pyproject.toml

# -------------------------------------------------------------------------
# Project metadata
# -------------------------------------------------------------------------
[project]
authors = [
  {name = "Arco Bast", email = "basta@janelia.hhmi.org"},
  {name = "Bjorge Meulemeester", email = "bjorge.meulemeester@mpinb.mpg.de"},
  {name = "Robert Egger"},
  {name = "Rieke Fruengel"},
  {name = "Maria Royo Cano" },
  {name = "Omar Valerio" },
  {name = "Shantanu Durgvanshi"}
  ]
description = "An In Silico Framework for the generation, simulation and analysis of neuron-network interactions during in vivo conditions."
name = "ISF"
requires-python = ">=3.8"
version = "0.7.2-beta"

[tool.pixi.workspace]
channels = ["conda-forge"]
platforms = ["linux-64", "osx-arm64", "win-64"]

[tool.pixi.system-requirements]
libc = "2.17"
linux = "3.10.0"

# -------------------------------------------------------------------------
# Build config
# -------------------------------------------------------------------------
[build-system]
build-backend = "hatchling.build"
requires = ["hatchling"]

# -------------------------------------------------------------------------
# Dependencies
# -------------------------------------------------------------------------
[tool.pixi.dependencies]
cmasher = ">=1.6.3,<2"
cython = ">=3.0.11,<4"
dash = ">=2.18.1,<3"
dask = "2.30.0.*"
fasteners = ">=0.17.3,<0.18"
flask = "==1.1.4"
ipywidgets = ">=8.1.5,<9"
jupyterlab = ">=3.5.3,<4"
jupyter-scatter = ">=0.19.1,<0.20"
kazoo = ">=2.10.0,<3"
matplotlib = ">=3.3.2,<4"
mock = ">=5.1.0,<6"
pandas = "1.1.3.*"
plotly = ">=5.24.1,<6"
pypdf2 = ">=3.0.1,<4"
pytest = ">=8.3.3,<9"
pytest-cov = ">=5.0.0,<6"
pytest-xdist = ">=3.6.1,<4"
pytest-timeout = ">=2.3.1,<3"
scikit-learn = "0.23.2.*"
seaborn = ">=0.12.2,<0.13"
scipy = "1.5.2.*"
wheel = ">=0.45.1,<0.46"
zarr = ">=2.15.0,<3"
pyarrow = ">=18.0.0,<22"
# for extracting barrel cortex data (optional)
7zip = ">=26.0,<27"

[tool.pixi.pypi-dependencies]
bluepyopt = "==1.9.126"
redis = ">=5.2.0,<6"
isf-pandas-msgpack = ">=0.4.0"
blosc = ">=1.11.1,<2"
blenderspike-py = { git = "https://github.com/ArtemKirsanov/BlenderSpike.git" }

# OS specific dependencies
[tool.pixi.target.osx]
# >=9 compiles to c++, not c, breaking our .mod files
pypi-dependencies = { neuron = ">=8.2,<9",   "distributed"= ">=2.30.0" }
dependencies = { numpy = "==1.21", pytables = ">=3.7.0,<4" }

[tool.pixi.target.linux]
dependencies = { neuron = "==7.8.2", numpy = "==1.19.2", distributed = "==2.30.0", gcc = "<15", gxx = "<15" }
pypi-dependencies = { tables = ">=3.8.0,<4" }

[tool.pixi.target.win]
dependencies = { numpy = "==1.19.2", distributed = "==2.30.0"}
pypi-dependencies = { tables = ">=3.8.0,<4" }

# Docs does not inherit the default dependencies
[tool.pixi.feature.docs.dependencies]
# astroid >=4 breaks autoapi API - filenames get mangled: last three chars are repeated
astroid="<4"
black = ">=21.12b0,<22"
cloudpickle = ">=3.1.1,<4"
dask = ">=2024.8.0,<2025"
flask = ">=2"
graphviz = ">=7.0.5,<13"
ipython = ">=8.18.1,<9"
jinja2 = ">=3.1.4,<4"
matplotlib = ">=3.9.4,<4"
nbsphinx = ">=0.9.6,<0.10"
nbsphinx-link = ">=1.3.0,<2"
pandoc = ">=3.6.2,<4"
python = ">=3.9"
sphinxcontrib-bibtex = ">=2.6.3,<3"
sphinxext-opengraph = ">=0.9.1,<0.10"
sphinx-copybutton = ">=0.5.2,<0.6"
sphinx = "<7.3.5"
sphinx-inline-tabs = ">=2023.4.21,<2024"
sphinx-design = ">=0.5.0,<0.6"
sphinxcontrib-video = ">=0.2.1,<0.3"
sphinx-immaterial = ">=0.12.5,<0.13"
sphinx-autoapi = ">=3.5.0,<4"
toml = ">=0.10.2,<0.11"
[tool.pixi.feature.docs.pypi-dependencies]
catppuccin = { version = ">=2.2.0,<3", extras = ["pygments"] }
isf-pandas-msgpack = ">=0.4.0,<0.5"
sphinx-paramlinks = ">=0.6.0,<0.7"

# -------------------------------------------------------------------------
# Environment config
# -------------------------------------------------------------------------
[tool.pixi.target.unix.activation.env]
PYTHONPATH = "$(pwd):$PYTHONPATH"
ISF_HOME="$(pwd)"
[tool.pixi.target.win.activation.env]
PYTHONPATH = "%cd%;%NEURONHOME%/lib/python;%PYTHONPATH%"
PATH = "%PATH%;%NEURONHOME%/bin"
ISF_HOME="%cd%"


[tool.pixi.environments]
docs = { features = ["docs"], no-default-feature = true }

# -------------------------------------------------------------------------
# Testing config
# -------------------------------------------------------------------------
[tool.pytest.ini_options]
markers = [
  "early: Mark a test as early, ensuring it is scheduled early in the test suite.",
  "statistical(n_runs, max_failure_rate): Mark tests to rerun multiple times to determine statistical significance."
]
# Don't schedule new tests if the previous exceeded this time
# Previous tests are gracefully finished until the timeout.
session_timeout = 600
timeout = 180
# Dask workers per pytest worker.
DASK_N_WORKERS = 4
DASK_MEM_LIMIT = "5GB"
log_cli = true
log_level = "INFO"

# -------------------------------------------------------------------------
# Pixi tasks
# -------------------------------------------------------------------------
[tool.pixi.tasks.configure]
# (re)configure ISF for local filesystem
args = [
  {arg = "force_recompile", default = "False" },
  {arg = "overwrite_param_files", default = "False" }
] 
cmd = [
  "python", 
  "config/isf_configure.py", 
  "--force-recompile={{ force_recompile }}",
  "--overwrite-param-files={{ overwrite_param_files }}",
]

[tool.pixi.tasks.install]
depends-on = ["configure"]
cmd = [
  "echo",
  "\nSuccessfully installed ISF.\n\n",
]

[tool.pixi.tasks.launch_dask_server]
args = [
  {arg = "port", default = "8786"},
  {arg = "dashboard_port", default = "8787"}
]
cmd = [
  "dask-scheduler", 
  "--port={{ port }}", 
  "--dashboard-address={{ dashboard_port }}", 
  "--host=localhost"
  ]
description = "Launch a Dask scheduler"

[tool.pixi.tasks.launch_dask_workers]
args = [
  {arg = "port",        default = "8786"},
  {arg = "dashboard_port",  default = "8787"},
  {arg = "num_workers", default = "4"},
  {arg = "mem_limit",   default = "3GB"}
]
cmd = [
  "dask-worker", 
  "localhost:{{ port }}", 
  "--nthreads=1", 
  "--nprocs={{  num_workers }}", 
  "--memory-limit={{  mem_limit }}", 
  "--dashboard-address={{  dashboard_port }}"
  ]
description = "Launch Dask workers"

[tool.pixi.tasks.launch_jupyter_server]
args = [
  {arg = "port", default = "11113"}
]
cmd = [
  "jupyter-lab", 
  "--ip='*'", 
  "--no-browser", 
  "--port={{ port }}", 
  "--NotebookApp.allow_origin='*'"
  ]
description = "Launch a Jupyter Lab server"

[tool.pixi.tasks.test]
args = [
  {arg = "n_pytest_workers", default = "3"},
]
depends-on = ["configure"]
cmd = [
  "rm", "-rf", "tests/logs", "&&",
  "mkdir", "-p", "tests/logs", "&&",
  "pytest", 
  "-rsx",   # print skipped and expected failures
  "-n",
  "{{ n_pytest_workers }}",
  "-vv",
  "--color=yes",
  "--durations=15",
  "tests",
]
env = {"DASK_CONFIG" = "tests/dask_config.yml"}
description = "Run test suite"

[tool.pixi.target.unix.tasks.download_bc_model]
cmd = ["./download_bc_model.sh"]
description = "Download ISF's barrel cortex model from Harvard Datverse"
cwd="installer"

[tool.pixi.target.win.tasks.download_bc_model]
cmd = ["./download_bc_model.bat"]
description = "Download ISF's barrel cortex model from Harvard Datverse"
cwd="installer"

[tool.pixi.feature.docs.tasks]
# Removing tutorials from doctrees and build is necessary to avoid slow recursion issues when building repeatedly
remove_tutorial_content = {cmd = [
  "rm", 
  "-rf", 
  "docs/_build/doctrees/_build",
  "docs/_build/doctrees/tutorials",
  "docs/_build/html/_build",
  "docs/_build/html/tutorials",
  "docs/_build/doctrees/nbsphinx"
  ], description = "Remove tutorial content from docs"}
build_docs = {cmd = ["make", "html"], description = "Build the documentation", cwd="docs", depends-on = ["remove_tutorial_content"]}
host_docs = {cmd = ["python", "-m", "http.server", "8000"], description = "Host the documentation", cwd="docs/_build/html"}


[tool.coverage.run]
# Ignore temporary dask files during test suite.
omit = ["dask-worker-space/*", "*/dask-worker-space/*"]

[tool.basedpyright]
pythonVersion = "3.8"
# we don't typehint arguments
reportUnknownArgumentType = false
reportArgumentType = false
# we don't typehint class instance variables
reportUnknownMemberType = false
# we don't typehing variables
reportUnknownVariableType = false
# Otherwise passing args to get or set gives error: No overloads for "__getitem__" match the provided arguments (basedpyrightreportCallIssue)
reportCallIssue = false
# We don't typehing parameters or functions
reportUnknownParameterType = false
reportMissingParameterType = false
# usually caught by the linter. there are many reasons why imports may remain unused, this clutters warnings
reportUnusedImport = false
# we allow "private" imports
reportPrivateLocalImportUsage = false
# When you call a function and don't care about the return value
reportUnusedCallResult = false
reportUnannotatedClassAttribute = false
ignore = ["**/*.ipynb"]
exclude = ["**/*.ipynb", "**.pixi**"]