Skip to content

Run the harness headlessly for plotly and matplotlib; un-exclude 001170 #209

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Merged
bendichter merged 1 commit into from
Aug 23, 2026
+74 −56
Merged

Run the harness headlessly for plotly and matplotlib; un-exclude 001170 #209

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
4 changes: 0 additions & 4 deletions .github/notebook-test-exclusions.txt
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -61,10 +61,6 @@ tutorials/cosyne_2023/advanced_asset_search.ipynb
# Works in Colab (which has libxcb preinstalled).
000559/dattalab/markowitz_gillis_nature_2023/read_avi.ipynb

# Calls webbrowser.open(), which raises "could not locate runnable browser"
# in headless CI. Works in Colab.
001170/ReimerLab/public_demo/001170_demo.ipynb

# =============================================================================
# Pre-existing notebook content bugs — track + fix in dedicated PRs.
# =============================================================================
Expand Down
13 changes: 12 additions & 1 deletion .github/scripts/run_notebook.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -25,6 +25,7 @@
import argparse
import copy
import json
import os
import re
import subprocess
import sys
Expand Down Expand Up @@ -227,8 +228,18 @@ def finalize(stage: str, ok: bool, error: str | None = None, **extra) -> int:
log_f = log_path.open("a")
log_f.write(f"\n=== execute (streaming) ===\n")
log_f.flush()
# Force both plotting libraries into a headless mode for this path. Outside
# a Jupyter kernel plotly resolves its default renderer to "browser", and
# fig.show() then calls webbrowser.open, which raises on a headless runner;
# matplotlib likewise picks a GUI backend when one is available, which opens
# windows when the harness is run on a developer's machine. A real kernel
# (Colab, or JupyterLab in the notebook image) selects inline rendering for
# both by itself, so neither setting applies to the kernel path above.
env = {**os.environ,
"PLOTLY_RENDERER": os.environ.get("PLOTLY_RENDERER", "json"),
"MPLBACKEND": os.environ.get("MPLBACKEND", "Agg")}
proc = subprocess.Popen(
cmd, cwd=str(nb_dir),
cmd, cwd=str(nb_dir), env=env,
stdout=subprocess.PIPE, stderr=subprocess.STDOUT,
text=True, bufsize=1,
)
Expand Down
103 changes: 52 additions & 51 deletions 001170/ReimerLab/public_demo/001170_demo.ipynb
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -28,112 +28,111 @@
"outputs": [],
"source": [
"#@title Installing requirements (click ▶ to run) { display-mode: \"form\" }\n",
"# Colab provides Python 3.12. We install with `uv --system` because Colab's\n",
"# Colab provides Python 3.13. We install with `uv --system` because Colab's\n",
"# kernel runs outside a virtualenv. All versions (direct + transitive) are\n",
"# pinned below so the notebook is reproducible regardless of resolver drift.\n",
"!pip install -q uv\n",
"!uv pip install --system \\\n",
" \"acres==0.5.0\" \\\n",
" \"aiohappyeyeballs==2.6.1\" \\\n",
" \"aiohttp==3.13.5\" \\\n",
" \"aiohappyeyeballs==2.7.1\" \\\n",
" \"aiohttp==3.14.3\" \\\n",
" \"aiosignal==1.4.0\" \\\n",
" \"annotated-types==0.7.0\" \\\n",
" \"annotated-types==0.8.0\" \\\n",
" \"arrow==1.4.0\" \\\n",
" \"asciitree==0.3.3\" \\\n",
" \"attrs==26.1.0\" \\\n",
" \"bids-validator-deno==2.4.1\" \\\n",
" \"bidsschematools==1.2.2\" \\\n",
" \"blessed==1.39.0\" \\\n",
" \"certifi==2026.4.22\" \\\n",
" \"cffi==2.0.0\" \\\n",
" \"charset-normalizer==3.4.7\" \\\n",
" \"bids-validator-deno==3.0.1\" \\\n",
" \"bidsschematools==1.2.7\" \\\n",
" \"blessed==1.48.0\" \\\n",
" \"certifi==2026.7.22\" \\\n",
" \"cffi==2.1.1\" \\\n",
" \"charset-normalizer==3.4.9\" \\\n",
" \"ci-info==0.4.0\" \\\n",
" \"click==8.1.8\" \\\n",
" \"click==8.4.2\" \\\n",
" \"click-didyoumean==0.3.1\" \\\n",
" \"contourpy==1.3.3\" \\\n",
" \"cryptography==48.0.0\" \\\n",
" \"cryptography==50.0.0\" \\\n",
" \"cycler==0.12.1\" \\\n",
" \"dandi==0.75.1\" \\\n",
" \"dandischema==0.12.1\" \\\n",
" \"deprecated==1.3.1\" \\\n",
" \"dandi==0.77.0\" \\\n",
" \"dandischema==0.14.0\" \\\n",
" \"deno==2.9.5\" \\\n",
" \"dnspython==2.8.0\" \\\n",
" \"donfig==0.8.1.post1\" \\\n",
" \"email-validator==2.3.0\" \\\n",
" \"etelemetry==0.3.1\" \\\n",
" \"fasteners==0.20\" \\\n",
" \"fonttools==4.62.1\" \\\n",
" \"fonttools==4.63.0\" \\\n",
" \"fqdn==1.5.1\" \\\n",
" \"frozenlist==1.8.0\" \\\n",
" \"fscacher==0.4.4\" \\\n",
" \"fsspec==2026.4.0\" \\\n",
" \"fsspec==2025.3.0\" \\\n",
" \"google-crc32c==1.8.0\" \\\n",
" \"h5py==3.16.0\" \\\n",
" \"hdmf==4.2.0\" \\\n",
" \"hdmf-zarr==0.12.0\" \\\n",
" \"humanize==4.15.0\" \\\n",
" \"idna==3.14\" \\\n",
" \"hdmf==4.3.1\" \\\n",
" \"humanize==4.16.0\" \\\n",
" \"idna==3.18\" \\\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==4.4.0\" \\\n",
" \"jaraco-functools==4.6.0\" \\\n",
" \"jeepney==0.9.0\" \\\n",
" \"jinxed==2.1.0\" \\\n",
" \"joblib==1.5.3\" \\\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",
" \"matplotlib==3.10.9\" \\\n",
" \"ml-dtypes==0.5.4\" \\\n",
" \"more-itertools==11.0.2\" \\\n",
" \"matplotlib==3.10.0\" \\\n",
" \"ml-dtypes==0.6.0\" \\\n",
" \"more-itertools==10.8.0\" \\\n",
" \"multidict==6.7.1\" \\\n",
" \"narwhals==2.21.0\" \\\n",
" \"natsort==8.4.0\" \\\n",
" \"numcodecs==0.15.1\" \\\n",
" \"numpy==2.4.4\" \\\n",
" \"nwbinspector==0.7.1\" \\\n",
" \"packaging==26.2\" \\\n",
" \"pandas==3.0.3\" \\\n",
" \"pillow==12.2.0\" \\\n",
" \"platformdirs==4.9.6\" \\\n",
" \"plotly==6.7.0\" \\\n",
" \"numcodecs==0.16.5\" \\\n",
" \"numpy==2.1.3\" \\\n",
" \"nwbinspector==0.7.2\" \\\n",
" \"packaging==26.3\" \\\n",
" \"pandas==2.2.3\" \\\n",
" \"pillow==11.3.0\" \\\n",
" \"platformdirs==4.11.3\" \\\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-settings==2.14.1\" \\\n",
" \"pydantic-settings==2.15.0\" \\\n",
" \"pynwb==3.1.3\" \\\n",
" \"pyout==0.8.1\" \\\n",
" \"pyparsing==3.3.2\" \\\n",
" \"python-dateutil==2.9.0.post0\" \\\n",
" \"python-dotenv==1.2.2\" \\\n",
" \"python-dotenv==1.2.3\" \\\n",
" \"pytz==2025.2\" \\\n",
" \"pyyaml==6.0.3\" \\\n",
" \"referencing==0.37.0\" \\\n",
" \"remfile==0.1.13\" \\\n",
" \"requests==2.34.0\" \\\n",
" \"remfile==0.1.14\" \\\n",
" \"requests==2.32.4\" \\\n",
" \"rfc3339-validator==0.1.4\" \\\n",
" \"rfc3987==1.3.8\" \\\n",
" \"rpds-py==0.30.0\" \\\n",
" \"rpds-py==2026.6.3\" \\\n",
" \"ruamel-yaml==0.19.1\" \\\n",
" \"secretstorage==3.5.0\" \\\n",
" \"semantic-version==2.10.0\" \\\n",
" \"six==1.17.0\" \\\n",
" \"tenacity==9.1.4\" \\\n",
" \"tensorstore==0.1.83\" \\\n",
" \"threadpoolctl==3.6.0\" \\\n",
" \"tensorstore==0.1.85\" \\\n",
" \"tqdm==4.67.3\" \\\n",
" \"typing-extensions==4.15.0\" \\\n",
" \"typing-inspection==0.4.2\" \\\n",
" \"tzdata==2026.2\" \\\n",
" \"typing-extensions==4.16.0\" \\\n",
" \"typing-inspection==0.4.4\" \\\n",
" \"tzdata==2026.3\" \\\n",
" \"uri-template==1.3.0\" \\\n",
" \"urllib3==2.7.0\" \\\n",
" \"wcwidth==0.7.0\" \\\n",
" \"urllib3==2.5.0\" \\\n",
" \"wcwidth==0.8.2\" \\\n",
" \"webcolors==25.10.0\" \\\n",
" \"wrapt==2.1.2\" \\\n",
" \"yarl==1.23.0\" \\\n",
" \"zarr==2.18.7\" \\\n",
" \"yarl==1.24.5\" \\\n",
" \"zarr==3.1.5\" \\\n",
" \"zarr-checksum==0.4.7\""
]
},
Expand Down Expand Up @@ -250,7 +249,9 @@
"import h5py\n",
"import remfile\n",
"\n",
"file = remfile.File(s3_url)\n",
"# The disk cache keeps blocks that have already been fetched, so repeated\n",
"# reads of the same part of the file do not go back over the network.\n",
"file = remfile.File(s3_url, disk_cache=remfile.DiskCache(\"nwb-cache\"))\n",
"h5_file = h5py.File(file, \"r\")"
]
},
Expand Down
10 changes: 10 additions & 0 deletions 001170/ReimerLab/public_demo/requirements.in
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1,10 @@
dandi
h5py
matplotlib
numpy
pandas
plotly
pynwb
remfile
pynwb<4
hdmf<5
Loading