fixes documentation, #56, #61, & codecov uploader

wdika · May 25, 2022 · e2c50f3 · e2c50f3
1 parent 60a429d
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diff --git a/.github/workflows/codecov.yml b/.github/workflows/codecov.yml
@@ -30,3 +30,4 @@ jobs:
         flags: pytests # optional
         name: codecov-umbrella # optional
         verbose: true # optional (default = false)
+        version: "v0.1.15"
diff --git a/.readthedocs.yaml b/.readthedocs.yaml
@@ -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:

diff --git a/CITATION.cff b/CITATION.cff
@@ -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
diff --git a/README.md b/README.md
@@ -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>
 
 ---
@@ -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
 

diff --git a/docs/build/doctrees/environment.pickle b/docs/build/doctrees/environment.pickle
diff --git a/docs/build/doctrees/index.doctree b/docs/build/doctrees/index.doctree
diff --git a/docs/build/doctrees/modules.doctree b/docs/build/doctrees/modules.doctree
diff --git a/docs/build/doctrees/mridc.collections.common.callbacks.doctree b/docs/build/doctrees/mridc.collections.common.callbacks.doctree
diff --git a/docs/build/doctrees/mridc.collections.common.data.doctree b/docs/build/doctrees/mridc.collections.common.data.doctree
diff --git a/docs/build/doctrees/mridc.collections.common.doctree b/docs/build/doctrees/mridc.collections.common.doctree
diff --git a/docs/build/doctrees/mridc.collections.common.losses.doctree b/docs/build/doctrees/mridc.collections.common.losses.doctree
diff --git a/docs/build/doctrees/mridc.collections.common.metrics.doctree b/docs/build/doctrees/mridc.collections.common.metrics.doctree
diff --git a/docs/build/doctrees/mridc.collections.common.parts.doctree b/docs/build/doctrees/mridc.collections.common.parts.doctree
diff --git a/docs/build/doctrees/mridc.collections.doctree b/docs/build/doctrees/mridc.collections.doctree
diff --git a/docs/build/doctrees/mridc.collections.reconstruction.data.doctree b/docs/build/doctrees/mridc.collections.reconstruction.data.doctree
diff --git a/docs/build/doctrees/mridc.collections.reconstruction.doctree b/docs/build/doctrees/mridc.collections.reconstruction.doctree
diff --git a/docs/build/doctrees/mridc.collections.reconstruction.metrics.doctree b/docs/build/doctrees/mridc.collections.reconstruction.metrics.doctree
diff --git a/docs/build/doctrees/mridc.collections.reconstruction.models.cascadenet.doctree b/docs/build/doctrees/mridc.collections.reconstruction.models.cascadenet.doctree
diff --git a/docs/build/doctrees/mridc.collections.reconstruction.models.conv.doctree b/docs/build/doctrees/mridc.collections.reconstruction.models.conv.doctree
diff --git a/docs/build/doctrees/mridc.collections.reconstruction.models.convrecnet.doctree b/docs/build/doctrees/mridc.collections.reconstruction.models.convrecnet.doctree
diff --git a/docs/build/doctrees/mridc.collections.reconstruction.models.crossdomain.doctree b/docs/build/doctrees/mridc.collections.reconstruction.models.crossdomain.doctree
diff --git a/docs/build/doctrees/mridc.collections.reconstruction.models.didn.doctree b/docs/build/doctrees/mridc.collections.reconstruction.models.didn.doctree
diff --git a/docs/build/doctrees/mridc.collections.reconstruction.models.doctree b/docs/build/doctrees/mridc.collections.reconstruction.models.doctree
diff --git a/docs/build/doctrees/mridc.collections.reconstruction.models.multidomain.doctree b/docs/build/doctrees/mridc.collections.reconstruction.models.multidomain.doctree
diff --git a/docs/build/doctrees/mridc.collections.reconstruction.models.mwcnn.doctree b/docs/build/doctrees/mridc.collections.reconstruction.models.mwcnn.doctree
diff --git a/docs/build/doctrees/mridc.collections.reconstruction.models.primaldual.doctree b/docs/build/doctrees/mridc.collections.reconstruction.models.primaldual.doctree
diff --git a/docs/build/doctrees/mridc.collections.reconstruction.models.recurrentvarnet.doctree b/docs/build/doctrees/mridc.collections.reconstruction.models.recurrentvarnet.doctree
diff --git a/docs/build/doctrees/mridc.collections.reconstruction.models.rim.doctree b/docs/build/doctrees/mridc.collections.reconstruction.models.rim.doctree
diff --git a/docs/build/doctrees/mridc.collections.reconstruction.models.sigmanet.doctree b/docs/build/doctrees/mridc.collections.reconstruction.models.sigmanet.doctree
diff --git a/docs/build/doctrees/mridc.collections.reconstruction.models.unet_base.doctree b/docs/build/doctrees/mridc.collections.reconstruction.models.unet_base.doctree
diff --git a/docs/build/doctrees/mridc.collections.reconstruction.models.variablesplittingnet.doctree b/docs/build/doctrees/mridc.collections.reconstruction.models.variablesplittingnet.doctree
diff --git a/docs/build/doctrees/mridc.collections.reconstruction.models.varnet.doctree b/docs/build/doctrees/mridc.collections.reconstruction.models.varnet.doctree
diff --git a/docs/build/doctrees/mridc.collections.reconstruction.parts.doctree b/docs/build/doctrees/mridc.collections.reconstruction.parts.doctree
diff --git a/docs/build/doctrees/mridc.core.classes.doctree b/docs/build/doctrees/mridc.core.classes.doctree
diff --git a/docs/build/doctrees/mridc.core.conf.doctree b/docs/build/doctrees/mridc.core.conf.doctree
diff --git a/docs/build/doctrees/mridc.core.connectors.doctree b/docs/build/doctrees/mridc.core.connectors.doctree
diff --git a/docs/build/doctrees/mridc.core.doctree b/docs/build/doctrees/mridc.core.doctree
diff --git a/docs/build/doctrees/mridc.core.neural_types.doctree b/docs/build/doctrees/mridc.core.neural_types.doctree
diff --git a/docs/build/doctrees/mridc.core.optim.doctree b/docs/build/doctrees/mridc.core.optim.doctree
diff --git a/docs/build/doctrees/mridc.core.utils.doctree b/docs/build/doctrees/mridc.core.utils.doctree
diff --git a/docs/build/doctrees/mridc.doctree b/docs/build/doctrees/mridc.doctree
diff --git a/docs/build/doctrees/mridc.utils.decorators.doctree b/docs/build/doctrees/mridc.utils.decorators.doctree
diff --git a/docs/build/doctrees/mridc.utils.doctree b/docs/build/doctrees/mridc.utils.doctree
diff --git a/docs/build/doctrees/mridc.utils.formaters.doctree b/docs/build/doctrees/mridc.utils.formaters.doctree
diff --git a/docs/build/html/.buildinfo b/docs/build/html/.buildinfo
@@ -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
diff --git a/docs/build/html/_modules/index.html b/docs/build/html/_modules/index.html
@@ -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>
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