Remove essential and advanced topics, merge into single topics category

Author: kinow

src/advanced-topics/index.md

@@ -93,33 +93,33 @@
 redirects = {
     '01-introduction/index.md': '../introduction/quick-start.html',
     '02-1st-example/index.md': '../introduction/quick-start.html',
-    '03-input/index.md': '../essential-topics/inputs.html',
-    '04-output/index.md': '../essential-topics/outputs.html',
-    '05-stdout/index.md': '../essential-topics/outputs.html',
-    '06-params/index.md': '../essential-topics/parameter-references.html',
-    '07-containers/index.md': '../advanced-topics/using-containers.html',
-    '08-arguments/index.md': '../essential-topics/additional-arguments-and-parameters.html',
-    '09-array-inputs/index.md': '../essential-topics/inputs.html',
-    '10-array-outputs/index.md': '../essential-topics/outputs.html',
-    '11-records/index.md': '../essential-topics/inputs.html',
-    '12-env/index.md': '../essential-topics/environment-variables.html',
-    '13-expressions/index.md': '../essential-topics/expressions.html',
-    '14-runtime/index.md': '../advanced-topics/creating-files-at-runtime.html',
-    '15-staging/index.md': '../advanced-topics/staging-input-files.html',
-    '16-file-formats/index.md': '../advanced-topics/file-formats.html',
-    '17-metadata/index.md': '../advanced-topics/metadata-and-authorship.html',
-    '19-custom-types/index.md': '../essential-topics/custom-types.html',
-    '20-software-requirements/index.md': '../advanced-topics/specifying-software-requirements.html',
-    '21-1st-workflow/index.md': '../essential-topics/workflows.html',
-    '22-nested-workflows/index.md': '../essential-topics/workflows.html#nested-workflows',
-    '23-scatter-workflow/index.md': '../essential-topics/workflows.html#scattering-workflows',
-    '24_conditional-workflow/index.md': '../essential-topics/workflows.html#conditional-workflows',
-    'rec-practices/index.md': '../advanced-topics/best-practices.html',
+    '03-input/index.md': '../topics/inputs.html',
+    '04-output/index.md': '../topics/outputs.html',
+    '05-stdout/index.md': '../topics/outputs.html',
+    '06-params/index.md': '../topics/parameter-references.html',
+    '07-containers/index.md': '../topics/using-containers.html',
+    '08-arguments/index.md': '../topics/additional-arguments-and-parameters.html',
+    '09-array-inputs/index.md': '../topics/inputs.html',
+    '10-array-outputs/index.md': '../topics/outputs.html',
+    '11-records/index.md': '../topics/inputs.html',
+    '12-env/index.md': '../topics/environment-variables.html',
+    '13-expressions/index.md': '../topics/expressions.html',
+    '14-runtime/index.md': '../topics/creating-files-at-runtime.html',
+    '15-staging/index.md': '../topics/staging-input-files.html',
+    '16-file-formats/index.md': '../topics/file-formats.html',
+    '17-metadata/index.md': '../topics/metadata-and-authorship.html',
+    '19-custom-types/index.md': '../topics/custom-types.html',
+    '20-software-requirements/index.md': '../topics/specifying-software-requirements.html',
+    '21-1st-workflow/index.md': '../topics/workflows.html',
+    '22-nested-workflows/index.md': '../topics/workflows.html#nested-workflows',
+    '23-scatter-workflow/index.md': '../topics/workflows.html#scattering-workflows',
+    '24_conditional-workflow/index.md': '../topics/workflows.html#conditional-workflows',
+    'rec-practices/index.md': '../topics/best-practices.html',
     'misc/index.md': '../faq.html',
     'episodes.md': 'index.html#table-of-contents',
     'setup.md': 'introduction/prerequisites.html',
     'extras.md': '/index.html',
-    'yaml/index.md': '../essential-topics/yaml-guide.html',
+    'yaml/index.md': '../topics/yaml-guide.html',
     'CODE_OF_CONDUCT.html': 'https://github.com/common-workflow-language/user_guide/blob/main/CODE_OF_CONDUCT.md'
 }
 

src/conf.py

@@ -17,7 +17,7 @@ each page.
 
 If you are a beginner user get started with the [Introduction](/introduction/index.md)
 section. For advanced users the subsections of the
-[Core Concepts](/essential-topics/index.md) have detailed information about the
+[Core Concepts](/topics/index.md) have detailed information about the
 most common topics for CWL.
 
 The Table of Contents is displayed at the top menu and also on the left sidebar.
@@ -32,8 +32,7 @@ the left sidebar.
 :numbered:
 
 introduction/index.md
-essential-topics/index.md
-advanced-topics/index.md
+topics/index.md
 tutorials.md
 faq.md
 LICENSE.md

src/index.md

@@ -181,4 +181,4 @@ vendors.
 - The current CWL specification on GitHub: {{ '<https://github.com/common-workflow-language/cwl-{}>'.format(cwl_version_text) }}
 - The list of Implementations in the CWL website: <https://www.commonwl.org/implementations/>
 - PROV-O: The PROV Ontology - <https://www.w3.org/TR/prov-o/>
-- CWL Operations are covered in the [Operations](../essential-topics/operations.md) section of this user guide.
+- CWL Operations are covered in the [Operations](../topics/operations.md) section of this user guide.

src/introduction/basic-concepts.md

@@ -9,7 +9,7 @@ must be comfortable following instructions for the command-line.
 ```{include} /_includes/what-is-cwl.md
 ```
 
-CWL documents are written in [YAML](../essential-topics/index.md) (and/or JSON).
+CWL documents are written in [YAML](../topics/index.md) (and/or JSON).
 The example below shows a simple CWL “Hello World” workflow annotated
 with comments:
 

src/introduction/quick-start.md

@@ -72,8 +72,8 @@ outputs:
 ```{note}
 
 The example above uses a simplified form to define inputs and outputs.
-You will learn more about in the [Inputs](../essential-topics/inputs.md)
-and in the [Outputs](../essential-topics/outputs.md) sections.
+You will learn more about in the [Inputs](../topics/inputs.md)
+and in the [Outputs](../topics/outputs.md) sections.
 ```
 
 % TODO

src/essential-topics/additional-arguments-and-parameters.md renamed to src/topics/additional-arguments-and-parameters.md

@@ -12,7 +12,7 @@ To generate such files we can use the `InitialWorkDirRequirement`.
 :name: createfile.cwl
 ```
 
-Any [expressions](../essential-topics/expressions.md) like `$(inputs.message)` are
+Any [expressions](../topics/expressions.md) like `$(inputs.message)` are
 expanded by the CWL engine before creating the file;
 here inserting the value at the input `message`.
 
@@ -48,7 +48,7 @@ which is YAML quoting syntax, and means that you are using a multiline string
 
 ```{note}
 
-See the [YAML Guide](../essential-topics/yaml-guide.md#maps) for more about the formatting.
+See the [YAML Guide](../topics/yaml-guide.md#maps) for more about the formatting.
 ```
 
 Now invoke `cwl-runner` with the tool wrapper and the input object on the

src/advanced-topics/best-practices.md renamed to src/topics/best-practices.md

@@ -10,7 +10,7 @@ JavaScript expressions should only be used when absolutely necessary.
 When manipulating file names, extensions, paths etc, consider whether one of the
 [built in `File` properties][file-prop] like `basename`, `nameroot`, `nameext`,
 etc, could be used instead.
-See the [list of best practices](../advanced-topics/best-practices).
+See the [list of best practices](best-practices.md).
 
 ```{literalinclude} /_includes/cwl/13-expressions/expression.cwl
 :language: cwl

src/essential-topics/command-line-tool.md renamed to src/topics/command-line-tool.md

@@ -1,7 +1,4 @@
-# Essential Topics
-
-In this section you will find fundamental concepts for CWL. This content
-should be enough to get you started reading and writing CWL workflows.
+# Topics
 
 ```{toctree}
 :maxdepth: 2
@@ -17,4 +14,11 @@ expression-tool.md
 workflows.md
 operations.md
 environment-variables.md
+using-containers.md
+creating-files-at-runtime.md
+staging-input-files.md
+best-practices.md
+file-formats.md
+metadata-and-authorship.md
+specifying-software-requirements.md
 ```

src/advanced-topics/creating-files-at-runtime.md renamed to src/topics/creating-files-at-runtime.md

@@ -123,7 +123,7 @@ parameter were not provided in the input, nothing would appear on the
 command line.
 
 Input files are read-only.  If you wish to update an input file, you must
-[first copy it to the output directory](../advanced-topics/staging-input-files.md).
+[first copy it to the output directory](staging-input-files.md).
 
 The value of `position` is used to determine where parameter should
 appear on the command line.  Positions are relative to one another, not