From ca308231f9587be90051771aa38bd897b5b84f69 Mon Sep 17 00:00:00 2001 From: "github-actions[bot]" <41898282+github-actions[bot]@users.noreply.github.com> Date: Mon, 28 Sep 2026 05:05:13 +0000 Subject: [PATCH] Refresh the Colab snapshot and re-lock notebooks --- .github/colab-preinstalled.txt | 158 +++++++++--------- .../chunglab/demo/2021-09-27_dandi-demo.ipynb | 22 +-- 000108/chunglab/demo/dashboard.ipynb | 22 +-- 000402/MICrONS/demo/000402_microns_demo.ipynb | 16 +- 000409/IBL/bwm_usage_notebook.ipynb | 22 +-- 000458/AllenInstitute/reanalysis.ipynb | 16 +- .../000_lindi_vs_fsspec_streaming.ipynb | 14 +- .../001_summarize_contents.ipynb | 14 +- .../reproduce_figure1d.ipynb | 20 +-- .../reproduce_figure_S1.ipynb | 20 +-- .../000582_Sargolini2006_demo.ipynb | 12 +- 000718/CaiLab/zaki_2024/000718_demo.ipynb | 16 +- .../simple_data_access/reading_data.ipynb | 16 +- .../visual_coding_ophys_tutorial.ipynb | 16 +- .../TurnerLab/public_demo/000947_demo.ipynb | 16 +- .../fiber_photometry_example_notebook.ipynb | 16 +- .../optogenetics_example_notebook.ipynb | 16 +- 001038/DombeckLab/001038_demo.ipynb | 20 +-- 001075/001075_paper_figure_1d.ipynb | 16 +- 001084/HoweLab/001084_demo.ipynb | 20 +-- .../ReimerLab/public_demo/001170_demo.ipynb | 16 +- 001172/HigleyLab/001172_demo.ipynb | 16 +- 001528/HnaskoLab/Lotfi_2025/001528_demo.ipynb | 16 +- .../figure_1E_dspn_somatic_excitability.ipynb | 16 +- .../zhai_2025/figure_2GH_oepsc_analysis.ipynb | 16 +- .../figure_5F_acetylcholine_biosensor.ipynb | 16 +- .../zhai_2025/how_to_use_this_dataset.ipynb | 16 +- 001550/PaganLab/01_behavior_demo.ipynb | 16 +- 001550/PaganLab/02_optogenetics_demo.ipynb | 16 +- .../antidromic_detection_tutorial.ipynb | 18 +- .../motor_cortex/turner_m1_glm.ipynb | 18 +- .../motor_cortex/turner_m1_peth.ipynb | 18 +- .../motor_cortex/turner_m1_usage.ipynb | 18 +- .../figure2_distance_tuning.ipynb | 16 +- .../public_demo/raw_widefield.ipynb | 16 +- 001754/CatalystNeuro/001754_demo.ipynb | 16 +- 001933/DombeckLab/001933_demo.ipynb | 16 +- dandi/DANDI User Guide, Part I.ipynb | 12 +- dandi/DANDI User Guide, Part II.ipynb | 12 +- demos/NWBWidget-demo.ipynb | 22 +-- tutorials/bcm_2024/analysis-demo.ipynb | 16 +- .../cosyne_2023/simple_dandiset_search.ipynb | 12 +- .../advanced_asset_search.ipynb | 12 +- .../simple_dandiset_search.ipynb | 12 +- .../Get-to-know-a-Dandiset.ipynb | 16 +- 45 files changed, 443 insertions(+), 439 deletions(-) diff --git a/.github/colab-preinstalled.txt b/.github/colab-preinstalled.txt index 79da44f..5577120 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: 2026-09-28 # # 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==0.2026.9.14.0.56.43 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==4.13.1 bokeh==3.8.2 Bottleneck==1.4.2 bqplot==0.12.47 @@ -82,11 +82,11 @@ colorlover==0.3.0 community==1.0.0b1 confection==1.3.3 cons==0.4.7 -contourpy==1.3.3 +contourpy==1.4.0 cramjam==2.12.1 cryptography==50.0.1 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 +104,9 @@ 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 +115,7 @@ 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 @@ -122,20 +123,20 @@ 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==2.2.28 +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==3.32.7 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==4.65.0 formulaic==1.2.2 fqdn==1.5.1 frozendict==2.4.7 @@ -146,7 +147,7 @@ gast==0.7.0 gcsfs==2025.12.0 GDAL==3.8.4 gdown==5.2.2 -geemap==0.38.4 +geemap==0.38.5 geocoder==1.38.1 geographiclib==2.1 geopandas==1.1.4 @@ -156,43 +157,41 @@ 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-auth==2.49.0 google-auth-httplib2==0.4.2 google-auth-oauthlib==1.4.1 -google-cloud-bigquery==3.44.0 +google-cloud-bigquery==3.45.1 google-cloud-bigquery-connection==1.22.0 -google-cloud-bigquery-storage==2.39.0 +google-cloud-bigquery-storage==2.41.0 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-dataproc==5.30.0 +google-cloud-datastore==2.26.1 +google-cloud-firestore==2.30.0 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==3.14.1 google-cloud-storage-control==1.12.0 google-cloud-translate==3.27.0 google-crc32c==1.8.0 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 +googleapis-common-protos==1.75.3 googledrivedownloader==1.1.0 -gradio==6.26.0 -gradio_client==2.6.1 +gradio==6.27.0 +gradio_client==2.7.0 grain==0.2.18 graphviz==0.21 -greenlet==3.5.5 +greenlet==3.5.6 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==1.84.0 grpcio-status==1.71.2 grpclib==0.4.9 gspread==6.2.1 @@ -203,23 +202,23 @@ 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==0.104 holoviews==1.23.2 hpack==4.2.0 html5lib==1.1 httpcore==1.0.9 -httpcore2==2.12.0 +httpcore2==2.13.0 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==2.13.0 +huggingface_hub==1.31.0 humanize==4.16.0 hyperframe==6.1.0 hyperopt==0.3.0 @@ -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 @@ -284,14 +283,14 @@ 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==1.4.0 +langchain-core==1.6.3 langchain-protocol==0.0.19 langgraph==1.2.11 langgraph-checkpoint==4.2.0 langgraph-prebuilt==1.1.0 langgraph-sdk==0.4.4 -langsmith==0.12.1 +langsmith==0.12.5 lark==1.3.1 launchpadlib==1.11.0 lazr.restfulclient==0.14.6 @@ -305,7 +304,8 @@ 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 @@ -330,14 +330,14 @@ more-itertools==10.8.0 moviepy==1.0.3 mpmath==1.3.0 msgpack==1.2.2 -multidict==6.7.1 +multidict==6.8.0 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 @@ -383,18 +383,18 @@ pandas-stubs==2.2.3.250527 pandocfilters==1.5.1 panel==1.9.4 panel-material-ui==0.14.2 -param==2.4.1 +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==4.5.1 +peft==0.21.0 pexpect==4.9.0 pickleshare==0.7.5 pillow==11.3.0 pip==24.1.2 -platformdirs==4.11.7 +platformdirs==4.11.8 plotly==5.24.1 plotnine==0.14.5 pluggy==1.6.0 @@ -411,13 +411,13 @@ 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==1.28.4 +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 py-cpuinfo==9.0.0 @@ -438,11 +438,11 @@ 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==2.14.0 pymc==5.28.5 pynndescent==0.6.0 pyogrio==0.13.0 @@ -451,7 +451,7 @@ PyOpenGL==3.1.10 pyOpenSSL==26.4.0 pyparsing==3.3.2 pyperclip==1.11.0 -pyproj==3.7.2 +pyproj==3.8.0 pyroaring==1.1.0 pysal==25.7 pyshp==3.1.6 @@ -463,16 +463,16 @@ 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==9.0.0 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 @@ -500,8 +500,8 @@ 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 +509,7 @@ 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==2.69.2 setuptools==80.10.2 shap==0.52.0 shapely==2.1.2 @@ -524,6 +524,7 @@ slicer==0.0.8 smart_open==8.0.1 sniffio==1.3.1 snowballstemmer==3.1.1 +sortedcontainers==2.4.0 soundfile==0.14.0 soupsieve==2.9.2 soxr==1.1.0 @@ -544,7 +545,7 @@ spint==1.1.0 splot==1.1.7 spopt==0.7.0 spreg==1.9.0 -SQLAlchemy==2.0.52 +SQLAlchemy==2.0.54 sqlglot==25.20.2 sqlparse==0.6.0 srsly==2.5.3 @@ -561,31 +562,32 @@ 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==2026.9.15 tiktoken==0.14.0 timm==1.0.29 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 @@ -597,7 +599,7 @@ tornado==6.5.7 tqdm==4.67.3 traitlets==5.7.1 traittypes==0.2.3 -transformers==5.16.1 +transformers==5.17.0 treescope==0.1.10 truststore==0.10.4 tsfresh==0.21.2 @@ -608,15 +610,15 @@ types-pytz==2026.3.1.20260727 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==0.53.0 uvloop==0.22.1 vega-datasets==0.9.0 wadllib==1.3.6 @@ -634,17 +636,19 @@ Werkzeug==3.1.8 wheel==0.48.0 widgetsnbextension==3.6.10 wordcloud==1.9.6 -wrapt==2.4.0 +wrapt==2.4.1 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 fb55b52..105e1db 100644 --- a/000108/chunglab/demo/2021-09-27_dandi-demo.ipynb +++ b/000108/chunglab/demo/2021-09-27_dandi-demo.ipynb @@ -51,7 +51,7 @@ " \"click==8.5.0\" \\\n", " \"click-didyoumean==0.3.1\" \\\n", " \"cloudpickle==3.1.2\" \\\n", - " \"contourpy==1.3.3\" \\\n", + " \"contourpy==1.4.0\" \\\n", " \"cryptography==50.0.1\" \\\n", " \"cycler==0.12.1\" \\\n", " \"dandi==0.77.0\" \\\n", @@ -62,13 +62,13 @@ " \"email-validator==2.3.0\" \\\n", " \"etelemetry==0.3.1\" \\\n", " \"fasteners==0.20\" \\\n", - " \"fonttools==4.64.0\" \\\n", + " \"fonttools==4.65.0\" \\\n", " \"fqdn==1.5.1\" \\\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", + " \"h5py==3.14.0\" \\\n", " \"hdmf==6.2.0\" \\\n", " \"humanize==4.16.0\" \\\n", " \"idna==3.19\" \\\n", @@ -94,8 +94,8 @@ " \"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==6.8.0\" \\\n", + " \"narwhals==2.26.0\" \\\n", " \"natsort==8.4.0\" \\\n", " \"networkx==3.6.1\" \\\n", " \"numcodecs==0.16.5\" \\\n", @@ -104,8 +104,8 @@ " \"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==4.11.8\" \\\n", + " \"propcache==0.5.4\" \\\n", " \"pycparser==3.0\" \\\n", " \"pycryptodomex==3.23.0\" \\\n", " \"pydantic==2.13.5\" \\\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==2026.9.15\" \\\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", " \"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 add50f6..6ed6550 100644 --- a/000108/chunglab/demo/dashboard.ipynb +++ b/000108/chunglab/demo/dashboard.ipynb @@ -51,7 +51,7 @@ " \"click==8.5.0\" \\\n", " \"click-didyoumean==0.3.1\" \\\n", " \"cloudpickle==3.1.2\" \\\n", - " \"contourpy==1.3.3\" \\\n", + " \"contourpy==1.4.0\" \\\n", " \"cryptography==50.0.1\" \\\n", " \"cycler==0.12.1\" \\\n", " \"dandi==0.77.0\" \\\n", @@ -62,13 +62,13 @@ " \"email-validator==2.3.0\" \\\n", " \"etelemetry==0.3.1\" \\\n", " \"fasteners==0.20\" \\\n", - " \"fonttools==4.64.0\" \\\n", + " \"fonttools==4.65.0\" \\\n", " \"fqdn==1.5.1\" \\\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", + " \"h5py==3.14.0\" \\\n", " \"hdmf==6.2.0\" \\\n", " \"humanize==4.16.0\" \\\n", " \"idna==3.19\" \\\n", @@ -94,8 +94,8 @@ " \"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==6.8.0\" \\\n", + " \"narwhals==2.26.0\" \\\n", " \"natsort==8.4.0\" \\\n", " \"networkx==3.6.1\" \\\n", " \"numcodecs==0.16.5\" \\\n", @@ -104,8 +104,8 @@ " \"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==4.11.8\" \\\n", + " \"propcache==0.5.4\" \\\n", " \"pycparser==3.0\" \\\n", " \"pycryptodomex==3.23.0\" \\\n", " \"pydantic==2.13.5\" \\\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==2026.9.15\" \\\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", " \"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 2b4c1ad..8d1eb5d 100644 --- a/000402/MICrONS/demo/000402_microns_demo.ipynb +++ b/000402/MICrONS/demo/000402_microns_demo.ipynb @@ -50,7 +50,7 @@ " \"click==8.5.0\" \\\n", " \"click-didyoumean==0.3.1\" \\\n", " \"cloudpickle==3.1.2\" \\\n", - " \"contourpy==1.3.3\" \\\n", + " \"contourpy==1.4.0\" \\\n", " \"cryptography==50.0.1\" \\\n", " \"cycler==0.12.1\" \\\n", " \"dandi==0.77.0\" \\\n", @@ -61,13 +61,13 @@ " \"email-validator==2.3.0\" \\\n", " \"etelemetry==0.3.1\" \\\n", " \"fasteners==0.20\" \\\n", - " \"fonttools==4.64.0\" \\\n", + " \"fonttools==4.65.0\" \\\n", " \"fqdn==1.5.1\" \\\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", + " \"h5py==3.14.0\" \\\n", " \"hdmf==4.3.1\" \\\n", " \"humanize==4.16.0\" \\\n", " \"idna==3.19\" \\\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==6.8.0\" \\\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==4.11.8\" \\\n", + " \"propcache==0.5.4\" \\\n", " \"pycparser==3.0\" \\\n", " \"pycryptodomex==3.23.0\" \\\n", " \"pydantic==2.13.5\" \\\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", " \"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 ab958b0..5728cd0 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", @@ -62,7 +62,7 @@ " \"click-didyoumean==0.3.1\" \\\n", " \"cloudpickle==3.1.2\" \\\n", " \"colorlog==6.12.0\" \\\n", - " \"contourpy==1.3.3\" \\\n", + " \"contourpy==1.4.0\" \\\n", " \"cryptography==50.0.1\" \\\n", " \"cycler==0.12.1\" \\\n", " \"dandi==0.77.0\" \\\n", @@ -78,13 +78,13 @@ " \"etelemetry==0.3.1\" \\\n", " \"fasteners==0.20\" \\\n", " \"fastjsonschema==2.22.2\" \\\n", - " \"fonttools==4.64.0\" \\\n", + " \"fonttools==4.65.0\" \\\n", " \"fqdn==1.5.1\" \\\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", + " \"h5py==3.14.0\" \\\n", " \"hdmf==4.3.1\" \\\n", " \"humanize==4.16.0\" \\\n", " \"iblatlas==1.2.0\" \\\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==6.8.0\" \\\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==4.11.8\" \\\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", @@ -203,7 +203,7 @@ " \"tenacity==9.1.4\" \\\n", " \"tensorstore==0.1.85\" \\\n", " \"terminado==0.18.1\" \\\n", - " \"tifffile==2026.8.23\" \\\n", + " \"tifffile==2026.9.15\" \\\n", " \"tinycss2==1.5.1\" \\\n", " \"tornado==6.5.7\" \\\n", " \"tqdm==4.67.3\" \\\n", @@ -211,7 +211,7 @@ " \"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", @@ -220,7 +220,7 @@ " \"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 f304ff3..7a8b0ce 100644 --- a/000458/AllenInstitute/reanalysis.ipynb +++ b/000458/AllenInstitute/reanalysis.ipynb @@ -50,7 +50,7 @@ " \"click==8.5.0\" \\\n", " \"click-didyoumean==0.3.1\" \\\n", " \"cloudpickle==3.1.2\" \\\n", - " \"contourpy==1.3.3\" \\\n", + " \"contourpy==1.4.0\" \\\n", " \"cryptography==50.0.1\" \\\n", " \"cycler==0.12.1\" \\\n", " \"dandi==0.77.0\" \\\n", @@ -61,13 +61,13 @@ " \"email-validator==2.3.0\" \\\n", " \"etelemetry==0.3.1\" \\\n", " \"fasteners==0.20\" \\\n", - " \"fonttools==4.64.0\" \\\n", + " \"fonttools==4.65.0\" \\\n", " \"fqdn==1.5.1\" \\\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", + " \"h5py==3.14.0\" \\\n", " \"hdmf==6.2.0\" \\\n", " \"humanize==4.16.0\" \\\n", " \"idna==3.19\" \\\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==6.8.0\" \\\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==4.11.8\" \\\n", + " \"propcache==0.5.4\" \\\n", " \"pycparser==3.0\" \\\n", " \"pycryptodomex==3.23.0\" \\\n", " \"pydantic==2.13.5\" \\\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", " \"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 0f45795..019edaf 100644 --- a/000458/FlatironInstitute/000_lindi_vs_fsspec_streaming.ipynb +++ b/000458/FlatironInstitute/000_lindi_vs_fsspec_streaming.ipynb @@ -66,7 +66,7 @@ " \"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", @@ -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==6.8.0\" \\\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==4.11.8\" \\\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", " \"webcolors==25.10.0\" \\\n", - " \"wrapt==2.4.0\" \\\n", - " \"yarl==1.24.5\" \\\n", + " \"wrapt==2.4.1\" \\\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 c7e79f2..4e9ad73 100644 --- a/000458/FlatironInstitute/001_summarize_contents.ipynb +++ b/000458/FlatironInstitute/001_summarize_contents.ipynb @@ -66,7 +66,7 @@ " \"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", @@ -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==6.8.0\" \\\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==4.11.8\" \\\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", " \"webcolors==25.10.0\" \\\n", - " \"wrapt==2.4.0\" \\\n", - " \"yarl==1.24.5\" \\\n", + " \"wrapt==2.4.1\" \\\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 5a0b2c9..5ecd181 100644 --- a/000559/dattalab/markowitz_gillis_nature_2023/reproduce_figure1d.ipynb +++ b/000559/dattalab/markowitz_gillis_nature_2023/reproduce_figure1d.ipynb @@ -52,7 +52,7 @@ " \"click-didyoumean==0.3.1\" \\\n", " \"cloudpickle==3.1.2\" \\\n", " \"colorcet==3.2.1\" \\\n", - " \"contourpy==1.3.3\" \\\n", + " \"contourpy==1.4.0\" \\\n", " \"cryptography==50.0.1\" \\\n", " \"cycler==0.12.1\" \\\n", " \"dandi==0.77.0\" \\\n", @@ -64,12 +64,12 @@ " \"email-validator==2.3.0\" \\\n", " \"etelemetry==0.3.1\" \\\n", " \"fasteners==0.20\" \\\n", - " \"fonttools==4.64.0\" \\\n", + " \"fonttools==4.65.0\" \\\n", " \"fqdn==1.5.1\" \\\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", @@ -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==6.8.0\" \\\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==4.11.8\" \\\n", + " \"propcache==0.5.4\" \\\n", " \"psutil==5.9.5\" \\\n", " \"pycparser==3.0\" \\\n", " \"pycryptodomex==3.23.0\" \\\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", " \"webcolors==25.10.0\" \\\n", - " \"wrapt==2.4.0\" \\\n", - " \"yarl==1.24.5\" \\\n", + " \"wrapt==2.4.1\" \\\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 b9c7a16..5c6e076 100644 --- a/000559/dattalab/markowitz_gillis_nature_2023/reproduce_figure_S1.ipynb +++ b/000559/dattalab/markowitz_gillis_nature_2023/reproduce_figure_S1.ipynb @@ -51,7 +51,7 @@ " \"click==8.5.0\" \\\n", " \"click-didyoumean==0.3.1\" \\\n", " \"cloudpickle==3.1.2\" \\\n", - " \"contourpy==1.3.3\" \\\n", + " \"contourpy==1.4.0\" \\\n", " \"cryptography==50.0.1\" \\\n", " \"cuda-bindings==12.9.4\" \\\n", " \"cuda-pathfinder==1.6.1\" \\\n", @@ -65,14 +65,14 @@ " \"etelemetry==0.3.1\" \\\n", " \"fasteners==0.20\" \\\n", " \"fastremap==1.20.0\" \\\n", - " \"filelock==3.32.5\" \\\n", - " \"fonttools==4.64.0\" \\\n", + " \"filelock==3.32.7\" \\\n", + " \"fonttools==4.65.0\" \\\n", " \"fqdn==1.5.1\" \\\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", + " \"h5py==3.14.0\" \\\n", " \"hdmf==4.3.1\" \\\n", " \"humanize==4.16.0\" \\\n", " \"idna==3.19\" \\\n", @@ -101,7 +101,7 @@ " \"ml-dtypes==0.6.0\" \\\n", " \"more-itertools==10.8.0\" \\\n", " \"mpmath==1.3.0\" \\\n", - " \"multidict==6.7.1\" \\\n", + " \"multidict==6.8.0\" \\\n", " \"natsort==8.4.0\" \\\n", " \"networkx==3.6.1\" \\\n", " \"numba==0.61.2\" \\\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==4.11.8\" \\\n", + " \"propcache==0.5.4\" \\\n", " \"pycparser==3.0\" \\\n", " \"pycryptodomex==3.23.0\" \\\n", " \"pydantic==2.13.5\" \\\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==2026.9.15\" \\\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", " \"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 f933d51..2d498d1 100644 --- a/000582/Sargolini2006/000582_Sargolini2006_demo.ipynb +++ b/000582/Sargolini2006/000582_Sargolini2006_demo.ipynb @@ -64,7 +64,7 @@ " \"fscacher==0.4.4\" \\\n", " \"fsspec==2025.12.0\" \\\n", " \"google-crc32c==1.8.0\" \\\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", @@ -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==6.8.0\" \\\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==4.11.8\" \\\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", " \"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 9abb76e..f967b9d 100644 --- a/000718/CaiLab/zaki_2024/000718_demo.ipynb +++ b/000718/CaiLab/zaki_2024/000718_demo.ipynb @@ -50,7 +50,7 @@ " \"click==8.5.0\" \\\n", " \"click-didyoumean==0.3.1\" \\\n", " \"cloudpickle==3.1.2\" \\\n", - " \"contourpy==1.3.3\" \\\n", + " \"contourpy==1.4.0\" \\\n", " \"cryptography==50.0.1\" \\\n", " \"cycler==0.12.1\" \\\n", " \"dandi==0.77.0\" \\\n", @@ -61,13 +61,13 @@ " \"email-validator==2.3.0\" \\\n", " \"etelemetry==0.3.1\" \\\n", " \"fasteners==0.20\" \\\n", - " \"fonttools==4.64.0\" \\\n", + " \"fonttools==4.65.0\" \\\n", " \"fqdn==1.5.1\" \\\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", + " \"h5py==3.14.0\" \\\n", " \"hdmf==4.3.1\" \\\n", " \"humanize==4.16.0\" \\\n", " \"idna==3.19\" \\\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==6.8.0\" \\\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==4.11.8\" \\\n", + " \"propcache==0.5.4\" \\\n", " \"pycparser==3.0\" \\\n", " \"pycryptodomex==3.23.0\" \\\n", " \"pydantic==2.13.5\" \\\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", " \"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 eae965e..2c98b73 100644 --- a/000727/clandinin/simple_data_access/reading_data.ipynb +++ b/000727/clandinin/simple_data_access/reading_data.ipynb @@ -50,7 +50,7 @@ " \"click==8.5.0\" \\\n", " \"click-didyoumean==0.3.1\" \\\n", " \"cloudpickle==3.1.2\" \\\n", - " \"contourpy==1.3.3\" \\\n", + " \"contourpy==1.4.0\" \\\n", " \"cryptography==50.0.1\" \\\n", " \"cycler==0.12.1\" \\\n", " \"dandi==0.77.0\" \\\n", @@ -61,13 +61,13 @@ " \"email-validator==2.3.0\" \\\n", " \"etelemetry==0.3.1\" \\\n", " \"fasteners==0.20\" \\\n", - " \"fonttools==4.64.0\" \\\n", + " \"fonttools==4.65.0\" \\\n", " \"fqdn==1.5.1\" \\\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", + " \"h5py==3.14.0\" \\\n", " \"hdmf==4.3.1\" \\\n", " \"humanize==4.16.0\" \\\n", " \"idna==3.19\" \\\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==6.8.0\" \\\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==4.11.8\" \\\n", + " \"propcache==0.5.4\" \\\n", " \"pycparser==3.0\" \\\n", " \"pycryptodomex==3.23.0\" \\\n", " \"pydantic==2.13.5\" \\\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", " \"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 6ca3f09..9287416 100644 --- a/000728/AllenInstitute/visual_coding_ophys_tutorial.ipynb +++ b/000728/AllenInstitute/visual_coding_ophys_tutorial.ipynb @@ -50,7 +50,7 @@ " \"click==8.5.0\" \\\n", " \"click-didyoumean==0.3.1\" \\\n", " \"cloudpickle==3.1.2\" \\\n", - " \"contourpy==1.3.3\" \\\n", + " \"contourpy==1.4.0\" \\\n", " \"cryptography==50.0.1\" \\\n", " \"cycler==0.12.1\" \\\n", " \"dandi==0.77.0\" \\\n", @@ -61,13 +61,13 @@ " \"email-validator==2.3.0\" \\\n", " \"etelemetry==0.3.1\" \\\n", " \"fasteners==0.20\" \\\n", - " \"fonttools==4.64.0\" \\\n", + " \"fonttools==4.65.0\" \\\n", " \"fqdn==1.5.1\" \\\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", + " \"h5py==3.14.0\" \\\n", " \"hdmf==4.3.1\" \\\n", " \"humanize==4.16.0\" \\\n", " \"idna==3.19\" \\\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==6.8.0\" \\\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==4.11.8\" \\\n", + " \"propcache==0.5.4\" \\\n", " \"pycparser==3.0\" \\\n", " \"pycryptodomex==3.23.0\" \\\n", " \"pydantic==2.13.5\" \\\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", " \"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 d5115bf..235a20f 100644 --- a/000947/TurnerLab/public_demo/000947_demo.ipynb +++ b/000947/TurnerLab/public_demo/000947_demo.ipynb @@ -50,7 +50,7 @@ " \"click==8.5.0\" \\\n", " \"click-didyoumean==0.3.1\" \\\n", " \"cloudpickle==3.1.2\" \\\n", - " \"contourpy==1.3.3\" \\\n", + " \"contourpy==1.4.0\" \\\n", " \"cryptography==50.0.1\" \\\n", " \"cycler==0.12.1\" \\\n", " \"dandi==0.77.0\" \\\n", @@ -61,13 +61,13 @@ " \"email-validator==2.3.0\" \\\n", " \"etelemetry==0.3.1\" \\\n", " \"fasteners==0.20\" \\\n", - " \"fonttools==4.64.0\" \\\n", + " \"fonttools==4.65.0\" \\\n", " \"fqdn==1.5.1\" \\\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", + " \"h5py==3.14.0\" \\\n", " \"hdmf==4.3.1\" \\\n", " \"humanize==4.16.0\" \\\n", " \"idna==3.19\" \\\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==6.8.0\" \\\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==4.11.8\" \\\n", + " \"propcache==0.5.4\" \\\n", " \"pycparser==3.0\" \\\n", " \"pycryptodomex==3.23.0\" \\\n", " \"pydantic==2.13.5\" \\\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", " \"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 aa5bb95..2059e44 100644 --- a/000971/lernerlab/seiler_2024/fiber_photometry_example_notebook.ipynb +++ b/000971/lernerlab/seiler_2024/fiber_photometry_example_notebook.ipynb @@ -50,7 +50,7 @@ " \"click==8.5.0\" \\\n", " \"click-didyoumean==0.3.1\" \\\n", " \"cloudpickle==3.1.2\" \\\n", - " \"contourpy==1.3.3\" \\\n", + " \"contourpy==1.4.0\" \\\n", " \"cryptography==50.0.1\" \\\n", " \"cycler==0.12.1\" \\\n", " \"dandi==0.77.0\" \\\n", @@ -61,13 +61,13 @@ " \"email-validator==2.3.0\" \\\n", " \"etelemetry==0.3.1\" \\\n", " \"fasteners==0.20\" \\\n", - " \"fonttools==4.64.0\" \\\n", + " \"fonttools==4.65.0\" \\\n", " \"fqdn==1.5.1\" \\\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", + " \"h5py==3.14.0\" \\\n", " \"hdmf==4.3.1\" \\\n", " \"humanize==4.16.0\" \\\n", " \"idna==3.19\" \\\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==6.8.0\" \\\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==4.11.8\" \\\n", + " \"propcache==0.5.4\" \\\n", " \"pycparser==3.0\" \\\n", " \"pycryptodomex==3.23.0\" \\\n", " \"pydantic==2.13.5\" \\\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", " \"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 cad6708..98d1dd7 100644 --- a/000971/lernerlab/seiler_2024/optogenetics_example_notebook.ipynb +++ b/000971/lernerlab/seiler_2024/optogenetics_example_notebook.ipynb @@ -50,7 +50,7 @@ " \"click==8.5.0\" \\\n", " \"click-didyoumean==0.3.1\" \\\n", " \"cloudpickle==3.1.2\" \\\n", - " \"contourpy==1.3.3\" \\\n", + " \"contourpy==1.4.0\" \\\n", " \"cryptography==50.0.1\" \\\n", " \"cycler==0.12.1\" \\\n", " \"dandi==0.77.0\" \\\n", @@ -61,13 +61,13 @@ " \"email-validator==2.3.0\" \\\n", " \"etelemetry==0.3.1\" \\\n", " \"fasteners==0.20\" \\\n", - " \"fonttools==4.64.0\" \\\n", + " \"fonttools==4.65.0\" \\\n", " \"fqdn==1.5.1\" \\\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", + " \"h5py==3.14.0\" \\\n", " \"hdmf==4.3.1\" \\\n", " \"humanize==4.16.0\" \\\n", " \"idna==3.19\" \\\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==6.8.0\" \\\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==4.11.8\" \\\n", + " \"propcache==0.5.4\" \\\n", " \"pycparser==3.0\" \\\n", " \"pycryptodomex==3.23.0\" \\\n", " \"pydantic==2.13.5\" \\\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", " \"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 72b69ce..f70c73b 100644 --- a/001038/DombeckLab/001038_demo.ipynb +++ b/001038/DombeckLab/001038_demo.ipynb @@ -52,7 +52,7 @@ " \"click==8.1.8\" \\\n", " \"click-didyoumean==0.3.1\" \\\n", " \"cloudpickle==3.1.2\" \\\n", - " \"contourpy==1.3.3\" \\\n", + " \"contourpy==1.4.0\" \\\n", " \"cryptography==50.0.1\" \\\n", " \"cycler==0.12.1\" \\\n", " \"dandi==0.74.3\" \\\n", @@ -64,12 +64,12 @@ " \"email-validator==2.3.0\" \\\n", " \"etelemetry==0.3.1\" \\\n", " \"fasteners==0.20\" \\\n", - " \"fonttools==4.64.0\" \\\n", + " \"fonttools==4.65.0\" \\\n", " \"fqdn==1.5.1\" \\\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", @@ -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==6.8.0\" \\\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==4.11.8\" \\\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", @@ -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", " \"webcolors==25.10.0\" \\\n", - " \"wrapt==2.4.0\" \\\n", - " \"yarl==1.24.5\" \\\n", + " \"wrapt==2.4.1\" \\\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 d9f2626..e9f7f69 100644 --- a/001075/001075_paper_figure_1d.ipynb +++ b/001075/001075_paper_figure_1d.ipynb @@ -50,7 +50,7 @@ " \"click==8.5.0\" \\\n", " \"click-didyoumean==0.3.1\" \\\n", " \"cloudpickle==3.1.2\" \\\n", - " \"contourpy==1.3.3\" \\\n", + " \"contourpy==1.4.0\" \\\n", " \"cryptography==50.0.1\" \\\n", " \"cycler==0.12.1\" \\\n", " \"dandi==0.77.0\" \\\n", @@ -61,13 +61,13 @@ " \"email-validator==2.3.0\" \\\n", " \"etelemetry==0.3.1\" \\\n", " \"fasteners==0.20\" \\\n", - " \"fonttools==4.64.0\" \\\n", + " \"fonttools==4.65.0\" \\\n", " \"fqdn==1.5.1\" \\\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", + " \"h5py==3.14.0\" \\\n", " \"hdmf==4.3.1\" \\\n", " \"humanize==4.16.0\" \\\n", " \"idna==3.19\" \\\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==6.8.0\" \\\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==4.11.8\" \\\n", + " \"propcache==0.5.4\" \\\n", " \"pycparser==3.0\" \\\n", " \"pycryptodomex==3.23.0\" \\\n", " \"pydantic==2.13.5\" \\\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", " \"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 67d94de..1cd2aa4 100644 --- a/001084/HoweLab/001084_demo.ipynb +++ b/001084/HoweLab/001084_demo.ipynb @@ -51,7 +51,7 @@ " \"click==8.1.8\" \\\n", " \"click-didyoumean==0.3.1\" \\\n", " \"cloudpickle==3.1.2\" \\\n", - " \"contourpy==1.3.3\" \\\n", + " \"contourpy==1.4.0\" \\\n", " \"cryptography==50.0.1\" \\\n", " \"cycler==0.12.1\" \\\n", " \"dandi==0.74.3\" \\\n", @@ -62,12 +62,12 @@ " \"email-validator==2.3.0\" \\\n", " \"etelemetry==0.3.1\" \\\n", " \"fasteners==0.20\" \\\n", - " \"fonttools==4.64.0\" \\\n", + " \"fonttools==4.65.0\" \\\n", " \"fqdn==1.5.1\" \\\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", @@ -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==6.8.0\" \\\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==4.11.8\" \\\n", + " \"propcache==0.5.4\" \\\n", " \"pycparser==3.0\" \\\n", " \"pycryptodomex==3.23.0\" \\\n", " \"pydantic==2.13.5\" \\\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", " \"webcolors==25.10.0\" \\\n", - " \"wrapt==2.4.0\" \\\n", - " \"yarl==1.24.5\" \\\n", + " \"wrapt==2.4.1\" \\\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 df112cd..6a1473a 100644 --- a/001170/ReimerLab/public_demo/001170_demo.ipynb +++ b/001170/ReimerLab/public_demo/001170_demo.ipynb @@ -50,7 +50,7 @@ " \"click==8.5.0\" \\\n", " \"click-didyoumean==0.3.1\" \\\n", " \"cloudpickle==3.1.2\" \\\n", - " \"contourpy==1.3.3\" \\\n", + " \"contourpy==1.4.0\" \\\n", " \"cryptography==50.0.1\" \\\n", " \"cycler==0.12.1\" \\\n", " \"dandi==0.77.0\" \\\n", @@ -61,13 +61,13 @@ " \"email-validator==2.3.0\" \\\n", " \"etelemetry==0.3.1\" \\\n", " \"fasteners==0.20\" \\\n", - " \"fonttools==4.64.0\" \\\n", + " \"fonttools==4.65.0\" \\\n", " \"fqdn==1.5.1\" \\\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", + " \"h5py==3.14.0\" \\\n", " \"hdmf==4.3.1\" \\\n", " \"humanize==4.16.0\" \\\n", " \"idna==3.19\" \\\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==6.8.0\" \\\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==4.11.8\" \\\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", @@ -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", " \"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 25c4bc4..8cd1d85 100644 --- a/001172/HigleyLab/001172_demo.ipynb +++ b/001172/HigleyLab/001172_demo.ipynb @@ -50,7 +50,7 @@ " \"click==8.5.0\" \\\n", " \"click-didyoumean==0.3.1\" \\\n", " \"cloudpickle==3.1.2\" \\\n", - " \"contourpy==1.3.3\" \\\n", + " \"contourpy==1.4.0\" \\\n", " \"cryptography==50.0.1\" \\\n", " \"cycler==0.12.1\" \\\n", " \"dandi==0.77.0\" \\\n", @@ -61,13 +61,13 @@ " \"email-validator==2.3.0\" \\\n", " \"etelemetry==0.3.1\" \\\n", " \"fasteners==0.20\" \\\n", - " \"fonttools==4.64.0\" \\\n", + " \"fonttools==4.65.0\" \\\n", " \"fqdn==1.5.1\" \\\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", + " \"h5py==3.14.0\" \\\n", " \"hdmf==4.3.1\" \\\n", " \"humanize==4.16.0\" \\\n", " \"idna==3.19\" \\\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==6.8.0\" \\\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==4.11.8\" \\\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", @@ -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", " \"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 2e4c1b3..389692e 100644 --- a/001528/HnaskoLab/Lotfi_2025/001528_demo.ipynb +++ b/001528/HnaskoLab/Lotfi_2025/001528_demo.ipynb @@ -50,7 +50,7 @@ " \"click==8.5.0\" \\\n", " \"click-didyoumean==0.3.1\" \\\n", " \"cloudpickle==3.1.2\" \\\n", - " \"contourpy==1.3.3\" \\\n", + " \"contourpy==1.4.0\" \\\n", " \"cryptography==50.0.1\" \\\n", " \"cycler==0.12.1\" \\\n", " \"dandi==0.77.0\" \\\n", @@ -61,13 +61,13 @@ " \"email-validator==2.3.0\" \\\n", " \"etelemetry==0.3.1\" \\\n", " \"fasteners==0.20\" \\\n", - " \"fonttools==4.64.0\" \\\n", + " \"fonttools==4.65.0\" \\\n", " \"fqdn==1.5.1\" \\\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", + " \"h5py==3.14.0\" \\\n", " \"hdmf==6.2.0\" \\\n", " \"humanize==4.16.0\" \\\n", " \"idna==3.19\" \\\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==6.8.0\" \\\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==4.11.8\" \\\n", + " \"propcache==0.5.4\" \\\n", " \"pycparser==3.0\" \\\n", " \"pycryptodomex==3.23.0\" \\\n", " \"pydantic==2.13.5\" \\\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", " \"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 d6c1db5..69a47d0 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 @@ -50,7 +50,7 @@ " \"click==8.5.0\" \\\n", " \"click-didyoumean==0.3.1\" \\\n", " \"cloudpickle==3.1.2\" \\\n", - " \"contourpy==1.3.3\" \\\n", + " \"contourpy==1.4.0\" \\\n", " \"cryptography==50.0.1\" \\\n", " \"cycler==0.12.1\" \\\n", " \"dandi==0.77.0\" \\\n", @@ -61,13 +61,13 @@ " \"email-validator==2.3.0\" \\\n", " \"etelemetry==0.3.1\" \\\n", " \"fasteners==0.20\" \\\n", - " \"fonttools==4.64.0\" \\\n", + " \"fonttools==4.65.0\" \\\n", " \"fqdn==1.5.1\" \\\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", + " \"h5py==3.14.0\" \\\n", " \"hdmf==4.3.1\" \\\n", " \"humanize==4.16.0\" \\\n", " \"idna==3.19\" \\\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==6.8.0\" \\\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==4.11.8\" \\\n", + " \"propcache==0.5.4\" \\\n", " \"pycparser==3.0\" \\\n", " \"pycryptodomex==3.23.0\" \\\n", " \"pydantic==2.13.5\" \\\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", " \"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 d9a5caa..e78ca50 100644 --- a/001538/catalyst_neuro/zhai_2025/figure_2GH_oepsc_analysis.ipynb +++ b/001538/catalyst_neuro/zhai_2025/figure_2GH_oepsc_analysis.ipynb @@ -50,7 +50,7 @@ " \"click==8.5.0\" \\\n", " \"click-didyoumean==0.3.1\" \\\n", " \"cloudpickle==3.1.2\" \\\n", - " \"contourpy==1.3.3\" \\\n", + " \"contourpy==1.4.0\" \\\n", " \"cryptography==50.0.1\" \\\n", " \"cycler==0.12.1\" \\\n", " \"dandi==0.77.0\" \\\n", @@ -61,13 +61,13 @@ " \"email-validator==2.3.0\" \\\n", " \"etelemetry==0.3.1\" \\\n", " \"fasteners==0.20\" \\\n", - " \"fonttools==4.64.0\" \\\n", + " \"fonttools==4.65.0\" \\\n", " \"fqdn==1.5.1\" \\\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", + " \"h5py==3.14.0\" \\\n", " \"hdmf==4.3.1\" \\\n", " \"humanize==4.16.0\" \\\n", " \"idna==3.19\" \\\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==6.8.0\" \\\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==4.11.8\" \\\n", + " \"propcache==0.5.4\" \\\n", " \"pycparser==3.0\" \\\n", " \"pycryptodomex==3.23.0\" \\\n", " \"pydantic==2.13.5\" \\\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", " \"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 2fdc1e8..36d996d 100644 --- a/001538/catalyst_neuro/zhai_2025/figure_5F_acetylcholine_biosensor.ipynb +++ b/001538/catalyst_neuro/zhai_2025/figure_5F_acetylcholine_biosensor.ipynb @@ -50,7 +50,7 @@ " \"click==8.5.0\" \\\n", " \"click-didyoumean==0.3.1\" \\\n", " \"cloudpickle==3.1.2\" \\\n", - " \"contourpy==1.3.3\" \\\n", + " \"contourpy==1.4.0\" \\\n", " \"cryptography==50.0.1\" \\\n", " \"cycler==0.12.1\" \\\n", " \"dandi==0.77.0\" \\\n", @@ -61,13 +61,13 @@ " \"email-validator==2.3.0\" \\\n", " \"etelemetry==0.3.1\" \\\n", " \"fasteners==0.20\" \\\n", - " \"fonttools==4.64.0\" \\\n", + " \"fonttools==4.65.0\" \\\n", " \"fqdn==1.5.1\" \\\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", + " \"h5py==3.14.0\" \\\n", " \"hdmf==4.3.1\" \\\n", " \"humanize==4.16.0\" \\\n", " \"idna==3.19\" \\\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==6.8.0\" \\\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==4.11.8\" \\\n", + " \"propcache==0.5.4\" \\\n", " \"pycparser==3.0\" \\\n", " \"pycryptodomex==3.23.0\" \\\n", " \"pydantic==2.13.5\" \\\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", " \"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 7437fae..fcc4feb 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 @@ -50,7 +50,7 @@ " \"click==8.5.0\" \\\n", " \"click-didyoumean==0.3.1\" \\\n", " \"cloudpickle==3.1.2\" \\\n", - " \"contourpy==1.3.3\" \\\n", + " \"contourpy==1.4.0\" \\\n", " \"cryptography==50.0.1\" \\\n", " \"cycler==0.12.1\" \\\n", " \"dandi==0.77.0\" \\\n", @@ -61,13 +61,13 @@ " \"email-validator==2.3.0\" \\\n", " \"etelemetry==0.3.1\" \\\n", " \"fasteners==0.20\" \\\n", - " \"fonttools==4.64.0\" \\\n", + " \"fonttools==4.65.0\" \\\n", " \"fqdn==1.5.1\" \\\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", + " \"h5py==3.14.0\" \\\n", " \"hdmf==4.3.1\" \\\n", " \"humanize==4.16.0\" \\\n", " \"idna==3.19\" \\\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==6.8.0\" \\\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==4.11.8\" \\\n", + " \"propcache==0.5.4\" \\\n", " \"pycparser==3.0\" \\\n", " \"pycryptodomex==3.23.0\" \\\n", " \"pydantic==2.13.5\" \\\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", " \"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 7828c8b..362b5c7 100644 --- a/001550/PaganLab/01_behavior_demo.ipynb +++ b/001550/PaganLab/01_behavior_demo.ipynb @@ -50,7 +50,7 @@ " \"click==8.5.0\" \\\n", " \"click-didyoumean==0.3.1\" \\\n", " \"cloudpickle==3.1.2\" \\\n", - " \"contourpy==1.3.3\" \\\n", + " \"contourpy==1.4.0\" \\\n", " \"cryptography==50.0.1\" \\\n", " \"cycler==0.12.1\" \\\n", " \"dandi==0.77.0\" \\\n", @@ -61,13 +61,13 @@ " \"email-validator==2.3.0\" \\\n", " \"etelemetry==0.3.1\" \\\n", " \"fasteners==0.20\" \\\n", - " \"fonttools==4.64.0\" \\\n", + " \"fonttools==4.65.0\" \\\n", " \"fqdn==1.5.1\" \\\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", + " \"h5py==3.14.0\" \\\n", " \"hdmf==4.3.1\" \\\n", " \"humanize==4.16.0\" \\\n", " \"idna==3.19\" \\\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==6.8.0\" \\\n", " \"natsort==8.4.0\" \\\n", " \"ndx-ophys-devices==0.3.1\" \\\n", " \"ndx-optogenetics==0.4.0\" \\\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==4.11.8\" \\\n", + " \"propcache==0.5.4\" \\\n", " \"pycparser==3.0\" \\\n", " \"pycryptodomex==3.23.0\" \\\n", " \"pydantic==2.13.5\" \\\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", " \"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 a168e1e..471dcca 100644 --- a/001550/PaganLab/02_optogenetics_demo.ipynb +++ b/001550/PaganLab/02_optogenetics_demo.ipynb @@ -50,7 +50,7 @@ " \"click==8.5.0\" \\\n", " \"click-didyoumean==0.3.1\" \\\n", " \"cloudpickle==3.1.2\" \\\n", - " \"contourpy==1.3.3\" \\\n", + " \"contourpy==1.4.0\" \\\n", " \"cryptography==50.0.1\" \\\n", " \"cycler==0.12.1\" \\\n", " \"dandi==0.77.0\" \\\n", @@ -61,13 +61,13 @@ " \"email-validator==2.3.0\" \\\n", " \"etelemetry==0.3.1\" \\\n", " \"fasteners==0.20\" \\\n", - " \"fonttools==4.64.0\" \\\n", + " \"fonttools==4.65.0\" \\\n", " \"fqdn==1.5.1\" \\\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", + " \"h5py==3.14.0\" \\\n", " \"hdmf==4.3.1\" \\\n", " \"humanize==4.16.0\" \\\n", " \"idna==3.19\" \\\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==6.8.0\" \\\n", " \"natsort==8.4.0\" \\\n", " \"ndx-ophys-devices==0.3.1\" \\\n", " \"ndx-optogenetics==0.4.0\" \\\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==4.11.8\" \\\n", + " \"propcache==0.5.4\" \\\n", " \"pycparser==3.0\" \\\n", " \"pycryptodomex==3.23.0\" \\\n", " \"pydantic==2.13.5\" \\\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", " \"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 8dcf476..36622c7 100644 --- a/001636/TurnerLab/motor_cortex/antidromic_detection_tutorial.ipynb +++ b/001636/TurnerLab/motor_cortex/antidromic_detection_tutorial.ipynb @@ -51,7 +51,7 @@ " \"click==8.5.0\" \\\n", " \"click-didyoumean==0.3.1\" \\\n", " \"cloudpickle==3.1.2\" \\\n", - " \"contourpy==1.3.3\" \\\n", + " \"contourpy==1.4.0\" \\\n", " \"cryptography==50.0.1\" \\\n", " \"cycler==0.12.1\" \\\n", " \"dandi==0.77.0\" \\\n", @@ -63,13 +63,13 @@ " \"equinox==0.13.8\" \\\n", " \"etelemetry==0.3.1\" \\\n", " \"fasteners==0.20\" \\\n", - " \"fonttools==4.64.0\" \\\n", + " \"fonttools==4.65.0\" \\\n", " \"fqdn==1.5.1\" \\\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", + " \"h5py==3.14.0\" \\\n", " \"hdmf==4.3.1\" \\\n", " \"humanize==4.16.0\" \\\n", " \"idna==3.19\" \\\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==6.8.0\" \\\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==4.11.8\" \\\n", + " \"propcache==0.5.4\" \\\n", " \"pycparser==3.0\" \\\n", " \"pycryptodomex==3.23.0\" \\\n", " \"pydantic==2.13.5\" \\\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", " \"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 1c139fd..7807e74 100644 --- a/001636/TurnerLab/motor_cortex/turner_m1_glm.ipynb +++ b/001636/TurnerLab/motor_cortex/turner_m1_glm.ipynb @@ -51,7 +51,7 @@ " \"click==8.5.0\" \\\n", " \"click-didyoumean==0.3.1\" \\\n", " \"cloudpickle==3.1.2\" \\\n", - " \"contourpy==1.3.3\" \\\n", + " \"contourpy==1.4.0\" \\\n", " \"cryptography==50.0.1\" \\\n", " \"cycler==0.12.1\" \\\n", " \"dandi==0.77.0\" \\\n", @@ -63,13 +63,13 @@ " \"equinox==0.13.8\" \\\n", " \"etelemetry==0.3.1\" \\\n", " \"fasteners==0.20\" \\\n", - " \"fonttools==4.64.0\" \\\n", + " \"fonttools==4.65.0\" \\\n", " \"fqdn==1.5.1\" \\\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", + " \"h5py==3.14.0\" \\\n", " \"hdmf==4.3.1\" \\\n", " \"humanize==4.16.0\" \\\n", " \"idna==3.19\" \\\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==6.8.0\" \\\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==4.11.8\" \\\n", + " \"propcache==0.5.4\" \\\n", " \"pycparser==3.0\" \\\n", " \"pycryptodomex==3.23.0\" \\\n", " \"pydantic==2.13.5\" \\\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", " \"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 a99d898..9d726bf 100644 --- a/001636/TurnerLab/motor_cortex/turner_m1_peth.ipynb +++ b/001636/TurnerLab/motor_cortex/turner_m1_peth.ipynb @@ -51,7 +51,7 @@ " \"click==8.5.0\" \\\n", " \"click-didyoumean==0.3.1\" \\\n", " \"cloudpickle==3.1.2\" \\\n", - " \"contourpy==1.3.3\" \\\n", + " \"contourpy==1.4.0\" \\\n", " \"cryptography==50.0.1\" \\\n", " \"cycler==0.12.1\" \\\n", " \"dandi==0.77.0\" \\\n", @@ -63,13 +63,13 @@ " \"equinox==0.13.8\" \\\n", " \"etelemetry==0.3.1\" \\\n", " \"fasteners==0.20\" \\\n", - " \"fonttools==4.64.0\" \\\n", + " \"fonttools==4.65.0\" \\\n", " \"fqdn==1.5.1\" \\\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", + " \"h5py==3.14.0\" \\\n", " \"hdmf==4.3.1\" \\\n", " \"humanize==4.16.0\" \\\n", " \"idna==3.19\" \\\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==6.8.0\" \\\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==4.11.8\" \\\n", + " \"propcache==0.5.4\" \\\n", " \"pycparser==3.0\" \\\n", " \"pycryptodomex==3.23.0\" \\\n", " \"pydantic==2.13.5\" \\\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", " \"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 aa3218e..057fde9 100644 --- a/001636/TurnerLab/motor_cortex/turner_m1_usage.ipynb +++ b/001636/TurnerLab/motor_cortex/turner_m1_usage.ipynb @@ -51,7 +51,7 @@ " \"click==8.5.0\" \\\n", " \"click-didyoumean==0.3.1\" \\\n", " \"cloudpickle==3.1.2\" \\\n", - " \"contourpy==1.3.3\" \\\n", + " \"contourpy==1.4.0\" \\\n", " \"cryptography==50.0.1\" \\\n", " \"cycler==0.12.1\" \\\n", " \"dandi==0.77.0\" \\\n", @@ -63,13 +63,13 @@ " \"equinox==0.13.8\" \\\n", " \"etelemetry==0.3.1\" \\\n", " \"fasteners==0.20\" \\\n", - " \"fonttools==4.64.0\" \\\n", + " \"fonttools==4.65.0\" \\\n", " \"fqdn==1.5.1\" \\\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", + " \"h5py==3.14.0\" \\\n", " \"hdmf==4.3.1\" \\\n", " \"humanize==4.16.0\" \\\n", " \"idna==3.19\" \\\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==6.8.0\" \\\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==4.11.8\" \\\n", + " \"propcache==0.5.4\" \\\n", " \"pycparser==3.0\" \\\n", " \"pycryptodomex==3.23.0\" \\\n", " \"pydantic==2.13.5\" \\\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", " \"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 0a03136..a87ba68 100644 --- a/001687/wanglab/figure2-distance-tuning/figure2_distance_tuning.ipynb +++ b/001687/wanglab/figure2-distance-tuning/figure2_distance_tuning.ipynb @@ -50,7 +50,7 @@ " \"click==8.5.0\" \\\n", " \"click-didyoumean==0.3.1\" \\\n", " \"cloudpickle==3.1.2\" \\\n", - " \"contourpy==1.3.3\" \\\n", + " \"contourpy==1.4.0\" \\\n", " \"cryptography==50.0.1\" \\\n", " \"cycler==0.12.1\" \\\n", " \"dandi==0.77.0\" \\\n", @@ -61,13 +61,13 @@ " \"email-validator==2.3.0\" \\\n", " \"etelemetry==0.3.1\" \\\n", " \"fasteners==0.20\" \\\n", - " \"fonttools==4.64.0\" \\\n", + " \"fonttools==4.65.0\" \\\n", " \"fqdn==1.5.1\" \\\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", + " \"h5py==3.14.0\" \\\n", " \"hdmf==6.2.0\" \\\n", " \"humanize==4.16.0\" \\\n", " \"idna==3.19\" \\\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==6.8.0\" \\\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==4.11.8\" \\\n", + " \"propcache==0.5.4\" \\\n", " \"pycparser==3.0\" \\\n", " \"pycryptodomex==3.23.0\" \\\n", " \"pydantic==2.13.5\" \\\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", " \"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 c388bd9..1e77646 100644 --- a/001712/IBL-Widefield/public_demo/raw_widefield.ipynb +++ b/001712/IBL-Widefield/public_demo/raw_widefield.ipynb @@ -50,7 +50,7 @@ " \"click==8.5.0\" \\\n", " \"click-didyoumean==0.3.1\" \\\n", " \"cloudpickle==3.1.2\" \\\n", - " \"contourpy==1.3.3\" \\\n", + " \"contourpy==1.4.0\" \\\n", " \"cryptography==50.0.1\" \\\n", " \"cycler==0.12.1\" \\\n", " \"dandi==0.77.0\" \\\n", @@ -61,13 +61,13 @@ " \"email-validator==2.3.0\" \\\n", " \"etelemetry==0.3.1\" \\\n", " \"fasteners==0.20\" \\\n", - " \"fonttools==4.64.0\" \\\n", + " \"fonttools==4.65.0\" \\\n", " \"fqdn==1.5.1\" \\\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", + " \"h5py==3.14.0\" \\\n", " \"hdmf==4.3.1\" \\\n", " \"humanize==4.16.0\" \\\n", " \"idna==3.19\" \\\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==6.8.0\" \\\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==4.11.8\" \\\n", + " \"propcache==0.5.4\" \\\n", " \"pycparser==3.0\" \\\n", " \"pycryptodomex==3.23.0\" \\\n", " \"pydantic==2.13.5\" \\\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", " \"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 0497774..dd612b3 100644 --- a/001754/CatalystNeuro/001754_demo.ipynb +++ b/001754/CatalystNeuro/001754_demo.ipynb @@ -50,7 +50,7 @@ " \"click==8.5.0\" \\\n", " \"click-didyoumean==0.3.1\" \\\n", " \"cloudpickle==3.1.2\" \\\n", - " \"contourpy==1.3.3\" \\\n", + " \"contourpy==1.4.0\" \\\n", " \"cryptography==50.0.1\" \\\n", " \"cycler==0.12.1\" \\\n", " \"dandi==0.77.0\" \\\n", @@ -61,13 +61,13 @@ " \"email-validator==2.3.0\" \\\n", " \"etelemetry==0.3.1\" \\\n", " \"fasteners==0.20\" \\\n", - " \"fonttools==4.64.0\" \\\n", + " \"fonttools==4.65.0\" \\\n", " \"fqdn==1.5.1\" \\\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", + " \"h5py==3.14.0\" \\\n", " \"hdmf==4.3.1\" \\\n", " \"humanize==4.16.0\" \\\n", " \"idna==3.19\" \\\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==6.8.0\" \\\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==4.11.8\" \\\n", + " \"propcache==0.5.4\" \\\n", " \"pycparser==3.0\" \\\n", " \"pycryptodomex==3.23.0\" \\\n", " \"pydantic==2.13.5\" \\\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", " \"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 055c6f5..789413f 100644 --- a/001933/DombeckLab/001933_demo.ipynb +++ b/001933/DombeckLab/001933_demo.ipynb @@ -50,7 +50,7 @@ " \"click==8.5.0\" \\\n", " \"click-didyoumean==0.3.1\" \\\n", " \"cloudpickle==3.1.2\" \\\n", - " \"contourpy==1.3.3\" \\\n", + " \"contourpy==1.4.0\" \\\n", " \"cryptography==50.0.1\" \\\n", " \"cycler==0.12.1\" \\\n", " \"dandi==0.77.0\" \\\n", @@ -61,13 +61,13 @@ " \"email-validator==2.3.0\" \\\n", " \"etelemetry==0.3.1\" \\\n", " \"fasteners==0.20\" \\\n", - " \"fonttools==4.64.0\" \\\n", + " \"fonttools==4.65.0\" \\\n", " \"fqdn==1.5.1\" \\\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", + " \"h5py==3.14.0\" \\\n", " \"hdmf==4.3.1\" \\\n", " \"humanize==4.16.0\" \\\n", " \"idna==3.19\" \\\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==6.8.0\" \\\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==4.11.8\" \\\n", + " \"propcache==0.5.4\" \\\n", " \"pycparser==3.0\" \\\n", " \"pycryptodomex==3.23.0\" \\\n", " \"pydantic==2.13.5\" \\\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", " \"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 a1a17cb..ff51004 100644 --- a/dandi/DANDI User Guide, Part I.ipynb +++ b/dandi/DANDI User Guide, Part I.ipynb @@ -64,7 +64,7 @@ " \"fscacher==0.4.4\" \\\n", " \"fsspec==2025.12.0\" \\\n", " \"google-crc32c==1.8.0\" \\\n", - " \"h5py==3.16.0\" \\\n", + " \"h5py==3.14.0\" \\\n", " \"hdmf==6.2.0\" \\\n", " \"humanize==4.16.0\" \\\n", " \"idna==3.19\" \\\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==6.8.0\" \\\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==4.11.8\" \\\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", " \"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 5506efd..511f2b6 100644 --- a/dandi/DANDI User Guide, Part II.ipynb +++ b/dandi/DANDI User Guide, Part II.ipynb @@ -64,7 +64,7 @@ " \"fscacher==0.4.4\" \\\n", " \"fsspec==2025.12.0\" \\\n", " \"google-crc32c==1.8.0\" \\\n", - " \"h5py==3.16.0\" \\\n", + " \"h5py==3.14.0\" \\\n", " \"hdmf==6.2.0\" \\\n", " \"humanize==4.16.0\" \\\n", " \"idna==3.19\" \\\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==6.8.0\" \\\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==4.11.8\" \\\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", " \"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 1ad7484..82d816e 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", @@ -63,11 +63,11 @@ " \"entrypoints==0.4\" \\\n", " \"fasteners==0.20\" \\\n", " \"fastjsonschema==2.22.2\" \\\n", - " \"fonttools==4.64.0\" \\\n", + " \"fonttools==4.65.0\" \\\n", " \"fqdn==1.5.1\" \\\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", @@ -108,7 +108,7 @@ " \"matplotlib==3.10.0\" \\\n", " \"matplotlib-inline==0.2.2\" \\\n", " \"mistune==3.3.4\" \\\n", - " \"multidict==6.7.1\" \\\n", + " \"multidict==6.8.0\" \\\n", " \"nbclassic==1.3.3\" \\\n", " \"nbclient==0.10.4\" \\\n", " \"nbconvert==7.17.1\" \\\n", @@ -131,11 +131,11 @@ " \"pexpect==4.9.0\" \\\n", " \"pickleshare==0.7.5\" \\\n", " \"pillow==11.3.0\" \\\n", - " \"platformdirs==4.11.7\" \\\n", + " \"platformdirs==4.11.8\" \\\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", @@ -164,7 +164,7 @@ " \"soupsieve==2.9.2\" \\\n", " \"tenacity==9.1.4\" \\\n", " \"terminado==0.18.1\" \\\n", - " \"tifffile==2026.8.23\" \\\n", + " \"tifffile==2026.9.15\" \\\n", " \"tinycss2==1.5.1\" \\\n", " \"toolz==0.12.1\" \\\n", " \"tornado==6.5.7\" \\\n", @@ -173,7 +173,7 @@ " \"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", @@ -181,9 +181,9 @@ " \"webencodings==0.6.1\" \\\n", " \"websocket-client==1.9.2\" \\\n", " \"widgetsnbextension==3.6.10\" \\\n", - " \"wrapt==2.4.0\" \\\n", + " \"wrapt==2.4.1\" \\\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 a3666fd..a3e8e0f 100644 --- a/tutorials/bcm_2024/analysis-demo.ipynb +++ b/tutorials/bcm_2024/analysis-demo.ipynb @@ -50,7 +50,7 @@ " \"click==8.5.0\" \\\n", " \"click-didyoumean==0.3.1\" \\\n", " \"cloudpickle==3.1.2\" \\\n", - " \"contourpy==1.3.3\" \\\n", + " \"contourpy==1.4.0\" \\\n", " \"cryptography==50.0.1\" \\\n", " \"cycler==0.12.1\" \\\n", " \"dandi==0.77.0\" \\\n", @@ -61,13 +61,13 @@ " \"email-validator==2.3.0\" \\\n", " \"etelemetry==0.3.1\" \\\n", " \"fasteners==0.20\" \\\n", - " \"fonttools==4.64.0\" \\\n", + " \"fonttools==4.65.0\" \\\n", " \"fqdn==1.5.1\" \\\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", + " \"h5py==3.14.0\" \\\n", " \"hdmf==4.3.1\" \\\n", " \"humanize==4.16.0\" \\\n", " \"idna==3.19\" \\\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==6.8.0\" \\\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==4.11.8\" \\\n", + " \"propcache==0.5.4\" \\\n", " \"pycparser==3.0\" \\\n", " \"pycryptodomex==3.23.0\" \\\n", " \"pydantic==2.13.5\" \\\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", " \"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 a1f07c4..1363512 100644 --- a/tutorials/cosyne_2023/simple_dandiset_search.ipynb +++ b/tutorials/cosyne_2023/simple_dandiset_search.ipynb @@ -64,7 +64,7 @@ " \"fscacher==0.4.4\" \\\n", " \"fsspec==2025.12.0\" \\\n", " \"google-crc32c==1.8.0\" \\\n", - " \"h5py==3.16.0\" \\\n", + " \"h5py==3.14.0\" \\\n", " \"hdmf==6.2.0\" \\\n", " \"humanize==4.16.0\" \\\n", " \"idna==3.19\" \\\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==6.8.0\" \\\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==4.11.8\" \\\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", " \"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 f5d9391..35f7391 100644 --- a/tutorials/neurodatarehack_2024/advanced_asset_search.ipynb +++ b/tutorials/neurodatarehack_2024/advanced_asset_search.ipynb @@ -64,7 +64,7 @@ " \"fscacher==0.4.4\" \\\n", " \"fsspec==2025.12.0\" \\\n", " \"google-crc32c==1.8.0\" \\\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", @@ -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==6.8.0\" \\\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==4.11.8\" \\\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", " \"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 8c94706..c6a5ffc 100644 --- a/tutorials/neurodatarehack_2024/simple_dandiset_search.ipynb +++ b/tutorials/neurodatarehack_2024/simple_dandiset_search.ipynb @@ -64,7 +64,7 @@ " \"fscacher==0.4.4\" \\\n", " \"fsspec==2025.12.0\" \\\n", " \"google-crc32c==1.8.0\" \\\n", - " \"h5py==3.16.0\" \\\n", + " \"h5py==3.14.0\" \\\n", " \"hdmf==6.2.0\" \\\n", " \"humanize==4.16.0\" \\\n", " \"idna==3.19\" \\\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==6.8.0\" \\\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==4.11.8\" \\\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", " \"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 e089466..f0c5488 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 @@ -50,7 +50,7 @@ " \"click==8.5.0\" \\\n", " \"click-didyoumean==0.3.1\" \\\n", " \"cloudpickle==3.1.2\" \\\n", - " \"contourpy==1.3.3\" \\\n", + " \"contourpy==1.4.0\" \\\n", " \"cryptography==50.0.1\" \\\n", " \"cycler==0.12.1\" \\\n", " \"dandi==0.77.0\" \\\n", @@ -61,13 +61,13 @@ " \"email-validator==2.3.0\" \\\n", " \"etelemetry==0.3.1\" \\\n", " \"fasteners==0.20\" \\\n", - " \"fonttools==4.64.0\" \\\n", + " \"fonttools==4.65.0\" \\\n", " \"fqdn==1.5.1\" \\\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", + " \"h5py==3.14.0\" \\\n", " \"hdmf==4.3.1\" \\\n", " \"humanize==4.16.0\" \\\n", " \"idna==3.19\" \\\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==6.8.0\" \\\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==4.11.8\" \\\n", + " \"propcache==0.5.4\" \\\n", " \"pycparser==3.0\" \\\n", " \"pycryptodomex==3.23.0\" \\\n", " \"pydantic==2.13.5\" \\\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", " \"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\"" ]