Merge pull request #105 from Materials-Data-Science-and-Informatics/feature/codemeta_overwrite

Feature/codemeta overwrite

Author: mustafasoylu

.somesy.toml

@@ -1,6 +1,6 @@
 [project]
 name = "somesy"
-version = "0.5.0"
+version = "0.6.0"
 description = "A CLI tool for synchronizing software project metadata."
 keywords = ["metadata", "FAIR"]
 license = "MIT"
@@ -54,7 +54,7 @@ orcid = "https://orcid.org/0000-0002-5149-603X"
 contribution = "Discussions and suggestions concerning tool scope and usability."
 contribution_begin = "2023-06-01"
 contribution_end = "2023-06-30"
-contribution_types = ["ideas"]
+contribution_types = ["ideas", "doc"]
 
 publication_author = true
 
@@ -67,17 +67,3 @@ orcid = "https://orcid.org/0000-0001-9560-4728"
 contribution_types = ["fundingFinding"]
 
 publication_author = true
-
-[config]
-no_sync_cff = false
-cff_file = "CITATION.cff"
-no_sync_pyproject = false
-pyproject_file = "pyproject.toml"
-no_sync_codemeta = false
-codemeta_file = "codemeta.json"
-no_sync_package_json = true
-no_sync_julia = true
-no_sync_fortran = true
-show_info = false
-verbose = false
-debug = true

CHANGELOG.md

@@ -6,12 +6,13 @@ Please consult the changelog to inform yourself about breaking changes and secur
 
 ## [v0.6.0](https://github.com/Materials-Data-Science-and-Informatics/somesy/tree/v0.6.0) <small>(2025-xx-xx)</small> { id="0.6.0" }
 
-- implement CFF Entity model for author/maintainer/contributor
+- implement CFF Entity (Organization) model for author/maintainer/contributor
+- add a new config option to use existing codemeta.json when syncing
 - fix SomesyBaseModel kwargs being overwritten
 
 ## [v0.5.0](https://github.com/Materials-Data-Science-and-Informatics/somesy/tree/v0.5.0) <small>(2025-01-15)</small> { id="0.5.0" }
 
-- make person argument email optional
+- make person (and entity) argument email optional
 
 ## [v0.4.3](https://github.com/Materials-Data-Science-and-Informatics/somesy/tree/v0.4.3) <small>(2024-07-29)</small> { id="0.4.3" }
 

CITATION.cff

@@ -3,7 +3,7 @@ type: software
 message: If you use this software, please cite it using this metadata.
 
 title: somesy
-version: 0.5.0
+version: 0.6.0
 abstract: A CLI tool for synchronizing software project metadata.
 url: https://materials-data-science-and-informatics.github.io/somesy
 repository-code: https://github.com/Materials-Data-Science-and-Informatics/somesy

README.md

@@ -118,10 +118,10 @@ rorid = "https://ror.org/02nv7yv05" # highly recommended set a ror id for your o
 verbose = true     # show detailed information about what somesy is doing
 ```
 
-As Helmholtz Metadata Collaboration (HMC), our goal is to increase usage of metadata and improve metadata quality. Therefore, some fields in `somesy.toml` are set as required fields. This is to increase rigour and completeness of metadata recorded with `somesy` .
-
 <!-- --8<-- [end:somesytoml] -->
 
+As Helmholtz Metadata Collaboration (HMC), our goal is to increase usage of metadata and improve metadata quality. Therefore, some fields in `somesy.toml` are set as required fields. This is to increase rigour and completeness of metadata recorded with `somesy` .
+
 Alternatively, you can also add the somesy configuration to an existing
 `pyproject.toml`, `package.json`, `Project.toml`, or `fpm.toml` file. The somesy [manual](https://materials-data-science-and-informatics.github.io/somesy/main/manual/#somesy-input-file) contains examples showing how to do that.
 
@@ -213,7 +213,7 @@ Here is an overview of all the currently supported files and formats.
 3. `fpm.toml` only supports one author and maintainer, so `somesy` will pick the _first_ listed author and maintainer
 4. `pom.xml` has no concept of `maintainers`, but it can have multiple licenses (somesy only supports one main project license)
 5. `mkdocs.yml` is a bit special, as it is not a project file, but a documentation file. `somesy` will only update it if it exists and is enabled in the configuration
-6. unlike other targets, `somesy` will _re-create_ the `codemeta.json` (i.e. do not edit it by hand!)
+6. For handling `codemeta.json` different options exists: Either (A) `somesy` removes any prior existing `codemata.json` files and re-creates it anew, or (B) `somesy` merges an existing `codemeta.json` with the information handled by `somesy`. See the [user manual](https://materials-data-science-and-informatics.github.io/somesy/main/manual/#codemeta) for additional details about CodeMeta handling.
 
 <!-- --8<-- [end:quickstart] -->
 

codemeta.json

@@ -27,7 +27,7 @@
   ],
   "name": "somesy",
   "description": "A CLI tool for synchronizing software project metadata.",
-  "version": "0.5.0",
+  "version": "0.6.0",
   "keywords": [
     "metadata",
     "FAIR"

docs/manual.md

@@ -253,10 +253,10 @@ one of the supported input formats:
 
 === "Project.toml"
 
-````toml
-name = "my-amazing-project"
-version = "0.1.0"
-uuid = "c7e460c6-3f3e-11ec-8d3d-0242ac130003"
+    ```toml
+    name = "my-amazing-project"
+    version = "0.1.0"
+    uuid = "c7e460c6-3f3e-11ec-8d3d-0242ac130003"
 
     [deps]
     ...
@@ -298,9 +298,10 @@ uuid = "c7e460c6-3f3e-11ec-8d3d-0242ac130003"
     ```
 
 === "fpm.toml"
-```toml
-name = "my-amazing-project"
-version = "0.1.0"
+
+    ```toml
+    name = "my-amazing-project"
+    version = "0.1.0"
 
     [tool.somesy.project]
     name = "my-amazing-project"
@@ -342,34 +343,34 @@ version = "0.1.0"
 
     ```json
     {
-      "name": "my-amazing-project",
-      "version": "0.1.0",
-      ...
+        "name": "my-amazing-project",
+        "version": "0.1.0",
+        ...
 
-      "somesy": {
+        "somesy": {
         "project": {
-          "name": "my-amazing-project",
-          "version": "0.1.0",
-          "description": "Brief description of my amazing software.",
-          "keywords": ["some", "descriptive", "keywords"],
-          "license": "MIT",
-          "repository": "https://github.com/username/my-amazing-project",
-          "people": [
+            "name": "my-amazing-project",
+            "version": "0.1.0",
+            "description": "Brief description of my amazing software.",
+            "keywords": ["some", "descriptive", "keywords"],
+            "license": "MIT",
+            "repository": "https://github.com/username/my-amazing-project",
+            "people": [
             {
-              "given-names": "Jane",
-              "family-names": "Doe",
-              "email": "j.doe@example.com",
-              "orcid": "https://orcid.org/0000-0000-0000-0001",
-              "author": true,
-              "maintainer": true
+                "given-names": "Jane",
+                "family-names": "Doe",
+                "email": "j.doe@example.com",
+                "orcid": "https://orcid.org/0000-0000-0000-0001",
+                "author": true,
+                "maintainer": true
             },
             {
-              "given-names": "Another",
-              "family-names": "Contributor",
-              "email": "a.contributor@example.com",
-              "orcid": "https://orcid.org/0000-0000-0000-0002"
+                "given-names": "Another",
+                "family-names": "Contributor",
+                "email": "a.contributor@example.com",
+                "orcid": "https://orcid.org/0000-0000-0000-0002"
             }
-          ]
+            ]
         },
         "entities":[
             {
@@ -380,9 +381,9 @@ version = "0.1.0"
             }
         ],
         "config": {
-          "verbose": true
+            "verbose": true
+        }
         }
-      }
     }
     ```
 
@@ -545,26 +546,47 @@ after running somesy (to remove the duplicate entries with the incorrect ROR ID)
 ### Codemeta
 
 While `somesy` is modifying existing files for most supported formats and implements
-features such as person identification and merging,
-[CodeMeta](https://codemeta.github.io/) is implemented differently.
+features such as person identification and merging, [CodeMeta](https://codemeta.github.io/)
+requires special handling.
+
+As `codemeta.json` is a [**JSON-LD**](https://json-ld.org/) file, it represents a graph and
+can have various equally valid representations in JSON format. The behavior of `somesy`
+when handling CodeMeta files is controlled by the `codemeta_merge` configuration option:
 
-As that `codemeta.json` is a [**JSON-LD**](https://json-ld.org/) file, it actually represents a graph,
-has various equally valid representations in a JSON file.
-Thus, supporting the same features as for other formats is technically much more
-challenging, if at all feasible. Therefore, for the time being, we regenerate the
-`codemeta.json` file directly from the source file, in order to avoid data inconsistency
-due to many pitfalls hiding in the details of the format.
+When `codemeta_merge = true`, `somesy` will:
+
+1. Read and parse any existing `codemeta.json` file
+2. Update only the fields that `somesy` manages. Values that are already present will be overwritten.
+3. Preserve any additional fields or metadata present in the file and append it to the record.
+
+
+When `codemeta_merge = false` (default), `somesy` will:
+
+1. Delete any existing `codemeta.json` file
+2. Create a new file containing only the metadata from your somesy project configuration
+
+!!! note
+
+    If you have additional CodeMeta fields you want to preserve, make sure to set
+    `codemeta_merge = true` in your somesy configuration.
 
 !!! warning
 
-    The `codemeta.json` is overwritten and regenerated from scratch every time you `sync`,
-    so **do not edit it** if you have the codemeta target enabled in `somesy`!
+    Unlike other formats, person and entity merging heuristics are not
+    implemented for CodeMeta. The author, maintainer, and contributor
+    fields are directly created from your somesy project metadata,
+    overwriting any existing entries in these fields.
+
+    Please note that due to the above behavior and the linked-data nature of values in
+    `codemeta.json` records using the option `codemeta_merge = true` can create
+    conflicts within the CodeMeta record, i.e. if values in `somesy.toml` and those
+    that get appended to the CodeMeta record show inconsistencies.
 
 As `codemeta.json` is considered a technical "backend-format" derived from other
-inputs, in most cases you probably do not need or should edit it by hand anyway.
+inputs, in most cases you probably do not need to edit it by hand anyway.
 
-Of course, you are welcome to contribute an improved CodeMeta writer for somesy that can correctly
-understand and update the linked data graph which the `codemeta.json` file represents!
+Of course, you are welcome to contribute improvements to the CodeMeta handling in somesy
+to make it even more robust and feature-complete!
 
 ## Using somesy to insert metadata into project documentation