diff --git a/.readthedocs.yaml b/.readthedocs.yaml index 9712e40..5e9e3c7 100644 --- a/.readthedocs.yaml +++ b/.readthedocs.yaml @@ -7,9 +7,9 @@ version: 2 # Set the version of Python and other tools you might need build: - os: ubuntu-22.04 + os: ubuntu-24.04 tools: - python: "3.11" + python: "3.12" # Build documentation in the docs/ directory with Sphinx sphinx: diff --git a/CHANGES.txt b/CHANGES.txt index 030f7c3..3c041a1 100644 --- a/CHANGES.txt +++ b/CHANGES.txt @@ -1,9 +1,10 @@ -v0.4.0 (2025/?/?) - Add an async version of the client - Replace requests HTTP library with the httpx library - Replace requests_cache caching library the hishel library - Update sphinx documentation and remove html build warning - Add CURIE id query support / testing +v0.4.0 (2025/01/10) + Dropped support for Python < 3.6 and added suport for Python up to 3.13 + Added an async version of the client + Replaced requests HTTP library with the httpx library + Replaced requests_cache caching library the hishel library + Updated sphinx documentation and removed html build warning + Added testing for CURIE id query supported by APIs v0.3.1 (2023/11/13) Use https URL for all BioThings APIs by default (thanks @@skumar951) diff --git a/docs/index.rst b/docs/index.rst index ed139a7..1401780 100644 --- a/docs/index.rst +++ b/docs/index.rst @@ -7,18 +7,23 @@ .. _MyGene.Info: http://mygene.info .. _MyVariant.Info: http://myvariant.info .. _MyChem.Info: http://mychem.info +.. _MyDisease.Info: http://mydisease.info .. _MyGene.py: https://pypi.org/project/mygene/ .. _MyVariant.py: https://pypi.org/project/myvariant/ Biothings_client.py =================== `Biothings_client.py `_ is a unified python client providing an easy-to-use wrapper -for accessing *any* `BioThings API `_ (e.g. MyGene.Info_, MyVariant.Info_, MyChem.Info_). It is the descendent and eventual replacement +for accessing *any* `BioThings API `_ (e.g. MyGene.Info_, MyVariant.Info_, MyChem.Info_, MyDisease.Info_). It is the descendent and eventual replacement of both the MyGene.py_ and MyVariant.py_ python clients. Requirements ============ - python >=3.7 + Python >=3.7 + +.. note:: Python 3.6 is still supported with some limitations (e.g. caching feature is not supported in Python 3.6). + +.. note:: Python<=3.5 (including Python 2.7) is no longer supported as of version 0.4.0. The last version supporting Python<=3.5 is 0.3.1. Installation ============= @@ -31,25 +36,32 @@ Installation * Option 2. Install the latest commit from the github repository using pip: - + .. code-block:: bash pip install -e git+https://github.com/biothings/biothings_client.py#egg=biothings_client + or + + .. code-block:: bash + + pip install biothings_client@git+https://github.com/biothings/biothings_client.py + + Optional features / dependencies ================================ * dataframe support (install using ``pip install biothings_client[dataframe]``) - + allows for formatting output from the client queries as a list of pandas `DataFrame `_ objects. - Requires the following optional dependenies + Requires the following optional dependenies * `pandas `_ * caching support (install using ``pip install biothings_client[caching]``) - + allows for local caching of client queries to a sqlite database. - Requires the following optional dependenies + Requires the following optional dependenies * `hishel `_ * `anysqlite `_ diff --git a/docs/requirements.txt b/docs/requirements.txt index 3176126..e81909e 100644 --- a/docs/requirements.txt +++ b/docs/requirements.txt @@ -1,6 +1 @@ -PyLD>=0.7.2 -anysqlite -hishel[sqlite] -httpx>=0.22.0 -pandas>=1.1.5 --e . +-e .[dataframe,caching,jsonld]