Skip to content

Reduce install size: make ipyparallel/matplotlib optional #13

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

Open
danifr wants to merge 6 commits into
base: master
Choose a base branch
from
Open

Reduce install size: make ipyparallel/matplotlib optional #13

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
6 commits
Select commit Hold shift + click to select a range
44fcee4
Reduce install size: make ipyparallel/matplotlib optional (ipyp extra…
danifr Oct 26, 2026
03519c0
Fix bpopt_tasksdb console-script entry point (module:callable)
danifr Oct 27, 2026
37323ef
Drop unused pickleshare and declare matplotlib in tests extras
danifr Oct 27, 2026
96349a2
Keep tests in sdist for downstream packagers (conda-forge)
danifr Oct 27, 2026
60437a0
Guard matplotlib import in bpopt_tasksdb with helpful error
danifr Oct 27, 2026
35cb3fa
Document that ipyparallel is now the bluepyopt[ipyp] extra
danifr Oct 27, 2026
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
2 changes: 1 addition & 1 deletion MANIFEST.in
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -6,7 +6,7 @@ include bluepyopt/ephys/templates/acc/_json_template.jinja2
include bluepyopt/ephys/templates/acc/decor_acc_template.jinja2
include bluepyopt/ephys/templates/acc/label_dict_acc_template.jinja2

include.txt
include README.rst
include AUTHORS.txt
include COPYING
include COPYING.lesser
Expand Down
21 changes: 20 additions & 1 deletion bluepyopt/ipyp/bpopt_tasksdb.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -29,7 +29,21 @@
import itertools

import numpy as np
import matplotlib.pyplot as plt


def _import_pyplot():
"""Import matplotlib.pyplot, with a helpful error if it is missing.

matplotlib is an optional dependency of bpopt_tasksdb; install it via
``pip install bluepyopt[ipyp]``.
"""
try:
import matplotlib.pyplot as plt
except ImportError as e:
raise ImportError(
"bpopt_tasksdb requires matplotlib: pip install bluepyopt[ipyp]"
) from e
return plt


def get_engine_data(tasksdb_filename):
Expand Down Expand Up @@ -67,6 +81,8 @@ def get_engine_data(tasksdb_filename):
def plot_usage(tasks, engine_number_map):
"""Plot usage stats"""

plt = _import_pyplot()

plt.figure(figsize=(8, 8))
for engine_uuid, task_list in tasks.items():
engine_number = engine_number_map[engine_uuid]
Expand All @@ -91,6 +107,8 @@ def plot_usage(tasks, engine_number_map):

def plot_duration_histogram(tasks):
"""Plot duration histogram"""
plt = _import_pyplot()

plt.figure(figsize=(8, 8))

durations = np.fromiter((t['duration']
Expand Down Expand Up @@ -137,6 +155,7 @@ def run(arg_list):
plot_usage(tasks, engine_number_map)
plot_duration_histogram(tasks)

plt = _import_pyplot()
plt.show()


Expand Down
5 changes: 5 additions & 0 deletions examples/BluePyOpt-ipyparallel.md
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -12,6 +12,11 @@ The `ipcontroller` gets its work from clients that connect to it.

## Installation

> **Note:** As of recent versions, `ipyparallel` is no longer installed
> automatically with `BluePyOpt`. Install it explicitly, either on its own
> (`pip install ipyparallel`) or together with BluePyOpt via the extra:
> `pip install bluepyopt[ipyp]`.

`ipyparallel` can be installed using pip:

# create and activate virtualenv
Expand Down
17 changes: 10 additions & 7 deletions pyproject.toml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -17,8 +17,6 @@ dependencies = [
"pandas>=0.18",
"deap>=1.3.3",
"efel>=2.13",
"ipyparallel",
"pickleshare>=0.7.3",

@darshanmandge darshanmandge Oct 26, 2026

Copy link
Copy Markdown
Collaborator

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

This could be a breaking change for packages that rely on ipyparallel being available indirectly through bluepyopt. The main l5PC example of bluepyopt also uses it. Maybe you can add a line to the example README or add the ipyparallel installation in the notebook or before launching the script.

@danifr danifr Oct 27, 2026

Copy link
Copy Markdown
Contributor Author

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

yep, I will add a new commit documenting the pip install bluepyopt[ipyp] requirement

"Jinja2>=2.8",
"Pebble>=4.6.0",
"NEURON>=7.8",
Expand All @@ -39,13 +37,15 @@ keywords = [
]

[project.optional-dependencies]
all = ["scoop>=0.7", "pyneuroml>=0.5.20", "libNeuroML>=0.3.1", "LFPy>=2.3", "arbor>=0.10,<0.12"]
tests = ["pyneuroml>=0.5.20", "libNeuroML>=0.3.1", "LFPy>=2.3", "arbor>=0.10,<0.12"]
tests-no-arbor = ["pyneuroml>=0.5.20", "libNeuroML>=0.3.1", "LFPy>=2.3"]
all = ["scoop>=0.7", "pyneuroml>=0.5.20", "libNeuroML>=0.3.1", "LFPy>=2.3", "arbor>=0.10,<0.12", "ipyparallel", "matplotlib"]
tests = ["pyneuroml>=0.5.20", "libNeuroML>=0.3.1", "LFPy>=2.3", "arbor>=0.10,<0.12", "matplotlib"]
tests-no-arbor = ["pyneuroml>=0.5.20", "libNeuroML>=0.3.1", "LFPy>=2.3", "matplotlib"]
scoop = ["scoop>=0.7"]
neuroml = ["pyneuroml>=0.5.20", "libNeuroML>=0.3.1"]
lfpy = ["LFPy>=2.3"]
arbor = ["arbor>=0.10,<0.12"]
# Dependencies for the optional ipyparallel-based bpopt_tasksdb helper script.
ipyp = ["ipyparallel", "matplotlib"]

[project.urls]
Homepage = "https://github.com/openbraininstitute/BluePyOpt"
Expand All @@ -55,7 +55,7 @@ Tracker = "https://github.com/openbraininstitute/BluePyOpt/issues"
Documentation = "https://bluepyopt.readthedocs.io/en/latest"

[project.scripts]
bpopt_tasksdb = "bluepyopt:ipyp.bpopt_tasksdb.main"
bpopt_tasksdb = "bluepyopt.ipyp.bpopt_tasksdb:main"

[tool.setuptools]
include-package-data = true
Expand All @@ -72,7 +72,10 @@ bluepyopt = [
]

[tool.setuptools.packages.find]
exclude = ["examples*"]
exclude = ["examples*", "bluepyopt.tests*"]

[tool.setuptools.exclude-package-data]
"*" = ["tests/*", "tests/**/*"]

[tool.setuptools_scm]
version_scheme = "python-simplified-semver"
Expand Down
Loading