From dbe09507dba7ca8e67b7559146f42181298046ba Mon Sep 17 00:00:00 2001 From: Yaroslav Halchenko Date: Fri, 26 Jan 2024 12:20:15 -0500 Subject: [PATCH 1/5] Add github action to codespell main on push and PRs --- .github/workflows/codespell.yml | 23 +++++++++++++++++++++++ 1 file changed, 23 insertions(+) create mode 100644 .github/workflows/codespell.yml diff --git a/.github/workflows/codespell.yml b/.github/workflows/codespell.yml new file mode 100644 index 0000000..7c9eafb --- /dev/null +++ b/.github/workflows/codespell.yml @@ -0,0 +1,23 @@ +# Codespell configuration is within .codespellrc +--- +name: Codespell + +on: + push: + branches: [main] + pull_request: + branches: [main] + +permissions: + contents: read + +jobs: + codespell: + name: Check for spelling errors + runs-on: ubuntu-latest + + steps: + - name: Checkout + uses: actions/checkout@v4 + - name: Codespell + uses: codespell-project/actions-codespell@v2 From 80de445b855f43e859582991edbb747dc2edf3d7 Mon Sep 17 00:00:00 2001 From: Yaroslav Halchenko Date: Fri, 26 Jan 2024 12:20:15 -0500 Subject: [PATCH 2/5] Add rudimentary codespell config --- .codespellrc | 6 ++++++ 1 file changed, 6 insertions(+) create mode 100644 .codespellrc diff --git a/.codespellrc b/.codespellrc new file mode 100644 index 0000000..d58f025 --- /dev/null +++ b/.codespellrc @@ -0,0 +1,6 @@ +[codespell] +# Ref: https://github.com/codespell-project/codespell#using-a-config-file +skip = .git,.codespellrc +check-hidden = true +# ignore-regex = +# ignore-words-list = From 0b007ef6d3ee0af4b47108f1ae9240d89e5dcdf5 Mon Sep 17 00:00:00 2001 From: Yaroslav Halchenko Date: Fri, 26 Jan 2024 12:20:35 -0500 Subject: [PATCH 3/5] [DATALAD RUNCMD] Do interactive fixing of typos === Do not change lines below === { "chain": [], "cmd": "codespell -w -i 3 -C 2", "exit": 0, "extra_inputs": [], "inputs": [], "outputs": [], "pwd": "." } ^^^ Do not change lines above ^^^ --- src/linkml/data-access-schema.yaml | 2 +- src/linkml/git-provenance-schema.yaml | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/src/linkml/data-access-schema.yaml b/src/linkml/data-access-schema.yaml index e23e5f3..1920ab0 100644 --- a/src/linkml/data-access-schema.yaml +++ b/src/linkml/data-access-schema.yaml @@ -110,7 +110,7 @@ classes: initialize the remote. range: string multivalued: true - # the next two must not be used, unless range is a class defintion + # the next two must not be used, unless range is a class definition # and not just a type #inlined: true #inlined_as_list: true diff --git a/src/linkml/git-provenance-schema.yaml b/src/linkml/git-provenance-schema.yaml index 625abbe..0fb338e 100644 --- a/src/linkml/git-provenance-schema.yaml +++ b/src/linkml/git-provenance-schema.yaml @@ -56,7 +56,7 @@ classes: A commit's GITSHA is a globally unique, content-based identifier of that commit. notes: - - The `gitsha` slot could have been labled to be the one identifier + - The `gitsha` slot could have been labeled to be the one identifier of a Commit-type object. However, we use `meta_type` for consistency and use its CURIE-format to assign an explicit namespace. From aff32ca56a8972d52a0aeb179f997a21e510875a Mon Sep 17 00:00:00 2001 From: Yaroslav Halchenko Date: Fri, 26 Jan 2024 12:22:13 -0500 Subject: [PATCH 4/5] Add pattern for gitsha I was curious why meta_id has it and not gitsha -- may be there is a reason? Asking as a PR --- src/linkml/git-provenance-schema.yaml | 1 + 1 file changed, 1 insertion(+) diff --git a/src/linkml/git-provenance-schema.yaml b/src/linkml/git-provenance-schema.yaml index 625abbe..a904d73 100644 --- a/src/linkml/git-provenance-schema.yaml +++ b/src/linkml/git-provenance-schema.yaml @@ -42,6 +42,7 @@ classes: - meta_id slot_usage: gitsha: + pattern: "^[0-9a-f]{40}$" description: >- SHA1 identifier of the commit object. meta_id: From 2fae171d75aa12f9f5ab4af76352f95f61203abe Mon Sep 17 00:00:00 2001 From: Michael Hanke Date: Tue, 13 Feb 2024 11:58:11 +0100 Subject: [PATCH 5/5] Fix typos Co-authored-by: Stephan Heunis --- src/linkml/datasets.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/src/linkml/datasets.yaml b/src/linkml/datasets.yaml index 6732467..057b61d 100644 --- a/src/linkml/datasets.yaml +++ b/src/linkml/datasets.yaml @@ -1,6 +1,6 @@ id: https://concepts.datalad.org/datasets name: datasets -title: Concepts for describing dataset +title: Concepts for describing datasets description: > Provided components are modeled after the DCAT v3 vocabulary (https://www.w3.org/TR/vocab-dcat-3). Within the DataLad concepts ontology @@ -241,7 +241,7 @@ classes: slots: - endpoint_url # although we do not expect any data service to have a unique identifier - # we must add this slow here, rather than in derived classes, due to + # we must add this slot here, rather than in derived classes, due to # a potential linkml limitation/bug # https://github.com/psychoinformatics-de/datalad-concepts/issues/30 - meta_id