v0.3.0 (#20)

* define specific CRUD functions

* add imports

* create class inheriting base client, add doc strings, define get_experiment

* initial get_experiment docstring

* return experiment model instance

* define get_scoreset

* return scoreset model instance

* define post_experiment and post_scoreset, docstring and return for post_experiment

* return confirmation of post scoreset

* delete duplicated code

* instantiate base client object

* update get_experiment function signature

* update get_experiment docstring

* edit parameter named in get_experiment docstring

* edit return value for get_experiment

* update variable name in return statement

* update get_scoreset function signature

* update get_scoreset docstring description

* edit get_scoreset docstring parameters

* edit get_scoreset docstring return value

* update parameters passed in return statement

* update create_experiment method signature

* update create_experiment docstring description

* update parameters in docstring

* change variable name in return statement

* update create_scoreset function signature

* update create_scoreset docstring description

* update create_scoreset docstring parameters

* change variable name in return statement

* add docstring to BaseClient

* add docstring to Client object

* reformat

* delete unused imports

* edit return type

* error is defined in self

* add init file

* delete redundant code files

* edit return type

* edit variable names to match json dict keys from API response

* edit variable names and mark new variables TODO, see where they should go

* mark new variables TODO, see where they should go

* edit variable names

* edit variable names, comment out variables not seen in json API response

* edit variable names to align with key values in json API response

* mark variable TODO as potentially optional

* edit arguments

* edit docstring parameters

* edit docstring returns

* set model urn

* edit return value and function parameters

* edit method docstring parameters and return values

* set model url

* add note to include mavecore validation

* fix typo

* edit request

* note where to include next request

* edit return type

* delete imports

* edit method return values

* edit method docstring parameters and return values

* edit method docstring parameters and return values

* edit method return values

* edit method return values

* change function signature

* fix typo

* delete output

* fix typo

* change base url

* edit method call

* change print type

* change version

* delete output

* edit base url

* change method call

* edit print type

* change version

* fix typo

* clear output

* edit import

* change base url

* edit experiment format

* post experiment

* change version

* update function signatures to be more readable

* update docstrings to reflect changes to function signatures

* update docstrings to reflect changes to function signatures

* update return description within docstrings

* change instance_url

* document additional error handling

* change error message

* set urn to None

* handle case where scores_df should not be None

* update request to reflect changes in API

* set urn after post request

* add additional request for data files to reflect changes in API

* log a successful request

* return urn

* import logging

* change method called

* change method called

* note where validation should occur and change method called

* edit function signature to be more readable

* edit docstring to reflect changes to function signature

* document added error handling

* add error handling and note where validation should occur

* set file_upload as dictionary

* create async client

* simple create dataset

* simple get dataset

* delete file

* create scoreset easy

* get scoreset easy

* get experiment easy

* create experiment easy

* edit title

* edit text inaccuracies

* edit imports

* edit url

* add detail to markdown

* remove redundant comment

* delete cell

* remove comment

* add markdown cell

* edit print statement

* change function called in code block

* edit title

* edit imports

* remove cells

* edit client instantiation

* edit markdown text

* create scoreset client

* reset cells

* edit import

* edit imports

* edit markdown

* delete cells

* edit client instantiation

* mak markdown text more readable

* make docstring more readable

* edit imports

* add session attribute to client

* define async functions

* edit exceptions

* configure requests for asyncio

* edit docstring to be more readable

* edit imports

* define functions as asynchronous

* add init file

* create client async notebooks

* change session instantiation

* delete methods, add await to return

* edit imports

* add await to return

* define and implement get_scoresets and run methods with new client sessions

* add await to return

* add await to return

* edit imports

* edit test urn

* call async methods

* print results

* define and implement get experiments

* define and implement create experiments

* define and implement create scoresets

* correct saving of URN

* change argument name

* update async client documentation

* update base url

* dont exit when error occurs

* update base url

* dont exit when error occurs

* add note

* automatically set base url in easy api

* update jupyter notebooks for creating multiple experiments

* update jupyter notebooks for easy api create experiment

* update jupyter notebooks for easy api get experiment

* update jupyter notebooks for easy api create scoreset

* update jupyter notebooks for easy api get scoreset

* update jupyter notebooks for getting multiple scoresets

* update jupyter notebooks for getting multiple experiments

* update jupyter notebooks for creating multiple scoresets

* dont require base url in easy api

* update urn

* rename python notebooks

* edit imports

* edit url to reflect changes in API

* update requests to httpx, add debugging print statements, mark TODO to resolve requests error

* reformat

* resolve timeout error, change requests to httpx

* remove debugging print statements

* change requests to httpx

* edit imports

* display errors in understandable way, remove requests module comments

* set ssl context for async requests

* set ssl context to resolve certificate error

* update imports

* add async requests to easy api

* add async POST requests to easy api

* edit imports

* edit imports

* update url to reflect changes in API

* reformat files

* display errors in readable way

* Release/0.3.0 (#12)

* Upload API convenience fixes (#9) (#10)

* return the HTTP response when posting a model

* drop internal MaveDB attributes

* make virtual method explicit

* update authors

* update version

* update version

* use pyproject.toml

* drop local validators

* fix deps

* API client rewrite (#13)

* drop local validators

* fix deps

* remove non-async client

* add missing deps

* remove BaseClient class in favor of a single Client class

* read the API url from an environment variable if not passed in

* minor syntax changes to deal with warnings

* update test case since rna isn't supported

* deduplication fix and test fixes

* add mavedb requirement

* refactor of API client creation and get method

* refactor dataset submission by POST

* delete thin wrapper functions

* allow get operations for private datasets

* make record type checking accept camel or snake case

* drop the basic wrappers that create a client for each call

* added local validation for dataframes

* add docstring

* Linting and pre-commit (#15)

* drop local validators

* fix deps

* add pre-commit hooks and linting options

* black formatting

* bump version

* delete old models that are now imported from mavedb-api

* delete old examples and data

* undo bump version

* clean up docs for removed code

* update to new API naming convention for score sets

* updates to imports to match latest mavedb version

* change to src/ layout

* use pyproject for flake8

* remove some locally maintained utility functions

* remove outdated/redundant functions

* minor refactor and remove unused tests

* clean up old enrich seqid conversion code

* add coverage to dev requirements

* drop unused import

* update codon sub to create a variant object instead of a string

* update infer_record_type for field name change

* remove local df validation until it can be updated

* don't use http keepalive to avoid disconnect errors

* add trailing slashes to urls

* add project.license

* update copyright

* add missing dependencies

* clean up docs for new version

* update badges

* update pre-commit versions

* add required server dependencies for validation

* add version check function

* add isort to precommit

* run isort

* add isort options to pyproject.toml

* add flake8-bugbear

* remove Enrich2-only tests from base

* flake8 cleanup

* flake8 compliance

* documentation updates for new version

---------

Co-authored-by: harmatt <[email protected]>

Author: afrubin

.gitignore

@@ -14,6 +14,7 @@ __pycache__/
 docs/build/
 develop-eggs/
 dist/
+build/
 downloads/
 eggs/
 .eggs/
@@ -110,6 +111,8 @@ celerybeat.pid
 # Environments
 .env
 .venv
+.envrc
+.direnv
 env/
 venv/
 ENV/

.pre-commit-config.yaml

@@ -0,0 +1,17 @@
+repos:
+  - repo: https://github.com/psf/black
+    rev: 25.1.0
+    hooks:
+      - id: black
+        language_version: python3.12
+  - repo: https://github.com/pycqa/flake8
+    rev: 7.1.1
+    hooks:
+    -   id: flake8
+        additional_dependencies:
+          - Flake8-pyproject
+          - flake8-bugbear
+  - repo: https://github.com/pycqa/isort
+    rev: 5.13.2
+    hooks:
+      - id: isort

.travis.yml

@@ -1,6 +1,6 @@
 BSD 3-Clause License
 
-Copyright (c) 2020-2022, MaveDB Developers
+Copyright (c) 2020-2025, MaveDB Developers
 All rights reserved.
 
 Redistribution and use in source and binary forms, with or without

LICENSE

@@ -1,5 +1,4 @@
-[![Build Status](https://travis-ci.com/VariantEffect/mavetools.svg?branch=main)](https://travis-ci.com/VariantEffect/mavetools)
-[![Coverage Status](https://coveralls.io/repos/github/VariantEffect/mavetools/badge.svg?branch=main)](https://coveralls.io/github/VariantEffect/mavetools?branch=main)
+[![PyPI version](https://badge.fury.io/py/mavetools.svg)](https://badge.fury.io/py/mavetools)
 [![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black)
 
 # mavetools