test: publish code coverage results (#6)

* doc: removed bitbucket pipeline [ci-skip]

* chore: moved pipeline and created reduced conda env spec

* test: publish code coverage results

* chore: fixed pipeline

* chore: another attempt

* chore: another pipeline try

* fix: removed tqdm from script template to match with mini env

* chore: added codecov upload

* chore: added conda cache

* chore: working on conda cache

* chore: removed conda cache. can't figure it out

* doc: added codecov badge to README.md

---------

Co-authored-by: Julien Lerat <[email protected]>

Author: jlerat

.github/workflows/python-package-conda.yml

@@ -19,27 +19,44 @@ jobs:
         uses: actions/setup-python@v3
         with:
           python-version: '3.10'
-          
+     
       - name: Add conda to system path
         run: |
           # $CONDA is an environment variable pointing to the root of the miniconda directory
           echo $CONDA/bin >> $GITHUB_PATH
+      
+      - name: Create conda environment if needed
+        run: |
+           source $CONDA/etc/profile.d/conda.sh
+           conda env create -f env_mini.yml
 
-      - name : Main pipeline 
+      - name : Install hydrodiy package in conda env 
         run: |
-          # Build conda
           source $CONDA/etc/profile.d/conda.sh
-          conda env create -f env_mini.yml
-          
-          # Activate conda
-          conda activate env_mini || true
-          
-          # Install hydrodiy
+          conda activate env_mini
           pip install -e .
-        
-          # Run test
+
+      - name: Run tests
+        run: |
+          source $CONDA/etc/profile.d/conda.sh
+          conda activate env_mini
           pytest --cov=hydrodiy --cov-config=.coveragerc --junitxml=junit/test-results.xml --cov-report=xml --cov-report=html hydrodiy
+      
+      - name: Upload pytest test results
+        uses: actions/upload-artifact@v3
+        with:
+          name: pytest-results
+          path: junit/test-results.xml
+        
+        # Use always() to always run this step to publish test results when there are test failures
+        if: ${{ always() }}
+
+      - name: Upload to codecov
+        uses: codecov/codecov-action@v3        
 
-          # Run examples
+      - name: Run examples
+        run: |
+          source $CONDA/etc/profile.d/conda.sh
+          conda activate env_mini
           python examples/run_all_examples.py
         

README.md

@@ -1,5 +1,5 @@
 # hydrodiy
-[![CI](https://github.com/csiro-hydroinformatics/hydrodiy/actions/workflows/python-package-conda.yml/badge.svg)](https://github.com/csiro-hydroinformatics/hydrodiy/actions/workflows/python-package-conda.yml)
+[![CI](https://github.com/csiro-hydroinformatics/hydrodiy/actions/workflows/python-package-conda.yml/badge.svg)](https://github.com/csiro-hydroinformatics/hydrodiy/actions/workflows/python-package-conda.yml) [![codecov](https://codecov.io/gh/csiro-hydroinformatics/hydrodiy/graph/badge.svg?token=ARBFW69TI3)](https://codecov.io/gh/csiro-hydroinformatics/hydrodiy)
 
 Python toolbox for hydrological data processing.
 

hydrodiy/io/script_template_plot.py

@@ -35,8 +35,6 @@
 import pyproj
 from hydrodiy.gis.oz import ozlayer
 
-import tqdm
-
 # Code to facilitate import of a "utils" package
 #import utils
 #import importlib

hydrodiy/io/script_template_simple.py

@@ -18,8 +18,6 @@
 
 from hydrodiy.io import csv, iutils
 
-from tqdm import tqdm
-
 #import importlib.util
 #spec = importlib.util.spec_from_file_location("foo", "/path/to/foo.py")
 #foo = importlib.util.module_from_spec(spec)
@@ -97,8 +95,8 @@
 # Process
 #----------------------------------------------------------------------
 nsites = len(sites)
-for isite, (siteid, sinfo) in tqdm(enumerate(sites.iterrows()), \
-                total=nsites, disable=not progress):
+for isite, (siteid, sinfo) in enumerate(sites.iterrows()):
+
     LOGGER.context = f"{siteid} ({isite+1}/{nsites})"
 
     LOGGER.info("Processing")