From 5bbc70bf41278a6621e827abad3742124e52f794 Mon Sep 17 00:00:00 2001
From: pswain <peter.swain@ed.ac.uk>
Date: Thu, 2 May 2024 17:25:12 +0100
Subject: [PATCH] change: update to 3.10; rm legacy.py
---
poetry.lock | 115 +-
poetry3_8.lock | 2896 ++++++++++++++++++++++++++++++++++
pyproject.toml | 2 +
src/logfile_parser/legacy.py | 62 -
4 files changed, 2959 insertions(+), 116 deletions(-)
create mode 100644 poetry3_8.lock
delete mode 100644 src/logfile_parser/legacy.py
diff --git a/poetry.lock b/poetry.lock
index 146dfa7..355f909 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -891,61 +891,69 @@ six = "*"
[[package]]
name = "grpcio"
-version = "1.63.0"
+version = "1.62.2"
description = "HTTP/2-based RPC framework"
optional = false
-python-versions = ">=3.8"
+python-versions = ">=3.7"
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+
+[[package]]
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+version = "2.16.1"
+description = "An implementation of chunked, compressed, N-dimensional arrays for Python"
+optional = false
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+fasteners = "*"
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+numpy = ">=1.20,<1.21.0 || >1.21.0"
+
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+jupyter = ["ipytree (>=0.2.2)", "ipywidgets (>=8.0.0)", "notebook"]
+
+[[package]]
+name = "zeroc-ice"
+version = "3.6.5"
+description = "Ice is a comprehensive RPC framework with support for Python, C++, .NET, Java, JavaScript and more."
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+version = "3.18.1"
+description = "Backport of pathlib-compatible object wrapper for zip files"
+optional = false
+python-versions = ">=3.8"
+files = [
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+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 = ">=3.8, <3.11"
+content-hash = "39094ed93d82943d98be0882b20d6b83511338adc467ab0c4155dab515529ac3"
diff --git a/pyproject.toml b/pyproject.toml
index c4a349e..545045f 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -38,11 +38,13 @@ zarr = ">=2.14.0"
tensorflow-io-gcs-filesystem = "0.34.0"
chardet = "^5.2.0"
+grpcio = "1.62.2"
tensorflow = "2.13.1"
baby-seg = ">=0.30.4"
omero-py = { version = ">=5.6.2", optional = true }
+
[tool.black]
line-length = 79
diff --git a/src/logfile_parser/legacy.py b/src/logfile_parser/legacy.py
deleted file mode 100644
index 7607318..0000000
--- a/src/logfile_parser/legacy.py
+++ /dev/null
@@ -1,62 +0,0 @@
-#!/usr/bin/env jupyter
-
-try:
- from importlib_resources import files
-except ModuleNotFoundError:
- from importlib.resources import files
-
-
-from logfile_parser import Parser
-
-grammars_dir = files("logfile_parser") / "grammars"
-
-
-def get_examples_dir():
- return files("aliby").parent.parent / "examples" / "logfile_parser"
-
-
-def get_logfile_grammars_dir():
- return files("logfile_parser") / "grammars"
-
-
-def get_legacy_log_example_interface() -> dict:
- parsed = {}
- examples_dir = get_examples_dir()
- grammars_dir = get_logfile_grammars_dir()
-
- for gram in ("acq", "log"):
- for gram_file in grammars_dir.glob(f"multiDGUI_{gram}_format.json"):
- parser = Parser(gram_file)
- for file_to_parse in examples_dir.glob(f"*{gram}.txt"):
- with open(file_to_parse, "r") as f:
- parsed = {**parsed, **parser.parse(f)}
- return parsed
-
-
-def to_legacy(parsed_logfile: dict) -> dict:
- """
- Convert the output of the new logfile parsing to legacy to a minimal working set of metadata.
- This converts the new more complex metadata structure to the previous one that did not have configuration profiles, but instead one configuration per channel.
- This is a temporal solution as we transition into a more general metadata structure that accounts for heterogeneous groups.
-
- We convert image configs to channels, and add general metadata to the root.
- """
- name_translation = {
- "Microscope name": "microscope",
- }
- channel_name_translation = {
- "Image config": "channel",
- "Channel": "channel_hardware",
- "Exposure (ms)": "exposure",
- "Z spacing (um)": "zsect",
- }
-
- # Translate general data
- general = {v: d["general"][k] for k, v in name_translation.items()}
- # Translate and cast image configs
- channels = {
- v: list(map(_cast_type, parsed_logfile["image_config"][k]))
- for k, v in channel_name_translation.items()
- }
- legacy_format = {"channels": channels, **general}
- return legacy_format
--
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