invenio-subjects-mesh-lite 2023.1.4__tar.gz → 2025.1.15__tar.gz

invenio_subjects_mesh_lite-2025.1.15/CHANGES.md

@@ -0,0 +1,21 @@
+# Changes
+
+Version 2025.1.15 (released 2025-01-15)
+
+- MeSH 2025
+
+Version 2024.3.6 (released 2024-08-09)
+
+- make compatible with InvenioRDM v12
+
+Version 2024.3.5 (released 2024-05-22)
+
+- patch fix from galter-subjects-utils
+
+Version 2023.1.4 (released 2023-11-7)
+
+- Polished release
+
+Version 0.1.0 (released 2023-10-30)
+
+- Initial public release.

{invenio-subjects-mesh-lite-2023.1.4 → invenio_subjects_mesh_lite-2025.1.15}/MANIFEST.in

@@ -15,3 +15,4 @@
 include *.md
 recursive-include invenio_subjects_mesh_lite *.yaml
 recursive-include invenio_subjects_mesh_lite *.jsonl
+recursive-include invenio_subjects_mesh_lite *.csv

{invenio-subjects-mesh-lite-2023.1.4/invenio_subjects_mesh_lite.egg-info → invenio_subjects_mesh_lite-2025.1.15}/PKG-INFO

@@ -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: invenio-search[opensearch2]<3.0,>=2.1.0; 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: 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/README.md

@@ -0,0 +1,122 @@
+# 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
+[invenio-subjects-mesh](https://github.com/galterlibrary/invenio-subjects-mesh) instead.
+
+> [!NOTE]
+> Both extensions map the `MeSH` subject id, so you can only install one of them. However, they
+> use the same pattern for subject ids, so you can switch from one to the other easily if your
+> needs change in the future.
+
+## Installation
+
+From your instance directory:
+
+```bash
+pipenv install invenio-subjects-mesh-lite
+```
+
+This will add it to your Pipfile.
+
+## Versions
+
+This repository follows [calendar versioning](https://calver.org/) for year and month:
+
+`2021.06.18` is both a valid semantic version and an indicator of the year-month corresponding to the loaded MeSH terms.
+`18` here is a patch number (not a day).
+
+So far the package is compatible with InvenioRDM 9.1+'s subjects "ABI". If there is a breaking change, a compatibility
+table will be provided to indicate version cross-compatibility.
+
+## Usage
+
+There are 2 types of users for this package. Instance operators and package maintainers.
+
+### Instance operators
+
+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.
+
+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.
+
+```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
+```
+
+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.
+
+
+### Maintainers
+
+When a new list of MeSH term comes out, this package should be updated. Here we show how.
+
+**Pre-requisite/Context**
+
+[Install the distribution package for development](#development) before you do anything.
+
+**Commands**
+
+Once you have it installed, you can run the following commands in the isolated virtualenv:
+
+```bash
+# 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
+```
+
+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
+
+Install the project in editable mode with `dev` dependencies in an isolated virtualenv (`(venv)` denotes that going forward):
+
+```bash
+(venv) pip install -e .[dev]
+# or if using pipenv
+pipenv run pip install -e .[dev]
+```
+
+Run tests:
+
+```bash
+(venv) invoke test
+# or shorter
+(venv) inv test
+# or if using pipenv
+pipenv run inv test
+```
+
+Check manifest:
+
+```bash
+(venv) inv check-manifest
+# or if using pipenv
+pipenv run inv check-manifest
+```
+
+Clean out artefacts:
+
+```bash
+(venv) inv clean
+# or if using pipenv
+pipenv run inv clean
+```