squash

book/_config.yml

@@ -92,9 +92,9 @@ parse:
     dwq2_add_2nd_transformer_commit_url: "{{dwq2_gh_commit_url.format(dwq2_add_2nd_transformer_commit)}}"
     dwq2_add_pipeline_commit: "1e601c41b86d98b22f4e16685e868f1c5710f3bf"
     dwq2_add_pipeline_commit_url: "{{dwq2_gh_commit_url.format(dwq2_add_pipeline_commit)}}"
-    dwq2_add_parallel_pipeline_commit_1: "a45f6fb85315843078c0777326031dbce9564802"
+    dwq2_add_parallel_pipeline_commit_1: "d0d5f38ca6d2e8cdc647660db8d1923b048f8e1e"
     dwq2_add_parallel_pipeline_commit_1_url: "{{dwq2_gh_commit_url.format(dwq2_add_parallel_pipeline_commit_1)}}"
-    dwq2_add_parallel_pipeline_commit_2: "fd36ec2ec8cf463ee568074a2ba25823e4f02352"
+    dwq2_add_parallel_pipeline_commit_2: "4ed7e01a6da9a10e7ddf1956877cf494740e35cd"
     dwq2_add_parallel_pipeline_commit_2_url: "{{dwq2_gh_commit_url.format(dwq2_add_parallel_pipeline_commit_2)}}"
-    dwq2_add_parallel_pipeline_commit_3: "f978c064a7e941081c7b2e697087be32a7db0e97"
+    dwq2_add_parallel_pipeline_commit_3: "590263ee9bb8c48df09fe62c0e966acfa99f9aff"
     dwq2_add_parallel_pipeline_commit_3_url: "{{dwq2_gh_commit_url.format(dwq2_add_parallel_pipeline_commit_3)}}"

book/plugins/tutorials/add-parallel-pipeline.md

@@ -7,9 +7,10 @@ This will enable your users to utilize multi-processor computers or multi-node h
 ```{admonition} tl;dr
 :class: tip
 
-The complete code that I wrote to add the second `Pipeline` to my plugin can be found here: {{ dwq2_add_parallel_pipeline_commit_1_url }}. The code that I developed to add parallel computing support to the new `Pipeline` can be found here: {{ dwq2_add_parallel_pipeline_commit_2_url }}.
-I also included a usage example at the end which you can use to compare the performance of serial and parallel runs of the new Pipeline here: {{ dwq2_add_parallel_pipeline_commit_3_url }}.
-That third commit does increase the runtime of the unit tests considerably (from about 30 seconds to about 6 minutes, on the computer that I'm developing on).
+1. The complete code that I wrote to add the second `Pipeline` to my plugin can be found here: {{ dwq2_add_parallel_pipeline_commit_1_url }}.
+2. The code that I developed to add parallel computing support to the new `Pipeline` can be found here: {{ dwq2_add_parallel_pipeline_commit_2_url }}.
+3. Finally, I added a usage example that can be used to compare the performance of serial and parallel runs of the new Pipeline here: {{ dwq2_add_parallel_pipeline_commit_3_url }}.
+Because the third commit includes (a small amount) of real data, as opposed to the toy-sized data we've been using in unit tests, it increases the runtime of the test suite considerably (from about 30 seconds to about 6 minutes, on the M3 MacBook Pro that that I'm developing on).
 ```
 
 ## Add a local alignment search `Pipeline`
@@ -396,6 +397,7 @@ After making all of the changes described here to your `_pipelines.py` and `test
 If all tests pass, you should be good to go.
 If not, compare your code to mine ({{ dwq2_add_parallel_pipeline_commit_2_url }}) to see what's different.
 
+(serial-parallel-runtime)=
 ## Compare the serial versus parallel run times of the `search-and-summarize`
 
 Now that we've added parallel computing support to our `search-and-summarize` Pipeline, we can try it out to see how it impacts run time.