.0 @@ -500,8 +501,8 @@ safetensors==0.8.0 scikit-image==0.25.2 scikit-learn==1.6.1 scipy==1.16.3 -scooby==0.11.2 -scs==3.2.11 +scooby==0.12.0 +scs==3.3.1 seaborn==0.13.2 SecretStorage==3.5.0 segregation==2.5.4 @@ -509,7 +510,7 @@ semantic-version==2.10.0 Send2Trash==2.1.0 sentence-transformers==5.7.0 sentencepiece==0.2.2 -sentry-sdk==2.68.1 +sentry-sdk==2.71.0 setuptools==80.10.2 shap==0.52.0 shapely==2.1.2 @@ -521,17 +522,18 @@ six==1.17.0 sklearn-compat==0.1.6 sklearn-pandas==2.2.0 slicer==0.0.8 -smart_open==8.0.1 +smart_open==8.0.2 sniffio==1.3.1 snowballstemmer==3.1.1 +sortedcontainers==2.4.0 soundfile==0.14.0 -soupsieve==2.9.2 +soupsieve==2.10 soxr==1.1.0 spacy==3.8.16 spacy-legacy==3.0.12 spacy-loggers==1.0.5 spaghetti==1.7.6 -spanner-graph-notebook==1.1.10 +spanner-graph-notebook==1.1.11 spglm==1.1.0 Sphinx==8.2.3 sphinxcontrib-applehelp==2.0.0 @@ -544,15 +546,15 @@ spint==1.1.0 splot==1.1.7 spopt==0.7.0 spreg==1.9.0 -SQLAlchemy==2.0.52 +SQLAlchemy==2.1.1 sqlglot==25.20.2 sqlparse==0.6.0 -srsly==2.5.3 +srsly==2.5.4 standard-aifc==3.13.0 standard-chunk==3.13.0 standard-sunau==3.13.0 stanio==0.5.1 -starlette==1.6.0 +starlette==1.7.0 statsmodels==0.15.0 strictyaml==1.7.3 stringzilla==5.1.2 @@ -561,31 +563,32 @@ sympy==1.14.0 tables==3.10.2 tabulate==0.9.0 tbb==2022.3.1 +tblib==3.2.2 tcmlib==1.5.0 tenacity==9.1.4 -tensorboard==2.20.0 +tensorboard==2.21.0 tensorboard-data-server==0.7.2 -tensorflow==2.20.0 +tensorflow==2.21.0 tensorflow-datasets==4.9.10 tensorflow-hub==0.16.1 tensorflow-metadata==1.21.0 tensorflow-probability==0.25.0 -tensorflow-text==2.20.1 +tensorflow-text==2.21.1 tensorstore==0.1.85 termcolor==3.3.0 terminado==0.18.1 text-unidecode==1.3 textblob==0.19.0 tf-slim==1.1.0 -tf_keras==2.20.1 +tf_keras==2.21.0 thinc==8.3.13 -threadpoolctl==3.6.0 -tifffile==2026.8.23 +threadpoolctl==3.7.0 +tifffile==2026.9.20 tiktoken==0.14.0 -timm==1.0.29 +timm==1.0.30 tinycss2==1.5.1 tobler==0.14.0 -tokenizers==0.23.1 +tokenizers==0.23.2 toml==0.10.2 tomlkit==0.14.0 toolz==0.12.1 @@ -597,54 +600,56 @@ tornado==6.5.7 tqdm==4.67.3 traitlets==5.7.1 traittypes==0.2.3 -transformers==5.16.1 +transformers==5.18.0 treescope==0.1.10 truststore==0.10.4 tsfresh==0.21.2 tweepy==4.17.0 typeguard==4.6.0 typer==0.27.2 -types-pytz==2026.3.1.20260727 +types-pytz==2026.4.0.20260926 types-setuptools==84.0.0.20260812 typing-inspection==0.4.4 typing_extensions==4.16.0 -tzdata==2026.3 +tzdata==2026.4 tzlocal==5.4.4 umap-learn==0.5.12 umf==1.0.3 uri-template==1.3.0 uritemplate==4.2.0 urllib3==2.5.0 -uuid_utils==0.17.0 -uvicorn==0.52.4 +uuid_utils==0.17.1 +uvicorn==0.54.0 uvloop==0.22.1 vega-datasets==0.9.0 wadllib==1.3.6 wandb==0.28.1 wasabi==1.1.3 watchdog==6.0.0 -watchfiles==1.2.0 -wcwidth==0.8.3 +watchfiles==1.3.0 +wcwidth==0.9.1 weasel==1.0.0 webcolors==25.10.0 webencodings==0.6.1 websocket-client==1.9.2 websockets==15.0.1 -Werkzeug==3.1.8 +Werkzeug==3.1.9 wheel==0.48.0 widgetsnbextension==3.6.10 wordcloud==1.9.6 -wrapt==2.4.0 +wrapt==2.5.0 xarray==2025.12.0 xarray-einstats==0.11.0 +xee==0.1.2 xgboost==3.4.1 xlrd==2.0.2 xxhash==4.0.1 -xyzservices==2026.3.0 -yarl==1.24.5 +xyzservices==2026.9.1 +yarl==1.25.1 ydf==0.15.0 -ydf_tf==2.20.0 +ydf_tf==2.21.0 yellowbrick==1.5 yfinance==0.2.66 +zict==3.0.0 zipp==4.1.0 zstandard==0.25.0 diff --git a/000108/chunglab/demo/2021-09-27_dandi-demo.ipynb b/000108/chunglab/demo/2021-09-27_dandi-demo.ipynb index fb55b52d..b71008e9 100644 --- a/000108/chunglab/demo/2021-09-27_dandi-demo.ipynb +++ b/000108/chunglab/demo/2021-09-27_dandi-demo.ipynb @@ -51,8 +51,8 @@ " \"click==8.5.0\" \\\n", " \"click-didyoumean==0.3.1\" \\\n", " \"cloudpickle==3.1.2\" \\\n", - " \"contourpy==1.3.3\" \\\n", - " \"cryptography==50.0.1\" \\\n", + " \"contourpy==1.4.0\" \\\n", + " \"cryptography==50.0.2\" \\\n", " \"cycler==0.12.1\" \\\n", " \"dandi==0.77.0\" \\\n", " \"dandischema==0.14.0\" \\\n", @@ -62,17 +62,17 @@ " \"email-validator==2.3.0\" \\\n", " \"etelemetry==0.3.1\" \\\n", " \"fasteners==0.20\" \\\n", - " \"fonttools==4.64.0\" \\\n", - " \"fqdn==1.5.1\" \\\n", + " \"fonttools==4.66.1\" \\\n", + " \"fqdn==1.6.0\" \\\n", " \"frozenlist==1.8.0\" \\\n", " \"fscacher==0.4.4\" \\\n", " \"fsspec==2025.12.0\" \\\n", - " \"google-crc32c==1.8.0\" \\\n", - " \"h5py==3.16.0\" \\\n", + " \"google-crc32c==1.9.0\" \\\n", + " \"h5py==3.14.0\" \\\n", " \"hdmf==6.2.0\" \\\n", " \"humanize==4.16.0\" \\\n", - " \"idna==3.19\" \\\n", - " \"imageio==2.37.4\" \\\n", + " \"idna==3.20\" \\\n", + " \"imageio==2.38.0\" \\\n", " \"interleave==0.3.0\" \\\n", " \"isodate==0.7.2\" \\\n", " \"isoduration==20.11.0\" \\\n", @@ -89,23 +89,23 @@ " \"keyring==25.7.0\" \\\n", " \"keyrings-alt==5.0.2\" \\\n", " \"kiwisolver==1.5.1\" \\\n", - " \"lazy-loader==0.5\" \\\n", + " \"lazy-loader==0.6\" \\\n", " \"markupsafe==3.0.3\" \\\n", " \"matplotlib==3.10.0\" \\\n", " \"ml-dtypes==0.6.0\" \\\n", " \"more-itertools==10.8.0\" \\\n", - " \"multidict==6.7.1\" \\\n", - " \"narwhals==2.25.0\" \\\n", + " \"multidict==6.9.1\" \\\n", + " \"narwhals==2.26.0\" \\\n", " \"natsort==8.4.0\" \\\n", - " \"networkx==3.6.1\" \\\n", + " \"networkx==3.7\" \\\n", " \"numcodecs==0.16.5\" \\\n", " \"numpy==2.1.3\" \\\n", " \"nwbinspector==0.7.2\" \\\n", " \"packaging==26.3\" \\\n", " \"pandas==2.2.3\" \\\n", " \"pillow==11.3.0\" \\\n", - " \"platformdirs==4.11.7\" \\\n", - " \"propcache==0.5.2\" \\\n", + " \"platformdirs==4.12.2\" \\\n", + " \"propcache==0.5.4\" \\\n", " \"pycparser==3.0\" \\\n", " \"pycryptodomex==3.23.0\" \\\n", " \"pydantic==2.13.5\" \\\n", @@ -113,7 +113,7 @@ " \"pydantic-settings==2.15.0\" \\\n", " \"pynwb==4.1.0\" \\\n", " \"pyout==0.8.1\" \\\n", - " \"pyparsing==3.3.2\" \\\n", + " \"pyparsing==3.3.3\" \\\n", " \"python-dateutil==2.9.0.post0\" \\\n", " \"python-dotenv==1.2.3\" \\\n", " \"pytz==2025.2\" \\\n", @@ -132,18 +132,18 @@ " \"six==1.17.0\" \\\n", " \"tenacity==9.1.4\" \\\n", " \"tensorstore==0.1.85\" \\\n", - " \"tifffile==2026.8.23\" \\\n", + " \"tifffile==2026.9.20\" \\\n", " \"tornado==6.5.7\" \\\n", " \"tqdm==4.67.3\" \\\n", " \"typing-extensions==4.16.0\" \\\n", " \"typing-inspection==0.4.4\" \\\n", - " \"tzdata==2026.3\" \\\n", + " \"tzdata==2026.4\" \\\n", " \"uri-template==1.3.0\" \\\n", " \"urllib3==2.5.0\" \\\n", - " \"wcwidth==0.8.3\" \\\n", + " \"wcwidth==0.9.1\" \\\n", " \"webcolors==25.10.0\" \\\n", - " \"xyzservices==2026.3.0\" \\\n", - " \"yarl==1.24.5\" \\\n", + " \"xyzservices==2026.9.1\" \\\n", + " \"yarl==1.25.1\" \\\n", " \"zarr==3.1.5\" \\\n", " \"zarr-checksum==0.4.7\"" ] diff --git a/000108/chunglab/demo/dashboard.ipynb b/000108/chunglab/demo/dashboard.ipynb index add50f6b..339e8335 100644 --- a/000108/chunglab/demo/dashboard.ipynb +++ b/000108/chunglab/demo/dashboard.ipynb @@ -51,8 +51,8 @@ " \"click==8.5.0\" \\\n", " \"click-didyoumean==0.3.1\" \\\n", " \"cloudpickle==3.1.2\" \\\n", - " \"contourpy==1.3.3\" \\\n", - " \"cryptography==50.0.1\" \\\n", + " \"contourpy==1.4.0\" \\\n", + " \"cryptography==50.0.2\" \\\n", " \"cycler==0.12.1\" \\\n", " \"dandi==0.77.0\" \\\n", " \"dandischema==0.14.0\" \\\n", @@ -62,17 +62,17 @@ " \"email-validator==2.3.0\" \\\n", " \"etelemetry==0.3.1\" \\\n", " \"fasteners==0.20\" \\\n", - " \"fonttools==4.64.0\" \\\n", - " \"fqdn==1.5.1\" \\\n", + " \"fonttools==4.66.1\" \\\n", + " \"fqdn==1.6.0\" \\\n", " \"frozenlist==1.8.0\" \\\n", " \"fscacher==0.4.4\" \\\n", " \"fsspec==2025.12.0\" \\\n", - " \"google-crc32c==1.8.0\" \\\n", - " \"h5py==3.16.0\" \\\n", + " \"google-crc32c==1.9.0\" \\\n", + " \"h5py==3.14.0\" \\\n", " \"hdmf==6.2.0\" \\\n", " \"humanize==4.16.0\" \\\n", - " \"idna==3.19\" \\\n", - " \"imageio==2.37.4\" \\\n", + " \"idna==3.20\" \\\n", + " \"imageio==2.38.0\" \\\n", " \"interleave==0.3.0\" \\\n", " \"isodate==0.7.2\" \\\n", " \"isoduration==20.11.0\" \\\n", @@ -89,23 +89,23 @@ " \"keyring==25.7.0\" \\\n", " \"keyrings-alt==5.0.2\" \\\n", " \"kiwisolver==1.5.1\" \\\n", - " \"lazy-loader==0.5\" \\\n", + " \"lazy-loader==0.6\" \\\n", " \"markupsafe==3.0.3\" \\\n", " \"matplotlib==3.10.0\" \\\n", " \"ml-dtypes==0.6.0\" \\\n", " \"more-itertools==10.8.0\" \\\n", - " \"multidict==6.7.1\" \\\n", - " \"narwhals==2.25.0\" \\\n", + " \"multidict==6.9.1\" \\\n", + " \"narwhals==2.26.0\" \\\n", " \"natsort==8.4.0\" \\\n", - " \"networkx==3.6.1\" \\\n", + " \"networkx==3.7\" \\\n", " \"numcodecs==0.16.5\" \\\n", " \"numpy==2.1.3\" \\\n", " \"nwbinspector==0.7.2\" \\\n", " \"packaging==26.3\" \\\n", " \"pandas==2.2.3\" \\\n", " \"pillow==11.3.0\" \\\n", - " \"platformdirs==4.11.7\" \\\n", - " \"propcache==0.5.2\" \\\n", + " \"platformdirs==4.12.2\" \\\n", + " \"propcache==0.5.4\" \\\n", " \"pycparser==3.0\" \\\n", " \"pycryptodomex==3.23.0\" \\\n", " \"pydantic==2.13.5\" \\\n", @@ -113,7 +113,7 @@ " \"pydantic-settings==2.15.0\" \\\n", " \"pynwb==4.1.0\" \\\n", " \"pyout==0.8.1\" \\\n", - " \"pyparsing==3.3.2\" \\\n", + " \"pyparsing==3.3.3\" \\\n", " \"python-dateutil==2.9.0.post0\" \\\n", " \"python-dotenv==1.2.3\" \\\n", " \"pytz==2025.2\" \\\n", @@ -132,18 +132,18 @@ " \"six==1.17.0\" \\\n", " \"tenacity==9.1.4\" \\\n", " \"tensorstore==0.1.85\" \\\n", - " \"tifffile==2026.8.23\" \\\n", + " \"tifffile==2026.9.20\" \\\n", " \"tornado==6.5.7\" \\\n", " \"tqdm==4.67.3\" \\\n", " \"typing-extensions==4.16.0\" \\\n", " \"typing-inspection==0.4.4\" \\\n", - " \"tzdata==2026.3\" \\\n", + " \"tzdata==2026.4\" \\\n", " \"uri-template==1.3.0\" \\\n", " \"urllib3==2.5.0\" \\\n", - " \"wcwidth==0.8.3\" \\\n", + " \"wcwidth==0.9.1\" \\\n", " \"webcolors==25.10.0\" \\\n", - " \"xyzservices==2026.3.0\" \\\n", - " \"yarl==1.24.5\" \\\n", + " \"xyzservices==2026.9.1\" \\\n", + " \"yarl==1.25.1\" \\\n", " \"zarr==3.1.5\" \\\n", " \"zarr-checksum==0.4.7\"" ] diff --git a/000402/MICrONS/demo/000402_microns_demo.ipynb b/000402/MICrONS/demo/000402_microns_demo.ipynb index 2b4c1ad8..bd24ca2a 100644 --- a/000402/MICrONS/demo/000402_microns_demo.ipynb +++ b/000402/MICrONS/demo/000402_microns_demo.ipynb @@ -50,8 +50,8 @@ " \"click==8.5.0\" \\\n", " \"click-didyoumean==0.3.1\" \\\n", " \"cloudpickle==3.1.2\" \\\n", - " \"contourpy==1.3.3\" \\\n", - " \"cryptography==50.0.1\" \\\n", + " \"contourpy==1.4.0\" \\\n", + " \"cryptography==50.0.2\" \\\n", " \"cycler==0.12.1\" \\\n", " \"dandi==0.77.0\" \\\n", " \"dandischema==0.14.0\" \\\n", @@ -61,16 +61,16 @@ " \"email-validator==2.3.0\" \\\n", " \"etelemetry==0.3.1\" \\\n", " \"fasteners==0.20\" \\\n", - " \"fonttools==4.64.0\" \\\n", - " \"fqdn==1.5.1\" \\\n", + " \"fonttools==4.66.1\" \\\n", + " \"fqdn==1.6.0\" \\\n", " \"frozenlist==1.8.0\" \\\n", " \"fscacher==0.4.4\" \\\n", " \"fsspec==2025.12.0\" \\\n", - " \"google-crc32c==1.8.0\" \\\n", - " \"h5py==3.16.0\" \\\n", + " \"google-crc32c==1.9.0\" \\\n", + " \"h5py==3.14.0\" \\\n", " \"hdmf==4.3.1\" \\\n", " \"humanize==4.16.0\" \\\n", - " \"idna==3.19\" \\\n", + " \"idna==3.20\" \\\n", " \"interleave==0.3.0\" \\\n", " \"isodate==0.7.2\" \\\n", " \"isoduration==20.11.0\" \\\n", @@ -89,7 +89,7 @@ " \"matplotlib==3.10.0\" \\\n", " \"ml-dtypes==0.6.0\" \\\n", " \"more-itertools==10.8.0\" \\\n", - " \"multidict==6.7.1\" \\\n", + " \"multidict==6.9.1\" \\\n", " \"natsort==8.4.0\" \\\n", " \"ndx-grayscalevolume==0.0.2\" \\\n", " \"ndx-icephys-meta==0.1.0\" \\\n", @@ -100,8 +100,8 @@ " \"packaging==26.3\" \\\n", " \"pandas==2.2.3\" \\\n", " \"pillow==11.3.0\" \\\n", - " \"platformdirs==4.11.7\" \\\n", - " \"propcache==0.5.2\" \\\n", + " \"platformdirs==4.12.2\" \\\n", + " \"propcache==0.5.4\" \\\n", " \"pycparser==3.0\" \\\n", " \"pycryptodomex==3.23.0\" \\\n", " \"pydantic==2.13.5\" \\\n", @@ -109,7 +109,7 @@ " \"pydantic-settings==2.15.0\" \\\n", " \"pynwb==3.1.3\" \\\n", " \"pyout==0.8.1\" \\\n", - " \"pyparsing==3.3.2\" \\\n", + " \"pyparsing==3.3.3\" \\\n", " \"python-dateutil==2.9.0.post0\" \\\n", " \"python-dotenv==1.2.3\" \\\n", " \"pytz==2025.2\" \\\n", @@ -128,12 +128,12 @@ " \"tqdm==4.67.3\" \\\n", " \"typing-extensions==4.16.0\" \\\n", " \"typing-inspection==0.4.4\" \\\n", - " \"tzdata==2026.3\" \\\n", + " \"tzdata==2026.4\" \\\n", " \"uri-template==1.3.0\" \\\n", " \"urllib3==2.5.0\" \\\n", - " \"wcwidth==0.8.3\" \\\n", + " \"wcwidth==0.9.1\" \\\n", " \"webcolors==25.10.0\" \\\n", - " \"yarl==1.24.5\" \\\n", + " \"yarl==1.25.1\" \\\n", " \"zarr==3.1.5\" \\\n", " \"zarr-checksum==0.4.7\"" ] diff --git a/000409/IBL/bwm_usage_notebook.ipynb b/000409/IBL/bwm_usage_notebook.ipynb index ab958b0f..0caeb279 100644 --- a/000409/IBL/bwm_usage_notebook.ipynb +++ b/000409/IBL/bwm_usage_notebook.ipynb @@ -38,7 +38,7 @@ " \"aiohttp==3.14.3\" \\\n", " \"aiosignal==1.4.0\" \\\n", " \"annotated-types==0.8.0\" \\\n", - " \"anyio==4.14.2\" \\\n", + " \"anyio==4.15.1\" \\\n", " \"anywidget==0.9.21\" \\\n", " \"argon2-cffi==25.1.0\" \\\n", " \"argon2-cffi-bindings==26.1.0\" \\\n", @@ -62,8 +62,8 @@ " \"click-didyoumean==0.3.1\" \\\n", " \"cloudpickle==3.1.2\" \\\n", " \"colorlog==6.12.0\" \\\n", - " \"contourpy==1.3.3\" \\\n", - " \"cryptography==50.0.1\" \\\n", + " \"contourpy==1.4.0\" \\\n", + " \"cryptography==50.0.2\" \\\n", " \"cycler==0.12.1\" \\\n", " \"dandi==0.77.0\" \\\n", " \"dandischema==0.14.0\" \\\n", @@ -78,18 +78,18 @@ " \"etelemetry==0.3.1\" \\\n", " \"fasteners==0.20\" \\\n", " \"fastjsonschema==2.22.2\" \\\n", - " \"fonttools==4.64.0\" \\\n", - " \"fqdn==1.5.1\" \\\n", + " \"fonttools==4.66.1\" \\\n", + " \"fqdn==1.6.0\" \\\n", " \"frozenlist==1.8.0\" \\\n", " \"fscacher==0.4.4\" \\\n", " \"fsspec==2025.12.0\" \\\n", - " \"google-crc32c==1.8.0\" \\\n", - " \"h5py==3.16.0\" \\\n", + " \"google-crc32c==1.9.0\" \\\n", + " \"h5py==3.14.0\" \\\n", " \"hdmf==4.3.1\" \\\n", " \"humanize==4.16.0\" \\\n", " \"iblatlas==1.2.0\" \\\n", " \"iblutil==1.20.0\" \\\n", - " \"idna==3.19\" \\\n", + " \"idna==3.20\" \\\n", " \"interleave==0.3.0\" \\\n", " \"ipykernel==6.17.1\" \\\n", " \"ipython==7.34.0\" \\\n", @@ -130,7 +130,7 @@ " \"mistune==3.3.4\" \\\n", " \"ml-dtypes==0.6.0\" \\\n", " \"more-itertools==10.8.0\" \\\n", - " \"multidict==6.7.1\" \\\n", + " \"multidict==6.9.1\" \\\n", " \"natsort==8.4.0\" \\\n", " \"nbclassic==1.3.3\" \\\n", " \"nbclient==0.10.4\" \\\n", @@ -153,13 +153,13 @@ " \"pexpect==4.9.0\" \\\n", " \"pickleshare==0.7.5\" \\\n", " \"pillow==11.3.0\" \\\n", - " \"platformdirs==4.11.7\" \\\n", + " \"platformdirs==4.12.2\" \\\n", " \"prometheus-client==0.26.0\" \\\n", " \"prompt-toolkit==3.0.53\" \\\n", - " \"propcache==0.5.2\" \\\n", + " \"propcache==0.5.4\" \\\n", " \"psutil==5.9.5\" \\\n", " \"psychofit==1.0.0.post0\" \\\n", - " \"psygnal==0.15.1\" \\\n", + " \"psygnal==0.16.1\" \\\n", " \"ptyprocess==0.7.0\" \\\n", " \"pyarrow==23.0.1\" \\\n", " \"pycparser==3.0\" \\\n", @@ -172,7 +172,7 @@ " \"pynrrd==1.1.3\" \\\n", " \"pynwb==3.1.3\" \\\n", " \"pyout==0.8.1\" \\\n", - " \"pyparsing==3.3.2\" \\\n", + " \"pyparsing==3.3.3\" \\\n", " \"python-dateutil==2.9.0.post0\" \\\n", " \"python-dotenv==1.2.3\" \\\n", " \"python-json-logger==4.2.0\" \\\n", @@ -198,12 +198,12 @@ " \"send2trash==2.1.0\" \\\n", " \"setuptools==80.10.2\" \\\n", " \"six==1.17.0\" \\\n", - " \"soupsieve==2.9.2\" \\\n", + " \"soupsieve==2.10\" \\\n", " \"tabulate==0.9.0\" \\\n", " \"tenacity==9.1.4\" \\\n", " \"tensorstore==0.1.85\" \\\n", " \"terminado==0.18.1\" \\\n", - " \"tifffile==2026.8.23\" \\\n", + " \"tifffile==2026.9.20\" \\\n", " \"tinycss2==1.5.1\" \\\n", " \"tornado==6.5.7\" \\\n", " \"tqdm==4.67.3\" \\\n", @@ -211,16 +211,16 @@ " \"treelib==1.8.0\" \\\n", " \"typing-extensions==4.16.0\" \\\n", " \"typing-inspection==0.4.4\" \\\n", - " \"tzdata==2026.3\" \\\n", + " \"tzdata==2026.4\" \\\n", " \"uri-template==1.3.0\" \\\n", " \"urllib3==2.5.0\" \\\n", - " \"wcwidth==0.8.3\" \\\n", + " \"wcwidth==0.9.1\" \\\n", " \"webcolors==25.10.0\" \\\n", " \"webencodings==0.6.1\" \\\n", " \"websocket-client==1.9.2\" \\\n", " \"widgetsnbextension==3.6.10\" \\\n", " \"xarray==2025.12.0\" \\\n", - " \"yarl==1.24.5\" \\\n", + " \"yarl==1.25.1\" \\\n", " \"zarr==3.1.5\" \\\n", " \"zarr-checksum==0.4.7\"" ] diff --git a/000458/AllenInstitute/reanalysis.ipynb b/000458/AllenInstitute/reanalysis.ipynb index f304ff31..1728c8a0 100644 --- a/000458/AllenInstitute/reanalysis.ipynb +++ b/000458/AllenInstitute/reanalysis.ipynb @@ -50,8 +50,8 @@ " \"click==8.5.0\" \\\n", " \"click-didyoumean==0.3.1\" \\\n", " \"cloudpickle==3.1.2\" \\\n", - " \"contourpy==1.3.3\" \\\n", - " \"cryptography==50.0.1\" \\\n", + " \"contourpy==1.4.0\" \\\n", + " \"cryptography==50.0.2\" \\\n", " \"cycler==0.12.1\" \\\n", " \"dandi==0.77.0\" \\\n", " \"dandischema==0.14.0\" \\\n", @@ -61,16 +61,16 @@ " \"email-validator==2.3.0\" \\\n", " \"etelemetry==0.3.1\" \\\n", " \"fasteners==0.20\" \\\n", - " \"fonttools==4.64.0\" \\\n", - " \"fqdn==1.5.1\" \\\n", + " \"fonttools==4.66.1\" \\\n", + " \"fqdn==1.6.0\" \\\n", " \"frozenlist==1.8.0\" \\\n", " \"fscacher==0.4.4\" \\\n", " \"fsspec==2025.12.0\" \\\n", - " \"google-crc32c==1.8.0\" \\\n", - " \"h5py==3.16.0\" \\\n", + " \"google-crc32c==1.9.0\" \\\n", + " \"h5py==3.14.0\" \\\n", " \"hdmf==6.2.0\" \\\n", " \"humanize==4.16.0\" \\\n", - " \"idna==3.19\" \\\n", + " \"idna==3.20\" \\\n", " \"interleave==0.3.0\" \\\n", " \"isodate==0.7.2\" \\\n", " \"isoduration==20.11.0\" \\\n", @@ -89,7 +89,7 @@ " \"matplotlib==3.10.0\" \\\n", " \"ml-dtypes==0.6.0\" \\\n", " \"more-itertools==10.8.0\" \\\n", - " \"multidict==6.7.1\" \\\n", + " \"multidict==6.9.1\" \\\n", " \"natsort==8.4.0\" \\\n", " \"numcodecs==0.16.5\" \\\n", " \"numpy==2.1.3\" \\\n", @@ -97,8 +97,8 @@ " \"packaging==26.3\" \\\n", " \"pandas==2.2.3\" \\\n", " \"pillow==11.3.0\" \\\n", - " \"platformdirs==4.11.7\" \\\n", - " \"propcache==0.5.2\" \\\n", + " \"platformdirs==4.12.2\" \\\n", + " \"propcache==0.5.4\" \\\n", " \"pycparser==3.0\" \\\n", " \"pycryptodomex==3.23.0\" \\\n", " \"pydantic==2.13.5\" \\\n", @@ -106,7 +106,7 @@ " \"pydantic-settings==2.15.0\" \\\n", " \"pynwb==4.1.0\" \\\n", " \"pyout==0.8.1\" \\\n", - " \"pyparsing==3.3.2\" \\\n", + " \"pyparsing==3.3.3\" \\\n", " \"python-dateutil==2.9.0.post0\" \\\n", " \"python-dotenv==1.2.3\" \\\n", " \"pytz==2025.2\" \\\n", @@ -126,12 +126,12 @@ " \"tqdm==4.67.3\" \\\n", " \"typing-extensions==4.16.0\" \\\n", " \"typing-inspection==0.4.4\" \\\n", - " \"tzdata==2026.3\" \\\n", + " \"tzdata==2026.4\" \\\n", " \"uri-template==1.3.0\" \\\n", " \"urllib3==2.5.0\" \\\n", - " \"wcwidth==0.8.3\" \\\n", + " \"wcwidth==0.9.1\" \\\n", " \"webcolors==25.10.0\" \\\n", - " \"yarl==1.24.5\" \\\n", + " \"yarl==1.25.1\" \\\n", " \"zarr==3.1.5\" \\\n", " \"zarr-checksum==0.4.7\"" ] diff --git a/000458/FlatironInstitute/000_lindi_vs_fsspec_streaming.ipynb b/000458/FlatironInstitute/000_lindi_vs_fsspec_streaming.ipynb index 0f457955..b6abffc6 100644 --- a/000458/FlatironInstitute/000_lindi_vs_fsspec_streaming.ipynb +++ b/000458/FlatironInstitute/000_lindi_vs_fsspec_streaming.ipynb @@ -52,7 +52,7 @@ " \"click==8.5.0\" \\\n", " \"click-didyoumean==0.3.1\" \\\n", " \"cloudpickle==3.1.2\" \\\n", - " \"cryptography==50.0.1\" \\\n", + " \"cryptography==50.0.2\" \\\n", " \"dandi==0.77.0\" \\\n", " \"dandischema==0.14.0\" \\\n", " \"decorator==4.4.2\" \\\n", @@ -62,14 +62,14 @@ " \"email-validator==2.3.0\" \\\n", " \"etelemetry==0.3.1\" \\\n", " \"fasteners==0.20\" \\\n", - " \"fqdn==1.5.1\" \\\n", + " \"fqdn==1.6.0\" \\\n", " \"frozenlist==1.8.0\" \\\n", " \"fscacher==0.4.4\" \\\n", " \"fsspec==2025.12.0\" \\\n", - " \"h5py==3.16.0\" \\\n", + " \"h5py==3.14.0\" \\\n", " \"hdmf==4.3.1\" \\\n", " \"humanize==4.16.0\" \\\n", - " \"idna==3.19\" \\\n", + " \"idna==3.20\" \\\n", " \"interleave==0.3.0\" \\\n", " \"ipython==7.34.0\" \\\n", " \"isodate==0.7.2\" \\\n", @@ -90,7 +90,7 @@ " \"matplotlib-inline==0.2.2\" \\\n", " \"ml-dtypes==0.6.0\" \\\n", " \"more-itertools==10.8.0\" \\\n", - " \"multidict==6.7.1\" \\\n", + " \"multidict==6.9.1\" \\\n", " \"natsort==8.4.0\" \\\n", " \"numcodecs==0.15.1\" \\\n", " \"numpy==2.1.3\" \\\n", @@ -100,9 +100,9 @@ " \"parso==0.8.7\" \\\n", " \"pexpect==4.9.0\" \\\n", " \"pickleshare==0.7.5\" \\\n", - " \"platformdirs==4.11.7\" \\\n", + " \"platformdirs==4.12.2\" \\\n", " \"prompt-toolkit==3.0.53\" \\\n", - " \"propcache==0.5.2\" \\\n", + " \"propcache==0.5.4\" \\\n", " \"ptyprocess==0.7.0\" \\\n", " \"pycparser==3.0\" \\\n", " \"pycryptodomex==3.23.0\" \\\n", @@ -132,13 +132,13 @@ " \"traitlets==5.7.1\" \\\n", " \"typing-extensions==4.16.0\" \\\n", " \"typing-inspection==0.4.4\" \\\n", - " \"tzdata==2026.3\" \\\n", + " \"tzdata==2026.4\" \\\n", " \"uri-template==1.3.0\" \\\n", " \"urllib3==2.5.0\" \\\n", - " \"wcwidth==0.8.3\" \\\n", + " \"wcwidth==0.9.1\" \\\n", " \"webcolors==25.10.0\" \\\n", - " \"wrapt==2.4.0\" \\\n", - " \"yarl==1.24.5\" \\\n", + " \"wrapt==2.5.0\" \\\n", + " \"yarl==1.25.1\" \\\n", " \"zarr==2.18.7\" \\\n", " \"zarr-checksum==0.4.7\"" ] diff --git a/000458/FlatironInstitute/001_summarize_contents.ipynb b/000458/FlatironInstitute/001_summarize_contents.ipynb index c7e79f2c..f65cc814 100644 --- a/000458/FlatironInstitute/001_summarize_contents.ipynb +++ b/000458/FlatironInstitute/001_summarize_contents.ipynb @@ -52,7 +52,7 @@ " \"click==8.5.0\" \\\n", " \"click-didyoumean==0.3.1\" \\\n", " \"cloudpickle==3.1.2\" \\\n", - " \"cryptography==50.0.1\" \\\n", + " \"cryptography==50.0.2\" \\\n", " \"dandi==0.77.0\" \\\n", " \"dandischema==0.14.0\" \\\n", " \"decorator==4.4.2\" \\\n", @@ -62,14 +62,14 @@ " \"email-validator==2.3.0\" \\\n", " \"etelemetry==0.3.1\" \\\n", " \"fasteners==0.20\" \\\n", - " \"fqdn==1.5.1\" \\\n", + " \"fqdn==1.6.0\" \\\n", " \"frozenlist==1.8.0\" \\\n", " \"fscacher==0.4.4\" \\\n", " \"fsspec==2025.12.0\" \\\n", - " \"h5py==3.16.0\" \\\n", + " \"h5py==3.14.0\" \\\n", " \"hdmf==4.3.1\" \\\n", " \"humanize==4.16.0\" \\\n", - " \"idna==3.19\" \\\n", + " \"idna==3.20\" \\\n", " \"interleave==0.3.0\" \\\n", " \"ipython==7.34.0\" \\\n", " \"isodate==0.7.2\" \\\n", @@ -90,7 +90,7 @@ " \"matplotlib-inline==0.2.2\" \\\n", " \"ml-dtypes==0.6.0\" \\\n", " \"more-itertools==10.8.0\" \\\n", - " \"multidict==6.7.1\" \\\n", + " \"multidict==6.9.1\" \\\n", " \"natsort==8.4.0\" \\\n", " \"numcodecs==0.15.1\" \\\n", " \"numpy==2.1.3\" \\\n", @@ -100,9 +100,9 @@ " \"parso==0.8.7\" \\\n", " \"pexpect==4.9.0\" \\\n", " \"pickleshare==0.7.5\" \\\n", - " \"platformdirs==4.11.7\" \\\n", + " \"platformdirs==4.12.2\" \\\n", " \"prompt-toolkit==3.0.53\" \\\n", - " \"propcache==0.5.2\" \\\n", + " \"propcache==0.5.4\" \\\n", " \"ptyprocess==0.7.0\" \\\n", " \"pycparser==3.0\" \\\n", " \"pycryptodomex==3.23.0\" \\\n", @@ -132,13 +132,13 @@ " \"traitlets==5.7.1\" \\\n", " \"typing-extensions==4.16.0\" \\\n", " \"typing-inspection==0.4.4\" \\\n", - " \"tzdata==2026.3\" \\\n", + " \"tzdata==2026.4\" \\\n", " \"uri-template==1.3.0\" \\\n", " \"urllib3==2.5.0\" \\\n", - " \"wcwidth==0.8.3\" \\\n", + " \"wcwidth==0.9.1\" \\\n", " \"webcolors==25.10.0\" \\\n", - " \"wrapt==2.4.0\" \\\n", - " \"yarl==1.24.5\" \\\n", + " \"wrapt==2.5.0\" \\\n", + " \"yarl==1.25.1\" \\\n", " \"zarr==2.18.7\" \\\n", " \"zarr-checksum==0.4.7\"\n", "!curl --create-dirs -sL -o helpers/stream_nwbfile.py https://raw.githubusercontent.com/dandi/example-notebooks/master/000458/FlatironInstitute/helpers/stream_nwbfile.py" diff --git a/000559/dattalab/markowitz_gillis_nature_2023/reproduce_figure1d.ipynb b/000559/dattalab/markowitz_gillis_nature_2023/reproduce_figure1d.ipynb index 5a0b2c96..bf097ebf 100644 --- a/000559/dattalab/markowitz_gillis_nature_2023/reproduce_figure1d.ipynb +++ b/000559/dattalab/markowitz_gillis_nature_2023/reproduce_figure1d.ipynb @@ -52,8 +52,8 @@ " \"click-didyoumean==0.3.1\" \\\n", " \"cloudpickle==3.1.2\" \\\n", " \"colorcet==3.2.1\" \\\n", - " \"contourpy==1.3.3\" \\\n", - " \"cryptography==50.0.1\" \\\n", + " \"contourpy==1.4.0\" \\\n", + " \"cryptography==50.0.2\" \\\n", " \"cycler==0.12.1\" \\\n", " \"dandi==0.77.0\" \\\n", " \"dandischema==0.14.0\" \\\n", @@ -64,16 +64,16 @@ " \"email-validator==2.3.0\" \\\n", " \"etelemetry==0.3.1\" \\\n", " \"fasteners==0.20\" \\\n", - " \"fonttools==4.64.0\" \\\n", - " \"fqdn==1.5.1\" \\\n", + " \"fonttools==4.66.1\" \\\n", + " \"fqdn==1.6.0\" \\\n", " \"frozenlist==1.8.0\" \\\n", " \"fscacher==0.4.4\" \\\n", " \"fsspec==2025.12.0\" \\\n", - " \"h5py==3.16.0\" \\\n", + " \"h5py==3.14.0\" \\\n", " \"hdmf==4.3.1\" \\\n", " \"hdmf-zarr==0.13.0\" \\\n", " \"humanize==4.16.0\" \\\n", - " \"idna==3.19\" \\\n", + " \"idna==3.20\" \\\n", " \"interleave==0.3.0\" \\\n", " \"isodate==0.7.2\" \\\n", " \"isoduration==20.11.0\" \\\n", @@ -92,7 +92,7 @@ " \"matplotlib==3.10.0\" \\\n", " \"ml-dtypes==0.6.0\" \\\n", " \"more-itertools==10.8.0\" \\\n", - " \"multidict==6.7.1\" \\\n", + " \"multidict==6.9.1\" \\\n", " \"natsort==8.4.0\" \\\n", " \"neuroconv==0.9.3\" \\\n", " \"numcodecs==0.15.1\" \\\n", @@ -102,8 +102,8 @@ " \"pandas==2.2.3\" \\\n", " \"parse==1.22.1\" \\\n", " \"pillow==11.3.0\" \\\n", - " \"platformdirs==4.11.7\" \\\n", - " \"propcache==0.5.2\" \\\n", + " \"platformdirs==4.12.2\" \\\n", + " \"propcache==0.5.4\" \\\n", " \"psutil==5.9.5\" \\\n", " \"pycparser==3.0\" \\\n", " \"pycryptodomex==3.23.0\" \\\n", @@ -112,7 +112,7 @@ " \"pydantic-settings==2.15.0\" \\\n", " \"pynwb==3.1.3\" \\\n", " \"pyout==0.8.1\" \\\n", - " \"pyparsing==3.3.2\" \\\n", + " \"pyparsing==3.3.3\" \\\n", " \"python-dateutil==2.9.0.post0\" \\\n", " \"python-dotenv==1.2.3\" \\\n", " \"pytz==2025.2\" \\\n", @@ -128,17 +128,17 @@ " \"six==1.17.0\" \\\n", " \"tenacity==9.1.4\" \\\n", " \"tensorstore==0.1.85\" \\\n", - " \"threadpoolctl==3.6.0\" \\\n", + " \"threadpoolctl==3.7.0\" \\\n", " \"tqdm==4.67.3\" \\\n", " \"typing-extensions==4.16.0\" \\\n", " \"typing-inspection==0.4.4\" \\\n", - " \"tzdata==2026.3\" \\\n", + " \"tzdata==2026.4\" \\\n", " \"uri-template==1.3.0\" \\\n", " \"urllib3==2.5.0\" \\\n", - " \"wcwidth==0.8.3\" \\\n", + " \"wcwidth==0.9.1\" \\\n", " \"webcolors==25.10.0\" \\\n", - " \"wrapt==2.4.0\" \\\n", - " \"yarl==1.24.5\" \\\n", + " \"wrapt==2.5.0\" \\\n", + " \"yarl==1.25.1\" \\\n", " \"zarr==2.18.7\" \\\n", " \"zarr-checksum==0.4.7\"\n", "!curl -sL -o stream_nwbfile.py https://raw.githubusercontent.com/dandi/example-notebooks/master/000559/dattalab/markowitz_gillis_nature_2023/stream_nwbfile.py" diff --git a/000559/dattalab/markowitz_gillis_nature_2023/reproduce_figure_S1.ipynb b/000559/dattalab/markowitz_gillis_nature_2023/reproduce_figure_S1.ipynb index b9c7a168..51d2bcd1 100644 --- a/000559/dattalab/markowitz_gillis_nature_2023/reproduce_figure_S1.ipynb +++ b/000559/dattalab/markowitz_gillis_nature_2023/reproduce_figure_S1.ipynb @@ -51,8 +51,8 @@ " \"click==8.5.0\" \\\n", " \"click-didyoumean==0.3.1\" \\\n", " \"cloudpickle==3.1.2\" \\\n", - " \"contourpy==1.3.3\" \\\n", - " \"cryptography==50.0.1\" \\\n", + " \"contourpy==1.4.0\" \\\n", + " \"cryptography==50.0.2\" \\\n", " \"cuda-bindings==12.9.4\" \\\n", " \"cuda-pathfinder==1.6.1\" \\\n", " \"cycler==0.12.1\" \\\n", @@ -65,19 +65,19 @@ " \"etelemetry==0.3.1\" \\\n", " \"fasteners==0.20\" \\\n", " \"fastremap==1.20.0\" \\\n", - " \"filelock==3.32.5\" \\\n", - " \"fonttools==4.64.0\" \\\n", - " \"fqdn==1.5.1\" \\\n", + " \"filelock==4.0.7\" \\\n", + " \"fonttools==4.66.1\" \\\n", + " \"fqdn==1.6.0\" \\\n", " \"frozenlist==1.8.0\" \\\n", " \"fscacher==0.4.4\" \\\n", " \"fsspec==2025.12.0\" \\\n", - " \"google-crc32c==1.8.0\" \\\n", - " \"h5py==3.16.0\" \\\n", + " \"google-crc32c==1.9.0\" \\\n", + " \"h5py==3.14.0\" \\\n", " \"hdmf==4.3.1\" \\\n", " \"humanize==4.16.0\" \\\n", - " \"idna==3.19\" \\\n", + " \"idna==3.20\" \\\n", " \"imagecodecs==2026.8.16\" \\\n", - " \"imageio==2.37.4\" \\\n", + " \"imageio==2.38.0\" \\\n", " \"interleave==0.3.0\" \\\n", " \"isodate==0.7.2\" \\\n", " \"isoduration==20.11.0\" \\\n", @@ -94,16 +94,16 @@ " \"keyring==25.7.0\" \\\n", " \"keyrings-alt==5.0.2\" \\\n", " \"kiwisolver==1.5.1\" \\\n", - " \"lazy-loader==0.5\" \\\n", + " \"lazy-loader==0.6\" \\\n", " \"llvmlite==0.44.0\" \\\n", " \"markupsafe==3.0.3\" \\\n", " \"matplotlib==3.10.0\" \\\n", " \"ml-dtypes==0.6.0\" \\\n", " \"more-itertools==10.8.0\" \\\n", " \"mpmath==1.3.0\" \\\n", - " \"multidict==6.7.1\" \\\n", + " \"multidict==6.9.1\" \\\n", " \"natsort==8.4.0\" \\\n", - " \"networkx==3.6.1\" \\\n", + " \"networkx==3.7\" \\\n", " \"numba==0.61.2\" \\\n", " \"numcodecs==0.16.5\" \\\n", " \"numpy==2.1.3\" \\\n", @@ -127,8 +127,8 @@ " \"packaging==26.3\" \\\n", " \"pandas==2.2.3\" \\\n", " \"pillow==11.3.0\" \\\n", - " \"platformdirs==4.11.7\" \\\n", - " \"propcache==0.5.2\" \\\n", + " \"platformdirs==4.12.2\" \\\n", + " \"propcache==0.5.4\" \\\n", " \"pycparser==3.0\" \\\n", " \"pycryptodomex==3.23.0\" \\\n", " \"pydantic==2.13.5\" \\\n", @@ -136,7 +136,7 @@ " \"pydantic-settings==2.15.0\" \\\n", " \"pynwb==3.1.3\" \\\n", " \"pyout==0.8.1\" \\\n", - " \"pyparsing==3.3.2\" \\\n", + " \"pyparsing==3.3.3\" \\\n", " \"python-dateutil==2.9.0.post0\" \\\n", " \"python-dotenv==1.2.3\" \\\n", " \"pytz==2025.2\" \\\n", @@ -158,18 +158,18 @@ " \"sympy==1.14.0\" \\\n", " \"tenacity==9.1.4\" \\\n", " \"tensorstore==0.1.85\" \\\n", - " \"tifffile==2026.8.23\" \\\n", + " \"tifffile==2026.9.20\" \\\n", " \"torch==2.10.0\" \\\n", " \"tqdm==4.67.3\" \\\n", " \"triton==3.6.0\" \\\n", " \"typing-extensions==4.16.0\" \\\n", " \"typing-inspection==0.4.4\" \\\n", - " \"tzdata==2026.3\" \\\n", + " \"tzdata==2026.4\" \\\n", " \"uri-template==1.3.0\" \\\n", " \"urllib3==2.5.0\" \\\n", - " \"wcwidth==0.8.3\" \\\n", + " \"wcwidth==0.9.1\" \\\n", " \"webcolors==25.10.0\" \\\n", - " \"yarl==1.24.5\" \\\n", + " \"yarl==1.25.1\" \\\n", " \"zarr==3.1.5\" \\\n", " \"zarr-checksum==0.4.7\"\n", "!curl -sL -o stream_nwbfile.py https://raw.githubusercontent.com/dandi/example-notebooks/master/000559/dattalab/markowitz_gillis_nature_2023/stream_nwbfile.py" diff --git a/000582/Sargolini2006/000582_Sargolini2006_demo.ipynb b/000582/Sargolini2006/000582_Sargolini2006_demo.ipynb index f933d514..e4625713 100644 --- a/000582/Sargolini2006/000582_Sargolini2006_demo.ipynb +++ b/000582/Sargolini2006/000582_Sargolini2006_demo.ipynb @@ -50,7 +50,7 @@ " \"click==8.5.0\" \\\n", " \"click-didyoumean==0.3.1\" \\\n", " \"cloudpickle==3.1.2\" \\\n", - " \"cryptography==50.0.1\" \\\n", + " \"cryptography==50.0.2\" \\\n", " \"dandi==0.77.0\" \\\n", " \"dandischema==0.14.0\" \\\n", " \"deno==2.9.5\" \\\n", @@ -59,15 +59,15 @@ " \"email-validator==2.3.0\" \\\n", " \"etelemetry==0.3.1\" \\\n", " \"fasteners==0.20\" \\\n", - " \"fqdn==1.5.1\" \\\n", + " \"fqdn==1.6.0\" \\\n", " \"frozenlist==1.8.0\" \\\n", " \"fscacher==0.4.4\" \\\n", " \"fsspec==2025.12.0\" \\\n", - " \"google-crc32c==1.8.0\" \\\n", - " \"h5py==3.16.0\" \\\n", + " \"google-crc32c==1.9.0\" \\\n", + " \"h5py==3.14.0\" \\\n", " \"hdmf==4.3.1\" \\\n", " \"humanize==4.16.0\" \\\n", - " \"idna==3.19\" \\\n", + " \"idna==3.20\" \\\n", " \"interleave==0.3.0\" \\\n", " \"isodate==0.7.2\" \\\n", " \"isoduration==20.11.0\" \\\n", @@ -87,7 +87,7 @@ " \"mdurl==0.1.2\" \\\n", " \"ml-dtypes==0.6.0\" \\\n", " \"more-itertools==10.8.0\" \\\n", - " \"multidict==6.7.1\" \\\n", + " \"multidict==6.9.1\" \\\n", " \"natsort==8.4.0\" \\\n", " \"neo==0.14.5\" \\\n", " \"numba==0.61.2\" \\\n", @@ -96,9 +96,9 @@ " \"nwbinspector==0.7.2\" \\\n", " \"packaging==26.3\" \\\n", " \"pandas==2.2.3\" \\\n", - " \"platformdirs==4.11.7\" \\\n", + " \"platformdirs==4.12.2\" \\\n", " \"plotly==5.24.1\" \\\n", - " \"propcache==0.5.2\" \\\n", + " \"propcache==0.5.4\" \\\n", " \"pycparser==3.0\" \\\n", " \"pycryptodomex==3.23.0\" \\\n", " \"pydantic==2.13.5\" \\\n", @@ -130,13 +130,13 @@ " \"tqdm==4.67.3\" \\\n", " \"typing-extensions==4.16.0\" \\\n", " \"typing-inspection==0.4.4\" \\\n", - " \"tzdata==2026.3\" \\\n", + " \"tzdata==2026.4\" \\\n", " \"uri-template==1.3.0\" \\\n", " \"urllib3==2.5.0\" \\\n", - " \"wcwidth==0.8.3\" \\\n", + " \"wcwidth==0.9.1\" \\\n", " \"webcolors==25.10.0\" \\\n", " \"xarray==2025.12.0\" \\\n", - " \"yarl==1.24.5\" \\\n", + " \"yarl==1.25.1\" \\\n", " \"zarr==3.1.5\" \\\n", " \"zarr-checksum==0.4.7\"" ] diff --git a/000718/CaiLab/zaki_2024/000718_demo.ipynb b/000718/CaiLab/zaki_2024/000718_demo.ipynb index 9abb76e6..8404f87c 100644 --- a/000718/CaiLab/zaki_2024/000718_demo.ipynb +++ b/000718/CaiLab/zaki_2024/000718_demo.ipynb @@ -50,8 +50,8 @@ " \"click==8.5.0\" \\\n", " \"click-didyoumean==0.3.1\" \\\n", " \"cloudpickle==3.1.2\" \\\n", - " \"contourpy==1.3.3\" \\\n", - " \"cryptography==50.0.1\" \\\n", + " \"contourpy==1.4.0\" \\\n", + " \"cryptography==50.0.2\" \\\n", " \"cycler==0.12.1\" \\\n", " \"dandi==0.77.0\" \\\n", " \"dandischema==0.14.0\" \\\n", @@ -61,16 +61,16 @@ " \"email-validator==2.3.0\" \\\n", " \"etelemetry==0.3.1\" \\\n", " \"fasteners==0.20\" \\\n", - " \"fonttools==4.64.0\" \\\n", - " \"fqdn==1.5.1\" \\\n", + " \"fonttools==4.66.1\" \\\n", + " \"fqdn==1.6.0\" \\\n", " \"frozenlist==1.8.0\" \\\n", " \"fscacher==0.4.4\" \\\n", " \"fsspec==2025.12.0\" \\\n", - " \"google-crc32c==1.8.0\" \\\n", - " \"h5py==3.16.0\" \\\n", + " \"google-crc32c==1.9.0\" \\\n", + " \"h5py==3.14.0\" \\\n", " \"hdmf==4.3.1\" \\\n", " \"humanize==4.16.0\" \\\n", - " \"idna==3.19\" \\\n", + " \"idna==3.20\" \\\n", " \"interleave==0.3.0\" \\\n", " \"isodate==0.7.2\" \\\n", " \"isoduration==20.11.0\" \\\n", @@ -89,7 +89,7 @@ " \"matplotlib==3.10.0\" \\\n", " \"ml-dtypes==0.6.0\" \\\n", " \"more-itertools==10.8.0\" \\\n", - " \"multidict==6.7.1\" \\\n", + " \"multidict==6.9.1\" \\\n", " \"natsort==8.4.0\" \\\n", " \"numcodecs==0.16.5\" \\\n", " \"numpy==2.1.3\" \\\n", @@ -97,8 +97,8 @@ " \"packaging==26.3\" \\\n", " \"pandas==2.2.3\" \\\n", " \"pillow==11.3.0\" \\\n", - " \"platformdirs==4.11.7\" \\\n", - " \"propcache==0.5.2\" \\\n", + " \"platformdirs==4.12.2\" \\\n", + " \"propcache==0.5.4\" \\\n", " \"pycparser==3.0\" \\\n", " \"pycryptodomex==3.23.0\" \\\n", " \"pydantic==2.13.5\" \\\n", @@ -106,7 +106,7 @@ " \"pydantic-settings==2.15.0\" \\\n", " \"pynwb==3.1.3\" \\\n", " \"pyout==0.8.1\" \\\n", - " \"pyparsing==3.3.2\" \\\n", + " \"pyparsing==3.3.3\" \\\n", " \"python-dateutil==2.9.0.post0\" \\\n", " \"python-dotenv==1.2.3\" \\\n", " \"pytz==2025.2\" \\\n", @@ -126,12 +126,12 @@ " \"tqdm==4.67.3\" \\\n", " \"typing-extensions==4.16.0\" \\\n", " \"typing-inspection==0.4.4\" \\\n", - " \"tzdata==2026.3\" \\\n", + " \"tzdata==2026.4\" \\\n", " \"uri-template==1.3.0\" \\\n", " \"urllib3==2.5.0\" \\\n", - " \"wcwidth==0.8.3\" \\\n", + " \"wcwidth==0.9.1\" \\\n", " \"webcolors==25.10.0\" \\\n", - " \"yarl==1.24.5\" \\\n", + " \"yarl==1.25.1\" \\\n", " \"zarr==3.1.5\" \\\n", " \"zarr-checksum==0.4.7\"" ] diff --git a/000727/clandinin/simple_data_access/reading_data.ipynb b/000727/clandinin/simple_data_access/reading_data.ipynb index eae965eb..1932144c 100644 --- a/000727/clandinin/simple_data_access/reading_data.ipynb +++ b/000727/clandinin/simple_data_access/reading_data.ipynb @@ -50,8 +50,8 @@ " \"click==8.5.0\" \\\n", " \"click-didyoumean==0.3.1\" \\\n", " \"cloudpickle==3.1.2\" \\\n", - " \"contourpy==1.3.3\" \\\n", - " \"cryptography==50.0.1\" \\\n", + " \"contourpy==1.4.0\" \\\n", + " \"cryptography==50.0.2\" \\\n", " \"cycler==0.12.1\" \\\n", " \"dandi==0.77.0\" \\\n", " \"dandischema==0.14.0\" \\\n", @@ -61,16 +61,16 @@ " \"email-validator==2.3.0\" \\\n", " \"etelemetry==0.3.1\" \\\n", " \"fasteners==0.20\" \\\n", - " \"fonttools==4.64.0\" \\\n", - " \"fqdn==1.5.1\" \\\n", + " \"fonttools==4.66.1\" \\\n", + " \"fqdn==1.6.0\" \\\n", " \"frozenlist==1.8.0\" \\\n", " \"fscacher==0.4.4\" \\\n", " \"fsspec==2025.12.0\" \\\n", - " \"google-crc32c==1.8.0\" \\\n", - " \"h5py==3.16.0\" \\\n", + " \"google-crc32c==1.9.0\" \\\n", + " \"h5py==3.14.0\" \\\n", " \"hdmf==4.3.1\" \\\n", " \"humanize==4.16.0\" \\\n", - " \"idna==3.19\" \\\n", + " \"idna==3.20\" \\\n", " \"interleave==0.3.0\" \\\n", " \"isodate==0.7.2\" \\\n", " \"isoduration==20.11.0\" \\\n", @@ -89,7 +89,7 @@ " \"matplotlib==3.10.0\" \\\n", " \"ml-dtypes==0.6.0\" \\\n", " \"more-itertools==10.8.0\" \\\n", - " \"multidict==6.7.1\" \\\n", + " \"multidict==6.9.1\" \\\n", " \"natsort==8.4.0\" \\\n", " \"numcodecs==0.16.5\" \\\n", " \"numpy==2.1.3\" \\\n", @@ -97,8 +97,8 @@ " \"packaging==26.3\" \\\n", " \"pandas==2.2.3\" \\\n", " \"pillow==11.3.0\" \\\n", - " \"platformdirs==4.11.7\" \\\n", - " \"propcache==0.5.2\" \\\n", + " \"platformdirs==4.12.2\" \\\n", + " \"propcache==0.5.4\" \\\n", " \"pycparser==3.0\" \\\n", " \"pycryptodomex==3.23.0\" \\\n", " \"pydantic==2.13.5\" \\\n", @@ -106,7 +106,7 @@ " \"pydantic-settings==2.15.0\" \\\n", " \"pynwb==3.1.3\" \\\n", " \"pyout==0.8.1\" \\\n", - " \"pyparsing==3.3.2\" \\\n", + " \"pyparsing==3.3.3\" \\\n", " \"python-dateutil==2.9.0.post0\" \\\n", " \"python-dotenv==1.2.3\" \\\n", " \"pytz==2025.2\" \\\n", @@ -126,12 +126,12 @@ " \"tqdm==4.67.3\" \\\n", " \"typing-extensions==4.16.0\" \\\n", " \"typing-inspection==0.4.4\" \\\n", - " \"tzdata==2026.3\" \\\n", + " \"tzdata==2026.4\" \\\n", " \"uri-template==1.3.0\" \\\n", " \"urllib3==2.5.0\" \\\n", - " \"wcwidth==0.8.3\" \\\n", + " \"wcwidth==0.9.1\" \\\n", " \"webcolors==25.10.0\" \\\n", - " \"yarl==1.24.5\" \\\n", + " \"yarl==1.25.1\" \\\n", " \"zarr==3.1.5\" \\\n", " \"zarr-checksum==0.4.7\"" ] diff --git a/000728/AllenInstitute/visual_coding_ophys_tutorial.ipynb b/000728/AllenInstitute/visual_coding_ophys_tutorial.ipynb index 6ca3f099..3e8de39b 100644 --- a/000728/AllenInstitute/visual_coding_ophys_tutorial.ipynb +++ b/000728/AllenInstitute/visual_coding_ophys_tutorial.ipynb @@ -50,8 +50,8 @@ " \"click==8.5.0\" \\\n", " \"click-didyoumean==0.3.1\" \\\n", " \"cloudpickle==3.1.2\" \\\n", - " \"contourpy==1.3.3\" \\\n", - " \"cryptography==50.0.1\" \\\n", + " \"contourpy==1.4.0\" \\\n", + " \"cryptography==50.0.2\" \\\n", " \"cycler==0.12.1\" \\\n", " \"dandi==0.77.0\" \\\n", " \"dandischema==0.14.0\" \\\n", @@ -61,16 +61,16 @@ " \"email-validator==2.3.0\" \\\n", " \"etelemetry==0.3.1\" \\\n", " \"fasteners==0.20\" \\\n", - " \"fonttools==4.64.0\" \\\n", - " \"fqdn==1.5.1\" \\\n", + " \"fonttools==4.66.1\" \\\n", + " \"fqdn==1.6.0\" \\\n", " \"frozenlist==1.8.0\" \\\n", " \"fscacher==0.4.4\" \\\n", " \"fsspec==2025.12.0\" \\\n", - " \"google-crc32c==1.8.0\" \\\n", - " \"h5py==3.16.0\" \\\n", + " \"google-crc32c==1.9.0\" \\\n", + " \"h5py==3.14.0\" \\\n", " \"hdmf==4.3.1\" \\\n", " \"humanize==4.16.0\" \\\n", - " \"idna==3.19\" \\\n", + " \"idna==3.20\" \\\n", " \"interleave==0.3.0\" \\\n", " \"isodate==0.7.2\" \\\n", " \"isoduration==20.11.0\" \\\n", @@ -89,7 +89,7 @@ " \"matplotlib==3.10.0\" \\\n", " \"ml-dtypes==0.6.0\" \\\n", " \"more-itertools==10.8.0\" \\\n", - " \"multidict==6.7.1\" \\\n", + " \"multidict==6.9.1\" \\\n", " \"natsort==8.4.0\" \\\n", " \"numcodecs==0.16.5\" \\\n", " \"numpy==2.1.3\" \\\n", @@ -97,8 +97,8 @@ " \"packaging==26.3\" \\\n", " \"pandas==2.2.3\" \\\n", " \"pillow==11.3.0\" \\\n", - " \"platformdirs==4.11.7\" \\\n", - " \"propcache==0.5.2\" \\\n", + " \"platformdirs==4.12.2\" \\\n", + " \"propcache==0.5.4\" \\\n", " \"pycparser==3.0\" \\\n", " \"pycryptodomex==3.23.0\" \\\n", " \"pydantic==2.13.5\" \\\n", @@ -106,7 +106,7 @@ " \"pydantic-settings==2.15.0\" \\\n", " \"pynwb==3.1.3\" \\\n", " \"pyout==0.8.1\" \\\n", - " \"pyparsing==3.3.2\" \\\n", + " \"pyparsing==3.3.3\" \\\n", " \"python-dateutil==2.9.0.post0\" \\\n", " \"python-dotenv==1.2.3\" \\\n", " \"pytz==2025.2\" \\\n", @@ -127,12 +127,12 @@ " \"tqdm==4.67.3\" \\\n", " \"typing-extensions==4.16.0\" \\\n", " \"typing-inspection==0.4.4\" \\\n", - " \"tzdata==2026.3\" \\\n", + " \"tzdata==2026.4\" \\\n", " \"uri-template==1.3.0\" \\\n", " \"urllib3==2.5.0\" \\\n", - " \"wcwidth==0.8.3\" \\\n", + " \"wcwidth==0.9.1\" \\\n", " \"webcolors==25.10.0\" \\\n", - " \"yarl==1.24.5\" \\\n", + " \"yarl==1.25.1\" \\\n", " \"zarr==3.1.5\" \\\n", " \"zarr-checksum==0.4.7\"" ] diff --git a/000947/TurnerLab/public_demo/000947_demo.ipynb b/000947/TurnerLab/public_demo/000947_demo.ipynb index d5115bff..70570e93 100644 --- a/000947/TurnerLab/public_demo/000947_demo.ipynb +++ b/000947/TurnerLab/public_demo/000947_demo.ipynb @@ -50,8 +50,8 @@ " \"click==8.5.0\" \\\n", " \"click-didyoumean==0.3.1\" \\\n", " \"cloudpickle==3.1.2\" \\\n", - " \"contourpy==1.3.3\" \\\n", - " \"cryptography==50.0.1\" \\\n", + " \"contourpy==1.4.0\" \\\n", + " \"cryptography==50.0.2\" \\\n", " \"cycler==0.12.1\" \\\n", " \"dandi==0.77.0\" \\\n", " \"dandischema==0.14.0\" \\\n", @@ -61,16 +61,16 @@ " \"email-validator==2.3.0\" \\\n", " \"etelemetry==0.3.1\" \\\n", " \"fasteners==0.20\" \\\n", - " \"fonttools==4.64.0\" \\\n", - " \"fqdn==1.5.1\" \\\n", + " \"fonttools==4.66.1\" \\\n", + " \"fqdn==1.6.0\" \\\n", " \"frozenlist==1.8.0\" \\\n", " \"fscacher==0.4.4\" \\\n", " \"fsspec==2025.12.0\" \\\n", - " \"google-crc32c==1.8.0\" \\\n", - " \"h5py==3.16.0\" \\\n", + " \"google-crc32c==1.9.0\" \\\n", + " \"h5py==3.14.0\" \\\n", " \"hdmf==4.3.1\" \\\n", " \"humanize==4.16.0\" \\\n", - " \"idna==3.19\" \\\n", + " \"idna==3.20\" \\\n", " \"interleave==0.3.0\" \\\n", " \"isodate==0.7.2\" \\\n", " \"isoduration==20.11.0\" \\\n", @@ -92,7 +92,7 @@ " \"mdurl==0.1.2\" \\\n", " \"ml-dtypes==0.6.0\" \\\n", " \"more-itertools==10.8.0\" \\\n", - " \"multidict==6.7.1\" \\\n", + " \"multidict==6.9.1\" \\\n", " \"natsort==8.4.0\" \\\n", " \"numba==0.61.2\" \\\n", " \"numcodecs==0.16.5\" \\\n", @@ -101,8 +101,8 @@ " \"packaging==26.3\" \\\n", " \"pandas==2.2.3\" \\\n", " \"pillow==11.3.0\" \\\n", - " \"platformdirs==4.11.7\" \\\n", - " \"propcache==0.5.2\" \\\n", + " \"platformdirs==4.12.2\" \\\n", + " \"propcache==0.5.4\" \\\n", " \"pycparser==3.0\" \\\n", " \"pycryptodomex==3.23.0\" \\\n", " \"pydantic==2.13.5\" \\\n", @@ -112,7 +112,7 @@ " \"pynapple==0.7.1\" \\\n", " \"pynwb==3.1.3\" \\\n", " \"pyout==0.8.1\" \\\n", - " \"pyparsing==3.3.2\" \\\n", + " \"pyparsing==3.3.3\" \\\n", " \"python-dateutil==2.9.0.post0\" \\\n", " \"python-dotenv==1.2.3\" \\\n", " \"pytz==2025.2\" \\\n", @@ -135,12 +135,12 @@ " \"tqdm==4.67.3\" \\\n", " \"typing-extensions==4.16.0\" \\\n", " \"typing-inspection==0.4.4\" \\\n", - " \"tzdata==2026.3\" \\\n", + " \"tzdata==2026.4\" \\\n", " \"uri-template==1.3.0\" \\\n", " \"urllib3==2.5.0\" \\\n", - " \"wcwidth==0.8.3\" \\\n", + " \"wcwidth==0.9.1\" \\\n", " \"webcolors==25.10.0\" \\\n", - " \"yarl==1.24.5\" \\\n", + " \"yarl==1.25.1\" \\\n", " \"zarr==3.1.5\" \\\n", " \"zarr-checksum==0.4.7\"" ] diff --git a/000971/lernerlab/seiler_2024/fiber_photometry_example_notebook.ipynb b/000971/lernerlab/seiler_2024/fiber_photometry_example_notebook.ipynb index aa5bb95b..358b1da4 100644 --- a/000971/lernerlab/seiler_2024/fiber_photometry_example_notebook.ipynb +++ b/000971/lernerlab/seiler_2024/fiber_photometry_example_notebook.ipynb @@ -50,8 +50,8 @@ " \"click==8.5.0\" \\\n", " \"click-didyoumean==0.3.1\" \\\n", " \"cloudpickle==3.1.2\" \\\n", - " \"contourpy==1.3.3\" \\\n", - " \"cryptography==50.0.1\" \\\n", + " \"contourpy==1.4.0\" \\\n", + " \"cryptography==50.0.2\" \\\n", " \"cycler==0.12.1\" \\\n", " \"dandi==0.77.0\" \\\n", " \"dandischema==0.14.0\" \\\n", @@ -61,16 +61,16 @@ " \"email-validator==2.3.0\" \\\n", " \"etelemetry==0.3.1\" \\\n", " \"fasteners==0.20\" \\\n", - " \"fonttools==4.64.0\" \\\n", - " \"fqdn==1.5.1\" \\\n", + " \"fonttools==4.66.1\" \\\n", + " \"fqdn==1.6.0\" \\\n", " \"frozenlist==1.8.0\" \\\n", " \"fscacher==0.4.4\" \\\n", " \"fsspec==2025.12.0\" \\\n", - " \"google-crc32c==1.8.0\" \\\n", - " \"h5py==3.16.0\" \\\n", + " \"google-crc32c==1.9.0\" \\\n", + " \"h5py==3.14.0\" \\\n", " \"hdmf==4.3.1\" \\\n", " \"humanize==4.16.0\" \\\n", - " \"idna==3.19\" \\\n", + " \"idna==3.20\" \\\n", " \"interleave==0.3.0\" \\\n", " \"isodate==0.7.2\" \\\n", " \"isoduration==20.11.0\" \\\n", @@ -89,7 +89,7 @@ " \"matplotlib==3.10.0\" \\\n", " \"ml-dtypes==0.6.0\" \\\n", " \"more-itertools==10.8.0\" \\\n", - " \"multidict==6.7.1\" \\\n", + " \"multidict==6.9.1\" \\\n", " \"natsort==8.4.0\" \\\n", " \"numcodecs==0.16.5\" \\\n", " \"numpy==2.1.3\" \\\n", @@ -97,8 +97,8 @@ " \"packaging==26.3\" \\\n", " \"pandas==2.2.3\" \\\n", " \"pillow==11.3.0\" \\\n", - " \"platformdirs==4.11.7\" \\\n", - " \"propcache==0.5.2\" \\\n", + " \"platformdirs==4.12.2\" \\\n", + " \"propcache==0.5.4\" \\\n", " \"pycparser==3.0\" \\\n", " \"pycryptodomex==3.23.0\" \\\n", " \"pydantic==2.13.5\" \\\n", @@ -106,7 +106,7 @@ " \"pydantic-settings==2.15.0\" \\\n", " \"pynwb==3.1.3\" \\\n", " \"pyout==0.8.1\" \\\n", - " \"pyparsing==3.3.2\" \\\n", + " \"pyparsing==3.3.3\" \\\n", " \"python-dateutil==2.9.0.post0\" \\\n", " \"python-dotenv==1.2.3\" \\\n", " \"pytz==2025.2\" \\\n", @@ -125,12 +125,12 @@ " \"tqdm==4.67.3\" \\\n", " \"typing-extensions==4.16.0\" \\\n", " \"typing-inspection==0.4.4\" \\\n", - " \"tzdata==2026.3\" \\\n", + " \"tzdata==2026.4\" \\\n", " \"uri-template==1.3.0\" \\\n", " \"urllib3==2.5.0\" \\\n", - " \"wcwidth==0.8.3\" \\\n", + " \"wcwidth==0.9.1\" \\\n", " \"webcolors==25.10.0\" \\\n", - " \"yarl==1.24.5\" \\\n", + " \"yarl==1.25.1\" \\\n", " \"zarr==3.1.5\" \\\n", " \"zarr-checksum==0.4.7\"\n", "!curl -sL -o stream_nwbfile.py https://raw.githubusercontent.com/dandi/example-notebooks/master/000971/lernerlab/seiler_2024/stream_nwbfile.py" diff --git a/000971/lernerlab/seiler_2024/optogenetics_example_notebook.ipynb b/000971/lernerlab/seiler_2024/optogenetics_example_notebook.ipynb index cad6708d..5c2eceb2 100644 --- a/000971/lernerlab/seiler_2024/optogenetics_example_notebook.ipynb +++ b/000971/lernerlab/seiler_2024/optogenetics_example_notebook.ipynb @@ -50,8 +50,8 @@ " \"click==8.5.0\" \\\n", " \"click-didyoumean==0.3.1\" \\\n", " \"cloudpickle==3.1.2\" \\\n", - " \"contourpy==1.3.3\" \\\n", - " \"cryptography==50.0.1\" \\\n", + " \"contourpy==1.4.0\" \\\n", + " \"cryptography==50.0.2\" \\\n", " \"cycler==0.12.1\" \\\n", " \"dandi==0.77.0\" \\\n", " \"dandischema==0.14.0\" \\\n", @@ -61,16 +61,16 @@ " \"email-validator==2.3.0\" \\\n", " \"etelemetry==0.3.1\" \\\n", " \"fasteners==0.20\" \\\n", - " \"fonttools==4.64.0\" \\\n", - " \"fqdn==1.5.1\" \\\n", + " \"fonttools==4.66.1\" \\\n", + " \"fqdn==1.6.0\" \\\n", " \"frozenlist==1.8.0\" \\\n", " \"fscacher==0.4.4\" \\\n", " \"fsspec==2025.12.0\" \\\n", - " \"google-crc32c==1.8.0\" \\\n", - " \"h5py==3.16.0\" \\\n", + " \"google-crc32c==1.9.0\" \\\n", + " \"h5py==3.14.0\" \\\n", " \"hdmf==4.3.1\" \\\n", " \"humanize==4.16.0\" \\\n", - " \"idna==3.19\" \\\n", + " \"idna==3.20\" \\\n", " \"interleave==0.3.0\" \\\n", " \"isodate==0.7.2\" \\\n", " \"isoduration==20.11.0\" \\\n", @@ -89,7 +89,7 @@ " \"matplotlib==3.10.0\" \\\n", " \"ml-dtypes==0.6.0\" \\\n", " \"more-itertools==10.8.0\" \\\n", - " \"multidict==6.7.1\" \\\n", + " \"multidict==6.9.1\" \\\n", " \"natsort==8.4.0\" \\\n", " \"numcodecs==0.16.5\" \\\n", " \"numpy==2.1.3\" \\\n", @@ -97,8 +97,8 @@ " \"packaging==26.3\" \\\n", " \"pandas==2.2.3\" \\\n", " \"pillow==11.3.0\" \\\n", - " \"platformdirs==4.11.7\" \\\n", - " \"propcache==0.5.2\" \\\n", + " \"platformdirs==4.12.2\" \\\n", + " \"propcache==0.5.4\" \\\n", " \"pycparser==3.0\" \\\n", " \"pycryptodomex==3.23.0\" \\\n", " \"pydantic==2.13.5\" \\\n", @@ -106,7 +106,7 @@ " \"pydantic-settings==2.15.0\" \\\n", " \"pynwb==3.1.3\" \\\n", " \"pyout==0.8.1\" \\\n", - " \"pyparsing==3.3.2\" \\\n", + " \"pyparsing==3.3.3\" \\\n", " \"python-dateutil==2.9.0.post0\" \\\n", " \"python-dotenv==1.2.3\" \\\n", " \"pytz==2025.2\" \\\n", @@ -125,12 +125,12 @@ " \"tqdm==4.67.3\" \\\n", " \"typing-extensions==4.16.0\" \\\n", " \"typing-inspection==0.4.4\" \\\n", - " \"tzdata==2026.3\" \\\n", + " \"tzdata==2026.4\" \\\n", " \"uri-template==1.3.0\" \\\n", " \"urllib3==2.5.0\" \\\n", - " \"wcwidth==0.8.3\" \\\n", + " \"wcwidth==0.9.1\" \\\n", " \"webcolors==25.10.0\" \\\n", - " \"yarl==1.24.5\" \\\n", + " \"yarl==1.25.1\" \\\n", " \"zarr==3.1.5\" \\\n", " \"zarr-checksum==0.4.7\"\n", "!curl -sL -o stream_nwbfile.py https://raw.githubusercontent.com/dandi/example-notebooks/master/000971/lernerlab/seiler_2024/stream_nwbfile.py" diff --git a/001038/DombeckLab/001038_demo.ipynb b/001038/DombeckLab/001038_demo.ipynb index 72b69ced..864b6910 100644 --- a/001038/DombeckLab/001038_demo.ipynb +++ b/001038/DombeckLab/001038_demo.ipynb @@ -52,8 +52,8 @@ " \"click==8.1.8\" \\\n", " \"click-didyoumean==0.3.1\" \\\n", " \"cloudpickle==3.1.2\" \\\n", - " \"contourpy==1.3.3\" \\\n", - " \"cryptography==50.0.1\" \\\n", + " \"contourpy==1.4.0\" \\\n", + " \"cryptography==50.0.2\" \\\n", " \"cycler==0.12.1\" \\\n", " \"dandi==0.74.3\" \\\n", " \"dandischema==0.12.1\" \\\n", @@ -64,16 +64,16 @@ " \"email-validator==2.3.0\" \\\n", " \"etelemetry==0.3.1\" \\\n", " \"fasteners==0.20\" \\\n", - " \"fonttools==4.64.0\" \\\n", - " \"fqdn==1.5.1\" \\\n", + " \"fonttools==4.66.1\" \\\n", + " \"fqdn==1.6.0\" \\\n", " \"frozenlist==1.8.0\" \\\n", " \"fscacher==0.4.4\" \\\n", " \"fsspec==2025.12.0\" \\\n", - " \"h5py==3.16.0\" \\\n", + " \"h5py==3.14.0\" \\\n", " \"hdmf==4.3.1\" \\\n", " \"hdmf-zarr==0.13.0\" \\\n", " \"humanize==4.16.0\" \\\n", - " \"idna==3.19\" \\\n", + " \"idna==3.20\" \\\n", " \"interleave==0.3.0\" \\\n", " \"ipython==7.34.0\" \\\n", " \"isodate==0.7.2\" \\\n", @@ -95,7 +95,7 @@ " \"matplotlib-inline==0.2.2\" \\\n", " \"ml-dtypes==0.6.0\" \\\n", " \"more-itertools==10.8.0\" \\\n", - " \"multidict==6.7.1\" \\\n", + " \"multidict==6.9.1\" \\\n", " \"natsort==8.4.0\" \\\n", " \"numcodecs==0.15.1\" \\\n", " \"numpy==2.1.3\" \\\n", @@ -106,9 +106,9 @@ " \"pexpect==4.9.0\" \\\n", " \"pickleshare==0.7.5\" \\\n", " \"pillow==11.3.0\" \\\n", - " \"platformdirs==4.11.7\" \\\n", + " \"platformdirs==4.12.2\" \\\n", " \"prompt-toolkit==3.0.53\" \\\n", - " \"propcache==0.5.2\" \\\n", + " \"propcache==0.5.4\" \\\n", " \"ptyprocess==0.7.0\" \\\n", " \"pycparser==3.0\" \\\n", " \"pycryptodomex==3.23.0\" \\\n", @@ -118,7 +118,7 @@ " \"pygments==2.21.0\" \\\n", " \"pynwb==3.0.0\" \\\n", " \"pyout==0.8.1\" \\\n", - " \"pyparsing==3.3.2\" \\\n", + " \"pyparsing==3.3.3\" \\\n", " \"python-dateutil==2.9.0.post0\" \\\n", " \"python-dotenv==1.2.3\" \\\n", " \"pytz==2025.2\" \\\n", @@ -136,18 +136,18 @@ " \"six==1.17.0\" \\\n", " \"tenacity==9.1.4\" \\\n", " \"tensorstore==0.1.85\" \\\n", - " \"threadpoolctl==3.6.0\" \\\n", + " \"threadpoolctl==3.7.0\" \\\n", " \"tqdm==4.67.3\" \\\n", " \"traitlets==5.7.1\" \\\n", " \"typing-extensions==4.16.0\" \\\n", " \"typing-inspection==0.4.4\" \\\n", - " \"tzdata==2026.3\" \\\n", + " \"tzdata==2026.4\" \\\n", " \"uri-template==1.3.0\" \\\n", " \"urllib3==2.5.0\" \\\n", - " \"wcwidth==0.8.3\" \\\n", + " \"wcwidth==0.9.1\" \\\n", " \"webcolors==25.10.0\" \\\n", - " \"wrapt==2.4.0\" \\\n", - " \"yarl==1.24.5\" \\\n", + " \"wrapt==2.5.0\" \\\n", + " \"yarl==1.25.1\" \\\n", " \"zarr==2.18.7\" \\\n", " \"zarr-checksum==0.4.7\"" ] diff --git a/001075/001075_paper_figure_1d.ipynb b/001075/001075_paper_figure_1d.ipynb index d9f2626d..fa084503 100644 --- a/001075/001075_paper_figure_1d.ipynb +++ b/001075/001075_paper_figure_1d.ipynb @@ -50,8 +50,8 @@ " \"click==8.5.0\" \\\n", " \"click-didyoumean==0.3.1\" \\\n", " \"cloudpickle==3.1.2\" \\\n", - " \"contourpy==1.3.3\" \\\n", - " \"cryptography==50.0.1\" \\\n", + " \"contourpy==1.4.0\" \\\n", + " \"cryptography==50.0.2\" \\\n", " \"cycler==0.12.1\" \\\n", " \"dandi==0.77.0\" \\\n", " \"dandischema==0.14.0\" \\\n", @@ -61,16 +61,16 @@ " \"email-validator==2.3.0\" \\\n", " \"etelemetry==0.3.1\" \\\n", " \"fasteners==0.20\" \\\n", - " \"fonttools==4.64.0\" \\\n", - " \"fqdn==1.5.1\" \\\n", + " \"fonttools==4.66.1\" \\\n", + " \"fqdn==1.6.0\" \\\n", " \"frozenlist==1.8.0\" \\\n", " \"fscacher==0.4.4\" \\\n", " \"fsspec==2025.12.0\" \\\n", - " \"google-crc32c==1.8.0\" \\\n", - " \"h5py==3.16.0\" \\\n", + " \"google-crc32c==1.9.0\" \\\n", + " \"h5py==3.14.0\" \\\n", " \"hdmf==4.3.1\" \\\n", " \"humanize==4.16.0\" \\\n", - " \"idna==3.19\" \\\n", + " \"idna==3.20\" \\\n", " \"interleave==0.3.0\" \\\n", " \"isodate==0.7.2\" \\\n", " \"isoduration==20.11.0\" \\\n", @@ -89,7 +89,7 @@ " \"matplotlib==3.10.0\" \\\n", " \"ml-dtypes==0.6.0\" \\\n", " \"more-itertools==10.8.0\" \\\n", - " \"multidict==6.7.1\" \\\n", + " \"multidict==6.9.1\" \\\n", " \"natsort==8.4.0\" \\\n", " \"numcodecs==0.16.5\" \\\n", " \"numpy==2.1.3\" \\\n", @@ -97,8 +97,8 @@ " \"packaging==26.3\" \\\n", " \"pandas==2.2.3\" \\\n", " \"pillow==11.3.0\" \\\n", - " \"platformdirs==4.11.7\" \\\n", - " \"propcache==0.5.2\" \\\n", + " \"platformdirs==4.12.2\" \\\n", + " \"propcache==0.5.4\" \\\n", " \"pycparser==3.0\" \\\n", " \"pycryptodomex==3.23.0\" \\\n", " \"pydantic==2.13.5\" \\\n", @@ -106,7 +106,7 @@ " \"pydantic-settings==2.15.0\" \\\n", " \"pynwb==3.1.3\" \\\n", " \"pyout==0.8.1\" \\\n", - " \"pyparsing==3.3.2\" \\\n", + " \"pyparsing==3.3.3\" \\\n", " \"python-dateutil==2.9.0.post0\" \\\n", " \"python-dotenv==1.2.3\" \\\n", " \"pytz==2025.2\" \\\n", @@ -127,12 +127,12 @@ " \"tqdm==4.67.3\" \\\n", " \"typing-extensions==4.16.0\" \\\n", " \"typing-inspection==0.4.4\" \\\n", - " \"tzdata==2026.3\" \\\n", + " \"tzdata==2026.4\" \\\n", " \"uri-template==1.3.0\" \\\n", " \"urllib3==2.5.0\" \\\n", - " \"wcwidth==0.8.3\" \\\n", + " \"wcwidth==0.9.1\" \\\n", " \"webcolors==25.10.0\" \\\n", - " \"yarl==1.24.5\" \\\n", + " \"yarl==1.25.1\" \\\n", " \"zarr==3.1.5\" \\\n", " \"zarr-checksum==0.4.7\"\n", "!curl --create-dirs -sL -o utils_001075/__init__.py https://raw.githubusercontent.com/dandi/example-notebooks/master/001075/utils_001075/__init__.py\n", diff --git a/001084/HoweLab/001084_demo.ipynb b/001084/HoweLab/001084_demo.ipynb index 67d94de3..5f88ff95 100644 --- a/001084/HoweLab/001084_demo.ipynb +++ b/001084/HoweLab/001084_demo.ipynb @@ -51,8 +51,8 @@ " \"click==8.1.8\" \\\n", " \"click-didyoumean==0.3.1\" \\\n", " \"cloudpickle==3.1.2\" \\\n", - " \"contourpy==1.3.3\" \\\n", - " \"cryptography==50.0.1\" \\\n", + " \"contourpy==1.4.0\" \\\n", + " \"cryptography==50.0.2\" \\\n", " \"cycler==0.12.1\" \\\n", " \"dandi==0.74.3\" \\\n", " \"dandischema==0.12.1\" \\\n", @@ -62,16 +62,16 @@ " \"email-validator==2.3.0\" \\\n", " \"etelemetry==0.3.1\" \\\n", " \"fasteners==0.20\" \\\n", - " \"fonttools==4.64.0\" \\\n", - " \"fqdn==1.5.1\" \\\n", + " \"fonttools==4.66.1\" \\\n", + " \"fqdn==1.6.0\" \\\n", " \"frozenlist==1.8.0\" \\\n", " \"fscacher==0.4.4\" \\\n", " \"fsspec==2025.12.0\" \\\n", - " \"h5py==3.16.0\" \\\n", + " \"h5py==3.14.0\" \\\n", " \"hdmf==4.3.1\" \\\n", " \"hdmf-zarr==0.13.0\" \\\n", " \"humanize==4.16.0\" \\\n", - " \"idna==3.19\" \\\n", + " \"idna==3.20\" \\\n", " \"interleave==0.3.0\" \\\n", " \"isodate==0.7.2\" \\\n", " \"isoduration==20.11.0\" \\\n", @@ -90,7 +90,7 @@ " \"matplotlib==3.10.0\" \\\n", " \"ml-dtypes==0.6.0\" \\\n", " \"more-itertools==10.8.0\" \\\n", - " \"multidict==6.7.1\" \\\n", + " \"multidict==6.9.1\" \\\n", " \"natsort==8.4.0\" \\\n", " \"numcodecs==0.15.1\" \\\n", " \"numpy==2.1.3\" \\\n", @@ -98,8 +98,8 @@ " \"packaging==26.3\" \\\n", " \"pandas==2.2.3\" \\\n", " \"pillow==11.3.0\" \\\n", - " \"platformdirs==4.11.7\" \\\n", - " \"propcache==0.5.2\" \\\n", + " \"platformdirs==4.12.2\" \\\n", + " \"propcache==0.5.4\" \\\n", " \"pycparser==3.0\" \\\n", " \"pycryptodomex==3.23.0\" \\\n", " \"pydantic==2.13.5\" \\\n", @@ -107,7 +107,7 @@ " \"pydantic-settings==2.15.0\" \\\n", " \"pynwb==3.0.0\" \\\n", " \"pyout==0.8.1\" \\\n", - " \"pyparsing==3.3.2\" \\\n", + " \"pyparsing==3.3.3\" \\\n", " \"python-dateutil==2.9.0.post0\" \\\n", " \"python-dotenv==1.2.3\" \\\n", " \"pytz==2025.2\" \\\n", @@ -124,17 +124,17 @@ " \"six==1.17.0\" \\\n", " \"tenacity==9.1.4\" \\\n", " \"tensorstore==0.1.85\" \\\n", - " \"threadpoolctl==3.6.0\" \\\n", + " \"threadpoolctl==3.7.0\" \\\n", " \"tqdm==4.67.3\" \\\n", " \"typing-extensions==4.16.0\" \\\n", " \"typing-inspection==0.4.4\" \\\n", - " \"tzdata==2026.3\" \\\n", + " \"tzdata==2026.4\" \\\n", " \"uri-template==1.3.0\" \\\n", " \"urllib3==2.5.0\" \\\n", - " \"wcwidth==0.8.3\" \\\n", + " \"wcwidth==0.9.1\" \\\n", " \"webcolors==25.10.0\" \\\n", - " \"wrapt==2.4.0\" \\\n", - " \"yarl==1.24.5\" \\\n", + " \"wrapt==2.5.0\" \\\n", + " \"yarl==1.25.1\" \\\n", " \"zarr==2.18.7\" \\\n", " \"zarr-checksum==0.4.7\"" ] diff --git a/001170/ReimerLab/public_demo/001170_demo.ipynb b/001170/ReimerLab/public_demo/001170_demo.ipynb index df112cd9..9561122e 100644 --- a/001170/ReimerLab/public_demo/001170_demo.ipynb +++ b/001170/ReimerLab/public_demo/001170_demo.ipynb @@ -50,8 +50,8 @@ " \"click==8.5.0\" \\\n", " \"click-didyoumean==0.3.1\" \\\n", " \"cloudpickle==3.1.2\" \\\n", - " \"contourpy==1.3.3\" \\\n", - " \"cryptography==50.0.1\" \\\n", + " \"contourpy==1.4.0\" \\\n", + " \"cryptography==50.0.2\" \\\n", " \"cycler==0.12.1\" \\\n", " \"dandi==0.77.0\" \\\n", " \"dandischema==0.14.0\" \\\n", @@ -61,16 +61,16 @@ " \"email-validator==2.3.0\" \\\n", " \"etelemetry==0.3.1\" \\\n", " \"fasteners==0.20\" \\\n", - " \"fonttools==4.64.0\" \\\n", - " \"fqdn==1.5.1\" \\\n", + " \"fonttools==4.66.1\" \\\n", + " \"fqdn==1.6.0\" \\\n", " \"frozenlist==1.8.0\" \\\n", " \"fscacher==0.4.4\" \\\n", " \"fsspec==2025.12.0\" \\\n", - " \"google-crc32c==1.8.0\" \\\n", - " \"h5py==3.16.0\" \\\n", + " \"google-crc32c==1.9.0\" \\\n", + " \"h5py==3.14.0\" \\\n", " \"hdmf==4.3.1\" \\\n", " \"humanize==4.16.0\" \\\n", - " \"idna==3.19\" \\\n", + " \"idna==3.20\" \\\n", " \"interleave==0.3.0\" \\\n", " \"isodate==0.7.2\" \\\n", " \"isoduration==20.11.0\" \\\n", @@ -89,7 +89,7 @@ " \"matplotlib==3.10.0\" \\\n", " \"ml-dtypes==0.6.0\" \\\n", " \"more-itertools==10.8.0\" \\\n", - " \"multidict==6.7.1\" \\\n", + " \"multidict==6.9.1\" \\\n", " \"natsort==8.4.0\" \\\n", " \"numcodecs==0.16.5\" \\\n", " \"numpy==2.1.3\" \\\n", @@ -97,9 +97,9 @@ " \"packaging==26.3\" \\\n", " \"pandas==2.2.3\" \\\n", " \"pillow==11.3.0\" \\\n", - " \"platformdirs==4.11.7\" \\\n", + " \"platformdirs==4.12.2\" \\\n", " \"plotly==5.24.1\" \\\n", - " \"propcache==0.5.2\" \\\n", + " \"propcache==0.5.4\" \\\n", " \"pycparser==3.0\" \\\n", " \"pycryptodomex==3.23.0\" \\\n", " \"pydantic==2.13.5\" \\\n", @@ -107,7 +107,7 @@ " \"pydantic-settings==2.15.0\" \\\n", " \"pynwb==3.1.3\" \\\n", " \"pyout==0.8.1\" \\\n", - " \"pyparsing==3.3.2\" \\\n", + " \"pyparsing==3.3.3\" \\\n", " \"python-dateutil==2.9.0.post0\" \\\n", " \"python-dotenv==1.2.3\" \\\n", " \"pytz==2025.2\" \\\n", @@ -127,12 +127,12 @@ " \"tqdm==4.67.3\" \\\n", " \"typing-extensions==4.16.0\" \\\n", " \"typing-inspection==0.4.4\" \\\n", - " \"tzdata==2026.3\" \\\n", + " \"tzdata==2026.4\" \\\n", " \"uri-template==1.3.0\" \\\n", " \"urllib3==2.5.0\" \\\n", - " \"wcwidth==0.8.3\" \\\n", + " \"wcwidth==0.9.1\" \\\n", " \"webcolors==25.10.0\" \\\n", - " \"yarl==1.24.5\" \\\n", + " \"yarl==1.25.1\" \\\n", " \"zarr==3.1.5\" \\\n", " \"zarr-checksum==0.4.7\"" ] diff --git a/001172/HigleyLab/001172_demo.ipynb b/001172/HigleyLab/001172_demo.ipynb index 25c4bc41..c7ec6707 100644 --- a/001172/HigleyLab/001172_demo.ipynb +++ b/001172/HigleyLab/001172_demo.ipynb @@ -50,8 +50,8 @@ " \"click==8.5.0\" \\\n", " \"click-didyoumean==0.3.1\" \\\n", " \"cloudpickle==3.1.2\" \\\n", - " \"contourpy==1.3.3\" \\\n", - " \"cryptography==50.0.1\" \\\n", + " \"contourpy==1.4.0\" \\\n", + " \"cryptography==50.0.2\" \\\n", " \"cycler==0.12.1\" \\\n", " \"dandi==0.77.0\" \\\n", " \"dandischema==0.14.0\" \\\n", @@ -61,16 +61,16 @@ " \"email-validator==2.3.0\" \\\n", " \"etelemetry==0.3.1\" \\\n", " \"fasteners==0.20\" \\\n", - " \"fonttools==4.64.0\" \\\n", - " \"fqdn==1.5.1\" \\\n", + " \"fonttools==4.66.1\" \\\n", + " \"fqdn==1.6.0\" \\\n", " \"frozenlist==1.8.0\" \\\n", " \"fscacher==0.4.4\" \\\n", " \"fsspec==2025.12.0\" \\\n", - " \"google-crc32c==1.8.0\" \\\n", - " \"h5py==3.16.0\" \\\n", + " \"google-crc32c==1.9.0\" \\\n", + " \"h5py==3.14.0\" \\\n", " \"hdmf==4.3.1\" \\\n", " \"humanize==4.16.0\" \\\n", - " \"idna==3.19\" \\\n", + " \"idna==3.20\" \\\n", " \"interleave==0.3.0\" \\\n", " \"isodate==0.7.2\" \\\n", " \"isoduration==20.11.0\" \\\n", @@ -89,7 +89,7 @@ " \"matplotlib==3.10.0\" \\\n", " \"ml-dtypes==0.6.0\" \\\n", " \"more-itertools==10.8.0\" \\\n", - " \"multidict==6.7.1\" \\\n", + " \"multidict==6.9.1\" \\\n", " \"natsort==8.4.0\" \\\n", " \"numcodecs==0.16.5\" \\\n", " \"numpy==2.1.3\" \\\n", @@ -97,9 +97,9 @@ " \"packaging==26.3\" \\\n", " \"pandas==2.2.3\" \\\n", " \"pillow==11.3.0\" \\\n", - " \"platformdirs==4.11.7\" \\\n", + " \"platformdirs==4.12.2\" \\\n", " \"plotly==5.24.1\" \\\n", - " \"propcache==0.5.2\" \\\n", + " \"propcache==0.5.4\" \\\n", " \"pycparser==3.0\" \\\n", " \"pycryptodomex==3.23.0\" \\\n", " \"pydantic==2.13.5\" \\\n", @@ -107,7 +107,7 @@ " \"pydantic-settings==2.15.0\" \\\n", " \"pynwb==3.1.3\" \\\n", " \"pyout==0.8.1\" \\\n", - " \"pyparsing==3.3.2\" \\\n", + " \"pyparsing==3.3.3\" \\\n", " \"python-dateutil==2.9.0.post0\" \\\n", " \"python-dotenv==1.2.3\" \\\n", " \"pytz==2025.2\" \\\n", @@ -127,12 +127,12 @@ " \"tqdm==4.67.3\" \\\n", " \"typing-extensions==4.16.0\" \\\n", " \"typing-inspection==0.4.4\" \\\n", - " \"tzdata==2026.3\" \\\n", + " \"tzdata==2026.4\" \\\n", " \"uri-template==1.3.0\" \\\n", " \"urllib3==2.5.0\" \\\n", - " \"wcwidth==0.8.3\" \\\n", + " \"wcwidth==0.9.1\" \\\n", " \"webcolors==25.10.0\" \\\n", - " \"yarl==1.24.5\" \\\n", + " \"yarl==1.25.1\" \\\n", " \"zarr==3.1.5\" \\\n", " \"zarr-checksum==0.4.7\"" ] diff --git a/001528/HnaskoLab/Lotfi_2025/001528_demo.ipynb b/001528/HnaskoLab/Lotfi_2025/001528_demo.ipynb index 2e4c1b3d..f96cecb1 100644 --- a/001528/HnaskoLab/Lotfi_2025/001528_demo.ipynb +++ b/001528/HnaskoLab/Lotfi_2025/001528_demo.ipynb @@ -50,8 +50,8 @@ " \"click==8.5.0\" \\\n", " \"click-didyoumean==0.3.1\" \\\n", " \"cloudpickle==3.1.2\" \\\n", - " \"contourpy==1.3.3\" \\\n", - " \"cryptography==50.0.1\" \\\n", + " \"contourpy==1.4.0\" \\\n", + " \"cryptography==50.0.2\" \\\n", " \"cycler==0.12.1\" \\\n", " \"dandi==0.77.0\" \\\n", " \"dandischema==0.14.0\" \\\n", @@ -61,16 +61,16 @@ " \"email-validator==2.3.0\" \\\n", " \"etelemetry==0.3.1\" \\\n", " \"fasteners==0.20\" \\\n", - " \"fonttools==4.64.0\" \\\n", - " \"fqdn==1.5.1\" \\\n", + " \"fonttools==4.66.1\" \\\n", + " \"fqdn==1.6.0\" \\\n", " \"frozenlist==1.8.0\" \\\n", " \"fscacher==0.4.4\" \\\n", " \"fsspec==2025.12.0\" \\\n", - " \"google-crc32c==1.8.0\" \\\n", - " \"h5py==3.16.0\" \\\n", + " \"google-crc32c==1.9.0\" \\\n", + " \"h5py==3.14.0\" \\\n", " \"hdmf==6.2.0\" \\\n", " \"humanize==4.16.0\" \\\n", - " \"idna==3.19\" \\\n", + " \"idna==3.20\" \\\n", " \"interleave==0.3.0\" \\\n", " \"isodate==0.7.2\" \\\n", " \"isoduration==20.11.0\" \\\n", @@ -89,7 +89,7 @@ " \"matplotlib==3.10.0\" \\\n", " \"ml-dtypes==0.6.0\" \\\n", " \"more-itertools==10.8.0\" \\\n", - " \"multidict==6.7.1\" \\\n", + " \"multidict==6.9.1\" \\\n", " \"natsort==8.4.0\" \\\n", " \"numcodecs==0.16.5\" \\\n", " \"numpy==2.1.3\" \\\n", @@ -97,8 +97,8 @@ " \"packaging==26.3\" \\\n", " \"pandas==2.2.3\" \\\n", " \"pillow==11.3.0\" \\\n", - " \"platformdirs==4.11.7\" \\\n", - " \"propcache==0.5.2\" \\\n", + " \"platformdirs==4.12.2\" \\\n", + " \"propcache==0.5.4\" \\\n", " \"pycparser==3.0\" \\\n", " \"pycryptodomex==3.23.0\" \\\n", " \"pydantic==2.13.5\" \\\n", @@ -106,7 +106,7 @@ " \"pydantic-settings==2.15.0\" \\\n", " \"pynwb==4.1.0\" \\\n", " \"pyout==0.8.1\" \\\n", - " \"pyparsing==3.3.2\" \\\n", + " \"pyparsing==3.3.3\" \\\n", " \"python-dateutil==2.9.0.post0\" \\\n", " \"python-dotenv==1.2.3\" \\\n", " \"pytz==2025.2\" \\\n", @@ -126,12 +126,12 @@ " \"tqdm==4.67.3\" \\\n", " \"typing-extensions==4.16.0\" \\\n", " \"typing-inspection==0.4.4\" \\\n", - " \"tzdata==2026.3\" \\\n", + " \"tzdata==2026.4\" \\\n", " \"uri-template==1.3.0\" \\\n", " \"urllib3==2.5.0\" \\\n", - " \"wcwidth==0.8.3\" \\\n", + " \"wcwidth==0.9.1\" \\\n", " \"webcolors==25.10.0\" \\\n", - " \"yarl==1.24.5\" \\\n", + " \"yarl==1.25.1\" \\\n", " \"zarr==3.1.5\" \\\n", " \"zarr-checksum==0.4.7\"" ] diff --git a/001538/catalyst_neuro/zhai_2025/figure_1E_dspn_somatic_excitability.ipynb b/001538/catalyst_neuro/zhai_2025/figure_1E_dspn_somatic_excitability.ipynb index d6c1db57..cb0f9cbe 100644 --- a/001538/catalyst_neuro/zhai_2025/figure_1E_dspn_somatic_excitability.ipynb +++ b/001538/catalyst_neuro/zhai_2025/figure_1E_dspn_somatic_excitability.ipynb @@ -50,8 +50,8 @@ " \"click==8.5.0\" \\\n", " \"click-didyoumean==0.3.1\" \\\n", " \"cloudpickle==3.1.2\" \\\n", - " \"contourpy==1.3.3\" \\\n", - " \"cryptography==50.0.1\" \\\n", + " \"contourpy==1.4.0\" \\\n", + " \"cryptography==50.0.2\" \\\n", " \"cycler==0.12.1\" \\\n", " \"dandi==0.77.0\" \\\n", " \"dandischema==0.14.0\" \\\n", @@ -61,16 +61,16 @@ " \"email-validator==2.3.0\" \\\n", " \"etelemetry==0.3.1\" \\\n", " \"fasteners==0.20\" \\\n", - " \"fonttools==4.64.0\" \\\n", - " \"fqdn==1.5.1\" \\\n", + " \"fonttools==4.66.1\" \\\n", + " \"fqdn==1.6.0\" \\\n", " \"frozenlist==1.8.0\" \\\n", " \"fscacher==0.4.4\" \\\n", " \"fsspec==2025.12.0\" \\\n", - " \"google-crc32c==1.8.0\" \\\n", - " \"h5py==3.16.0\" \\\n", + " \"google-crc32c==1.9.0\" \\\n", + " \"h5py==3.14.0\" \\\n", " \"hdmf==4.3.1\" \\\n", " \"humanize==4.16.0\" \\\n", - " \"idna==3.19\" \\\n", + " \"idna==3.20\" \\\n", " \"interleave==0.3.0\" \\\n", " \"isodate==0.7.2\" \\\n", " \"isoduration==20.11.0\" \\\n", @@ -89,7 +89,7 @@ " \"matplotlib==3.10.0\" \\\n", " \"ml-dtypes==0.6.0\" \\\n", " \"more-itertools==10.8.0\" \\\n", - " \"multidict==6.7.1\" \\\n", + " \"multidict==6.9.1\" \\\n", " \"natsort==8.4.0\" \\\n", " \"numcodecs==0.16.5\" \\\n", " \"numpy==2.1.3\" \\\n", @@ -97,8 +97,8 @@ " \"packaging==26.3\" \\\n", " \"pandas==2.2.3\" \\\n", " \"pillow==11.3.0\" \\\n", - " \"platformdirs==4.11.7\" \\\n", - " \"propcache==0.5.2\" \\\n", + " \"platformdirs==4.12.2\" \\\n", + " \"propcache==0.5.4\" \\\n", " \"pycparser==3.0\" \\\n", " \"pycryptodomex==3.23.0\" \\\n", " \"pydantic==2.13.5\" \\\n", @@ -106,7 +106,7 @@ " \"pydantic-settings==2.15.0\" \\\n", " \"pynwb==3.1.3\" \\\n", " \"pyout==0.8.1\" \\\n", - " \"pyparsing==3.3.2\" \\\n", + " \"pyparsing==3.3.3\" \\\n", " \"python-dateutil==2.9.0.post0\" \\\n", " \"python-dotenv==1.2.3\" \\\n", " \"pytz==2025.2\" \\\n", @@ -128,12 +128,12 @@ " \"tqdm==4.67.3\" \\\n", " \"typing-extensions==4.16.0\" \\\n", " \"typing-inspection==0.4.4\" \\\n", - " \"tzdata==2026.3\" \\\n", + " \"tzdata==2026.4\" \\\n", " \"uri-template==1.3.0\" \\\n", " \"urllib3==2.5.0\" \\\n", - " \"wcwidth==0.8.3\" \\\n", + " \"wcwidth==0.9.1\" \\\n", " \"webcolors==25.10.0\" \\\n", - " \"yarl==1.24.5\" \\\n", + " \"yarl==1.25.1\" \\\n", " \"zarr==3.1.5\" \\\n", " \"zarr-checksum==0.4.7\"" ] diff --git a/001538/catalyst_neuro/zhai_2025/figure_2GH_oepsc_analysis.ipynb b/001538/catalyst_neuro/zhai_2025/figure_2GH_oepsc_analysis.ipynb index d9a5caa8..f28367a4 100644 --- a/001538/catalyst_neuro/zhai_2025/figure_2GH_oepsc_analysis.ipynb +++ b/001538/catalyst_neuro/zhai_2025/figure_2GH_oepsc_analysis.ipynb @@ -50,8 +50,8 @@ " \"click==8.5.0\" \\\n", " \"click-didyoumean==0.3.1\" \\\n", " \"cloudpickle==3.1.2\" \\\n", - " \"contourpy==1.3.3\" \\\n", - " \"cryptography==50.0.1\" \\\n", + " \"contourpy==1.4.0\" \\\n", + " \"cryptography==50.0.2\" \\\n", " \"cycler==0.12.1\" \\\n", " \"dandi==0.77.0\" \\\n", " \"dandischema==0.14.0\" \\\n", @@ -61,16 +61,16 @@ " \"email-validator==2.3.0\" \\\n", " \"etelemetry==0.3.1\" \\\n", " \"fasteners==0.20\" \\\n", - " \"fonttools==4.64.0\" \\\n", - " \"fqdn==1.5.1\" \\\n", + " \"fonttools==4.66.1\" \\\n", + " \"fqdn==1.6.0\" \\\n", " \"frozenlist==1.8.0\" \\\n", " \"fscacher==0.4.4\" \\\n", " \"fsspec==2025.12.0\" \\\n", - " \"google-crc32c==1.8.0\" \\\n", - " \"h5py==3.16.0\" \\\n", + " \"google-crc32c==1.9.0\" \\\n", + " \"h5py==3.14.0\" \\\n", " \"hdmf==4.3.1\" \\\n", " \"humanize==4.16.0\" \\\n", - " \"idna==3.19\" \\\n", + " \"idna==3.20\" \\\n", " \"interleave==0.3.0\" \\\n", " \"isodate==0.7.2\" \\\n", " \"isoduration==20.11.0\" \\\n", @@ -89,7 +89,7 @@ " \"matplotlib==3.10.0\" \\\n", " \"ml-dtypes==0.6.0\" \\\n", " \"more-itertools==10.8.0\" \\\n", - " \"multidict==6.7.1\" \\\n", + " \"multidict==6.9.1\" \\\n", " \"natsort==8.4.0\" \\\n", " \"numcodecs==0.16.5\" \\\n", " \"numpy==2.1.3\" \\\n", @@ -97,8 +97,8 @@ " \"packaging==26.3\" \\\n", " \"pandas==2.2.3\" \\\n", " \"pillow==11.3.0\" \\\n", - " \"platformdirs==4.11.7\" \\\n", - " \"propcache==0.5.2\" \\\n", + " \"platformdirs==4.12.2\" \\\n", + " \"propcache==0.5.4\" \\\n", " \"pycparser==3.0\" \\\n", " \"pycryptodomex==3.23.0\" \\\n", " \"pydantic==2.13.5\" \\\n", @@ -106,7 +106,7 @@ " \"pydantic-settings==2.15.0\" \\\n", " \"pynwb==3.1.3\" \\\n", " \"pyout==0.8.1\" \\\n", - " \"pyparsing==3.3.2\" \\\n", + " \"pyparsing==3.3.3\" \\\n", " \"python-dateutil==2.9.0.post0\" \\\n", " \"python-dotenv==1.2.3\" \\\n", " \"pytz==2025.2\" \\\n", @@ -128,12 +128,12 @@ " \"tqdm==4.67.3\" \\\n", " \"typing-extensions==4.16.0\" \\\n", " \"typing-inspection==0.4.4\" \\\n", - " \"tzdata==2026.3\" \\\n", + " \"tzdata==2026.4\" \\\n", " \"uri-template==1.3.0\" \\\n", " \"urllib3==2.5.0\" \\\n", - " \"wcwidth==0.8.3\" \\\n", + " \"wcwidth==0.9.1\" \\\n", " \"webcolors==25.10.0\" \\\n", - " \"yarl==1.24.5\" \\\n", + " \"yarl==1.25.1\" \\\n", " \"zarr==3.1.5\" \\\n", " \"zarr-checksum==0.4.7\"" ] diff --git a/001538/catalyst_neuro/zhai_2025/figure_5F_acetylcholine_biosensor.ipynb b/001538/catalyst_neuro/zhai_2025/figure_5F_acetylcholine_biosensor.ipynb index 2fdc1e8b..a93314c1 100644 --- a/001538/catalyst_neuro/zhai_2025/figure_5F_acetylcholine_biosensor.ipynb +++ b/001538/catalyst_neuro/zhai_2025/figure_5F_acetylcholine_biosensor.ipynb @@ -50,8 +50,8 @@ " \"click==8.5.0\" \\\n", " \"click-didyoumean==0.3.1\" \\\n", " \"cloudpickle==3.1.2\" \\\n", - " \"contourpy==1.3.3\" \\\n", - " \"cryptography==50.0.1\" \\\n", + " \"contourpy==1.4.0\" \\\n", + " \"cryptography==50.0.2\" \\\n", " \"cycler==0.12.1\" \\\n", " \"dandi==0.77.0\" \\\n", " \"dandischema==0.14.0\" \\\n", @@ -61,16 +61,16 @@ " \"email-validator==2.3.0\" \\\n", " \"etelemetry==0.3.1\" \\\n", " \"fasteners==0.20\" \\\n", - " \"fonttools==4.64.0\" \\\n", - " \"fqdn==1.5.1\" \\\n", + " \"fonttools==4.66.1\" \\\n", + " \"fqdn==1.6.0\" \\\n", " \"frozenlist==1.8.0\" \\\n", " \"fscacher==0.4.4\" \\\n", " \"fsspec==2025.12.0\" \\\n", - " \"google-crc32c==1.8.0\" \\\n", - " \"h5py==3.16.0\" \\\n", + " \"google-crc32c==1.9.0\" \\\n", + " \"h5py==3.14.0\" \\\n", " \"hdmf==4.3.1\" \\\n", " \"humanize==4.16.0\" \\\n", - " \"idna==3.19\" \\\n", + " \"idna==3.20\" \\\n", " \"interleave==0.3.0\" \\\n", " \"isodate==0.7.2\" \\\n", " \"isoduration==20.11.0\" \\\n", @@ -89,7 +89,7 @@ " \"matplotlib==3.10.0\" \\\n", " \"ml-dtypes==0.6.0\" \\\n", " \"more-itertools==10.8.0\" \\\n", - " \"multidict==6.7.1\" \\\n", + " \"multidict==6.9.1\" \\\n", " \"natsort==8.4.0\" \\\n", " \"numcodecs==0.16.5\" \\\n", " \"numpy==2.1.3\" \\\n", @@ -97,8 +97,8 @@ " \"packaging==26.3\" \\\n", " \"pandas==2.2.3\" \\\n", " \"pillow==11.3.0\" \\\n", - " \"platformdirs==4.11.7\" \\\n", - " \"propcache==0.5.2\" \\\n", + " \"platformdirs==4.12.2\" \\\n", + " \"propcache==0.5.4\" \\\n", " \"pycparser==3.0\" \\\n", " \"pycryptodomex==3.23.0\" \\\n", " \"pydantic==2.13.5\" \\\n", @@ -106,7 +106,7 @@ " \"pydantic-settings==2.15.0\" \\\n", " \"pynwb==3.1.3\" \\\n", " \"pyout==0.8.1\" \\\n", - " \"pyparsing==3.3.2\" \\\n", + " \"pyparsing==3.3.3\" \\\n", " \"python-dateutil==2.9.0.post0\" \\\n", " \"python-dotenv==1.2.3\" \\\n", " \"pytz==2025.2\" \\\n", @@ -128,12 +128,12 @@ " \"tqdm==4.67.3\" \\\n", " \"typing-extensions==4.16.0\" \\\n", " \"typing-inspection==0.4.4\" \\\n", - " \"tzdata==2026.3\" \\\n", + " \"tzdata==2026.4\" \\\n", " \"uri-template==1.3.0\" \\\n", " \"urllib3==2.5.0\" \\\n", - " \"wcwidth==0.8.3\" \\\n", + " \"wcwidth==0.9.1\" \\\n", " \"webcolors==25.10.0\" \\\n", - " \"yarl==1.24.5\" \\\n", + " \"yarl==1.25.1\" \\\n", " \"zarr==3.1.5\" \\\n", " \"zarr-checksum==0.4.7\"" ] diff --git a/001538/catalyst_neuro/zhai_2025/how_to_use_this_dataset.ipynb b/001538/catalyst_neuro/zhai_2025/how_to_use_this_dataset.ipynb index 7437fae5..8e8efc21 100644 --- a/001538/catalyst_neuro/zhai_2025/how_to_use_this_dataset.ipynb +++ b/001538/catalyst_neuro/zhai_2025/how_to_use_this_dataset.ipynb @@ -50,8 +50,8 @@ " \"click==8.5.0\" \\\n", " \"click-didyoumean==0.3.1\" \\\n", " \"cloudpickle==3.1.2\" \\\n", - " \"contourpy==1.3.3\" \\\n", - " \"cryptography==50.0.1\" \\\n", + " \"contourpy==1.4.0\" \\\n", + " \"cryptography==50.0.2\" \\\n", " \"cycler==0.12.1\" \\\n", " \"dandi==0.77.0\" \\\n", " \"dandischema==0.14.0\" \\\n", @@ -61,16 +61,16 @@ " \"email-validator==2.3.0\" \\\n", " \"etelemetry==0.3.1\" \\\n", " \"fasteners==0.20\" \\\n", - " \"fonttools==4.64.0\" \\\n", - " \"fqdn==1.5.1\" \\\n", + " \"fonttools==4.66.1\" \\\n", + " \"fqdn==1.6.0\" \\\n", " \"frozenlist==1.8.0\" \\\n", " \"fscacher==0.4.4\" \\\n", " \"fsspec==2025.12.0\" \\\n", - " \"google-crc32c==1.8.0\" \\\n", - " \"h5py==3.16.0\" \\\n", + " \"google-crc32c==1.9.0\" \\\n", + " \"h5py==3.14.0\" \\\n", " \"hdmf==4.3.1\" \\\n", " \"humanize==4.16.0\" \\\n", - " \"idna==3.19\" \\\n", + " \"idna==3.20\" \\\n", " \"interleave==0.3.0\" \\\n", " \"isodate==0.7.2\" \\\n", " \"isoduration==20.11.0\" \\\n", @@ -89,7 +89,7 @@ " \"matplotlib==3.10.0\" \\\n", " \"ml-dtypes==0.6.0\" \\\n", " \"more-itertools==10.8.0\" \\\n", - " \"multidict==6.7.1\" \\\n", + " \"multidict==6.9.1\" \\\n", " \"natsort==8.4.0\" \\\n", " \"numcodecs==0.16.5\" \\\n", " \"numpy==2.1.3\" \\\n", @@ -97,8 +97,8 @@ " \"packaging==26.3\" \\\n", " \"pandas==2.2.3\" \\\n", " \"pillow==11.3.0\" \\\n", - " \"platformdirs==4.11.7\" \\\n", - " \"propcache==0.5.2\" \\\n", + " \"platformdirs==4.12.2\" \\\n", + " \"propcache==0.5.4\" \\\n", " \"pycparser==3.0\" \\\n", " \"pycryptodomex==3.23.0\" \\\n", " \"pydantic==2.13.5\" \\\n", @@ -106,7 +106,7 @@ " \"pydantic-settings==2.15.0\" \\\n", " \"pynwb==3.1.3\" \\\n", " \"pyout==0.8.1\" \\\n", - " \"pyparsing==3.3.2\" \\\n", + " \"pyparsing==3.3.3\" \\\n", " \"python-dateutil==2.9.0.post0\" \\\n", " \"python-dotenv==1.2.3\" \\\n", " \"pytz==2025.2\" \\\n", @@ -128,12 +128,12 @@ " \"tqdm==4.67.3\" \\\n", " \"typing-extensions==4.16.0\" \\\n", " \"typing-inspection==0.4.4\" \\\n", - " \"tzdata==2026.3\" \\\n", + " \"tzdata==2026.4\" \\\n", " \"uri-template==1.3.0\" \\\n", " \"urllib3==2.5.0\" \\\n", - " \"wcwidth==0.8.3\" \\\n", + " \"wcwidth==0.9.1\" \\\n", " \"webcolors==25.10.0\" \\\n", - " \"yarl==1.24.5\" \\\n", + " \"yarl==1.25.1\" \\\n", " \"zarr==3.1.5\" \\\n", " \"zarr-checksum==0.4.7\"" ] diff --git a/001550/PaganLab/01_behavior_demo.ipynb b/001550/PaganLab/01_behavior_demo.ipynb index 7828c8b8..abc6712a 100644 --- a/001550/PaganLab/01_behavior_demo.ipynb +++ b/001550/PaganLab/01_behavior_demo.ipynb @@ -50,8 +50,8 @@ " \"click==8.5.0\" \\\n", " \"click-didyoumean==0.3.1\" \\\n", " \"cloudpickle==3.1.2\" \\\n", - " \"contourpy==1.3.3\" \\\n", - " \"cryptography==50.0.1\" \\\n", + " \"contourpy==1.4.0\" \\\n", + " \"cryptography==50.0.2\" \\\n", " \"cycler==0.12.1\" \\\n", " \"dandi==0.77.0\" \\\n", " \"dandischema==0.14.0\" \\\n", @@ -61,16 +61,16 @@ " \"email-validator==2.3.0\" \\\n", " \"etelemetry==0.3.1\" \\\n", " \"fasteners==0.20\" \\\n", - " \"fonttools==4.64.0\" \\\n", - " \"fqdn==1.5.1\" \\\n", + " \"fonttools==4.66.1\" \\\n", + " \"fqdn==1.6.0\" \\\n", " \"frozenlist==1.8.0\" \\\n", " \"fscacher==0.4.4\" \\\n", " \"fsspec==2025.12.0\" \\\n", - " \"google-crc32c==1.8.0\" \\\n", - " \"h5py==3.16.0\" \\\n", + " \"google-crc32c==1.9.0\" \\\n", + " \"h5py==3.14.0\" \\\n", " \"hdmf==4.3.1\" \\\n", " \"humanize==4.16.0\" \\\n", - " \"idna==3.19\" \\\n", + " \"idna==3.20\" \\\n", " \"interleave==0.3.0\" \\\n", " \"isodate==0.7.2\" \\\n", " \"isoduration==20.11.0\" \\\n", @@ -89,20 +89,20 @@ " \"matplotlib==3.10.0\" \\\n", " \"ml-dtypes==0.6.0\" \\\n", " \"more-itertools==10.8.0\" \\\n", - " \"multidict==6.7.1\" \\\n", + " \"multidict==6.9.1\" \\\n", " \"natsort==8.4.0\" \\\n", " \"ndx-ophys-devices==0.3.1\" \\\n", " \"ndx-optogenetics==0.4.0\" \\\n", " \"ndx-structured-behavior @ git+https://github.com/rly/ndx-structured-behavior.git@b31692480fa8c7e005dea7d843528582c02ef7e2\" \\\n", - " \"networkx==3.6.1\" \\\n", + " \"networkx==3.7\" \\\n", " \"numcodecs==0.16.5\" \\\n", " \"numpy==2.1.3\" \\\n", " \"nwbinspector==0.7.2\" \\\n", " \"packaging==26.3\" \\\n", " \"pandas==2.2.3\" \\\n", " \"pillow==11.3.0\" \\\n", - " \"platformdirs==4.11.7\" \\\n", - " \"propcache==0.5.2\" \\\n", + " \"platformdirs==4.12.2\" \\\n", + " \"propcache==0.5.4\" \\\n", " \"pycparser==3.0\" \\\n", " \"pycryptodomex==3.23.0\" \\\n", " \"pydantic==2.13.5\" \\\n", @@ -110,7 +110,7 @@ " \"pydantic-settings==2.15.0\" \\\n", " \"pynwb==3.1.3\" \\\n", " \"pyout==0.8.1\" \\\n", - " \"pyparsing==3.3.2\" \\\n", + " \"pyparsing==3.3.3\" \\\n", " \"python-dateutil==2.9.0.post0\" \\\n", " \"python-dotenv==1.2.3\" \\\n", " \"pytz==2025.2\" \\\n", @@ -131,12 +131,12 @@ " \"tqdm==4.67.3\" \\\n", " \"typing-extensions==4.16.0\" \\\n", " \"typing-inspection==0.4.4\" \\\n", - " \"tzdata==2026.3\" \\\n", + " \"tzdata==2026.4\" \\\n", " \"uri-template==1.3.0\" \\\n", " \"urllib3==2.5.0\" \\\n", - " \"wcwidth==0.8.3\" \\\n", + " \"wcwidth==0.9.1\" \\\n", " \"webcolors==25.10.0\" \\\n", - " \"yarl==1.24.5\" \\\n", + " \"yarl==1.25.1\" \\\n", " \"zarr==3.1.5\" \\\n", " \"zarr-checksum==0.4.7\"" ] diff --git a/001550/PaganLab/02_optogenetics_demo.ipynb b/001550/PaganLab/02_optogenetics_demo.ipynb index a168e1e0..a1304e47 100644 --- a/001550/PaganLab/02_optogenetics_demo.ipynb +++ b/001550/PaganLab/02_optogenetics_demo.ipynb @@ -50,8 +50,8 @@ " \"click==8.5.0\" \\\n", " \"click-didyoumean==0.3.1\" \\\n", " \"cloudpickle==3.1.2\" \\\n", - " \"contourpy==1.3.3\" \\\n", - " \"cryptography==50.0.1\" \\\n", + " \"contourpy==1.4.0\" \\\n", + " \"cryptography==50.0.2\" \\\n", " \"cycler==0.12.1\" \\\n", " \"dandi==0.77.0\" \\\n", " \"dandischema==0.14.0\" \\\n", @@ -61,16 +61,16 @@ " \"email-validator==2.3.0\" \\\n", " \"etelemetry==0.3.1\" \\\n", " \"fasteners==0.20\" \\\n", - " \"fonttools==4.64.0\" \\\n", - " \"fqdn==1.5.1\" \\\n", + " \"fonttools==4.66.1\" \\\n", + " \"fqdn==1.6.0\" \\\n", " \"frozenlist==1.8.0\" \\\n", " \"fscacher==0.4.4\" \\\n", " \"fsspec==2025.12.0\" \\\n", - " \"google-crc32c==1.8.0\" \\\n", - " \"h5py==3.16.0\" \\\n", + " \"google-crc32c==1.9.0\" \\\n", + " \"h5py==3.14.0\" \\\n", " \"hdmf==4.3.1\" \\\n", " \"humanize==4.16.0\" \\\n", - " \"idna==3.19\" \\\n", + " \"idna==3.20\" \\\n", " \"interleave==0.3.0\" \\\n", " \"isodate==0.7.2\" \\\n", " \"isoduration==20.11.0\" \\\n", @@ -89,20 +89,20 @@ " \"matplotlib==3.10.0\" \\\n", " \"ml-dtypes==0.6.0\" \\\n", " \"more-itertools==10.8.0\" \\\n", - " \"multidict==6.7.1\" \\\n", + " \"multidict==6.9.1\" \\\n", " \"natsort==8.4.0\" \\\n", " \"ndx-ophys-devices==0.3.1\" \\\n", " \"ndx-optogenetics==0.4.0\" \\\n", " \"ndx-structured-behavior @ git+https://github.com/rly/ndx-structured-behavior.git@b31692480fa8c7e005dea7d843528582c02ef7e2\" \\\n", - " \"networkx==3.6.1\" \\\n", + " \"networkx==3.7\" \\\n", " \"numcodecs==0.16.5\" \\\n", " \"numpy==2.1.3\" \\\n", " \"nwbinspector==0.7.2\" \\\n", " \"packaging==26.3\" \\\n", " \"pandas==2.2.3\" \\\n", " \"pillow==11.3.0\" \\\n", - " \"platformdirs==4.11.7\" \\\n", - " \"propcache==0.5.2\" \\\n", + " \"platformdirs==4.12.2\" \\\n", + " \"propcache==0.5.4\" \\\n", " \"pycparser==3.0\" \\\n", " \"pycryptodomex==3.23.0\" \\\n", " \"pydantic==2.13.5\" \\\n", @@ -110,7 +110,7 @@ " \"pydantic-settings==2.15.0\" \\\n", " \"pynwb==3.1.3\" \\\n", " \"pyout==0.8.1\" \\\n", - " \"pyparsing==3.3.2\" \\\n", + " \"pyparsing==3.3.3\" \\\n", " \"python-dateutil==2.9.0.post0\" \\\n", " \"python-dotenv==1.2.3\" \\\n", " \"pytz==2025.2\" \\\n", @@ -131,12 +131,12 @@ " \"tqdm==4.67.3\" \\\n", " \"typing-extensions==4.16.0\" \\\n", " \"typing-inspection==0.4.4\" \\\n", - " \"tzdata==2026.3\" \\\n", + " \"tzdata==2026.4\" \\\n", " \"uri-template==1.3.0\" \\\n", " \"urllib3==2.5.0\" \\\n", - " \"wcwidth==0.8.3\" \\\n", + " \"wcwidth==0.9.1\" \\\n", " \"webcolors==25.10.0\" \\\n", - " \"yarl==1.24.5\" \\\n", + " \"yarl==1.25.1\" \\\n", " \"zarr==3.1.5\" \\\n", " \"zarr-checksum==0.4.7\"" ] diff --git a/001636/TurnerLab/motor_cortex/antidromic_detection_tutorial.ipynb b/001636/TurnerLab/motor_cortex/antidromic_detection_tutorial.ipynb index 8dcf4766..36fd82ec 100644 --- a/001636/TurnerLab/motor_cortex/antidromic_detection_tutorial.ipynb +++ b/001636/TurnerLab/motor_cortex/antidromic_detection_tutorial.ipynb @@ -51,8 +51,8 @@ " \"click==8.5.0\" \\\n", " \"click-didyoumean==0.3.1\" \\\n", " \"cloudpickle==3.1.2\" \\\n", - " \"contourpy==1.3.3\" \\\n", - " \"cryptography==50.0.1\" \\\n", + " \"contourpy==1.4.0\" \\\n", + " \"cryptography==50.0.2\" \\\n", " \"cycler==0.12.1\" \\\n", " \"dandi==0.77.0\" \\\n", " \"dandischema==0.14.0\" \\\n", @@ -63,16 +63,16 @@ " \"equinox==0.13.8\" \\\n", " \"etelemetry==0.3.1\" \\\n", " \"fasteners==0.20\" \\\n", - " \"fonttools==4.64.0\" \\\n", - " \"fqdn==1.5.1\" \\\n", + " \"fonttools==4.66.1\" \\\n", + " \"fqdn==1.6.0\" \\\n", " \"frozenlist==1.8.0\" \\\n", " \"fscacher==0.4.4\" \\\n", " \"fsspec==2025.12.0\" \\\n", - " \"google-crc32c==1.8.0\" \\\n", - " \"h5py==3.16.0\" \\\n", + " \"google-crc32c==1.9.0\" \\\n", + " \"h5py==3.14.0\" \\\n", " \"hdmf==4.3.1\" \\\n", " \"humanize==4.16.0\" \\\n", - " \"idna==3.19\" \\\n", + " \"idna==3.20\" \\\n", " \"interleave==0.3.0\" \\\n", " \"isodate==0.7.2\" \\\n", " \"isoduration==20.11.0\" \\\n", @@ -98,7 +98,7 @@ " \"mdurl==0.1.2\" \\\n", " \"ml-dtypes==0.6.0\" \\\n", " \"more-itertools==10.8.0\" \\\n", - " \"multidict==6.7.1\" \\\n", + " \"multidict==6.9.1\" \\\n", " \"natsort==8.4.0\" \\\n", " \"nemos==0.2.6\" \\\n", " \"numba==0.61.2\" \\\n", @@ -111,8 +111,8 @@ " \"packaging==26.3\" \\\n", " \"pandas==2.2.3\" \\\n", " \"pillow==11.3.0\" \\\n", - " \"platformdirs==4.11.7\" \\\n", - " \"propcache==0.5.2\" \\\n", + " \"platformdirs==4.12.2\" \\\n", + " \"propcache==0.5.4\" \\\n", " \"pycparser==3.0\" \\\n", " \"pycryptodomex==3.23.0\" \\\n", " \"pydantic==2.13.5\" \\\n", @@ -122,7 +122,7 @@ " \"pynapple==0.10.3\" \\\n", " \"pynwb==3.1.3\" \\\n", " \"pyout==0.8.1\" \\\n", - " \"pyparsing==3.3.2\" \\\n", + " \"pyparsing==3.3.3\" \\\n", " \"python-dateutil==2.9.0.post0\" \\\n", " \"python-dotenv==1.2.3\" \\\n", " \"pytz==2025.2\" \\\n", @@ -143,18 +143,18 @@ " \"tabulate==0.9.0\" \\\n", " \"tenacity==9.1.4\" \\\n", " \"tensorstore==0.1.85\" \\\n", - " \"threadpoolctl==3.6.0\" \\\n", + " \"threadpoolctl==3.7.0\" \\\n", " \"tqdm==4.67.3\" \\\n", " \"typing-extensions==4.16.0\" \\\n", " \"typing-inspection==0.4.4\" \\\n", - " \"tzdata==2026.3\" \\\n", + " \"tzdata==2026.4\" \\\n", " \"uri-template==1.3.0\" \\\n", " \"urllib3==2.5.0\" \\\n", " \"wadler-lindig==0.1.7\" \\\n", - " \"wcwidth==0.8.3\" \\\n", + " \"wcwidth==0.9.1\" \\\n", " \"webcolors==25.10.0\" \\\n", " \"xarray==2025.12.0\" \\\n", - " \"yarl==1.24.5\" \\\n", + " \"yarl==1.25.1\" \\\n", " \"zarr==3.1.5\" \\\n", " \"zarr-checksum==0.4.7\"\n", "!curl -sL -o notebook_helpers.py https://raw.githubusercontent.com/dandi/example-notebooks/master/001636/TurnerLab/motor_cortex/notebook_helpers.py" diff --git a/001636/TurnerLab/motor_cortex/turner_m1_glm.ipynb b/001636/TurnerLab/motor_cortex/turner_m1_glm.ipynb index 1c139fda..061de572 100644 --- a/001636/TurnerLab/motor_cortex/turner_m1_glm.ipynb +++ b/001636/TurnerLab/motor_cortex/turner_m1_glm.ipynb @@ -51,8 +51,8 @@ " \"click==8.5.0\" \\\n", " \"click-didyoumean==0.3.1\" \\\n", " \"cloudpickle==3.1.2\" \\\n", - " \"contourpy==1.3.3\" \\\n", - " \"cryptography==50.0.1\" \\\n", + " \"contourpy==1.4.0\" \\\n", + " \"cryptography==50.0.2\" \\\n", " \"cycler==0.12.1\" \\\n", " \"dandi==0.77.0\" \\\n", " \"dandischema==0.14.0\" \\\n", @@ -63,16 +63,16 @@ " \"equinox==0.13.8\" \\\n", " \"etelemetry==0.3.1\" \\\n", " \"fasteners==0.20\" \\\n", - " \"fonttools==4.64.0\" \\\n", - " \"fqdn==1.5.1\" \\\n", + " \"fonttools==4.66.1\" \\\n", + " \"fqdn==1.6.0\" \\\n", " \"frozenlist==1.8.0\" \\\n", " \"fscacher==0.4.4\" \\\n", " \"fsspec==2025.12.0\" \\\n", - " \"google-crc32c==1.8.0\" \\\n", - " \"h5py==3.16.0\" \\\n", + " \"google-crc32c==1.9.0\" \\\n", + " \"h5py==3.14.0\" \\\n", " \"hdmf==4.3.1\" \\\n", " \"humanize==4.16.0\" \\\n", - " \"idna==3.19\" \\\n", + " \"idna==3.20\" \\\n", " \"interleave==0.3.0\" \\\n", " \"isodate==0.7.2\" \\\n", " \"isoduration==20.11.0\" \\\n", @@ -98,7 +98,7 @@ " \"mdurl==0.1.2\" \\\n", " \"ml-dtypes==0.6.0\" \\\n", " \"more-itertools==10.8.0\" \\\n", - " \"multidict==6.7.1\" \\\n", + " \"multidict==6.9.1\" \\\n", " \"natsort==8.4.0\" \\\n", " \"nemos==0.2.6\" \\\n", " \"numba==0.61.2\" \\\n", @@ -111,8 +111,8 @@ " \"packaging==26.3\" \\\n", " \"pandas==2.2.3\" \\\n", " \"pillow==11.3.0\" \\\n", - " \"platformdirs==4.11.7\" \\\n", - " \"propcache==0.5.2\" \\\n", + " \"platformdirs==4.12.2\" \\\n", + " \"propcache==0.5.4\" \\\n", " \"pycparser==3.0\" \\\n", " \"pycryptodomex==3.23.0\" \\\n", " \"pydantic==2.13.5\" \\\n", @@ -122,7 +122,7 @@ " \"pynapple==0.10.3\" \\\n", " \"pynwb==3.1.3\" \\\n", " \"pyout==0.8.1\" \\\n", - " \"pyparsing==3.3.2\" \\\n", + " \"pyparsing==3.3.3\" \\\n", " \"python-dateutil==2.9.0.post0\" \\\n", " \"python-dotenv==1.2.3\" \\\n", " \"pytz==2025.2\" \\\n", @@ -143,18 +143,18 @@ " \"tabulate==0.9.0\" \\\n", " \"tenacity==9.1.4\" \\\n", " \"tensorstore==0.1.85\" \\\n", - " \"threadpoolctl==3.6.0\" \\\n", + " \"threadpoolctl==3.7.0\" \\\n", " \"tqdm==4.67.3\" \\\n", " \"typing-extensions==4.16.0\" \\\n", " \"typing-inspection==0.4.4\" \\\n", - " \"tzdata==2026.3\" \\\n", + " \"tzdata==2026.4\" \\\n", " \"uri-template==1.3.0\" \\\n", " \"urllib3==2.5.0\" \\\n", " \"wadler-lindig==0.1.7\" \\\n", - " \"wcwidth==0.8.3\" \\\n", + " \"wcwidth==0.9.1\" \\\n", " \"webcolors==25.10.0\" \\\n", " \"xarray==2025.12.0\" \\\n", - " \"yarl==1.24.5\" \\\n", + " \"yarl==1.25.1\" \\\n", " \"zarr==3.1.5\" \\\n", " \"zarr-checksum==0.4.7\"" ] diff --git a/001636/TurnerLab/motor_cortex/turner_m1_peth.ipynb b/001636/TurnerLab/motor_cortex/turner_m1_peth.ipynb index a99d8987..a2d4b1bf 100644 --- a/001636/TurnerLab/motor_cortex/turner_m1_peth.ipynb +++ b/001636/TurnerLab/motor_cortex/turner_m1_peth.ipynb @@ -51,8 +51,8 @@ " \"click==8.5.0\" \\\n", " \"click-didyoumean==0.3.1\" \\\n", " \"cloudpickle==3.1.2\" \\\n", - " \"contourpy==1.3.3\" \\\n", - " \"cryptography==50.0.1\" \\\n", + " \"contourpy==1.4.0\" \\\n", + " \"cryptography==50.0.2\" \\\n", " \"cycler==0.12.1\" \\\n", " \"dandi==0.77.0\" \\\n", " \"dandischema==0.14.0\" \\\n", @@ -63,16 +63,16 @@ " \"equinox==0.13.8\" \\\n", " \"etelemetry==0.3.1\" \\\n", " \"fasteners==0.20\" \\\n", - " \"fonttools==4.64.0\" \\\n", - " \"fqdn==1.5.1\" \\\n", + " \"fonttools==4.66.1\" \\\n", + " \"fqdn==1.6.0\" \\\n", " \"frozenlist==1.8.0\" \\\n", " \"fscacher==0.4.4\" \\\n", " \"fsspec==2025.12.0\" \\\n", - " \"google-crc32c==1.8.0\" \\\n", - " \"h5py==3.16.0\" \\\n", + " \"google-crc32c==1.9.0\" \\\n", + " \"h5py==3.14.0\" \\\n", " \"hdmf==4.3.1\" \\\n", " \"humanize==4.16.0\" \\\n", - " \"idna==3.19\" \\\n", + " \"idna==3.20\" \\\n", " \"interleave==0.3.0\" \\\n", " \"isodate==0.7.2\" \\\n", " \"isoduration==20.11.0\" \\\n", @@ -98,7 +98,7 @@ " \"mdurl==0.1.2\" \\\n", " \"ml-dtypes==0.6.0\" \\\n", " \"more-itertools==10.8.0\" \\\n", - " \"multidict==6.7.1\" \\\n", + " \"multidict==6.9.1\" \\\n", " \"natsort==8.4.0\" \\\n", " \"nemos==0.2.6\" \\\n", " \"numba==0.61.2\" \\\n", @@ -111,8 +111,8 @@ " \"packaging==26.3\" \\\n", " \"pandas==2.2.3\" \\\n", " \"pillow==11.3.0\" \\\n", - " \"platformdirs==4.11.7\" \\\n", - " \"propcache==0.5.2\" \\\n", + " \"platformdirs==4.12.2\" \\\n", + " \"propcache==0.5.4\" \\\n", " \"pycparser==3.0\" \\\n", " \"pycryptodomex==3.23.0\" \\\n", " \"pydantic==2.13.5\" \\\n", @@ -122,7 +122,7 @@ " \"pynapple==0.10.3\" \\\n", " \"pynwb==3.1.3\" \\\n", " \"pyout==0.8.1\" \\\n", - " \"pyparsing==3.3.2\" \\\n", + " \"pyparsing==3.3.3\" \\\n", " \"python-dateutil==2.9.0.post0\" \\\n", " \"python-dotenv==1.2.3\" \\\n", " \"pytz==2025.2\" \\\n", @@ -143,18 +143,18 @@ " \"tabulate==0.9.0\" \\\n", " \"tenacity==9.1.4\" \\\n", " \"tensorstore==0.1.85\" \\\n", - " \"threadpoolctl==3.6.0\" \\\n", + " \"threadpoolctl==3.7.0\" \\\n", " \"tqdm==4.67.3\" \\\n", " \"typing-extensions==4.16.0\" \\\n", " \"typing-inspection==0.4.4\" \\\n", - " \"tzdata==2026.3\" \\\n", + " \"tzdata==2026.4\" \\\n", " \"uri-template==1.3.0\" \\\n", " \"urllib3==2.5.0\" \\\n", " \"wadler-lindig==0.1.7\" \\\n", - " \"wcwidth==0.8.3\" \\\n", + " \"wcwidth==0.9.1\" \\\n", " \"webcolors==25.10.0\" \\\n", " \"xarray==2025.12.0\" \\\n", - " \"yarl==1.24.5\" \\\n", + " \"yarl==1.25.1\" \\\n", " \"zarr==3.1.5\" \\\n", " \"zarr-checksum==0.4.7\"" ] diff --git a/001636/TurnerLab/motor_cortex/turner_m1_usage.ipynb b/001636/TurnerLab/motor_cortex/turner_m1_usage.ipynb index aa3218ed..a3b3bc29 100644 --- a/001636/TurnerLab/motor_cortex/turner_m1_usage.ipynb +++ b/001636/TurnerLab/motor_cortex/turner_m1_usage.ipynb @@ -51,8 +51,8 @@ " \"click==8.5.0\" \\\n", " \"click-didyoumean==0.3.1\" \\\n", " \"cloudpickle==3.1.2\" \\\n", - " \"contourpy==1.3.3\" \\\n", - " \"cryptography==50.0.1\" \\\n", + " \"contourpy==1.4.0\" \\\n", + " \"cryptography==50.0.2\" \\\n", " \"cycler==0.12.1\" \\\n", " \"dandi==0.77.0\" \\\n", " \"dandischema==0.14.0\" \\\n", @@ -63,16 +63,16 @@ " \"equinox==0.13.8\" \\\n", " \"etelemetry==0.3.1\" \\\n", " \"fasteners==0.20\" \\\n", - " \"fonttools==4.64.0\" \\\n", - " \"fqdn==1.5.1\" \\\n", + " \"fonttools==4.66.1\" \\\n", + " \"fqdn==1.6.0\" \\\n", " \"frozenlist==1.8.0\" \\\n", " \"fscacher==0.4.4\" \\\n", " \"fsspec==2025.12.0\" \\\n", - " \"google-crc32c==1.8.0\" \\\n", - " \"h5py==3.16.0\" \\\n", + " \"google-crc32c==1.9.0\" \\\n", + " \"h5py==3.14.0\" \\\n", " \"hdmf==4.3.1\" \\\n", " \"humanize==4.16.0\" \\\n", - " \"idna==3.19\" \\\n", + " \"idna==3.20\" \\\n", " \"interleave==0.3.0\" \\\n", " \"isodate==0.7.2\" \\\n", " \"isoduration==20.11.0\" \\\n", @@ -98,7 +98,7 @@ " \"mdurl==0.1.2\" \\\n", " \"ml-dtypes==0.6.0\" \\\n", " \"more-itertools==10.8.0\" \\\n", - " \"multidict==6.7.1\" \\\n", + " \"multidict==6.9.1\" \\\n", " \"natsort==8.4.0\" \\\n", " \"nemos==0.2.6\" \\\n", " \"numba==0.61.2\" \\\n", @@ -111,8 +111,8 @@ " \"packaging==26.3\" \\\n", " \"pandas==2.2.3\" \\\n", " \"pillow==11.3.0\" \\\n", - " \"platformdirs==4.11.7\" \\\n", - " \"propcache==0.5.2\" \\\n", + " \"platformdirs==4.12.2\" \\\n", + " \"propcache==0.5.4\" \\\n", " \"pycparser==3.0\" \\\n", " \"pycryptodomex==3.23.0\" \\\n", " \"pydantic==2.13.5\" \\\n", @@ -122,7 +122,7 @@ " \"pynapple==0.10.3\" \\\n", " \"pynwb==3.1.3\" \\\n", " \"pyout==0.8.1\" \\\n", - " \"pyparsing==3.3.2\" \\\n", + " \"pyparsing==3.3.3\" \\\n", " \"python-dateutil==2.9.0.post0\" \\\n", " \"python-dotenv==1.2.3\" \\\n", " \"pytz==2025.2\" \\\n", @@ -143,18 +143,18 @@ " \"tabulate==0.9.0\" \\\n", " \"tenacity==9.1.4\" \\\n", " \"tensorstore==0.1.85\" \\\n", - " \"threadpoolctl==3.6.0\" \\\n", + " \"threadpoolctl==3.7.0\" \\\n", " \"tqdm==4.67.3\" \\\n", " \"typing-extensions==4.16.0\" \\\n", " \"typing-inspection==0.4.4\" \\\n", - " \"tzdata==2026.3\" \\\n", + " \"tzdata==2026.4\" \\\n", " \"uri-template==1.3.0\" \\\n", " \"urllib3==2.5.0\" \\\n", " \"wadler-lindig==0.1.7\" \\\n", - " \"wcwidth==0.8.3\" \\\n", + " \"wcwidth==0.9.1\" \\\n", " \"webcolors==25.10.0\" \\\n", " \"xarray==2025.12.0\" \\\n", - " \"yarl==1.24.5\" \\\n", + " \"yarl==1.25.1\" \\\n", " \"zarr==3.1.5\" \\\n", " \"zarr-checksum==0.4.7\"\n", "!curl -sL -o trial_structure_plot.py https://raw.githubusercontent.com/dandi/example-notebooks/master/001636/TurnerLab/motor_cortex/trial_structure_plot.py" diff --git a/001687/wanglab/figure2-distance-tuning/figure2_distance_tuning.ipynb b/001687/wanglab/figure2-distance-tuning/figure2_distance_tuning.ipynb index 0a031361..0c4b9af6 100644 --- a/001687/wanglab/figure2-distance-tuning/figure2_distance_tuning.ipynb +++ b/001687/wanglab/figure2-distance-tuning/figure2_distance_tuning.ipynb @@ -50,8 +50,8 @@ " \"click==8.5.0\" \\\n", " \"click-didyoumean==0.3.1\" \\\n", " \"cloudpickle==3.1.2\" \\\n", - " \"contourpy==1.3.3\" \\\n", - " \"cryptography==50.0.1\" \\\n", + " \"contourpy==1.4.0\" \\\n", + " \"cryptography==50.0.2\" \\\n", " \"cycler==0.12.1\" \\\n", " \"dandi==0.77.0\" \\\n", " \"dandischema==0.14.0\" \\\n", @@ -61,16 +61,16 @@ " \"email-validator==2.3.0\" \\\n", " \"etelemetry==0.3.1\" \\\n", " \"fasteners==0.20\" \\\n", - " \"fonttools==4.64.0\" \\\n", - " \"fqdn==1.5.1\" \\\n", + " \"fonttools==4.66.1\" \\\n", + " \"fqdn==1.6.0\" \\\n", " \"frozenlist==1.8.0\" \\\n", " \"fscacher==0.4.4\" \\\n", " \"fsspec==2025.12.0\" \\\n", - " \"google-crc32c==1.8.0\" \\\n", - " \"h5py==3.16.0\" \\\n", + " \"google-crc32c==1.9.0\" \\\n", + " \"h5py==3.14.0\" \\\n", " \"hdmf==6.2.0\" \\\n", " \"humanize==4.16.0\" \\\n", - " \"idna==3.19\" \\\n", + " \"idna==3.20\" \\\n", " \"interleave==0.3.0\" \\\n", " \"isodate==0.7.2\" \\\n", " \"isoduration==20.11.0\" \\\n", @@ -89,7 +89,7 @@ " \"matplotlib==3.10.0\" \\\n", " \"ml-dtypes==0.6.0\" \\\n", " \"more-itertools==10.8.0\" \\\n", - " \"multidict==6.7.1\" \\\n", + " \"multidict==6.9.1\" \\\n", " \"natsort==8.4.0\" \\\n", " \"numcodecs==0.16.5\" \\\n", " \"numpy==2.1.3\" \\\n", @@ -97,8 +97,8 @@ " \"packaging==26.3\" \\\n", " \"pandas==2.2.3\" \\\n", " \"pillow==11.3.0\" \\\n", - " \"platformdirs==4.11.7\" \\\n", - " \"propcache==0.5.2\" \\\n", + " \"platformdirs==4.12.2\" \\\n", + " \"propcache==0.5.4\" \\\n", " \"pycparser==3.0\" \\\n", " \"pycryptodomex==3.23.0\" \\\n", " \"pydantic==2.13.5\" \\\n", @@ -106,7 +106,7 @@ " \"pydantic-settings==2.15.0\" \\\n", " \"pynwb==4.1.0\" \\\n", " \"pyout==0.8.1\" \\\n", - " \"pyparsing==3.3.2\" \\\n", + " \"pyparsing==3.3.3\" \\\n", " \"python-dateutil==2.9.0.post0\" \\\n", " \"python-dotenv==1.2.3\" \\\n", " \"pytz==2025.2\" \\\n", @@ -126,12 +126,12 @@ " \"tqdm==4.67.3\" \\\n", " \"typing-extensions==4.16.0\" \\\n", " \"typing-inspection==0.4.4\" \\\n", - " \"tzdata==2026.3\" \\\n", + " \"tzdata==2026.4\" \\\n", " \"uri-template==1.3.0\" \\\n", " \"urllib3==2.5.0\" \\\n", - " \"wcwidth==0.8.3\" \\\n", + " \"wcwidth==0.9.1\" \\\n", " \"webcolors==25.10.0\" \\\n", - " \"yarl==1.24.5\" \\\n", + " \"yarl==1.25.1\" \\\n", " \"zarr==3.1.5\" \\\n", " \"zarr-checksum==0.4.7\"" ] diff --git a/001712/IBL-Widefield/public_demo/raw_widefield.ipynb b/001712/IBL-Widefield/public_demo/raw_widefield.ipynb index c388bd9a..6abac964 100644 --- a/001712/IBL-Widefield/public_demo/raw_widefield.ipynb +++ b/001712/IBL-Widefield/public_demo/raw_widefield.ipynb @@ -50,8 +50,8 @@ " \"click==8.5.0\" \\\n", " \"click-didyoumean==0.3.1\" \\\n", " \"cloudpickle==3.1.2\" \\\n", - " \"contourpy==1.3.3\" \\\n", - " \"cryptography==50.0.1\" \\\n", + " \"contourpy==1.4.0\" \\\n", + " \"cryptography==50.0.2\" \\\n", " \"cycler==0.12.1\" \\\n", " \"dandi==0.77.0\" \\\n", " \"dandischema==0.14.0\" \\\n", @@ -61,16 +61,16 @@ " \"email-validator==2.3.0\" \\\n", " \"etelemetry==0.3.1\" \\\n", " \"fasteners==0.20\" \\\n", - " \"fonttools==4.64.0\" \\\n", - " \"fqdn==1.5.1\" \\\n", + " \"fonttools==4.66.1\" \\\n", + " \"fqdn==1.6.0\" \\\n", " \"frozenlist==1.8.0\" \\\n", " \"fscacher==0.4.4\" \\\n", " \"fsspec==2025.12.0\" \\\n", - " \"google-crc32c==1.8.0\" \\\n", - " \"h5py==3.16.0\" \\\n", + " \"google-crc32c==1.9.0\" \\\n", + " \"h5py==3.14.0\" \\\n", " \"hdmf==4.3.1\" \\\n", " \"humanize==4.16.0\" \\\n", - " \"idna==3.19\" \\\n", + " \"idna==3.20\" \\\n", " \"interleave==0.3.0\" \\\n", " \"isodate==0.7.2\" \\\n", " \"isoduration==20.11.0\" \\\n", @@ -89,7 +89,7 @@ " \"matplotlib==3.10.0\" \\\n", " \"ml-dtypes==0.6.0\" \\\n", " \"more-itertools==10.8.0\" \\\n", - " \"multidict==6.7.1\" \\\n", + " \"multidict==6.9.1\" \\\n", " \"natsort==8.4.0\" \\\n", " \"numcodecs==0.16.5\" \\\n", " \"numpy==2.1.3\" \\\n", @@ -97,8 +97,8 @@ " \"packaging==26.3\" \\\n", " \"pandas==2.2.3\" \\\n", " \"pillow==11.3.0\" \\\n", - " \"platformdirs==4.11.7\" \\\n", - " \"propcache==0.5.2\" \\\n", + " \"platformdirs==4.12.2\" \\\n", + " \"propcache==0.5.4\" \\\n", " \"pycparser==3.0\" \\\n", " \"pycryptodomex==3.23.0\" \\\n", " \"pydantic==2.13.5\" \\\n", @@ -106,7 +106,7 @@ " \"pydantic-settings==2.15.0\" \\\n", " \"pynwb==3.1.3\" \\\n", " \"pyout==0.8.1\" \\\n", - " \"pyparsing==3.3.2\" \\\n", + " \"pyparsing==3.3.3\" \\\n", " \"python-dateutil==2.9.0.post0\" \\\n", " \"python-dotenv==1.2.3\" \\\n", " \"pytz==2025.2\" \\\n", @@ -126,12 +126,12 @@ " \"tqdm==4.67.3\" \\\n", " \"typing-extensions==4.16.0\" \\\n", " \"typing-inspection==0.4.4\" \\\n", - " \"tzdata==2026.3\" \\\n", + " \"tzdata==2026.4\" \\\n", " \"uri-template==1.3.0\" \\\n", " \"urllib3==2.5.0\" \\\n", - " \"wcwidth==0.8.3\" \\\n", + " \"wcwidth==0.9.1\" \\\n", " \"webcolors==25.10.0\" \\\n", - " \"yarl==1.24.5\" \\\n", + " \"yarl==1.25.1\" \\\n", " \"zarr==3.1.5\" \\\n", " \"zarr-checksum==0.4.7\"\n", "!curl --create-dirs -sL -o load_nwb_utils.py https://raw.githubusercontent.com/dandi/example-notebooks/master/001712/IBL-Widefield/public_demo/load_nwb_utils.py" diff --git a/001754/CatalystNeuro/001754_demo.ipynb b/001754/CatalystNeuro/001754_demo.ipynb index 04977741..1a60f8fb 100644 --- a/001754/CatalystNeuro/001754_demo.ipynb +++ b/001754/CatalystNeuro/001754_demo.ipynb @@ -50,8 +50,8 @@ " \"click==8.5.0\" \\\n", " \"click-didyoumean==0.3.1\" \\\n", " \"cloudpickle==3.1.2\" \\\n", - " \"contourpy==1.3.3\" \\\n", - " \"cryptography==50.0.1\" \\\n", + " \"contourpy==1.4.0\" \\\n", + " \"cryptography==50.0.2\" \\\n", " \"cycler==0.12.1\" \\\n", " \"dandi==0.77.0\" \\\n", " \"dandischema==0.14.0\" \\\n", @@ -61,16 +61,16 @@ " \"email-validator==2.3.0\" \\\n", " \"etelemetry==0.3.1\" \\\n", " \"fasteners==0.20\" \\\n", - " \"fonttools==4.64.0\" \\\n", - " \"fqdn==1.5.1\" \\\n", + " \"fonttools==4.66.1\" \\\n", + " \"fqdn==1.6.0\" \\\n", " \"frozenlist==1.8.0\" \\\n", " \"fscacher==0.4.4\" \\\n", " \"fsspec==2025.12.0\" \\\n", - " \"google-crc32c==1.8.0\" \\\n", - " \"h5py==3.16.0\" \\\n", + " \"google-crc32c==1.9.0\" \\\n", + " \"h5py==3.14.0\" \\\n", " \"hdmf==4.3.1\" \\\n", " \"humanize==4.16.0\" \\\n", - " \"idna==3.19\" \\\n", + " \"idna==3.20\" \\\n", " \"interleave==0.3.0\" \\\n", " \"isodate==0.7.2\" \\\n", " \"isoduration==20.11.0\" \\\n", @@ -92,7 +92,7 @@ " \"mdurl==0.1.2\" \\\n", " \"ml-dtypes==0.6.0\" \\\n", " \"more-itertools==10.8.0\" \\\n", - " \"multidict==6.7.1\" \\\n", + " \"multidict==6.9.1\" \\\n", " \"natsort==8.4.0\" \\\n", " \"neo==0.14.5\" \\\n", " \"numba==0.61.2\" \\\n", @@ -102,8 +102,8 @@ " \"packaging==26.3\" \\\n", " \"pandas==2.2.3\" \\\n", " \"pillow==11.3.0\" \\\n", - " \"platformdirs==4.11.7\" \\\n", - " \"propcache==0.5.2\" \\\n", + " \"platformdirs==4.12.2\" \\\n", + " \"propcache==0.5.4\" \\\n", " \"pycparser==3.0\" \\\n", " \"pycryptodomex==3.23.0\" \\\n", " \"pydantic==2.13.5\" \\\n", @@ -113,7 +113,7 @@ " \"pynapple==0.11.4\" \\\n", " \"pynwb==3.1.3\" \\\n", " \"pyout==0.8.1\" \\\n", - " \"pyparsing==3.3.2\" \\\n", + " \"pyparsing==3.3.3\" \\\n", " \"python-dateutil==2.9.0.post0\" \\\n", " \"python-dotenv==1.2.3\" \\\n", " \"pytz==2025.2\" \\\n", @@ -137,13 +137,13 @@ " \"tqdm==4.67.3\" \\\n", " \"typing-extensions==4.16.0\" \\\n", " \"typing-inspection==0.4.4\" \\\n", - " \"tzdata==2026.3\" \\\n", + " \"tzdata==2026.4\" \\\n", " \"uri-template==1.3.0\" \\\n", " \"urllib3==2.5.0\" \\\n", - " \"wcwidth==0.8.3\" \\\n", + " \"wcwidth==0.9.1\" \\\n", " \"webcolors==25.10.0\" \\\n", " \"xarray==2025.12.0\" \\\n", - " \"yarl==1.24.5\" \\\n", + " \"yarl==1.25.1\" \\\n", " \"zarr==3.1.5\" \\\n", " \"zarr-checksum==0.4.7\"" ] diff --git a/001933/DombeckLab/001933_demo.ipynb b/001933/DombeckLab/001933_demo.ipynb index 055c6f51..d8896fde 100644 --- a/001933/DombeckLab/001933_demo.ipynb +++ b/001933/DombeckLab/001933_demo.ipynb @@ -50,8 +50,8 @@ " \"click==8.5.0\" \\\n", " \"click-didyoumean==0.3.1\" \\\n", " \"cloudpickle==3.1.2\" \\\n", - " \"contourpy==1.3.3\" \\\n", - " \"cryptography==50.0.1\" \\\n", + " \"contourpy==1.4.0\" \\\n", + " \"cryptography==50.0.2\" \\\n", " \"cycler==0.12.1\" \\\n", " \"dandi==0.77.0\" \\\n", " \"dandischema==0.14.0\" \\\n", @@ -61,16 +61,16 @@ " \"email-validator==2.3.0\" \\\n", " \"etelemetry==0.3.1\" \\\n", " \"fasteners==0.20\" \\\n", - " \"fonttools==4.64.0\" \\\n", - " \"fqdn==1.5.1\" \\\n", + " \"fonttools==4.66.1\" \\\n", + " \"fqdn==1.6.0\" \\\n", " \"frozenlist==1.8.0\" \\\n", " \"fscacher==0.4.4\" \\\n", " \"fsspec==2025.12.0\" \\\n", - " \"google-crc32c==1.8.0\" \\\n", - " \"h5py==3.16.0\" \\\n", + " \"google-crc32c==1.9.0\" \\\n", + " \"h5py==3.14.0\" \\\n", " \"hdmf==4.3.1\" \\\n", " \"humanize==4.16.0\" \\\n", - " \"idna==3.19\" \\\n", + " \"idna==3.20\" \\\n", " \"interleave==0.3.0\" \\\n", " \"isodate==0.7.2\" \\\n", " \"isoduration==20.11.0\" \\\n", @@ -89,7 +89,7 @@ " \"matplotlib==3.10.0\" \\\n", " \"ml-dtypes==0.6.0\" \\\n", " \"more-itertools==10.8.0\" \\\n", - " \"multidict==6.7.1\" \\\n", + " \"multidict==6.9.1\" \\\n", " \"natsort==8.4.0\" \\\n", " \"ndx-fiber-photometry==0.2.3\" \\\n", " \"ndx-ophys-devices==0.3.1\" \\\n", @@ -100,8 +100,8 @@ " \"packaging==26.3\" \\\n", " \"pandas==2.2.3\" \\\n", " \"pillow==11.3.0\" \\\n", - " \"platformdirs==4.11.7\" \\\n", - " \"propcache==0.5.2\" \\\n", + " \"platformdirs==4.12.2\" \\\n", + " \"propcache==0.5.4\" \\\n", " \"pycparser==3.0\" \\\n", " \"pycryptodomex==3.23.0\" \\\n", " \"pydantic==2.13.5\" \\\n", @@ -109,7 +109,7 @@ " \"pydantic-settings==2.15.0\" \\\n", " \"pynwb==3.1.3\" \\\n", " \"pyout==0.8.1\" \\\n", - " \"pyparsing==3.3.2\" \\\n", + " \"pyparsing==3.3.3\" \\\n", " \"python-dateutil==2.9.0.post0\" \\\n", " \"python-dotenv==1.2.3\" \\\n", " \"pytz==2025.2\" \\\n", @@ -129,12 +129,12 @@ " \"tqdm==4.67.3\" \\\n", " \"typing-extensions==4.16.0\" \\\n", " \"typing-inspection==0.4.4\" \\\n", - " \"tzdata==2026.3\" \\\n", + " \"tzdata==2026.4\" \\\n", " \"uri-template==1.3.0\" \\\n", " \"urllib3==2.5.0\" \\\n", - " \"wcwidth==0.8.3\" \\\n", + " \"wcwidth==0.9.1\" \\\n", " \"webcolors==25.10.0\" \\\n", - " \"yarl==1.24.5\" \\\n", + " \"yarl==1.25.1\" \\\n", " \"zarr==3.1.5\" \\\n", " \"zarr-checksum==0.4.7\"" ] diff --git a/dandi/DANDI User Guide, Part I.ipynb b/dandi/DANDI User Guide, Part I.ipynb index a1a17cbc..bffd255e 100644 --- a/dandi/DANDI User Guide, Part I.ipynb +++ b/dandi/DANDI User Guide, Part I.ipynb @@ -50,7 +50,7 @@ " \"click==8.5.0\" \\\n", " \"click-didyoumean==0.3.1\" \\\n", " \"cloudpickle==3.1.2\" \\\n", - " \"cryptography==50.0.1\" \\\n", + " \"cryptography==50.0.2\" \\\n", " \"dandi==0.77.0\" \\\n", " \"dandischema==0.14.0\" \\\n", " \"deno==2.9.5\" \\\n", @@ -59,15 +59,15 @@ " \"email-validator==2.3.0\" \\\n", " \"etelemetry==0.3.1\" \\\n", " \"fasteners==0.20\" \\\n", - " \"fqdn==1.5.1\" \\\n", + " \"fqdn==1.6.0\" \\\n", " \"frozenlist==1.8.0\" \\\n", " \"fscacher==0.4.4\" \\\n", " \"fsspec==2025.12.0\" \\\n", - " \"google-crc32c==1.8.0\" \\\n", - " \"h5py==3.16.0\" \\\n", + " \"google-crc32c==1.9.0\" \\\n", + " \"h5py==3.14.0\" \\\n", " \"hdmf==6.2.0\" \\\n", " \"humanize==4.16.0\" \\\n", - " \"idna==3.19\" \\\n", + " \"idna==3.20\" \\\n", " \"interleave==0.3.0\" \\\n", " \"isodate==0.7.2\" \\\n", " \"isoduration==20.11.0\" \\\n", @@ -84,15 +84,15 @@ " \"keyrings-alt==5.0.2\" \\\n", " \"ml-dtypes==0.6.0\" \\\n", " \"more-itertools==10.8.0\" \\\n", - " \"multidict==6.7.1\" \\\n", + " \"multidict==6.9.1\" \\\n", " \"natsort==8.4.0\" \\\n", " \"numcodecs==0.16.5\" \\\n", " \"numpy==2.1.3\" \\\n", " \"nwbinspector==0.7.2\" \\\n", " \"packaging==26.3\" \\\n", " \"pandas==2.2.3\" \\\n", - " \"platformdirs==4.11.7\" \\\n", - " \"propcache==0.5.2\" \\\n", + " \"platformdirs==4.12.2\" \\\n", + " \"propcache==0.5.4\" \\\n", " \"pycparser==3.0\" \\\n", " \"pycryptodomex==3.23.0\" \\\n", " \"pydantic==2.13.5\" \\\n", @@ -119,12 +119,12 @@ " \"tqdm==4.67.3\" \\\n", " \"typing-extensions==4.16.0\" \\\n", " \"typing-inspection==0.4.4\" \\\n", - " \"tzdata==2026.3\" \\\n", + " \"tzdata==2026.4\" \\\n", " \"uri-template==1.3.0\" \\\n", " \"urllib3==2.5.0\" \\\n", - " \"wcwidth==0.8.3\" \\\n", + " \"wcwidth==0.9.1\" \\\n", " \"webcolors==25.10.0\" \\\n", - " \"yarl==1.24.5\" \\\n", + " \"yarl==1.25.1\" \\\n", " \"zarr==3.1.5\" \\\n", " \"zarr-checksum==0.4.7\"" ] diff --git a/dandi/DANDI User Guide, Part II.ipynb b/dandi/DANDI User Guide, Part II.ipynb index 5506efdb..8faf65d9 100644 --- a/dandi/DANDI User Guide, Part II.ipynb +++ b/dandi/DANDI User Guide, Part II.ipynb @@ -50,7 +50,7 @@ " \"click==8.5.0\" \\\n", " \"click-didyoumean==0.3.1\" \\\n", " \"cloudpickle==3.1.2\" \\\n", - " \"cryptography==50.0.1\" \\\n", + " \"cryptography==50.0.2\" \\\n", " \"dandi==0.77.0\" \\\n", " \"dandischema==0.14.0\" \\\n", " \"deno==2.9.5\" \\\n", @@ -59,15 +59,15 @@ " \"email-validator==2.3.0\" \\\n", " \"etelemetry==0.3.1\" \\\n", " \"fasteners==0.20\" \\\n", - " \"fqdn==1.5.1\" \\\n", + " \"fqdn==1.6.0\" \\\n", " \"frozenlist==1.8.0\" \\\n", " \"fscacher==0.4.4\" \\\n", " \"fsspec==2025.12.0\" \\\n", - " \"google-crc32c==1.8.0\" \\\n", - " \"h5py==3.16.0\" \\\n", + " \"google-crc32c==1.9.0\" \\\n", + " \"h5py==3.14.0\" \\\n", " \"hdmf==6.2.0\" \\\n", " \"humanize==4.16.0\" \\\n", - " \"idna==3.19\" \\\n", + " \"idna==3.20\" \\\n", " \"interleave==0.3.0\" \\\n", " \"isodate==0.7.2\" \\\n", " \"isoduration==20.11.0\" \\\n", @@ -84,15 +84,15 @@ " \"keyrings-alt==5.0.2\" \\\n", " \"ml-dtypes==0.6.0\" \\\n", " \"more-itertools==10.8.0\" \\\n", - " \"multidict==6.7.1\" \\\n", + " \"multidict==6.9.1\" \\\n", " \"natsort==8.4.0\" \\\n", " \"numcodecs==0.16.5\" \\\n", " \"numpy==2.1.3\" \\\n", " \"nwbinspector==0.7.2\" \\\n", " \"packaging==26.3\" \\\n", " \"pandas==2.2.3\" \\\n", - " \"platformdirs==4.11.7\" \\\n", - " \"propcache==0.5.2\" \\\n", + " \"platformdirs==4.12.2\" \\\n", + " \"propcache==0.5.4\" \\\n", " \"pycparser==3.0\" \\\n", " \"pycryptodomex==3.23.0\" \\\n", " \"pydantic==2.13.5\" \\\n", @@ -118,12 +118,12 @@ " \"tqdm==4.67.3\" \\\n", " \"typing-extensions==4.16.0\" \\\n", " \"typing-inspection==0.4.4\" \\\n", - " \"tzdata==2026.3\" \\\n", + " \"tzdata==2026.4\" \\\n", " \"uri-template==1.3.0\" \\\n", " \"urllib3==2.5.0\" \\\n", - " \"wcwidth==0.8.3\" \\\n", + " \"wcwidth==0.9.1\" \\\n", " \"webcolors==25.10.0\" \\\n", - " \"yarl==1.24.5\" \\\n", + " \"yarl==1.25.1\" \\\n", " \"zarr==3.1.5\" \\\n", " \"zarr-checksum==0.4.7\"" ] diff --git a/demos/NWBWidget-demo.ipynb b/demos/NWBWidget-demo.ipynb index 1ad74842..b5ff7bc0 100644 --- a/demos/NWBWidget-demo.ipynb +++ b/demos/NWBWidget-demo.ipynb @@ -36,7 +36,7 @@ " \"aiohappyeyeballs==2.7.1\" \\\n", " \"aiohttp==3.14.3\" \\\n", " \"aiosignal==1.4.0\" \\\n", - " \"anyio==4.14.2\" \\\n", + " \"anyio==4.15.1\" \\\n", " \"argon2-cffi==25.1.0\" \\\n", " \"argon2-cffi-bindings==26.1.0\" \\\n", " \"arrow==1.4.0\" \\\n", @@ -53,7 +53,7 @@ " \"click==8.5.0\" \\\n", " \"cloudpickle==3.1.2\" \\\n", " \"colorcet==3.2.1\" \\\n", - " \"contourpy==1.3.3\" \\\n", + " \"contourpy==1.4.0\" \\\n", " \"cycler==0.12.1\" \\\n", " \"dask==2026.8.0\" \\\n", " \"debugpy==1.8.15\" \\\n", @@ -63,14 +63,14 @@ " \"entrypoints==0.4\" \\\n", " \"fasteners==0.20\" \\\n", " \"fastjsonschema==2.22.2\" \\\n", - " \"fonttools==4.64.0\" \\\n", - " \"fqdn==1.5.1\" \\\n", + " \"fonttools==4.66.1\" \\\n", + " \"fqdn==1.6.0\" \\\n", " \"frozenlist==1.8.0\" \\\n", " \"fsspec==2025.12.0\" \\\n", - " \"h5py==3.16.0\" \\\n", + " \"h5py==3.14.0\" \\\n", " \"hdmf==3.14.6\" \\\n", - " \"idna==3.19\" \\\n", - " \"imageio==2.37.4\" \\\n", + " \"idna==3.20\" \\\n", + " \"imageio==2.38.0\" \\\n", " \"ipydatawidgets==4.3.5\" \\\n", " \"ipykernel==6.17.1\" \\\n", " \"ipympl==0.10.0\" \\\n", @@ -102,13 +102,13 @@ " \"jupyterlab-widgets==3.0.17\" \\\n", " \"kiwisolver==1.5.1\" \\\n", " \"lark==1.3.1\" \\\n", - " \"lazy-loader==0.5\" \\\n", + " \"lazy-loader==0.6\" \\\n", " \"locket==1.0.0\" \\\n", " \"markupsafe==3.0.3\" \\\n", " \"matplotlib==3.10.0\" \\\n", " \"matplotlib-inline==0.2.2\" \\\n", " \"mistune==3.3.4\" \\\n", - " \"multidict==6.7.1\" \\\n", + " \"multidict==6.9.1\" \\\n", " \"nbclassic==1.3.3\" \\\n", " \"nbclient==0.10.4\" \\\n", " \"nbconvert==7.17.1\" \\\n", @@ -117,7 +117,7 @@ " \"ndx-icephys-meta==0.1.0\" \\\n", " \"ndx-spectrum==0.2.2\" \\\n", " \"nest-asyncio==1.6.0\" \\\n", - " \"networkx==3.6.1\" \\\n", + " \"networkx==3.7\" \\\n", " \"notebook==6.5.7\" \\\n", " \"notebook-shim==0.2.4\" \\\n", " \"numcodecs==0.15.1\" \\\n", @@ -131,17 +131,17 @@ " \"pexpect==4.9.0\" \\\n", " \"pickleshare==0.7.5\" \\\n", " \"pillow==11.3.0\" \\\n", - " \"platformdirs==4.11.7\" \\\n", + " \"platformdirs==4.12.2\" \\\n", " \"plotly==5.24.1\" \\\n", " \"prometheus-client==0.26.0\" \\\n", " \"prompt-toolkit==3.0.53\" \\\n", - " \"propcache==0.5.2\" \\\n", + " \"propcache==0.5.4\" \\\n", " \"psutil==5.9.5\" \\\n", " \"ptyprocess==0.7.0\" \\\n", " \"pycparser==3.0\" \\\n", " \"pygments==2.21.0\" \\\n", " \"pynwb==2.8.3\" \\\n", - " \"pyparsing==3.3.2\" \\\n", + " \"pyparsing==3.3.3\" \\\n", " \"python-dateutil==2.9.0.post0\" \\\n", " \"python-json-logger==4.2.0\" \\\n", " \"pythreejs==2.4.2\" \\\n", @@ -161,10 +161,10 @@ " \"send2trash==2.1.0\" \\\n", " \"setuptools==80.10.2\" \\\n", " \"six==1.17.0\" \\\n", - " \"soupsieve==2.9.2\" \\\n", + " \"soupsieve==2.10\" \\\n", " \"tenacity==9.1.4\" \\\n", " \"terminado==0.18.1\" \\\n", - " \"tifffile==2026.8.23\" \\\n", + " \"tifffile==2026.9.20\" \\\n", " \"tinycss2==1.5.1\" \\\n", " \"toolz==0.12.1\" \\\n", " \"tornado==6.5.7\" \\\n", @@ -173,17 +173,17 @@ " \"traittypes==0.2.3\" \\\n", " \"trimesh==5.0.0\" \\\n", " \"typing-extensions==4.16.0\" \\\n", - " \"tzdata==2026.3\" \\\n", + " \"tzdata==2026.4\" \\\n", " \"uri-template==1.3.0\" \\\n", " \"urllib3==2.5.0\" \\\n", - " \"wcwidth==0.8.3\" \\\n", + " \"wcwidth==0.9.1\" \\\n", " \"webcolors==25.10.0\" \\\n", " \"webencodings==0.6.1\" \\\n", " \"websocket-client==1.9.2\" \\\n", " \"widgetsnbextension==3.6.10\" \\\n", - " \"wrapt==2.4.0\" \\\n", + " \"wrapt==2.5.0\" \\\n", " \"xarray==2025.12.0\" \\\n", - " \"yarl==1.24.5\" \\\n", + " \"yarl==1.25.1\" \\\n", " \"zarr==2.18.7\" \\\n", " \"zstandard==0.25.0\"" ] diff --git a/tutorials/bcm_2024/analysis-demo.ipynb b/tutorials/bcm_2024/analysis-demo.ipynb index a3666fdf..420428fa 100644 --- a/tutorials/bcm_2024/analysis-demo.ipynb +++ b/tutorials/bcm_2024/analysis-demo.ipynb @@ -50,8 +50,8 @@ " \"click==8.5.0\" \\\n", " \"click-didyoumean==0.3.1\" \\\n", " \"cloudpickle==3.1.2\" \\\n", - " \"contourpy==1.3.3\" \\\n", - " \"cryptography==50.0.1\" \\\n", + " \"contourpy==1.4.0\" \\\n", + " \"cryptography==50.0.2\" \\\n", " \"cycler==0.12.1\" \\\n", " \"dandi==0.77.0\" \\\n", " \"dandischema==0.14.0\" \\\n", @@ -61,16 +61,16 @@ " \"email-validator==2.3.0\" \\\n", " \"etelemetry==0.3.1\" \\\n", " \"fasteners==0.20\" \\\n", - " \"fonttools==4.64.0\" \\\n", - " \"fqdn==1.5.1\" \\\n", + " \"fonttools==4.66.1\" \\\n", + " \"fqdn==1.6.0\" \\\n", " \"frozenlist==1.8.0\" \\\n", " \"fscacher==0.4.4\" \\\n", " \"fsspec==2025.12.0\" \\\n", - " \"google-crc32c==1.8.0\" \\\n", - " \"h5py==3.16.0\" \\\n", + " \"google-crc32c==1.9.0\" \\\n", + " \"h5py==3.14.0\" \\\n", " \"hdmf==4.3.1\" \\\n", " \"humanize==4.16.0\" \\\n", - " \"idna==3.19\" \\\n", + " \"idna==3.20\" \\\n", " \"interleave==0.3.0\" \\\n", " \"isodate==0.7.2\" \\\n", " \"isoduration==20.11.0\" \\\n", @@ -92,7 +92,7 @@ " \"mdurl==0.1.2\" \\\n", " \"ml-dtypes==0.6.0\" \\\n", " \"more-itertools==10.8.0\" \\\n", - " \"multidict==6.7.1\" \\\n", + " \"multidict==6.9.1\" \\\n", " \"natsort==8.4.0\" \\\n", " \"neo==0.14.5\" \\\n", " \"numba==0.61.2\" \\\n", @@ -102,8 +102,8 @@ " \"packaging==26.3\" \\\n", " \"pandas==2.2.3\" \\\n", " \"pillow==11.3.0\" \\\n", - " \"platformdirs==4.11.7\" \\\n", - " \"propcache==0.5.2\" \\\n", + " \"platformdirs==4.12.2\" \\\n", + " \"propcache==0.5.4\" \\\n", " \"pycparser==3.0\" \\\n", " \"pycryptodomex==3.23.0\" \\\n", " \"pydantic==2.13.5\" \\\n", @@ -113,7 +113,7 @@ " \"pynapple==0.11.4\" \\\n", " \"pynwb==3.1.3\" \\\n", " \"pyout==0.8.1\" \\\n", - " \"pyparsing==3.3.2\" \\\n", + " \"pyparsing==3.3.3\" \\\n", " \"python-dateutil==2.9.0.post0\" \\\n", " \"python-dotenv==1.2.3\" \\\n", " \"pytz==2025.2\" \\\n", @@ -137,13 +137,13 @@ " \"tqdm==4.67.3\" \\\n", " \"typing-extensions==4.16.0\" \\\n", " \"typing-inspection==0.4.4\" \\\n", - " \"tzdata==2026.3\" \\\n", + " \"tzdata==2026.4\" \\\n", " \"uri-template==1.3.0\" \\\n", " \"urllib3==2.5.0\" \\\n", - " \"wcwidth==0.8.3\" \\\n", + " \"wcwidth==0.9.1\" \\\n", " \"webcolors==25.10.0\" \\\n", " \"xarray==2025.12.0\" \\\n", - " \"yarl==1.24.5\" \\\n", + " \"yarl==1.25.1\" \\\n", " \"zarr==3.1.5\" \\\n", " \"zarr-checksum==0.4.7\"" ] diff --git a/tutorials/cosyne_2023/simple_dandiset_search.ipynb b/tutorials/cosyne_2023/simple_dandiset_search.ipynb index a1f07c4c..ec97de35 100644 --- a/tutorials/cosyne_2023/simple_dandiset_search.ipynb +++ b/tutorials/cosyne_2023/simple_dandiset_search.ipynb @@ -50,7 +50,7 @@ " \"click==8.5.0\" \\\n", " \"click-didyoumean==0.3.1\" \\\n", " \"cloudpickle==3.1.2\" \\\n", - " \"cryptography==50.0.1\" \\\n", + " \"cryptography==50.0.2\" \\\n", " \"dandi==0.77.0\" \\\n", " \"dandischema==0.14.0\" \\\n", " \"deno==2.9.5\" \\\n", @@ -59,15 +59,15 @@ " \"email-validator==2.3.0\" \\\n", " \"etelemetry==0.3.1\" \\\n", " \"fasteners==0.20\" \\\n", - " \"fqdn==1.5.1\" \\\n", + " \"fqdn==1.6.0\" \\\n", " \"frozenlist==1.8.0\" \\\n", " \"fscacher==0.4.4\" \\\n", " \"fsspec==2025.12.0\" \\\n", - " \"google-crc32c==1.8.0\" \\\n", - " \"h5py==3.16.0\" \\\n", + " \"google-crc32c==1.9.0\" \\\n", + " \"h5py==3.14.0\" \\\n", " \"hdmf==6.2.0\" \\\n", " \"humanize==4.16.0\" \\\n", - " \"idna==3.19\" \\\n", + " \"idna==3.20\" \\\n", " \"interleave==0.3.0\" \\\n", " \"isodate==0.7.2\" \\\n", " \"isoduration==20.11.0\" \\\n", @@ -84,15 +84,15 @@ " \"keyrings-alt==5.0.2\" \\\n", " \"ml-dtypes==0.6.0\" \\\n", " \"more-itertools==10.8.0\" \\\n", - " \"multidict==6.7.1\" \\\n", + " \"multidict==6.9.1\" \\\n", " \"natsort==8.4.0\" \\\n", " \"numcodecs==0.16.5\" \\\n", " \"numpy==2.1.3\" \\\n", " \"nwbinspector==0.7.2\" \\\n", " \"packaging==26.3\" \\\n", " \"pandas==2.2.3\" \\\n", - " \"platformdirs==4.11.7\" \\\n", - " \"propcache==0.5.2\" \\\n", + " \"platformdirs==4.12.2\" \\\n", + " \"propcache==0.5.4\" \\\n", " \"pycparser==3.0\" \\\n", " \"pycryptodomex==3.23.0\" \\\n", " \"pydantic==2.13.5\" \\\n", @@ -118,12 +118,12 @@ " \"tqdm==4.67.3\" \\\n", " \"typing-extensions==4.16.0\" \\\n", " \"typing-inspection==0.4.4\" \\\n", - " \"tzdata==2026.3\" \\\n", + " \"tzdata==2026.4\" \\\n", " \"uri-template==1.3.0\" \\\n", " \"urllib3==2.5.0\" \\\n", - " \"wcwidth==0.8.3\" \\\n", + " \"wcwidth==0.9.1\" \\\n", " \"webcolors==25.10.0\" \\\n", - " \"yarl==1.24.5\" \\\n", + " \"yarl==1.25.1\" \\\n", " \"zarr==3.1.5\" \\\n", " \"zarr-checksum==0.4.7\"" ] diff --git a/tutorials/neurodatarehack_2024/advanced_asset_search.ipynb b/tutorials/neurodatarehack_2024/advanced_asset_search.ipynb index f5d93917..49b2bf63 100644 --- a/tutorials/neurodatarehack_2024/advanced_asset_search.ipynb +++ b/tutorials/neurodatarehack_2024/advanced_asset_search.ipynb @@ -50,7 +50,7 @@ " \"click==8.5.0\" \\\n", " \"click-didyoumean==0.3.1\" \\\n", " \"cloudpickle==3.1.2\" \\\n", - " \"cryptography==50.0.1\" \\\n", + " \"cryptography==50.0.2\" \\\n", " \"dandi==0.77.0\" \\\n", " \"dandischema==0.14.0\" \\\n", " \"deno==2.9.5\" \\\n", @@ -59,15 +59,15 @@ " \"email-validator==2.3.0\" \\\n", " \"etelemetry==0.3.1\" \\\n", " \"fasteners==0.20\" \\\n", - " \"fqdn==1.5.1\" \\\n", + " \"fqdn==1.6.0\" \\\n", " \"frozenlist==1.8.0\" \\\n", " \"fscacher==0.4.4\" \\\n", " \"fsspec==2025.12.0\" \\\n", - " \"google-crc32c==1.8.0\" \\\n", - " \"h5py==3.16.0\" \\\n", + " \"google-crc32c==1.9.0\" \\\n", + " \"h5py==3.14.0\" \\\n", " \"hdmf==4.3.1\" \\\n", " \"humanize==4.16.0\" \\\n", - " \"idna==3.19\" \\\n", + " \"idna==3.20\" \\\n", " \"interleave==0.3.0\" \\\n", " \"isodate==0.7.2\" \\\n", " \"isoduration==20.11.0\" \\\n", @@ -84,15 +84,15 @@ " \"keyrings-alt==5.0.2\" \\\n", " \"ml-dtypes==0.6.0\" \\\n", " \"more-itertools==10.8.0\" \\\n", - " \"multidict==6.7.1\" \\\n", + " \"multidict==6.9.1\" \\\n", " \"natsort==8.4.0\" \\\n", " \"numcodecs==0.16.5\" \\\n", " \"numpy==2.1.3\" \\\n", " \"nwbinspector==0.7.2\" \\\n", " \"packaging==26.3\" \\\n", " \"pandas==2.2.3\" \\\n", - " \"platformdirs==4.11.7\" \\\n", - " \"propcache==0.5.2\" \\\n", + " \"platformdirs==4.12.2\" \\\n", + " \"propcache==0.5.4\" \\\n", " \"pycparser==3.0\" \\\n", " \"pycryptodomex==3.23.0\" \\\n", " \"pydantic==2.13.5\" \\\n", @@ -119,12 +119,12 @@ " \"tqdm==4.67.3\" \\\n", " \"typing-extensions==4.16.0\" \\\n", " \"typing-inspection==0.4.4\" \\\n", - " \"tzdata==2026.3\" \\\n", + " \"tzdata==2026.4\" \\\n", " \"uri-template==1.3.0\" \\\n", " \"urllib3==2.5.0\" \\\n", - " \"wcwidth==0.8.3\" \\\n", + " \"wcwidth==0.9.1\" \\\n", " \"webcolors==25.10.0\" \\\n", - " \"yarl==1.24.5\" \\\n", + " \"yarl==1.25.1\" \\\n", " \"zarr==3.1.5\" \\\n", " \"zarr-checksum==0.4.7\"" ] diff --git a/tutorials/neurodatarehack_2024/simple_dandiset_search.ipynb b/tutorials/neurodatarehack_2024/simple_dandiset_search.ipynb index 8c947065..e6170dd0 100644 --- a/tutorials/neurodatarehack_2024/simple_dandiset_search.ipynb +++ b/tutorials/neurodatarehack_2024/simple_dandiset_search.ipynb @@ -50,7 +50,7 @@ " \"click==8.5.0\" \\\n", " \"click-didyoumean==0.3.1\" \\\n", " \"cloudpickle==3.1.2\" \\\n", - " \"cryptography==50.0.1\" \\\n", + " \"cryptography==50.0.2\" \\\n", " \"dandi==0.77.0\" \\\n", " \"dandischema==0.14.0\" \\\n", " \"deno==2.9.5\" \\\n", @@ -59,15 +59,15 @@ " \"email-validator==2.3.0\" \\\n", " \"etelemetry==0.3.1\" \\\n", " \"fasteners==0.20\" \\\n", - " \"fqdn==1.5.1\" \\\n", + " \"fqdn==1.6.0\" \\\n", " \"frozenlist==1.8.0\" \\\n", " \"fscacher==0.4.4\" \\\n", " \"fsspec==2025.12.0\" \\\n", - " \"google-crc32c==1.8.0\" \\\n", - " \"h5py==3.16.0\" \\\n", + " \"google-crc32c==1.9.0\" \\\n", + " \"h5py==3.14.0\" \\\n", " \"hdmf==6.2.0\" \\\n", " \"humanize==4.16.0\" \\\n", - " \"idna==3.19\" \\\n", + " \"idna==3.20\" \\\n", " \"interleave==0.3.0\" \\\n", " \"isodate==0.7.2\" \\\n", " \"isoduration==20.11.0\" \\\n", @@ -84,15 +84,15 @@ " \"keyrings-alt==5.0.2\" \\\n", " \"ml-dtypes==0.6.0\" \\\n", " \"more-itertools==10.8.0\" \\\n", - " \"multidict==6.7.1\" \\\n", + " \"multidict==6.9.1\" \\\n", " \"natsort==8.4.0\" \\\n", " \"numcodecs==0.16.5\" \\\n", " \"numpy==2.1.3\" \\\n", " \"nwbinspector==0.7.2\" \\\n", " \"packaging==26.3\" \\\n", " \"pandas==2.2.3\" \\\n", - " \"platformdirs==4.11.7\" \\\n", - " \"propcache==0.5.2\" \\\n", + " \"platformdirs==4.12.2\" \\\n", + " \"propcache==0.5.4\" \\\n", " \"pycparser==3.0\" \\\n", " \"pycryptodomex==3.23.0\" \\\n", " \"pydantic==2.13.5\" \\\n", @@ -118,12 +118,12 @@ " \"tqdm==4.67.3\" \\\n", " \"typing-extensions==4.16.0\" \\\n", " \"typing-inspection==0.4.4\" \\\n", - " \"tzdata==2026.3\" \\\n", + " \"tzdata==2026.4\" \\\n", " \"uri-template==1.3.0\" \\\n", " \"urllib3==2.5.0\" \\\n", - " \"wcwidth==0.8.3\" \\\n", + " \"wcwidth==0.9.1\" \\\n", " \"webcolors==25.10.0\" \\\n", - " \"yarl==1.24.5\" \\\n", + " \"yarl==1.25.1\" \\\n", " \"zarr==3.1.5\" \\\n", " \"zarr-checksum==0.4.7\"" ] diff --git a/tutorials/open_data_quick_start_2026/Get-to-know-a-Dandiset.ipynb b/tutorials/open_data_quick_start_2026/Get-to-know-a-Dandiset.ipynb index e0894667..1a97778e 100644 --- a/tutorials/open_data_quick_start_2026/Get-to-know-a-Dandiset.ipynb +++ b/tutorials/open_data_quick_start_2026/Get-to-know-a-Dandiset.ipynb @@ -50,8 +50,8 @@ " \"click==8.5.0\" \\\n", " \"click-didyoumean==0.3.1\" \\\n", " \"cloudpickle==3.1.2\" \\\n", - " \"contourpy==1.3.3\" \\\n", - " \"cryptography==50.0.1\" \\\n", + " \"contourpy==1.4.0\" \\\n", + " \"cryptography==50.0.2\" \\\n", " \"cycler==0.12.1\" \\\n", " \"dandi==0.77.0\" \\\n", " \"dandischema==0.14.0\" \\\n", @@ -61,16 +61,16 @@ " \"email-validator==2.3.0\" \\\n", " \"etelemetry==0.3.1\" \\\n", " \"fasteners==0.20\" \\\n", - " \"fonttools==4.64.0\" \\\n", - " \"fqdn==1.5.1\" \\\n", + " \"fonttools==4.66.1\" \\\n", + " \"fqdn==1.6.0\" \\\n", " \"frozenlist==1.8.0\" \\\n", " \"fscacher==0.4.4\" \\\n", " \"fsspec==2025.12.0\" \\\n", - " \"google-crc32c==1.8.0\" \\\n", - " \"h5py==3.16.0\" \\\n", + " \"google-crc32c==1.9.0\" \\\n", + " \"h5py==3.14.0\" \\\n", " \"hdmf==4.3.1\" \\\n", " \"humanize==4.16.0\" \\\n", - " \"idna==3.19\" \\\n", + " \"idna==3.20\" \\\n", " \"interleave==0.3.0\" \\\n", " \"isodate==0.7.2\" \\\n", " \"isoduration==20.11.0\" \\\n", @@ -89,7 +89,7 @@ " \"matplotlib==3.10.0\" \\\n", " \"ml-dtypes==0.6.0\" \\\n", " \"more-itertools==10.8.0\" \\\n", - " \"multidict==6.7.1\" \\\n", + " \"multidict==6.9.1\" \\\n", " \"natsort==8.4.0\" \\\n", " \"numcodecs==0.16.5\" \\\n", " \"numpy==2.1.3\" \\\n", @@ -98,8 +98,8 @@ " \"packaging==26.3\" \\\n", " \"pandas==2.2.3\" \\\n", " \"pillow==11.3.0\" \\\n", - " \"platformdirs==4.11.7\" \\\n", - " \"propcache==0.5.2\" \\\n", + " \"platformdirs==4.12.2\" \\\n", + " \"propcache==0.5.4\" \\\n", " \"pycparser==3.0\" \\\n", " \"pycryptodomex==3.23.0\" \\\n", " \"pydantic==2.13.5\" \\\n", @@ -107,7 +107,7 @@ " \"pydantic-settings==2.15.0\" \\\n", " \"pynwb==3.1.3\" \\\n", " \"pyout==0.8.1\" \\\n", - " \"pyparsing==3.3.2\" \\\n", + " \"pyparsing==3.3.3\" \\\n", " \"python-dateutil==2.9.0.post0\" \\\n", " \"python-dotenv==1.2.3\" \\\n", " \"pytz==2025.2\" \\\n", @@ -127,12 +127,12 @@ " \"tqdm==4.67.3\" \\\n", " \"typing-extensions==4.16.0\" \\\n", " \"typing-inspection==0.4.4\" \\\n", - " \"tzdata==2026.3\" \\\n", + " \"tzdata==2026.4\" \\\n", " \"uri-template==1.3.0\" \\\n", " \"urllib3==2.5.0\" \\\n", - " \"wcwidth==0.8.3\" \\\n", + " \"wcwidth==0.9.1\" \\\n", " \"webcolors==25.10.0\" \\\n", - " \"yarl==1.24.5\" \\\n", + " \"yarl==1.25.1\" \\\n", " \"zarr==3.1.5\" \\\n", " \"zarr-checksum==0.4.7\"" ]