From 1a10f55cd2396a94c241f068d0ec65d4cf423a78 Mon Sep 17 00:00:00 2001 From: mattloose Date: Mon, 26 Aug 2024 19:36:33 +0100 Subject: [PATCH 1/3] Minor change to readme to better reflect update to 6.0 and deprecation of guppy. --- README.md | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/README.md b/README.md index 83f5c68..c63c008 100644 --- a/README.md +++ b/README.md @@ -128,9 +128,9 @@ conda env create -f development.yml conda activate readfish_dev ``` -|

‼️ Important !!

| -|:------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------| -| MinKNOW is transitioning from Guppy to Dorado. Until MinKNOW version 5.9 both Guppy and Dorado used ont-pyguppy-client-lib.
As of MinKNOW version 5.9 and Dorado server version 7.3.9 and greater Dorado requires an alternate library, `ont-pybasecall-client-lib`.
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. | +|

‼️ Important !!

| +|:------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------| +| MinKNOW has now transitioned from Guppy to Dorado. Until MinKNOW version 5.9 both Guppy and Dorado used ont-pyguppy-client-lib.
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.
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. From 2da0fb7b32a4f2e7de2a3f03611e3fef0faa0c6f Mon Sep 17 00:00:00 2001 From: Adoni5 Date: Thu, 12 Sep 2024 14:53:12 +0100 Subject: [PATCH 2/3] Allow hidden files, warn if file not found --- .github/workflows/CI.yml | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/.github/workflows/CI.yml b/.github/workflows/CI.yml index f33939c..0cc74f6 100644 --- 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 From e13e456a10df4d18d4dc1dd4263d7336b2d7d0e3 Mon Sep 17 00:00:00 2001 From: Adoni5 Date: Thu, 12 Sep 2024 14:58:31 +0100 Subject: [PATCH 3/3] Include hidden files in merge When did this become a thing --- .github/workflows/CI.yml | 1 + 1 file changed, 1 insertion(+) diff --git a/.github/workflows/CI.yml b/.github/workflows/CI.yml index 0cc74f6..9c9fb53 100644 --- a/.github/workflows/CI.yml +++ b/.github/workflows/CI.yml @@ -66,6 +66,7 @@ jobs: with: name: coverage-data pattern: my-artifact-* + include-hidden-files: true coverage: name: Combine coverage