From 3ceea0de258dea879de70e58d86c503e706d7045 Mon Sep 17 00:00:00 2001 From: Ben Dichter Date: Mon, 21 Sep 2026 15:14:22 -0400 Subject: [PATCH 1/2] Add a weekly job that refreshes the Colab snapshot Colab rebuilds its runtime image every week or two, and the notebooks' install cells are locked against a snapshot of its preinstalled versions. Once the snapshot is stale, the install cell downgrades the packages Colab has since bumped, which is slow and forces a runtime restart. refresh_colab_snapshot.py rewrites .github/colab-preinstalled.txt from googlecolab/backend-info and re-locks every CI-tested notebook. A new workflow runs it on Mondays and opens or updates one PR when the snapshot has drifted. lock_notebook.py now hands the notebook's current pins to uv as the previous lock, so a re-lock moves only what the snapshot or requirements.in forces. Packages Colab does not ship (dandi, pynwb, ...) stay at the versions the notebook was tested with. --upgrade restores the old behavior of resolving everything afresh. Co-Authored-By: Claude Fable 5.1 --- .github/scripts/lock_notebook.py | 40 +++++- .github/scripts/refresh_colab_snapshot.py | 133 +++++++++++++++++++ .github/workflows/refresh-colab-snapshot.yml | 80 +++++++++++ docs/adding-notebooks.md | 18 ++- 4 files changed, 263 insertions(+), 8 deletions(-) create mode 100644 .github/scripts/refresh_colab_snapshot.py create mode 100644 .github/workflows/refresh-colab-snapshot.yml diff --git a/.github/scripts/lock_notebook.py b/.github/scripts/lock_notebook.py index 264afcd..aedf129 100644 --- a/.github/scripts/lock_notebook.py +++ b/.github/scripts/lock_notebook.py @@ -14,8 +14,12 @@ their pin sets identical, so they are tested against one environment and are published together in one container image (see ../docker/README.md). +Re-locking keeps each package at its currently pinned version unless the Colab +snapshot or the requirements file forces a change; pass `--upgrade` to resolve +everything to the newest allowed versions instead. + Usage: - python .github/scripts/lock_notebook.py [...] + python .github/scripts/lock_notebook.py [--upgrade] [...] Assumes `uv` is on PATH and `nbformat` is importable. """ @@ -99,7 +103,15 @@ def overrides_in(requirements: Path) -> list[str]: ] -def compile_pins(requirements: Path) -> list[str]: +def compile_pins(requirements: Path, existing: list[str] | None = None) -> list[str]: + """Resolve `requirements` to a full pin set under the Colab constraints. + + `existing` is the notebook's current pin set. It is handed to uv as the + previous lock, so packages keep their current version unless a constraint + or requirement forces a change. A refresh of the Colab snapshot then moves + only what Colab moved, and packages Colab does not ship (dandi, pynwb, ...) + stay where they were tested. Pass None to resolve everything afresh. + """ overrides = overrides_in(requirements) constraint = CONSTRAINT if overrides: @@ -120,11 +132,20 @@ def compile_pins(requirements: Path) -> list[str]: "--constraint", str(constraint), "--no-header", "--no-annotate", ] + previous = None + if existing: + # uv reads an existing --output-file as preferences for the new lock. + with tempfile.NamedTemporaryFile("w", suffix=".lock.txt", delete=False) as f: + f.write("\n".join(existing) + "\n") + previous = Path(f.name) + cmd += ["--output-file", str(previous)] try: r = subprocess.run(cmd, capture_output=True, text=True, stdin=subprocess.DEVNULL) finally: if constraint is not CONSTRAINT: constraint.unlink(missing_ok=True) + if previous is not None: + previous.unlink(missing_ok=True) if r.returncode != 0: raise RuntimeError(f"uv pip compile failed for {requirements}:\n{r.stderr}") pins = [ @@ -145,15 +166,17 @@ def install_cell_source(pins: list[str], helpers: list[str]) -> str: return "\n".join(lines) -def lock(nb_path: Path) -> None: +def lock(nb_path: Path, upgrade: bool = False) -> None: requirements = requirements_for(nb_path) - pins = compile_pins(requirements) nb = nbformat.read(nb_path, as_version=4) try: - _, helpers, install_idx = find_install_cell(nb) + existing, helpers, install_idx = find_install_cell(nb) except RuntimeError: - helpers, install_idx = [], None + existing, helpers, install_idx = [], [], None + # Only `name==version` entries are usable as preferences (not git pins). + existing = [p for p in existing if re.fullmatch(r"[A-Za-z0-9._\[\],-]+==\S+", p)] + pins = compile_pins(requirements, None if upgrade else existing) if install_idx is not None: nb.cells[install_idx].source = install_cell_source(pins, helpers) @@ -182,11 +205,14 @@ def lock(nb_path: Path) -> None: def main() -> int: parser = argparse.ArgumentParser(description=__doc__) parser.add_argument("notebooks", nargs="+", type=Path) + parser.add_argument("--upgrade", action="store_true", + help="Ignore the notebook's current pins and resolve every " + "package to the newest version the constraints allow") args = parser.parse_args() failures = 0 for nb_path in args.notebooks: try: - lock(nb_path) + lock(nb_path, upgrade=args.upgrade) except Exception as e: print(f"error: {nb_path}: {e}", file=sys.stderr) failures += 1 diff --git a/.github/scripts/refresh_colab_snapshot.py b/.github/scripts/refresh_colab_snapshot.py new file mode 100644 index 0000000..21db2f1 --- /dev/null +++ b/.github/scripts/refresh_colab_snapshot.py @@ -0,0 +1,133 @@ +"""Refresh `.github/colab-preinstalled.txt` from Colab's published pip freeze. + +Colab rebuilds its runtime image every week or two, and each rebuild bumps some +of the preinstalled packages. The notebooks' install cells are locked against +the snapshot in `.github/colab-preinstalled.txt`, so once the snapshot is stale +the install cell downgrades those packages back to the old pins, which is slow +and forces a runtime restart. This script rewrites the snapshot from +googlecolab/backend-info and, with `--relock`, re-locks every notebook that +already has a bootstrap install cell and is tested by CI. + +Only `name==version` lines are kept. Colab's freeze also lists direct-URL +installs (torch, google-colab, ...), which cannot be used as constraints. + +Usage: + python .github/scripts/refresh_colab_snapshot.py [--relock] + +Exits 0 whether or not anything changed; prints `changed=true|false` and, when +$GITHUB_OUTPUT is set, writes the same line there. +""" + +from __future__ import annotations + +import argparse +import datetime +import os +import re +import subprocess +import sys +import urllib.request +from pathlib import Path + +import nbformat + +sys.path.insert(0, str(Path(__file__).resolve().parent)) +from list_notebooks import REPO_ROOT, is_excluded, load_exclusions # noqa: E402 +from lock_notebook import CONSTRAINT, requirements_for # noqa: E402 +from run_notebook import find_install_cell # noqa: E402 + +SOURCE_URL = "https://raw.githubusercontent.com/googlecolab/backend-info/main/pip-freeze.txt" +PIN_RE = re.compile(r"^[A-Za-z0-9][A-Za-z0-9._-]*==\S+$") +REFRESHED_RE = re.compile(r"^# Last refreshed: .*$", re.MULTILINE) + + +def fetch_pins() -> list[str]: + with urllib.request.urlopen(SOURCE_URL, timeout=60) as r: + text = r.read().decode() + pins = [line.strip() for line in text.splitlines() if PIN_RE.match(line.strip())] + # Guard against an empty or truncated response replacing a good snapshot. + if len(pins) < 300: + raise RuntimeError(f"Only {len(pins)} pins in {SOURCE_URL}; refusing to refresh") + return pins + + +def split_snapshot(text: str) -> tuple[str, list[str]]: + lines = text.splitlines() + header = [line for line in lines if line.startswith("#") or not line.strip()] + pins = [line.strip() for line in lines if line.strip() and not line.startswith("#")] + return "\n".join(header).rstrip("\n"), pins + + +def describe_changes(old: list[str], new: list[str]) -> list[str]: + old_map = dict(p.split("==", 1) for p in old) + new_map = dict(p.split("==", 1) for p in new) + out = [] + for name in sorted(set(old_map) | set(new_map), key=str.lower): + before, after = old_map.get(name), new_map.get(name) + if before != after: + out.append(f"{name}: {before or '(absent)'} -> {after or '(removed)'}") + return out + + +def bootstrapped_notebooks() -> list[Path]: + """Notebooks that carry a locked install cell and a requirements file. + + Notebooks excluded from CI are left alone: their pins cannot be verified + after a re-lock, and several are held on an older stack on purpose. + """ + exclusions = load_exclusions() + found = [] + for nb_path in sorted(REPO_ROOT.rglob("*.ipynb")): + if ".ipynb_checkpoints" in nb_path.parts: + continue + if is_excluded(str(nb_path.relative_to(REPO_ROOT)), exclusions): + continue + try: + find_install_cell(nbformat.read(nb_path, as_version=4)) + requirements_for(nb_path) + except Exception: + continue + found.append(nb_path) + return found + + +def main() -> int: + parser = argparse.ArgumentParser(description=__doc__) + parser.add_argument("--relock", action="store_true", + help="Re-lock every bootstrapped notebook when the snapshot changed") + parser.add_argument("--force-relock", action="store_true", + help="Re-lock even when the snapshot did not change") + args = parser.parse_args() + + header, old_pins = split_snapshot(CONSTRAINT.read_text()) + new_pins = fetch_pins() + changes = describe_changes(old_pins, new_pins) + changed = bool(changes) + + if changed: + today = datetime.date.today().isoformat() + header = REFRESHED_RE.sub(f"# Last refreshed: {today}", header) + CONSTRAINT.write_text(header + "\n" + "\n".join(new_pins) + "\n") + print(f"Refreshed {CONSTRAINT.relative_to(REPO_ROOT)}: {len(changes)} package(s) changed") + for line in changes: + print(f" {line}") + else: + print("Snapshot already matches Colab's current pip freeze") + + rc = 0 + if (changed and args.relock) or args.force_relock: + notebooks = bootstrapped_notebooks() + print(f"Re-locking {len(notebooks)} notebook(s)") + rc = subprocess.run( + [sys.executable, str(Path(__file__).with_name("lock_notebook.py")), *map(str, notebooks)] + ).returncode + + print(f"changed={'true' if changed else 'false'}") + if os.environ.get("GITHUB_OUTPUT"): + with open(os.environ["GITHUB_OUTPUT"], "a") as f: + f.write(f"changed={'true' if changed else 'false'}\n") + return rc + + +if __name__ == "__main__": + sys.exit(main()) diff --git a/.github/workflows/refresh-colab-snapshot.yml b/.github/workflows/refresh-colab-snapshot.yml new file mode 100644 index 0000000..a3f6a6e --- /dev/null +++ b/.github/workflows/refresh-colab-snapshot.yml @@ -0,0 +1,80 @@ +name: Refresh Colab snapshot (weekly) + +# Colab rebuilds its runtime image every week or two. When its preinstalled +# versions move past `.github/colab-preinstalled.txt`, the notebooks' install +# cells start downgrading packages on Colab. This job compares the snapshot with +# googlecolab/backend-info and, when they differ, opens (or updates) one PR that +# refreshes the snapshot and re-locks the notebooks against it. + +on: + schedule: + # Mondays at 05:00 UTC, an hour before the weekly notebook test run + - cron: '0 5 * * 1' + workflow_dispatch: + +permissions: + contents: write + pull-requests: write + +concurrency: + group: refresh-colab-snapshot + cancel-in-progress: false + +env: + BRANCH: bot/refresh-colab-snapshot + +jobs: + refresh: + name: Refresh snapshot and re-lock + runs-on: ubuntu-latest + steps: + - uses: actions/checkout@v4 + with: + # A PAT lets the PR trigger "Test changed notebooks"; PRs opened with + # the default GITHUB_TOKEN do not trigger other workflows. + token: ${{ secrets.COLAB_REFRESH_TOKEN || github.token }} + + - uses: actions/setup-python@v5 + with: + python-version: '3.13' + + - name: Install tooling + run: pip install --no-cache-dir uv nbformat + + - name: Refresh snapshot and re-lock notebooks + id: refresh + run: python .github/scripts/refresh_colab_snapshot.py --relock | tee refresh.log + + - name: Open or update the PR + if: steps.refresh.outputs.changed == 'true' + env: + GH_TOKEN: ${{ secrets.COLAB_REFRESH_TOKEN || github.token }} + run: | + set -euo pipefail + { + echo "Colab's preinstalled package versions have moved past \`.github/colab-preinstalled.txt\`, so the notebooks' install cells were downgrading those packages on Colab. This refreshes the snapshot from [googlecolab/backend-info](https://github.com/googlecolab/backend-info) and re-locks every CI-tested notebook against it. Packages that Colab does not ship keep their current pins." + echo + echo "
Snapshot changes" + echo + echo '```' + grep -E '^ \S+: ' refresh.log || true + echo '```' + echo + echo "
" + } > pr-body.md + rm -f refresh.log + + git config user.name "github-actions[bot]" + git config user.email "41898282+github-actions[bot]@users.noreply.github.com" + git checkout -B "$BRANCH" + git add -A -- .github/colab-preinstalled.txt '*.ipynb' + git commit -m "Refresh the Colab snapshot and re-lock notebooks" + git push --force origin "$BRANCH" + + if [ -n "$(gh pr list --head "$BRANCH" --state open --json number --jq '.[].number')" ]; then + gh pr edit "$BRANCH" --body-file pr-body.md + else + gh pr create --head "$BRANCH" --base "${{ github.event.repository.default_branch }}" \ + --title "Refresh the Colab snapshot and re-lock notebooks" \ + --body-file pr-body.md + fi diff --git a/docs/adding-notebooks.md b/docs/adding-notebooks.md index 8bf0056..7a656bc 100644 --- a/docs/adding-notebooks.md +++ b/docs/adding-notebooks.md @@ -236,7 +236,23 @@ other. Add a notebook to whichever applies, always with a one-line reason. [`.github/colab-preinstalled.txt`](../.github/colab-preinstalled.txt) — **not** an exclusion list. It's a snapshot of Colab's preinstalled package versions, used as the `uv pip compile --constraint` when generating install-cell pins (see -[above](#generating-the-install-cell)). Refresh it when Colab bumps its runtime. +[above](#generating-the-install-cell)). Colab rebuilds its image every week or +two, and once the snapshot is stale the install cells downgrade Colab's newer +packages back to the old pins. The +[`refresh-colab-snapshot`](../.github/workflows/refresh-colab-snapshot.yml) +workflow checks weekly and opens a PR when the snapshot has drifted. To do the +same by hand: + +``` +python .github/scripts/refresh_colab_snapshot.py --relock +``` + +This rewrites the snapshot from +[googlecolab/backend-info](https://github.com/googlecolab/backend-info) and +re-locks every CI-tested notebook. A re-lock keeps each package at its current +pin unless the snapshot or `requirements.in` forces a change, so packages Colab +does not ship (dandi, pynwb, ...) stay at the versions the notebook was tested +with. Pass `--upgrade` to `lock_notebook.py` to float those as well. ### `notebook-test-exclusions.txt` → "skip in CI" [`.github/notebook-test-exclusions.txt`](../.github/notebook-test-exclusions.txt) From 2e8dc6c29ffbe31ea0675c7989f1c78090e4257b Mon Sep 17 00:00:00 2001 From: Ben Dichter Date: Mon, 21 Sep 2026 15:14:23 -0400 Subject: [PATCH 2/2] Refresh the Colab snapshot and re-lock notebooks Colab's image has changed several times since the 2026-08-22 snapshot, most recently with the move to Ubuntu 24.04 on 2026-09-04, and 88 preinstalled packages now differ. Install cells were pulling click, cryptography, fsspec, pydantic, and others back to the August versions. This refreshes the snapshot and re-locks the 44 CI-tested notebooks. Every changed pin matches Colab's current version; no package outside the snapshot moved. Co-Authored-By: Claude Fable 5.1 --- .github/colab-preinstalled.txt | 174 +++++++++--------- .../chunglab/demo/2021-09-27_dandi-demo.ipynb | 27 +-- 000108/chunglab/demo/dashboard.ipynb | 27 +-- 000402/MICrONS/demo/000402_microns_demo.ipynb | 23 +-- 000409/IBL/bwm_usage_notebook.ipynb | 35 ++-- 000458/AllenInstitute/reanalysis.ipynb | 23 +-- .../000_lindi_vs_fsspec_streaming.ipynb | 23 +-- .../001_summarize_contents.ipynb | 23 +-- .../reproduce_figure1d.ipynb | 25 +-- .../reproduce_figure_S1.ipynb | 29 +-- .../000582_Sargolini2006_demo.ipynb | 19 +- 000718/CaiLab/zaki_2024/000718_demo.ipynb | 23 +-- .../simple_data_access/reading_data.ipynb | 23 +-- .../visual_coding_ophys_tutorial.ipynb | 23 +-- .../TurnerLab/public_demo/000947_demo.ipynb | 23 +-- .../fiber_photometry_example_notebook.ipynb | 23 +-- .../optogenetics_example_notebook.ipynb | 23 +-- 001038/DombeckLab/001038_demo.ipynb | 25 +-- 001075/001075_paper_figure_1d.ipynb | 23 +-- 001084/HoweLab/001084_demo.ipynb | 23 +-- .../ReimerLab/public_demo/001170_demo.ipynb | 23 +-- 001172/HigleyLab/001172_demo.ipynb | 23 +-- 001528/HnaskoLab/Lotfi_2025/001528_demo.ipynb | 23 +-- .../figure_1E_dspn_somatic_excitability.ipynb | 23 +-- .../zhai_2025/figure_2GH_oepsc_analysis.ipynb | 23 +-- .../figure_5F_acetylcholine_biosensor.ipynb | 23 +-- .../zhai_2025/how_to_use_this_dataset.ipynb | 23 +-- 001550/PaganLab/01_behavior_demo.ipynb | 23 +-- 001550/PaganLab/02_optogenetics_demo.ipynb | 23 +-- .../antidromic_detection_tutorial.ipynb | 27 +-- .../motor_cortex/turner_m1_glm.ipynb | 27 +-- .../motor_cortex/turner_m1_peth.ipynb | 27 +-- .../motor_cortex/turner_m1_usage.ipynb | 27 +-- .../figure2_distance_tuning.ipynb | 23 +-- .../public_demo/raw_widefield.ipynb | 23 +-- 001754/CatalystNeuro/001754_demo.ipynb | 23 +-- 001933/DombeckLab/001933_demo.ipynb | 23 +-- dandi/DANDI User Guide, Part I.ipynb | 19 +- dandi/DANDI User Guide, Part II.ipynb | 19 +- demos/NWBWidget-demo.ipynb | 28 +-- tutorials/bcm_2024/analysis-demo.ipynb | 23 +-- .../cosyne_2023/simple_dandiset_search.ipynb | 19 +- .../advanced_asset_search.ipynb | 19 +- .../simple_dandiset_search.ipynb | 19 +- .../Get-to-know-a-Dandiset.ipynb | 23 +-- 45 files changed, 629 insertions(+), 584 deletions(-) diff --git a/.github/colab-preinstalled.txt b/.github/colab-preinstalled.txt index 0b2f859..79da44f 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: 2026-08-22 +# Last refreshed: 2026-09-21 # # 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 @@ -15,7 +15,7 @@ absl-py==1.4.0 accelerate==1.14.0 access==1.1.10.post3 -affine==3.0.0 +affine==3.0.1 aiofiles==25.1.0 aiohappyeyeballs==2.7.1 aiohttp==3.14.3 @@ -33,31 +33,31 @@ anyio==4.14.2 anywidget==0.9.21 apsw==3.53.4.0 argon2-cffi==25.1.0 -argon2-cffi-bindings==25.1.0 +argon2-cffi-bindings==26.1.0 array_record==0.8.3 arrow==1.4.0 arviz==0.22.0 astropy==7.2.2 -astropy-iers-data==0.2026.8.10.0.32.39 +astropy-iers-data==0.2026.8.31.0.57.9 astunparse==1.6.3 atpublic==5.1 attrs==26.1.0 audioop-lts==0.2.2 audioread==3.1.0 -Authlib==1.7.2 +Authlib==1.8.0 autograd==1.9.1 babel==2.18.0 backcall==0.2.0 beartype==0.22.9 beautifulsoup4==4.13.5 betterproto==2.0.0b7 -bigframes==2.42.0 +bigframes==2.48.0 bigquery-magics==0.14.0 bleach==6.4.0 blinker==1.9.0 blis==1.3.3 -blobfile==3.2.0 -blosc2==4.11.0 +blobfile==3.3.0 +blosc2==4.12.0 bokeh==3.8.2 Bottleneck==1.4.2 bqplot==0.12.47 @@ -71,9 +71,9 @@ cffi==2.1.1 chardet==5.2.0 charset-normalizer==3.4.9 clarabel==0.11.1 -click==8.4.2 +click==8.5.0 cligj==0.7.2 -cloudpathlib==0.24.0 +cloudpathlib==0.25.0 cloudpickle==3.1.2 cmake==3.31.10 cmdstanpy==1.3.0 @@ -83,27 +83,27 @@ community==1.0.0b1 confection==1.3.3 cons==0.4.7 contourpy==1.3.3 -cramjam==2.11.0 -cryptography==50.0.0 +cramjam==2.12.1 +cryptography==50.0.1 cufflinks==0.17.3 -curl_cffi==0.16.0 +curl_cffi==0.16.2 cvxopt==1.3.2 cvxpy==1.6.7 cycler==0.12.1 cyipopt==1.5.0 cymem==2.0.13 Cython==3.0.12 -dask==2026.7.1 +dask==2026.8.0 dataproc-spark-connect==1.1.0 -datasets==4.0.0 +datasets==4.8.5 db-dtypes==1.7.1 -dbus-python==1.2.18 +dbus-python==1.3.2 debugpy==1.8.15 decorator==4.4.2 defusedxml==0.7.1 deprecation==2.1.0 -diffusers==0.39.0 -dill==0.3.8 +diffusers==0.40.0 +dill==0.4.1 distro==1.9.0 dlib==19.24.6 dm-tree==0.1.10 @@ -124,28 +124,29 @@ etuples==0.3.10 Farama-Notifications==0.0.6 fastai==2.8.8 fastapi==0.141.1 -fastcore==2.2.12 +fastcore==2.2.19 fastdownload==0.0.7 fastjsonschema==2.22.2 fastprogress==1.1.6 fasttransform==0.0.2 -filelock==3.32.3 +filelock==3.32.5 firebase-admin==6.9.0 Flask==3.1.3 flatbuffers==25.12.19 flax==0.11.2 folium==0.20.0 -fonttools==4.63.0 +fonttools==4.64.0 +formulaic==1.2.2 fqdn==1.5.1 frozendict==2.4.7 frozenlist==1.8.0 -fsspec==2025.3.0 +fsspec==2025.12.0 future==1.0.0 gast==0.7.0 -gcsfs==2025.3.0 +gcsfs==2025.12.0 GDAL==3.8.4 gdown==5.2.2 -geemap==0.38.3 +geemap==0.38.4 geocoder==1.38.1 geographiclib==2.1 geopandas==1.1.4 @@ -157,14 +158,14 @@ 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==2.198.0 +google-api-python-client==2.200.0 google-auth==2.49.0 -google-auth-httplib2==0.4.1 -google-auth-oauthlib==1.4.0 -google-cloud-bigquery==3.43.0 +google-auth-httplib2==0.4.2 +google-auth-oauthlib==1.4.1 +google-cloud-bigquery==3.44.0 google-cloud-bigquery-connection==1.22.0 google-cloud-bigquery-storage==2.39.0 -google-cloud-core==2.6.1 +google-cloud-core==2.7.0 google-cloud-dataproc==5.28.0 google-cloud-datastore==2.25.0 google-cloud-firestore==2.27.0 @@ -174,23 +175,24 @@ google-cloud-monitoring==2.31.0 google-cloud-resource-manager==1.18.0 google-cloud-spanner==3.68.0 google-cloud-storage==3.13.1 +google-cloud-storage-control==1.12.0 google-cloud-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==2.10.1 +google-resumable-media==2.10.2 googleapis-common-protos==1.75.0 googledrivedownloader==1.1.0 -gradio==6.24.0 -gradio_client==2.6.0 +gradio==6.26.0 +gradio_client==2.6.1 grain==0.2.18 graphviz==0.21 greenlet==3.5.5 groovy==0.1.2 grpc-google-iam-v1==0.14.4 grpc-interceptor==0.15.4 -grpcio==1.83.0 +grpcio==1.83.1 grpcio-status==1.71.2 grpclib==0.4.9 gspread==6.2.1 @@ -207,34 +209,35 @@ hf-gradio==0.4.1 hf-xet==1.6.0 highspy==1.15.1 holidays==0.103 -holoviews==1.23.1 +holoviews==1.23.2 hpack==4.2.0 html5lib==1.1 httpcore==1.0.9 -httpcore2==2.10.0 +httpcore2==2.12.0 httpimport==1.4.1 httplib2==0.32.0 httptools==0.8.0 httpx==0.28.1 -httpx2==2.10.0 -huggingface_hub==1.27.0 +httpx2==2.12.0 +huggingface_hub==1.29.0 humanize==4.16.0 hyperframe==6.1.0 hyperopt==0.3.0 ibis-framework==9.5.0 -idna==3.18 +idna==3.19 ImageIO==2.37.4 imageio-ffmpeg==0.6.0 -imagesize==2.0.0 +imagesize==2.0.1 imbalanced-learn==0.14.2 immutabledict==4.3.1 -importlib_metadata==9.0.0 +importlib_metadata==9.0.1 imutils==0.5.4 inequality==1.1.2 inflect==7.5.0 iniconfig==2.3.0 intel-cmplr-lib-ur==2025.3.3 intel-openmp==2025.3.3 +interface_meta==2.0.1 ipyevents==2.0.4 ipyfilechooser==0.6.0 ipykernel==6.17.1 @@ -249,14 +252,14 @@ itsdangerous==2.2.0 jaraco.classes==3.4.0 jaraco.context==6.1.2 jaraco.functools==4.6.0 -jax==0.7.2 -jaxlib==0.7.2 +jax==0.11.1 +jaxlib==0.11.1 jeepney==0.9.0 jieba==0.42.1 Jinja2==3.1.6 jiter==0.16.0 -joblib==1.5.3 -joserfc==1.7.4 +joblib==1.6.0 +joserfc==1.7.5 jsonpatch==1.33 jsonpickle==4.1.2 jsonpointer==3.1.1 @@ -270,7 +273,7 @@ jupyter_core==5.9.1 jupyter_server==2.20.0 jupyter_server_terminals==0.5.4 jupyterlab_pygments==0.3.0 -jupyterlab_widgets==3.0.16 +jupyterlab_widgets==3.0.17 jupytext==1.19.5 kaggle==2.0.2 kagglehub==1.0.2 @@ -280,30 +283,30 @@ keras-hub==0.26.0 keras-nlp==0.26.0 keyring==25.7.0 keyrings.google-artifactregistry-auth==1.1.2 -kiwisolver==1.5.0 -langchain==1.3.15 -langchain-core==1.5.5 -langchain-protocol==0.0.18 +kiwisolver==1.5.1 +langchain==1.3.18 +langchain-core==1.6.1 +langchain-protocol==0.0.19 langgraph==1.2.11 langgraph-checkpoint==4.2.0 langgraph-prebuilt==1.1.0 -langgraph-sdk==0.4.2 -langsmith==0.11.0 +langgraph-sdk==0.4.4 +langsmith==0.12.1 lark==1.3.1 -launchpadlib==1.10.16 -lazr.restfulclient==0.14.4 +launchpadlib==1.11.0 +lazr.restfulclient==0.14.6 lazr.uri==1.0.6 lazy-loader==0.5 libclang==18.1.1 libpysal==4.14.1 librosa==0.11.0 lightgbm==4.6.0 -linkify-it-py==2.1.0 +linkify-it-py==2.2.0 llvmlite==0.44.0 locket==1.0.0 logical-unification==0.4.7 -lxml==6.1.1 -Mako==1.1.3 +lxml==6.1.2 +Mako==1.3.2.dev0 mapclassify==2.10.0 Markdown==3.10.3 markdown-it-py==4.2.0 @@ -321,20 +324,20 @@ mizani==0.13.5 mkl==2025.3.1 ml_dtypes==0.6.0 mlxtend==0.23.4 -mmh3==5.2.1 +mmh3==5.3.0 momepy==0.11.0 more-itertools==10.8.0 moviepy==1.0.3 mpmath==1.3.0 -msgpack==1.2.1 +msgpack==1.2.2 multidict==6.7.1 multipledispatch==1.0.0 -multiprocess==0.70.16 +multiprocess==0.70.19 multitasking==0.0.13 murmurhash==1.0.15 music21==9.9.2 namex==0.1.0 -narwhals==2.24.0 +narwhals==2.25.0 natsort==8.4.0 nbclassic==1.3.3 nbclient==0.10.4 @@ -343,7 +346,7 @@ nbformat==5.11.1 ndindex==1.10.1 nest-asyncio==1.6.0 networkx==3.6.1 -nh3==0.3.6 +nh3==0.3.7 nibabel==5.4.2 nltk==3.9.1 notebook==6.5.7 @@ -367,7 +370,7 @@ opentelemetry-sdk==1.42.1 opentelemetry-semantic-conventions==0.63b1 opt_einsum==3.4.0 optax==0.2.8 -optree==0.19.1 +optree==0.20.0 orbax-checkpoint==0.12.4 orjson==3.12.0 ormsgpack==1.12.2 @@ -384,14 +387,14 @@ param==2.4.1 parso==0.8.7 parsy==2.2 partd==1.4.2 -patsy==1.0.2 -peewee==4.3.0 +patsy==1.0.3 +peewee==4.4.0 peft==0.20.0 pexpect==4.9.0 pickleshare==0.7.5 pillow==11.3.0 pip==24.1.2 -platformdirs==4.11.3 +platformdirs==4.11.7 plotly==5.24.1 plotnine==0.14.5 pluggy==1.6.0 @@ -419,15 +422,15 @@ ptyprocess==0.7.0 PuLP==3.3.2 py-cpuinfo==9.0.0 py4j==0.10.9.9 -pyarrow==18.1.0 +pyarrow==23.0.1 pyasn1==0.6.4 pyasn1_modules==0.4.2 pycairo==1.29.1 pycocotools==2.0.11 pycparser==3.0 pycryptodomex==3.23.0 -pydantic==2.13.4 -pydantic_core==2.46.4 +pydantic==2.13.5 +pydantic_core==2.46.5 pydata-google-auth==1.9.1 pydot==4.0.1 pydotplus==2.0.2 @@ -438,7 +441,7 @@ pygame==2.6.1 pygit2==1.20.0 Pygments==2.21.0 PyGObject==3.48.2 -pyiceberg==0.11.1 +pyiceberg==0.12.0 PyJWT==2.13.0 pymc==5.28.5 pynndescent==0.6.0 @@ -460,13 +463,13 @@ python-apt==0.0.0 python-box==7.4.1 python-dateutil==2.9.0.post0 python-dotenv==1.2.3 -python-fasthtml==0.14.11 +python-fasthtml==0.14.12 python-json-logger==4.2.0 python-louvain==0.16 python-multipart==0.0.32 python-slugify==8.0.4 python-snappy==0.7.3 -python-utils==4.0.0 +python-utils==4.0.1 pytz==2025.2 pyviz_comms==3.0.6 PyWavelets==1.9.0 @@ -506,13 +509,13 @@ semantic-version==2.10.0 Send2Trash==2.1.0 sentence-transformers==5.7.0 sentencepiece==0.2.2 -sentry-sdk==2.68.0 -setuptools==75.2.0 +sentry-sdk==2.68.1 +setuptools==80.10.2 shap==0.52.0 shapely==2.1.2 shellingham==1.5.4 simple-parsing==0.1.9 -simplejson==4.1.1 +simplejson==4.1.2 simsimd==6.5.16 six==1.17.0 sklearn-compat==0.1.6 @@ -524,7 +527,7 @@ snowballstemmer==3.1.1 soundfile==0.14.0 soupsieve==2.9.2 soxr==1.1.0 -spacy==3.8.15 +spacy==3.8.16 spacy-legacy==3.0.12 spacy-loggers==1.0.5 spaghetti==1.7.6 @@ -550,7 +553,7 @@ standard-chunk==3.13.0 standard-sunau==3.13.0 stanio==0.5.1 starlette==1.6.0 -statsmodels==0.14.6 +statsmodels==0.15.0 strictyaml==1.7.3 stringzilla==5.1.2 stumpy==1.14.1 @@ -577,12 +580,12 @@ tf-slim==1.1.0 tf_keras==2.20.1 thinc==8.3.13 threadpoolctl==3.6.0 -tifffile==2026.8.16 +tifffile==2026.8.23 tiktoken==0.14.0 -timm==1.0.28 +timm==1.0.29 tinycss2==1.5.1 tobler==0.14.0 -tokenizers==0.22.2 +tokenizers==0.23.1 toml==0.10.2 tomlkit==0.14.0 toolz==0.12.1 @@ -594,27 +597,26 @@ tornado==6.5.7 tqdm==4.67.3 traitlets==5.7.1 traittypes==0.2.3 -transformers==5.15.0 +transformers==5.16.1 treescope==0.1.10 truststore==0.10.4 tsfresh==0.21.2 tweepy==4.17.0 typeguard==4.6.0 -typer==0.27.1 +typer==0.27.2 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 tzlocal==5.4.4 -uc-micro-py==2.0.0 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==0.52.3 +uvicorn==0.52.4 uvloop==0.22.1 vega-datasets==0.9.0 wadllib==1.3.6 @@ -622,17 +624,17 @@ wandb==0.28.1 wasabi==1.1.3 watchdog==6.0.0 watchfiles==1.2.0 -wcwidth==0.8.2 +wcwidth==0.8.3 weasel==1.0.0 webcolors==25.10.0 webencodings==0.6.1 -websocket-client==1.9.0 +websocket-client==1.9.2 websockets==15.0.1 Werkzeug==3.1.8 wheel==0.48.0 widgetsnbextension==3.6.10 wordcloud==1.9.6 -wrapt==2.3.0 +wrapt==2.4.0 xarray==2025.12.0 xarray-einstats==0.11.0 xgboost==3.4.1 diff --git a/000108/chunglab/demo/2021-09-27_dandi-demo.ipynb b/000108/chunglab/demo/2021-09-27_dandi-demo.ipynb index 311a639..fb55b52 100644 --- a/000108/chunglab/demo/2021-09-27_dandi-demo.ipynb +++ b/000108/chunglab/demo/2021-09-27_dandi-demo.ipynb @@ -48,10 +48,11 @@ " \"cffi==2.1.1\" \\\n", " \"charset-normalizer==3.4.9\" \\\n", " \"ci-info==0.4.0\" \\\n", - " \"click==8.4.2\" \\\n", + " \"click==8.5.0\" \\\n", " \"click-didyoumean==0.3.1\" \\\n", + " \"cloudpickle==3.1.2\" \\\n", " \"contourpy==1.3.3\" \\\n", - " \"cryptography==50.0.0\" \\\n", + " \"cryptography==50.0.1\" \\\n", " \"cycler==0.12.1\" \\\n", " \"dandi==0.77.0\" \\\n", " \"dandischema==0.14.0\" \\\n", @@ -61,16 +62,16 @@ " \"email-validator==2.3.0\" \\\n", " \"etelemetry==0.3.1\" \\\n", " \"fasteners==0.20\" \\\n", - " \"fonttools==4.63.0\" \\\n", + " \"fonttools==4.64.0\" \\\n", " \"fqdn==1.5.1\" \\\n", " \"frozenlist==1.8.0\" \\\n", " \"fscacher==0.4.4\" \\\n", - " \"fsspec==2025.3.0\" \\\n", + " \"fsspec==2025.12.0\" \\\n", " \"google-crc32c==1.8.0\" \\\n", " \"h5py==3.16.0\" \\\n", " \"hdmf==6.2.0\" \\\n", " \"humanize==4.16.0\" \\\n", - " \"idna==3.18\" \\\n", + " \"idna==3.19\" \\\n", " \"imageio==2.37.4\" \\\n", " \"interleave==0.3.0\" \\\n", " \"isodate==0.7.2\" \\\n", @@ -81,20 +82,20 @@ " \"jeepney==0.9.0\" \\\n", " \"jinja2==3.1.6\" \\\n", " \"jinxed==2.1.0\" \\\n", - " \"joblib==1.5.3\" \\\n", + " \"joblib==1.6.0\" \\\n", " \"jsonpointer==3.1.1\" \\\n", " \"jsonschema==4.26.0\" \\\n", " \"jsonschema-specifications==2025.9.1\" \\\n", " \"keyring==25.7.0\" \\\n", " \"keyrings-alt==5.0.2\" \\\n", - " \"kiwisolver==1.5.0\" \\\n", + " \"kiwisolver==1.5.1\" \\\n", " \"lazy-loader==0.5\" \\\n", " \"markupsafe==3.0.3\" \\\n", " \"matplotlib==3.10.0\" \\\n", " \"ml-dtypes==0.6.0\" \\\n", " \"more-itertools==10.8.0\" \\\n", " \"multidict==6.7.1\" \\\n", - " \"narwhals==2.24.0\" \\\n", + " \"narwhals==2.25.0\" \\\n", " \"natsort==8.4.0\" \\\n", " \"networkx==3.6.1\" \\\n", " \"numcodecs==0.16.5\" \\\n", @@ -103,12 +104,12 @@ " \"packaging==26.3\" \\\n", " \"pandas==2.2.3\" \\\n", " \"pillow==11.3.0\" \\\n", - " \"platformdirs==4.11.3\" \\\n", + " \"platformdirs==4.11.7\" \\\n", " \"propcache==0.5.2\" \\\n", " \"pycparser==3.0\" \\\n", " \"pycryptodomex==3.23.0\" \\\n", - " \"pydantic==2.13.4\" \\\n", - " \"pydantic-core==2.46.4\" \\\n", + " \"pydantic==2.13.5\" \\\n", + " \"pydantic-core==2.46.5\" \\\n", " \"pydantic-settings==2.15.0\" \\\n", " \"pynwb==4.1.0\" \\\n", " \"pyout==0.8.1\" \\\n", @@ -131,7 +132,7 @@ " \"six==1.17.0\" \\\n", " \"tenacity==9.1.4\" \\\n", " \"tensorstore==0.1.85\" \\\n", - " \"tifffile==2026.8.16\" \\\n", + " \"tifffile==2026.8.23\" \\\n", " \"tornado==6.5.7\" \\\n", " \"tqdm==4.67.3\" \\\n", " \"typing-extensions==4.16.0\" \\\n", @@ -139,7 +140,7 @@ " \"tzdata==2026.3\" \\\n", " \"uri-template==1.3.0\" \\\n", " \"urllib3==2.5.0\" \\\n", - " \"wcwidth==0.8.2\" \\\n", + " \"wcwidth==0.8.3\" \\\n", " \"webcolors==25.10.0\" \\\n", " \"xyzservices==2026.3.0\" \\\n", " \"yarl==1.24.5\" \\\n", diff --git a/000108/chunglab/demo/dashboard.ipynb b/000108/chunglab/demo/dashboard.ipynb index 23be337..add50f6 100644 --- a/000108/chunglab/demo/dashboard.ipynb +++ b/000108/chunglab/demo/dashboard.ipynb @@ -48,10 +48,11 @@ " \"cffi==2.1.1\" \\\n", " \"charset-normalizer==3.4.9\" \\\n", " \"ci-info==0.4.0\" \\\n", - " \"click==8.4.2\" \\\n", + " \"click==8.5.0\" \\\n", " \"click-didyoumean==0.3.1\" \\\n", + " \"cloudpickle==3.1.2\" \\\n", " \"contourpy==1.3.3\" \\\n", - " \"cryptography==50.0.0\" \\\n", + " \"cryptography==50.0.1\" \\\n", " \"cycler==0.12.1\" \\\n", " \"dandi==0.77.0\" \\\n", " \"dandischema==0.14.0\" \\\n", @@ -61,16 +62,16 @@ " \"email-validator==2.3.0\" \\\n", " \"etelemetry==0.3.1\" \\\n", " \"fasteners==0.20\" \\\n", - " \"fonttools==4.63.0\" \\\n", + " \"fonttools==4.64.0\" \\\n", " \"fqdn==1.5.1\" \\\n", " \"frozenlist==1.8.0\" \\\n", " \"fscacher==0.4.4\" \\\n", - " \"fsspec==2025.3.0\" \\\n", + " \"fsspec==2025.12.0\" \\\n", " \"google-crc32c==1.8.0\" \\\n", " \"h5py==3.16.0\" \\\n", " \"hdmf==6.2.0\" \\\n", " \"humanize==4.16.0\" \\\n", - " \"idna==3.18\" \\\n", + " \"idna==3.19\" \\\n", " \"imageio==2.37.4\" \\\n", " \"interleave==0.3.0\" \\\n", " \"isodate==0.7.2\" \\\n", @@ -81,20 +82,20 @@ " \"jeepney==0.9.0\" \\\n", " \"jinja2==3.1.6\" \\\n", " \"jinxed==2.1.0\" \\\n", - " \"joblib==1.5.3\" \\\n", + " \"joblib==1.6.0\" \\\n", " \"jsonpointer==3.1.1\" \\\n", " \"jsonschema==4.26.0\" \\\n", " \"jsonschema-specifications==2025.9.1\" \\\n", " \"keyring==25.7.0\" \\\n", " \"keyrings-alt==5.0.2\" \\\n", - " \"kiwisolver==1.5.0\" \\\n", + " \"kiwisolver==1.5.1\" \\\n", " \"lazy-loader==0.5\" \\\n", " \"markupsafe==3.0.3\" \\\n", " \"matplotlib==3.10.0\" \\\n", " \"ml-dtypes==0.6.0\" \\\n", " \"more-itertools==10.8.0\" \\\n", " \"multidict==6.7.1\" \\\n", - " \"narwhals==2.24.0\" \\\n", + " \"narwhals==2.25.0\" \\\n", " \"natsort==8.4.0\" \\\n", " \"networkx==3.6.1\" \\\n", " \"numcodecs==0.16.5\" \\\n", @@ -103,12 +104,12 @@ " \"packaging==26.3\" \\\n", " \"pandas==2.2.3\" \\\n", " \"pillow==11.3.0\" \\\n", - " \"platformdirs==4.11.3\" \\\n", + " \"platformdirs==4.11.7\" \\\n", " \"propcache==0.5.2\" \\\n", " \"pycparser==3.0\" \\\n", " \"pycryptodomex==3.23.0\" \\\n", - " \"pydantic==2.13.4\" \\\n", - " \"pydantic-core==2.46.4\" \\\n", + " \"pydantic==2.13.5\" \\\n", + " \"pydantic-core==2.46.5\" \\\n", " \"pydantic-settings==2.15.0\" \\\n", " \"pynwb==4.1.0\" \\\n", " \"pyout==0.8.1\" \\\n", @@ -131,7 +132,7 @@ " \"six==1.17.0\" \\\n", " \"tenacity==9.1.4\" \\\n", " \"tensorstore==0.1.85\" \\\n", - " \"tifffile==2026.8.16\" \\\n", + " \"tifffile==2026.8.23\" \\\n", " \"tornado==6.5.7\" \\\n", " \"tqdm==4.67.3\" \\\n", " \"typing-extensions==4.16.0\" \\\n", @@ -139,7 +140,7 @@ " \"tzdata==2026.3\" \\\n", " \"uri-template==1.3.0\" \\\n", " \"urllib3==2.5.0\" \\\n", - " \"wcwidth==0.8.2\" \\\n", + " \"wcwidth==0.8.3\" \\\n", " \"webcolors==25.10.0\" \\\n", " \"xyzservices==2026.3.0\" \\\n", " \"yarl==1.24.5\" \\\n", diff --git a/000402/MICrONS/demo/000402_microns_demo.ipynb b/000402/MICrONS/demo/000402_microns_demo.ipynb index 989d0e7..2b4c1ad 100644 --- a/000402/MICrONS/demo/000402_microns_demo.ipynb +++ b/000402/MICrONS/demo/000402_microns_demo.ipynb @@ -47,10 +47,11 @@ " \"cffi==2.1.1\" \\\n", " \"charset-normalizer==3.4.9\" \\\n", " \"ci-info==0.4.0\" \\\n", - " \"click==8.4.2\" \\\n", + " \"click==8.5.0\" \\\n", " \"click-didyoumean==0.3.1\" \\\n", + " \"cloudpickle==3.1.2\" \\\n", " \"contourpy==1.3.3\" \\\n", - " \"cryptography==50.0.0\" \\\n", + " \"cryptography==50.0.1\" \\\n", " \"cycler==0.12.1\" \\\n", " \"dandi==0.77.0\" \\\n", " \"dandischema==0.14.0\" \\\n", @@ -60,16 +61,16 @@ " \"email-validator==2.3.0\" \\\n", " \"etelemetry==0.3.1\" \\\n", " \"fasteners==0.20\" \\\n", - " \"fonttools==4.63.0\" \\\n", + " \"fonttools==4.64.0\" \\\n", " \"fqdn==1.5.1\" \\\n", " \"frozenlist==1.8.0\" \\\n", " \"fscacher==0.4.4\" \\\n", - " \"fsspec==2025.3.0\" \\\n", + " \"fsspec==2025.12.0\" \\\n", " \"google-crc32c==1.8.0\" \\\n", " \"h5py==3.16.0\" \\\n", " \"hdmf==4.3.1\" \\\n", " \"humanize==4.16.0\" \\\n", - " \"idna==3.18\" \\\n", + " \"idna==3.19\" \\\n", " \"interleave==0.3.0\" \\\n", " \"isodate==0.7.2\" \\\n", " \"isoduration==20.11.0\" \\\n", @@ -78,13 +79,13 @@ " \"jaraco-functools==4.6.0\" \\\n", " \"jeepney==0.9.0\" \\\n", " \"jinxed==2.1.0\" \\\n", - " \"joblib==1.5.3\" \\\n", + " \"joblib==1.6.0\" \\\n", " \"jsonpointer==3.1.1\" \\\n", " \"jsonschema==4.26.0\" \\\n", " \"jsonschema-specifications==2025.9.1\" \\\n", " \"keyring==25.7.0\" \\\n", " \"keyrings-alt==5.0.2\" \\\n", - " \"kiwisolver==1.5.0\" \\\n", + " \"kiwisolver==1.5.1\" \\\n", " \"matplotlib==3.10.0\" \\\n", " \"ml-dtypes==0.6.0\" \\\n", " \"more-itertools==10.8.0\" \\\n", @@ -99,12 +100,12 @@ " \"packaging==26.3\" \\\n", " \"pandas==2.2.3\" \\\n", " \"pillow==11.3.0\" \\\n", - " \"platformdirs==4.11.3\" \\\n", + " \"platformdirs==4.11.7\" \\\n", " \"propcache==0.5.2\" \\\n", " \"pycparser==3.0\" \\\n", " \"pycryptodomex==3.23.0\" \\\n", - " \"pydantic==2.13.4\" \\\n", - " \"pydantic-core==2.46.4\" \\\n", + " \"pydantic==2.13.5\" \\\n", + " \"pydantic-core==2.46.5\" \\\n", " \"pydantic-settings==2.15.0\" \\\n", " \"pynwb==3.1.3\" \\\n", " \"pyout==0.8.1\" \\\n", @@ -130,7 +131,7 @@ " \"tzdata==2026.3\" \\\n", " \"uri-template==1.3.0\" \\\n", " \"urllib3==2.5.0\" \\\n", - " \"wcwidth==0.8.2\" \\\n", + " \"wcwidth==0.8.3\" \\\n", " \"webcolors==25.10.0\" \\\n", " \"yarl==1.24.5\" \\\n", " \"zarr==3.1.5\" \\\n", diff --git a/000409/IBL/bwm_usage_notebook.ipynb b/000409/IBL/bwm_usage_notebook.ipynb index 4eb0a2a..ab958b0 100644 --- a/000409/IBL/bwm_usage_notebook.ipynb +++ b/000409/IBL/bwm_usage_notebook.ipynb @@ -41,7 +41,7 @@ " \"anyio==4.14.2\" \\\n", " \"anywidget==0.9.21\" \\\n", " \"argon2-cffi==25.1.0\" \\\n", - " \"argon2-cffi-bindings==25.1.0\" \\\n", + " \"argon2-cffi-bindings==26.1.0\" \\\n", " \"arrow==1.4.0\" \\\n", " \"attrs==26.1.0\" \\\n", " \"backcall==0.2.0\" \\\n", @@ -58,11 +58,12 @@ " \"cffi==2.1.1\" \\\n", " \"charset-normalizer==3.4.9\" \\\n", " \"ci-info==0.4.0\" \\\n", - " \"click==8.4.2\" \\\n", + " \"click==8.5.0\" \\\n", " \"click-didyoumean==0.3.1\" \\\n", + " \"cloudpickle==3.1.2\" \\\n", " \"colorlog==6.12.0\" \\\n", " \"contourpy==1.3.3\" \\\n", - " \"cryptography==50.0.0\" \\\n", + " \"cryptography==50.0.1\" \\\n", " \"cycler==0.12.1\" \\\n", " \"dandi==0.77.0\" \\\n", " \"dandischema==0.14.0\" \\\n", @@ -77,18 +78,18 @@ " \"etelemetry==0.3.1\" \\\n", " \"fasteners==0.20\" \\\n", " \"fastjsonschema==2.22.2\" \\\n", - " \"fonttools==4.63.0\" \\\n", + " \"fonttools==4.64.0\" \\\n", " \"fqdn==1.5.1\" \\\n", " \"frozenlist==1.8.0\" \\\n", " \"fscacher==0.4.4\" \\\n", - " \"fsspec==2025.3.0\" \\\n", + " \"fsspec==2025.12.0\" \\\n", " \"google-crc32c==1.8.0\" \\\n", " \"h5py==3.16.0\" \\\n", " \"hdmf==4.3.1\" \\\n", " \"humanize==4.16.0\" \\\n", " \"iblatlas==1.2.0\" \\\n", " \"iblutil==1.20.0\" \\\n", - " \"idna==3.18\" \\\n", + " \"idna==3.19\" \\\n", " \"interleave==0.3.0\" \\\n", " \"ipykernel==6.17.1\" \\\n", " \"ipython==7.34.0\" \\\n", @@ -104,7 +105,7 @@ " \"jinja2==3.1.6\" \\\n", " \"jinxed==2.1.0\" \\\n", " \"jmespath==1.1.0\" \\\n", - " \"joblib==1.5.3\" \\\n", + " \"joblib==1.6.0\" \\\n", " \"jsonpointer==3.1.1\" \\\n", " \"jsonschema==4.26.0\" \\\n", " \"jsonschema-specifications==2025.9.1\" \\\n", @@ -114,10 +115,10 @@ " \"jupyter-server==2.20.0\" \\\n", " \"jupyter-server-terminals==0.5.4\" \\\n", " \"jupyterlab-pygments==0.3.0\" \\\n", - " \"jupyterlab-widgets==3.0.16\" \\\n", + " \"jupyterlab-widgets==3.0.17\" \\\n", " \"keyring==25.7.0\" \\\n", " \"keyrings-alt==5.0.2\" \\\n", - " \"kiwisolver==1.5.0\" \\\n", + " \"kiwisolver==1.5.1\" \\\n", " \"lark==1.3.1\" \\\n", " \"llvmlite==0.44.0\" \\\n", " \"markdown-it-py==4.2.0\" \\\n", @@ -152,7 +153,7 @@ " \"pexpect==4.9.0\" \\\n", " \"pickleshare==0.7.5\" \\\n", " \"pillow==11.3.0\" \\\n", - " \"platformdirs==4.11.3\" \\\n", + " \"platformdirs==4.11.7\" \\\n", " \"prometheus-client==0.26.0\" \\\n", " \"prompt-toolkit==3.0.53\" \\\n", " \"propcache==0.5.2\" \\\n", @@ -160,11 +161,11 @@ " \"psychofit==1.0.0.post0\" \\\n", " \"psygnal==0.15.1\" \\\n", " \"ptyprocess==0.7.0\" \\\n", - " \"pyarrow==18.1.0\" \\\n", + " \"pyarrow==23.0.1\" \\\n", " \"pycparser==3.0\" \\\n", " \"pycryptodomex==3.23.0\" \\\n", - " \"pydantic==2.13.4\" \\\n", - " \"pydantic-core==2.46.4\" \\\n", + " \"pydantic==2.13.5\" \\\n", + " \"pydantic-core==2.46.5\" \\\n", " \"pydantic-settings==2.15.0\" \\\n", " \"pygments==2.21.0\" \\\n", " \"pynapple==0.11.4\" \\\n", @@ -195,14 +196,14 @@ " \"secretstorage==3.5.0\" \\\n", " \"semantic-version==2.10.0\" \\\n", " \"send2trash==2.1.0\" \\\n", - " \"setuptools==75.2.0\" \\\n", + " \"setuptools==80.10.2\" \\\n", " \"six==1.17.0\" \\\n", " \"soupsieve==2.9.2\" \\\n", " \"tabulate==0.9.0\" \\\n", " \"tenacity==9.1.4\" \\\n", " \"tensorstore==0.1.85\" \\\n", " \"terminado==0.18.1\" \\\n", - " \"tifffile==2026.8.16\" \\\n", + " \"tifffile==2026.8.23\" \\\n", " \"tinycss2==1.5.1\" \\\n", " \"tornado==6.5.7\" \\\n", " \"tqdm==4.67.3\" \\\n", @@ -213,10 +214,10 @@ " \"tzdata==2026.3\" \\\n", " \"uri-template==1.3.0\" \\\n", " \"urllib3==2.5.0\" \\\n", - " \"wcwidth==0.8.2\" \\\n", + " \"wcwidth==0.8.3\" \\\n", " \"webcolors==25.10.0\" \\\n", " \"webencodings==0.6.1\" \\\n", - " \"websocket-client==1.9.0\" \\\n", + " \"websocket-client==1.9.2\" \\\n", " \"widgetsnbextension==3.6.10\" \\\n", " \"xarray==2025.12.0\" \\\n", " \"yarl==1.24.5\" \\\n", diff --git a/000458/AllenInstitute/reanalysis.ipynb b/000458/AllenInstitute/reanalysis.ipynb index 8d94bf8..f304ff3 100644 --- a/000458/AllenInstitute/reanalysis.ipynb +++ b/000458/AllenInstitute/reanalysis.ipynb @@ -47,10 +47,11 @@ " \"cffi==2.1.1\" \\\n", " \"charset-normalizer==3.4.9\" \\\n", " \"ci-info==0.4.0\" \\\n", - " \"click==8.4.2\" \\\n", + " \"click==8.5.0\" \\\n", " \"click-didyoumean==0.3.1\" \\\n", + " \"cloudpickle==3.1.2\" \\\n", " \"contourpy==1.3.3\" \\\n", - " \"cryptography==50.0.0\" \\\n", + " \"cryptography==50.0.1\" \\\n", " \"cycler==0.12.1\" \\\n", " \"dandi==0.77.0\" \\\n", " \"dandischema==0.14.0\" \\\n", @@ -60,16 +61,16 @@ " \"email-validator==2.3.0\" \\\n", " \"etelemetry==0.3.1\" \\\n", " \"fasteners==0.20\" \\\n", - " \"fonttools==4.63.0\" \\\n", + " \"fonttools==4.64.0\" \\\n", " \"fqdn==1.5.1\" \\\n", " \"frozenlist==1.8.0\" \\\n", " \"fscacher==0.4.4\" \\\n", - " \"fsspec==2025.3.0\" \\\n", + " \"fsspec==2025.12.0\" \\\n", " \"google-crc32c==1.8.0\" \\\n", " \"h5py==3.16.0\" \\\n", " \"hdmf==6.2.0\" \\\n", " \"humanize==4.16.0\" \\\n", - " \"idna==3.18\" \\\n", + " \"idna==3.19\" \\\n", " \"interleave==0.3.0\" \\\n", " \"isodate==0.7.2\" \\\n", " \"isoduration==20.11.0\" \\\n", @@ -78,13 +79,13 @@ " \"jaraco-functools==4.6.0\" \\\n", " \"jeepney==0.9.0\" \\\n", " \"jinxed==2.1.0\" \\\n", - " \"joblib==1.5.3\" \\\n", + " \"joblib==1.6.0\" \\\n", " \"jsonpointer==3.1.1\" \\\n", " \"jsonschema==4.26.0\" \\\n", " \"jsonschema-specifications==2025.9.1\" \\\n", " \"keyring==25.7.0\" \\\n", " \"keyrings-alt==5.0.2\" \\\n", - " \"kiwisolver==1.5.0\" \\\n", + " \"kiwisolver==1.5.1\" \\\n", " \"matplotlib==3.10.0\" \\\n", " \"ml-dtypes==0.6.0\" \\\n", " \"more-itertools==10.8.0\" \\\n", @@ -96,12 +97,12 @@ " \"packaging==26.3\" \\\n", " \"pandas==2.2.3\" \\\n", " \"pillow==11.3.0\" \\\n", - " \"platformdirs==4.11.3\" \\\n", + " \"platformdirs==4.11.7\" \\\n", " \"propcache==0.5.2\" \\\n", " \"pycparser==3.0\" \\\n", " \"pycryptodomex==3.23.0\" \\\n", - " \"pydantic==2.13.4\" \\\n", - " \"pydantic-core==2.46.4\" \\\n", + " \"pydantic==2.13.5\" \\\n", + " \"pydantic-core==2.46.5\" \\\n", " \"pydantic-settings==2.15.0\" \\\n", " \"pynwb==4.1.0\" \\\n", " \"pyout==0.8.1\" \\\n", @@ -128,7 +129,7 @@ " \"tzdata==2026.3\" \\\n", " \"uri-template==1.3.0\" \\\n", " \"urllib3==2.5.0\" \\\n", - " \"wcwidth==0.8.2\" \\\n", + " \"wcwidth==0.8.3\" \\\n", " \"webcolors==25.10.0\" \\\n", " \"yarl==1.24.5\" \\\n", " \"zarr==3.1.5\" \\\n", diff --git a/000458/FlatironInstitute/000_lindi_vs_fsspec_streaming.ipynb b/000458/FlatironInstitute/000_lindi_vs_fsspec_streaming.ipynb index 1a746e7..0f45795 100644 --- a/000458/FlatironInstitute/000_lindi_vs_fsspec_streaming.ipynb +++ b/000458/FlatironInstitute/000_lindi_vs_fsspec_streaming.ipynb @@ -49,9 +49,10 @@ " \"cffi==2.1.1\" \\\n", " \"charset-normalizer==3.4.9\" \\\n", " \"ci-info==0.4.0\" \\\n", - " \"click==8.4.2\" \\\n", + " \"click==8.5.0\" \\\n", " \"click-didyoumean==0.3.1\" \\\n", - " \"cryptography==50.0.0\" \\\n", + " \"cloudpickle==3.1.2\" \\\n", + " \"cryptography==50.0.1\" \\\n", " \"dandi==0.77.0\" \\\n", " \"dandischema==0.14.0\" \\\n", " \"decorator==4.4.2\" \\\n", @@ -64,11 +65,11 @@ " \"fqdn==1.5.1\" \\\n", " \"frozenlist==1.8.0\" \\\n", " \"fscacher==0.4.4\" \\\n", - " \"fsspec==2025.3.0\" \\\n", + " \"fsspec==2025.12.0\" \\\n", " \"h5py==3.16.0\" \\\n", " \"hdmf==4.3.1\" \\\n", " \"humanize==4.16.0\" \\\n", - " \"idna==3.18\" \\\n", + " \"idna==3.19\" \\\n", " \"interleave==0.3.0\" \\\n", " \"ipython==7.34.0\" \\\n", " \"isodate==0.7.2\" \\\n", @@ -79,7 +80,7 @@ " \"jedi==0.20.0\" \\\n", " \"jeepney==0.9.0\" \\\n", " \"jinxed==2.1.0\" \\\n", - " \"joblib==1.5.3\" \\\n", + " \"joblib==1.6.0\" \\\n", " \"jsonpointer==3.1.1\" \\\n", " \"jsonschema==4.26.0\" \\\n", " \"jsonschema-specifications==2025.9.1\" \\\n", @@ -99,14 +100,14 @@ " \"parso==0.8.7\" \\\n", " \"pexpect==4.9.0\" \\\n", " \"pickleshare==0.7.5\" \\\n", - " \"platformdirs==4.11.3\" \\\n", + " \"platformdirs==4.11.7\" \\\n", " \"prompt-toolkit==3.0.53\" \\\n", " \"propcache==0.5.2\" \\\n", " \"ptyprocess==0.7.0\" \\\n", " \"pycparser==3.0\" \\\n", " \"pycryptodomex==3.23.0\" \\\n", - " \"pydantic==2.13.4\" \\\n", - " \"pydantic-core==2.46.4\" \\\n", + " \"pydantic==2.13.5\" \\\n", + " \"pydantic-core==2.46.5\" \\\n", " \"pydantic-settings==2.15.0\" \\\n", " \"pygments==2.21.0\" \\\n", " \"pynwb==3.1.3\" \\\n", @@ -123,7 +124,7 @@ " \"ruamel-yaml==0.19.1\" \\\n", " \"secretstorage==3.5.0\" \\\n", " \"semantic-version==2.10.0\" \\\n", - " \"setuptools==75.2.0\" \\\n", + " \"setuptools==80.10.2\" \\\n", " \"six==1.17.0\" \\\n", " \"tenacity==9.1.4\" \\\n", " \"tensorstore==0.1.85\" \\\n", @@ -134,9 +135,9 @@ " \"tzdata==2026.3\" \\\n", " \"uri-template==1.3.0\" \\\n", " \"urllib3==2.5.0\" \\\n", - " \"wcwidth==0.8.2\" \\\n", + " \"wcwidth==0.8.3\" \\\n", " \"webcolors==25.10.0\" \\\n", - " \"wrapt==2.3.0\" \\\n", + " \"wrapt==2.4.0\" \\\n", " \"yarl==1.24.5\" \\\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 3e120b9..c7e79f2 100644 --- a/000458/FlatironInstitute/001_summarize_contents.ipynb +++ b/000458/FlatironInstitute/001_summarize_contents.ipynb @@ -49,9 +49,10 @@ " \"cffi==2.1.1\" \\\n", " \"charset-normalizer==3.4.9\" \\\n", " \"ci-info==0.4.0\" \\\n", - " \"click==8.4.2\" \\\n", + " \"click==8.5.0\" \\\n", " \"click-didyoumean==0.3.1\" \\\n", - " \"cryptography==50.0.0\" \\\n", + " \"cloudpickle==3.1.2\" \\\n", + " \"cryptography==50.0.1\" \\\n", " \"dandi==0.77.0\" \\\n", " \"dandischema==0.14.0\" \\\n", " \"decorator==4.4.2\" \\\n", @@ -64,11 +65,11 @@ " \"fqdn==1.5.1\" \\\n", " \"frozenlist==1.8.0\" \\\n", " \"fscacher==0.4.4\" \\\n", - " \"fsspec==2025.3.0\" \\\n", + " \"fsspec==2025.12.0\" \\\n", " \"h5py==3.16.0\" \\\n", " \"hdmf==4.3.1\" \\\n", " \"humanize==4.16.0\" \\\n", - " \"idna==3.18\" \\\n", + " \"idna==3.19\" \\\n", " \"interleave==0.3.0\" \\\n", " \"ipython==7.34.0\" \\\n", " \"isodate==0.7.2\" \\\n", @@ -79,7 +80,7 @@ " \"jedi==0.20.0\" \\\n", " \"jeepney==0.9.0\" \\\n", " \"jinxed==2.1.0\" \\\n", - " \"joblib==1.5.3\" \\\n", + " \"joblib==1.6.0\" \\\n", " \"jsonpointer==3.1.1\" \\\n", " \"jsonschema==4.26.0\" \\\n", " \"jsonschema-specifications==2025.9.1\" \\\n", @@ -99,14 +100,14 @@ " \"parso==0.8.7\" \\\n", " \"pexpect==4.9.0\" \\\n", " \"pickleshare==0.7.5\" \\\n", - " \"platformdirs==4.11.3\" \\\n", + " \"platformdirs==4.11.7\" \\\n", " \"prompt-toolkit==3.0.53\" \\\n", " \"propcache==0.5.2\" \\\n", " \"ptyprocess==0.7.0\" \\\n", " \"pycparser==3.0\" \\\n", " \"pycryptodomex==3.23.0\" \\\n", - " \"pydantic==2.13.4\" \\\n", - " \"pydantic-core==2.46.4\" \\\n", + " \"pydantic==2.13.5\" \\\n", + " \"pydantic-core==2.46.5\" \\\n", " \"pydantic-settings==2.15.0\" \\\n", " \"pygments==2.21.0\" \\\n", " \"pynwb==3.1.3\" \\\n", @@ -123,7 +124,7 @@ " \"ruamel-yaml==0.19.1\" \\\n", " \"secretstorage==3.5.0\" \\\n", " \"semantic-version==2.10.0\" \\\n", - " \"setuptools==75.2.0\" \\\n", + " \"setuptools==80.10.2\" \\\n", " \"six==1.17.0\" \\\n", " \"tenacity==9.1.4\" \\\n", " \"tensorstore==0.1.85\" \\\n", @@ -134,9 +135,9 @@ " \"tzdata==2026.3\" \\\n", " \"uri-template==1.3.0\" \\\n", " \"urllib3==2.5.0\" \\\n", - " \"wcwidth==0.8.2\" \\\n", + " \"wcwidth==0.8.3\" \\\n", " \"webcolors==25.10.0\" \\\n", - " \"wrapt==2.3.0\" \\\n", + " \"wrapt==2.4.0\" \\\n", " \"yarl==1.24.5\" \\\n", " \"zarr==2.18.7\" \\\n", " \"zarr-checksum==0.4.7\"\n", diff --git a/000559/dattalab/markowitz_gillis_nature_2023/reproduce_figure1d.ipynb b/000559/dattalab/markowitz_gillis_nature_2023/reproduce_figure1d.ipynb index 43be919..5a0b2c9 100644 --- a/000559/dattalab/markowitz_gillis_nature_2023/reproduce_figure1d.ipynb +++ b/000559/dattalab/markowitz_gillis_nature_2023/reproduce_figure1d.ipynb @@ -48,11 +48,12 @@ " \"cffi==2.1.1\" \\\n", " \"charset-normalizer==3.4.9\" \\\n", " \"ci-info==0.4.0\" \\\n", - " \"click==8.4.2\" \\\n", + " \"click==8.5.0\" \\\n", " \"click-didyoumean==0.3.1\" \\\n", + " \"cloudpickle==3.1.2\" \\\n", " \"colorcet==3.2.1\" \\\n", " \"contourpy==1.3.3\" \\\n", - " \"cryptography==50.0.0\" \\\n", + " \"cryptography==50.0.1\" \\\n", " \"cycler==0.12.1\" \\\n", " \"dandi==0.77.0\" \\\n", " \"dandischema==0.14.0\" \\\n", @@ -63,16 +64,16 @@ " \"email-validator==2.3.0\" \\\n", " \"etelemetry==0.3.1\" \\\n", " \"fasteners==0.20\" \\\n", - " \"fonttools==4.63.0\" \\\n", + " \"fonttools==4.64.0\" \\\n", " \"fqdn==1.5.1\" \\\n", " \"frozenlist==1.8.0\" \\\n", " \"fscacher==0.4.4\" \\\n", - " \"fsspec==2025.3.0\" \\\n", + " \"fsspec==2025.12.0\" \\\n", " \"h5py==3.16.0\" \\\n", " \"hdmf==4.3.1\" \\\n", " \"hdmf-zarr==0.13.0\" \\\n", " \"humanize==4.16.0\" \\\n", - " \"idna==3.18\" \\\n", + " \"idna==3.19\" \\\n", " \"interleave==0.3.0\" \\\n", " \"isodate==0.7.2\" \\\n", " \"isoduration==20.11.0\" \\\n", @@ -81,13 +82,13 @@ " \"jaraco-functools==4.6.0\" \\\n", " \"jeepney==0.9.0\" \\\n", " \"jinxed==2.1.0\" \\\n", - " \"joblib==1.5.3\" \\\n", + " \"joblib==1.6.0\" \\\n", " \"jsonpointer==3.1.1\" \\\n", " \"jsonschema==4.26.0\" \\\n", " \"jsonschema-specifications==2025.9.1\" \\\n", " \"keyring==25.7.0\" \\\n", " \"keyrings-alt==5.0.2\" \\\n", - " \"kiwisolver==1.5.0\" \\\n", + " \"kiwisolver==1.5.1\" \\\n", " \"matplotlib==3.10.0\" \\\n", " \"ml-dtypes==0.6.0\" \\\n", " \"more-itertools==10.8.0\" \\\n", @@ -101,13 +102,13 @@ " \"pandas==2.2.3\" \\\n", " \"parse==1.22.1\" \\\n", " \"pillow==11.3.0\" \\\n", - " \"platformdirs==4.11.3\" \\\n", + " \"platformdirs==4.11.7\" \\\n", " \"propcache==0.5.2\" \\\n", " \"psutil==5.9.5\" \\\n", " \"pycparser==3.0\" \\\n", " \"pycryptodomex==3.23.0\" \\\n", - " \"pydantic==2.13.4\" \\\n", - " \"pydantic-core==2.46.4\" \\\n", + " \"pydantic==2.13.5\" \\\n", + " \"pydantic-core==2.46.5\" \\\n", " \"pydantic-settings==2.15.0\" \\\n", " \"pynwb==3.1.3\" \\\n", " \"pyout==0.8.1\" \\\n", @@ -134,9 +135,9 @@ " \"tzdata==2026.3\" \\\n", " \"uri-template==1.3.0\" \\\n", " \"urllib3==2.5.0\" \\\n", - " \"wcwidth==0.8.2\" \\\n", + " \"wcwidth==0.8.3\" \\\n", " \"webcolors==25.10.0\" \\\n", - " \"wrapt==2.3.0\" \\\n", + " \"wrapt==2.4.0\" \\\n", " \"yarl==1.24.5\" \\\n", " \"zarr==2.18.7\" \\\n", " \"zarr-checksum==0.4.7\"\n", 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 24aa3f3..b9c7a16 100644 --- a/000559/dattalab/markowitz_gillis_nature_2023/reproduce_figure_S1.ipynb +++ b/000559/dattalab/markowitz_gillis_nature_2023/reproduce_figure_S1.ipynb @@ -48,10 +48,11 @@ " \"cffi==2.1.1\" \\\n", " \"charset-normalizer==3.4.9\" \\\n", " \"ci-info==0.4.0\" \\\n", - " \"click==8.4.2\" \\\n", + " \"click==8.5.0\" \\\n", " \"click-didyoumean==0.3.1\" \\\n", + " \"cloudpickle==3.1.2\" \\\n", " \"contourpy==1.3.3\" \\\n", - " \"cryptography==50.0.0\" \\\n", + " \"cryptography==50.0.1\" \\\n", " \"cuda-bindings==12.9.4\" \\\n", " \"cuda-pathfinder==1.6.1\" \\\n", " \"cycler==0.12.1\" \\\n", @@ -64,17 +65,17 @@ " \"etelemetry==0.3.1\" \\\n", " \"fasteners==0.20\" \\\n", " \"fastremap==1.20.0\" \\\n", - " \"filelock==3.32.3\" \\\n", - " \"fonttools==4.63.0\" \\\n", + " \"filelock==3.32.5\" \\\n", + " \"fonttools==4.64.0\" \\\n", " \"fqdn==1.5.1\" \\\n", " \"frozenlist==1.8.0\" \\\n", " \"fscacher==0.4.4\" \\\n", - " \"fsspec==2025.3.0\" \\\n", + " \"fsspec==2025.12.0\" \\\n", " \"google-crc32c==1.8.0\" \\\n", " \"h5py==3.16.0\" \\\n", " \"hdmf==4.3.1\" \\\n", " \"humanize==4.16.0\" \\\n", - " \"idna==3.18\" \\\n", + " \"idna==3.19\" \\\n", " \"imagecodecs==2026.8.16\" \\\n", " \"imageio==2.37.4\" \\\n", " \"interleave==0.3.0\" \\\n", @@ -86,13 +87,13 @@ " \"jeepney==0.9.0\" \\\n", " \"jinja2==3.1.6\" \\\n", " \"jinxed==2.1.0\" \\\n", - " \"joblib==1.5.3\" \\\n", + " \"joblib==1.6.0\" \\\n", " \"jsonpointer==3.1.1\" \\\n", " \"jsonschema==4.26.0\" \\\n", " \"jsonschema-specifications==2025.9.1\" \\\n", " \"keyring==25.7.0\" \\\n", " \"keyrings-alt==5.0.2\" \\\n", - " \"kiwisolver==1.5.0\" \\\n", + " \"kiwisolver==1.5.1\" \\\n", " \"lazy-loader==0.5\" \\\n", " \"llvmlite==0.44.0\" \\\n", " \"markupsafe==3.0.3\" \\\n", @@ -126,12 +127,12 @@ " \"packaging==26.3\" \\\n", " \"pandas==2.2.3\" \\\n", " \"pillow==11.3.0\" \\\n", - " \"platformdirs==4.11.3\" \\\n", + " \"platformdirs==4.11.7\" \\\n", " \"propcache==0.5.2\" \\\n", " \"pycparser==3.0\" \\\n", " \"pycryptodomex==3.23.0\" \\\n", - " \"pydantic==2.13.4\" \\\n", - " \"pydantic-core==2.46.4\" \\\n", + " \"pydantic==2.13.5\" \\\n", + " \"pydantic-core==2.46.5\" \\\n", " \"pydantic-settings==2.15.0\" \\\n", " \"pynwb==3.1.3\" \\\n", " \"pyout==0.8.1\" \\\n", @@ -152,12 +153,12 @@ " \"seaborn==0.13.2\" \\\n", " \"secretstorage==3.5.0\" \\\n", " \"semantic-version==2.10.0\" \\\n", - " \"setuptools==75.2.0\" \\\n", + " \"setuptools==80.10.2\" \\\n", " \"six==1.17.0\" \\\n", " \"sympy==1.14.0\" \\\n", " \"tenacity==9.1.4\" \\\n", " \"tensorstore==0.1.85\" \\\n", - " \"tifffile==2026.8.16\" \\\n", + " \"tifffile==2026.8.23\" \\\n", " \"torch==2.10.0\" \\\n", " \"tqdm==4.67.3\" \\\n", " \"triton==3.6.0\" \\\n", @@ -166,7 +167,7 @@ " \"tzdata==2026.3\" \\\n", " \"uri-template==1.3.0\" \\\n", " \"urllib3==2.5.0\" \\\n", - " \"wcwidth==0.8.2\" \\\n", + " \"wcwidth==0.8.3\" \\\n", " \"webcolors==25.10.0\" \\\n", " \"yarl==1.24.5\" \\\n", " \"zarr==3.1.5\" \\\n", diff --git a/000582/Sargolini2006/000582_Sargolini2006_demo.ipynb b/000582/Sargolini2006/000582_Sargolini2006_demo.ipynb index 05e1504..f933d51 100644 --- a/000582/Sargolini2006/000582_Sargolini2006_demo.ipynb +++ b/000582/Sargolini2006/000582_Sargolini2006_demo.ipynb @@ -47,9 +47,10 @@ " \"cffi==2.1.1\" \\\n", " \"charset-normalizer==3.4.9\" \\\n", " \"ci-info==0.4.0\" \\\n", - " \"click==8.4.2\" \\\n", + " \"click==8.5.0\" \\\n", " \"click-didyoumean==0.3.1\" \\\n", - " \"cryptography==50.0.0\" \\\n", + " \"cloudpickle==3.1.2\" \\\n", + " \"cryptography==50.0.1\" \\\n", " \"dandi==0.77.0\" \\\n", " \"dandischema==0.14.0\" \\\n", " \"deno==2.9.5\" \\\n", @@ -61,12 +62,12 @@ " \"fqdn==1.5.1\" \\\n", " \"frozenlist==1.8.0\" \\\n", " \"fscacher==0.4.4\" \\\n", - " \"fsspec==2025.3.0\" \\\n", + " \"fsspec==2025.12.0\" \\\n", " \"google-crc32c==1.8.0\" \\\n", " \"h5py==3.16.0\" \\\n", " \"hdmf==4.3.1\" \\\n", " \"humanize==4.16.0\" \\\n", - " \"idna==3.18\" \\\n", + " \"idna==3.19\" \\\n", " \"interleave==0.3.0\" \\\n", " \"isodate==0.7.2\" \\\n", " \"isoduration==20.11.0\" \\\n", @@ -75,7 +76,7 @@ " \"jaraco-functools==4.6.0\" \\\n", " \"jeepney==0.9.0\" \\\n", " \"jinxed==2.1.0\" \\\n", - " \"joblib==1.5.3\" \\\n", + " \"joblib==1.6.0\" \\\n", " \"jsonpointer==3.1.1\" \\\n", " \"jsonschema==4.26.0\" \\\n", " \"jsonschema-specifications==2025.9.1\" \\\n", @@ -95,13 +96,13 @@ " \"nwbinspector==0.7.2\" \\\n", " \"packaging==26.3\" \\\n", " \"pandas==2.2.3\" \\\n", - " \"platformdirs==4.11.3\" \\\n", + " \"platformdirs==4.11.7\" \\\n", " \"plotly==5.24.1\" \\\n", " \"propcache==0.5.2\" \\\n", " \"pycparser==3.0\" \\\n", " \"pycryptodomex==3.23.0\" \\\n", - " \"pydantic==2.13.4\" \\\n", - " \"pydantic-core==2.46.4\" \\\n", + " \"pydantic==2.13.5\" \\\n", + " \"pydantic-core==2.46.5\" \\\n", " \"pydantic-settings==2.15.0\" \\\n", " \"pygments==2.21.0\" \\\n", " \"pynapple==0.11.4\" \\\n", @@ -132,7 +133,7 @@ " \"tzdata==2026.3\" \\\n", " \"uri-template==1.3.0\" \\\n", " \"urllib3==2.5.0\" \\\n", - " \"wcwidth==0.8.2\" \\\n", + " \"wcwidth==0.8.3\" \\\n", " \"webcolors==25.10.0\" \\\n", " \"xarray==2025.12.0\" \\\n", " \"yarl==1.24.5\" \\\n", diff --git a/000718/CaiLab/zaki_2024/000718_demo.ipynb b/000718/CaiLab/zaki_2024/000718_demo.ipynb index 92599e1..9abb76e 100644 --- a/000718/CaiLab/zaki_2024/000718_demo.ipynb +++ b/000718/CaiLab/zaki_2024/000718_demo.ipynb @@ -47,10 +47,11 @@ " \"cffi==2.1.1\" \\\n", " \"charset-normalizer==3.4.9\" \\\n", " \"ci-info==0.4.0\" \\\n", - " \"click==8.4.2\" \\\n", + " \"click==8.5.0\" \\\n", " \"click-didyoumean==0.3.1\" \\\n", + " \"cloudpickle==3.1.2\" \\\n", " \"contourpy==1.3.3\" \\\n", - " \"cryptography==50.0.0\" \\\n", + " \"cryptography==50.0.1\" \\\n", " \"cycler==0.12.1\" \\\n", " \"dandi==0.77.0\" \\\n", " \"dandischema==0.14.0\" \\\n", @@ -60,16 +61,16 @@ " \"email-validator==2.3.0\" \\\n", " \"etelemetry==0.3.1\" \\\n", " \"fasteners==0.20\" \\\n", - " \"fonttools==4.63.0\" \\\n", + " \"fonttools==4.64.0\" \\\n", " \"fqdn==1.5.1\" \\\n", " \"frozenlist==1.8.0\" \\\n", " \"fscacher==0.4.4\" \\\n", - " \"fsspec==2025.3.0\" \\\n", + " \"fsspec==2025.12.0\" \\\n", " \"google-crc32c==1.8.0\" \\\n", " \"h5py==3.16.0\" \\\n", " \"hdmf==4.3.1\" \\\n", " \"humanize==4.16.0\" \\\n", - " \"idna==3.18\" \\\n", + " \"idna==3.19\" \\\n", " \"interleave==0.3.0\" \\\n", " \"isodate==0.7.2\" \\\n", " \"isoduration==20.11.0\" \\\n", @@ -78,13 +79,13 @@ " \"jaraco-functools==4.6.0\" \\\n", " \"jeepney==0.9.0\" \\\n", " \"jinxed==2.1.0\" \\\n", - " \"joblib==1.5.3\" \\\n", + " \"joblib==1.6.0\" \\\n", " \"jsonpointer==3.1.1\" \\\n", " \"jsonschema==4.26.0\" \\\n", " \"jsonschema-specifications==2025.9.1\" \\\n", " \"keyring==25.7.0\" \\\n", " \"keyrings-alt==5.0.2\" \\\n", - " \"kiwisolver==1.5.0\" \\\n", + " \"kiwisolver==1.5.1\" \\\n", " \"matplotlib==3.10.0\" \\\n", " \"ml-dtypes==0.6.0\" \\\n", " \"more-itertools==10.8.0\" \\\n", @@ -96,12 +97,12 @@ " \"packaging==26.3\" \\\n", " \"pandas==2.2.3\" \\\n", " \"pillow==11.3.0\" \\\n", - " \"platformdirs==4.11.3\" \\\n", + " \"platformdirs==4.11.7\" \\\n", " \"propcache==0.5.2\" \\\n", " \"pycparser==3.0\" \\\n", " \"pycryptodomex==3.23.0\" \\\n", - " \"pydantic==2.13.4\" \\\n", - " \"pydantic-core==2.46.4\" \\\n", + " \"pydantic==2.13.5\" \\\n", + " \"pydantic-core==2.46.5\" \\\n", " \"pydantic-settings==2.15.0\" \\\n", " \"pynwb==3.1.3\" \\\n", " \"pyout==0.8.1\" \\\n", @@ -128,7 +129,7 @@ " \"tzdata==2026.3\" \\\n", " \"uri-template==1.3.0\" \\\n", " \"urllib3==2.5.0\" \\\n", - " \"wcwidth==0.8.2\" \\\n", + " \"wcwidth==0.8.3\" \\\n", " \"webcolors==25.10.0\" \\\n", " \"yarl==1.24.5\" \\\n", " \"zarr==3.1.5\" \\\n", diff --git a/000727/clandinin/simple_data_access/reading_data.ipynb b/000727/clandinin/simple_data_access/reading_data.ipynb index b2f26ca..eae965e 100644 --- a/000727/clandinin/simple_data_access/reading_data.ipynb +++ b/000727/clandinin/simple_data_access/reading_data.ipynb @@ -47,10 +47,11 @@ " \"cffi==2.1.1\" \\\n", " \"charset-normalizer==3.4.9\" \\\n", " \"ci-info==0.4.0\" \\\n", - " \"click==8.4.2\" \\\n", + " \"click==8.5.0\" \\\n", " \"click-didyoumean==0.3.1\" \\\n", + " \"cloudpickle==3.1.2\" \\\n", " \"contourpy==1.3.3\" \\\n", - " \"cryptography==50.0.0\" \\\n", + " \"cryptography==50.0.1\" \\\n", " \"cycler==0.12.1\" \\\n", " \"dandi==0.77.0\" \\\n", " \"dandischema==0.14.0\" \\\n", @@ -60,16 +61,16 @@ " \"email-validator==2.3.0\" \\\n", " \"etelemetry==0.3.1\" \\\n", " \"fasteners==0.20\" \\\n", - " \"fonttools==4.63.0\" \\\n", + " \"fonttools==4.64.0\" \\\n", " \"fqdn==1.5.1\" \\\n", " \"frozenlist==1.8.0\" \\\n", " \"fscacher==0.4.4\" \\\n", - " \"fsspec==2025.3.0\" \\\n", + " \"fsspec==2025.12.0\" \\\n", " \"google-crc32c==1.8.0\" \\\n", " \"h5py==3.16.0\" \\\n", " \"hdmf==4.3.1\" \\\n", " \"humanize==4.16.0\" \\\n", - " \"idna==3.18\" \\\n", + " \"idna==3.19\" \\\n", " \"interleave==0.3.0\" \\\n", " \"isodate==0.7.2\" \\\n", " \"isoduration==20.11.0\" \\\n", @@ -78,13 +79,13 @@ " \"jaraco-functools==4.6.0\" \\\n", " \"jeepney==0.9.0\" \\\n", " \"jinxed==2.1.0\" \\\n", - " \"joblib==1.5.3\" \\\n", + " \"joblib==1.6.0\" \\\n", " \"jsonpointer==3.1.1\" \\\n", " \"jsonschema==4.26.0\" \\\n", " \"jsonschema-specifications==2025.9.1\" \\\n", " \"keyring==25.7.0\" \\\n", " \"keyrings-alt==5.0.2\" \\\n", - " \"kiwisolver==1.5.0\" \\\n", + " \"kiwisolver==1.5.1\" \\\n", " \"matplotlib==3.10.0\" \\\n", " \"ml-dtypes==0.6.0\" \\\n", " \"more-itertools==10.8.0\" \\\n", @@ -96,12 +97,12 @@ " \"packaging==26.3\" \\\n", " \"pandas==2.2.3\" \\\n", " \"pillow==11.3.0\" \\\n", - " \"platformdirs==4.11.3\" \\\n", + " \"platformdirs==4.11.7\" \\\n", " \"propcache==0.5.2\" \\\n", " \"pycparser==3.0\" \\\n", " \"pycryptodomex==3.23.0\" \\\n", - " \"pydantic==2.13.4\" \\\n", - " \"pydantic-core==2.46.4\" \\\n", + " \"pydantic==2.13.5\" \\\n", + " \"pydantic-core==2.46.5\" \\\n", " \"pydantic-settings==2.15.0\" \\\n", " \"pynwb==3.1.3\" \\\n", " \"pyout==0.8.1\" \\\n", @@ -128,7 +129,7 @@ " \"tzdata==2026.3\" \\\n", " \"uri-template==1.3.0\" \\\n", " \"urllib3==2.5.0\" \\\n", - " \"wcwidth==0.8.2\" \\\n", + " \"wcwidth==0.8.3\" \\\n", " \"webcolors==25.10.0\" \\\n", " \"yarl==1.24.5\" \\\n", " \"zarr==3.1.5\" \\\n", diff --git a/000728/AllenInstitute/visual_coding_ophys_tutorial.ipynb b/000728/AllenInstitute/visual_coding_ophys_tutorial.ipynb index 38a9a26..6ca3f09 100644 --- a/000728/AllenInstitute/visual_coding_ophys_tutorial.ipynb +++ b/000728/AllenInstitute/visual_coding_ophys_tutorial.ipynb @@ -47,10 +47,11 @@ " \"cffi==2.1.1\" \\\n", " \"charset-normalizer==3.4.9\" \\\n", " \"ci-info==0.4.0\" \\\n", - " \"click==8.4.2\" \\\n", + " \"click==8.5.0\" \\\n", " \"click-didyoumean==0.3.1\" \\\n", + " \"cloudpickle==3.1.2\" \\\n", " \"contourpy==1.3.3\" \\\n", - " \"cryptography==50.0.0\" \\\n", + " \"cryptography==50.0.1\" \\\n", " \"cycler==0.12.1\" \\\n", " \"dandi==0.77.0\" \\\n", " \"dandischema==0.14.0\" \\\n", @@ -60,16 +61,16 @@ " \"email-validator==2.3.0\" \\\n", " \"etelemetry==0.3.1\" \\\n", " \"fasteners==0.20\" \\\n", - " \"fonttools==4.63.0\" \\\n", + " \"fonttools==4.64.0\" \\\n", " \"fqdn==1.5.1\" \\\n", " \"frozenlist==1.8.0\" \\\n", " \"fscacher==0.4.4\" \\\n", - " \"fsspec==2025.3.0\" \\\n", + " \"fsspec==2025.12.0\" \\\n", " \"google-crc32c==1.8.0\" \\\n", " \"h5py==3.16.0\" \\\n", " \"hdmf==4.3.1\" \\\n", " \"humanize==4.16.0\" \\\n", - " \"idna==3.18\" \\\n", + " \"idna==3.19\" \\\n", " \"interleave==0.3.0\" \\\n", " \"isodate==0.7.2\" \\\n", " \"isoduration==20.11.0\" \\\n", @@ -78,13 +79,13 @@ " \"jaraco-functools==4.6.0\" \\\n", " \"jeepney==0.9.0\" \\\n", " \"jinxed==2.1.0\" \\\n", - " \"joblib==1.5.3\" \\\n", + " \"joblib==1.6.0\" \\\n", " \"jsonpointer==3.1.1\" \\\n", " \"jsonschema==4.26.0\" \\\n", " \"jsonschema-specifications==2025.9.1\" \\\n", " \"keyring==25.7.0\" \\\n", " \"keyrings-alt==5.0.2\" \\\n", - " \"kiwisolver==1.5.0\" \\\n", + " \"kiwisolver==1.5.1\" \\\n", " \"matplotlib==3.10.0\" \\\n", " \"ml-dtypes==0.6.0\" \\\n", " \"more-itertools==10.8.0\" \\\n", @@ -96,12 +97,12 @@ " \"packaging==26.3\" \\\n", " \"pandas==2.2.3\" \\\n", " \"pillow==11.3.0\" \\\n", - " \"platformdirs==4.11.3\" \\\n", + " \"platformdirs==4.11.7\" \\\n", " \"propcache==0.5.2\" \\\n", " \"pycparser==3.0\" \\\n", " \"pycryptodomex==3.23.0\" \\\n", - " \"pydantic==2.13.4\" \\\n", - " \"pydantic-core==2.46.4\" \\\n", + " \"pydantic==2.13.5\" \\\n", + " \"pydantic-core==2.46.5\" \\\n", " \"pydantic-settings==2.15.0\" \\\n", " \"pynwb==3.1.3\" \\\n", " \"pyout==0.8.1\" \\\n", @@ -129,7 +130,7 @@ " \"tzdata==2026.3\" \\\n", " \"uri-template==1.3.0\" \\\n", " \"urllib3==2.5.0\" \\\n", - " \"wcwidth==0.8.2\" \\\n", + " \"wcwidth==0.8.3\" \\\n", " \"webcolors==25.10.0\" \\\n", " \"yarl==1.24.5\" \\\n", " \"zarr==3.1.5\" \\\n", diff --git a/000947/TurnerLab/public_demo/000947_demo.ipynb b/000947/TurnerLab/public_demo/000947_demo.ipynb index 2e4d406..d5115bf 100644 --- a/000947/TurnerLab/public_demo/000947_demo.ipynb +++ b/000947/TurnerLab/public_demo/000947_demo.ipynb @@ -47,10 +47,11 @@ " \"cffi==2.1.1\" \\\n", " \"charset-normalizer==3.4.9\" \\\n", " \"ci-info==0.4.0\" \\\n", - " \"click==8.4.2\" \\\n", + " \"click==8.5.0\" \\\n", " \"click-didyoumean==0.3.1\" \\\n", + " \"cloudpickle==3.1.2\" \\\n", " \"contourpy==1.3.3\" \\\n", - " \"cryptography==50.0.0\" \\\n", + " \"cryptography==50.0.1\" \\\n", " \"cycler==0.12.1\" \\\n", " \"dandi==0.77.0\" \\\n", " \"dandischema==0.14.0\" \\\n", @@ -60,16 +61,16 @@ " \"email-validator==2.3.0\" \\\n", " \"etelemetry==0.3.1\" \\\n", " \"fasteners==0.20\" \\\n", - " \"fonttools==4.63.0\" \\\n", + " \"fonttools==4.64.0\" \\\n", " \"fqdn==1.5.1\" \\\n", " \"frozenlist==1.8.0\" \\\n", " \"fscacher==0.4.4\" \\\n", - " \"fsspec==2025.3.0\" \\\n", + " \"fsspec==2025.12.0\" \\\n", " \"google-crc32c==1.8.0\" \\\n", " \"h5py==3.16.0\" \\\n", " \"hdmf==4.3.1\" \\\n", " \"humanize==4.16.0\" \\\n", - " \"idna==3.18\" \\\n", + " \"idna==3.19\" \\\n", " \"interleave==0.3.0\" \\\n", " \"isodate==0.7.2\" \\\n", " \"isoduration==20.11.0\" \\\n", @@ -78,13 +79,13 @@ " \"jaraco-functools==4.6.0\" \\\n", " \"jeepney==0.9.0\" \\\n", " \"jinxed==2.1.0\" \\\n", - " \"joblib==1.5.3\" \\\n", + " \"joblib==1.6.0\" \\\n", " \"jsonpointer==3.1.1\" \\\n", " \"jsonschema==4.26.0\" \\\n", " \"jsonschema-specifications==2025.9.1\" \\\n", " \"keyring==25.7.0\" \\\n", " \"keyrings-alt==5.0.2\" \\\n", - " \"kiwisolver==1.5.0\" \\\n", + " \"kiwisolver==1.5.1\" \\\n", " \"llvmlite==0.44.0\" \\\n", " \"markdown-it-py==4.2.0\" \\\n", " \"matplotlib==3.10.0\" \\\n", @@ -100,12 +101,12 @@ " \"packaging==26.3\" \\\n", " \"pandas==2.2.3\" \\\n", " \"pillow==11.3.0\" \\\n", - " \"platformdirs==4.11.3\" \\\n", + " \"platformdirs==4.11.7\" \\\n", " \"propcache==0.5.2\" \\\n", " \"pycparser==3.0\" \\\n", " \"pycryptodomex==3.23.0\" \\\n", - " \"pydantic==2.13.4\" \\\n", - " \"pydantic-core==2.46.4\" \\\n", + " \"pydantic==2.13.5\" \\\n", + " \"pydantic-core==2.46.5\" \\\n", " \"pydantic-settings==2.15.0\" \\\n", " \"pygments==2.21.0\" \\\n", " \"pynapple==0.7.1\" \\\n", @@ -137,7 +138,7 @@ " \"tzdata==2026.3\" \\\n", " \"uri-template==1.3.0\" \\\n", " \"urllib3==2.5.0\" \\\n", - " \"wcwidth==0.8.2\" \\\n", + " \"wcwidth==0.8.3\" \\\n", " \"webcolors==25.10.0\" \\\n", " \"yarl==1.24.5\" \\\n", " \"zarr==3.1.5\" \\\n", diff --git a/000971/lernerlab/seiler_2024/fiber_photometry_example_notebook.ipynb b/000971/lernerlab/seiler_2024/fiber_photometry_example_notebook.ipynb index 2296c10..aa5bb95 100644 --- a/000971/lernerlab/seiler_2024/fiber_photometry_example_notebook.ipynb +++ b/000971/lernerlab/seiler_2024/fiber_photometry_example_notebook.ipynb @@ -47,10 +47,11 @@ " \"cffi==2.1.1\" \\\n", " \"charset-normalizer==3.4.9\" \\\n", " \"ci-info==0.4.0\" \\\n", - " \"click==8.4.2\" \\\n", + " \"click==8.5.0\" \\\n", " \"click-didyoumean==0.3.1\" \\\n", + " \"cloudpickle==3.1.2\" \\\n", " \"contourpy==1.3.3\" \\\n", - " \"cryptography==50.0.0\" \\\n", + " \"cryptography==50.0.1\" \\\n", " \"cycler==0.12.1\" \\\n", " \"dandi==0.77.0\" \\\n", " \"dandischema==0.14.0\" \\\n", @@ -60,16 +61,16 @@ " \"email-validator==2.3.0\" \\\n", " \"etelemetry==0.3.1\" \\\n", " \"fasteners==0.20\" \\\n", - " \"fonttools==4.63.0\" \\\n", + " \"fonttools==4.64.0\" \\\n", " \"fqdn==1.5.1\" \\\n", " \"frozenlist==1.8.0\" \\\n", " \"fscacher==0.4.4\" \\\n", - " \"fsspec==2025.3.0\" \\\n", + " \"fsspec==2025.12.0\" \\\n", " \"google-crc32c==1.8.0\" \\\n", " \"h5py==3.16.0\" \\\n", " \"hdmf==4.3.1\" \\\n", " \"humanize==4.16.0\" \\\n", - " \"idna==3.18\" \\\n", + " \"idna==3.19\" \\\n", " \"interleave==0.3.0\" \\\n", " \"isodate==0.7.2\" \\\n", " \"isoduration==20.11.0\" \\\n", @@ -78,13 +79,13 @@ " \"jaraco-functools==4.6.0\" \\\n", " \"jeepney==0.9.0\" \\\n", " \"jinxed==2.1.0\" \\\n", - " \"joblib==1.5.3\" \\\n", + " \"joblib==1.6.0\" \\\n", " \"jsonpointer==3.1.1\" \\\n", " \"jsonschema==4.26.0\" \\\n", " \"jsonschema-specifications==2025.9.1\" \\\n", " \"keyring==25.7.0\" \\\n", " \"keyrings-alt==5.0.2\" \\\n", - " \"kiwisolver==1.5.0\" \\\n", + " \"kiwisolver==1.5.1\" \\\n", " \"matplotlib==3.10.0\" \\\n", " \"ml-dtypes==0.6.0\" \\\n", " \"more-itertools==10.8.0\" \\\n", @@ -96,12 +97,12 @@ " \"packaging==26.3\" \\\n", " \"pandas==2.2.3\" \\\n", " \"pillow==11.3.0\" \\\n", - " \"platformdirs==4.11.3\" \\\n", + " \"platformdirs==4.11.7\" \\\n", " \"propcache==0.5.2\" \\\n", " \"pycparser==3.0\" \\\n", " \"pycryptodomex==3.23.0\" \\\n", - " \"pydantic==2.13.4\" \\\n", - " \"pydantic-core==2.46.4\" \\\n", + " \"pydantic==2.13.5\" \\\n", + " \"pydantic-core==2.46.5\" \\\n", " \"pydantic-settings==2.15.0\" \\\n", " \"pynwb==3.1.3\" \\\n", " \"pyout==0.8.1\" \\\n", @@ -127,7 +128,7 @@ " \"tzdata==2026.3\" \\\n", " \"uri-template==1.3.0\" \\\n", " \"urllib3==2.5.0\" \\\n", - " \"wcwidth==0.8.2\" \\\n", + " \"wcwidth==0.8.3\" \\\n", " \"webcolors==25.10.0\" \\\n", " \"yarl==1.24.5\" \\\n", " \"zarr==3.1.5\" \\\n", diff --git a/000971/lernerlab/seiler_2024/optogenetics_example_notebook.ipynb b/000971/lernerlab/seiler_2024/optogenetics_example_notebook.ipynb index b67724b..cad6708 100644 --- a/000971/lernerlab/seiler_2024/optogenetics_example_notebook.ipynb +++ b/000971/lernerlab/seiler_2024/optogenetics_example_notebook.ipynb @@ -47,10 +47,11 @@ " \"cffi==2.1.1\" \\\n", " \"charset-normalizer==3.4.9\" \\\n", " \"ci-info==0.4.0\" \\\n", - " \"click==8.4.2\" \\\n", + " \"click==8.5.0\" \\\n", " \"click-didyoumean==0.3.1\" \\\n", + " \"cloudpickle==3.1.2\" \\\n", " \"contourpy==1.3.3\" \\\n", - " \"cryptography==50.0.0\" \\\n", + " \"cryptography==50.0.1\" \\\n", " \"cycler==0.12.1\" \\\n", " \"dandi==0.77.0\" \\\n", " \"dandischema==0.14.0\" \\\n", @@ -60,16 +61,16 @@ " \"email-validator==2.3.0\" \\\n", " \"etelemetry==0.3.1\" \\\n", " \"fasteners==0.20\" \\\n", - " \"fonttools==4.63.0\" \\\n", + " \"fonttools==4.64.0\" \\\n", " \"fqdn==1.5.1\" \\\n", " \"frozenlist==1.8.0\" \\\n", " \"fscacher==0.4.4\" \\\n", - " \"fsspec==2025.3.0\" \\\n", + " \"fsspec==2025.12.0\" \\\n", " \"google-crc32c==1.8.0\" \\\n", " \"h5py==3.16.0\" \\\n", " \"hdmf==4.3.1\" \\\n", " \"humanize==4.16.0\" \\\n", - " \"idna==3.18\" \\\n", + " \"idna==3.19\" \\\n", " \"interleave==0.3.0\" \\\n", " \"isodate==0.7.2\" \\\n", " \"isoduration==20.11.0\" \\\n", @@ -78,13 +79,13 @@ " \"jaraco-functools==4.6.0\" \\\n", " \"jeepney==0.9.0\" \\\n", " \"jinxed==2.1.0\" \\\n", - " \"joblib==1.5.3\" \\\n", + " \"joblib==1.6.0\" \\\n", " \"jsonpointer==3.1.1\" \\\n", " \"jsonschema==4.26.0\" \\\n", " \"jsonschema-specifications==2025.9.1\" \\\n", " \"keyring==25.7.0\" \\\n", " \"keyrings-alt==5.0.2\" \\\n", - " \"kiwisolver==1.5.0\" \\\n", + " \"kiwisolver==1.5.1\" \\\n", " \"matplotlib==3.10.0\" \\\n", " \"ml-dtypes==0.6.0\" \\\n", " \"more-itertools==10.8.0\" \\\n", @@ -96,12 +97,12 @@ " \"packaging==26.3\" \\\n", " \"pandas==2.2.3\" \\\n", " \"pillow==11.3.0\" \\\n", - " \"platformdirs==4.11.3\" \\\n", + " \"platformdirs==4.11.7\" \\\n", " \"propcache==0.5.2\" \\\n", " \"pycparser==3.0\" \\\n", " \"pycryptodomex==3.23.0\" \\\n", - " \"pydantic==2.13.4\" \\\n", - " \"pydantic-core==2.46.4\" \\\n", + " \"pydantic==2.13.5\" \\\n", + " \"pydantic-core==2.46.5\" \\\n", " \"pydantic-settings==2.15.0\" \\\n", " \"pynwb==3.1.3\" \\\n", " \"pyout==0.8.1\" \\\n", @@ -127,7 +128,7 @@ " \"tzdata==2026.3\" \\\n", " \"uri-template==1.3.0\" \\\n", " \"urllib3==2.5.0\" \\\n", - " \"wcwidth==0.8.2\" \\\n", + " \"wcwidth==0.8.3\" \\\n", " \"webcolors==25.10.0\" \\\n", " \"yarl==1.24.5\" \\\n", " \"zarr==3.1.5\" \\\n", diff --git a/001038/DombeckLab/001038_demo.ipynb b/001038/DombeckLab/001038_demo.ipynb index 43f00c3..72b69ce 100644 --- a/001038/DombeckLab/001038_demo.ipynb +++ b/001038/DombeckLab/001038_demo.ipynb @@ -51,8 +51,9 @@ " \"ci-info==0.4.0\" \\\n", " \"click==8.1.8\" \\\n", " \"click-didyoumean==0.3.1\" \\\n", + " \"cloudpickle==3.1.2\" \\\n", " \"contourpy==1.3.3\" \\\n", - " \"cryptography==50.0.0\" \\\n", + " \"cryptography==50.0.1\" \\\n", " \"cycler==0.12.1\" \\\n", " \"dandi==0.74.3\" \\\n", " \"dandischema==0.12.1\" \\\n", @@ -63,16 +64,16 @@ " \"email-validator==2.3.0\" \\\n", " \"etelemetry==0.3.1\" \\\n", " \"fasteners==0.20\" \\\n", - " \"fonttools==4.63.0\" \\\n", + " \"fonttools==4.64.0\" \\\n", " \"fqdn==1.5.1\" \\\n", " \"frozenlist==1.8.0\" \\\n", " \"fscacher==0.4.4\" \\\n", - " \"fsspec==2025.3.0\" \\\n", + " \"fsspec==2025.12.0\" \\\n", " \"h5py==3.16.0\" \\\n", " \"hdmf==4.3.1\" \\\n", " \"hdmf-zarr==0.13.0\" \\\n", " \"humanize==4.16.0\" \\\n", - " \"idna==3.18\" \\\n", + " \"idna==3.19\" \\\n", " \"interleave==0.3.0\" \\\n", " \"ipython==7.34.0\" \\\n", " \"isodate==0.7.2\" \\\n", @@ -83,13 +84,13 @@ " \"jedi==0.20.0\" \\\n", " \"jeepney==0.9.0\" \\\n", " \"jinxed==2.1.0\" \\\n", - " \"joblib==1.5.3\" \\\n", + " \"joblib==1.6.0\" \\\n", " \"jsonpointer==3.1.1\" \\\n", " \"jsonschema==4.26.0\" \\\n", " \"jsonschema-specifications==2025.9.1\" \\\n", " \"keyring==25.7.0\" \\\n", " \"keyrings-alt==5.0.2\" \\\n", - " \"kiwisolver==1.5.0\" \\\n", + " \"kiwisolver==1.5.1\" \\\n", " \"matplotlib==3.10.0\" \\\n", " \"matplotlib-inline==0.2.2\" \\\n", " \"ml-dtypes==0.6.0\" \\\n", @@ -105,14 +106,14 @@ " \"pexpect==4.9.0\" \\\n", " \"pickleshare==0.7.5\" \\\n", " \"pillow==11.3.0\" \\\n", - " \"platformdirs==4.11.3\" \\\n", + " \"platformdirs==4.11.7\" \\\n", " \"prompt-toolkit==3.0.53\" \\\n", " \"propcache==0.5.2\" \\\n", " \"ptyprocess==0.7.0\" \\\n", " \"pycparser==3.0\" \\\n", " \"pycryptodomex==3.23.0\" \\\n", - " \"pydantic==2.13.4\" \\\n", - " \"pydantic-core==2.46.4\" \\\n", + " \"pydantic==2.13.5\" \\\n", + " \"pydantic-core==2.46.5\" \\\n", " \"pydantic-settings==2.15.0\" \\\n", " \"pygments==2.21.0\" \\\n", " \"pynwb==3.0.0\" \\\n", @@ -131,7 +132,7 @@ " \"ruamel-yaml==0.19.1\" \\\n", " \"secretstorage==3.5.0\" \\\n", " \"semantic-version==2.10.0\" \\\n", - " \"setuptools==75.2.0\" \\\n", + " \"setuptools==80.10.2\" \\\n", " \"six==1.17.0\" \\\n", " \"tenacity==9.1.4\" \\\n", " \"tensorstore==0.1.85\" \\\n", @@ -143,9 +144,9 @@ " \"tzdata==2026.3\" \\\n", " \"uri-template==1.3.0\" \\\n", " \"urllib3==2.5.0\" \\\n", - " \"wcwidth==0.8.2\" \\\n", + " \"wcwidth==0.8.3\" \\\n", " \"webcolors==25.10.0\" \\\n", - " \"wrapt==2.3.0\" \\\n", + " \"wrapt==2.4.0\" \\\n", " \"yarl==1.24.5\" \\\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 67fbfa2..d9f2626 100644 --- a/001075/001075_paper_figure_1d.ipynb +++ b/001075/001075_paper_figure_1d.ipynb @@ -47,10 +47,11 @@ " \"cffi==2.1.1\" \\\n", " \"charset-normalizer==3.4.9\" \\\n", " \"ci-info==0.4.0\" \\\n", - " \"click==8.4.2\" \\\n", + " \"click==8.5.0\" \\\n", " \"click-didyoumean==0.3.1\" \\\n", + " \"cloudpickle==3.1.2\" \\\n", " \"contourpy==1.3.3\" \\\n", - " \"cryptography==50.0.0\" \\\n", + " \"cryptography==50.0.1\" \\\n", " \"cycler==0.12.1\" \\\n", " \"dandi==0.77.0\" \\\n", " \"dandischema==0.14.0\" \\\n", @@ -60,16 +61,16 @@ " \"email-validator==2.3.0\" \\\n", " \"etelemetry==0.3.1\" \\\n", " \"fasteners==0.20\" \\\n", - " \"fonttools==4.63.0\" \\\n", + " \"fonttools==4.64.0\" \\\n", " \"fqdn==1.5.1\" \\\n", " \"frozenlist==1.8.0\" \\\n", " \"fscacher==0.4.4\" \\\n", - " \"fsspec==2025.3.0\" \\\n", + " \"fsspec==2025.12.0\" \\\n", " \"google-crc32c==1.8.0\" \\\n", " \"h5py==3.16.0\" \\\n", " \"hdmf==4.3.1\" \\\n", " \"humanize==4.16.0\" \\\n", - " \"idna==3.18\" \\\n", + " \"idna==3.19\" \\\n", " \"interleave==0.3.0\" \\\n", " \"isodate==0.7.2\" \\\n", " \"isoduration==20.11.0\" \\\n", @@ -78,13 +79,13 @@ " \"jaraco-functools==4.6.0\" \\\n", " \"jeepney==0.9.0\" \\\n", " \"jinxed==2.1.0\" \\\n", - " \"joblib==1.5.3\" \\\n", + " \"joblib==1.6.0\" \\\n", " \"jsonpointer==3.1.1\" \\\n", " \"jsonschema==4.26.0\" \\\n", " \"jsonschema-specifications==2025.9.1\" \\\n", " \"keyring==25.7.0\" \\\n", " \"keyrings-alt==5.0.2\" \\\n", - " \"kiwisolver==1.5.0\" \\\n", + " \"kiwisolver==1.5.1\" \\\n", " \"matplotlib==3.10.0\" \\\n", " \"ml-dtypes==0.6.0\" \\\n", " \"more-itertools==10.8.0\" \\\n", @@ -96,12 +97,12 @@ " \"packaging==26.3\" \\\n", " \"pandas==2.2.3\" \\\n", " \"pillow==11.3.0\" \\\n", - " \"platformdirs==4.11.3\" \\\n", + " \"platformdirs==4.11.7\" \\\n", " \"propcache==0.5.2\" \\\n", " \"pycparser==3.0\" \\\n", " \"pycryptodomex==3.23.0\" \\\n", - " \"pydantic==2.13.4\" \\\n", - " \"pydantic-core==2.46.4\" \\\n", + " \"pydantic==2.13.5\" \\\n", + " \"pydantic-core==2.46.5\" \\\n", " \"pydantic-settings==2.15.0\" \\\n", " \"pynwb==3.1.3\" \\\n", " \"pyout==0.8.1\" \\\n", @@ -129,7 +130,7 @@ " \"tzdata==2026.3\" \\\n", " \"uri-template==1.3.0\" \\\n", " \"urllib3==2.5.0\" \\\n", - " \"wcwidth==0.8.2\" \\\n", + " \"wcwidth==0.8.3\" \\\n", " \"webcolors==25.10.0\" \\\n", " \"yarl==1.24.5\" \\\n", " \"zarr==3.1.5\" \\\n", diff --git a/001084/HoweLab/001084_demo.ipynb b/001084/HoweLab/001084_demo.ipynb index e0bd5e6..67d94de 100644 --- a/001084/HoweLab/001084_demo.ipynb +++ b/001084/HoweLab/001084_demo.ipynb @@ -50,8 +50,9 @@ " \"ci-info==0.4.0\" \\\n", " \"click==8.1.8\" \\\n", " \"click-didyoumean==0.3.1\" \\\n", + " \"cloudpickle==3.1.2\" \\\n", " \"contourpy==1.3.3\" \\\n", - " \"cryptography==50.0.0\" \\\n", + " \"cryptography==50.0.1\" \\\n", " \"cycler==0.12.1\" \\\n", " \"dandi==0.74.3\" \\\n", " \"dandischema==0.12.1\" \\\n", @@ -61,16 +62,16 @@ " \"email-validator==2.3.0\" \\\n", " \"etelemetry==0.3.1\" \\\n", " \"fasteners==0.20\" \\\n", - " \"fonttools==4.63.0\" \\\n", + " \"fonttools==4.64.0\" \\\n", " \"fqdn==1.5.1\" \\\n", " \"frozenlist==1.8.0\" \\\n", " \"fscacher==0.4.4\" \\\n", - " \"fsspec==2025.3.0\" \\\n", + " \"fsspec==2025.12.0\" \\\n", " \"h5py==3.16.0\" \\\n", " \"hdmf==4.3.1\" \\\n", " \"hdmf-zarr==0.13.0\" \\\n", " \"humanize==4.16.0\" \\\n", - " \"idna==3.18\" \\\n", + " \"idna==3.19\" \\\n", " \"interleave==0.3.0\" \\\n", " \"isodate==0.7.2\" \\\n", " \"isoduration==20.11.0\" \\\n", @@ -79,13 +80,13 @@ " \"jaraco-functools==4.6.0\" \\\n", " \"jeepney==0.9.0\" \\\n", " \"jinxed==2.1.0\" \\\n", - " \"joblib==1.5.3\" \\\n", + " \"joblib==1.6.0\" \\\n", " \"jsonpointer==3.1.1\" \\\n", " \"jsonschema==4.26.0\" \\\n", " \"jsonschema-specifications==2025.9.1\" \\\n", " \"keyring==25.7.0\" \\\n", " \"keyrings-alt==5.0.2\" \\\n", - " \"kiwisolver==1.5.0\" \\\n", + " \"kiwisolver==1.5.1\" \\\n", " \"matplotlib==3.10.0\" \\\n", " \"ml-dtypes==0.6.0\" \\\n", " \"more-itertools==10.8.0\" \\\n", @@ -97,12 +98,12 @@ " \"packaging==26.3\" \\\n", " \"pandas==2.2.3\" \\\n", " \"pillow==11.3.0\" \\\n", - " \"platformdirs==4.11.3\" \\\n", + " \"platformdirs==4.11.7\" \\\n", " \"propcache==0.5.2\" \\\n", " \"pycparser==3.0\" \\\n", " \"pycryptodomex==3.23.0\" \\\n", - " \"pydantic==2.13.4\" \\\n", - " \"pydantic-core==2.46.4\" \\\n", + " \"pydantic==2.13.5\" \\\n", + " \"pydantic-core==2.46.5\" \\\n", " \"pydantic-settings==2.15.0\" \\\n", " \"pynwb==3.0.0\" \\\n", " \"pyout==0.8.1\" \\\n", @@ -130,9 +131,9 @@ " \"tzdata==2026.3\" \\\n", " \"uri-template==1.3.0\" \\\n", " \"urllib3==2.5.0\" \\\n", - " \"wcwidth==0.8.2\" \\\n", + " \"wcwidth==0.8.3\" \\\n", " \"webcolors==25.10.0\" \\\n", - " \"wrapt==2.3.0\" \\\n", + " \"wrapt==2.4.0\" \\\n", " \"yarl==1.24.5\" \\\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 022e1ce..df112cd 100644 --- a/001170/ReimerLab/public_demo/001170_demo.ipynb +++ b/001170/ReimerLab/public_demo/001170_demo.ipynb @@ -47,10 +47,11 @@ " \"cffi==2.1.1\" \\\n", " \"charset-normalizer==3.4.9\" \\\n", " \"ci-info==0.4.0\" \\\n", - " \"click==8.4.2\" \\\n", + " \"click==8.5.0\" \\\n", " \"click-didyoumean==0.3.1\" \\\n", + " \"cloudpickle==3.1.2\" \\\n", " \"contourpy==1.3.3\" \\\n", - " \"cryptography==50.0.0\" \\\n", + " \"cryptography==50.0.1\" \\\n", " \"cycler==0.12.1\" \\\n", " \"dandi==0.77.0\" \\\n", " \"dandischema==0.14.0\" \\\n", @@ -60,16 +61,16 @@ " \"email-validator==2.3.0\" \\\n", " \"etelemetry==0.3.1\" \\\n", " \"fasteners==0.20\" \\\n", - " \"fonttools==4.63.0\" \\\n", + " \"fonttools==4.64.0\" \\\n", " \"fqdn==1.5.1\" \\\n", " \"frozenlist==1.8.0\" \\\n", " \"fscacher==0.4.4\" \\\n", - " \"fsspec==2025.3.0\" \\\n", + " \"fsspec==2025.12.0\" \\\n", " \"google-crc32c==1.8.0\" \\\n", " \"h5py==3.16.0\" \\\n", " \"hdmf==4.3.1\" \\\n", " \"humanize==4.16.0\" \\\n", - " \"idna==3.18\" \\\n", + " \"idna==3.19\" \\\n", " \"interleave==0.3.0\" \\\n", " \"isodate==0.7.2\" \\\n", " \"isoduration==20.11.0\" \\\n", @@ -78,13 +79,13 @@ " \"jaraco-functools==4.6.0\" \\\n", " \"jeepney==0.9.0\" \\\n", " \"jinxed==2.1.0\" \\\n", - " \"joblib==1.5.3\" \\\n", + " \"joblib==1.6.0\" \\\n", " \"jsonpointer==3.1.1\" \\\n", " \"jsonschema==4.26.0\" \\\n", " \"jsonschema-specifications==2025.9.1\" \\\n", " \"keyring==25.7.0\" \\\n", " \"keyrings-alt==5.0.2\" \\\n", - " \"kiwisolver==1.5.0\" \\\n", + " \"kiwisolver==1.5.1\" \\\n", " \"matplotlib==3.10.0\" \\\n", " \"ml-dtypes==0.6.0\" \\\n", " \"more-itertools==10.8.0\" \\\n", @@ -96,13 +97,13 @@ " \"packaging==26.3\" \\\n", " \"pandas==2.2.3\" \\\n", " \"pillow==11.3.0\" \\\n", - " \"platformdirs==4.11.3\" \\\n", + " \"platformdirs==4.11.7\" \\\n", " \"plotly==5.24.1\" \\\n", " \"propcache==0.5.2\" \\\n", " \"pycparser==3.0\" \\\n", " \"pycryptodomex==3.23.0\" \\\n", - " \"pydantic==2.13.4\" \\\n", - " \"pydantic-core==2.46.4\" \\\n", + " \"pydantic==2.13.5\" \\\n", + " \"pydantic-core==2.46.5\" \\\n", " \"pydantic-settings==2.15.0\" \\\n", " \"pynwb==3.1.3\" \\\n", " \"pyout==0.8.1\" \\\n", @@ -129,7 +130,7 @@ " \"tzdata==2026.3\" \\\n", " \"uri-template==1.3.0\" \\\n", " \"urllib3==2.5.0\" \\\n", - " \"wcwidth==0.8.2\" \\\n", + " \"wcwidth==0.8.3\" \\\n", " \"webcolors==25.10.0\" \\\n", " \"yarl==1.24.5\" \\\n", " \"zarr==3.1.5\" \\\n", diff --git a/001172/HigleyLab/001172_demo.ipynb b/001172/HigleyLab/001172_demo.ipynb index b264f10..25c4bc4 100644 --- a/001172/HigleyLab/001172_demo.ipynb +++ b/001172/HigleyLab/001172_demo.ipynb @@ -47,10 +47,11 @@ " \"cffi==2.1.1\" \\\n", " \"charset-normalizer==3.4.9\" \\\n", " \"ci-info==0.4.0\" \\\n", - " \"click==8.4.2\" \\\n", + " \"click==8.5.0\" \\\n", " \"click-didyoumean==0.3.1\" \\\n", + " \"cloudpickle==3.1.2\" \\\n", " \"contourpy==1.3.3\" \\\n", - " \"cryptography==50.0.0\" \\\n", + " \"cryptography==50.0.1\" \\\n", " \"cycler==0.12.1\" \\\n", " \"dandi==0.77.0\" \\\n", " \"dandischema==0.14.0\" \\\n", @@ -60,16 +61,16 @@ " \"email-validator==2.3.0\" \\\n", " \"etelemetry==0.3.1\" \\\n", " \"fasteners==0.20\" \\\n", - " \"fonttools==4.63.0\" \\\n", + " \"fonttools==4.64.0\" \\\n", " \"fqdn==1.5.1\" \\\n", " \"frozenlist==1.8.0\" \\\n", " \"fscacher==0.4.4\" \\\n", - " \"fsspec==2025.3.0\" \\\n", + " \"fsspec==2025.12.0\" \\\n", " \"google-crc32c==1.8.0\" \\\n", " \"h5py==3.16.0\" \\\n", " \"hdmf==4.3.1\" \\\n", " \"humanize==4.16.0\" \\\n", - " \"idna==3.18\" \\\n", + " \"idna==3.19\" \\\n", " \"interleave==0.3.0\" \\\n", " \"isodate==0.7.2\" \\\n", " \"isoduration==20.11.0\" \\\n", @@ -78,13 +79,13 @@ " \"jaraco-functools==4.6.0\" \\\n", " \"jeepney==0.9.0\" \\\n", " \"jinxed==2.1.0\" \\\n", - " \"joblib==1.5.3\" \\\n", + " \"joblib==1.6.0\" \\\n", " \"jsonpointer==3.1.1\" \\\n", " \"jsonschema==4.26.0\" \\\n", " \"jsonschema-specifications==2025.9.1\" \\\n", " \"keyring==25.7.0\" \\\n", " \"keyrings-alt==5.0.2\" \\\n", - " \"kiwisolver==1.5.0\" \\\n", + " \"kiwisolver==1.5.1\" \\\n", " \"matplotlib==3.10.0\" \\\n", " \"ml-dtypes==0.6.0\" \\\n", " \"more-itertools==10.8.0\" \\\n", @@ -96,13 +97,13 @@ " \"packaging==26.3\" \\\n", " \"pandas==2.2.3\" \\\n", " \"pillow==11.3.0\" \\\n", - " \"platformdirs==4.11.3\" \\\n", + " \"platformdirs==4.11.7\" \\\n", " \"plotly==5.24.1\" \\\n", " \"propcache==0.5.2\" \\\n", " \"pycparser==3.0\" \\\n", " \"pycryptodomex==3.23.0\" \\\n", - " \"pydantic==2.13.4\" \\\n", - " \"pydantic-core==2.46.4\" \\\n", + " \"pydantic==2.13.5\" \\\n", + " \"pydantic-core==2.46.5\" \\\n", " \"pydantic-settings==2.15.0\" \\\n", " \"pynwb==3.1.3\" \\\n", " \"pyout==0.8.1\" \\\n", @@ -129,7 +130,7 @@ " \"tzdata==2026.3\" \\\n", " \"uri-template==1.3.0\" \\\n", " \"urllib3==2.5.0\" \\\n", - " \"wcwidth==0.8.2\" \\\n", + " \"wcwidth==0.8.3\" \\\n", " \"webcolors==25.10.0\" \\\n", " \"yarl==1.24.5\" \\\n", " \"zarr==3.1.5\" \\\n", diff --git a/001528/HnaskoLab/Lotfi_2025/001528_demo.ipynb b/001528/HnaskoLab/Lotfi_2025/001528_demo.ipynb index 21fec2a..2e4c1b3 100644 --- a/001528/HnaskoLab/Lotfi_2025/001528_demo.ipynb +++ b/001528/HnaskoLab/Lotfi_2025/001528_demo.ipynb @@ -47,10 +47,11 @@ " \"cffi==2.1.1\" \\\n", " \"charset-normalizer==3.4.9\" \\\n", " \"ci-info==0.4.0\" \\\n", - " \"click==8.4.2\" \\\n", + " \"click==8.5.0\" \\\n", " \"click-didyoumean==0.3.1\" \\\n", + " \"cloudpickle==3.1.2\" \\\n", " \"contourpy==1.3.3\" \\\n", - " \"cryptography==50.0.0\" \\\n", + " \"cryptography==50.0.1\" \\\n", " \"cycler==0.12.1\" \\\n", " \"dandi==0.77.0\" \\\n", " \"dandischema==0.14.0\" \\\n", @@ -60,16 +61,16 @@ " \"email-validator==2.3.0\" \\\n", " \"etelemetry==0.3.1\" \\\n", " \"fasteners==0.20\" \\\n", - " \"fonttools==4.63.0\" \\\n", + " \"fonttools==4.64.0\" \\\n", " \"fqdn==1.5.1\" \\\n", " \"frozenlist==1.8.0\" \\\n", " \"fscacher==0.4.4\" \\\n", - " \"fsspec==2025.3.0\" \\\n", + " \"fsspec==2025.12.0\" \\\n", " \"google-crc32c==1.8.0\" \\\n", " \"h5py==3.16.0\" \\\n", " \"hdmf==6.2.0\" \\\n", " \"humanize==4.16.0\" \\\n", - " \"idna==3.18\" \\\n", + " \"idna==3.19\" \\\n", " \"interleave==0.3.0\" \\\n", " \"isodate==0.7.2\" \\\n", " \"isoduration==20.11.0\" \\\n", @@ -78,13 +79,13 @@ " \"jaraco-functools==4.6.0\" \\\n", " \"jeepney==0.9.0\" \\\n", " \"jinxed==2.1.0\" \\\n", - " \"joblib==1.5.3\" \\\n", + " \"joblib==1.6.0\" \\\n", " \"jsonpointer==3.1.1\" \\\n", " \"jsonschema==4.26.0\" \\\n", " \"jsonschema-specifications==2025.9.1\" \\\n", " \"keyring==25.7.0\" \\\n", " \"keyrings-alt==5.0.2\" \\\n", - " \"kiwisolver==1.5.0\" \\\n", + " \"kiwisolver==1.5.1\" \\\n", " \"matplotlib==3.10.0\" \\\n", " \"ml-dtypes==0.6.0\" \\\n", " \"more-itertools==10.8.0\" \\\n", @@ -96,12 +97,12 @@ " \"packaging==26.3\" \\\n", " \"pandas==2.2.3\" \\\n", " \"pillow==11.3.0\" \\\n", - " \"platformdirs==4.11.3\" \\\n", + " \"platformdirs==4.11.7\" \\\n", " \"propcache==0.5.2\" \\\n", " \"pycparser==3.0\" \\\n", " \"pycryptodomex==3.23.0\" \\\n", - " \"pydantic==2.13.4\" \\\n", - " \"pydantic-core==2.46.4\" \\\n", + " \"pydantic==2.13.5\" \\\n", + " \"pydantic-core==2.46.5\" \\\n", " \"pydantic-settings==2.15.0\" \\\n", " \"pynwb==4.1.0\" \\\n", " \"pyout==0.8.1\" \\\n", @@ -128,7 +129,7 @@ " \"tzdata==2026.3\" \\\n", " \"uri-template==1.3.0\" \\\n", " \"urllib3==2.5.0\" \\\n", - " \"wcwidth==0.8.2\" \\\n", + " \"wcwidth==0.8.3\" \\\n", " \"webcolors==25.10.0\" \\\n", " \"yarl==1.24.5\" \\\n", " \"zarr==3.1.5\" \\\n", 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 2cdf896..d6c1db5 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 @@ -47,10 +47,11 @@ " \"cffi==2.1.1\" \\\n", " \"charset-normalizer==3.4.9\" \\\n", " \"ci-info==0.4.0\" \\\n", - " \"click==8.4.2\" \\\n", + " \"click==8.5.0\" \\\n", " \"click-didyoumean==0.3.1\" \\\n", + " \"cloudpickle==3.1.2\" \\\n", " \"contourpy==1.3.3\" \\\n", - " \"cryptography==50.0.0\" \\\n", + " \"cryptography==50.0.1\" \\\n", " \"cycler==0.12.1\" \\\n", " \"dandi==0.77.0\" \\\n", " \"dandischema==0.14.0\" \\\n", @@ -60,16 +61,16 @@ " \"email-validator==2.3.0\" \\\n", " \"etelemetry==0.3.1\" \\\n", " \"fasteners==0.20\" \\\n", - " \"fonttools==4.63.0\" \\\n", + " \"fonttools==4.64.0\" \\\n", " \"fqdn==1.5.1\" \\\n", " \"frozenlist==1.8.0\" \\\n", " \"fscacher==0.4.4\" \\\n", - " \"fsspec==2025.3.0\" \\\n", + " \"fsspec==2025.12.0\" \\\n", " \"google-crc32c==1.8.0\" \\\n", " \"h5py==3.16.0\" \\\n", " \"hdmf==4.3.1\" \\\n", " \"humanize==4.16.0\" \\\n", - " \"idna==3.18\" \\\n", + " \"idna==3.19\" \\\n", " \"interleave==0.3.0\" \\\n", " \"isodate==0.7.2\" \\\n", " \"isoduration==20.11.0\" \\\n", @@ -78,13 +79,13 @@ " \"jaraco-functools==4.6.0\" \\\n", " \"jeepney==0.9.0\" \\\n", " \"jinxed==2.1.0\" \\\n", - " \"joblib==1.5.3\" \\\n", + " \"joblib==1.6.0\" \\\n", " \"jsonpointer==3.1.1\" \\\n", " \"jsonschema==4.26.0\" \\\n", " \"jsonschema-specifications==2025.9.1\" \\\n", " \"keyring==25.7.0\" \\\n", " \"keyrings-alt==5.0.2\" \\\n", - " \"kiwisolver==1.5.0\" \\\n", + " \"kiwisolver==1.5.1\" \\\n", " \"matplotlib==3.10.0\" \\\n", " \"ml-dtypes==0.6.0\" \\\n", " \"more-itertools==10.8.0\" \\\n", @@ -96,12 +97,12 @@ " \"packaging==26.3\" \\\n", " \"pandas==2.2.3\" \\\n", " \"pillow==11.3.0\" \\\n", - " \"platformdirs==4.11.3\" \\\n", + " \"platformdirs==4.11.7\" \\\n", " \"propcache==0.5.2\" \\\n", " \"pycparser==3.0\" \\\n", " \"pycryptodomex==3.23.0\" \\\n", - " \"pydantic==2.13.4\" \\\n", - " \"pydantic-core==2.46.4\" \\\n", + " \"pydantic==2.13.5\" \\\n", + " \"pydantic-core==2.46.5\" \\\n", " \"pydantic-settings==2.15.0\" \\\n", " \"pynwb==3.1.3\" \\\n", " \"pyout==0.8.1\" \\\n", @@ -130,7 +131,7 @@ " \"tzdata==2026.3\" \\\n", " \"uri-template==1.3.0\" \\\n", " \"urllib3==2.5.0\" \\\n", - " \"wcwidth==0.8.2\" \\\n", + " \"wcwidth==0.8.3\" \\\n", " \"webcolors==25.10.0\" \\\n", " \"yarl==1.24.5\" \\\n", " \"zarr==3.1.5\" \\\n", 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 b0884a7..d9a5caa 100644 --- a/001538/catalyst_neuro/zhai_2025/figure_2GH_oepsc_analysis.ipynb +++ b/001538/catalyst_neuro/zhai_2025/figure_2GH_oepsc_analysis.ipynb @@ -47,10 +47,11 @@ " \"cffi==2.1.1\" \\\n", " \"charset-normalizer==3.4.9\" \\\n", " \"ci-info==0.4.0\" \\\n", - " \"click==8.4.2\" \\\n", + " \"click==8.5.0\" \\\n", " \"click-didyoumean==0.3.1\" \\\n", + " \"cloudpickle==3.1.2\" \\\n", " \"contourpy==1.3.3\" \\\n", - " \"cryptography==50.0.0\" \\\n", + " \"cryptography==50.0.1\" \\\n", " \"cycler==0.12.1\" \\\n", " \"dandi==0.77.0\" \\\n", " \"dandischema==0.14.0\" \\\n", @@ -60,16 +61,16 @@ " \"email-validator==2.3.0\" \\\n", " \"etelemetry==0.3.1\" \\\n", " \"fasteners==0.20\" \\\n", - " \"fonttools==4.63.0\" \\\n", + " \"fonttools==4.64.0\" \\\n", " \"fqdn==1.5.1\" \\\n", " \"frozenlist==1.8.0\" \\\n", " \"fscacher==0.4.4\" \\\n", - " \"fsspec==2025.3.0\" \\\n", + " \"fsspec==2025.12.0\" \\\n", " \"google-crc32c==1.8.0\" \\\n", " \"h5py==3.16.0\" \\\n", " \"hdmf==4.3.1\" \\\n", " \"humanize==4.16.0\" \\\n", - " \"idna==3.18\" \\\n", + " \"idna==3.19\" \\\n", " \"interleave==0.3.0\" \\\n", " \"isodate==0.7.2\" \\\n", " \"isoduration==20.11.0\" \\\n", @@ -78,13 +79,13 @@ " \"jaraco-functools==4.6.0\" \\\n", " \"jeepney==0.9.0\" \\\n", " \"jinxed==2.1.0\" \\\n", - " \"joblib==1.5.3\" \\\n", + " \"joblib==1.6.0\" \\\n", " \"jsonpointer==3.1.1\" \\\n", " \"jsonschema==4.26.0\" \\\n", " \"jsonschema-specifications==2025.9.1\" \\\n", " \"keyring==25.7.0\" \\\n", " \"keyrings-alt==5.0.2\" \\\n", - " \"kiwisolver==1.5.0\" \\\n", + " \"kiwisolver==1.5.1\" \\\n", " \"matplotlib==3.10.0\" \\\n", " \"ml-dtypes==0.6.0\" \\\n", " \"more-itertools==10.8.0\" \\\n", @@ -96,12 +97,12 @@ " \"packaging==26.3\" \\\n", " \"pandas==2.2.3\" \\\n", " \"pillow==11.3.0\" \\\n", - " \"platformdirs==4.11.3\" \\\n", + " \"platformdirs==4.11.7\" \\\n", " \"propcache==0.5.2\" \\\n", " \"pycparser==3.0\" \\\n", " \"pycryptodomex==3.23.0\" \\\n", - " \"pydantic==2.13.4\" \\\n", - " \"pydantic-core==2.46.4\" \\\n", + " \"pydantic==2.13.5\" \\\n", + " \"pydantic-core==2.46.5\" \\\n", " \"pydantic-settings==2.15.0\" \\\n", " \"pynwb==3.1.3\" \\\n", " \"pyout==0.8.1\" \\\n", @@ -130,7 +131,7 @@ " \"tzdata==2026.3\" \\\n", " \"uri-template==1.3.0\" \\\n", " \"urllib3==2.5.0\" \\\n", - " \"wcwidth==0.8.2\" \\\n", + " \"wcwidth==0.8.3\" \\\n", " \"webcolors==25.10.0\" \\\n", " \"yarl==1.24.5\" \\\n", " \"zarr==3.1.5\" \\\n", 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 f0fe376..2fdc1e8 100644 --- a/001538/catalyst_neuro/zhai_2025/figure_5F_acetylcholine_biosensor.ipynb +++ b/001538/catalyst_neuro/zhai_2025/figure_5F_acetylcholine_biosensor.ipynb @@ -47,10 +47,11 @@ " \"cffi==2.1.1\" \\\n", " \"charset-normalizer==3.4.9\" \\\n", " \"ci-info==0.4.0\" \\\n", - " \"click==8.4.2\" \\\n", + " \"click==8.5.0\" \\\n", " \"click-didyoumean==0.3.1\" \\\n", + " \"cloudpickle==3.1.2\" \\\n", " \"contourpy==1.3.3\" \\\n", - " \"cryptography==50.0.0\" \\\n", + " \"cryptography==50.0.1\" \\\n", " \"cycler==0.12.1\" \\\n", " \"dandi==0.77.0\" \\\n", " \"dandischema==0.14.0\" \\\n", @@ -60,16 +61,16 @@ " \"email-validator==2.3.0\" \\\n", " \"etelemetry==0.3.1\" \\\n", " \"fasteners==0.20\" \\\n", - " \"fonttools==4.63.0\" \\\n", + " \"fonttools==4.64.0\" \\\n", " \"fqdn==1.5.1\" \\\n", " \"frozenlist==1.8.0\" \\\n", " \"fscacher==0.4.4\" \\\n", - " \"fsspec==2025.3.0\" \\\n", + " \"fsspec==2025.12.0\" \\\n", " \"google-crc32c==1.8.0\" \\\n", " \"h5py==3.16.0\" \\\n", " \"hdmf==4.3.1\" \\\n", " \"humanize==4.16.0\" \\\n", - " \"idna==3.18\" \\\n", + " \"idna==3.19\" \\\n", " \"interleave==0.3.0\" \\\n", " \"isodate==0.7.2\" \\\n", " \"isoduration==20.11.0\" \\\n", @@ -78,13 +79,13 @@ " \"jaraco-functools==4.6.0\" \\\n", " \"jeepney==0.9.0\" \\\n", " \"jinxed==2.1.0\" \\\n", - " \"joblib==1.5.3\" \\\n", + " \"joblib==1.6.0\" \\\n", " \"jsonpointer==3.1.1\" \\\n", " \"jsonschema==4.26.0\" \\\n", " \"jsonschema-specifications==2025.9.1\" \\\n", " \"keyring==25.7.0\" \\\n", " \"keyrings-alt==5.0.2\" \\\n", - " \"kiwisolver==1.5.0\" \\\n", + " \"kiwisolver==1.5.1\" \\\n", " \"matplotlib==3.10.0\" \\\n", " \"ml-dtypes==0.6.0\" \\\n", " \"more-itertools==10.8.0\" \\\n", @@ -96,12 +97,12 @@ " \"packaging==26.3\" \\\n", " \"pandas==2.2.3\" \\\n", " \"pillow==11.3.0\" \\\n", - " \"platformdirs==4.11.3\" \\\n", + " \"platformdirs==4.11.7\" \\\n", " \"propcache==0.5.2\" \\\n", " \"pycparser==3.0\" \\\n", " \"pycryptodomex==3.23.0\" \\\n", - " \"pydantic==2.13.4\" \\\n", - " \"pydantic-core==2.46.4\" \\\n", + " \"pydantic==2.13.5\" \\\n", + " \"pydantic-core==2.46.5\" \\\n", " \"pydantic-settings==2.15.0\" \\\n", " \"pynwb==3.1.3\" \\\n", " \"pyout==0.8.1\" \\\n", @@ -130,7 +131,7 @@ " \"tzdata==2026.3\" \\\n", " \"uri-template==1.3.0\" \\\n", " \"urllib3==2.5.0\" \\\n", - " \"wcwidth==0.8.2\" \\\n", + " \"wcwidth==0.8.3\" \\\n", " \"webcolors==25.10.0\" \\\n", " \"yarl==1.24.5\" \\\n", " \"zarr==3.1.5\" \\\n", 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 320c38f..7437fae 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 @@ -47,10 +47,11 @@ " \"cffi==2.1.1\" \\\n", " \"charset-normalizer==3.4.9\" \\\n", " \"ci-info==0.4.0\" \\\n", - " \"click==8.4.2\" \\\n", + " \"click==8.5.0\" \\\n", " \"click-didyoumean==0.3.1\" \\\n", + " \"cloudpickle==3.1.2\" \\\n", " \"contourpy==1.3.3\" \\\n", - " \"cryptography==50.0.0\" \\\n", + " \"cryptography==50.0.1\" \\\n", " \"cycler==0.12.1\" \\\n", " \"dandi==0.77.0\" \\\n", " \"dandischema==0.14.0\" \\\n", @@ -60,16 +61,16 @@ " \"email-validator==2.3.0\" \\\n", " \"etelemetry==0.3.1\" \\\n", " \"fasteners==0.20\" \\\n", - " \"fonttools==4.63.0\" \\\n", + " \"fonttools==4.64.0\" \\\n", " \"fqdn==1.5.1\" \\\n", " \"frozenlist==1.8.0\" \\\n", " \"fscacher==0.4.4\" \\\n", - " \"fsspec==2025.3.0\" \\\n", + " \"fsspec==2025.12.0\" \\\n", " \"google-crc32c==1.8.0\" \\\n", " \"h5py==3.16.0\" \\\n", " \"hdmf==4.3.1\" \\\n", " \"humanize==4.16.0\" \\\n", - " \"idna==3.18\" \\\n", + " \"idna==3.19\" \\\n", " \"interleave==0.3.0\" \\\n", " \"isodate==0.7.2\" \\\n", " \"isoduration==20.11.0\" \\\n", @@ -78,13 +79,13 @@ " \"jaraco-functools==4.6.0\" \\\n", " \"jeepney==0.9.0\" \\\n", " \"jinxed==2.1.0\" \\\n", - " \"joblib==1.5.3\" \\\n", + " \"joblib==1.6.0\" \\\n", " \"jsonpointer==3.1.1\" \\\n", " \"jsonschema==4.26.0\" \\\n", " \"jsonschema-specifications==2025.9.1\" \\\n", " \"keyring==25.7.0\" \\\n", " \"keyrings-alt==5.0.2\" \\\n", - " \"kiwisolver==1.5.0\" \\\n", + " \"kiwisolver==1.5.1\" \\\n", " \"matplotlib==3.10.0\" \\\n", " \"ml-dtypes==0.6.0\" \\\n", " \"more-itertools==10.8.0\" \\\n", @@ -96,12 +97,12 @@ " \"packaging==26.3\" \\\n", " \"pandas==2.2.3\" \\\n", " \"pillow==11.3.0\" \\\n", - " \"platformdirs==4.11.3\" \\\n", + " \"platformdirs==4.11.7\" \\\n", " \"propcache==0.5.2\" \\\n", " \"pycparser==3.0\" \\\n", " \"pycryptodomex==3.23.0\" \\\n", - " \"pydantic==2.13.4\" \\\n", - " \"pydantic-core==2.46.4\" \\\n", + " \"pydantic==2.13.5\" \\\n", + " \"pydantic-core==2.46.5\" \\\n", " \"pydantic-settings==2.15.0\" \\\n", " \"pynwb==3.1.3\" \\\n", " \"pyout==0.8.1\" \\\n", @@ -130,7 +131,7 @@ " \"tzdata==2026.3\" \\\n", " \"uri-template==1.3.0\" \\\n", " \"urllib3==2.5.0\" \\\n", - " \"wcwidth==0.8.2\" \\\n", + " \"wcwidth==0.8.3\" \\\n", " \"webcolors==25.10.0\" \\\n", " \"yarl==1.24.5\" \\\n", " \"zarr==3.1.5\" \\\n", diff --git a/001550/PaganLab/01_behavior_demo.ipynb b/001550/PaganLab/01_behavior_demo.ipynb index 61cc8c5..7828c8b 100644 --- a/001550/PaganLab/01_behavior_demo.ipynb +++ b/001550/PaganLab/01_behavior_demo.ipynb @@ -47,10 +47,11 @@ " \"cffi==2.1.1\" \\\n", " \"charset-normalizer==3.4.9\" \\\n", " \"ci-info==0.4.0\" \\\n", - " \"click==8.4.2\" \\\n", + " \"click==8.5.0\" \\\n", " \"click-didyoumean==0.3.1\" \\\n", + " \"cloudpickle==3.1.2\" \\\n", " \"contourpy==1.3.3\" \\\n", - " \"cryptography==50.0.0\" \\\n", + " \"cryptography==50.0.1\" \\\n", " \"cycler==0.12.1\" \\\n", " \"dandi==0.77.0\" \\\n", " \"dandischema==0.14.0\" \\\n", @@ -60,16 +61,16 @@ " \"email-validator==2.3.0\" \\\n", " \"etelemetry==0.3.1\" \\\n", " \"fasteners==0.20\" \\\n", - " \"fonttools==4.63.0\" \\\n", + " \"fonttools==4.64.0\" \\\n", " \"fqdn==1.5.1\" \\\n", " \"frozenlist==1.8.0\" \\\n", " \"fscacher==0.4.4\" \\\n", - " \"fsspec==2025.3.0\" \\\n", + " \"fsspec==2025.12.0\" \\\n", " \"google-crc32c==1.8.0\" \\\n", " \"h5py==3.16.0\" \\\n", " \"hdmf==4.3.1\" \\\n", " \"humanize==4.16.0\" \\\n", - " \"idna==3.18\" \\\n", + " \"idna==3.19\" \\\n", " \"interleave==0.3.0\" \\\n", " \"isodate==0.7.2\" \\\n", " \"isoduration==20.11.0\" \\\n", @@ -78,13 +79,13 @@ " \"jaraco-functools==4.6.0\" \\\n", " \"jeepney==0.9.0\" \\\n", " \"jinxed==2.1.0\" \\\n", - " \"joblib==1.5.3\" \\\n", + " \"joblib==1.6.0\" \\\n", " \"jsonpointer==3.1.1\" \\\n", " \"jsonschema==4.26.0\" \\\n", " \"jsonschema-specifications==2025.9.1\" \\\n", " \"keyring==25.7.0\" \\\n", " \"keyrings-alt==5.0.2\" \\\n", - " \"kiwisolver==1.5.0\" \\\n", + " \"kiwisolver==1.5.1\" \\\n", " \"matplotlib==3.10.0\" \\\n", " \"ml-dtypes==0.6.0\" \\\n", " \"more-itertools==10.8.0\" \\\n", @@ -100,12 +101,12 @@ " \"packaging==26.3\" \\\n", " \"pandas==2.2.3\" \\\n", " \"pillow==11.3.0\" \\\n", - " \"platformdirs==4.11.3\" \\\n", + " \"platformdirs==4.11.7\" \\\n", " \"propcache==0.5.2\" \\\n", " \"pycparser==3.0\" \\\n", " \"pycryptodomex==3.23.0\" \\\n", - " \"pydantic==2.13.4\" \\\n", - " \"pydantic-core==2.46.4\" \\\n", + " \"pydantic==2.13.5\" \\\n", + " \"pydantic-core==2.46.5\" \\\n", " \"pydantic-settings==2.15.0\" \\\n", " \"pynwb==3.1.3\" \\\n", " \"pyout==0.8.1\" \\\n", @@ -133,7 +134,7 @@ " \"tzdata==2026.3\" \\\n", " \"uri-template==1.3.0\" \\\n", " \"urllib3==2.5.0\" \\\n", - " \"wcwidth==0.8.2\" \\\n", + " \"wcwidth==0.8.3\" \\\n", " \"webcolors==25.10.0\" \\\n", " \"yarl==1.24.5\" \\\n", " \"zarr==3.1.5\" \\\n", diff --git a/001550/PaganLab/02_optogenetics_demo.ipynb b/001550/PaganLab/02_optogenetics_demo.ipynb index f735db1..a168e1e 100644 --- a/001550/PaganLab/02_optogenetics_demo.ipynb +++ b/001550/PaganLab/02_optogenetics_demo.ipynb @@ -47,10 +47,11 @@ " \"cffi==2.1.1\" \\\n", " \"charset-normalizer==3.4.9\" \\\n", " \"ci-info==0.4.0\" \\\n", - " \"click==8.4.2\" \\\n", + " \"click==8.5.0\" \\\n", " \"click-didyoumean==0.3.1\" \\\n", + " \"cloudpickle==3.1.2\" \\\n", " \"contourpy==1.3.3\" \\\n", - " \"cryptography==50.0.0\" \\\n", + " \"cryptography==50.0.1\" \\\n", " \"cycler==0.12.1\" \\\n", " \"dandi==0.77.0\" \\\n", " \"dandischema==0.14.0\" \\\n", @@ -60,16 +61,16 @@ " \"email-validator==2.3.0\" \\\n", " \"etelemetry==0.3.1\" \\\n", " \"fasteners==0.20\" \\\n", - " \"fonttools==4.63.0\" \\\n", + " \"fonttools==4.64.0\" \\\n", " \"fqdn==1.5.1\" \\\n", " \"frozenlist==1.8.0\" \\\n", " \"fscacher==0.4.4\" \\\n", - " \"fsspec==2025.3.0\" \\\n", + " \"fsspec==2025.12.0\" \\\n", " \"google-crc32c==1.8.0\" \\\n", " \"h5py==3.16.0\" \\\n", " \"hdmf==4.3.1\" \\\n", " \"humanize==4.16.0\" \\\n", - " \"idna==3.18\" \\\n", + " \"idna==3.19\" \\\n", " \"interleave==0.3.0\" \\\n", " \"isodate==0.7.2\" \\\n", " \"isoduration==20.11.0\" \\\n", @@ -78,13 +79,13 @@ " \"jaraco-functools==4.6.0\" \\\n", " \"jeepney==0.9.0\" \\\n", " \"jinxed==2.1.0\" \\\n", - " \"joblib==1.5.3\" \\\n", + " \"joblib==1.6.0\" \\\n", " \"jsonpointer==3.1.1\" \\\n", " \"jsonschema==4.26.0\" \\\n", " \"jsonschema-specifications==2025.9.1\" \\\n", " \"keyring==25.7.0\" \\\n", " \"keyrings-alt==5.0.2\" \\\n", - " \"kiwisolver==1.5.0\" \\\n", + " \"kiwisolver==1.5.1\" \\\n", " \"matplotlib==3.10.0\" \\\n", " \"ml-dtypes==0.6.0\" \\\n", " \"more-itertools==10.8.0\" \\\n", @@ -100,12 +101,12 @@ " \"packaging==26.3\" \\\n", " \"pandas==2.2.3\" \\\n", " \"pillow==11.3.0\" \\\n", - " \"platformdirs==4.11.3\" \\\n", + " \"platformdirs==4.11.7\" \\\n", " \"propcache==0.5.2\" \\\n", " \"pycparser==3.0\" \\\n", " \"pycryptodomex==3.23.0\" \\\n", - " \"pydantic==2.13.4\" \\\n", - " \"pydantic-core==2.46.4\" \\\n", + " \"pydantic==2.13.5\" \\\n", + " \"pydantic-core==2.46.5\" \\\n", " \"pydantic-settings==2.15.0\" \\\n", " \"pynwb==3.1.3\" \\\n", " \"pyout==0.8.1\" \\\n", @@ -133,7 +134,7 @@ " \"tzdata==2026.3\" \\\n", " \"uri-template==1.3.0\" \\\n", " \"urllib3==2.5.0\" \\\n", - " \"wcwidth==0.8.2\" \\\n", + " \"wcwidth==0.8.3\" \\\n", " \"webcolors==25.10.0\" \\\n", " \"yarl==1.24.5\" \\\n", " \"zarr==3.1.5\" \\\n", diff --git a/001636/TurnerLab/motor_cortex/antidromic_detection_tutorial.ipynb b/001636/TurnerLab/motor_cortex/antidromic_detection_tutorial.ipynb index ae7d489..8dcf476 100644 --- a/001636/TurnerLab/motor_cortex/antidromic_detection_tutorial.ipynb +++ b/001636/TurnerLab/motor_cortex/antidromic_detection_tutorial.ipynb @@ -48,10 +48,11 @@ " \"cffi==2.1.1\" \\\n", " \"charset-normalizer==3.4.9\" \\\n", " \"ci-info==0.4.0\" \\\n", - " \"click==8.4.2\" \\\n", + " \"click==8.5.0\" \\\n", " \"click-didyoumean==0.3.1\" \\\n", + " \"cloudpickle==3.1.2\" \\\n", " \"contourpy==1.3.3\" \\\n", - " \"cryptography==50.0.0\" \\\n", + " \"cryptography==50.0.1\" \\\n", " \"cycler==0.12.1\" \\\n", " \"dandi==0.77.0\" \\\n", " \"dandischema==0.14.0\" \\\n", @@ -62,34 +63,34 @@ " \"equinox==0.13.8\" \\\n", " \"etelemetry==0.3.1\" \\\n", " \"fasteners==0.20\" \\\n", - " \"fonttools==4.63.0\" \\\n", + " \"fonttools==4.64.0\" \\\n", " \"fqdn==1.5.1\" \\\n", " \"frozenlist==1.8.0\" \\\n", " \"fscacher==0.4.4\" \\\n", - " \"fsspec==2025.3.0\" \\\n", + " \"fsspec==2025.12.0\" \\\n", " \"google-crc32c==1.8.0\" \\\n", " \"h5py==3.16.0\" \\\n", " \"hdmf==4.3.1\" \\\n", " \"humanize==4.16.0\" \\\n", - " \"idna==3.18\" \\\n", + " \"idna==3.19\" \\\n", " \"interleave==0.3.0\" \\\n", " \"isodate==0.7.2\" \\\n", " \"isoduration==20.11.0\" \\\n", " \"jaraco-classes==3.4.0\" \\\n", " \"jaraco-context==6.1.2\" \\\n", " \"jaraco-functools==4.6.0\" \\\n", - " \"jax==0.7.2\" \\\n", - " \"jaxlib==0.7.2\" \\\n", + " \"jax==0.11.1\" \\\n", + " \"jaxlib==0.11.1\" \\\n", " \"jaxtyping==0.3.11\" \\\n", " \"jeepney==0.9.0\" \\\n", " \"jinxed==2.1.0\" \\\n", - " \"joblib==1.5.3\" \\\n", + " \"joblib==1.6.0\" \\\n", " \"jsonpointer==3.1.1\" \\\n", " \"jsonschema==4.26.0\" \\\n", " \"jsonschema-specifications==2025.9.1\" \\\n", " \"keyring==25.7.0\" \\\n", " \"keyrings-alt==5.0.2\" \\\n", - " \"kiwisolver==1.5.0\" \\\n", + " \"kiwisolver==1.5.1\" \\\n", " \"lineax==0.1.0\" \\\n", " \"llvmlite==0.44.0\" \\\n", " \"markdown-it-py==4.2.0\" \\\n", @@ -110,12 +111,12 @@ " \"packaging==26.3\" \\\n", " \"pandas==2.2.3\" \\\n", " \"pillow==11.3.0\" \\\n", - " \"platformdirs==4.11.3\" \\\n", + " \"platformdirs==4.11.7\" \\\n", " \"propcache==0.5.2\" \\\n", " \"pycparser==3.0\" \\\n", " \"pycryptodomex==3.23.0\" \\\n", - " \"pydantic==2.13.4\" \\\n", - " \"pydantic-core==2.46.4\" \\\n", + " \"pydantic==2.13.5\" \\\n", + " \"pydantic-core==2.46.5\" \\\n", " \"pydantic-settings==2.15.0\" \\\n", " \"pygments==2.21.0\" \\\n", " \"pynapple==0.10.3\" \\\n", @@ -150,7 +151,7 @@ " \"uri-template==1.3.0\" \\\n", " \"urllib3==2.5.0\" \\\n", " \"wadler-lindig==0.1.7\" \\\n", - " \"wcwidth==0.8.2\" \\\n", + " \"wcwidth==0.8.3\" \\\n", " \"webcolors==25.10.0\" \\\n", " \"xarray==2025.12.0\" \\\n", " \"yarl==1.24.5\" \\\n", diff --git a/001636/TurnerLab/motor_cortex/turner_m1_glm.ipynb b/001636/TurnerLab/motor_cortex/turner_m1_glm.ipynb index 09463d7..1c139fd 100644 --- a/001636/TurnerLab/motor_cortex/turner_m1_glm.ipynb +++ b/001636/TurnerLab/motor_cortex/turner_m1_glm.ipynb @@ -48,10 +48,11 @@ " \"cffi==2.1.1\" \\\n", " \"charset-normalizer==3.4.9\" \\\n", " \"ci-info==0.4.0\" \\\n", - " \"click==8.4.2\" \\\n", + " \"click==8.5.0\" \\\n", " \"click-didyoumean==0.3.1\" \\\n", + " \"cloudpickle==3.1.2\" \\\n", " \"contourpy==1.3.3\" \\\n", - " \"cryptography==50.0.0\" \\\n", + " \"cryptography==50.0.1\" \\\n", " \"cycler==0.12.1\" \\\n", " \"dandi==0.77.0\" \\\n", " \"dandischema==0.14.0\" \\\n", @@ -62,34 +63,34 @@ " \"equinox==0.13.8\" \\\n", " \"etelemetry==0.3.1\" \\\n", " \"fasteners==0.20\" \\\n", - " \"fonttools==4.63.0\" \\\n", + " \"fonttools==4.64.0\" \\\n", " \"fqdn==1.5.1\" \\\n", " \"frozenlist==1.8.0\" \\\n", " \"fscacher==0.4.4\" \\\n", - " \"fsspec==2025.3.0\" \\\n", + " \"fsspec==2025.12.0\" \\\n", " \"google-crc32c==1.8.0\" \\\n", " \"h5py==3.16.0\" \\\n", " \"hdmf==4.3.1\" \\\n", " \"humanize==4.16.0\" \\\n", - " \"idna==3.18\" \\\n", + " \"idna==3.19\" \\\n", " \"interleave==0.3.0\" \\\n", " \"isodate==0.7.2\" \\\n", " \"isoduration==20.11.0\" \\\n", " \"jaraco-classes==3.4.0\" \\\n", " \"jaraco-context==6.1.2\" \\\n", " \"jaraco-functools==4.6.0\" \\\n", - " \"jax==0.7.2\" \\\n", - " \"jaxlib==0.7.2\" \\\n", + " \"jax==0.11.1\" \\\n", + " \"jaxlib==0.11.1\" \\\n", " \"jaxtyping==0.3.11\" \\\n", " \"jeepney==0.9.0\" \\\n", " \"jinxed==2.1.0\" \\\n", - " \"joblib==1.5.3\" \\\n", + " \"joblib==1.6.0\" \\\n", " \"jsonpointer==3.1.1\" \\\n", " \"jsonschema==4.26.0\" \\\n", " \"jsonschema-specifications==2025.9.1\" \\\n", " \"keyring==25.7.0\" \\\n", " \"keyrings-alt==5.0.2\" \\\n", - " \"kiwisolver==1.5.0\" \\\n", + " \"kiwisolver==1.5.1\" \\\n", " \"lineax==0.1.0\" \\\n", " \"llvmlite==0.44.0\" \\\n", " \"markdown-it-py==4.2.0\" \\\n", @@ -110,12 +111,12 @@ " \"packaging==26.3\" \\\n", " \"pandas==2.2.3\" \\\n", " \"pillow==11.3.0\" \\\n", - " \"platformdirs==4.11.3\" \\\n", + " \"platformdirs==4.11.7\" \\\n", " \"propcache==0.5.2\" \\\n", " \"pycparser==3.0\" \\\n", " \"pycryptodomex==3.23.0\" \\\n", - " \"pydantic==2.13.4\" \\\n", - " \"pydantic-core==2.46.4\" \\\n", + " \"pydantic==2.13.5\" \\\n", + " \"pydantic-core==2.46.5\" \\\n", " \"pydantic-settings==2.15.0\" \\\n", " \"pygments==2.21.0\" \\\n", " \"pynapple==0.10.3\" \\\n", @@ -150,7 +151,7 @@ " \"uri-template==1.3.0\" \\\n", " \"urllib3==2.5.0\" \\\n", " \"wadler-lindig==0.1.7\" \\\n", - " \"wcwidth==0.8.2\" \\\n", + " \"wcwidth==0.8.3\" \\\n", " \"webcolors==25.10.0\" \\\n", " \"xarray==2025.12.0\" \\\n", " \"yarl==1.24.5\" \\\n", diff --git a/001636/TurnerLab/motor_cortex/turner_m1_peth.ipynb b/001636/TurnerLab/motor_cortex/turner_m1_peth.ipynb index 84dc1b1..a99d898 100644 --- a/001636/TurnerLab/motor_cortex/turner_m1_peth.ipynb +++ b/001636/TurnerLab/motor_cortex/turner_m1_peth.ipynb @@ -48,10 +48,11 @@ " \"cffi==2.1.1\" \\\n", " \"charset-normalizer==3.4.9\" \\\n", " \"ci-info==0.4.0\" \\\n", - " \"click==8.4.2\" \\\n", + " \"click==8.5.0\" \\\n", " \"click-didyoumean==0.3.1\" \\\n", + " \"cloudpickle==3.1.2\" \\\n", " \"contourpy==1.3.3\" \\\n", - " \"cryptography==50.0.0\" \\\n", + " \"cryptography==50.0.1\" \\\n", " \"cycler==0.12.1\" \\\n", " \"dandi==0.77.0\" \\\n", " \"dandischema==0.14.0\" \\\n", @@ -62,34 +63,34 @@ " \"equinox==0.13.8\" \\\n", " \"etelemetry==0.3.1\" \\\n", " \"fasteners==0.20\" \\\n", - " \"fonttools==4.63.0\" \\\n", + " \"fonttools==4.64.0\" \\\n", " \"fqdn==1.5.1\" \\\n", " \"frozenlist==1.8.0\" \\\n", " \"fscacher==0.4.4\" \\\n", - " \"fsspec==2025.3.0\" \\\n", + " \"fsspec==2025.12.0\" \\\n", " \"google-crc32c==1.8.0\" \\\n", " \"h5py==3.16.0\" \\\n", " \"hdmf==4.3.1\" \\\n", " \"humanize==4.16.0\" \\\n", - " \"idna==3.18\" \\\n", + " \"idna==3.19\" \\\n", " \"interleave==0.3.0\" \\\n", " \"isodate==0.7.2\" \\\n", " \"isoduration==20.11.0\" \\\n", " \"jaraco-classes==3.4.0\" \\\n", " \"jaraco-context==6.1.2\" \\\n", " \"jaraco-functools==4.6.0\" \\\n", - " \"jax==0.7.2\" \\\n", - " \"jaxlib==0.7.2\" \\\n", + " \"jax==0.11.1\" \\\n", + " \"jaxlib==0.11.1\" \\\n", " \"jaxtyping==0.3.11\" \\\n", " \"jeepney==0.9.0\" \\\n", " \"jinxed==2.1.0\" \\\n", - " \"joblib==1.5.3\" \\\n", + " \"joblib==1.6.0\" \\\n", " \"jsonpointer==3.1.1\" \\\n", " \"jsonschema==4.26.0\" \\\n", " \"jsonschema-specifications==2025.9.1\" \\\n", " \"keyring==25.7.0\" \\\n", " \"keyrings-alt==5.0.2\" \\\n", - " \"kiwisolver==1.5.0\" \\\n", + " \"kiwisolver==1.5.1\" \\\n", " \"lineax==0.1.0\" \\\n", " \"llvmlite==0.44.0\" \\\n", " \"markdown-it-py==4.2.0\" \\\n", @@ -110,12 +111,12 @@ " \"packaging==26.3\" \\\n", " \"pandas==2.2.3\" \\\n", " \"pillow==11.3.0\" \\\n", - " \"platformdirs==4.11.3\" \\\n", + " \"platformdirs==4.11.7\" \\\n", " \"propcache==0.5.2\" \\\n", " \"pycparser==3.0\" \\\n", " \"pycryptodomex==3.23.0\" \\\n", - " \"pydantic==2.13.4\" \\\n", - " \"pydantic-core==2.46.4\" \\\n", + " \"pydantic==2.13.5\" \\\n", + " \"pydantic-core==2.46.5\" \\\n", " \"pydantic-settings==2.15.0\" \\\n", " \"pygments==2.21.0\" \\\n", " \"pynapple==0.10.3\" \\\n", @@ -150,7 +151,7 @@ " \"uri-template==1.3.0\" \\\n", " \"urllib3==2.5.0\" \\\n", " \"wadler-lindig==0.1.7\" \\\n", - " \"wcwidth==0.8.2\" \\\n", + " \"wcwidth==0.8.3\" \\\n", " \"webcolors==25.10.0\" \\\n", " \"xarray==2025.12.0\" \\\n", " \"yarl==1.24.5\" \\\n", diff --git a/001636/TurnerLab/motor_cortex/turner_m1_usage.ipynb b/001636/TurnerLab/motor_cortex/turner_m1_usage.ipynb index ee5e0ef..aa3218e 100644 --- a/001636/TurnerLab/motor_cortex/turner_m1_usage.ipynb +++ b/001636/TurnerLab/motor_cortex/turner_m1_usage.ipynb @@ -48,10 +48,11 @@ " \"cffi==2.1.1\" \\\n", " \"charset-normalizer==3.4.9\" \\\n", " \"ci-info==0.4.0\" \\\n", - " \"click==8.4.2\" \\\n", + " \"click==8.5.0\" \\\n", " \"click-didyoumean==0.3.1\" \\\n", + " \"cloudpickle==3.1.2\" \\\n", " \"contourpy==1.3.3\" \\\n", - " \"cryptography==50.0.0\" \\\n", + " \"cryptography==50.0.1\" \\\n", " \"cycler==0.12.1\" \\\n", " \"dandi==0.77.0\" \\\n", " \"dandischema==0.14.0\" \\\n", @@ -62,34 +63,34 @@ " \"equinox==0.13.8\" \\\n", " \"etelemetry==0.3.1\" \\\n", " \"fasteners==0.20\" \\\n", - " \"fonttools==4.63.0\" \\\n", + " \"fonttools==4.64.0\" \\\n", " \"fqdn==1.5.1\" \\\n", " \"frozenlist==1.8.0\" \\\n", " \"fscacher==0.4.4\" \\\n", - " \"fsspec==2025.3.0\" \\\n", + " \"fsspec==2025.12.0\" \\\n", " \"google-crc32c==1.8.0\" \\\n", " \"h5py==3.16.0\" \\\n", " \"hdmf==4.3.1\" \\\n", " \"humanize==4.16.0\" \\\n", - " \"idna==3.18\" \\\n", + " \"idna==3.19\" \\\n", " \"interleave==0.3.0\" \\\n", " \"isodate==0.7.2\" \\\n", " \"isoduration==20.11.0\" \\\n", " \"jaraco-classes==3.4.0\" \\\n", " \"jaraco-context==6.1.2\" \\\n", " \"jaraco-functools==4.6.0\" \\\n", - " \"jax==0.7.2\" \\\n", - " \"jaxlib==0.7.2\" \\\n", + " \"jax==0.11.1\" \\\n", + " \"jaxlib==0.11.1\" \\\n", " \"jaxtyping==0.3.11\" \\\n", " \"jeepney==0.9.0\" \\\n", " \"jinxed==2.1.0\" \\\n", - " \"joblib==1.5.3\" \\\n", + " \"joblib==1.6.0\" \\\n", " \"jsonpointer==3.1.1\" \\\n", " \"jsonschema==4.26.0\" \\\n", " \"jsonschema-specifications==2025.9.1\" \\\n", " \"keyring==25.7.0\" \\\n", " \"keyrings-alt==5.0.2\" \\\n", - " \"kiwisolver==1.5.0\" \\\n", + " \"kiwisolver==1.5.1\" \\\n", " \"lineax==0.1.0\" \\\n", " \"llvmlite==0.44.0\" \\\n", " \"markdown-it-py==4.2.0\" \\\n", @@ -110,12 +111,12 @@ " \"packaging==26.3\" \\\n", " \"pandas==2.2.3\" \\\n", " \"pillow==11.3.0\" \\\n", - " \"platformdirs==4.11.3\" \\\n", + " \"platformdirs==4.11.7\" \\\n", " \"propcache==0.5.2\" \\\n", " \"pycparser==3.0\" \\\n", " \"pycryptodomex==3.23.0\" \\\n", - " \"pydantic==2.13.4\" \\\n", - " \"pydantic-core==2.46.4\" \\\n", + " \"pydantic==2.13.5\" \\\n", + " \"pydantic-core==2.46.5\" \\\n", " \"pydantic-settings==2.15.0\" \\\n", " \"pygments==2.21.0\" \\\n", " \"pynapple==0.10.3\" \\\n", @@ -150,7 +151,7 @@ " \"uri-template==1.3.0\" \\\n", " \"urllib3==2.5.0\" \\\n", " \"wadler-lindig==0.1.7\" \\\n", - " \"wcwidth==0.8.2\" \\\n", + " \"wcwidth==0.8.3\" \\\n", " \"webcolors==25.10.0\" \\\n", " \"xarray==2025.12.0\" \\\n", " \"yarl==1.24.5\" \\\n", diff --git a/001687/wanglab/figure2-distance-tuning/figure2_distance_tuning.ipynb b/001687/wanglab/figure2-distance-tuning/figure2_distance_tuning.ipynb index f83ff34..0a03136 100644 --- a/001687/wanglab/figure2-distance-tuning/figure2_distance_tuning.ipynb +++ b/001687/wanglab/figure2-distance-tuning/figure2_distance_tuning.ipynb @@ -47,10 +47,11 @@ " \"cffi==2.1.1\" \\\n", " \"charset-normalizer==3.4.9\" \\\n", " \"ci-info==0.4.0\" \\\n", - " \"click==8.4.2\" \\\n", + " \"click==8.5.0\" \\\n", " \"click-didyoumean==0.3.1\" \\\n", + " \"cloudpickle==3.1.2\" \\\n", " \"contourpy==1.3.3\" \\\n", - " \"cryptography==50.0.0\" \\\n", + " \"cryptography==50.0.1\" \\\n", " \"cycler==0.12.1\" \\\n", " \"dandi==0.77.0\" \\\n", " \"dandischema==0.14.0\" \\\n", @@ -60,16 +61,16 @@ " \"email-validator==2.3.0\" \\\n", " \"etelemetry==0.3.1\" \\\n", " \"fasteners==0.20\" \\\n", - " \"fonttools==4.63.0\" \\\n", + " \"fonttools==4.64.0\" \\\n", " \"fqdn==1.5.1\" \\\n", " \"frozenlist==1.8.0\" \\\n", " \"fscacher==0.4.4\" \\\n", - " \"fsspec==2025.3.0\" \\\n", + " \"fsspec==2025.12.0\" \\\n", " \"google-crc32c==1.8.0\" \\\n", " \"h5py==3.16.0\" \\\n", " \"hdmf==6.2.0\" \\\n", " \"humanize==4.16.0\" \\\n", - " \"idna==3.18\" \\\n", + " \"idna==3.19\" \\\n", " \"interleave==0.3.0\" \\\n", " \"isodate==0.7.2\" \\\n", " \"isoduration==20.11.0\" \\\n", @@ -78,13 +79,13 @@ " \"jaraco-functools==4.6.0\" \\\n", " \"jeepney==0.9.0\" \\\n", " \"jinxed==2.1.0\" \\\n", - " \"joblib==1.5.3\" \\\n", + " \"joblib==1.6.0\" \\\n", " \"jsonpointer==3.1.1\" \\\n", " \"jsonschema==4.26.0\" \\\n", " \"jsonschema-specifications==2025.9.1\" \\\n", " \"keyring==25.7.0\" \\\n", " \"keyrings-alt==5.0.2\" \\\n", - " \"kiwisolver==1.5.0\" \\\n", + " \"kiwisolver==1.5.1\" \\\n", " \"matplotlib==3.10.0\" \\\n", " \"ml-dtypes==0.6.0\" \\\n", " \"more-itertools==10.8.0\" \\\n", @@ -96,12 +97,12 @@ " \"packaging==26.3\" \\\n", " \"pandas==2.2.3\" \\\n", " \"pillow==11.3.0\" \\\n", - " \"platformdirs==4.11.3\" \\\n", + " \"platformdirs==4.11.7\" \\\n", " \"propcache==0.5.2\" \\\n", " \"pycparser==3.0\" \\\n", " \"pycryptodomex==3.23.0\" \\\n", - " \"pydantic==2.13.4\" \\\n", - " \"pydantic-core==2.46.4\" \\\n", + " \"pydantic==2.13.5\" \\\n", + " \"pydantic-core==2.46.5\" \\\n", " \"pydantic-settings==2.15.0\" \\\n", " \"pynwb==4.1.0\" \\\n", " \"pyout==0.8.1\" \\\n", @@ -128,7 +129,7 @@ " \"tzdata==2026.3\" \\\n", " \"uri-template==1.3.0\" \\\n", " \"urllib3==2.5.0\" \\\n", - " \"wcwidth==0.8.2\" \\\n", + " \"wcwidth==0.8.3\" \\\n", " \"webcolors==25.10.0\" \\\n", " \"yarl==1.24.5\" \\\n", " \"zarr==3.1.5\" \\\n", diff --git a/001712/IBL-Widefield/public_demo/raw_widefield.ipynb b/001712/IBL-Widefield/public_demo/raw_widefield.ipynb index 7586665..c388bd9 100644 --- a/001712/IBL-Widefield/public_demo/raw_widefield.ipynb +++ b/001712/IBL-Widefield/public_demo/raw_widefield.ipynb @@ -47,10 +47,11 @@ " \"cffi==2.1.1\" \\\n", " \"charset-normalizer==3.4.9\" \\\n", " \"ci-info==0.4.0\" \\\n", - " \"click==8.4.2\" \\\n", + " \"click==8.5.0\" \\\n", " \"click-didyoumean==0.3.1\" \\\n", + " \"cloudpickle==3.1.2\" \\\n", " \"contourpy==1.3.3\" \\\n", - " \"cryptography==50.0.0\" \\\n", + " \"cryptography==50.0.1\" \\\n", " \"cycler==0.12.1\" \\\n", " \"dandi==0.77.0\" \\\n", " \"dandischema==0.14.0\" \\\n", @@ -60,16 +61,16 @@ " \"email-validator==2.3.0\" \\\n", " \"etelemetry==0.3.1\" \\\n", " \"fasteners==0.20\" \\\n", - " \"fonttools==4.63.0\" \\\n", + " \"fonttools==4.64.0\" \\\n", " \"fqdn==1.5.1\" \\\n", " \"frozenlist==1.8.0\" \\\n", " \"fscacher==0.4.4\" \\\n", - " \"fsspec==2025.3.0\" \\\n", + " \"fsspec==2025.12.0\" \\\n", " \"google-crc32c==1.8.0\" \\\n", " \"h5py==3.16.0\" \\\n", " \"hdmf==4.3.1\" \\\n", " \"humanize==4.16.0\" \\\n", - " \"idna==3.18\" \\\n", + " \"idna==3.19\" \\\n", " \"interleave==0.3.0\" \\\n", " \"isodate==0.7.2\" \\\n", " \"isoduration==20.11.0\" \\\n", @@ -78,13 +79,13 @@ " \"jaraco-functools==4.6.0\" \\\n", " \"jeepney==0.9.0\" \\\n", " \"jinxed==2.1.0\" \\\n", - " \"joblib==1.5.3\" \\\n", + " \"joblib==1.6.0\" \\\n", " \"jsonpointer==3.1.1\" \\\n", " \"jsonschema==4.26.0\" \\\n", " \"jsonschema-specifications==2025.9.1\" \\\n", " \"keyring==25.7.0\" \\\n", " \"keyrings-alt==5.0.2\" \\\n", - " \"kiwisolver==1.5.0\" \\\n", + " \"kiwisolver==1.5.1\" \\\n", " \"matplotlib==3.10.0\" \\\n", " \"ml-dtypes==0.6.0\" \\\n", " \"more-itertools==10.8.0\" \\\n", @@ -96,12 +97,12 @@ " \"packaging==26.3\" \\\n", " \"pandas==2.2.3\" \\\n", " \"pillow==11.3.0\" \\\n", - " \"platformdirs==4.11.3\" \\\n", + " \"platformdirs==4.11.7\" \\\n", " \"propcache==0.5.2\" \\\n", " \"pycparser==3.0\" \\\n", " \"pycryptodomex==3.23.0\" \\\n", - " \"pydantic==2.13.4\" \\\n", - " \"pydantic-core==2.46.4\" \\\n", + " \"pydantic==2.13.5\" \\\n", + " \"pydantic-core==2.46.5\" \\\n", " \"pydantic-settings==2.15.0\" \\\n", " \"pynwb==3.1.3\" \\\n", " \"pyout==0.8.1\" \\\n", @@ -128,7 +129,7 @@ " \"tzdata==2026.3\" \\\n", " \"uri-template==1.3.0\" \\\n", " \"urllib3==2.5.0\" \\\n", - " \"wcwidth==0.8.2\" \\\n", + " \"wcwidth==0.8.3\" \\\n", " \"webcolors==25.10.0\" \\\n", " \"yarl==1.24.5\" \\\n", " \"zarr==3.1.5\" \\\n", diff --git a/001754/CatalystNeuro/001754_demo.ipynb b/001754/CatalystNeuro/001754_demo.ipynb index ff9f78e..0497774 100644 --- a/001754/CatalystNeuro/001754_demo.ipynb +++ b/001754/CatalystNeuro/001754_demo.ipynb @@ -47,10 +47,11 @@ " \"cffi==2.1.1\" \\\n", " \"charset-normalizer==3.4.9\" \\\n", " \"ci-info==0.4.0\" \\\n", - " \"click==8.4.2\" \\\n", + " \"click==8.5.0\" \\\n", " \"click-didyoumean==0.3.1\" \\\n", + " \"cloudpickle==3.1.2\" \\\n", " \"contourpy==1.3.3\" \\\n", - " \"cryptography==50.0.0\" \\\n", + " \"cryptography==50.0.1\" \\\n", " \"cycler==0.12.1\" \\\n", " \"dandi==0.77.0\" \\\n", " \"dandischema==0.14.0\" \\\n", @@ -60,16 +61,16 @@ " \"email-validator==2.3.0\" \\\n", " \"etelemetry==0.3.1\" \\\n", " \"fasteners==0.20\" \\\n", - " \"fonttools==4.63.0\" \\\n", + " \"fonttools==4.64.0\" \\\n", " \"fqdn==1.5.1\" \\\n", " \"frozenlist==1.8.0\" \\\n", " \"fscacher==0.4.4\" \\\n", - " \"fsspec==2025.3.0\" \\\n", + " \"fsspec==2025.12.0\" \\\n", " \"google-crc32c==1.8.0\" \\\n", " \"h5py==3.16.0\" \\\n", " \"hdmf==4.3.1\" \\\n", " \"humanize==4.16.0\" \\\n", - " \"idna==3.18\" \\\n", + " \"idna==3.19\" \\\n", " \"interleave==0.3.0\" \\\n", " \"isodate==0.7.2\" \\\n", " \"isoduration==20.11.0\" \\\n", @@ -78,13 +79,13 @@ " \"jaraco-functools==4.6.0\" \\\n", " \"jeepney==0.9.0\" \\\n", " \"jinxed==2.1.0\" \\\n", - " \"joblib==1.5.3\" \\\n", + " \"joblib==1.6.0\" \\\n", " \"jsonpointer==3.1.1\" \\\n", " \"jsonschema==4.26.0\" \\\n", " \"jsonschema-specifications==2025.9.1\" \\\n", " \"keyring==25.7.0\" \\\n", " \"keyrings-alt==5.0.2\" \\\n", - " \"kiwisolver==1.5.0\" \\\n", + " \"kiwisolver==1.5.1\" \\\n", " \"llvmlite==0.44.0\" \\\n", " \"markdown-it-py==4.2.0\" \\\n", " \"matplotlib==3.10.0\" \\\n", @@ -101,12 +102,12 @@ " \"packaging==26.3\" \\\n", " \"pandas==2.2.3\" \\\n", " \"pillow==11.3.0\" \\\n", - " \"platformdirs==4.11.3\" \\\n", + " \"platformdirs==4.11.7\" \\\n", " \"propcache==0.5.2\" \\\n", " \"pycparser==3.0\" \\\n", " \"pycryptodomex==3.23.0\" \\\n", - " \"pydantic==2.13.4\" \\\n", - " \"pydantic-core==2.46.4\" \\\n", + " \"pydantic==2.13.5\" \\\n", + " \"pydantic-core==2.46.5\" \\\n", " \"pydantic-settings==2.15.0\" \\\n", " \"pygments==2.21.0\" \\\n", " \"pynapple==0.11.4\" \\\n", @@ -139,7 +140,7 @@ " \"tzdata==2026.3\" \\\n", " \"uri-template==1.3.0\" \\\n", " \"urllib3==2.5.0\" \\\n", - " \"wcwidth==0.8.2\" \\\n", + " \"wcwidth==0.8.3\" \\\n", " \"webcolors==25.10.0\" \\\n", " \"xarray==2025.12.0\" \\\n", " \"yarl==1.24.5\" \\\n", diff --git a/001933/DombeckLab/001933_demo.ipynb b/001933/DombeckLab/001933_demo.ipynb index 49795aa..055c6f5 100644 --- a/001933/DombeckLab/001933_demo.ipynb +++ b/001933/DombeckLab/001933_demo.ipynb @@ -47,10 +47,11 @@ " \"cffi==2.1.1\" \\\n", " \"charset-normalizer==3.4.9\" \\\n", " \"ci-info==0.4.0\" \\\n", - " \"click==8.4.2\" \\\n", + " \"click==8.5.0\" \\\n", " \"click-didyoumean==0.3.1\" \\\n", + " \"cloudpickle==3.1.2\" \\\n", " \"contourpy==1.3.3\" \\\n", - " \"cryptography==50.0.0\" \\\n", + " \"cryptography==50.0.1\" \\\n", " \"cycler==0.12.1\" \\\n", " \"dandi==0.77.0\" \\\n", " \"dandischema==0.14.0\" \\\n", @@ -60,16 +61,16 @@ " \"email-validator==2.3.0\" \\\n", " \"etelemetry==0.3.1\" \\\n", " \"fasteners==0.20\" \\\n", - " \"fonttools==4.63.0\" \\\n", + " \"fonttools==4.64.0\" \\\n", " \"fqdn==1.5.1\" \\\n", " \"frozenlist==1.8.0\" \\\n", " \"fscacher==0.4.4\" \\\n", - " \"fsspec==2025.3.0\" \\\n", + " \"fsspec==2025.12.0\" \\\n", " \"google-crc32c==1.8.0\" \\\n", " \"h5py==3.16.0\" \\\n", " \"hdmf==4.3.1\" \\\n", " \"humanize==4.16.0\" \\\n", - " \"idna==3.18\" \\\n", + " \"idna==3.19\" \\\n", " \"interleave==0.3.0\" \\\n", " \"isodate==0.7.2\" \\\n", " \"isoduration==20.11.0\" \\\n", @@ -78,13 +79,13 @@ " \"jaraco-functools==4.6.0\" \\\n", " \"jeepney==0.9.0\" \\\n", " \"jinxed==2.1.0\" \\\n", - " \"joblib==1.5.3\" \\\n", + " \"joblib==1.6.0\" \\\n", " \"jsonpointer==3.1.1\" \\\n", " \"jsonschema==4.26.0\" \\\n", " \"jsonschema-specifications==2025.9.1\" \\\n", " \"keyring==25.7.0\" \\\n", " \"keyrings-alt==5.0.2\" \\\n", - " \"kiwisolver==1.5.0\" \\\n", + " \"kiwisolver==1.5.1\" \\\n", " \"matplotlib==3.10.0\" \\\n", " \"ml-dtypes==0.6.0\" \\\n", " \"more-itertools==10.8.0\" \\\n", @@ -99,12 +100,12 @@ " \"packaging==26.3\" \\\n", " \"pandas==2.2.3\" \\\n", " \"pillow==11.3.0\" \\\n", - " \"platformdirs==4.11.3\" \\\n", + " \"platformdirs==4.11.7\" \\\n", " \"propcache==0.5.2\" \\\n", " \"pycparser==3.0\" \\\n", " \"pycryptodomex==3.23.0\" \\\n", - " \"pydantic==2.13.4\" \\\n", - " \"pydantic-core==2.46.4\" \\\n", + " \"pydantic==2.13.5\" \\\n", + " \"pydantic-core==2.46.5\" \\\n", " \"pydantic-settings==2.15.0\" \\\n", " \"pynwb==3.1.3\" \\\n", " \"pyout==0.8.1\" \\\n", @@ -131,7 +132,7 @@ " \"tzdata==2026.3\" \\\n", " \"uri-template==1.3.0\" \\\n", " \"urllib3==2.5.0\" \\\n", - " \"wcwidth==0.8.2\" \\\n", + " \"wcwidth==0.8.3\" \\\n", " \"webcolors==25.10.0\" \\\n", " \"yarl==1.24.5\" \\\n", " \"zarr==3.1.5\" \\\n", diff --git a/dandi/DANDI User Guide, Part I.ipynb b/dandi/DANDI User Guide, Part I.ipynb index 8727394..a1a17cb 100644 --- a/dandi/DANDI User Guide, Part I.ipynb +++ b/dandi/DANDI User Guide, Part I.ipynb @@ -47,9 +47,10 @@ " \"cffi==2.1.1\" \\\n", " \"charset-normalizer==3.4.9\" \\\n", " \"ci-info==0.4.0\" \\\n", - " \"click==8.4.2\" \\\n", + " \"click==8.5.0\" \\\n", " \"click-didyoumean==0.3.1\" \\\n", - " \"cryptography==50.0.0\" \\\n", + " \"cloudpickle==3.1.2\" \\\n", + " \"cryptography==50.0.1\" \\\n", " \"dandi==0.77.0\" \\\n", " \"dandischema==0.14.0\" \\\n", " \"deno==2.9.5\" \\\n", @@ -61,12 +62,12 @@ " \"fqdn==1.5.1\" \\\n", " \"frozenlist==1.8.0\" \\\n", " \"fscacher==0.4.4\" \\\n", - " \"fsspec==2025.3.0\" \\\n", + " \"fsspec==2025.12.0\" \\\n", " \"google-crc32c==1.8.0\" \\\n", " \"h5py==3.16.0\" \\\n", " \"hdmf==6.2.0\" \\\n", " \"humanize==4.16.0\" \\\n", - " \"idna==3.18\" \\\n", + " \"idna==3.19\" \\\n", " \"interleave==0.3.0\" \\\n", " \"isodate==0.7.2\" \\\n", " \"isoduration==20.11.0\" \\\n", @@ -75,7 +76,7 @@ " \"jaraco-functools==4.6.0\" \\\n", " \"jeepney==0.9.0\" \\\n", " \"jinxed==2.1.0\" \\\n", - " \"joblib==1.5.3\" \\\n", + " \"joblib==1.6.0\" \\\n", " \"jsonpointer==3.1.1\" \\\n", " \"jsonschema==4.26.0\" \\\n", " \"jsonschema-specifications==2025.9.1\" \\\n", @@ -90,12 +91,12 @@ " \"nwbinspector==0.7.2\" \\\n", " \"packaging==26.3\" \\\n", " \"pandas==2.2.3\" \\\n", - " \"platformdirs==4.11.3\" \\\n", + " \"platformdirs==4.11.7\" \\\n", " \"propcache==0.5.2\" \\\n", " \"pycparser==3.0\" \\\n", " \"pycryptodomex==3.23.0\" \\\n", - " \"pydantic==2.13.4\" \\\n", - " \"pydantic-core==2.46.4\" \\\n", + " \"pydantic==2.13.5\" \\\n", + " \"pydantic-core==2.46.5\" \\\n", " \"pydantic-settings==2.15.0\" \\\n", " \"pynwb==4.1.0\" \\\n", " \"pyout==0.8.1\" \\\n", @@ -121,7 +122,7 @@ " \"tzdata==2026.3\" \\\n", " \"uri-template==1.3.0\" \\\n", " \"urllib3==2.5.0\" \\\n", - " \"wcwidth==0.8.2\" \\\n", + " \"wcwidth==0.8.3\" \\\n", " \"webcolors==25.10.0\" \\\n", " \"yarl==1.24.5\" \\\n", " \"zarr==3.1.5\" \\\n", diff --git a/dandi/DANDI User Guide, Part II.ipynb b/dandi/DANDI User Guide, Part II.ipynb index addd216..5506efd 100644 --- a/dandi/DANDI User Guide, Part II.ipynb +++ b/dandi/DANDI User Guide, Part II.ipynb @@ -47,9 +47,10 @@ " \"cffi==2.1.1\" \\\n", " \"charset-normalizer==3.4.9\" \\\n", " \"ci-info==0.4.0\" \\\n", - " \"click==8.4.2\" \\\n", + " \"click==8.5.0\" \\\n", " \"click-didyoumean==0.3.1\" \\\n", - " \"cryptography==50.0.0\" \\\n", + " \"cloudpickle==3.1.2\" \\\n", + " \"cryptography==50.0.1\" \\\n", " \"dandi==0.77.0\" \\\n", " \"dandischema==0.14.0\" \\\n", " \"deno==2.9.5\" \\\n", @@ -61,12 +62,12 @@ " \"fqdn==1.5.1\" \\\n", " \"frozenlist==1.8.0\" \\\n", " \"fscacher==0.4.4\" \\\n", - " \"fsspec==2025.3.0\" \\\n", + " \"fsspec==2025.12.0\" \\\n", " \"google-crc32c==1.8.0\" \\\n", " \"h5py==3.16.0\" \\\n", " \"hdmf==6.2.0\" \\\n", " \"humanize==4.16.0\" \\\n", - " \"idna==3.18\" \\\n", + " \"idna==3.19\" \\\n", " \"interleave==0.3.0\" \\\n", " \"isodate==0.7.2\" \\\n", " \"isoduration==20.11.0\" \\\n", @@ -75,7 +76,7 @@ " \"jaraco-functools==4.6.0\" \\\n", " \"jeepney==0.9.0\" \\\n", " \"jinxed==2.1.0\" \\\n", - " \"joblib==1.5.3\" \\\n", + " \"joblib==1.6.0\" \\\n", " \"jsonpointer==3.1.1\" \\\n", " \"jsonschema==4.26.0\" \\\n", " \"jsonschema-specifications==2025.9.1\" \\\n", @@ -90,12 +91,12 @@ " \"nwbinspector==0.7.2\" \\\n", " \"packaging==26.3\" \\\n", " \"pandas==2.2.3\" \\\n", - " \"platformdirs==4.11.3\" \\\n", + " \"platformdirs==4.11.7\" \\\n", " \"propcache==0.5.2\" \\\n", " \"pycparser==3.0\" \\\n", " \"pycryptodomex==3.23.0\" \\\n", - " \"pydantic==2.13.4\" \\\n", - " \"pydantic-core==2.46.4\" \\\n", + " \"pydantic==2.13.5\" \\\n", + " \"pydantic-core==2.46.5\" \\\n", " \"pydantic-settings==2.15.0\" \\\n", " \"pynwb==4.1.0\" \\\n", " \"pyout==0.8.1\" \\\n", @@ -120,7 +121,7 @@ " \"tzdata==2026.3\" \\\n", " \"uri-template==1.3.0\" \\\n", " \"urllib3==2.5.0\" \\\n", - " \"wcwidth==0.8.2\" \\\n", + " \"wcwidth==0.8.3\" \\\n", " \"webcolors==25.10.0\" \\\n", " \"yarl==1.24.5\" \\\n", " \"zarr==3.1.5\" \\\n", diff --git a/demos/NWBWidget-demo.ipynb b/demos/NWBWidget-demo.ipynb index 6467efd..1ad7484 100644 --- a/demos/NWBWidget-demo.ipynb +++ b/demos/NWBWidget-demo.ipynb @@ -38,7 +38,7 @@ " \"aiosignal==1.4.0\" \\\n", " \"anyio==4.14.2\" \\\n", " \"argon2-cffi==25.1.0\" \\\n", - " \"argon2-cffi-bindings==25.1.0\" \\\n", + " \"argon2-cffi-bindings==26.1.0\" \\\n", " \"arrow==1.4.0\" \\\n", " \"asciitree==0.3.3\" \\\n", " \"attrs==26.1.0\" \\\n", @@ -50,12 +50,12 @@ " \"certifi==2026.7.22\" \\\n", " \"cffi==2.1.1\" \\\n", " \"charset-normalizer==3.4.9\" \\\n", - " \"click==8.4.2\" \\\n", + " \"click==8.5.0\" \\\n", " \"cloudpickle==3.1.2\" \\\n", " \"colorcet==3.2.1\" \\\n", " \"contourpy==1.3.3\" \\\n", " \"cycler==0.12.1\" \\\n", - " \"dask==2026.7.1\" \\\n", + " \"dask==2026.8.0\" \\\n", " \"debugpy==1.8.15\" \\\n", " \"decorator==4.4.2\" \\\n", " \"defusedxml==0.7.1\" \\\n", @@ -63,13 +63,13 @@ " \"entrypoints==0.4\" \\\n", " \"fasteners==0.20\" \\\n", " \"fastjsonschema==2.22.2\" \\\n", - " \"fonttools==4.63.0\" \\\n", + " \"fonttools==4.64.0\" \\\n", " \"fqdn==1.5.1\" \\\n", " \"frozenlist==1.8.0\" \\\n", - " \"fsspec==2025.3.0\" \\\n", + " \"fsspec==2025.12.0\" \\\n", " \"h5py==3.16.0\" \\\n", " \"hdmf==3.14.6\" \\\n", - " \"idna==3.18\" \\\n", + " \"idna==3.19\" \\\n", " \"imageio==2.37.4\" \\\n", " \"ipydatawidgets==4.3.5\" \\\n", " \"ipykernel==6.17.1\" \\\n", @@ -99,8 +99,8 @@ " \"jupyter-server==2.20.0\" \\\n", " \"jupyter-server-terminals==0.5.4\" \\\n", " \"jupyterlab-pygments==0.3.0\" \\\n", - " \"jupyterlab-widgets==3.0.16\" \\\n", - " \"kiwisolver==1.5.0\" \\\n", + " \"jupyterlab-widgets==3.0.17\" \\\n", + " \"kiwisolver==1.5.1\" \\\n", " \"lark==1.3.1\" \\\n", " \"lazy-loader==0.5\" \\\n", " \"locket==1.0.0\" \\\n", @@ -131,7 +131,7 @@ " \"pexpect==4.9.0\" \\\n", " \"pickleshare==0.7.5\" \\\n", " \"pillow==11.3.0\" \\\n", - " \"platformdirs==4.11.3\" \\\n", + " \"platformdirs==4.11.7\" \\\n", " \"plotly==5.24.1\" \\\n", " \"prometheus-client==0.26.0\" \\\n", " \"prompt-toolkit==3.0.53\" \\\n", @@ -159,12 +159,12 @@ " \"scikit-image==0.25.2\" \\\n", " \"scipy==1.16.3\" \\\n", " \"send2trash==2.1.0\" \\\n", - " \"setuptools==75.2.0\" \\\n", + " \"setuptools==80.10.2\" \\\n", " \"six==1.17.0\" \\\n", " \"soupsieve==2.9.2\" \\\n", " \"tenacity==9.1.4\" \\\n", " \"terminado==0.18.1\" \\\n", - " \"tifffile==2026.8.16\" \\\n", + " \"tifffile==2026.8.23\" \\\n", " \"tinycss2==1.5.1\" \\\n", " \"toolz==0.12.1\" \\\n", " \"tornado==6.5.7\" \\\n", @@ -176,12 +176,12 @@ " \"tzdata==2026.3\" \\\n", " \"uri-template==1.3.0\" \\\n", " \"urllib3==2.5.0\" \\\n", - " \"wcwidth==0.8.2\" \\\n", + " \"wcwidth==0.8.3\" \\\n", " \"webcolors==25.10.0\" \\\n", " \"webencodings==0.6.1\" \\\n", - " \"websocket-client==1.9.0\" \\\n", + " \"websocket-client==1.9.2\" \\\n", " \"widgetsnbextension==3.6.10\" \\\n", - " \"wrapt==2.3.0\" \\\n", + " \"wrapt==2.4.0\" \\\n", " \"xarray==2025.12.0\" \\\n", " \"yarl==1.24.5\" \\\n", " \"zarr==2.18.7\" \\\n", diff --git a/tutorials/bcm_2024/analysis-demo.ipynb b/tutorials/bcm_2024/analysis-demo.ipynb index c3a4465..a3666fd 100644 --- a/tutorials/bcm_2024/analysis-demo.ipynb +++ b/tutorials/bcm_2024/analysis-demo.ipynb @@ -47,10 +47,11 @@ " \"cffi==2.1.1\" \\\n", " \"charset-normalizer==3.4.9\" \\\n", " \"ci-info==0.4.0\" \\\n", - " \"click==8.4.2\" \\\n", + " \"click==8.5.0\" \\\n", " \"click-didyoumean==0.3.1\" \\\n", + " \"cloudpickle==3.1.2\" \\\n", " \"contourpy==1.3.3\" \\\n", - " \"cryptography==50.0.0\" \\\n", + " \"cryptography==50.0.1\" \\\n", " \"cycler==0.12.1\" \\\n", " \"dandi==0.77.0\" \\\n", " \"dandischema==0.14.0\" \\\n", @@ -60,16 +61,16 @@ " \"email-validator==2.3.0\" \\\n", " \"etelemetry==0.3.1\" \\\n", " \"fasteners==0.20\" \\\n", - " \"fonttools==4.63.0\" \\\n", + " \"fonttools==4.64.0\" \\\n", " \"fqdn==1.5.1\" \\\n", " \"frozenlist==1.8.0\" \\\n", " \"fscacher==0.4.4\" \\\n", - " \"fsspec==2025.3.0\" \\\n", + " \"fsspec==2025.12.0\" \\\n", " \"google-crc32c==1.8.0\" \\\n", " \"h5py==3.16.0\" \\\n", " \"hdmf==4.3.1\" \\\n", " \"humanize==4.16.0\" \\\n", - " \"idna==3.18\" \\\n", + " \"idna==3.19\" \\\n", " \"interleave==0.3.0\" \\\n", " \"isodate==0.7.2\" \\\n", " \"isoduration==20.11.0\" \\\n", @@ -78,13 +79,13 @@ " \"jaraco-functools==4.6.0\" \\\n", " \"jeepney==0.9.0\" \\\n", " \"jinxed==2.1.0\" \\\n", - " \"joblib==1.5.3\" \\\n", + " \"joblib==1.6.0\" \\\n", " \"jsonpointer==3.1.1\" \\\n", " \"jsonschema==4.26.0\" \\\n", " \"jsonschema-specifications==2025.9.1\" \\\n", " \"keyring==25.7.0\" \\\n", " \"keyrings-alt==5.0.2\" \\\n", - " \"kiwisolver==1.5.0\" \\\n", + " \"kiwisolver==1.5.1\" \\\n", " \"llvmlite==0.44.0\" \\\n", " \"markdown-it-py==4.2.0\" \\\n", " \"matplotlib==3.10.0\" \\\n", @@ -101,12 +102,12 @@ " \"packaging==26.3\" \\\n", " \"pandas==2.2.3\" \\\n", " \"pillow==11.3.0\" \\\n", - " \"platformdirs==4.11.3\" \\\n", + " \"platformdirs==4.11.7\" \\\n", " \"propcache==0.5.2\" \\\n", " \"pycparser==3.0\" \\\n", " \"pycryptodomex==3.23.0\" \\\n", - " \"pydantic==2.13.4\" \\\n", - " \"pydantic-core==2.46.4\" \\\n", + " \"pydantic==2.13.5\" \\\n", + " \"pydantic-core==2.46.5\" \\\n", " \"pydantic-settings==2.15.0\" \\\n", " \"pygments==2.21.0\" \\\n", " \"pynapple==0.11.4\" \\\n", @@ -139,7 +140,7 @@ " \"tzdata==2026.3\" \\\n", " \"uri-template==1.3.0\" \\\n", " \"urllib3==2.5.0\" \\\n", - " \"wcwidth==0.8.2\" \\\n", + " \"wcwidth==0.8.3\" \\\n", " \"webcolors==25.10.0\" \\\n", " \"xarray==2025.12.0\" \\\n", " \"yarl==1.24.5\" \\\n", diff --git a/tutorials/cosyne_2023/simple_dandiset_search.ipynb b/tutorials/cosyne_2023/simple_dandiset_search.ipynb index 6ca43fa..a1f07c4 100644 --- a/tutorials/cosyne_2023/simple_dandiset_search.ipynb +++ b/tutorials/cosyne_2023/simple_dandiset_search.ipynb @@ -47,9 +47,10 @@ " \"cffi==2.1.1\" \\\n", " \"charset-normalizer==3.4.9\" \\\n", " \"ci-info==0.4.0\" \\\n", - " \"click==8.4.2\" \\\n", + " \"click==8.5.0\" \\\n", " \"click-didyoumean==0.3.1\" \\\n", - " \"cryptography==50.0.0\" \\\n", + " \"cloudpickle==3.1.2\" \\\n", + " \"cryptography==50.0.1\" \\\n", " \"dandi==0.77.0\" \\\n", " \"dandischema==0.14.0\" \\\n", " \"deno==2.9.5\" \\\n", @@ -61,12 +62,12 @@ " \"fqdn==1.5.1\" \\\n", " \"frozenlist==1.8.0\" \\\n", " \"fscacher==0.4.4\" \\\n", - " \"fsspec==2025.3.0\" \\\n", + " \"fsspec==2025.12.0\" \\\n", " \"google-crc32c==1.8.0\" \\\n", " \"h5py==3.16.0\" \\\n", " \"hdmf==6.2.0\" \\\n", " \"humanize==4.16.0\" \\\n", - " \"idna==3.18\" \\\n", + " \"idna==3.19\" \\\n", " \"interleave==0.3.0\" \\\n", " \"isodate==0.7.2\" \\\n", " \"isoduration==20.11.0\" \\\n", @@ -75,7 +76,7 @@ " \"jaraco-functools==4.6.0\" \\\n", " \"jeepney==0.9.0\" \\\n", " \"jinxed==2.1.0\" \\\n", - " \"joblib==1.5.3\" \\\n", + " \"joblib==1.6.0\" \\\n", " \"jsonpointer==3.1.1\" \\\n", " \"jsonschema==4.26.0\" \\\n", " \"jsonschema-specifications==2025.9.1\" \\\n", @@ -90,12 +91,12 @@ " \"nwbinspector==0.7.2\" \\\n", " \"packaging==26.3\" \\\n", " \"pandas==2.2.3\" \\\n", - " \"platformdirs==4.11.3\" \\\n", + " \"platformdirs==4.11.7\" \\\n", " \"propcache==0.5.2\" \\\n", " \"pycparser==3.0\" \\\n", " \"pycryptodomex==3.23.0\" \\\n", - " \"pydantic==2.13.4\" \\\n", - " \"pydantic-core==2.46.4\" \\\n", + " \"pydantic==2.13.5\" \\\n", + " \"pydantic-core==2.46.5\" \\\n", " \"pydantic-settings==2.15.0\" \\\n", " \"pynwb==4.1.0\" \\\n", " \"pyout==0.8.1\" \\\n", @@ -120,7 +121,7 @@ " \"tzdata==2026.3\" \\\n", " \"uri-template==1.3.0\" \\\n", " \"urllib3==2.5.0\" \\\n", - " \"wcwidth==0.8.2\" \\\n", + " \"wcwidth==0.8.3\" \\\n", " \"webcolors==25.10.0\" \\\n", " \"yarl==1.24.5\" \\\n", " \"zarr==3.1.5\" \\\n", diff --git a/tutorials/neurodatarehack_2024/advanced_asset_search.ipynb b/tutorials/neurodatarehack_2024/advanced_asset_search.ipynb index 7bb3ea4..f5d9391 100644 --- a/tutorials/neurodatarehack_2024/advanced_asset_search.ipynb +++ b/tutorials/neurodatarehack_2024/advanced_asset_search.ipynb @@ -47,9 +47,10 @@ " \"cffi==2.1.1\" \\\n", " \"charset-normalizer==3.4.9\" \\\n", " \"ci-info==0.4.0\" \\\n", - " \"click==8.4.2\" \\\n", + " \"click==8.5.0\" \\\n", " \"click-didyoumean==0.3.1\" \\\n", - " \"cryptography==50.0.0\" \\\n", + " \"cloudpickle==3.1.2\" \\\n", + " \"cryptography==50.0.1\" \\\n", " \"dandi==0.77.0\" \\\n", " \"dandischema==0.14.0\" \\\n", " \"deno==2.9.5\" \\\n", @@ -61,12 +62,12 @@ " \"fqdn==1.5.1\" \\\n", " \"frozenlist==1.8.0\" \\\n", " \"fscacher==0.4.4\" \\\n", - " \"fsspec==2025.3.0\" \\\n", + " \"fsspec==2025.12.0\" \\\n", " \"google-crc32c==1.8.0\" \\\n", " \"h5py==3.16.0\" \\\n", " \"hdmf==4.3.1\" \\\n", " \"humanize==4.16.0\" \\\n", - " \"idna==3.18\" \\\n", + " \"idna==3.19\" \\\n", " \"interleave==0.3.0\" \\\n", " \"isodate==0.7.2\" \\\n", " \"isoduration==20.11.0\" \\\n", @@ -75,7 +76,7 @@ " \"jaraco-functools==4.6.0\" \\\n", " \"jeepney==0.9.0\" \\\n", " \"jinxed==2.1.0\" \\\n", - " \"joblib==1.5.3\" \\\n", + " \"joblib==1.6.0\" \\\n", " \"jsonpointer==3.1.1\" \\\n", " \"jsonschema==4.26.0\" \\\n", " \"jsonschema-specifications==2025.9.1\" \\\n", @@ -90,12 +91,12 @@ " \"nwbinspector==0.7.2\" \\\n", " \"packaging==26.3\" \\\n", " \"pandas==2.2.3\" \\\n", - " \"platformdirs==4.11.3\" \\\n", + " \"platformdirs==4.11.7\" \\\n", " \"propcache==0.5.2\" \\\n", " \"pycparser==3.0\" \\\n", " \"pycryptodomex==3.23.0\" \\\n", - " \"pydantic==2.13.4\" \\\n", - " \"pydantic-core==2.46.4\" \\\n", + " \"pydantic==2.13.5\" \\\n", + " \"pydantic-core==2.46.5\" \\\n", " \"pydantic-settings==2.15.0\" \\\n", " \"pynwb==3.1.3\" \\\n", " \"pyout==0.8.1\" \\\n", @@ -121,7 +122,7 @@ " \"tzdata==2026.3\" \\\n", " \"uri-template==1.3.0\" \\\n", " \"urllib3==2.5.0\" \\\n", - " \"wcwidth==0.8.2\" \\\n", + " \"wcwidth==0.8.3\" \\\n", " \"webcolors==25.10.0\" \\\n", " \"yarl==1.24.5\" \\\n", " \"zarr==3.1.5\" \\\n", diff --git a/tutorials/neurodatarehack_2024/simple_dandiset_search.ipynb b/tutorials/neurodatarehack_2024/simple_dandiset_search.ipynb index d8983a8..8c94706 100644 --- a/tutorials/neurodatarehack_2024/simple_dandiset_search.ipynb +++ b/tutorials/neurodatarehack_2024/simple_dandiset_search.ipynb @@ -47,9 +47,10 @@ " \"cffi==2.1.1\" \\\n", " \"charset-normalizer==3.4.9\" \\\n", " \"ci-info==0.4.0\" \\\n", - " \"click==8.4.2\" \\\n", + " \"click==8.5.0\" \\\n", " \"click-didyoumean==0.3.1\" \\\n", - " \"cryptography==50.0.0\" \\\n", + " \"cloudpickle==3.1.2\" \\\n", + " \"cryptography==50.0.1\" \\\n", " \"dandi==0.77.0\" \\\n", " \"dandischema==0.14.0\" \\\n", " \"deno==2.9.5\" \\\n", @@ -61,12 +62,12 @@ " \"fqdn==1.5.1\" \\\n", " \"frozenlist==1.8.0\" \\\n", " \"fscacher==0.4.4\" \\\n", - " \"fsspec==2025.3.0\" \\\n", + " \"fsspec==2025.12.0\" \\\n", " \"google-crc32c==1.8.0\" \\\n", " \"h5py==3.16.0\" \\\n", " \"hdmf==6.2.0\" \\\n", " \"humanize==4.16.0\" \\\n", - " \"idna==3.18\" \\\n", + " \"idna==3.19\" \\\n", " \"interleave==0.3.0\" \\\n", " \"isodate==0.7.2\" \\\n", " \"isoduration==20.11.0\" \\\n", @@ -75,7 +76,7 @@ " \"jaraco-functools==4.6.0\" \\\n", " \"jeepney==0.9.0\" \\\n", " \"jinxed==2.1.0\" \\\n", - " \"joblib==1.5.3\" \\\n", + " \"joblib==1.6.0\" \\\n", " \"jsonpointer==3.1.1\" \\\n", " \"jsonschema==4.26.0\" \\\n", " \"jsonschema-specifications==2025.9.1\" \\\n", @@ -90,12 +91,12 @@ " \"nwbinspector==0.7.2\" \\\n", " \"packaging==26.3\" \\\n", " \"pandas==2.2.3\" \\\n", - " \"platformdirs==4.11.3\" \\\n", + " \"platformdirs==4.11.7\" \\\n", " \"propcache==0.5.2\" \\\n", " \"pycparser==3.0\" \\\n", " \"pycryptodomex==3.23.0\" \\\n", - " \"pydantic==2.13.4\" \\\n", - " \"pydantic-core==2.46.4\" \\\n", + " \"pydantic==2.13.5\" \\\n", + " \"pydantic-core==2.46.5\" \\\n", " \"pydantic-settings==2.15.0\" \\\n", " \"pynwb==4.1.0\" \\\n", " \"pyout==0.8.1\" \\\n", @@ -120,7 +121,7 @@ " \"tzdata==2026.3\" \\\n", " \"uri-template==1.3.0\" \\\n", " \"urllib3==2.5.0\" \\\n", - " \"wcwidth==0.8.2\" \\\n", + " \"wcwidth==0.8.3\" \\\n", " \"webcolors==25.10.0\" \\\n", " \"yarl==1.24.5\" \\\n", " \"zarr==3.1.5\" \\\n", 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 b509205..e089466 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 @@ -47,10 +47,11 @@ " \"cffi==2.1.1\" \\\n", " \"charset-normalizer==3.4.9\" \\\n", " \"ci-info==0.4.0\" \\\n", - " \"click==8.4.2\" \\\n", + " \"click==8.5.0\" \\\n", " \"click-didyoumean==0.3.1\" \\\n", + " \"cloudpickle==3.1.2\" \\\n", " \"contourpy==1.3.3\" \\\n", - " \"cryptography==50.0.0\" \\\n", + " \"cryptography==50.0.1\" \\\n", " \"cycler==0.12.1\" \\\n", " \"dandi==0.77.0\" \\\n", " \"dandischema==0.14.0\" \\\n", @@ -60,16 +61,16 @@ " \"email-validator==2.3.0\" \\\n", " \"etelemetry==0.3.1\" \\\n", " \"fasteners==0.20\" \\\n", - " \"fonttools==4.63.0\" \\\n", + " \"fonttools==4.64.0\" \\\n", " \"fqdn==1.5.1\" \\\n", " \"frozenlist==1.8.0\" \\\n", " \"fscacher==0.4.4\" \\\n", - " \"fsspec==2025.3.0\" \\\n", + " \"fsspec==2025.12.0\" \\\n", " \"google-crc32c==1.8.0\" \\\n", " \"h5py==3.16.0\" \\\n", " \"hdmf==4.3.1\" \\\n", " \"humanize==4.16.0\" \\\n", - " \"idna==3.18\" \\\n", + " \"idna==3.19\" \\\n", " \"interleave==0.3.0\" \\\n", " \"isodate==0.7.2\" \\\n", " \"isoduration==20.11.0\" \\\n", @@ -78,13 +79,13 @@ " \"jaraco-functools==4.6.0\" \\\n", " \"jeepney==0.9.0\" \\\n", " \"jinxed==2.1.0\" \\\n", - " \"joblib==1.5.3\" \\\n", + " \"joblib==1.6.0\" \\\n", " \"jsonpointer==3.1.1\" \\\n", " \"jsonschema==4.26.0\" \\\n", " \"jsonschema-specifications==2025.9.1\" \\\n", " \"keyring==25.7.0\" \\\n", " \"keyrings-alt==5.0.2\" \\\n", - " \"kiwisolver==1.5.0\" \\\n", + " \"kiwisolver==1.5.1\" \\\n", " \"matplotlib==3.10.0\" \\\n", " \"ml-dtypes==0.6.0\" \\\n", " \"more-itertools==10.8.0\" \\\n", @@ -97,12 +98,12 @@ " \"packaging==26.3\" \\\n", " \"pandas==2.2.3\" \\\n", " \"pillow==11.3.0\" \\\n", - " \"platformdirs==4.11.3\" \\\n", + " \"platformdirs==4.11.7\" \\\n", " \"propcache==0.5.2\" \\\n", " \"pycparser==3.0\" \\\n", " \"pycryptodomex==3.23.0\" \\\n", - " \"pydantic==2.13.4\" \\\n", - " \"pydantic-core==2.46.4\" \\\n", + " \"pydantic==2.13.5\" \\\n", + " \"pydantic-core==2.46.5\" \\\n", " \"pydantic-settings==2.15.0\" \\\n", " \"pynwb==3.1.3\" \\\n", " \"pyout==0.8.1\" \\\n", @@ -129,7 +130,7 @@ " \"tzdata==2026.3\" \\\n", " \"uri-template==1.3.0\" \\\n", " \"urllib3==2.5.0\" \\\n", - " \"wcwidth==0.8.2\" \\\n", + " \"wcwidth==0.8.3\" \\\n", " \"webcolors==25.10.0\" \\\n", " \"yarl==1.24.5\" \\\n", " \"zarr==3.1.5\" \\\n",