From 5493c24904015b2f777dc2bd3af8296b6cf1fc8e Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Al=C3=A1n=20Mu=C3=B1oz?= <amuoz@ed.ac.uk>
Date: Tue, 1 Feb 2022 13:09:40 +0000
Subject: [PATCH] update tomlock
---
poetry.lock | 365 +++++++++++++++++++++++++------------------------
pyproject.toml | 20 ++-
2 files changed, 194 insertions(+), 191 deletions(-)
diff --git a/poetry.lock b/poetry.lock
index 339baa67..ac5aac82 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -78,7 +78,7 @@ python-versions = "*"
[[package]]
name = "aliby-agora"
-version = "0.2.11"
+version = "0.2.15"
description = "A gathering of shared utilities for the Swain Lab image processing pipeline."
category = "main"
optional = false
@@ -86,14 +86,15 @@ python-versions = ">=3.7.1,<3.11"
[package.dependencies]
h5py = "2.10"
-opencv-python = ">=4.5.5,<5.0.0"
-pandas = ">=1.3.5,<2.0.0"
+numpy = ">=1.6.0"
+opencv-python = "*"
+pandas = ">=1.1.4,<2.0.0"
py-find-1st = ">=1.1.5,<2.0.0"
PyYAML = ">=6.0,<7.0"
[[package]]
name = "aliby-baby"
-version = "0.1.2"
+version = "0.1.4"
description = "Birth Annotator for Budding Yeast"
category = "main"
optional = false
@@ -102,32 +103,33 @@ python-versions = ">=3.7.1,<3.11"
[package.dependencies]
imageio = "2.8.0"
matplotlib = ">=3.5.1,<4.0.0"
-numpy = ">=1.21.4,<2.0.0"
-pandas = ">=1.3.5,<2.0.0"
+numpy = ">=1.16.0,<2.0.0"
+pandas = ">=1.1.4"
Pillow = ">=9.0.0,<10.0.0"
+ray = {version = "1.4.0", extras = ["tune"]}
scikit-image = ">=0.19.1,<0.20.0"
scikit-learn = "0.22.2.post1"
-tensorflow = ">=1.15,<=2.3"
+tensorflow = "2.1.4"
tqdm = ">=4.62.3,<5.0.0"
tune-sklearn = ">=0.4.1,<0.5.0"
xgboost = "1.4.2"
[[package]]
name = "aliby-post"
-version = "0.1.9"
+version = "0.1.13"
description = "Post-processing tools for aliby pipeline."
category = "main"
optional = false
python-versions = ">=3.7.1,<3.11"
[package.dependencies]
-aliby-agora = ">=0.2.11,<0.3.0"
+aliby-agora = ">=0.2.14,<0.3.0"
catch22 = ">=0.2.0,<0.3.0"
leidenalg = ">=0.8.8,<0.9.0"
more-itertools = ">=8.12.0,<9.0.0"
numpy = ">=1.17.3"
-omni-gaussian = "*"
-pandas = ">=1.3.5,<2.0.0"
+omni-gaussian = ">=0.1.3,<0.2.0"
+pandas = ">=1.1.4,<2.0.0"
pathos = ">=0.2.8,<0.3.0"
PyYAML = ">=6.0,<7.0"
scipy = ">=1.4.1"
@@ -734,7 +736,7 @@ tests = ["pytest", "pytest-pep8", "pytest-xdist", "pytest-cov"]
[[package]]
name = "keras-preprocessing"
-version = "1.1.2"
+version = "1.1.0"
description = "Easy data preprocessing and data augmentation for deep learning models"
category = "main"
optional = false
@@ -747,7 +749,7 @@ six = ">=1.9.0"
[package.extras]
image = ["scipy (>=0.14)", "Pillow (>=5.2.0)"]
pep8 = ["flake8"]
-tests = ["pandas", "pillow", "tensorflow", "keras", "pytest", "pytest-xdist", "pytest-cov"]
+tests = ["pandas", "pillow", "tensorflow (==1.7)", "keras", "pytest", "pytest-xdist", "pytest-cov"]
[[package]]
name = "kiwisolver"
@@ -893,25 +895,13 @@ doc = ["sphinx (>=4.0,<5.0)", "pydata-sphinx-theme (>=0.6,<1.0)", "sphinx-galler
extra = ["lxml (>=4.5)", "pygraphviz (>=1.7)", "pydot (>=1.4.1)"]
test = ["pytest (>=6.2)", "pytest-cov (>=2.12)", "codecov (>=2.1)"]
-[[package]]
-name = "numexpr"
-version = "2.8.1"
-description = "Fast numerical expression evaluator for NumPy"
-category = "main"
-optional = false
-python-versions = "*"
-
-[package.dependencies]
-numpy = ">=1.13.3"
-packaging = "*"
-
[[package]]
name = "numpy"
-version = "1.21.5"
+version = "1.18.5"
description = "NumPy is the fundamental package for array computing with Python."
category = "main"
optional = false
-python-versions = ">=3.7,<3.11"
+python-versions = ">=3.5"
[[package]]
name = "nvidia-ml-py3"
@@ -954,7 +944,7 @@ zeroc-ice = ">=3.6.4,<3.7"
[[package]]
name = "omni-gaussian"
-version = "0.1.1"
+version = "0.1.3"
description = "For using Gaussian processes to smooth data nad estimate first and second derivatives"
category = "main"
optional = false
@@ -962,8 +952,8 @@ python-versions = ">=3.7.1,<3.11"
[package.dependencies]
matplotlib = ">=3.5.1,<4.0.0"
-numpy = ">=1.21.4,<2.0.0"
-scipy = ">=1.7.3,<2.0.0"
+numpy = ">=1.16.0,<2.0.0"
+scipy = ">=1.4.1"
[[package]]
name = "opencensus"
@@ -985,6 +975,17 @@ category = "main"
optional = false
python-versions = "*"
+[[package]]
+name = "opencv-python"
+version = "4.5.2.54"
+description = "Wrapper package for OpenCV python bindings."
+category = "main"
+optional = false
+python-versions = ">=3.6"
+
+[package.dependencies]
+numpy = ">=1.13.3"
+
[[package]]
name = "opencv-python"
version = "4.5.5.62"
@@ -995,8 +996,6 @@ python-versions = ">=3.6"
[package.dependencies]
numpy = [
- {version = ">=1.21.2", markers = "python_version >= \"3.10\" or python_version >= \"3.6\" and platform_system == \"Darwin\" and platform_machine == \"arm64\""},
- {version = ">=1.19.3", markers = "python_version >= \"3.6\" and platform_system == \"Linux\" and platform_machine == \"aarch64\" or python_version >= \"3.9\""},
{version = ">=1.14.5", markers = "python_version >= \"3.7\""},
{version = ">=1.17.3", markers = "python_version >= \"3.8\""},
]
@@ -1027,6 +1026,38 @@ python-versions = ">=3.6"
[package.dependencies]
pyparsing = ">=2.0.2,<3.0.5 || >3.0.5"
+[[package]]
+name = "pandas"
+version = "1.3.3"
+description = "Powerful data structures for data analysis, time series, and statistics"
+category = "main"
+optional = false
+python-versions = ">=3.7.1"
+
+[package.dependencies]
+numpy = ">=1.17.3"
+python-dateutil = ">=2.7.3"
+pytz = ">=2017.3"
+
+[package.extras]
+test = ["hypothesis (>=3.58)", "pytest (>=6.0)", "pytest-xdist"]
+
+[[package]]
+name = "pandas"
+version = "1.3.4"
+description = "Powerful data structures for data analysis, time series, and statistics"
+category = "main"
+optional = false
+python-versions = ">=3.7.1"
+
+[package.dependencies]
+numpy = {version = ">=1.17.3", markers = "platform_machine != \"aarch64\" and platform_machine != \"arm64\" and python_version < \"3.10\""}
+python-dateutil = ">=2.7.3"
+pytz = ">=2017.3"
+
+[package.extras]
+test = ["hypothesis (>=3.58)", "pytest (>=6.0)", "pytest-xdist"]
+
[[package]]
name = "pandas"
version = "1.3.5"
@@ -1036,12 +1067,7 @@ optional = false
python-versions = ">=3.7.1"
[package.dependencies]
-numpy = [
- {version = ">=1.17.3", markers = "platform_machine != \"aarch64\" and platform_machine != \"arm64\" and python_version < \"3.10\""},
- {version = ">=1.19.2", markers = "platform_machine == \"aarch64\" and python_version < \"3.10\""},
- {version = ">=1.20.0", markers = "platform_machine == \"arm64\" and python_version < \"3.10\""},
- {version = ">=1.21.0", markers = "python_version >= \"3.10\""},
-]
+numpy = {version = ">=1.17.3", markers = "platform_machine != \"aarch64\" and platform_machine != \"arm64\" and python_version < \"3.10\""}
python-dateutil = ">=2.7.3"
pytz = ">=2017.3"
@@ -1141,11 +1167,11 @@ dill = ["dill (>=0.3.4)"]
[[package]]
name = "prometheus-client"
-version = "0.12.0"
+version = "0.13.0"
description = "Python client for the Prometheus monitoring system."
category = "main"
optional = false
-python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
+python-versions = ">=3.6"
[package.extras]
twisted = ["twisted"]
@@ -1385,7 +1411,7 @@ tune = ["pandas", "tabulate", "tensorboardx"]
[[package]]
name = "redis"
-version = "4.1.1"
+version = "4.1.2"
description = "Python client for Redis database and key-value store"
category = "main"
optional = false
@@ -1641,22 +1667,6 @@ python-versions = ">=3.5"
lint = ["flake8", "mypy", "docutils-stubs"]
test = ["pytest"]
-[[package]]
-name = "tables"
-version = "3.7.0"
-description = "Hierarchical datasets for Python"
-category = "main"
-optional = false
-python-versions = ">=3.6"
-
-[package.dependencies]
-numexpr = ">=2.6.2"
-numpy = ">=1.19.0"
-packaging = "*"
-
-[package.extras]
-doc = ["sphinx (>=1.1)", "sphinx-rtd-theme", "numpydoc", "ipython"]
-
[[package]]
name = "tabulate"
version = "0.8.9"
@@ -1670,7 +1680,7 @@ widechars = ["wcwidth"]
[[package]]
name = "tensorboard"
-version = "2.0.2"
+version = "2.1.1"
description = "TensorBoard lets you watch Tensors Flow"
category = "main"
optional = false
@@ -1702,7 +1712,7 @@ protobuf = ">=3.8.0"
[[package]]
name = "tensorflow"
-version = "2.0.2"
+version = "2.1.4"
description = "TensorFlow is an open source machine learning framework for everyone."
category = "main"
optional = false
@@ -1714,20 +1724,21 @@ astor = ">=0.6.0"
gast = "0.2.2"
google-pasta = ">=0.1.6"
grpcio = ">=1.8.6"
+h5py = "<=2.10.0"
keras-applications = ">=1.0.8"
-keras-preprocessing = ">=1.0.5"
-numpy = ">=1.16.0,<2.0"
+keras-preprocessing = "1.1.0"
+numpy = ">=1.16.0,<1.19.0"
opt-einsum = ">=2.3.2"
-protobuf = ">=3.6.1"
-six = ">=1.10.0"
-tensorboard = ">=2.0.0,<2.1.0"
-tensorflow-estimator = ">=2.0.0,<2.1.0"
+protobuf = ">=3.8.0"
+six = ">=1.12.0"
+tensorboard = ">=2.1.0,<2.2.0"
+tensorflow-estimator = ">=2.1.0rc0,<2.2.0"
termcolor = ">=1.1.0"
wrapt = ">=1.11.1"
[[package]]
name = "tensorflow-estimator"
-version = "2.0.1"
+version = "2.1.0"
description = "TensorFlow Estimator."
category = "main"
optional = false
@@ -1920,7 +1931,7 @@ testing = ["pytest (>=6)", "pytest-checkdocs (>=2.4)", "pytest-flake8", "pytest-
[metadata]
lock-version = "1.1"
python-versions = ">=3.7.1,<3.11"
-content-hash = "d85b736014517401ba6cbd663015246c8fce0395297fab7dcd7a51487add7da0"
+content-hash = "7774509cdf681d86462b6c56d58da04a4598a146648283d2e98b6590e91e3bf8"
[metadata.files]
absl-py = [
@@ -2018,16 +2029,16 @@ alabaster = [
{file = "alabaster-0.7.12.tar.gz", hash = "sha256:a661d72d58e6ea8a57f7a86e37d86716863ee5e92788398526d58b26a4e4dc02"},
]
aliby-agora = [
- {file = "aliby-agora-0.2.11.tar.gz", hash = "sha256:9979349a937adcf0b1288b22e2d6fe62d2d3eadd3f9a07855debf8307642a9d0"},
- {file = "aliby_agora-0.2.11-py3-none-any.whl", hash = "sha256:3675cd754340623ecf3acc7ae0b9efa35afd9d69ccfbcedd0d116cd0d2c53d36"},
+ {file = "aliby-agora-0.2.15.tar.gz", hash = "sha256:2799b03aceaee9d2040693df56a6732edbf4d169224c27fdfdf2015b0bf8391f"},
+ {file = "aliby_agora-0.2.15-py3-none-any.whl", hash = "sha256:2ad45eb8d64ec740ebf8c526ccf2ef40bd8386526c2e7efd3fa5d300a742dbf4"},
]
aliby-baby = [
- {file = "aliby-baby-0.1.2.tar.gz", hash = "sha256:564a12b44fc7e4889fb70d5a82e39e7fb01f37eeb60669c684bd18677160de93"},
- {file = "aliby_baby-0.1.2-py3-none-any.whl", hash = "sha256:f8f11b82db89a74ad8cc48059370af889f246a83d4cbc45ce75d9475a15605f7"},
+ {file = "aliby-baby-0.1.4.tar.gz", hash = "sha256:c8393a698850e559466e7cbc5d9887b003ee498af1401b9fc055e5e1781ae9f9"},
+ {file = "aliby_baby-0.1.4-py3-none-any.whl", hash = "sha256:74035d05c3b2fe6652ec52b494c9f88c6587fd64102b224aaa88d91aa66872c0"},
]
aliby-post = [
- {file = "aliby-post-0.1.9.tar.gz", hash = "sha256:900fb4c51e99a1ae722bb510f80230258d9226c6d302bbcbde84122d48096930"},
- {file = "aliby_post-0.1.9-py3-none-any.whl", hash = "sha256:0ca6b4bb0597684c13da3782e9255fb341cbef6925cbb6ba78a83dbbeb20c057"},
+ {file = "aliby-post-0.1.13.tar.gz", hash = "sha256:49366e6b9f451d5324bdd1ee23edaa2279cf27540725b62ca5d778cf72b0c326"},
+ {file = "aliby_post-0.1.13-py3-none-any.whl", hash = "sha256:af8e95ea7eb8c47933cc8bf246731a4255ee4914ff551dcffc05d73ed3e7a56d"},
]
appdirs = [
{file = "appdirs-1.4.4-py2.py3-none-any.whl", hash = "sha256:a841dacd6b99318a741b166adb07e19ee71a274450e68237b4650ca1055ab128"},
@@ -2379,8 +2390,8 @@ keras-applications = [
{file = "Keras_Applications-1.0.8.tar.gz", hash = "sha256:5579f9a12bcde9748f4a12233925a59b93b73ae6947409ff34aa2ba258189fe5"},
]
keras-preprocessing = [
- {file = "Keras_Preprocessing-1.1.2-py2.py3-none-any.whl", hash = "sha256:7b82029b130ff61cc99b55f3bd27427df4838576838c5b2f65940e4fcec99a7b"},
- {file = "Keras_Preprocessing-1.1.2.tar.gz", hash = "sha256:add82567c50c8bc648c14195bf544a5ce7c1f76761536956c3d2978970179ef3"},
+ {file = "Keras_Preprocessing-1.1.0-py2.py3-none-any.whl", hash = "sha256:44aee5f2c4d80c3b29f208359fcb336df80f293a0bb6b1c738da43ca206656fb"},
+ {file = "Keras_Preprocessing-1.1.0.tar.gz", hash = "sha256:5a8debe01d840de93d49e05ccf1c9b81ae30e210d34dacbcc47aeb3049b528e5"},
]
kiwisolver = [
{file = "kiwisolver-1.3.2-cp310-cp310-macosx_10_9_universal2.whl", hash = "sha256:1d819553730d3c2724582124aee8a03c846ec4362ded1034c16fb3ef309264e6"},
@@ -2719,65 +2730,28 @@ networkx = [
{file = "networkx-2.6.3-py3-none-any.whl", hash = "sha256:80b6b89c77d1dfb64a4c7854981b60aeea6360ac02c6d4e4913319e0a313abef"},
{file = "networkx-2.6.3.tar.gz", hash = "sha256:c0946ed31d71f1b732b5aaa6da5a0388a345019af232ce2f49c766e2d6795c51"},
]
-numexpr = [
- {file = "numexpr-2.8.1-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:d148e99483e15de22d0acd5100136d39a336e91c8f8d37bf2e84e9f0ab4c0610"},
- {file = "numexpr-2.8.1-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:ebf31aeed426840aefe1e94c89bb0b7530a72be36444ed4c73e4411865b79be5"},
- {file = "numexpr-2.8.1-cp310-cp310-musllinux_1_1_x86_64.whl", hash = "sha256:3bab5add6628fa8bb66fba7b1f0eed5d8d0ce05fdd2dcc326dde8a297a961c46"},
- {file = "numexpr-2.8.1-cp310-cp310-win32.whl", hash = "sha256:79ec94295aa57f5a9d212116bb7359744cd2f9e05d477df0dee383b7f44b9588"},
- {file = "numexpr-2.8.1-cp310-cp310-win_amd64.whl", hash = "sha256:cfd89f63028f8df3c9b11bf2c98085184f967a09f543a77c3335f4a0ec54f124"},
- {file = "numexpr-2.8.1-cp36-cp36m-macosx_10_9_x86_64.whl", hash = "sha256:517f299c4bc8491b5117aa276e8f3cf7ee2e89223922e92e2ea78a32985d5087"},
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+ {file = "tensorflow-2.1.4-cp37-cp37m-macosx_10_11_x86_64.whl", hash = "sha256:d82b846a2c3f450f908321699d66b03924377a272ca81e16ca93c4955431c33a"},
+ {file = "tensorflow-2.1.4-cp37-cp37m-manylinux2010_x86_64.whl", hash = "sha256:b0a8bbab58bab297ec9cffa2df4dae0d03560acefe89ef6a31db00ce4cce022c"},
+ {file = "tensorflow-2.1.4-cp37-cp37m-win_amd64.whl", hash = "sha256:1d427d9b71bd42a49a83bcc08f56290f9cdb608e184537a13d0f9bad767be223"},
]
tensorflow-estimator = [
- {file = "tensorflow_estimator-2.0.1-py2.py3-none-any.whl", hash = "sha256:aa8deab25d09a9730dfbae8ec58f4eb00ec2a90b5ca3dcbd8fa0717103d3bbb3"},
+ {file = "tensorflow_estimator-2.1.0-py2.py3-none-any.whl", hash = "sha256:e5c5f648a636f18d1be4cf7ed46132b108a2f0f3fd9f1c850eba924263dc6972"},
]
termcolor = [
{file = "termcolor-1.1.0.tar.gz", hash = "sha256:1d6d69ce66211143803fbc56652b41d73b4a400a2891d7bf7a1cdf4c02de613b"},
diff --git a/pyproject.toml b/pyproject.toml
index b14a1c12..7a0c821e 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,6 +1,6 @@
[tool.poetry]
name = "aliby"
-version = "0.1.14"
+version = "0.1.15"
description = ""
authors = ["Alan Munoz <alan.munoz@ed.ac.uk>"]
packages = [
@@ -10,28 +10,24 @@ packages = [
[tool.poetry.dependencies]
python = ">=3.7.1,<3.11"
-ray = {version = "1.4.0", extras = ["tune"]}
-numpy = "^1.21.4"
+numpy = "^1.16.0"
dask = "^2021.12.0"
pathos = "^0.2.8"
tqdm = "^4.62.3"
-pandas = "^1.3.5"
scikit-learn = "0.22.2.post1"
-more-itertools = "^8.12.0"
+# more-itertools = "^8.12.0"
py-find-1st = "^1.1.5"
scikit-image = "^0.19.1"
-opencv-python = "^4.5.4"
+opencv-python = "*"
requests-toolbelt = "^0.9.1"
h5py = "2.10"
-tables = "^3.6.1"
+# tables = "^3.6.1"
imageio = "2.8.0"
omero-py = ">=5.6.2"
zeroc-ice = "3.6.5"
-tensorflow = ">=1.15,<=2.3"
-aliby-agora = "^0.2.11"
-aliby-baby = "^0.1.2"
-omni-gaussian = "^0.1.1"
-aliby-post = "^0.1.9"
+aliby-agora = "^0.2.14"
+aliby-baby = "^0.1.4"
+aliby-post = "^0.1.13"
[tool.poetry.dev-dependencies]
--
GitLab