Rename notebook folders to have no spaces (Add Sphinx docs - Part 1)

README.md

@@ -10,13 +10,12 @@ The DCP welcomes any contributed notebooks or other tutorials to the list below.
 
 ## Vignettes Table of Contents:
 
-* [Explore an HCA Data Set in Scanpy (May 2019)](Explore%20an%20HCA%20Data%20Set%20in%20Scanpy%20(May%202019)/README.md)
-* [Download Expression Matrix for Scanpy](Download%20Expression%20Matrix%20for%20Scanpy/README.md)
-* [Explore an HCA Data Set in Scanpy (Nov 2018)](Explore%20an%20HCA%20Data%20Set%20in%20Scanpy%20(Nov%202018)/README.md)
-* [SPARK Example](SPARK%20Example/README.md)
-* [Login to the DSS](Login%20to%20the%20DSS/README.md)
-* [Download all .fastq files in a project](Download%20all%20.fastq%20files%20in%20a%20project/README.md)
-* [Download Any BAM File](Download%20Any%20BAM%20File/README.md)
-* [Find Cell Type Count](Find%20Cell%20Type%20Count/README.md)
-* [Install the HCA CLI tools](Install%20the%20HCA%20CLI%20tools/README.md)
-* [Download 10x Seq T-cell Bundles](Download%2010x%20Seq%20T-cell%20Bundles/README.md)
+* [Install the HCA CLI tools](install-hca/install-hca.ipynb)
+* [Login to the DSS](login/login.ipynb)
+* [Writing ElasticSearch Queries](elasticsearch-queries/elasticsearch-queries.ipynb)
+* [Download 10x Liver Cell Data](download-10x-seq-tcell/download-10x-liver.ipynb)
+* [Download All Fastq Files in a Project](download-all-fastq-files/download-all-fastq-files.ipynb)
+* [Download Any BAM File](download-any-bam-file/download-any-bam-file.ipynb)
+* [Download Smartseq2 Expression Matrix as an Input to Scanpy](download-smartseq2-matrix-scanpy/download-smartseq2-matrix-scanpy.ipynb)
+* [Explore an HCA Data Set in Scanpy](explore-hca-dataset-scanpy/explore-hca-dataset-scanpy.ipynb)
+* [Find Cell Type Count](find-cell-type-count/find-cell-type-count.ipynb)

Download 10x Seq T-cell Bundles/README.md → download-10x-seq-tcell/README.md

@@ -1,5 +1,5 @@
-# Download All Bundles for T-Cells Sequenced with 10x
-
-In this task, the goal is to download all bundles containing data on T-cells and 10x sequencing.
-
-See the [notebook](https://github.com/HumanCellAtlas/data-consumer-vignettes/blob/jk-download-t-cells-with-10x/tasks/Download%2010x%20Seq%20T-cell%20Bundles/Download%20All%20Bundles%20for%20T-cells%20Sequenced%20with%2010x.ipynb).
+# Download All Bundles for T-Cells Sequenced with 10x
+
+In this task, the goal is to download all bundles containing data on T-cells and 10x sequencing.
+
+See the [notebook](https://github.com/HumanCellAtlas/data-consumer-vignettes/blob/jk-download-t-cells-with-10x/tasks/Download%2010x%20Seq%20T-cell%20Bundles/Download%20All%20Bundles%20for%20T-cells%20Sequenced%20with%2010x.ipynb).

Download Expression Matrix for Scanpy/README.md → download-smartseq2-matrix-scanpy/README.md

@@ -1,5 +1,5 @@
-# Download SmartSeq2 Expression Matrix as an Input to Scanpy
-
-In this task, suppose you want to download an expression matrix for use in Python's scanpy module.
-
-See the [notebook](https://github.com/HumanCellAtlas/data-consumer-vignettes/blob/feature/download-expression-matrix/tasks/Download%20Expression%20Matrix%20for%20Scanpy/Download%20SmartSeq2%20Expression%20Matrix%20as%20Input%20to%20Scanpy.ipynb).
+# Download SmartSeq2 Expression Matrix as an Input to Scanpy
+
+In this task, suppose you want to download an expression matrix for use in Python's scanpy module.
+
+See the [notebook](https://github.com/HumanCellAtlas/data-consumer-vignettes/blob/feature/download-expression-matrix/tasks/Download%20Expression%20Matrix%20for%20Scanpy/Download%20SmartSeq2%20Expression%20Matrix%20as%20Input%20to%20Scanpy.ipynb).

Explore an HCA Data Set in Scanpy (Nov 2018)/README.md → explore-hca-dataset-scanpy-nov-2018/README.md

@@ -1,14 +1,14 @@
 # HCA Scanpy Demo
 
-The vignette in this folder demonstrates the ability to load an expression matrix downloaded 
+The vignette in this folder demonstrates the ability to load an expression matrix downloaded
 from the HCA browser into scanpy and briefly explore the data. The downloaded file, `pancreas.loom`, is the result of end-to-end processing in the Data Coordination Platform workflow, and is included in this repo.
 
 The file `ENSG_to_name.csv` contains the Gencode identifiers for the genes in the HCA expression matrices, along with the more commonly used gene symbol (i.e. `ENSG00000115263.14,GCG`). This might be generally useful in your exploration of HCA expression matrices.
 
 
 ## Installation
 
-This notebook assumes that you have installed python 3 on your system, 
+This notebook assumes that you have installed python 3 on your system,
 and that the `pip` executable installs packages for that python
 distribution. For some users, it may be necessary to use `pip3` instead.
 

Find Cell Type Count/README.md → find-cell-type-count/README.md

@@ -1,6 +1,6 @@
-# Find Cell Type Count
-
-In this task, you want to count the number of available cells of a certain cell type. For instance,
-you might ask, "How many _hematopoietic system_ cells are available in the database?"
-
-See the [notebook](Find%20Cell%20Type%20Count.ipynb).
+# Find Cell Type Count
+
+In this task, you want to count the number of available cells of a certain cell type. For instance,
+you might ask, "How many _hematopoietic system_ cells are available in the database?"
+
+See the [notebook](Find%20Cell%20Type%20Count.ipynb).

SPARK Example/README.md → spark-example/README.md

@@ -193,7 +193,7 @@ d03e1fb5-0bd6-41ad-9744-c87af0fbdc33	40	TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTCT
 
 This is an extremely basic example of how to access HCA data on AWS using
 SPARK.  A future iteration of this code could do something much more interesting.  I'm
-thinking of implementing what Titus Brown covers in this [blog post](http://ivory.idyll.org/blog/2016-sourmash.html).  
+thinking of implementing what Titus Brown covers in this [blog post](http://ivory.idyll.org/blog/2016-sourmash.html).
 Specifically it would be super cool to calculate MinHash signature for each
 of the biomaterials in HCA and use these to quickly compare samples by samples.
 Perhaps this would be useful in building a feature to ask "what cells are

SPARK Example/src/main/java/kmer/Retriable.java → spark-example/src/main/java/kmer/Retriable.java

@@ -47,4 +47,3 @@ static <T> Optional<T> runWithRetries(
         return runWithRetries(maxRetries, maxInterval, supplier, t -> true);
     }
 };
-

SPARK Example/src/main/java/kmer/SparkUtil.java → spark-example/src/main/java/kmer/SparkUtil.java

@@ -4,14 +4,14 @@
 import org.apache.spark.api.java.JavaSparkContext;
 
 /**
- * This is a utility class to create JavaSparkContext 
- * and other objects required by Spark. There are many 
- * ways to create JavaSparkContext object. Here we offer 
+ * This is a utility class to create JavaSparkContext
+ * and other objects required by Spark. There are many
+ * ways to create JavaSparkContext object. Here we offer
  * 2 ways to create it:
  *
  *   1. by using YARN's resource manager host name
  *
- *   2. by using spark master URL, which is expressed as: 
+ *   2. by using spark master URL, which is expressed as:
  *
  *           spark://<spark-master-host-name>:7077
  *

SPARK Example/src/test/java/kmer/DataStoreClientTest.java → spark-example/src/test/java/kmer/DataStoreClientTest.java

@@ -70,4 +70,3 @@ public void testSerialize() throws IOException {
         oos.writeObject(new DataStoreClient("https://somewhere.com/"));
     }
 }
-

SPARK Example/src/test/java/kmer/RetriableTest.java → spark-example/src/test/java/kmer/RetriableTest.java

@@ -22,5 +22,3 @@ public void runWithRetriesShouldReturnSuccessfulValue() throws InterruptedExcept
         assertTrue(opt.get() == 2);
     }
 }
-
-