invenio-subjects-mesh-lite 2023.1.4__py3-none-any.whl → 2025.1.15__py3-none-any.whl

invenio_subjects_mesh_lite/vocabularies/vocabularies.yaml

@@ -2,6 +2,6 @@ subjects:
   pid-type: sub
   schemes:
     - id: MeSH
-      data-file: subjects_mesh.jsonl
+      data-file: subjects_mesh.csv
       name: Medical Subject Headings
       uri: "https://www.nlm.nih.gov/mesh/meshhome.html"

{invenio_subjects_mesh_lite-2023.1.4.dist-info → invenio_subjects_mesh_lite-2025.1.15.dist-info}/METADATA

@@ -1,6 +1,6 @@
-Metadata-Version: 2.1
+Metadata-Version: 2.2
 Name: invenio-subjects-mesh-lite
-Version: 2023.1.4
+Version: 2025.1.15
 Summary: MeSH subject terms without qualifiers
 Author-email: Northwestern University <DL_FSM_GDS@e.northwestern.edu>
 License: MIT License
@@ -35,28 +35,28 @@ Classifier: Programming Language :: Python
 Classifier: Topic :: Internet :: WWW/HTTP :: Dynamic Content
 Classifier: Topic :: Software Development :: Libraries :: Python Modules
 Classifier: Programming Language :: Python :: 3
-Classifier: Programming Language :: Python :: 3.8
 Classifier: Programming Language :: Python :: 3.9
-Classifier: Programming Language :: Python :: 3.10
 Classifier: Programming Language :: Python :: 3.11
-Requires-Python: >=3.8
+Classifier: Programming Language :: Python :: 3.12
+Requires-Python: >=3.9
 Description-Content-Type: text/markdown
 License-File: LICENSE
+Requires-Dist: galter-subjects-utils<2.0,>=0.4.2
 Provides-Extra: dev
-Requires-Dist: check-manifest >=0.49 ; extra == 'dev'
-Requires-Dist: invoke <3.0,>=2.2 ; extra == 'dev'
-Requires-Dist: galter-subjects-utils <2.0,>=0.1.0 ; extra == 'dev'
-Requires-Dist: pyyaml >=5.4.1 ; extra == 'dev'
-Requires-Dist: pytest >=7.2.0 ; extra == 'dev'
-Requires-Dist: pytest-cov >=3.0.0 ; extra == 'dev'
-Requires-Dist: pytest-isort >=3.0.0 ; extra == 'dev'
-Requires-Dist: pytest-pycodestyle >=2.2.0 ; extra == 'dev'
-Requires-Dist: pytest-pydocstyle >=2.2.3 ; extra == 'dev'
+Requires-Dist: check-manifest>=0.49; extra == "dev"
+Requires-Dist: invenio-search[opensearch2]<3.0,>=2.1.0; extra == "dev"
+Requires-Dist: invoke<3.0,>=2.2; extra == "dev"
+Requires-Dist: pyyaml>=5.4.1; extra == "dev"
+Requires-Dist: pytest-invenio<3.0.0,>=2.1.1; extra == "dev"
 
 # invenio-subjects-mesh-lite
 
 *MeSH topical subject terms without qualifiers for InvenioRDM*
 
+<a href="https://pypi.org/project/invenio-subjects-mesh-lite/">
+  <img src="https://img.shields.io/pypi/v/invenio-subjects-mesh-lite.svg">
+</a>
+
 Install this extension to get Medical Subject Headings topics without qualifiers into your instance.
 
 If you are looking for a larger MeSH vocabulary with qualifiers, use
@@ -89,44 +89,52 @@ table will be provided to indicate version cross-compatibility.
 
 ## Usage
 
-There are 2 types of users for this package. Instance administrators and package maintainers.
+There are 2 types of users for this package. Instance operators and package maintainers.
 
-### Instance administrators
+### Instance operators
 
-For instance administrators, after you have installed the extension as per the steps above, you will want to reload your instance's fixtures: `pipenv run invenio rdm-records fixtures`. This will install the new terms in your instance.
+For instance operators, after you have installed the extension as per the steps above, you will want to reload your instance's fixtures: `pipenv run invenio rdm-records fixtures`. This will install the new terms in your instance.
 
-Updating existing terms currently requires manual replacement.
+Alternatively, or if you want to update your already loaded subjects to a new listing (e.g. from one year's list to another), you can update your instance's MeSH subjects as per below. Updating subjects this way takes care of everything for you: the subjects themselves and the records/drafts using those subjects. **WARNING** This operation can _remove_ subjects.
 
-### Maintainers
+```bash
+# In your instance's project
+# Download up-to-date listings
+pipenv run invenio galter_subjects mesh download -d /path/to/downloads/storage/ -y YEAR
+# Generate file containg deltas to transition your instance to the downloaded listing
+pipenv run invenio galter_subjects mesh deltas -d /path/to/downloads/storage/ -y YEAR -f topic -o deltas_mesh.csv
+# Update your instance - *this operation will modify your instance*
+pipenv run invenio galter_subjects update deltas_mesh.csv
+```
 
-When a new list of MeSH term comes out, this package should be updated. Here we show how.
+Look at the help text for these commands to see additional options that can be passed.
+In particular, options for `galter_subjects update` allow you to store renamed, replaced or removed subjects on records according to a template of your choice.
 
-0. Install this package locally with the `dev` extra:
 
-```bash
-pipenv run pip install -e .[dev]
-```
+### Maintainers
 
-1. Use the installed `galter-subjects-utils` tool to get the new list:
+When a new list of MeSH term comes out, this package should be updated. Here we show how.
 
-```bash
-pipenv run galter-subjects-utils mesh --filter topic --output-file invenio_subjects_mesh_lite/vocabularies/subjects_mesh.jsonl
-```
+**Pre-requisite/Context**
 
-   This will
+[Install the distribution package for development](#development) before you do anything.
 
-   1. Download the new list(s)
-   2. Read it filtering for topics
-   3. Convert terms to InvenioRDM subjects format
-   4. Write those to the specified file
+**Commands**
 
-2. Check the manifest (it should typically be all good)
+Once you have it installed, you can run the following commands in the isolated virtualenv:
 
 ```bash
-pipenv run inv check-manifest
+# In this project
+# Download up-to-date listings
+(venv) invenio galter_subjects mesh download -d /path/to/downloads/storage/ -y YEAR
+# Generate file containing initial listing
+(venv) invenio galter_subjects mesh file -d /path/to/downloads/storage/ -y YEAR -f topic -o invenio_subjects_mesh_lite/vocabularies/subjects_mesh.csv
 ```
 
-3. When you are happy with the list, bump the version in `pyproject.toml` and release it.
+Sorting the resulting csv is a nice touch for humans to better parse the changes between versions.
+
+When you are happy with the list, bump the version in `pyproject.toml` and release it.
+
 
 ## Development
 

invenio_subjects_mesh_lite-2025.1.15.dist-info/RECORD

@@ -0,0 +1,10 @@
+invenio_subjects_mesh_lite/__init__.py,sha256=OMjv34qKJaCfpWkviS2Flm5-x102etEeCDeZxwfg-fk,279
+invenio_subjects_mesh_lite/vocabularies/__init__.py,sha256=Jan6XCvJwfPkOh2K9HsMvKN2aL3uNbfYaGyWcesfwHI,251
+invenio_subjects_mesh_lite/vocabularies/subjects_mesh.csv,sha256=H_1_WFU4_AHFEGOyJCB4dgqxaIex-hcw-U9PIhPPqZw,1854040
+invenio_subjects_mesh_lite/vocabularies/vocabularies.yaml,sha256=GZNfEe-5B10X0xcJxR780orv7Z7H0mu5lWUxug8agTg,180
+invenio_subjects_mesh_lite-2025.1.15.dist-info/LICENSE,sha256=pvn4sHeXv1itkPsbMsOgqg14rm28oYDUbLm8UNiCYbE,1086
+invenio_subjects_mesh_lite-2025.1.15.dist-info/METADATA,sha256=4SQcVXvUrPIGPs5X98dLx6lLsbX98vrXlbMHlsyoL0E,6763
+invenio_subjects_mesh_lite-2025.1.15.dist-info/WHEEL,sha256=In9FTNxeP60KnTkGw7wk6mJPYd_dQSjEZmXdBdMCI-8,91
+invenio_subjects_mesh_lite-2025.1.15.dist-info/entry_points.txt,sha256=e7moK0iCK4p9usRWiwQIHW_zjN3P9d5fxtx-WZW7-a0,100
+invenio_subjects_mesh_lite-2025.1.15.dist-info/top_level.txt,sha256=V6HkvobY26xog1stvPmVbhG5Xh3fclE4LtcTajmeu3c,27
+invenio_subjects_mesh_lite-2025.1.15.dist-info/RECORD,,

{invenio_subjects_mesh_lite-2023.1.4.dist-info → invenio_subjects_mesh_lite-2025.1.15.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: bdist_wheel (0.41.3)
+Generator: setuptools (75.8.0)
 Root-Is-Purelib: true
 Tag: py3-none-any