Update logo links in README (#166)

* Update logo links in README

* Update linting, formatting, and testing scripts

- Added `--fix` option to notebook formatting check
- Introduced a new script for running Jupyter notebooks
- Included functional tests in the test runner script

* Fix typo in CI workflow for notebook checks

Author: AndrewSazonov

.github/workflows/ci-testing.yaml

@@ -14,7 +14,7 @@
 #    - Download the Python package from the previous job
 #    - Install the downloaded Python package
 #    - Test the code base
-#    - Check if Jupiter Notebooks run without errors
+#    - Check if Jupyter Notebooks run without errors
 
 name: Test code, notebooks and package
 
@@ -251,7 +251,7 @@ jobs:
         run: >
           pytest tests/ --color=yes -n auto
 
-      - name: Check if Jupiter Notebooks run without errors
+      - name: Check if Jupyter Notebooks run without errors
         shell: bash
         run: >
           pytest --nbmake examples/ --ignore-glob='examples/*emcee*'

README.md

@@ -1,11 +1,11 @@
 <p align='left'>
   <picture>
     <!-- light mode logo -->
-    <source media='(prefers-color-scheme: light)' srcset='https://raw.githubusercontent.com/EasyScience/EasyDiffraction/master/resources/logo/EasyDiffractionLib-logo_lightmode.svg'>
+    <source media='(prefers-color-scheme: light)' srcset='https://raw.githubusercontent.com/EasyScience/BrandingResources/refs/heads/master/EasyDiffraction/logos/ed-logo_light.svg'>
     <!-- dark mode logo -->
-    <source media='(prefers-color-scheme: dark)' srcset='https://raw.githubusercontent.com/EasyScience/EasyDiffraction/master/resources/logo/EasyDiffractionLib-logo_darkmode.svg'>
+    <source media='(prefers-color-scheme: dark)' srcset='https://raw.githubusercontent.com/EasyScience/BrandingResources/refs/heads/master/EasyDiffraction/logos/ed-logo_dark.svg'>
     <!-- default logo == light mode logo -->
-    <img src='https://raw.githubusercontent.com/EasyScience/EasyDiffraction/master/resources/logo/EasyDiffractionLib-logo_lightmode.svg' alt='EasyCrystallography'>
+    <img src='https://raw.githubusercontent.com/EasyScience/BrandingResources/refs/heads/master/EasyDiffraction/logos/ed-logo_light.svg' alt='EasyDiffraction'>
   </picture>
 </p>
 

tools/linting_and_formatting.sh

@@ -5,7 +5,7 @@ echo "\033[0;33m:::::: Check and fix code formatting\033[0m"
 ruff format .
 
 echo "\033[0;33m:::::: Check and fix notebook formatting\033[0m"
-nbqa ruff examples/
+nbqa ruff examples/ --fix
 
 echo "\033[0;33m:::::: Check and fix non-code formatting\033[0m"
 npx prettier . --write --config=prettierrc.toml

tools/run_notebooks.sh

@@ -0,0 +1,6 @@
+echo "\033[0;33m:::::: Add src to pythonpath\033[0m"
+export PYTHONPATH="${PWD}/src:${PYTHONPATH}"
+echo "PYTHONPATH: ${PYTHONPATH}"
+
+echo "\033[0;33m:::::: Run Jupyter notebooks\033[0m"
+pytest --nbmake examples/ --ignore-glob='examples/*emcee*' --nbmake-timeout=300 --color=yes -n=auto

tools/run_tests.sh

@@ -5,5 +5,8 @@ echo "PYTHONPATH: ${PYTHONPATH}"
 echo "\033[0;33m:::::: Run unit tests\033[0m"
 pytest tests/unit_tests/ --color=yes --disable-warnings
 
+echo "\033[0;33m:::::: Run functional tests\033[0m"
+pytest tests/functional_tests/ --color=yes --disable-warnings
+
 echo "\033[0;33m:::::: Run integration tests\033[0m"
 pytest tests/integration_tests/ --color=yes --disable-warnings