From eac53e591057e398149a2717943391c93bae308e Mon Sep 17 00:00:00 2001
From: Peter Swain <pswain@Home-iMac.local>
Date: Thu, 2 May 2024 09:35:56 +0100
Subject: [PATCH] change: updated pyproject.toml

Includes pathos and napari.
---
 examples/run_gr.py |    6 +-
 growth_rate.py     |    3 +-
 poetry.lock        | 3838 ++++++++++++++++++++++++++++++++++++++------
 pyproject.toml     |   20 +-
 4 files changed, 3328 insertions(+), 539 deletions(-)

diff --git a/examples/run_gr.py b/examples/run_gr.py
index 159dbca..d7dd307 100644
--- a/examples/run_gr.py
+++ b/examples/run_gr.py
@@ -1,5 +1,5 @@
-from wela.growth_rate import find_all_grs, add_gr_from_pkl
 from wela.dataloader import dataloader
+from wela.growth_rate import add_gr_from_pkl, find_all_grs
 
 run_GP = True
 
@@ -27,8 +27,8 @@ datasets = [
 for dataname in datasets:
     if run_GP:
         # generate pkl files and pdf files for inspection
-        # run first with max_no_cells=2 to check the results
-        find_all_grs(
+        # run first with max_no_cells=20 to check the results
+        res_b, res_m = find_all_grs(
             dataname,
             max_no_cells=20,
             wdir=wdir,
diff --git a/growth_rate.py b/growth_rate.py
index a255410..e95fbf8 100644
--- a/growth_rate.py
+++ b/growth_rate.py
@@ -223,7 +223,7 @@ def run_parallel(t, volume, buddings_df, buddings, no_cells, config):
 
     The CPU cores either run mothers or buds from the same mother.
     """
-    batch_size = multiprocessing.cpu_count()
+    batch_size = np.max([multiprocessing.cpu_count() - 1, 1])
     pool = ProcessingPool(nodes=batch_size)
 
     def batch_GP(x, y):
@@ -250,6 +250,7 @@ def run_parallel(t, volume, buddings_df, buddings, no_cells, config):
         for idx in range(no_cells):
             print(f" buds for {idx:d}/{no_cells-1:d}")
             ivol = volume[idx, :]
+            # indices for buds
             bs = np.concatenate(([0], np.where(buddings[idx, :])[0], [t.size]))
             # get bud data
             t_batch = [t[start:end] for start, end in zip(bs, bs[1:])]
diff --git a/poetry.lock b/poetry.lock
index 5e06f0b..2ad4622 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -1,667 +1,3451 @@
-# This file is automatically @generated by Poetry 1.4.0 and should not be changed by hand.
+# This file is automatically @generated by Poetry 1.8.2 and should not be changed by hand.
 
 [[package]]
-name = "black"
-version = "23.3.0"
-description = "The uncompromising code formatter."
-category = "dev"
+name = "alabaster"
+version = "0.7.13"
+description = "A configurable sidebar-enabled Sphinx theme"
+optional = false
+python-versions = ">=3.6"
+files = [
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+    {file = "alabaster-0.7.13.tar.gz", hash = "sha256:a27a4a084d5e690e16e01e03ad2b2e552c61a65469419b907243193de1a84ae2"},
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+
+[[package]]
+name = "annotated-types"
+version = "0.6.0"
+description = "Reusable constraint types to use with typing.Annotated"
+optional = false
+python-versions = ">=3.8"
+files = [
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+version = "0.2.6"
+description = "Generic application schema implemented in python"
+optional = false
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+pydantic-compat = ">=0.1.1"
+typing-extensions = "*"
+
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+dev = ["app-model[test-qt]", "ipython", "mypy", "pdbpp", "pre-commit", "rich"]
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+test = ["pytest (>=6.0)", "pytest-cov"]
+test-qt = ["app-model[qt]", "app-model[test]", "fonticon-fontawesome6", "pytest-qt"]
+
+[[package]]
+name = "appdirs"
+version = "1.4.4"
+description = "A small Python module for determining appropriate platform-specific dirs, e.g. a \"user data dir\"."
+optional = false
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+
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 ]
 
 [[package]]
 name = "zipp"
-version = "3.15.0"
+version = "3.18.1"
 description = "Backport of pathlib-compatible object wrapper for zip files"
-category = "dev"
 optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.8"
 files = [
-    {file = "zipp-3.15.0-py3-none-any.whl", hash = "sha256:48904fc76a60e542af151aded95726c1a5c34ed43ab4134b597665c86d7ad556"},
-    {file = "zipp-3.15.0.tar.gz", hash = "sha256:112929ad649da941c23de50f356a2b5570c954b65150642bccdd66bf194d224b"},
+    {file = "zipp-3.18.1-py3-none-any.whl", hash = "sha256:206f5a15f2af3dbaee80769fb7dc6f249695e940acca08dfb2a4769fe61e538b"},
+    {file = "zipp-3.18.1.tar.gz", hash = "sha256:2884ed22e7d8961de1c9a05142eb69a247f120291bc0206a00a7642f09b5b715"},
 ]
 
 [package.extras]
-docs = ["furo", "jaraco.packaging (>=9)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-lint"]
-testing = ["big-O", "flake8 (<5)", "jaraco.functools", "jaraco.itertools", "more-itertools", "pytest (>=6)", "pytest-black (>=0.3.7)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=1.3)", "pytest-flake8", "pytest-mypy (>=0.9.1)"]
+docs = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-lint"]
+testing = ["big-O", "jaraco.functools", "jaraco.itertools", "more-itertools", "pytest (>=6)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=2.2)", "pytest-ignore-flaky", "pytest-mypy", "pytest-ruff (>=0.2.1)"]
 
 [metadata]
 lock-version = "2.0"
-python-versions = "^3.7.1,<3.11"
-content-hash = "a42d56686148708909b220389d2088456d499aec6c63497f81a9e996f4fd4ac1"
+python-versions = ">=3.8,<3.11"
+content-hash = "a1303c2bc789c7c01c91791e25fe3035ce6c8a396735925b70cc01bd8e0661cd"
diff --git a/pyproject.toml b/pyproject.toml
index 8c5465e..fcc6f75 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -4,19 +4,23 @@ version = "0.1.0"
 description = "Time-series analysis"
 authors = ["Swainlab"]
 
+[build-system]
+requires = ["poetry-core>=1.0.0"]
+build-backend = "poetry.core.masonry.api"
 
 [tool.poetry.dependencies]
-python = "^3.7.1,<3.11"
-numpy = ">=1.6.0"
-scipy = ">=1.7.3"
+python = ">=3.8,<3.11"
+numpy = ">=1.21.6"
 matplotlib = ">=3.5.2"
+pandas = ">=2.0.3"
+scipy = ">=1.7.3"
 
-[tool.poetry.dev-dependencies]
-black = ">=22.3.0"
+h5py = ">=3.11.0"
+gaussianprocessderivatives = ">=0.1.65"
+pathos = ">=0.3.2"
+
+napari = ">=0.4.19.post1"
 
 [tool.black]
 line-length = 79
 
-[build-system]
-requires = ["poetry-core>=1.0.0"]
-build-backend = "poetry.core.masonry.api"
-- 
GitLab