Skip to content
This repository has been archived by the owner on Apr 29, 2024. It is now read-only.

Commit

Permalink
fixes documentation, #56, #61, & codecov uploader
Browse files Browse the repository at this point in the history
  • Loading branch information
wdika committed May 25, 2022
1 parent 60a429d commit e2c50f3
Show file tree
Hide file tree
Showing 349 changed files with 73,754 additions and 567 deletions.
1 change: 1 addition & 0 deletions .github/workflows/codecov.yml
Original file line number Diff line number Diff line change
Expand Up @@ -30,3 +30,4 @@ jobs:
flags: pytests # optional
name: codecov-umbrella # optional
verbose: true # optional (default = false)
version: "v0.1.15"
4 changes: 0 additions & 4 deletions .readthedocs.yaml
Original file line number Diff line number Diff line change
Expand Up @@ -10,10 +10,6 @@ build:
os: ubuntu-20.04
tools:
python: "3.9"
# You can also specify other tool versions:
# nodejs: "16"
# rust: "1.55"
# golang: "1.17"

# Build documentation in the docs/ directory with Sphinx
sphinx:
Expand Down
4 changes: 2 additions & 2 deletions CITATION.cff
Original file line number Diff line number Diff line change
Expand Up @@ -9,5 +9,5 @@ authors:
orcid: https://orcid.org/0000-0002-5162-8880
title: "MRI Data Consistency"
url: "https://github.com/wdika/mridc"
version: 0.0.1
date-released: 2021-29-11
version: 0.1.0
date-released: 2022-25-05
7 changes: 2 additions & 5 deletions README.md
Original file line number Diff line number Diff line change
Expand Up @@ -3,9 +3,6 @@
[![CodeQL](https://github.com/wdika/mridc/actions/workflows/codeql-analysis.yml/badge.svg)](https://github.com/wdika/mridc/actions/workflows/codeql-analysis.yml)
[![CircleCI](https://circleci.com/gh/wdika/mridc/tree/main.svg?style=svg)](https://circleci.com/gh/wdika/mridc/tree/main)
[![codecov](https://codecov.io/gh/wdika/mridc/branch/main/graph/badge.svg?token=KPPQ33DOTF)](https://codecov.io/gh/wdika/mridc)
[![DeepSource](https://deepsource.io/gh/wdika/mridc.svg/?label=active+issues&show_trend=true&token=txj87v43GA6vhpbSwPEUTQtX)](https://deepsource.io/gh/wdika/mridc/?ref=repository-badge)
[![DeepSource](https://deepsource.io/gh/wdika/mridc.svg/?label=resolved+issues&show_trend=true&token=txj87v43GA6vhpbSwPEUTQtX)](https://deepsource.io/gh/wdika/mridc/?ref=repository-badge)
[![Total alerts](https://img.shields.io/lgtm/alerts/g/wdika/mridc.svg?logo=lgtm&logoWidth=18)](https://lgtm.com/projects/g/wdika/mridc/alerts/)
<a href="https://github.com/psf/black"><img alt="Code style: black" src="https://img.shields.io/badge/code%20style-black-000000.svg"></a>

---
Expand Down Expand Up @@ -76,11 +73,11 @@ Recommended public datasets to use with this repo:
- [fastMRI](http://arxiv.org/abs/1811.08839),
- [Fully Sampled Knees](http://old.mridata.org/fullysampled/knees/).

## Documentation
## API Documentation

[![Documentation Status](https://readthedocs.org/projects/mridc/badge/?version=latest)](https://mridc.readthedocs.io/en/latest/?badge=latest)

Read the docs [here](https://mridc.readthedocs.io/en/latest/index.html)
Access the API Documentation [here](https://mridc.readthedocs.io/en/latest/modules.html)

## License

Expand Down
Binary file added docs/build/doctrees/environment.pickle
Binary file not shown.
Binary file added docs/build/doctrees/index.doctree
Binary file not shown.
Binary file added docs/build/doctrees/modules.doctree
Binary file not shown.
Binary file not shown.
Binary file not shown.
Binary file not shown.
Binary file not shown.
Binary file not shown.
Binary file not shown.
Binary file added docs/build/doctrees/mridc.collections.doctree
Binary file not shown.
Binary file not shown.
Binary file not shown.
Binary file not shown.
Binary file not shown.
Binary file not shown.
Binary file not shown.
Binary file not shown.
Binary file not shown.
Binary file not shown.
Binary file not shown.
Binary file not shown.
Binary file not shown.
Binary file not shown.
Binary file not shown.
Binary file not shown.
Binary file not shown.
Binary file not shown.
Binary file not shown.
Binary file not shown.
Binary file added docs/build/doctrees/mridc.core.classes.doctree
Binary file not shown.
Binary file added docs/build/doctrees/mridc.core.conf.doctree
Binary file not shown.
Binary file added docs/build/doctrees/mridc.core.connectors.doctree
Binary file not shown.
Binary file added docs/build/doctrees/mridc.core.doctree
Binary file not shown.
Binary file not shown.
Binary file added docs/build/doctrees/mridc.core.optim.doctree
Binary file not shown.
Binary file added docs/build/doctrees/mridc.core.utils.doctree
Binary file not shown.
Binary file added docs/build/doctrees/mridc.doctree
Binary file not shown.
Binary file not shown.
Binary file added docs/build/doctrees/mridc.utils.doctree
Binary file not shown.
Binary file not shown.
4 changes: 4 additions & 0 deletions docs/build/html/.buildinfo
Original file line number Diff line number Diff line change
@@ -0,0 +1,4 @@
# Sphinx build info version 1
# This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
config: 46554dcb68b067ce402ab476ee469479
tags: 645f666f9bcd5a90fca523b33c5a78b7
193 changes: 193 additions & 0 deletions docs/build/html/_modules/index.html
Original file line number Diff line number Diff line change
@@ -0,0 +1,193 @@
<!DOCTYPE html>
<html class="writer-html5" lang="en" >
<head>
<meta charset="utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1.0" />
<title>Overview: module code &mdash; mridc v.0.0.1 documentation</title>
<link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
<link rel="stylesheet" href="../_static/css/theme.css" type="text/css" />
<!--[if lt IE 9]>
<script src="../_static/js/html5shiv.min.js"></script>
<![endif]-->

<script data-url_root="../" id="documentation_options" src="../_static/documentation_options.js"></script>
<script src="../_static/jquery.js"></script>
<script src="../_static/underscore.js"></script>
<script src="../_static/doctools.js"></script>
<script src="../_static/js/theme.js"></script>
<link rel="index" title="Index" href="../genindex.html" />
<link rel="search" title="Search" href="../search.html" />
</head>

<body class="wy-body-for-nav">
<div class="wy-grid-for-nav">
<nav data-toggle="wy-nav-shift" class="wy-nav-side">
<div class="wy-side-scroll">
<div class="wy-side-nav-search" >
<a href="../index.html" class="icon icon-home"> mridc
</a>
<div role="search">
<form id="rtd-search-form" class="wy-form" action="../search.html" method="get">
<input type="text" name="q" placeholder="Search docs" />
<input type="hidden" name="check_keywords" value="yes" />
<input type="hidden" name="area" value="default" />
</form>
</div>
</div><div class="wy-menu wy-menu-vertical" data-spy="affix" role="navigation" aria-label="Navigation menu">
<p class="caption" role="heading"><span class="caption-text">API Documentation:</span></p>
<ul>
<li class="toctree-l1"><a class="reference internal" href="../modules.html">mridc</a></li>
</ul>

</div>
</div>
</nav>

<section data-toggle="wy-nav-shift" class="wy-nav-content-wrap"><nav class="wy-nav-top" aria-label="Mobile navigation menu" >
<i data-toggle="wy-nav-top" class="fa fa-bars"></i>
<a href="../index.html">mridc</a>
</nav>

<div class="wy-nav-content">
<div class="rst-content">
<div role="navigation" aria-label="Page navigation">
<ul class="wy-breadcrumbs">
<li><a href="../index.html" class="icon icon-home"></a> &raquo;</li>
<li>Overview: module code</li>
<li class="wy-breadcrumbs-aside">
</li>
</ul>
<hr/>
</div>
<div role="main" class="document" itemscope="itemscope" itemtype="http://schema.org/Article">
<div itemprop="articleBody">

<h1>All modules for which code is available</h1>
<ul><li><a href="mridc/collections/common/callbacks/callbacks.html">mridc.collections.common.callbacks.callbacks</a></li>
<li><a href="mridc/collections/common/data/dataset.html">mridc.collections.common.data.dataset</a></li>
<li><a href="mridc/collections/common/losses/aggregator.html">mridc.collections.common.losses.aggregator</a></li>
<li><a href="mridc/collections/common/losses/ssim.html">mridc.collections.common.losses.ssim</a></li>
<li><a href="mridc/collections/common/metrics/global_average_loss_metric.html">mridc.collections.common.metrics.global_average_loss_metric</a></li>
<li><a href="mridc/collections/common/parts/fft.html">mridc.collections.common.parts.fft</a></li>
<li><a href="mridc/collections/common/parts/ptl_overrides.html">mridc.collections.common.parts.ptl_overrides</a></li>
<li><a href="mridc/collections/common/parts/rnn_utils.html">mridc.collections.common.parts.rnn_utils</a></li>
<li><a href="mridc/collections/common/parts/utils.html">mridc.collections.common.parts.utils</a></li>
<li><a href="mridc/collections/reconstruction/data/mri_data.html">mridc.collections.reconstruction.data.mri_data</a></li>
<li><a href="mridc/collections/reconstruction/data/subsample.html">mridc.collections.reconstruction.data.subsample</a></li>
<li><a href="mridc/collections/reconstruction/metrics/evaluate.html">mridc.collections.reconstruction.metrics.evaluate</a></li>
<li><a href="mridc/collections/reconstruction/models/base.html">mridc.collections.reconstruction.models.base</a></li>
<li><a href="mridc/collections/reconstruction/models/cascadenet/ccnn_block.html">mridc.collections.reconstruction.models.cascadenet.ccnn_block</a></li>
<li><a href="mridc/collections/reconstruction/models/ccnn.html">mridc.collections.reconstruction.models.ccnn</a></li>
<li><a href="mridc/collections/reconstruction/models/cirim.html">mridc.collections.reconstruction.models.cirim</a></li>
<li><a href="mridc/collections/reconstruction/models/conv/conv2d.html">mridc.collections.reconstruction.models.conv.conv2d</a></li>
<li><a href="mridc/collections/reconstruction/models/conv/gruconv2d.html">mridc.collections.reconstruction.models.conv.gruconv2d</a></li>
<li><a href="mridc/collections/reconstruction/models/convrecnet/crnn_block.html">mridc.collections.reconstruction.models.convrecnet.crnn_block</a></li>
<li><a href="mridc/collections/reconstruction/models/crnn.html">mridc.collections.reconstruction.models.crnn</a></li>
<li><a href="mridc/collections/reconstruction/models/crossdomain/crossdomain.html">mridc.collections.reconstruction.models.crossdomain.crossdomain</a></li>
<li><a href="mridc/collections/reconstruction/models/crossdomain/multicoil.html">mridc.collections.reconstruction.models.crossdomain.multicoil</a></li>
<li><a href="mridc/collections/reconstruction/models/didn/didn.html">mridc.collections.reconstruction.models.didn.didn</a></li>
<li><a href="mridc/collections/reconstruction/models/dunet.html">mridc.collections.reconstruction.models.dunet</a></li>
<li><a href="mridc/collections/reconstruction/models/jointicnet.html">mridc.collections.reconstruction.models.jointicnet</a></li>
<li><a href="mridc/collections/reconstruction/models/kikinet.html">mridc.collections.reconstruction.models.kikinet</a></li>
<li><a href="mridc/collections/reconstruction/models/lpd.html">mridc.collections.reconstruction.models.lpd</a></li>
<li><a href="mridc/collections/reconstruction/models/multidomain/multidomain.html">mridc.collections.reconstruction.models.multidomain.multidomain</a></li>
<li><a href="mridc/collections/reconstruction/models/multidomainnet.html">mridc.collections.reconstruction.models.multidomainnet</a></li>
<li><a href="mridc/collections/reconstruction/models/mwcnn/mwcnn.html">mridc.collections.reconstruction.models.mwcnn.mwcnn</a></li>
<li><a href="mridc/collections/reconstruction/models/pics.html">mridc.collections.reconstruction.models.pics</a></li>
<li><a href="mridc/collections/reconstruction/models/primaldual/pd.html">mridc.collections.reconstruction.models.primaldual.pd</a></li>
<li><a href="mridc/collections/reconstruction/models/recurrentvarnet/conv2gru.html">mridc.collections.reconstruction.models.recurrentvarnet.conv2gru</a></li>
<li><a href="mridc/collections/reconstruction/models/recurrentvarnet/recurentvarnet.html">mridc.collections.reconstruction.models.recurrentvarnet.recurentvarnet</a></li>
<li><a href="mridc/collections/reconstruction/models/rim/conv_layers.html">mridc.collections.reconstruction.models.rim.conv_layers</a></li>
<li><a href="mridc/collections/reconstruction/models/rim/rim_block.html">mridc.collections.reconstruction.models.rim.rim_block</a></li>
<li><a href="mridc/collections/reconstruction/models/rim/rnn_cells.html">mridc.collections.reconstruction.models.rim.rnn_cells</a></li>
<li><a href="mridc/collections/reconstruction/models/rim/utils.html">mridc.collections.reconstruction.models.rim.utils</a></li>
<li><a href="mridc/collections/reconstruction/models/rvn.html">mridc.collections.reconstruction.models.rvn</a></li>
<li><a href="mridc/collections/reconstruction/models/sigmanet/dc_layers.html">mridc.collections.reconstruction.models.sigmanet.dc_layers</a></li>
<li><a href="mridc/collections/reconstruction/models/sigmanet/sensitivity_net.html">mridc.collections.reconstruction.models.sigmanet.sensitivity_net</a></li>
<li><a href="mridc/collections/reconstruction/models/unet.html">mridc.collections.reconstruction.models.unet</a></li>
<li><a href="mridc/collections/reconstruction/models/unet_base/unet_block.html">mridc.collections.reconstruction.models.unet_base.unet_block</a></li>
<li><a href="mridc/collections/reconstruction/models/variablesplittingnet/vsnet_block.html">mridc.collections.reconstruction.models.variablesplittingnet.vsnet_block</a></li>
<li><a href="mridc/collections/reconstruction/models/varnet/vn_block.html">mridc.collections.reconstruction.models.varnet.vn_block</a></li>
<li><a href="mridc/collections/reconstruction/models/vn.html">mridc.collections.reconstruction.models.vn</a></li>
<li><a href="mridc/collections/reconstruction/models/vsnet.html">mridc.collections.reconstruction.models.vsnet</a></li>
<li><a href="mridc/collections/reconstruction/models/xpdnet.html">mridc.collections.reconstruction.models.xpdnet</a></li>
<li><a href="mridc/collections/reconstruction/models/zf.html">mridc.collections.reconstruction.models.zf</a></li>
<li><a href="mridc/collections/reconstruction/parts/transforms.html">mridc.collections.reconstruction.parts.transforms</a></li>
<li><a href="mridc/collections/reconstruction/parts/utils.html">mridc.collections.reconstruction.parts.utils</a></li>
<li><a href="mridc/core/classes/common.html">mridc.core.classes.common</a></li>
<li><a href="mridc/core/classes/dataset.html">mridc.core.classes.dataset</a></li>
<li><a href="mridc/core/classes/export.html">mridc.core.classes.export</a></li>
<li><a href="mridc/core/classes/loss.html">mridc.core.classes.loss</a></li>
<li><a href="mridc/core/classes/modelPT.html">mridc.core.classes.modelPT</a></li>
<li><a href="mridc/core/classes/module.html">mridc.core.classes.module</a></li>
<li><a href="mridc/core/conf/base_config.html">mridc.core.conf.base_config</a></li>
<li><a href="mridc/core/conf/dataloader.html">mridc.core.conf.dataloader</a></li>
<li><a href="mridc/core/conf/hydra_runner.html">mridc.core.conf.hydra_runner</a></li>
<li><a href="mridc/core/conf/modelPT.html">mridc.core.conf.modelPT</a></li>
<li><a href="mridc/core/conf/optimizers.html">mridc.core.conf.optimizers</a></li>
<li><a href="mridc/core/conf/schedulers.html">mridc.core.conf.schedulers</a></li>
<li><a href="mridc/core/conf/trainer.html">mridc.core.conf.trainer</a></li>
<li><a href="mridc/core/connectors/save_restore_connector.html">mridc.core.connectors.save_restore_connector</a></li>
<li><a href="mridc/core/neural_types/axes.html">mridc.core.neural_types.axes</a></li>
<li><a href="mridc/core/neural_types/comparison.html">mridc.core.neural_types.comparison</a></li>
<li><a href="mridc/core/neural_types/elements.html">mridc.core.neural_types.elements</a></li>
<li><a href="mridc/core/neural_types/neural_type.html">mridc.core.neural_types.neural_type</a></li>
<li><a href="mridc/core/optim/adafactor.html">mridc.core.optim.adafactor</a></li>
<li><a href="mridc/core/optim/lr_scheduler.html">mridc.core.optim.lr_scheduler</a></li>
<li><a href="mridc/core/optim/novograd.html">mridc.core.optim.novograd</a></li>
<li><a href="mridc/core/optim/optimizer_with_master_params.html">mridc.core.optim.optimizer_with_master_params</a></li>
<li><a href="mridc/core/optim/optimizers.html">mridc.core.optim.optimizers</a></li>
<li><a href="mridc/core/utils/neural_type_utils.html">mridc.core.utils.neural_type_utils</a></li>
<li><a href="mridc/core/utils/numba_utils.html">mridc.core.utils.numba_utils</a></li>
<li><a href="mridc/launch.html">mridc.launch</a></li>
<li><a href="mridc/utils/app_state.html">mridc.utils.app_state</a></li>
<li><a href="mridc/utils/arguments.html">mridc.utils.arguments</a></li>
<li><a href="mridc/utils/cloud.html">mridc.utils.cloud</a></li>
<li><a href="mridc/utils/config_utils.html">mridc.utils.config_utils</a></li>
<li><a href="mridc/utils/decorators/deprecated.html">mridc.utils.decorators.deprecated</a></li>
<li><a href="mridc/utils/decorators/experimental.html">mridc.utils.decorators.experimental</a></li>
<li><a href="mridc/utils/decorators/port_docs.html">mridc.utils.decorators.port_docs</a></li>
<li><a href="mridc/utils/distributed.html">mridc.utils.distributed</a></li>
<li><a href="mridc/utils/env_var_parsing.html">mridc.utils.env_var_parsing</a></li>
<li><a href="mridc/utils/exceptions.html">mridc.utils.exceptions</a></li>
<li><a href="mridc/utils/exp_manager.html">mridc.utils.exp_manager</a></li>
<li><a href="mridc/utils/export_utils.html">mridc.utils.export_utils</a></li>
<li><a href="mridc/utils/formaters/base.html">mridc.utils.formaters.base</a></li>
<li><a href="mridc/utils/formaters/colors.html">mridc.utils.formaters.colors</a></li>
<li><a href="mridc/utils/formaters/utils.html">mridc.utils.formaters.utils</a></li>
<li><a href="mridc/utils/get_rank.html">mridc.utils.get_rank</a></li>
<li><a href="mridc/utils/lightning_logger_patch.html">mridc.utils.lightning_logger_patch</a></li>
<li><a href="mridc/utils/metaclasses.html">mridc.utils.metaclasses</a></li>
<li><a href="mridc/utils/model_utils.html">mridc.utils.model_utils</a></li>
<li><a href="mridc/utils/mridc_logging.html">mridc.utils.mridc_logging</a></li>
<li><a href="mridc/utils/timers.html">mridc.utils.timers</a></li>
</ul>

</div>
</div>
<footer>

<hr/>

<div role="contentinfo">
<p>&#169; Copyright 2022, Dimitrios Karkalousos.</p>
</div>

Built with <a href="https://www.sphinx-doc.org/">Sphinx</a> using a
<a href="https://github.com/readthedocs/sphinx_rtd_theme">theme</a>
provided by <a href="https://readthedocs.org">Read the Docs</a>.


</footer>
</div>
</div>
</section>
</div>
<script>
jQuery(function () {
SphinxRtdTheme.Navigation.enable(true);
});
</script>

</body>
</html>
Loading

0 comments on commit e2c50f3

Please sign in to comment.