From f2e6557b764a4edcbd8d2b49e9c087563fb3ce11 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Al=C3=A1n=20Mu=C3=B1oz?= <alan.munoz@ed.ac.uk>
Date: Sat, 24 Sep 2022 20:02:46 +0100
Subject: [PATCH] tweak(all): migrate to src/ layout
---
poetry.lock | 153 ++++++++++++++++--
pyproject.toml | 15 +-
{agora => src/agora}/__init__.py | 0
{agora => src/agora}/abc.py | 0
{agora => src/agora}/io/__init__.py | 0
{agora => src/agora}/io/bridge.py | 0
{agora => src/agora}/io/cells.py | 0
{agora => src/agora}/io/metadata.py | 0
{agora => src/agora}/io/reader.py | 0
{agora => src/agora}/io/signal.py | 0
{agora => src/agora}/io/utils.py | 0
{agora => src/agora}/io/writer.py | 0
{agora => src/agora}/utils/__init__.py | 0
{agora => src/agora}/utils/example.py | 0
{agora => src/agora}/utils/lineage.py | 0
{aliby => src/aliby}/__init__.py | 0
{aliby => src/aliby}/baby_client.py | 0
{aliby => src/aliby}/haystack.py | 0
{aliby => src/aliby}/io/__init__.py | 0
{aliby => src/aliby}/io/dataset.py | 0
{aliby => src/aliby}/io/image.py | 0
{aliby => src/aliby}/io/omero.py | 0
{aliby => src/aliby}/io/utils.py | 0
{aliby => src/aliby}/pipeline.py | 0
{aliby => src/aliby}/tile/__init__.py | 0
{aliby => src/aliby}/tile/tiler.py | 0
{aliby => src/aliby}/tile/traps.py | 0
{aliby => src/aliby}/utils/__init__.py | 0
{aliby => src/aliby}/utils/argo.py | 0
{aliby => src/aliby}/utils/cache.py | 0
{aliby => src/aliby}/utils/imageViewer.py | 0
{extraction => src/extraction}/__init__.py | 0
.../extraction}/core/__init__.py | 0
.../extraction}/core/extractor.py | 0
.../extraction}/core/functions/__init__.py | 0
.../extraction}/core/functions/cell.py | 0
.../core/functions/custom/__init__.py | 0
.../core/functions/custom/localisation.py | 0
.../extraction}/core/functions/defaults.py | 0
.../core/functions/distributors.py | 0
.../extraction}/core/functions/io.py | 0
.../extraction}/core/functions/loaders.py | 0
.../extraction}/core/functions/math_utils.py | 0
.../extraction}/core/functions/trap.py | 0
.../extraction}/core/functions/utils.py | 0
.../extraction}/core/functions/versioning.py | 0
{extraction => src/extraction}/core/omero.py | 0
.../extraction}/examples/data.py | 0
.../extraction}/examples/pos_example.py | 0
.../extraction}/examples/tiler_error.py | 0
.../logfile_parser}/README.md | 0
.../logfile_parser}/__init__.py | 0
.../grammars/cExperiment_log_format.json | 0
.../grammars/multiDGUI_acq_format.json | 0
.../grammars/multiDGUI_log_format.json | 0
.../logfile_parser}/logfile_parser.py | 0
.../postprocessor}/__init__.py | 0
.../benchmarks/post_processing.py | 0
.../postprocessor}/compiler.py | 0
.../postprocessor}/core/__init__.py | 0
.../postprocessor}/core/abc.py | 0
.../postprocessor}/core/export_pdf.py | 0
.../postprocessor}/core/functions/__init__.py | 0
.../postprocessor}/core/functions/tracks.py | 0
.../postprocessor}/core/group.py | 0
.../postprocessor}/core/lineageprocess.py | 0
.../core/multisignal/__init__.py | 0
.../core/multisignal/aggregate.py | 0
.../postprocessor}/core/multisignal/align.py | 0
.../core/multisignal/crosscorr.py | 0
.../postprocessor}/core/multisignal/mi.py | 0
.../postprocessor}/core/processes/__init__.py | 0
.../postprocessor}/core/processes/autoreg.py | 0
.../core/processes/bud_metric.py | 0
.../postprocessor}/core/processes/buddings.py | 0
.../postprocessor}/core/processes/butter.py | 0
.../postprocessor}/core/processes/catch22.py | 0
.../postprocessor}/core/processes/detrend.py | 0
.../postprocessor}/core/processes/dsignal.py | 0
.../postprocessor}/core/processes/fft.py | 0
.../core/processes/findpeaks.py | 0
.../postprocessor}/core/processes/gpsignal.py | 0
.../postprocessor}/core/processes/knngraph.py | 0
.../postprocessor}/core/processes/leiden.py | 0
.../core/processes/lineageprocess.py | 0
.../postprocessor}/core/processes/merger.py | 0
.../postprocessor}/core/processes/picker.py | 0
.../postprocessor}/core/processes/savgol.py | 0
.../core/processes/standardscaler.py | 0
.../postprocessor}/core/processes/template.py | 0
.../core/processes/umapembedding.py | 0
.../postprocessor}/core/processor.py | 0
.../postprocessor}/core/report.py | 0
.../postprocessor}/grouper.py | 0
.../postprocessor}/routines/__init__.py | 0
.../postprocessor}/routines/boxplot.py | 0
.../postprocessor}/routines/heatmap.py | 0
.../postprocessor}/routines/histogram.py | 0
.../postprocessor}/routines/mean_plot.py | 0
.../postprocessor}/routines/median_plot.py | 0
.../postprocessor}/routines/plot_utils.py | 0
.../postprocessor}/routines/plottingabc.py | 0
.../routines/single_birth_plot.py | 0
.../postprocessor}/routines/single_plot.py | 0
104 files changed, 146 insertions(+), 22 deletions(-)
rename {agora => src/agora}/__init__.py (100%)
rename {agora => src/agora}/abc.py (100%)
rename {agora => src/agora}/io/__init__.py (100%)
rename {agora => src/agora}/io/bridge.py (100%)
rename {agora => src/agora}/io/cells.py (100%)
rename {agora => src/agora}/io/metadata.py (100%)
rename {agora => src/agora}/io/reader.py (100%)
rename {agora => src/agora}/io/signal.py (100%)
rename {agora => src/agora}/io/utils.py (100%)
rename {agora => src/agora}/io/writer.py (100%)
rename {agora => src/agora}/utils/__init__.py (100%)
rename {agora => src/agora}/utils/example.py (100%)
rename {agora => src/agora}/utils/lineage.py (100%)
rename {aliby => src/aliby}/__init__.py (100%)
rename {aliby => src/aliby}/baby_client.py (100%)
rename {aliby => src/aliby}/haystack.py (100%)
rename {aliby => src/aliby}/io/__init__.py (100%)
rename {aliby => src/aliby}/io/dataset.py (100%)
rename {aliby => src/aliby}/io/image.py (100%)
rename {aliby => src/aliby}/io/omero.py (100%)
rename {aliby => src/aliby}/io/utils.py (100%)
rename {aliby => src/aliby}/pipeline.py (100%)
rename {aliby => src/aliby}/tile/__init__.py (100%)
rename {aliby => src/aliby}/tile/tiler.py (100%)
rename {aliby => src/aliby}/tile/traps.py (100%)
rename {aliby => src/aliby}/utils/__init__.py (100%)
rename {aliby => src/aliby}/utils/argo.py (100%)
rename {aliby => src/aliby}/utils/cache.py (100%)
rename {aliby => src/aliby}/utils/imageViewer.py (100%)
rename {extraction => src/extraction}/__init__.py (100%)
rename {extraction => src/extraction}/core/__init__.py (100%)
rename {extraction => src/extraction}/core/extractor.py (100%)
rename {extraction => src/extraction}/core/functions/__init__.py (100%)
rename {extraction => src/extraction}/core/functions/cell.py (100%)
rename {extraction => src/extraction}/core/functions/custom/__init__.py (100%)
rename {extraction => src/extraction}/core/functions/custom/localisation.py (100%)
rename {extraction => src/extraction}/core/functions/defaults.py (100%)
rename {extraction => src/extraction}/core/functions/distributors.py (100%)
rename {extraction => src/extraction}/core/functions/io.py (100%)
rename {extraction => src/extraction}/core/functions/loaders.py (100%)
rename {extraction => src/extraction}/core/functions/math_utils.py (100%)
rename {extraction => src/extraction}/core/functions/trap.py (100%)
rename {extraction => src/extraction}/core/functions/utils.py (100%)
rename {extraction => src/extraction}/core/functions/versioning.py (100%)
rename {extraction => src/extraction}/core/omero.py (100%)
rename {extraction => src/extraction}/examples/data.py (100%)
rename {extraction => src/extraction}/examples/pos_example.py (100%)
rename {extraction => src/extraction}/examples/tiler_error.py (100%)
rename {logfile_parser => src/logfile_parser}/README.md (100%)
rename {logfile_parser => src/logfile_parser}/__init__.py (100%)
rename {logfile_parser => src/logfile_parser}/grammars/cExperiment_log_format.json (100%)
rename {logfile_parser => src/logfile_parser}/grammars/multiDGUI_acq_format.json (100%)
rename {logfile_parser => src/logfile_parser}/grammars/multiDGUI_log_format.json (100%)
rename {logfile_parser => src/logfile_parser}/logfile_parser.py (100%)
rename {postprocessor => src/postprocessor}/__init__.py (100%)
rename {postprocessor => src/postprocessor}/benchmarks/post_processing.py (100%)
rename {postprocessor => src/postprocessor}/compiler.py (100%)
rename {postprocessor => src/postprocessor}/core/__init__.py (100%)
rename {postprocessor => src/postprocessor}/core/abc.py (100%)
rename {postprocessor => src/postprocessor}/core/export_pdf.py (100%)
rename {postprocessor => src/postprocessor}/core/functions/__init__.py (100%)
rename {postprocessor => src/postprocessor}/core/functions/tracks.py (100%)
rename {postprocessor => src/postprocessor}/core/group.py (100%)
rename {postprocessor => src/postprocessor}/core/lineageprocess.py (100%)
rename {postprocessor => src/postprocessor}/core/multisignal/__init__.py (100%)
rename {postprocessor => src/postprocessor}/core/multisignal/aggregate.py (100%)
rename {postprocessor => src/postprocessor}/core/multisignal/align.py (100%)
rename {postprocessor => src/postprocessor}/core/multisignal/crosscorr.py (100%)
rename {postprocessor => src/postprocessor}/core/multisignal/mi.py (100%)
rename {postprocessor => src/postprocessor}/core/processes/__init__.py (100%)
rename {postprocessor => src/postprocessor}/core/processes/autoreg.py (100%)
rename {postprocessor => src/postprocessor}/core/processes/bud_metric.py (100%)
rename {postprocessor => src/postprocessor}/core/processes/buddings.py (100%)
rename {postprocessor => src/postprocessor}/core/processes/butter.py (100%)
rename {postprocessor => src/postprocessor}/core/processes/catch22.py (100%)
rename {postprocessor => src/postprocessor}/core/processes/detrend.py (100%)
rename {postprocessor => src/postprocessor}/core/processes/dsignal.py (100%)
rename {postprocessor => src/postprocessor}/core/processes/fft.py (100%)
rename {postprocessor => src/postprocessor}/core/processes/findpeaks.py (100%)
rename {postprocessor => src/postprocessor}/core/processes/gpsignal.py (100%)
rename {postprocessor => src/postprocessor}/core/processes/knngraph.py (100%)
rename {postprocessor => src/postprocessor}/core/processes/leiden.py (100%)
rename {postprocessor => src/postprocessor}/core/processes/lineageprocess.py (100%)
rename {postprocessor => src/postprocessor}/core/processes/merger.py (100%)
rename {postprocessor => src/postprocessor}/core/processes/picker.py (100%)
rename {postprocessor => src/postprocessor}/core/processes/savgol.py (100%)
rename {postprocessor => src/postprocessor}/core/processes/standardscaler.py (100%)
rename {postprocessor => src/postprocessor}/core/processes/template.py (100%)
rename {postprocessor => src/postprocessor}/core/processes/umapembedding.py (100%)
rename {postprocessor => src/postprocessor}/core/processor.py (100%)
rename {postprocessor => src/postprocessor}/core/report.py (100%)
rename {postprocessor => src/postprocessor}/grouper.py (100%)
rename {postprocessor => src/postprocessor}/routines/__init__.py (100%)
rename {postprocessor => src/postprocessor}/routines/boxplot.py (100%)
rename {postprocessor => src/postprocessor}/routines/heatmap.py (100%)
rename {postprocessor => src/postprocessor}/routines/histogram.py (100%)
rename {postprocessor => src/postprocessor}/routines/mean_plot.py (100%)
rename {postprocessor => src/postprocessor}/routines/median_plot.py (100%)
rename {postprocessor => src/postprocessor}/routines/plot_utils.py (100%)
rename {postprocessor => src/postprocessor}/routines/plottingabc.py (100%)
rename {postprocessor => src/postprocessor}/routines/single_birth_plot.py (100%)
rename {postprocessor => src/postprocessor}/routines/single_plot.py (100%)
diff --git a/poetry.lock b/poetry.lock
index bb99e24b..8957a2b5 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -1076,6 +1076,27 @@ importlib-metadata = {version = ">=4.4", markers = "python_version < \"3.10\""}
[package.extras]
testing = ["coverage", "pyyaml"]
+[[package]]
+name = "markdown-it-py"
+version = "2.1.0"
+description = "Python port of markdown-it. Markdown parsing, done right!"
+category = "dev"
+optional = false
+python-versions = ">=3.7"
+
+[package.dependencies]
+mdurl = ">=0.1,<1.0"
+
+[package.extras]
+benchmarking = ["psutil", "pytest", "pytest-benchmark (>=3.2,<4.0)"]
+code_style = ["pre-commit (==2.6)"]
+compare = ["commonmark (>=0.9.1,<0.10.0)", "markdown (>=3.3.6,<3.4.0)", "mistletoe (>=0.8.1,<0.9.0)", "mistune (>=2.0.2,<2.1.0)", "panflute (>=2.1.3,<2.2.0)"]
+linkify = ["linkify-it-py (>=1.0,<2.0)"]
+plugins = ["mdit-py-plugins"]
+profiling = ["gprof2dot"]
+rtd = ["attrs", "myst-parser", "pyyaml", "sphinx", "sphinx-copybutton", "sphinx-design", "sphinx_book_theme"]
+testing = ["coverage", "pytest", "pytest-cov", "pytest-regressions"]
+
[[package]]
name = "MarkupSafe"
version = "2.1.1"
@@ -1123,6 +1144,30 @@ category = "dev"
optional = false
python-versions = "*"
+[[package]]
+name = "mdit-py-plugins"
+version = "0.3.0"
+description = "Collection of plugins for markdown-it-py"
+category = "dev"
+optional = false
+python-versions = "~=3.6"
+
+[package.dependencies]
+markdown-it-py = ">=1.0.0,<3.0.0"
+
+[package.extras]
+code_style = ["pre-commit (==2.6)"]
+rtd = ["myst-parser (>=0.14.0,<0.15.0)", "sphinx-book-theme (>=0.1.0,<0.2.0)"]
+testing = ["coverage", "pytest (>=3.6,<4)", "pytest-cov", "pytest-regressions"]
+
+[[package]]
+name = "mdurl"
+version = "0.1.2"
+description = "Markdown URL utilities"
+category = "dev"
+optional = false
+python-versions = ">=3.7"
+
[[package]]
name = "mistune"
version = "2.0.4"
@@ -1183,6 +1228,29 @@ category = "dev"
optional = false
python-versions = "*"
+[[package]]
+name = "myst-parser"
+version = "0.18.0"
+description = "An extended commonmark compliant parser, with bridges to docutils & sphinx."
+category = "dev"
+optional = false
+python-versions = ">=3.7"
+
+[package.dependencies]
+docutils = ">=0.15,<0.19"
+jinja2 = "*"
+markdown-it-py = ">=1.0.0,<3.0.0"
+mdit-py-plugins = ">=0.3.0,<0.4.0"
+pyyaml = "*"
+sphinx = ">=4,<6"
+typing-extensions = "*"
+
+[package.extras]
+code_style = ["pre-commit (>=2.12,<3.0)"]
+linkify = ["linkify-it-py (>=1.0,<2.0)"]
+rtd = ["ipython", "sphinx-book-theme", "sphinx-design", "sphinxcontrib.mermaid (>=0.7.1,<0.8.0)", "sphinxext-opengraph (>=0.6.3,<0.7.0)", "sphinxext-rediraffe (>=0.2.7,<0.3.0)"]
+testing = ["beautifulsoup4", "coverage[toml]", "pytest (>=6,<7)", "pytest-cov", "pytest-param-files (>=0.3.4,<0.4.0)", "pytest-regressions", "sphinx-pytest"]
+
[[package]]
name = "nbclient"
version = "0.6.8"
@@ -2128,7 +2196,7 @@ python-versions = ">=3.6"
[[package]]
name = "Sphinx"
-version = "4.5.0"
+version = "5.2.0"
description = "Python documentation generator"
category = "dev"
optional = false
@@ -2136,16 +2204,16 @@ python-versions = ">=3.6"
[package.dependencies]
alabaster = ">=0.7,<0.8"
-babel = ">=1.3"
-colorama = {version = ">=0.3.5", markers = "sys_platform == \"win32\""}
-docutils = ">=0.14,<0.18"
-imagesize = "*"
-importlib-metadata = {version = ">=4.4", markers = "python_version < \"3.10\""}
-Jinja2 = ">=2.3"
-packaging = "*"
-Pygments = ">=2.0"
+babel = ">=2.9"
+colorama = {version = ">=0.4.5", markers = "sys_platform == \"win32\""}
+docutils = ">=0.14,<0.20"
+imagesize = ">=1.3"
+importlib-metadata = {version = ">=4.8", markers = "python_version < \"3.10\""}
+Jinja2 = ">=3.0"
+packaging = ">=21.0"
+Pygments = ">=2.12"
requests = ">=2.5.0"
-snowballstemmer = ">=1.1"
+snowballstemmer = ">=2.0"
sphinxcontrib-applehelp = "*"
sphinxcontrib-devhelp = "*"
sphinxcontrib-htmlhelp = ">=2.0.0"
@@ -2155,8 +2223,38 @@ sphinxcontrib-serializinghtml = ">=1.1.5"
[package.extras]
docs = ["sphinxcontrib-websupport"]
-lint = ["docutils-stubs", "flake8 (>=3.5.0)", "isort", "mypy (>=0.931)", "types-requests", "types-typed-ast"]
-test = ["cython", "html5lib", "pytest", "pytest-cov", "typed-ast"]
+lint = ["docutils-stubs", "flake8 (>=3.5.0)", "flake8-bugbear", "flake8-comprehensions", "flake8-simplify", "isort", "mypy (>=0.971)", "sphinx-lint", "types-requests", "types-typed-ast"]
+test = ["cython", "html5lib", "pytest (>=4.6)", "typed_ast"]
+
+[[package]]
+name = "sphinx-autodoc-typehints"
+version = "1.19.2"
+description = "Type hints (PEP 484) support for the Sphinx autodoc extension"
+category = "dev"
+optional = false
+python-versions = ">=3.7"
+
+[package.dependencies]
+Sphinx = ">=5.1.1"
+
+[package.extras]
+testing = ["covdefaults (>=2.2)", "coverage (>=6.4.2)", "diff-cover (>=6.5.1)", "nptyping (>=2.2)", "pytest (>=7.1.2)", "pytest-cov (>=3)", "sphobjinv (>=2.2.2)", "typing-extensions (>=4.3)"]
+type_comments = ["typed-ast (>=1.5.4)"]
+
+[[package]]
+name = "sphinx-rtd-theme"
+version = "1.0.0"
+description = "Read the Docs theme for Sphinx"
+category = "dev"
+optional = false
+python-versions = ">=2.7,!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*"
+
+[package.dependencies]
+docutils = "<0.18"
+sphinx = ">=1.6"
+
+[package.extras]
+dev = ["bump2version", "sphinxcontrib-httpdomain", "transifex-client"]
[[package]]
name = "sphinxcontrib-applehelp"
@@ -2661,12 +2759,11 @@ testing = ["func-timeout", "jaraco.itertools", "pytest (>=6)", "pytest-black (>=
[extras]
network = ["omero-py", "zeroc-ice"]
omero = ["omero-py"]
-zeroc = ["zeroc-ice"]
[metadata]
lock-version = "1.1"
python-versions = ">=3.8, <3.11"
-content-hash = "5e430e3617c6ad4ef44736d752fa032e7b3c2ef99e865927a8230e5ff2c39a58"
+content-hash = "3af4a2c14311ac198966c9a895edd9067626203228e97a7de5505cd5cfc05da0"
[metadata.files]
absl-py = [
@@ -3552,6 +3649,10 @@ Markdown = [
{file = "Markdown-3.4.1-py3-none-any.whl", hash = "sha256:08fb8465cffd03d10b9dd34a5c3fea908e20391a2a90b88d66362cb05beed186"},
{file = "Markdown-3.4.1.tar.gz", hash = "sha256:3b809086bb6efad416156e00a0da66fe47618a5d6918dd688f53f40c8e4cfeff"},
]
+markdown-it-py = [
+ {file = "markdown-it-py-2.1.0.tar.gz", hash = "sha256:cf7e59fed14b5ae17c0006eff14a2d9a00ed5f3a846148153899a0224e2c07da"},
+ {file = "markdown_it_py-2.1.0-py3-none-any.whl", hash = "sha256:93de681e5c021a432c63147656fe21790bc01231e0cd2da73626f1aa3ac0fe27"},
+]
MarkupSafe = [
{file = "MarkupSafe-2.1.1-cp310-cp310-macosx_10_9_universal2.whl", hash = "sha256:86b1f75c4e7c2ac2ccdaec2b9022845dbb81880ca318bb7a0a01fbf7813e3812"},
{file = "MarkupSafe-2.1.1-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:f121a1420d4e173a5d96e47e9a0c0dcff965afdf1626d28de1460815f7c4ee7a"},
@@ -3645,6 +3746,14 @@ mccabe = [
{file = "mccabe-0.6.1-py2.py3-none-any.whl", hash = "sha256:ab8a6258860da4b6677da4bd2fe5dc2c659cff31b3ee4f7f5d64e79735b80d42"},
{file = "mccabe-0.6.1.tar.gz", hash = "sha256:dd8d182285a0fe56bace7f45b5e7d1a6ebcbf524e8f3bd87eb0f125271b8831f"},
]
+mdit-py-plugins = [
+ {file = "mdit-py-plugins-0.3.0.tar.gz", hash = "sha256:ecc24f51eeec6ab7eecc2f9724e8272c2fb191c2e93cf98109120c2cace69750"},
+ {file = "mdit_py_plugins-0.3.0-py3-none-any.whl", hash = "sha256:b1279701cee2dbf50e188d3da5f51fee8d78d038cdf99be57c6b9d1aa93b4073"},
+]
+mdurl = [
+ {file = "mdurl-0.1.2-py3-none-any.whl", hash = "sha256:84008a41e51615a49fc9966191ff91509e3c40b939176e643fd50a5c2196b8f8"},
+ {file = "mdurl-0.1.2.tar.gz", hash = "sha256:bb413d29f5eea38f31dd4754dd7377d4465116fb207585f97bf925588687c1ba"},
+]
mistune = [
{file = "mistune-2.0.4-py2.py3-none-any.whl", hash = "sha256:182cc5ee6f8ed1b807de6b7bb50155df7b66495412836b9a74c8fbdfc75fe36d"},
{file = "mistune-2.0.4.tar.gz", hash = "sha256:9ee0a66053e2267aba772c71e06891fa8f1af6d4b01d5e84e267b4570d4d9808"},
@@ -3756,6 +3865,10 @@ mypy-extensions = [
{file = "mypy_extensions-0.4.3-py2.py3-none-any.whl", hash = "sha256:090fedd75945a69ae91ce1303b5824f428daf5a028d2f6ab8a299250a846f15d"},
{file = "mypy_extensions-0.4.3.tar.gz", hash = "sha256:2d82818f5bb3e369420cb3c4060a7970edba416647068eb4c5343488a6c604a8"},
]
+myst-parser = [
+ {file = "myst-parser-0.18.0.tar.gz", hash = "sha256:739a4d96773a8e55a2cacd3941ce46a446ee23dcd6b37e06f73f551ad7821d86"},
+ {file = "myst_parser-0.18.0-py3-none-any.whl", hash = "sha256:4965e51918837c13bf1c6f6fe2c6bddddf193148360fbdaefe743a4981358f6a"},
+]
nbclient = [
{file = "nbclient-0.6.8-py3-none-any.whl", hash = "sha256:7cce8b415888539180535953f80ea2385cdbb444944cdeb73ffac1556fdbc228"},
{file = "nbclient-0.6.8.tar.gz", hash = "sha256:268fde3457cafe1539e32eb1c6d796bbedb90b9e92bacd3e43d83413734bb0e8"},
@@ -4470,8 +4583,16 @@ soupsieve = [
{file = "soupsieve-2.3.2.post1.tar.gz", hash = "sha256:fc53893b3da2c33de295667a0e19f078c14bf86544af307354de5fcf12a3f30d"},
]
Sphinx = [
- {file = "Sphinx-4.5.0-py3-none-any.whl", hash = "sha256:ebf612653238bcc8f4359627a9b7ce44ede6fdd75d9d30f68255c7383d3a6226"},
- {file = "Sphinx-4.5.0.tar.gz", hash = "sha256:7bf8ca9637a4ee15af412d1a1d9689fec70523a68ca9bb9127c2f3eeb344e2e6"},
+ {file = "Sphinx-5.2.0.tar.gz", hash = "sha256:1790c2098937dcfa7871c9d102c24eccd4a8b883b67c5c1e26892fb52d102542"},
+ {file = "sphinx-5.2.0-py3-none-any.whl", hash = "sha256:422812bdf2dacab55c47ee4dd4746bb82e739fe4c97ce16dd68bcc208e348e73"},
+]
+sphinx-autodoc-typehints = [
+ {file = "sphinx_autodoc_typehints-1.19.2-py3-none-any.whl", hash = "sha256:3d761de928d5a86901331133d6d4a2552afa2e798ebcfc0886791792aeb4dd9a"},
+ {file = "sphinx_autodoc_typehints-1.19.2.tar.gz", hash = "sha256:872fb2d7b3d794826c28e36edf6739e93549491447dcabeb07c58855e9f914de"},
+]
+sphinx-rtd-theme = [
+ {file = "sphinx_rtd_theme-1.0.0-py2.py3-none-any.whl", hash = "sha256:4d35a56f4508cfee4c4fb604373ede6feae2a306731d533f409ef5c3496fdbd8"},
+ {file = "sphinx_rtd_theme-1.0.0.tar.gz", hash = "sha256:eec6d497e4c2195fa0e8b2016b337532b8a699a68bcb22a512870e16925c6a5c"},
]
sphinxcontrib-applehelp = [
{file = "sphinxcontrib-applehelp-1.0.2.tar.gz", hash = "sha256:a072735ec80e7675e3f432fcae8610ecf509c5f1869d17e2eecff44389cdbc58"},
diff --git a/pyproject.toml b/pyproject.toml
index 46acf218..1e51eb83 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -4,11 +4,11 @@ version = "0.1.43"
description = "Process and analyse live-cell imaging data"
authors = ["Alan Munoz <alan.munoz@ed.ac.uk>"]
packages = [
- { include = "aliby" },
- { include = "extraction" },
- { include = "agora" },
- { include = "postprocessor" },
- { include = "logfile_parser" },
+ { include = "aliby", from="src" },
+ { include = "extraction", from="src" },
+ { include = "agora", from="src" },
+ { include = "postprocessor", from="src" },
+ { include = "logfile_parser", from="src" },
]
readme = "README.md"
@@ -70,7 +70,10 @@ seaborn = "^0.11.2"
optional = true
[tool.poetry.group.docs.dependencies]
-Sphinx = "^4.3.2"
+Sphinx = "^5.2.0"
+sphinx-rtd-theme = "^1.0.0"
+sphinx-autodoc-typehints = "^1.19.2"
+myst-parser = "^0.18.0"
[tool.poetry.group.test]
optional = true
diff --git a/agora/__init__.py b/src/agora/__init__.py
similarity index 100%
rename from agora/__init__.py
rename to src/agora/__init__.py
diff --git a/agora/abc.py b/src/agora/abc.py
similarity index 100%
rename from agora/abc.py
rename to src/agora/abc.py
diff --git a/agora/io/__init__.py b/src/agora/io/__init__.py
similarity index 100%
rename from agora/io/__init__.py
rename to src/agora/io/__init__.py
diff --git a/agora/io/bridge.py b/src/agora/io/bridge.py
similarity index 100%
rename from agora/io/bridge.py
rename to src/agora/io/bridge.py
diff --git a/agora/io/cells.py b/src/agora/io/cells.py
similarity index 100%
rename from agora/io/cells.py
rename to src/agora/io/cells.py
diff --git a/agora/io/metadata.py b/src/agora/io/metadata.py
similarity index 100%
rename from agora/io/metadata.py
rename to src/agora/io/metadata.py
diff --git a/agora/io/reader.py b/src/agora/io/reader.py
similarity index 100%
rename from agora/io/reader.py
rename to src/agora/io/reader.py
diff --git a/agora/io/signal.py b/src/agora/io/signal.py
similarity index 100%
rename from agora/io/signal.py
rename to src/agora/io/signal.py
diff --git a/agora/io/utils.py b/src/agora/io/utils.py
similarity index 100%
rename from agora/io/utils.py
rename to src/agora/io/utils.py
diff --git a/agora/io/writer.py b/src/agora/io/writer.py
similarity index 100%
rename from agora/io/writer.py
rename to src/agora/io/writer.py
diff --git a/agora/utils/__init__.py b/src/agora/utils/__init__.py
similarity index 100%
rename from agora/utils/__init__.py
rename to src/agora/utils/__init__.py
diff --git a/agora/utils/example.py b/src/agora/utils/example.py
similarity index 100%
rename from agora/utils/example.py
rename to src/agora/utils/example.py
diff --git a/agora/utils/lineage.py b/src/agora/utils/lineage.py
similarity index 100%
rename from agora/utils/lineage.py
rename to src/agora/utils/lineage.py
diff --git a/aliby/__init__.py b/src/aliby/__init__.py
similarity index 100%
rename from aliby/__init__.py
rename to src/aliby/__init__.py
diff --git a/aliby/baby_client.py b/src/aliby/baby_client.py
similarity index 100%
rename from aliby/baby_client.py
rename to src/aliby/baby_client.py
diff --git a/aliby/haystack.py b/src/aliby/haystack.py
similarity index 100%
rename from aliby/haystack.py
rename to src/aliby/haystack.py
diff --git a/aliby/io/__init__.py b/src/aliby/io/__init__.py
similarity index 100%
rename from aliby/io/__init__.py
rename to src/aliby/io/__init__.py
diff --git a/aliby/io/dataset.py b/src/aliby/io/dataset.py
similarity index 100%
rename from aliby/io/dataset.py
rename to src/aliby/io/dataset.py
diff --git a/aliby/io/image.py b/src/aliby/io/image.py
similarity index 100%
rename from aliby/io/image.py
rename to src/aliby/io/image.py
diff --git a/aliby/io/omero.py b/src/aliby/io/omero.py
similarity index 100%
rename from aliby/io/omero.py
rename to src/aliby/io/omero.py
diff --git a/aliby/io/utils.py b/src/aliby/io/utils.py
similarity index 100%
rename from aliby/io/utils.py
rename to src/aliby/io/utils.py
diff --git a/aliby/pipeline.py b/src/aliby/pipeline.py
similarity index 100%
rename from aliby/pipeline.py
rename to src/aliby/pipeline.py
diff --git a/aliby/tile/__init__.py b/src/aliby/tile/__init__.py
similarity index 100%
rename from aliby/tile/__init__.py
rename to src/aliby/tile/__init__.py
diff --git a/aliby/tile/tiler.py b/src/aliby/tile/tiler.py
similarity index 100%
rename from aliby/tile/tiler.py
rename to src/aliby/tile/tiler.py
diff --git a/aliby/tile/traps.py b/src/aliby/tile/traps.py
similarity index 100%
rename from aliby/tile/traps.py
rename to src/aliby/tile/traps.py
diff --git a/aliby/utils/__init__.py b/src/aliby/utils/__init__.py
similarity index 100%
rename from aliby/utils/__init__.py
rename to src/aliby/utils/__init__.py
diff --git a/aliby/utils/argo.py b/src/aliby/utils/argo.py
similarity index 100%
rename from aliby/utils/argo.py
rename to src/aliby/utils/argo.py
diff --git a/aliby/utils/cache.py b/src/aliby/utils/cache.py
similarity index 100%
rename from aliby/utils/cache.py
rename to src/aliby/utils/cache.py
diff --git a/aliby/utils/imageViewer.py b/src/aliby/utils/imageViewer.py
similarity index 100%
rename from aliby/utils/imageViewer.py
rename to src/aliby/utils/imageViewer.py
diff --git a/extraction/__init__.py b/src/extraction/__init__.py
similarity index 100%
rename from extraction/__init__.py
rename to src/extraction/__init__.py
diff --git a/extraction/core/__init__.py b/src/extraction/core/__init__.py
similarity index 100%
rename from extraction/core/__init__.py
rename to src/extraction/core/__init__.py
diff --git a/extraction/core/extractor.py b/src/extraction/core/extractor.py
similarity index 100%
rename from extraction/core/extractor.py
rename to src/extraction/core/extractor.py
diff --git a/extraction/core/functions/__init__.py b/src/extraction/core/functions/__init__.py
similarity index 100%
rename from extraction/core/functions/__init__.py
rename to src/extraction/core/functions/__init__.py
diff --git a/extraction/core/functions/cell.py b/src/extraction/core/functions/cell.py
similarity index 100%
rename from extraction/core/functions/cell.py
rename to src/extraction/core/functions/cell.py
diff --git a/extraction/core/functions/custom/__init__.py b/src/extraction/core/functions/custom/__init__.py
similarity index 100%
rename from extraction/core/functions/custom/__init__.py
rename to src/extraction/core/functions/custom/__init__.py
diff --git a/extraction/core/functions/custom/localisation.py b/src/extraction/core/functions/custom/localisation.py
similarity index 100%
rename from extraction/core/functions/custom/localisation.py
rename to src/extraction/core/functions/custom/localisation.py
diff --git a/extraction/core/functions/defaults.py b/src/extraction/core/functions/defaults.py
similarity index 100%
rename from extraction/core/functions/defaults.py
rename to src/extraction/core/functions/defaults.py
diff --git a/extraction/core/functions/distributors.py b/src/extraction/core/functions/distributors.py
similarity index 100%
rename from extraction/core/functions/distributors.py
rename to src/extraction/core/functions/distributors.py
diff --git a/extraction/core/functions/io.py b/src/extraction/core/functions/io.py
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rename from extraction/core/functions/io.py
rename to src/extraction/core/functions/io.py
diff --git a/extraction/core/functions/loaders.py b/src/extraction/core/functions/loaders.py
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rename from extraction/core/functions/loaders.py
rename to src/extraction/core/functions/loaders.py
diff --git a/extraction/core/functions/math_utils.py b/src/extraction/core/functions/math_utils.py
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rename from extraction/core/functions/math_utils.py
rename to src/extraction/core/functions/math_utils.py
diff --git a/extraction/core/functions/trap.py b/src/extraction/core/functions/trap.py
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rename from extraction/core/functions/trap.py
rename to src/extraction/core/functions/trap.py
diff --git a/extraction/core/functions/utils.py b/src/extraction/core/functions/utils.py
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rename from extraction/core/functions/utils.py
rename to src/extraction/core/functions/utils.py
diff --git a/extraction/core/functions/versioning.py b/src/extraction/core/functions/versioning.py
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rename from extraction/core/functions/versioning.py
rename to src/extraction/core/functions/versioning.py
diff --git a/extraction/core/omero.py b/src/extraction/core/omero.py
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rename from extraction/core/omero.py
rename to src/extraction/core/omero.py
diff --git a/extraction/examples/data.py b/src/extraction/examples/data.py
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rename from extraction/examples/data.py
rename to src/extraction/examples/data.py
diff --git a/extraction/examples/pos_example.py b/src/extraction/examples/pos_example.py
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rename from extraction/examples/pos_example.py
rename to src/extraction/examples/pos_example.py
diff --git a/extraction/examples/tiler_error.py b/src/extraction/examples/tiler_error.py
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rename from extraction/examples/tiler_error.py
rename to src/extraction/examples/tiler_error.py
diff --git a/logfile_parser/README.md b/src/logfile_parser/README.md
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diff --git a/logfile_parser/__init__.py b/src/logfile_parser/__init__.py
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diff --git a/logfile_parser/grammars/cExperiment_log_format.json b/src/logfile_parser/grammars/cExperiment_log_format.json
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rename from logfile_parser/grammars/cExperiment_log_format.json
rename to src/logfile_parser/grammars/cExperiment_log_format.json
diff --git a/logfile_parser/grammars/multiDGUI_acq_format.json b/src/logfile_parser/grammars/multiDGUI_acq_format.json
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rename from logfile_parser/grammars/multiDGUI_acq_format.json
rename to src/logfile_parser/grammars/multiDGUI_acq_format.json
diff --git a/logfile_parser/grammars/multiDGUI_log_format.json b/src/logfile_parser/grammars/multiDGUI_log_format.json
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rename from logfile_parser/grammars/multiDGUI_log_format.json
rename to src/logfile_parser/grammars/multiDGUI_log_format.json
diff --git a/logfile_parser/logfile_parser.py b/src/logfile_parser/logfile_parser.py
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rename from logfile_parser/logfile_parser.py
rename to src/logfile_parser/logfile_parser.py
diff --git a/postprocessor/__init__.py b/src/postprocessor/__init__.py
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rename from postprocessor/__init__.py
rename to src/postprocessor/__init__.py
diff --git a/postprocessor/benchmarks/post_processing.py b/src/postprocessor/benchmarks/post_processing.py
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rename from postprocessor/benchmarks/post_processing.py
rename to src/postprocessor/benchmarks/post_processing.py
diff --git a/postprocessor/compiler.py b/src/postprocessor/compiler.py
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rename from postprocessor/compiler.py
rename to src/postprocessor/compiler.py
diff --git a/postprocessor/core/__init__.py b/src/postprocessor/core/__init__.py
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rename from postprocessor/core/__init__.py
rename to src/postprocessor/core/__init__.py
diff --git a/postprocessor/core/abc.py b/src/postprocessor/core/abc.py
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rename from postprocessor/core/abc.py
rename to src/postprocessor/core/abc.py
diff --git a/postprocessor/core/export_pdf.py b/src/postprocessor/core/export_pdf.py
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rename from postprocessor/core/export_pdf.py
rename to src/postprocessor/core/export_pdf.py
diff --git a/postprocessor/core/functions/__init__.py b/src/postprocessor/core/functions/__init__.py
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rename from postprocessor/core/functions/__init__.py
rename to src/postprocessor/core/functions/__init__.py
diff --git a/postprocessor/core/functions/tracks.py b/src/postprocessor/core/functions/tracks.py
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rename to src/postprocessor/core/functions/tracks.py
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rename from postprocessor/core/lineageprocess.py
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rename to src/postprocessor/core/processes/template.py
diff --git a/postprocessor/core/processes/umapembedding.py b/src/postprocessor/core/processes/umapembedding.py
similarity index 100%
rename from postprocessor/core/processes/umapembedding.py
rename to src/postprocessor/core/processes/umapembedding.py
diff --git a/postprocessor/core/processor.py b/src/postprocessor/core/processor.py
similarity index 100%
rename from postprocessor/core/processor.py
rename to src/postprocessor/core/processor.py
diff --git a/postprocessor/core/report.py b/src/postprocessor/core/report.py
similarity index 100%
rename from postprocessor/core/report.py
rename to src/postprocessor/core/report.py
diff --git a/postprocessor/grouper.py b/src/postprocessor/grouper.py
similarity index 100%
rename from postprocessor/grouper.py
rename to src/postprocessor/grouper.py
diff --git a/postprocessor/routines/__init__.py b/src/postprocessor/routines/__init__.py
similarity index 100%
rename from postprocessor/routines/__init__.py
rename to src/postprocessor/routines/__init__.py
diff --git a/postprocessor/routines/boxplot.py b/src/postprocessor/routines/boxplot.py
similarity index 100%
rename from postprocessor/routines/boxplot.py
rename to src/postprocessor/routines/boxplot.py
diff --git a/postprocessor/routines/heatmap.py b/src/postprocessor/routines/heatmap.py
similarity index 100%
rename from postprocessor/routines/heatmap.py
rename to src/postprocessor/routines/heatmap.py
diff --git a/postprocessor/routines/histogram.py b/src/postprocessor/routines/histogram.py
similarity index 100%
rename from postprocessor/routines/histogram.py
rename to src/postprocessor/routines/histogram.py
diff --git a/postprocessor/routines/mean_plot.py b/src/postprocessor/routines/mean_plot.py
similarity index 100%
rename from postprocessor/routines/mean_plot.py
rename to src/postprocessor/routines/mean_plot.py
diff --git a/postprocessor/routines/median_plot.py b/src/postprocessor/routines/median_plot.py
similarity index 100%
rename from postprocessor/routines/median_plot.py
rename to src/postprocessor/routines/median_plot.py
diff --git a/postprocessor/routines/plot_utils.py b/src/postprocessor/routines/plot_utils.py
similarity index 100%
rename from postprocessor/routines/plot_utils.py
rename to src/postprocessor/routines/plot_utils.py
diff --git a/postprocessor/routines/plottingabc.py b/src/postprocessor/routines/plottingabc.py
similarity index 100%
rename from postprocessor/routines/plottingabc.py
rename to src/postprocessor/routines/plottingabc.py
diff --git a/postprocessor/routines/single_birth_plot.py b/src/postprocessor/routines/single_birth_plot.py
similarity index 100%
rename from postprocessor/routines/single_birth_plot.py
rename to src/postprocessor/routines/single_birth_plot.py
diff --git a/postprocessor/routines/single_plot.py b/src/postprocessor/routines/single_plot.py
similarity index 100%
rename from postprocessor/routines/single_plot.py
rename to src/postprocessor/routines/single_plot.py
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