Merge pull request #38 from pepkit/dev

Release 0.4.1

Author: khoroshevskyi

.github/workflows/cli-coverage.yml

@@ -0,0 +1,40 @@
+name: test coverage
+
+on:
+  push:
+    branches: [master, dev]
+
+jobs:
+  cli-coverage-report:
+    strategy:
+      matrix:
+        python-version: [ "3.11" ]
+        os: [ ubuntu-latest ]
+        r: [ release ]
+    runs-on: ${{ matrix.os }}
+    steps:
+      - uses: actions/checkout@v2
+
+      - uses: actions/setup-python@v1
+        with:
+          python-version: '3.10'
+
+      - name: Install test dependencies
+        run: if [ -f requirements/requirements-test.txt ]; then pip install -r requirements/requirements-test.txt; fi
+
+      - run: pip install .
+
+      - name: Run tests
+        run: coverage run -m pytest
+
+      - name: build coverage
+        run: coverage html -i
+
+      - run: smokeshow upload htmlcov
+        env:
+          SMOKESHOW_GITHUB_STATUS_DESCRIPTION: Coverage {coverage-percentage}
+          SMOKESHOW_GITHUB_COVERAGE_THRESHOLD: 80
+          SMOKESHOW_GITHUB_CONTEXT: coverage
+          SMOKESHOW_GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+          SMOKESHOW_GITHUB_PR_HEAD_SHA: ${{ github.event.pull_request.head.sha }}
+          SMOKESHOW_AUTH_KEY: ${{ secrets.SMOKESHOW_AUTH_KEY }}

.github/workflows/run-codecov.yml

@@ -1,14 +1,38 @@
-# `PEPHubClient`
+<h1 align="center">PEPHubClient</h1>
 
 [![PEP compatible](https://pepkit.github.io/img/PEP-compatible-green.svg)](https://pepkit.github.io)
 ![Run pytests](https://github.com/pepkit/pephubclient/workflows/Run%20pytests/badge.svg)
-[![codecov](https://codecov.io/gh/pepkit/pephubclient/branch/dev/graph/badge.svg)](https://codecov.io/gh/pepkit/pephubclient)
-[![pypi-badge](https://img.shields.io/pypi/v/pephubclient)](https://pypi.org/project/pephubclient)
+[![pypi-badge](https://img.shields.io/pypi/v/pephubclient?color=%2334D058)](https://pypi.org/project/pephubclient)
+[![pypi-version](https://img.shields.io/pypi/pyversions/pephubclient.svg?color=%2334D058)](https://pypi.org/project/pephubclient)
+[![Coverage](https://coverage-badge.samuelcolvin.workers.dev/pepkit/pephubclient.svg)](https://coverage-badge.samuelcolvin.workers.dev/redirect/pepkit/pephubclient)
+[![Github badge](https://img.shields.io/badge/source-github-354a75?logo=github)](https://github.com/pepkit/pephubclient)
 [![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black)
 
+
 `PEPHubClient` is a tool to provide Python API and CLI for [PEPhub](https://pephub.databio.org).
 
-`pephubclient` features: 
+
+---
+
+**Documentation**: <a href="https://pep.databio.org/" target="_blank">https://pep.databio.org</a>
+
+**Source Code**: <a href="https://github.com/pepkit/pephubclient" target="_blank">https://github.com/pepkit/pephubclient</a>
+
+---
+
+## Installation
+To install `pepdbagent` use this command: 
+```
+pip install pephubclient
+```
+or install the latest version from the GitHub repository:
+```
+pip install git+https://github.com/pepkit/pephubclient.git
+```
+
+---
+
+### `pephubclient` features: 
 1) `push` (upload) projects)
 2) `pull` (download projects)
 
@@ -17,7 +41,7 @@ The authorization process is based on pephub device authorization protocol.
 To upload projects or to download private projects, user must be authorized through pephub.
 
 If you want to use your own pephub instance, you can specify it by setting `PEPHUB_BASE_URL` environment variable.
-e.g. `export PEPHUB_BASE_URL=https://pephub.databio.org` (This is original pephub instance)
+e.g. `export PEPHUB_BASE_URL=https://pephub.databio.org/` (This is original pephub instance)
 
 To login, use the `login` argument; to logout, use `logout`.
 

README.md

@@ -2,6 +2,10 @@
 
 This project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html) and [Keep a Changelog](https://keepachangelog.com/en/1.0.0/) format.
 
+## [0.4.1] - 2024-03-07
+### Fixed
+- Expired token error handling  ([#17](https://github.com/pepkit/pephubclient/issues/17))
+
 ## [0.4.0] - 2024-02-12
 ### Added
 - a parameter that points to where peps should be saved ([#32](https://github.com/pepkit/pephubclient/issues/32))

codecov.yml

@@ -4,7 +4,7 @@
 import coloredlogs
 
 __app_name__ = "pephubclient"
-__version__ = "0.4.0"
+__version__ = "0.4.1"
 __author__ = "Oleksandr Khoroshevskyi, Rafal Stepien"
 
 

docs/changelog.md

@@ -37,7 +37,7 @@ def send_request(
         params: Optional[dict] = None,
         json: Optional[dict] = None,
     ) -> requests.Response:
-        return requests.request(
+        request_return = requests.request(
             method=method,
             url=url,
             verify=False,
@@ -46,6 +46,15 @@ def send_request(
             params=params,
             json=json,
         )
+        if request_return.status_code == 401:
+            if (
+                RequestManager.decode_response(request_return, output_json=True).get(
+                    "detail"
+                )
+                == "JWT has expired"
+            ):
+                raise ResponseError("JWT has expired. Please log in again.")
+        return request_return
 
     @staticmethod
     def decode_response(

pephubclient/__init__.py

@@ -6,4 +6,6 @@ pytest-mock
 flake8
 coveralls
 pytest-cov
-pre-commit
+pre-commit
+coverage
+smokeshow

pephubclient/helpers.py

@@ -49,14 +49,14 @@ def read_reqs(reqs_name):
     keywords="project, bioinformatics, metadata",
     url=f"https://github.com/databio/{PACKAGE}/",
     author=AUTHOR,
+    author_email="[email protected]",
     license="BSD2",
     entry_points={
         "console_scripts": [
             "phc = pephubclient.__main__:main",
         ],
     },
     package_data={PACKAGE: ["templates/*"]},
-    scripts=None,
     include_package_data=True,
     test_suite="tests",
     tests_require=read_reqs("test"),