Merge pull request #119 from inab/full_circle

Merge removed JSON Schema documentation bits

Author: jmfernandez

.github/workflows/schemas-doc-generator.yml

@@ -0,0 +1,35 @@
+name: Create a pull request against readthedocs_merge branch updating the tag being pulled
+on:
+  workflow_dispatch:
+  push:
+    tags:
+      # Push events to every tag not containing /
+      # based on https://stackoverflow.com/a/61892639
+      - '[1-9]*'
+
+jobs:
+  update_wfexs_requirement_at_readthedocs_merge:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Documentation branch checkout
+        uses: actions/checkout@v4
+        with:
+          ref: readthedocs_merge
+      - name: Write requirement
+        run: |
+          echo "wfexs_backend @ git+${{ github.server_url }}/${{ github.repository }}.git@${{ github.ref_name }}" > docs/source/requirement-wfexs.txt
+      - name: Create Pull Request
+        id: cpr
+        uses: peter-evans/create-pull-request@v7
+        with:
+          title: Updated WfExS-backend version being documented to ${{ github.ref_name }}
+          add-paths: |
+            docs/source/requirement-wfexs.txt
+          branch: create-pull-request/patch-documented-wfexs-version
+          delete-branch: true
+          commit-message: "[create-pull-request] Automatically commit updated contents (changed referred WfExS version to ${{ github.ref_name }})"
+      - name: Check outputs
+        if: ${{ steps.cpr.outputs.pull-request-number }}
+        run: |
+          echo "Pull Request Number - ${{ steps.cpr.outputs.pull-request-number }}"
+          echo "Pull Request URL - ${{ steps.cpr.outputs.pull-request-url }}"

.github/workflows/update-documented-wfexs.yml

@@ -27,7 +27,7 @@ and [cwltool](https://github.com/common-workflow-language/cwltool)).
 
 * [README_REPLICATOR.md](README_REPLICATOR.md): It briefly describes `WfExS-config-replicator.py` usage.
 
-Additional present and future documentation is hosted at [development-docs](development-docs/index.md) subfolder, until it is migrated to a proper documentation service.
+Additional present and future documentation is hosted at [development-docs](development-docs/index.md) subfolder, until it is migrated to [WfExS-backend ReadTheDocs](https://wfexs-backend.readthedocs.io).
 
 ##  Cite as
 
@@ -108,7 +108,7 @@ Also, a description about the different WfExS commands is available [at the comm
 
 The program uses three different types of configuration files:
 
-* Local configuration file: YAML formatted file which describes the local setup of the backend (example at [workflow_examples/local_config.yaml](workflow_examples/local_config.yaml)). JSON Schema describing the format (and used for validation) is available at [wfexs_backend/schemas/config.json](wfexs_backend/schemas/config.json) and there is also automatically generated documentation (see [config_schema.md](development-docs/schemas/config_schema.md)). Relative paths in this configuration file use as reference the directory where the local configuration file is living.
+* Local configuration file: YAML formatted file which describes the local setup of the backend (example at [workflow_examples/local_config.yaml](workflow_examples/local_config.yaml)). JSON Schema describing the format (and used for validation) is available at [wfexs_backend/schemas/config.json](wfexs_backend/schemas/config.json) and there is also automatically generated documentation on each release (see [config.json.html](https://wfexs-backend.readthedocs.io/en/latest/schemadocs/config.json.html)). Relative paths in this configuration file use as reference the directory where the local configuration file is living.
 
   - `cacheDir`: The path in this key sets up the place where all the contents which can be cached are hold. It contains downloaded RO-Crate,
      downloaded workflow git repositories, downloaded workflow engines. It is recommended to have it outside `/tmp` directory when
@@ -146,9 +146,9 @@ The program uses three different types of configuration files:
 
   - `tools.encrypted_fs.idle`: Number of minutes of inactivity before the encrypted FUSE filesystem is automatically unmounted. The default is 5 minutes.
 
-* Workflow configuration file: YAML formatted file which describes the workflow staging before being executed, like where inputs are located and can be fetched, the security contexts to be used on specific inputs to get those controlled access resources, the parameters, the outputs to capture, ... ([Nextflow example](workflow_examples/wetlab2variations_execution_nxf.wfex.stage), [CWL example](workflow_examples/wetlab2variations_execution_cwl.wfex.stage)). JSON Schema describing the format and valid keys (and used for validation), is available at [wfexs_backend/schemas/stage-definition.json](wfexs_backend/schemas/stage-definition.json) and there is also automatically generated documentation (see [stage-definition_schema.md](development-docs/schemas/stage-definition_schema.md)).
+* Workflow configuration file: YAML formatted file which describes the workflow staging before being executed, like where inputs are located and can be fetched, the security contexts to be used on specific inputs to get those controlled access resources, the parameters, the outputs to capture, ... ([Nextflow example](workflow_examples/wetlab2variations_execution_nxf.wfex.stage), [CWL example](workflow_examples/wetlab2variations_execution_cwl.wfex.stage)). JSON Schema describing the format and valid keys (and used for validation), is available at [wfexs_backend/schemas/stage-definition.json](wfexs_backend/schemas/stage-definition.json) and there is also automatically generated documentation on each release (see [stage-definition.json.html](https://wfexs-backend.readthedocs.io/en/latest/schemadocs/stage-definition.json.html)).
 
-* Security contexts file: YAML formatted file which holds the `user`/`password` pairs, security tokens or keys needed on different steps, like input fetching. ([Nextflow example](workflow_examples/wetlab2variations_credentials_nxf.wfex.ctxt), [CWL example](workflow_examples/wetlab2variations_credentials_cwl.wfex.ctxt)). JSON Schema describing the format and valid keys (and used for validation), is available at [wfexs_backend/schemas/security-context.json](wfexs_backend/schemas/security-context.json) and there is also automatically generated documentation (see [security-context_schema.md](development-docs/schemas/security-context_schema.md)).
+* Security contexts file: YAML formatted file which holds the `user`/`password` pairs, security tokens or keys needed on different steps, like input fetching. ([Nextflow example](workflow_examples/wetlab2variations_credentials_nxf.wfex.ctxt), [CWL example](workflow_examples/wetlab2variations_credentials_cwl.wfex.ctxt)). JSON Schema describing the format and valid keys (and used for validation), is available at [wfexs_backend/schemas/security-context.json](wfexs_backend/schemas/security-context.json) and there is also automatically generated documentation on each release (see [security-context.json.html](https://wfexs-backend.readthedocs.io/en/latest/schemadocs/security-context.json.html)).
 
 ## License
 * © 2020-2024 Barcelona Supercomputing Center (BSC), ES

README.md

@@ -13,7 +13,8 @@ flake8 < 6.0.0 ; python_version < '3.8'
 flake8 >= 6.0.0 ; python_version >= '3.8'
 mccabe >= 0.7.0
 mypy >= 1.1.1
-json-schema-for-humans >= 0.45.1
+# This one is now managed by the ReadTheDocs documentation
+# json-schema-for-humans >= 0.45.1
 pre-commit >= 2.17.0
 # This is the last version of black supporting Python 3.7
 black == 23.3.0