Add badges (#721)

* Add.

* Fixes.

* Add covecov to CI.

* More fix.es

* try fix ci issue.

* Update.

* Enhance debugging output in CI workflow

Added diagnostic echo statements for conda environment and Python/pip paths during installation steps.

* Simplify workflow by removing debug steps and adding packages

Removed debugging steps from the workflow and added conda-packages specification.

* Update code_test_and_deploy.yml

* Fix cov argument.

* Update README.md

* fix DOI badge

* Update DOI badge in README

Updated DOI badge to the latest version.

Author: JoeZiminski

.github/workflows/code_test_and_deploy.yml

@@ -98,31 +98,48 @@ jobs:
         # run Linux containers because nested containerisation is disabled.
       - name: Test SSH (Linux only)
         if: runner.os == 'Linux'
+        env:
+          COVERAGE_FILE: .coverage.ssh
         run: |
           sudo service mysql stop  # free up port 3306 for ssh tests
-          pytest tests/tests_transfers/ssh
+          pytest tests/tests_transfers/ssh --cov=datashuttle --cov-report=
 
       - name: Test all except central connections
+        env:
+          COVERAGE_FILE: .coverage.main
         run: |
-          pytest --ignore=tests/tests_transfers/ssh --ignore=tests/tests_transfers/gdrive --ignore=tests/tests_transfers/aws
+          pytest --ignore=tests/tests_transfers/ssh --ignore=tests/tests_transfers/gdrive --ignore=tests/tests_transfers/aws --cov=datashuttle --cov-report=
 
       - name: Test Google Drive
         env:
           GDRIVE_CLIENT_ID: ${{ secrets.GDRIVE_CLIENT_ID }}
           GDRIVE_CLIENT_SECRET: ${{ secrets.GDRIVE_CLIENT_SECRET }}
           GDRIVE_ROOT_FOLDER_ID: ${{ secrets.GDRIVE_ROOT_FOLDER_ID }}
           GDRIVE_CONFIG_TOKEN: ${{ secrets.GDRIVE_CONFIG_TOKEN }}
+          COVERAGE_FILE: .coverage.gdrive
         run: |
-          pytest tests/tests_transfers/gdrive
+          pytest tests/tests_transfers/gdrive --cov=datashuttle --cov-report=
 
       - name: Test AWS
         env:
           AWS_ACCESS_KEY_ID: ${{ secrets.AWS_ACCESS_KEY_ID }}
           AWS_SECRET_ACCESS_KEY: ${{ secrets.AWS_SECRET_ACCESS_KEY }}
           AWS_REGION: ${{ secrets.AWS_REGION }}
           AWS_BUCKET_NAME: ${{ secrets.AWS_BUCKET_NAME }}
+          COVERAGE_FILE: .coverage.aws
+        run: |
+          pytest tests/tests_transfers/aws --cov=datashuttle --cov-report=
+
+      - name: Combine coverage reports
         run: |
-          pytest tests/tests_transfers/aws
+          coverage combine
+          coverage xml
+
+      - name: Upload coverage reports to Codecov
+        uses: codecov/codecov-action@v5
+        with:
+          token: ${{ secrets.CODECOV_TOKEN }}
+          slug: neuroinformatics-unit/datashuttle
 
   build_sdist_wheels:
     name: Build source distribution

README.md

@@ -1,3 +1,12 @@
+[![Python Version](https://img.shields.io/pypi/pyversions/datashuttle.svg)](https://pypi.org/project/datashuttle)
+[![Downloads](https://pepy.tech/badge/datashuttle)](https://pepy.tech/project/datashuttle)
+[![License](https://img.shields.io/badge/License-BSD_3--Clause-orange.svg)](https://opensource.org/licenses/BSD-3-Clause)
+[![CI](https://img.shields.io/github/actions/workflow/status/neuroinformatics-unit/datashuttle/code_test_and_deploy.yml?label=CI)](https://github.com/neuroinformatics-unit/datashuttle/actions)
+[![codecov](https://codecov.io/gh/neuroinformatics-unit/datashuttle/branch/main/graph/badge.svg?token=P8CCH3TI8K)](https://codecov.io/gh/neuroinformatics-unit/datashuttle)
+[![pre-commit](https://img.shields.io/badge/pre--commit-enabled-brightgreen?logo=pre-commit&logoColor=white)](https://github.com/pre-commit/pre-commit)
+[![project chat](https://img.shields.io/badge/zulip-join_chat-brightgreen.svg)](https://neuroinformatics.zulipchat.com/#narrow/channel/405999-DataShuttle)
+[![DOI](https://zenodo.org/badge/531897428.svg)](https://zenodo.org/badge/latestdoi/531897428)
+
 # **datashuttle**
 
 **datashuttle** is a tool to automate creation, validation and transfer of neuroscience project folders.