Merge pull request #169 from nextflow-io/revert-to-1.1.3-b

revert to v1.1.3

.github/workflows/build-docs.yml

@@ -12,27 +12,15 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v3
-        with:
-          fetch-depth: 0 # fetch all commits/branches
       - uses: actions/setup-python@v4
         with:
           python-version: 3.x
       - run: echo "cache_id=$(date --utc '+%V')" >> $GITHUB_ENV
-      - name: Obtain version from MANIFEST.MF
-        run: echo "plugin_version=$(grep "Plugin-Version" plugins/nf-validation/src/resources/META-INF/MANIFEST.MF | awk '{print $2}' | awk -F '.' '{print $1"."$2}')" >> $GITHUB_ENV
-      - name: Setup git user
-        run: |
-          git config --global user.name "${{github.actor}}"
-          git config --global user.email "${{github.actor}}@users.noreply.github.com"
       - uses: actions/cache@v3
         with:
           key: mkdocs-material-${{ env.cache_id }}
           path: .cache
           restore-keys: |
             mkdocs-material-
-      - name: Install dependencies
-        run: pip install mkdocs-material pymdown-extensions pillow cairosvg mike
-      - name: Build docs
-        run: mike deploy --push --update-aliases ${{ env.plugin_version }} latest
-      - name: Set default docs
-        run: mike set-default --push latest
+      - run: pip install mkdocs-material pymdown-extensions pillow cairosvg
+      - run: mkdocs gh-deploy --force

CHANGELOG.md

@@ -1,31 +1,5 @@
 # nextflow-io/nf-validation: Changelog
 
-# Version 2.0.0 - Kagoshima
-
-:warning: This version contains a number of breaking changes. Please read the changelog carefully before upgrading. :warning:
-
-To migrate your schemas please follow the [migration guide](https://nextflow-io.github.io/nf-validation/latest/migration_guide/)
-
-## New features
-
-- Added the `uniqueEntries` keyword. This keyword takes a list of strings corresponding to names of fields that need to be a unique combination. e.g. `uniqueEntries: ['sample', 'replicate']` will make sure that the combination of the `sample` and `replicate` fields is unique. ([#141](https://github.com/nextflow-io/nf-validation/pull/141))
-
-## Changes
-
-- Changed the used draft for the schema from `draft-07` to `draft-2020-12`. See the [2019-09](https://json-schema.org/draft/2019-09/release-notes) and [2020-12](https://json-schema.org/draft/2020-12/release-notes) release notes for all changes ([#141](https://github.com/nextflow-io/nf-validation/pull/141))
-- Removed all validation code from the `.fromSamplesheet()` channel factory. The validation is now solely done in the `validateParameters()` function. A custom error message will now be displayed if any error has been encountered during the conversion ([#141](https://github.com/nextflow-io/nf-validation/pull/141))
-- Removed the `unique` keyword from the samplesheet schema. You should now use [`uniqueItems`](https://json-schema.org/understanding-json-schema/reference/array#uniqueItems) or `uniqueEntries` instead ([#141](https://github.com/nextflow-io/nf-validation/pull/141))
-- Removed the `skip_duplicate_check` option from the `fromSamplesheet()` channel factory and the `--validationSkipDuplicateCheck` parameter. You should now use the `uniqueEntries` or [`uniqueItems`](https://json-schema.org/understanding-json-schema/reference/array#uniqueItems) keywords in the schema instead ([#141](https://github.com/nextflow-io/nf-validation/pull/141))
-- `.fromSamplesheet()` now does dynamic typecasting instead of using the `type` fields in the JSON schema. This is done due to the complexity of `draft-2020-12` JSON schemas. This should not have that much impact but keep in mind that some types can be different between this and earlier versions because of this ([#141](https://github.com/nextflow-io/nf-validation/pull/141))
-- `.fromSamplesheet()` will now set all missing values as `[]` instead of the type specific defaults (because of the changes in the previous point). This should not change that much as this will also result in `false` when used in conditions. ([#141](https://github.com/nextflow-io/nf-validation/pull/141))
-
-## Improvements
-
-- Setting the `exists` keyword to `false` will now check if the path does not exist ([#141](https://github.com/nextflow-io/nf-validation/pull/141))
-- The `schema` keyword will now work in all schemas. ([#141](https://github.com/nextflow-io/nf-validation/pull/141))
-- Improved the error messages ([#141](https://github.com/nextflow-io/nf-validation/pull/141))
-- `.fromSamplesheet()` now supports deeply nested samplesheets ([#141](https://github.com/nextflow-io/nf-validation/pull/141))
-
 # Version 1.1.3 - Asahikawa
 
 ## Improvements

README.md

@@ -14,7 +14,7 @@ This [Nextflow plugin](https://www.nextflow.io/docs/latest/plugins.html#plugins)
 - 📋 Validate the contents of supplied sample sheet files
 - 🛠️ Create a Nextflow channel with a parsed sample sheet
 
-Supported sample sheet formats are CSV, TSV, JSON and YAML.
+Supported sample sheet formats are CSV, TSV and YAML (simple).
 
 ## Quick Start
 
@@ -31,7 +31,7 @@ This is all that is needed - Nextflow will automatically fetch the plugin code a
 > [!NOTE]
 > The snippet above will always try to install the latest version, good to make sure
 > that the latest bug fixes are included! However, this can cause difficulties if running
-> offline. You can pin a specific release using the syntax `nf-validation@2.0.0`
+> offline. You can pin a specific release using the syntax `nf-validation@0.3.2`
 
 You can now include the plugin helper functions into your Nextflow pipeline:
 
@@ -58,7 +58,7 @@ ch_input = Channel.fromSamplesheet("input")
 ## Dependencies
 
 - Java 11 or later
-- <https://github.com/harrel56/json-schema>
+- <https://github.com/everit-org/json-schema>
 
 ## Slack channel
 
@@ -75,4 +75,3 @@ We would like to thank the key contributors who include (but are not limited to)
 - Nicolas Vannieuwkerke ([@nvnieuwk](https://github.com/nvnieuwk))
 - Kevin Menden ([@KevinMenden](https://github.com/KevinMenden))
 - Phil Ewels ([@ewels](https://github.com/ewels))
-- Arthur ([@awgymer](https://github.com/awgymer))

docs/nextflow_schema/create_schema.md

@@ -46,15 +46,6 @@ go to the pipeline root and run the following:
 nf-core schema build
 ```
 
-!!! warning
-
-    The current version of `nf-core` tools (v2.12.1) does not support the new schema draft used in `nf-validation`. Running this command after building the schema will convert the schema to the right draft:
-
-    ```bash
-    sed -i -e 's/http:\/\/json-schema.org\/draft-07\/schema/https:\/\/json-schema.org\/draft\/2020-12\/schema/g' -e 's/definitions/defs/g' nextflow_schema.json
-    ```
-    A new version of the nf-core schema builder will be available soon. Keep an eye out!
-
 The tool will run the `nextflow config` command to extract your pipeline's configuration
 and compare the output to your `nextflow_schema.json` file (if it exists).
 It will prompt you to update the schema file with any changes, then it will ask if you