Merge branch 'master' into qurator-omni

.markdownlint.jsonc

@@ -0,0 +1,7 @@
+{
+  "default": true,
+  "no-blanks-blockquote": false,
+  "no-duplicate-heading": {
+    "siblings_only": true
+  }
+}

.markdownlintignore

@@ -1,10 +1,8 @@
 # Not ready for lint yet
 gendocs
-lambdas
-py-shared
 testdocs
 
-# Autogenerated 
+# Autogenerated
 docs/api-reference
 
 .git

catalog/app/containers/Admin/Buckets/Buckets.tsx

@@ -1187,7 +1187,7 @@ function TabulatorCard({
     <Card
       className={className}
       disabled={disabled}
-      title="Tabulation (Longitudinal Querying)"
+      title="Tabulator (Longitudinal Querying)"
     >
       <TabulatorForm bucket={bucket} tables={tabulatorTables} />
     </Card>

catalog/app/containers/Admin/Buckets/Tabulator/Tabulator.tsx

@@ -30,7 +30,7 @@ const ConfigEditor = React.lazy(() =>
 
 const defaultConfig = `schema:
     - name: column1 # specify the schema
-      type: Utf8
+      type: STRING
 source:
     type: quilt-packages
     package_name: "" # specify a RegEx for matching packages

lambdas/indexer/README.md

@@ -1,11 +1,14 @@
+<!-- markdownlint-configure-file {"line-length": {"code_blocks": false}} -->
 # Notes on message formats
+
 `indexer.py` consumes messages from an SQS Queue.
 Each message contains one or more S3 events (these may be synthetic events
 created by the bulk indexing process).
 
 ## Sample message
-```
-message: {
+
+```python
+{
   'messageId': 'f4feb40f-16a5-47af-89dc-091bd0fae1e2',
   'receiptHandle': 'AQEBv6rRxc4+CRSi3RWY64HqOIzu+dJEWnMCAwVgyogUBDY4a1fBoEp6mnx3qy5AO/A+qvTVRWq6lWS3D2iDc8pUGfj8BAJ2/G21/mA2OqDF8e0JdItwu+haRiFzsH87W+5HAwGjIi13Yltf1UjaZoBbrdX+jOlx2lbMTgJOgAzK6ZrHnYaJdTsY72izxAY+3zm4x7U4Cg79uGj6IezWNW+ZjlsEg20tkvexQXPr6AaTbJ0cei+IVueSTy5WUiBMjTgmKxvJEWoLr3BzUvy7uI1ECJx/6m2ya5+M0161ufyYMFqYljYFe2InV2G79fXdW2pYkHy0xnbMKLlQpmOkQyJWyyYV9J6i9MO9Qkp9l0gnyxykw9eOZ/9bn0iV5p+aoRwhkopS6e1jhx8HMtTAs30TM6Uw1TFU+vPAMPu6syIMABs=',
   'body': '{"Message": "{\\"Records\\": [{\\"eventName\\": \\"ObjectCreated:Put\\", \\"s3\\": {\\"bucket\\": {\\"name\\": \\"quilt-search-test\\"}}},]}"}',
@@ -24,7 +27,8 @@ message: {
 ```
 
 ## Sample event
-```
+
+```python
 {
   'eventName': 'ObjectCreated:Put',
   's3': {
@@ -40,4 +44,3 @@ message: {
   }
 }
 ```
-

lambdas/indexer/test/README.md

@@ -1,9 +1,10 @@
 # Rudimentary tests
 
 ## TODO
+
 * [ ] run inside of Docker container that mimics Lambda env
-		* https://blog.quiltdata.com/an-easier-way-to-build-lambda-deployment-packages-with-docker-instead-of-ec2-9050cd486ba8
-		* https://nvbn.github.io/2015/09/09/pytest-docker/
+  * <https://blog.quiltdata.com/an-easier-way-to-build-lambda-deployment-packages-with-docker-instead-of-ec2-9050cd486ba8>
+  * <https://nvbn.github.io/2015/09/09/pytest-docker/>
 
 * [ ] parameterize Python version (Lambda functions can be 2.7, 3.6, etc.)
 * [ ] integrate withe rest of unit testing suite?

lambdas/indexer/test/data/extended/README.md

@@ -1,3 +1,4 @@
+<!-- markdownlint-disable first-line-h1 -->
 If you run `pytest --extended` the test harness will look for parquet, etc. files
 in this folder and run a few conditional tests. This is useful for testing
 one-off / customer issues

lambdas/s3hash/CHANGELOG.md

@@ -1,3 +1,4 @@
+<!-- markdownlint-disable line-length -->
 # Changelog
 
 Changes are listed in reverse chronological order (newer entries at the top).

lambdas/shared/tests/data/fcs/README.md

@@ -1,4 +1,5 @@
+<!-- markdownlint-disable first-line-h1 -->
 See notebook for original source of files
 
-normal.fcs was Accuri - C6 - A01 H2O.fcs
-meta-only.fcs was BD - FACS Aria II - Compensation Controls_G710 Stained Control.fcs  
+* normal.fcs was Accuri - C6 - A01 H2O.fcs
+* meta-only.fcs was BD - FACS Aria II - Compensation Controls_G710 Stained Control.fcs

lambdas/thumbnail/tests/data/pdf2image-README.md

@@ -1,63 +1,68 @@
+<!-- markdownlint-configure-file {"line-length": {"code_blocks": false}} -->
 # Developer notes
+
 * How we get pdftoppm running with MS fonts
 * On MacBook testing: jpeg faster than png, pdftoppm faster than pdftocairo
 
 ## Extracting pdftoppm, pdftocairo (via poppler-utils) as standalones
-```
+
+```sh
 yum install yum-utils rpmdevtools
-yumdownloader poppler-utils 
+yumdownloader poppler-utils
 
 # Extract files from .rpm
 rpmdev-extract *.rpm
 ```
 
-Then you need to run the binaries by hand and discover which .o files are missing. These files
-were found to be children of /usr/lib64 and when they are copied to the same, /usr/bin/pdftoppm works.
+Then you need to run the binaries by hand and discover which .o files are
+missing. These files were found to be children of /usr/lib64 and when they
+are copied to the same, /usr/bin/pdftoppm works.
 
 Consider setting [`LD_LIBRARY_PATH`](https://docs.aws.amazon.com/lambda/latest/dg/configuration-envvars.html#configuration-envvars-runtime)
 to include /somedir/usr/lib64 so Linux can find the libs.
 
-
 ## Getting MS fonts
 
 * [Installing cabextract on Amazon Linux](https://aws.amazon.com/premiumsupport/knowledge-center/ec2-enable-epel/)
 * [Adding MS fonts to linux](http://mscorefonts2.sourceforge.net/)
 
 Above step will add fonts to `cp -r /usr/share/fonts`
 
-## Making the fonts discoverable via pdftoppm, etc.
+## Making the fonts discoverable via pdftoppm, etc
 
 * [fonts.conf](https://stackoverflow.com/questions/46486261/include-custom-fonts-in-aws-lambda)
 * `fc-cache` (unix util)
 
-```
+```sh
 export FONTCONFIG_PATH=/io/fonts/
 ```
 
 ## `pdftoppm`
+
 * Page numbering starts at 1 (not 0)
 * Providing size=INT to a convert function ensures largest dimension == INT
 * first_page can be negative (lib rounds up to 1)
 * last_page can be > than total pages (lib takes min)
 
 No format (=ppm) faster than JPEG faster than PNG
 
-``` (=ppm)(=ppm) 
-In [8]: %timeit imgs = pdf2image.convert_from_path("tests/data/MUMmer.pdf", fmt="png",size=(1024,768))                                                             
+```Python console
+In [8]: %timeit imgs = pdf2image.convert_from_path("tests/data/MUMmer.pdf", fmt="png",size=(1024,768))
 4.3 s ± 162 ms per loop (mean ± std. dev. of 7 runs, 1 loop each)
 
-In [9]: %timeit imgs = pdf2image.convert_from_path("tests/data/MUMmer.pdf", fmt="jpeg", size=(1024,768))                                                            
+In [9]: %timeit imgs = pdf2image.convert_from_path("tests/data/MUMmer.pdf", fmt="jpeg", size=(1024,768))
 970 ms ± 58.2 ms per loop (mean ± std. dev. of 7 runs, 1 loop each)
 
-In [10]: %timeit imgs = pdf2image.convert_from_path("tests/data/MUMmer.pdf", size=(1024,768))                                                                      
+In [10]: %timeit imgs = pdf2image.convert_from_path("tests/data/MUMmer.pdf", size=(1024,768))
 798 ms ± 37.2 ms per loop (mean ± std. dev. of 7 runs, 1 loop each)
 ```
 
 jpeg also outputs faster:
-```
-In [14]: %timeit imgs[3].save("tmp-1024-768.png")                                     
+
+```Python console
+In [14]: %timeit imgs[3].save("tmp-1024-768.png")
 198 ms ± 4.97 ms per loop (mean ± std. dev. of 7 runs, 10 loops each)
 
-In [15]: %timeit imgs[3].save("tmp-1024-768.jpeg")                                    
+In [15]: %timeit imgs[3].save("tmp-1024-768.jpeg")
 44.1 ms ± 4.36 ms per loop (mean ± std. dev. of 7 runs, 10 loops each)
-```
+```

py-shared/CHANGELOG.md

@@ -1,3 +1,4 @@
+<!-- markdownlint-disable line-length -->
 # Changelog
 
 Changes are listed in reverse chronological order (newer entries at the top).