Minor change to readme to better reflect update to 6.0 and deprecatio… (

#382) * Minor change to readme to better reflect update to 6.0 and deprecation of guppy. * Allow hidden files in upload CI action, warn if file not found * Include hidden files in merge action When did this become a thing --------- Co-authored-by: Rory Munro <[email protected]>
LooseLab · Sep 12, 2024 · 2c63712 · 2c63712
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diff --git a/.github/workflows/CI.yml b/.github/workflows/CI.yml
@@ -53,7 +53,8 @@ jobs:
         with:
           name: my-artifact-${{ matrix.python-version }}
           path: .coverage*
-          if-no-files-found: ignore
+          if-no-files-found: warn
+          include-hidden-files: true
 
   merge:
     name: merge
@@ -65,6 +66,7 @@ jobs:
           with:
             name: coverage-data
             pattern: my-artifact-*
+            include-hidden-files: true
 
   coverage:
     name: Combine coverage

diff --git a/README.md b/README.md
@@ -128,9 +128,9 @@ conda env create -f development.yml
 conda activate readfish_dev
 ```
 
-| <h2>‼️ Important !! </h2>                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   |
-|:------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
-| MinKNOW is transitioning from Guppy to Dorado. Until MinKNOW version 5.9 both Guppy and Dorado used ont-pyguppy-client-lib.<br/>As of MinKNOW version 5.9 and Dorado server version 7.3.9 and greater Dorado requires an alternate library, `ont-pybasecall-client-lib`.<br/>The listed `ont-pyguppy-client-lib` or `ont-pybasecaller-client-lib` version may not match the version installed on your system. To fix this, Please see this [issue](https://github.com/LooseLab/readfish/issues/221#issuecomment-1381529409), using the appropriate library. |
+| <h2>‼️ Important !! </h2>                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 |
+|:------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
+| MinKNOW has now transitioned from Guppy to Dorado. Until MinKNOW version 5.9 both Guppy and Dorado used ont-pyguppy-client-lib.<br/>As of MinKNOW version 5.9 and Dorado server version 7.3.9 and greater Dorado required an alternate library, `ont-pybasecall-client-lib`, but guppy could still be used. <br/> As of MinKNOW 6.0 Guppy support has been deprecated and only Dorado support is provided. It is important to ensure the correct library is installed for your specific configuration and the listed `ont-pyguppy-client-lib` or `ont-pybasecaller-client-lib` version may not match the versions installed on your system. To fix this, Please see this [issue](https://github.com/LooseLab/readfish/issues/221#issuecomment-1381529409), using the appropriate library. |
 
 
 [ONT's Dorado Basecall Server GPU](https://community.nanoporetech.com/downloads) should be installed and running as a server.