From 9c49829ccc99295b24f2494ed3e5cee297c4566b Mon Sep 17 00:00:00 2001
From: Yohsuke Fukai <ysk@yfukai.net>
Date: Wed, 16 Feb 2022 13:14:50 +0900
Subject: [PATCH 1/4] initial try to add ray for parallel first translation
 comp.

---
 poetry.lock               | 374 +++++++++++++++++++++++++++++++++++++-
 pyproject.toml            |   1 +
 src/m2stitch/stitching.py |  68 ++++---
 3 files changed, 406 insertions(+), 37 deletions(-)

diff --git a/poetry.lock b/poetry.lock
index 4864d78..1177c89 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -18,7 +18,7 @@ python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
 name = "attrs"
 version = "21.4.0"
 description = "Classes Without Boilerplate"
-category = "dev"
+category = "main"
 optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*"
 
@@ -99,6 +99,20 @@ tomli = {version = "*", optional = true, markers = "extra == \"toml\""}
 [package.extras]
 toml = ["tomli"]
 
+[[package]]
+name = "deprecated"
+version = "1.2.13"
+description = "Python @deprecated decorator to deprecate old python classes, functions or methods."
+category = "main"
+optional = false
+python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
+
+[package.dependencies]
+wrapt = ">=1.10,<2"
+
+[package.extras]
+dev = ["tox", "bump2version (<1)", "sphinx (<2)", "importlib-metadata (<3)", "importlib-resources (<4)", "configparser (<5)", "sphinxcontrib-websupport (<2)", "zipp (<2)", "PyTest (<5)", "PyTest-Cov (<2.6)", "pytest", "pytest-cov"]
+
 [[package]]
 name = "distlib"
 version = "0.3.4"
@@ -135,7 +149,7 @@ pipenv = ["pipenv"]
 name = "filelock"
 version = "3.4.2"
 description = "A platform independent file lock."
-category = "dev"
+category = "main"
 optional = false
 python-versions = ">=3.7"
 
@@ -143,6 +157,20 @@ python-versions = ">=3.7"
 docs = ["furo (>=2021.8.17b43)", "sphinx (>=4.1)", "sphinx-autodoc-typehints (>=1.12)"]
 testing = ["covdefaults (>=1.2.0)", "coverage (>=4)", "pytest (>=4)", "pytest-cov", "pytest-timeout (>=1.4.2)"]
 
+[[package]]
+name = "grpcio"
+version = "1.43.0"
+description = "HTTP/2-based RPC framework"
+category = "main"
+optional = false
+python-versions = ">=3.6"
+
+[package.dependencies]
+six = ">=1.5.2"
+
+[package.extras]
+protobuf = ["grpcio-tools (>=1.43.0)"]
+
 [[package]]
 name = "identify"
 version = "2.4.9"
@@ -186,6 +214,21 @@ docs = ["sphinx", "jaraco.packaging (>=8.2)", "rst.linker (>=1.9)"]
 perf = ["ipython"]
 testing = ["pytest (>=6)", "pytest-checkdocs (>=2.4)", "pytest-flake8", "pytest-cov", "pytest-enabler (>=1.0.1)", "packaging", "pyfakefs", "flufl.flake8", "pytest-perf (>=0.9.2)", "pytest-black (>=0.3.7)", "pytest-mypy", "importlib-resources (>=1.3)"]
 
+[[package]]
+name = "importlib-resources"
+version = "5.4.0"
+description = "Read resources from Python packages"
+category = "main"
+optional = false
+python-versions = ">=3.6"
+
+[package.dependencies]
+zipp = {version = ">=3.1.0", markers = "python_version < \"3.10\""}
+
+[package.extras]
+docs = ["sphinx", "jaraco.packaging (>=8.2)", "rst.linker (>=1.9)"]
+testing = ["pytest (>=6)", "pytest-checkdocs (>=2.4)", "pytest-flake8", "pytest-cov", "pytest-enabler (>=1.0.1)", "pytest-black (>=0.3.7)", "pytest-mypy"]
+
 [[package]]
 name = "iniconfig"
 version = "1.1.1"
@@ -216,6 +259,23 @@ category = "main"
 optional = false
 python-versions = ">=3.6"
 
+[[package]]
+name = "jsonschema"
+version = "4.4.0"
+description = "An implementation of JSON Schema validation for Python"
+category = "main"
+optional = false
+python-versions = ">=3.7"
+
+[package.dependencies]
+attrs = ">=17.4.0"
+importlib-resources = {version = ">=1.4.0", markers = "python_version < \"3.9\""}
+pyrsistent = ">=0.14.0,<0.17.0 || >0.17.0,<0.17.1 || >0.17.1,<0.17.2 || >0.17.2"
+
+[package.extras]
+format = ["fqdn", "idna", "isoduration", "jsonpointer (>1.13)", "rfc3339-validator", "rfc3987", "uri-template", "webcolors (>=1.11)"]
+format_nongpl = ["fqdn", "idna", "isoduration", "jsonpointer (>1.13)", "rfc3339-validator", "rfc3986-validator (>0.1.0)", "uri-template", "webcolors (>=1.11)"]
+
 [[package]]
 name = "livereload"
 version = "2.6.3"
@@ -236,6 +296,14 @@ category = "dev"
 optional = false
 python-versions = ">=3.6"
 
+[[package]]
+name = "msgpack"
+version = "1.0.3"
+description = "MessagePack (de)serializer."
+category = "main"
+optional = false
+python-versions = "*"
+
 [[package]]
 name = "mypy"
 version = "0.930"
@@ -296,7 +364,7 @@ python-versions = ">=3.8"
 name = "packaging"
 version = "21.3"
 description = "Core utilities for Python packages"
-category = "dev"
+category = "main"
 optional = false
 python-versions = ">=3.6"
 
@@ -384,6 +452,14 @@ python-versions = ">=3.6.1"
 "ruamel.yaml" = ">=0.15"
 toml = "*"
 
+[[package]]
+name = "protobuf"
+version = "3.19.4"
+description = "Protocol Buffers"
+category = "main"
+optional = false
+python-versions = ">=3.5"
+
 [[package]]
 name = "py"
 version = "1.11.0"
@@ -404,13 +480,21 @@ python-versions = ">=3.5"
 name = "pyparsing"
 version = "3.0.7"
 description = "Python parsing module"
-category = "dev"
+category = "main"
 optional = false
 python-versions = ">=3.6"
 
 [package.extras]
 diagrams = ["jinja2", "railroad-diagrams"]
 
+[[package]]
+name = "pyrsistent"
+version = "0.18.1"
+description = "Persistent/Functional/Immutable data structures"
+category = "main"
+optional = false
+python-versions = ">=3.7"
+
 [[package]]
 name = "pytest"
 version = "7.0.1"
@@ -466,10 +550,60 @@ python-versions = "*"
 name = "pyyaml"
 version = "6.0"
 description = "YAML parser and emitter for Python"
-category = "dev"
+category = "main"
+optional = false
+python-versions = ">=3.6"
+
+[[package]]
+name = "ray"
+version = "1.10.0"
+description = "Ray provides a simple, universal API for building distributed applications."
+category = "main"
+optional = false
+python-versions = "*"
+
+[package.dependencies]
+attrs = "*"
+click = ">=7.0"
+filelock = "*"
+grpcio = ">=1.28.1"
+jsonschema = "*"
+msgpack = ">=1.0.0,<2.0.0"
+numpy = [
+    {version = ">=1.16", markers = "python_version < \"3.9\""},
+    {version = ">=1.19.3", markers = "python_version >= \"3.9\""},
+]
+protobuf = ">=3.15.3"
+pyyaml = "*"
+redis = ">=3.5.0"
+
+[package.extras]
+all = ["pandas", "colorful", "aiohttp-cors", "scikit-image", "numpy (>=1.19)", "aiosignal", "gpustat (>=1.0.0b1)", "tensorboardX (>=1.9)", "scipy", "aiohttp (>=3.7)", "dm-tree", "ray-cpp (==1.10.0)", "requests", "kubernetes", "frozenlist", "urllib3", "opentelemetry-exporter-otlp (==1.1.0)", "gym", "matplotlib (!=3.4.3)", "smart-open", "fsspec", "opencensus", "aiorwlock", "py-spy (>=0.2.0)", "fastapi", "lz4", "aioredis (<2)", "tabulate", "starlette", "pyarrow (>=4.0.1)", "opentelemetry-api (==1.1.0)", "prometheus-client (>=0.7.1)", "pyyaml", "uvicorn", "opentelemetry-sdk (==1.1.0)"]
+cpp = ["ray-cpp (==1.10.0)"]
+data = ["pandas", "pyarrow (>=4.0.1)", "fsspec", "numpy (>=1.19)"]
+default = ["aiohttp (>=3.7)", "aiosignal", "aiohttp-cors", "aioredis (<2)", "colorful", "frozenlist", "py-spy (>=0.2.0)", "requests", "gpustat (>=1.0.0b1)", "opencensus", "prometheus-client (>=0.7.1)", "smart-open"]
+k8s = ["kubernetes", "urllib3"]
+observability = ["opentelemetry-api (==1.1.0)", "opentelemetry-sdk (==1.1.0)", "opentelemetry-exporter-otlp (==1.1.0)"]
+rllib = ["pandas", "tabulate", "tensorboardX (>=1.9)", "requests", "dm-tree", "gym", "lz4", "matplotlib (!=3.4.3)", "scikit-image", "pyyaml", "scipy"]
+serve = ["frozenlist", "starlette", "aiohttp-cors", "colorful", "aiosignal", "gpustat (>=1.0.0b1)", "prometheus-client (>=0.7.1)", "aiorwlock", "opencensus", "py-spy (>=0.2.0)", "requests", "fastapi", "aiohttp (>=3.7)", "smart-open", "uvicorn", "aioredis (<2)"]
+tune = ["pandas", "tabulate", "tensorboardX (>=1.9)", "requests"]
+
+[[package]]
+name = "redis"
+version = "4.1.3"
+description = "Python client for Redis database and key-value store"
+category = "main"
 optional = false
 python-versions = ">=3.6"
 
+[package.dependencies]
+deprecated = ">=1.2.3"
+packaging = ">=20.4"
+
+[package.extras]
+hiredis = ["hiredis (>=1.0.0)"]
+ocsp = ["cryptography (>=36.0.1)", "pyopenssl (==20.0.1)", "requests (>=2.26.0)"]
+
 [[package]]
 name = "requests"
 version = "2.27.1"
@@ -818,6 +952,14 @@ six = ">=1.9.0,<2"
 docs = ["proselint (>=0.10.2)", "sphinx (>=3)", "sphinx-argparse (>=0.2.5)", "sphinx-rtd-theme (>=0.4.3)", "towncrier (>=21.3)"]
 testing = ["coverage (>=4)", "coverage-enable-subprocess (>=1)", "flaky (>=3)", "pytest (>=4)", "pytest-env (>=0.6.2)", "pytest-freezegun (>=0.4.1)", "pytest-mock (>=2)", "pytest-randomly (>=1)", "pytest-timeout (>=1)", "packaging (>=20.0)"]
 
+[[package]]
+name = "wrapt"
+version = "1.13.3"
+description = "Module for decorators, wrappers and monkey patching."
+category = "main"
+optional = false
+python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,>=2.7"
+
 [[package]]
 name = "xdoctest"
 version = "0.15.10"
@@ -842,7 +984,7 @@ tests = ["codecov", "scikit-build", "cmake", "ninja", "pybind11", "pytest", "pyt
 name = "zipp"
 version = "3.7.0"
 description = "Backport of pathlib-compatible object wrapper for zip files"
-category = "dev"
+category = "main"
 optional = false
 python-versions = ">=3.7"
 
@@ -853,7 +995,7 @@ testing = ["pytest (>=6)", "pytest-checkdocs (>=2.4)", "pytest-flake8", "pytest-
 [metadata]
 lock-version = "1.1"
 python-versions = ">=3.8,<3.11"
-content-hash = "88805c27fb4349cb5f380857ec941ba68659eb7db25e710856e1d79aa120832e"
+content-hash = "c4653366015035cbd5ed0e3e60195f5f934b820ccb2565604090b20d4390d5ff"
 
 [metadata.files]
 alabaster = [
@@ -935,6 +1077,10 @@ coverage = [
     {file = "coverage-6.3.1-pp36.pp37.pp38-none-any.whl", hash = "sha256:463e52616ea687fd323888e86bf25e864a3cc6335a043fad6bbb037dbf49bbe2"},
     {file = "coverage-6.3.1.tar.gz", hash = "sha256:6c3f6158b02ac403868eea390930ae64e9a9a2a5bbfafefbb920d29258d9f2f8"},
 ]
+deprecated = [
+    {file = "Deprecated-1.2.13-py2.py3-none-any.whl", hash = "sha256:64756e3e14c8c5eea9795d93c524551432a0be75629f8f29e67ab8caf076c76d"},
+    {file = "Deprecated-1.2.13.tar.gz", hash = "sha256:43ac5335da90c31c24ba028af536a91d41d53f9e6901ddb021bcc572ce44e38d"},
+]
 distlib = [
     {file = "distlib-0.3.4-py2.py3-none-any.whl", hash = "sha256:6564fe0a8f51e734df6333d08b8b94d4ea8ee6b99b5ed50613f731fd4089f34b"},
     {file = "distlib-0.3.4.zip", hash = "sha256:e4b58818180336dc9c529bfb9a0b58728ffc09ad92027a3f30b7cd91e3458579"},
@@ -951,6 +1097,52 @@ filelock = [
     {file = "filelock-3.4.2-py3-none-any.whl", hash = "sha256:cf0fc6a2f8d26bd900f19bf33915ca70ba4dd8c56903eeb14e1e7a2fd7590146"},
     {file = "filelock-3.4.2.tar.gz", hash = "sha256:38b4f4c989f9d06d44524df1b24bd19e167d851f19b50bf3e3559952dddc5b80"},
 ]
+grpcio = [
+    {file = "grpcio-1.43.0-cp310-cp310-linux_armv7l.whl", hash = "sha256:a4e786a8ee8b30b25d70ee52cda6d1dbba2a8ca2f1208d8e20ed8280774f15c8"},
+    {file = "grpcio-1.43.0-cp310-cp310-macosx_10_10_universal2.whl", hash = "sha256:af9c3742f6c13575c0d4147a8454da0ff5308c4d9469462ff18402c6416942fe"},
+    {file = "grpcio-1.43.0-cp310-cp310-manylinux_2_17_aarch64.whl", hash = "sha256:fdac966699707b5554b815acc272d81e619dd0999f187cd52a61aef075f870ee"},
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+    {file = "grpcio-1.43.0-cp310-cp310-win32.whl", hash = "sha256:c36f418c925a41fccada8f7ae9a3d3e227bfa837ddbfddd3d8b0ac252d12dda9"},
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 pytest = [
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@@ -1218,6 +1505,26 @@ pyyaml = [
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 ]
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 requests = [
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@@ -1439,6 +1746,59 @@ virtualenv = [
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 ]
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+]
 xdoctest = [
     {file = "xdoctest-0.15.10-py3-none-any.whl", hash = "sha256:7666bd0511df59275dfe94ef94b0fde9654afd14f00bf88902fdc9bcee77d527"},
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diff --git a/pyproject.toml b/pyproject.toml
index fafc200..1ef6387 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -33,6 +33,7 @@ networkx = "^2.5.1"
 scipy = "^1.6.3"
 tqdm = "^4.60.0"
 scikit-learn = "^1.0.2"
+ray = "^1.10.0"
 
 [tool.poetry.dev-dependencies]
 pytest = "^7.0.0"
diff --git a/src/m2stitch/stitching.py b/src/m2stitch/stitching.py
index 1dc5802..3ee15df 100644
--- a/src/m2stitch/stitching.py
+++ b/src/m2stitch/stitching.py
@@ -10,8 +10,8 @@
 
 import numpy as np
 import pandas as pd
+import ray
 from sklearn.covariance import EllipticEnvelope
-from tqdm import tqdm
 
 from ._constrained_refinement import refine_translations
 from ._global_optimization import compute_final_position
@@ -157,36 +157,44 @@ def get_index(col, row):
                 )
 
     ###### translationComputation ######
-    for direction in ["left", "top"]:
-        for i2, g in tqdm(grid.iterrows(), total=len(grid)):
-            i1 = g[direction]
-            if pd.isna(i1):
-                continue
-            image1 = images[i1]
-            image2 = images[i2]
-
-            PCM = pcm(image1, image2).real
-            if position_initial_guess is not None:
-
-                def get_lims(dimension, size):
-                    val = g[f"{direction}_{dimension}_init_guess"]
-                    r = size * overlap_diff_threshold / 100.0
-                    return np.round([val - r, val + r]).astype(np.int64)
-
-                lims = np.array(
-                    [
-                        get_lims(dimension, size)
-                        for dimension, size in zip("yx", [sizeY, sizeX])
-                    ]
-                )
-            else:
-                lims = np.array([[-sizeY, sizeY], [-sizeX, sizeX]])
-            yins, xins, _ = multi_peak_max(PCM)
-            max_peak = interpret_translation(
-                image1, image2, yins, xins, *lims[0], *lims[1]
+    @ray.remote
+    def calc_first_translation(i2, direction):
+        g = grid.loc[i2]
+        i1 = g[direction]
+        if pd.isna(i1):
+            return None
+        image1 = images[i1]
+        image2 = images[i2]
+
+        PCM = pcm(image1, image2).real
+        if position_initial_guess is not None:
+
+            def get_lims(dimension, size):
+                val = g[f"{direction}_{dimension}_init_guess"]
+                r = size * overlap_diff_threshold / 100.0
+                return np.round([val - r, val + r]).astype(np.int64)
+
+            lims = np.array(
+                [
+                    get_lims(dimension, size)
+                    for dimension, size in zip("yx", [sizeY, sizeX])
+                ]
             )
-            for j, key in enumerate(["ncc", "y", "x"]):
-                grid.loc[i2, f"{direction}_{key}_first"] = max_peak[j]
+        else:
+            lims = np.array([[-sizeY, sizeY], [-sizeX, sizeX]])
+        yins, xins, _ = multi_peak_max(PCM)
+        max_peak = interpret_translation(image1, image2, yins, xins, *lims[0], *lims[1])
+        return max_peak
+
+    for direction in ["left", "top"]:
+        print("computing translation for", direction)
+        res = ray.get(
+            [calc_first_translation.remote(i2, direction) for i2 in grid.index]
+        )
+        for i2, max_peak in zip(grid.index, res):
+            if max_peak is not None:
+                for j, key in enumerate(["ncc", "y", "x"]):
+                    grid.loc[i2, f"{direction}_{key}_first"] = max_peak[j]
 
     # TODO make threshold adjustable
     assert np.any(grid["top_ncc_first"] > 0.5), "there is no good top pair"

From dea7131a4c3d7be2ae4d1454b49431cedb06bbb8 Mon Sep 17 00:00:00 2001
From: Yohsuke Fukai <ysk@yfukai.net>
Date: Wed, 16 Feb 2022 13:17:29 +0900
Subject: [PATCH 2/4] minor version update

---
 poetry.lock    | 32 ++++++++++++++++----------------
 pyproject.toml |  2 +-
 2 files changed, 17 insertions(+), 17 deletions(-)

diff --git a/poetry.lock b/poetry.lock
index 1177c89..f7186c2 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -147,7 +147,7 @@ pipenv = ["pipenv"]
 
 [[package]]
 name = "filelock"
-version = "3.4.2"
+version = "3.5.0"
 description = "A platform independent file lock."
 category = "main"
 optional = false
@@ -173,7 +173,7 @@ protobuf = ["grpcio-tools (>=1.43.0)"]
 
 [[package]]
 name = "identify"
-version = "2.4.9"
+version = "2.4.10"
 description = "File identification library for Python"
 category = "dev"
 optional = false
@@ -200,7 +200,7 @@ python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
 
 [[package]]
 name = "importlib-metadata"
-version = "4.11.0"
+version = "4.11.1"
 description = "Read metadata from Python packages"
 category = "dev"
 optional = false
@@ -212,7 +212,7 @@ zipp = ">=0.5"
 [package.extras]
 docs = ["sphinx", "jaraco.packaging (>=8.2)", "rst.linker (>=1.9)"]
 perf = ["ipython"]
-testing = ["pytest (>=6)", "pytest-checkdocs (>=2.4)", "pytest-flake8", "pytest-cov", "pytest-enabler (>=1.0.1)", "packaging", "pyfakefs", "flufl.flake8", "pytest-perf (>=0.9.2)", "pytest-black (>=0.3.7)", "pytest-mypy", "importlib-resources (>=1.3)"]
+testing = ["pytest (>=6)", "pytest-checkdocs (>=2.4)", "pytest-flake8", "pytest-cov", "pytest-enabler (>=1.0.1)", "packaging", "pyfakefs", "flufl.flake8", "pytest-perf (>=0.9.2)", "pytest-black (>=0.3.7)", "pytest-mypy (>=0.9.1)", "importlib-resources (>=1.3)"]
 
 [[package]]
 name = "importlib-resources"
@@ -394,7 +394,7 @@ test = ["hypothesis (>=5.5.3)", "pytest (>=6.0)", "pytest-xdist (>=1.31)"]
 
 [[package]]
 name = "pandas-stubs"
-version = "1.2.0.47"
+version = "1.2.0.48"
 description = "Type annotations for Pandas"
 category = "main"
 optional = false
@@ -915,7 +915,7 @@ test = ["pytest", "typing-extensions", "mypy"]
 
 [[package]]
 name = "typing-extensions"
-version = "4.1.0"
+version = "4.1.1"
 description = "Backported and Experimental Type Hints for Python 3.6+"
 category = "dev"
 optional = false
@@ -1094,8 +1094,8 @@ dparse = [
     {file = "dparse-0.5.1.tar.gz", hash = "sha256:a1b5f169102e1c894f9a7d5ccf6f9402a836a5d24be80a986c7ce9eaed78f367"},
 ]
 filelock = [
-    {file = "filelock-3.4.2-py3-none-any.whl", hash = "sha256:cf0fc6a2f8d26bd900f19bf33915ca70ba4dd8c56903eeb14e1e7a2fd7590146"},
-    {file = "filelock-3.4.2.tar.gz", hash = "sha256:38b4f4c989f9d06d44524df1b24bd19e167d851f19b50bf3e3559952dddc5b80"},
+    {file = "filelock-3.5.0-py3-none-any.whl", hash = "sha256:a7141afb4feca60925cfc090b411fb9faaf542d06d58ece4f93d940265e6b995"},
+    {file = "filelock-3.5.0.tar.gz", hash = "sha256:137b661e657f7850eec9def2a001efadba3414be523b87cd3f9a037372d80a15"},
 ]
 grpcio = [
     {file = "grpcio-1.43.0-cp310-cp310-linux_armv7l.whl", hash = "sha256:a4e786a8ee8b30b25d70ee52cda6d1dbba2a8ca2f1208d8e20ed8280774f15c8"},
@@ -1144,8 +1144,8 @@ grpcio = [
     {file = "grpcio-1.43.0.tar.gz", hash = "sha256:735d9a437c262ab039d02defddcb9f8f545d7009ae61c0114e19dda3843febe5"},
 ]
 identify = [
-    {file = "identify-2.4.9-py2.py3-none-any.whl", hash = "sha256:bff7c4959d68510bc28b99d664b6a623e36c6eadc933f89a4e0a9ddff9b4fee4"},
-    {file = "identify-2.4.9.tar.gz", hash = "sha256:e926ae3b3dc142b6a7a9c65433eb14ccac751b724ee255f7c2ed3b5970d764fb"},
+    {file = "identify-2.4.10-py2.py3-none-any.whl", hash = "sha256:7d10baf6ba6f1912a0a49f4c1c2c49fa1718765c3a37d72d13b07779567c5b85"},
+    {file = "identify-2.4.10.tar.gz", hash = "sha256:e12b2aea3cf108de73ae055c2260783bde6601de09718f6768cf8e9f6f6322a6"},
 ]
 idna = [
     {file = "idna-3.3-py3-none-any.whl", hash = "sha256:84d9dd047ffa80596e0f246e2eab0b391788b0503584e8945f2368256d2735ff"},
@@ -1156,8 +1156,8 @@ imagesize = [
     {file = "imagesize-1.3.0.tar.gz", hash = "sha256:cd1750d452385ca327479d45b64d9c7729ecf0b3969a58148298c77092261f9d"},
 ]
 importlib-metadata = [
-    {file = "importlib_metadata-4.11.0-py3-none-any.whl", hash = "sha256:6affcdb3aec542dd98df8211e730bba6c5f2bec8288d47bacacde898f548c9ad"},
-    {file = "importlib_metadata-4.11.0.tar.gz", hash = "sha256:9e5e553bbba1843cb4a00823014b907616be46ee503d2b9ba001d214a8da218f"},
+    {file = "importlib_metadata-4.11.1-py3-none-any.whl", hash = "sha256:e0bc84ff355328a4adfc5240c4f211e0ab386f80aa640d1b11f0618a1d282094"},
+    {file = "importlib_metadata-4.11.1.tar.gz", hash = "sha256:175f4ee440a0317f6e8d81b7f8d4869f93316170a65ad2b007d2929186c8052c"},
 ]
 importlib-resources = [
     {file = "importlib_resources-5.4.0-py3-none-any.whl", hash = "sha256:33a95faed5fc19b4bc16b29a6eeae248a3fe69dd55d4d229d2b480e23eeaad45"},
@@ -1372,8 +1372,8 @@ pandas = [
     {file = "pandas-1.4.1.tar.gz", hash = "sha256:8db93ec98ac7cb5f8ac1420c10f5e3c43533153f253fe7fb6d891cf5aa2b80d2"},
 ]
 pandas-stubs = [
-    {file = "pandas-stubs-1.2.0.47.tar.gz", hash = "sha256:78801efb504abe75c2cf73cb3469b97003080e80fb03aa2a406ca4928f3fd887"},
-    {file = "pandas_stubs-1.2.0.47-py3-none-any.whl", hash = "sha256:54df4b9d344f2bbb5b65646a77d420b6f0250d2bb6742e5b04e65006acc60e8a"},
+    {file = "pandas-stubs-1.2.0.48.tar.gz", hash = "sha256:53cf78af9671acd6731941b852904d15ae4cf534e8d4f3ce1d5bd5a4e52057c5"},
+    {file = "pandas_stubs-1.2.0.48-py3-none-any.whl", hash = "sha256:a2555093f7e58f8b6cd0b8d73222ca03b8154e6787336957c16a4a4e9447a71f"},
 ]
 platformdirs = [
     {file = "platformdirs-2.5.0-py3-none-any.whl", hash = "sha256:30671902352e97b1eafd74ade8e4a694782bd3471685e78c32d0fdfd3aa7e7bb"},
@@ -1735,8 +1735,8 @@ typeguard = [
     {file = "typeguard-2.13.3.tar.gz", hash = "sha256:00edaa8da3a133674796cf5ea87d9f4b4c367d77476e185e80251cc13dfbb8c4"},
 ]
 typing-extensions = [
-    {file = "typing_extensions-4.1.0-py3-none-any.whl", hash = "sha256:c13180fbaa7cd97065a4915ceba012bdb31dc34743e63ddee16360161d358414"},
-    {file = "typing_extensions-4.1.0.tar.gz", hash = "sha256:ba97c5143e5bb067b57793c726dd857b1671d4b02ced273ca0538e71ff009095"},
+    {file = "typing_extensions-4.1.1-py3-none-any.whl", hash = "sha256:21c85e0fe4b9a155d0799430b0ad741cdce7e359660ccbd8b530613e8df88ce2"},
+    {file = "typing_extensions-4.1.1.tar.gz", hash = "sha256:1a9462dcc3347a79b1f1c0271fbe79e844580bb598bafa1ed208b94da3cdcd42"},
 ]
 urllib3 = [
     {file = "urllib3-1.26.8-py2.py3-none-any.whl", hash = "sha256:000ca7f471a233c2251c6c7023ee85305721bfdf18621ebff4fd17a8653427ed"},
diff --git a/pyproject.toml b/pyproject.toml
index 1ef6387..fe12a16 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "m2stitch"
-version = "0.6.0"
+version = "0.7.0"
 description = "M2Stitch"
 authors = ["Yohsuke Fukai <ysk@yfukai.net>"]
 license = "MIT"

From 104aa05cb4027072a434bdc0a204076c84db8790 Mon Sep 17 00:00:00 2001
From: Yohsuke Fukai <ysk@yfukai.net>
Date: Wed, 16 Feb 2022 13:20:28 +0900
Subject: [PATCH 3/4] update ray version

---
 poetry.lock    | 2 +-
 pyproject.toml | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/poetry.lock b/poetry.lock
index f7186c2..f0cc41d 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -995,7 +995,7 @@ testing = ["pytest (>=6)", "pytest-checkdocs (>=2.4)", "pytest-flake8", "pytest-
 [metadata]
 lock-version = "1.1"
 python-versions = ">=3.8,<3.11"
-content-hash = "c4653366015035cbd5ed0e3e60195f5f934b820ccb2565604090b20d4390d5ff"
+content-hash = "5185ecac027745527648836550f139ce8846fcb83ef7ec9aaae69320f03dcca4"
 
 [metadata.files]
 alabaster = [
diff --git a/pyproject.toml b/pyproject.toml
index fe12a16..8948690 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -33,7 +33,7 @@ networkx = "^2.5.1"
 scipy = "^1.6.3"
 tqdm = "^4.60.0"
 scikit-learn = "^1.0.2"
-ray = "^1.10.0"
+ray = "^1.8.0"
 
 [tool.poetry.dev-dependencies]
 pytest = "^7.0.0"

From 3a1921a813750142c9bb341bd95bc0fd02062d41 Mon Sep 17 00:00:00 2001
From: Yohsuke Fukai <ysk@yfukai.net>
Date: Thu, 3 Mar 2022 22:38:28 +0900
Subject: [PATCH 4/4] updated dependency

---
 poetry.lock | 374 +++++++++++++++++++++++++++++++++++++++++++++++++++-
 1 file changed, 367 insertions(+), 7 deletions(-)

diff --git a/poetry.lock b/poetry.lock
index 3840a27..417db8c 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -18,7 +18,7 @@ python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
 name = "attrs"
 version = "21.4.0"
 description = "Classes Without Boilerplate"
-category = "dev"
+category = "main"
 optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*"
 
@@ -99,6 +99,20 @@ tomli = {version = "*", optional = true, markers = "extra == \"toml\""}
 [package.extras]
 toml = ["tomli"]
 
+[[package]]
+name = "deprecated"
+version = "1.2.13"
+description = "Python @deprecated decorator to deprecate old python classes, functions or methods."
+category = "main"
+optional = false
+python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
+
+[package.dependencies]
+wrapt = ">=1.10,<2"
+
+[package.extras]
+dev = ["tox", "bump2version (<1)", "sphinx (<2)", "importlib-metadata (<3)", "importlib-resources (<4)", "configparser (<5)", "sphinxcontrib-websupport (<2)", "zipp (<2)", "PyTest (<5)", "PyTest-Cov (<2.6)", "pytest", "pytest-cov"]
+
 [[package]]
 name = "distlib"
 version = "0.3.4"
@@ -135,7 +149,7 @@ pipenv = ["pipenv"]
 name = "filelock"
 version = "3.6.0"
 description = "A platform independent file lock."
-category = "dev"
+category = "main"
 optional = false
 python-versions = ">=3.7"
 
@@ -143,6 +157,20 @@ python-versions = ">=3.7"
 docs = ["furo (>=2021.8.17b43)", "sphinx (>=4.1)", "sphinx-autodoc-typehints (>=1.12)"]
 testing = ["covdefaults (>=1.2.0)", "coverage (>=4)", "pytest (>=4)", "pytest-cov", "pytest-timeout (>=1.4.2)"]
 
+[[package]]
+name = "grpcio"
+version = "1.44.0"
+description = "HTTP/2-based RPC framework"
+category = "main"
+optional = false
+python-versions = ">=3.6"
+
+[package.dependencies]
+six = ">=1.5.2"
+
+[package.extras]
+protobuf = ["grpcio-tools (>=1.44.0)"]
+
 [[package]]
 name = "identify"
 version = "2.4.11"
@@ -186,6 +214,21 @@ docs = ["sphinx", "jaraco.packaging (>=9)", "rst.linker (>=1.9)"]
 perf = ["ipython"]
 testing = ["pytest (>=6)", "pytest-checkdocs (>=2.4)", "pytest-flake8", "pytest-cov", "pytest-enabler (>=1.0.1)", "packaging", "pyfakefs", "flufl.flake8", "pytest-perf (>=0.9.2)", "pytest-black (>=0.3.7)", "pytest-mypy (>=0.9.1)", "importlib-resources (>=1.3)"]
 
+[[package]]
+name = "importlib-resources"
+version = "5.4.0"
+description = "Read resources from Python packages"
+category = "main"
+optional = false
+python-versions = ">=3.6"
+
+[package.dependencies]
+zipp = {version = ">=3.1.0", markers = "python_version < \"3.10\""}
+
+[package.extras]
+docs = ["sphinx", "jaraco.packaging (>=8.2)", "rst.linker (>=1.9)"]
+testing = ["pytest (>=6)", "pytest-checkdocs (>=2.4)", "pytest-flake8", "pytest-cov", "pytest-enabler (>=1.0.1)", "pytest-black (>=0.3.7)", "pytest-mypy"]
+
 [[package]]
 name = "iniconfig"
 version = "1.1.1"
@@ -216,6 +259,23 @@ category = "main"
 optional = false
 python-versions = ">=3.6"
 
+[[package]]
+name = "jsonschema"
+version = "4.4.0"
+description = "An implementation of JSON Schema validation for Python"
+category = "main"
+optional = false
+python-versions = ">=3.7"
+
+[package.dependencies]
+attrs = ">=17.4.0"
+importlib-resources = {version = ">=1.4.0", markers = "python_version < \"3.9\""}
+pyrsistent = ">=0.14.0,<0.17.0 || >0.17.0,<0.17.1 || >0.17.1,<0.17.2 || >0.17.2"
+
+[package.extras]
+format = ["fqdn", "idna", "isoduration", "jsonpointer (>1.13)", "rfc3339-validator", "rfc3987", "uri-template", "webcolors (>=1.11)"]
+format_nongpl = ["fqdn", "idna", "isoduration", "jsonpointer (>1.13)", "rfc3339-validator", "rfc3986-validator (>0.1.0)", "uri-template", "webcolors (>=1.11)"]
+
 [[package]]
 name = "livereload"
 version = "2.6.3"
@@ -236,6 +296,14 @@ category = "dev"
 optional = false
 python-versions = ">=3.7"
 
+[[package]]
+name = "msgpack"
+version = "1.0.3"
+description = "MessagePack (de)serializer."
+category = "main"
+optional = false
+python-versions = "*"
+
 [[package]]
 name = "mypy"
 version = "0.930"
@@ -296,7 +364,7 @@ python-versions = ">=3.8"
 name = "packaging"
 version = "21.3"
 description = "Core utilities for Python packages"
-category = "dev"
+category = "main"
 optional = false
 python-versions = ">=3.6"
 
@@ -384,6 +452,14 @@ python-versions = ">=3.6.1"
 "ruamel.yaml" = ">=0.15"
 toml = "*"
 
+[[package]]
+name = "protobuf"
+version = "3.19.4"
+description = "Protocol Buffers"
+category = "main"
+optional = false
+python-versions = ">=3.5"
+
 [[package]]
 name = "py"
 version = "1.11.0"
@@ -404,13 +480,21 @@ python-versions = ">=3.5"
 name = "pyparsing"
 version = "3.0.7"
 description = "Python parsing module"
-category = "dev"
+category = "main"
 optional = false
 python-versions = ">=3.6"
 
 [package.extras]
 diagrams = ["jinja2", "railroad-diagrams"]
 
+[[package]]
+name = "pyrsistent"
+version = "0.18.1"
+description = "Persistent/Functional/Immutable data structures"
+category = "main"
+optional = false
+python-versions = ">=3.7"
+
 [[package]]
 name = "pytest"
 version = "7.0.1"
@@ -466,10 +550,60 @@ python-versions = "*"
 name = "pyyaml"
 version = "6.0"
 description = "YAML parser and emitter for Python"
-category = "dev"
+category = "main"
+optional = false
+python-versions = ">=3.6"
+
+[[package]]
+name = "ray"
+version = "1.10.0"
+description = "Ray provides a simple, universal API for building distributed applications."
+category = "main"
+optional = false
+python-versions = "*"
+
+[package.dependencies]
+attrs = "*"
+click = ">=7.0"
+filelock = "*"
+grpcio = ">=1.28.1"
+jsonschema = "*"
+msgpack = ">=1.0.0,<2.0.0"
+numpy = [
+    {version = ">=1.16", markers = "python_version < \"3.9\""},
+    {version = ">=1.19.3", markers = "python_version >= \"3.9\""},
+]
+protobuf = ">=3.15.3"
+pyyaml = "*"
+redis = ">=3.5.0"
+
+[package.extras]
+all = ["pandas", "colorful", "aiohttp-cors", "scikit-image", "numpy (>=1.19)", "aiosignal", "gpustat (>=1.0.0b1)", "tensorboardX (>=1.9)", "scipy", "aiohttp (>=3.7)", "dm-tree", "ray-cpp (==1.10.0)", "requests", "kubernetes", "frozenlist", "urllib3", "opentelemetry-exporter-otlp (==1.1.0)", "gym", "matplotlib (!=3.4.3)", "smart-open", "fsspec", "opencensus", "aiorwlock", "py-spy (>=0.2.0)", "fastapi", "lz4", "aioredis (<2)", "tabulate", "starlette", "pyarrow (>=4.0.1)", "opentelemetry-api (==1.1.0)", "prometheus-client (>=0.7.1)", "pyyaml", "uvicorn", "opentelemetry-sdk (==1.1.0)"]
+cpp = ["ray-cpp (==1.10.0)"]
+data = ["pandas", "pyarrow (>=4.0.1)", "fsspec", "numpy (>=1.19)"]
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+observability = ["opentelemetry-api (==1.1.0)", "opentelemetry-sdk (==1.1.0)", "opentelemetry-exporter-otlp (==1.1.0)"]
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+tune = ["pandas", "tabulate", "tensorboardX (>=1.9)", "requests"]
+
+[[package]]
+name = "redis"
+version = "4.1.4"
+description = "Python client for Redis database and key-value store"
+category = "main"
 optional = false
 python-versions = ">=3.6"
 
+[package.dependencies]
+deprecated = ">=1.2.3"
+packaging = ">=20.4"
+
+[package.extras]
+hiredis = ["hiredis (>=1.0.0)"]
+ocsp = ["cryptography (>=36.0.1)", "pyopenssl (==20.0.1)", "requests (>=2.26.0)"]
+
 [[package]]
 name = "requests"
 version = "2.27.1"
@@ -818,6 +952,14 @@ six = ">=1.9.0,<2"
 docs = ["proselint (>=0.10.2)", "sphinx (>=3)", "sphinx-argparse (>=0.2.5)", "sphinx-rtd-theme (>=0.4.3)", "towncrier (>=21.3)"]
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+[[package]]
+name = "wrapt"
+version = "1.13.3"
+description = "Module for decorators, wrappers and monkey patching."
+category = "main"
+optional = false
+python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,>=2.7"
+
 [[package]]
 name = "xdoctest"
 version = "0.15.10"
@@ -842,7 +984,7 @@ tests = ["codecov", "scikit-build", "cmake", "ninja", "pybind11", "pytest", "pyt
 name = "zipp"
 version = "3.7.0"
 description = "Backport of pathlib-compatible object wrapper for zip files"
-category = "dev"
+category = "main"
 optional = false
 python-versions = ">=3.7"
 
@@ -853,7 +995,7 @@ testing = ["pytest (>=6)", "pytest-checkdocs (>=2.4)", "pytest-flake8", "pytest-
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