From 573ed998fa866a591e175ff67858cf4f6ed98dea 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 20:44:00 +0100
Subject: [PATCH] docs(all): make docs great again
---
docs/source/index.rst | 6 ++++
poetry.lock | 44 +++++++++++++++++++++++++++-
pyproject.toml | 1 +
src/agora/io/bridge.py | 14 +++++----
src/logfile_parser/__init__.py | 10 -------
src/logfile_parser/logfile_parser.py | 9 ------
6 files changed, 58 insertions(+), 26 deletions(-)
diff --git a/docs/source/index.rst b/docs/source/index.rst
index 21a5748d..0f8de1dc 100644
--- a/docs/source/index.rst
+++ b/docs/source/index.rst
@@ -7,6 +7,12 @@
:hidden:
Home page <self>
+ Installation <INSTALL.md>
+ ..
+ Examples <examples.rst>
+ Reference <api.rst>
+ ..
+ Contributing <CONTRIBUTING.md>
ALIBY reference <_autosummary/aliby>
extraction reference <_autosummary/extraction>
agora reference <_autosummary/agora>
diff --git a/poetry.lock b/poetry.lock
index 8957a2b5..c35b798c 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -552,6 +552,28 @@ matplotlib = ">=3.5.1,<4.0.0"
numpy = ">=1.16.0,<2.0.0"
scipy = ">=1.7.3,<2.0.0"
+[[package]]
+name = "gitdb"
+version = "4.0.9"
+description = "Git Object Database"
+category = "main"
+optional = false
+python-versions = ">=3.6"
+
+[package.dependencies]
+smmap = ">=3.0.1,<6"
+
+[[package]]
+name = "GitPython"
+version = "3.1.27"
+description = "GitPython is a python library used to interact with Git repositories"
+category = "main"
+optional = false
+python-versions = ">=3.7"
+
+[package.dependencies]
+gitdb = ">=4.0.1,<5"
+
[[package]]
name = "google-auth"
version = "2.11.1"
@@ -2178,6 +2200,14 @@ category = "main"
optional = false
python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*"
+[[package]]
+name = "smmap"
+version = "5.0.0"
+description = "A pure Python implementation of a sliding window memory map manager"
+category = "main"
+optional = false
+python-versions = ">=3.6"
+
[[package]]
name = "snowballstemmer"
version = "2.2.0"
@@ -2763,7 +2793,7 @@ omero = ["omero-py"]
[metadata]
lock-version = "1.1"
python-versions = ">=3.8, <3.11"
-content-hash = "3af4a2c14311ac198966c9a895edd9067626203228e97a7de5505cd5cfc05da0"
+content-hash = "3a558cdc2c34c8a9864c4983c7e445167ab8040927f00a3dae3d4745421da2a0"
[metadata.files]
absl-py = [
@@ -3194,6 +3224,14 @@ gaussianprocessderivatives = [
{file = "gaussianprocessderivatives-0.1.5-py3-none-any.whl", hash = "sha256:c1639d3c3e9b007bb63424e3db605ee675cb63410f5aa499bbf6c025f316ed21"},
{file = "gaussianprocessderivatives-0.1.5.tar.gz", hash = "sha256:3bd2142668a0d9b8876ba1a15a406a7f9bcbb8564547a7027a9839024dd81838"},
]
+gitdb = [
+ {file = "gitdb-4.0.9-py3-none-any.whl", hash = "sha256:8033ad4e853066ba6ca92050b9df2f89301b8fc8bf7e9324d412a63f8bf1a8fd"},
+ {file = "gitdb-4.0.9.tar.gz", hash = "sha256:bac2fd45c0a1c9cf619e63a90d62bdc63892ef92387424b855792a6cabe789aa"},
+]
+GitPython = [
+ {file = "GitPython-3.1.27-py3-none-any.whl", hash = "sha256:5b68b000463593e05ff2b261acff0ff0972df8ab1b70d3cdbd41b546c8b8fc3d"},
+ {file = "GitPython-3.1.27.tar.gz", hash = "sha256:1c885ce809e8ba2d88a29befeb385fcea06338d3640712b59ca623c220bb5704"},
+]
google-auth = [
{file = "google-auth-2.11.1.tar.gz", hash = "sha256:516e6623038b81430dd062a1a25ecd24f173d7c15cdf4e48a9e78bc87e97aeec"},
{file = "google_auth-2.11.1-py2.py3-none-any.whl", hash = "sha256:53bdc0c2b4e25895575779caef4cfb3a6bdff1b7b32dc38a654d71aba35bb5f8"},
@@ -4574,6 +4612,10 @@ six = [
{file = "six-1.16.0-py2.py3-none-any.whl", hash = "sha256:8abb2f1d86890a2dfb989f9a77cfcfd3e47c2a354b01111771326f8aa26e0254"},
{file = "six-1.16.0.tar.gz", hash = "sha256:1e61c37477a1626458e36f7b1d82aa5c9b094fa4802892072e49de9c60c4c926"},
]
+smmap = [
+ {file = "smmap-5.0.0-py3-none-any.whl", hash = "sha256:2aba19d6a040e78d8b09de5c57e96207b09ed71d8e55ce0959eeee6c8e190d94"},
+ {file = "smmap-5.0.0.tar.gz", hash = "sha256:c840e62059cd3be204b0c9c9f74be2c09d5648eddd4580d9314c3ecde0b30936"},
+]
snowballstemmer = [
{file = "snowballstemmer-2.2.0-py2.py3-none-any.whl", hash = "sha256:c8e1716e83cc398ae16824e5572ae04e0d9fc2c6b985fb0f900f5f0c96ecba1a"},
{file = "snowballstemmer-2.2.0.tar.gz", hash = "sha256:09b16deb8547d3412ad7b590689584cd0fe25ec8db3be37788be3810cbf19cb1"},
diff --git a/pyproject.toml b/pyproject.toml
index 1e51eb83..bb7a558d 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -44,6 +44,7 @@ pycatch22 = "^0.4.2"
# [tool.poetry.group.network.dependencies]
omero-py = { version = ">=5.6.2", optional = true } # contact omero server
zeroc-ice = { version="3.6.5", optional = true } # networking interface, slow to build
+GitPython = "^3.1.27"
[tool.poetry.extras]
omero = [ "omero-py" ]
diff --git a/src/agora/io/bridge.py b/src/agora/io/bridge.py
index f797f07b..4a2f6093 100644
--- a/src/agora/io/bridge.py
+++ b/src/agora/io/bridge.py
@@ -95,18 +95,20 @@ class BridgeH5:
Default hierarchy is:
- trap
- - time point
- - cell label
+ - time point
+ - cell label
This function currently produces trees of depth 3, but it can easily be
extended for deeper trees if needed (e.g. considering groups,
chambers and/or positions).
- input
- :fields: Fields to fetch from 'cell_info' inside the hdf5 storage
+ Parameters
+ ----------
+ fields: Fields to fetch from 'cell_info' inside the hdf5 storage
- returns
- :tree: Nested dictionary where keys (or branches) are the upper levels
+ Returns
+ ----------
+ Nested dictionary where keys (or branches) are the upper levels
and the leaves are the last element of :fields:.
"""
zipped_info = (*zip(*[self._hdf["cell_info"][f][()] for f in fields]),)
diff --git a/src/logfile_parser/__init__.py b/src/logfile_parser/__init__.py
index 55973d48..3e552539 100644
--- a/src/logfile_parser/__init__.py
+++ b/src/logfile_parser/__init__.py
@@ -1,12 +1,2 @@
# -*- coding: utf-8 -*-
-"""
-logfile_parser
-~~~~~~~~~~~~
-
-Simple log file parsing according to grammars specified in JSON
-
-:copyright: (c) 2020 by Julian Pietsch.
-:license: LGPL
-"""
-
from .logfile_parser import Parser
diff --git a/src/logfile_parser/logfile_parser.py b/src/logfile_parser/logfile_parser.py
index cb850573..4b73129d 100644
--- a/src/logfile_parser/logfile_parser.py
+++ b/src/logfile_parser/logfile_parser.py
@@ -1,13 +1,4 @@
# -*- coding: utf-8 -*-
-"""
-logfile_parser
-~~~~~~~~~~~~
-
-Simple log file parsing according to grammars specified in JSON
-
-:copyright: (c) 2020 by Julian Pietsch.
-:license: LGPL
-"""
import json
import pkgutil
--
GitLab