From 515d17d2d1802e0e384f3553374016c6d27c29db Mon Sep 17 00:00:00 2001 From: Joris Van den Bossche Date: Tue, 13 Jan 2026 17:13:59 +0100 Subject: [PATCH 1/5] Update to Python 3.13 in env --- environment.yml | 8 ++++---- web/templates/setup.md.tmpl | 2 +- web/templates/slides.html.tmpl | 2 +- 3 files changed, 6 insertions(+), 6 deletions(-) diff --git a/environment.yml b/environment.yml index 0aad3dc..cf9f5ca 100644 --- a/environment.yml +++ b/environment.yml @@ -1,13 +1,13 @@ -name: course-python +name: course-python2 channels: - conda-forge dependencies: -- python=3.12 +- python=3.13 - ipython - jupyter -- jupyterlab>=3 +- jupyterlab>=4 - numpy -- pandas=2.2 +- pandas=2.3 - matplotlib>3 - mplleaflet - ipympl diff --git a/web/templates/setup.md.tmpl b/web/templates/setup.md.tmpl index aa61997..da68326 100644 --- a/web/templates/setup.md.tmpl +++ b/web/templates/setup.md.tmpl @@ -86,7 +86,7 @@ name: {{ conda_environment }} channels: - conda-forge dependencies: -- python=3.12 +- python=3.13 - geopandas - ... ``` diff --git a/web/templates/slides.html.tmpl b/web/templates/slides.html.tmpl index 4a82c7e..f9a6c4c 100644 --- a/web/templates/slides.html.tmpl +++ b/web/templates/slides.html.tmpl @@ -153,7 +153,7 @@ class: middle, section_background Creating a new environment: ``` -conda create -n my_env python=3.9 pandas +conda create -n my_env python=3.3 pandas # or from environment file conda env create -f environment.yml From 256e5346afe480747143ee438b5d6baba95cc615 Mon Sep 17 00:00:00 2001 From: Joris Van den Bossche Date: Tue, 13 Jan 2026 17:18:46 +0100 Subject: [PATCH 2/5] update copyright year and notebook metadata --- notebooks/00-jupyter_introduction.ipynb | 5 +++-- notebooks/00-jupyter_introduction.md | 4 ++-- notebooks/case1_bike_count.ipynb | 5 +++-- notebooks/case1_bike_count.md | 4 ++-- notebooks/case2_observations.ipynb | 5 +++-- notebooks/case2_observations.md | 4 ++-- notebooks/case3_bacterial_resistance_lab_experiment.ipynb | 5 +++-- notebooks/case3_bacterial_resistance_lab_experiment.md | 4 ++-- notebooks/case4_air_quality_analysis.ipynb | 5 +++-- notebooks/case4_air_quality_analysis.md | 4 ++-- notebooks/case4_air_quality_processing.ipynb | 5 +++-- notebooks/case4_air_quality_processing.md | 4 ++-- notebooks/pandas_01_data_structures.ipynb | 5 +++-- notebooks/pandas_01_data_structures.md | 4 ++-- notebooks/pandas_02_basic_operations.ipynb | 5 +++-- notebooks/pandas_02_basic_operations.md | 4 ++-- notebooks/pandas_03a_selecting_data.ipynb | 5 +++-- notebooks/pandas_03a_selecting_data.md | 4 ++-- notebooks/pandas_03b_indexing.ipynb | 5 +++-- notebooks/pandas_03b_indexing.md | 4 ++-- notebooks/pandas_04_time_series_data.ipynb | 5 +++-- notebooks/pandas_04_time_series_data.md | 4 ++-- notebooks/pandas_05_groupby_operations.ipynb | 5 +++-- notebooks/pandas_05_groupby_operations.md | 4 ++-- notebooks/pandas_06_data_cleaning.ipynb | 7 +++++-- notebooks/pandas_06_data_cleaning.md | 4 ++-- notebooks/pandas_07_missing_values.ipynb | 5 +++-- notebooks/pandas_07_missing_values.md | 4 ++-- notebooks/pandas_08_reshaping_data.ipynb | 5 +++-- notebooks/pandas_08_reshaping_data.md | 4 ++-- notebooks/pandas_09_combining_datasets.ipynb | 5 +++-- notebooks/pandas_09_combining_datasets.md | 4 ++-- notebooks/visualization_01_matplotlib.ipynb | 5 +++-- notebooks/visualization_01_matplotlib.md | 4 ++-- notebooks/visualization_02_seaborn.ipynb | 5 +++-- notebooks/visualization_02_seaborn.md | 4 ++-- notebooks/visualization_03_landscape.ipynb | 5 +++-- notebooks/visualization_03_landscape.md | 4 ++-- 38 files changed, 97 insertions(+), 76 deletions(-) diff --git a/notebooks/00-jupyter_introduction.ipynb b/notebooks/00-jupyter_introduction.ipynb index df88434..6eb38e0 100644 --- a/notebooks/00-jupyter_introduction.ipynb +++ b/notebooks/00-jupyter_introduction.ipynb @@ -6,7 +6,7 @@ "source": [ "

Jupyter notebook INTRODUCTION

\n", "\n", - "> *© 2025, Joris Van den Bossche and Stijn Van Hoey (, ). Licensed under [CC BY 4.0 Creative Commons](http://creativecommons.org/licenses/by/4.0/)*\n", + "> *© 2026, Joris Van den Bossche and Stijn Van Hoey (, ). Licensed under [CC BY 4.0 Creative Commons](http://creativecommons.org/licenses/by/4.0/)*\n", "\n", "---" ] @@ -1023,6 +1023,7 @@ ], "metadata": { "jupytext": { + "default_lexer": "ipython3", "formats": "ipynb,md:myst" }, "kernelspec": { @@ -1040,7 +1041,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.12.8" + "version": "3.13.11" }, "nav_menu": {}, "toc": { diff --git a/notebooks/00-jupyter_introduction.md b/notebooks/00-jupyter_introduction.md index 440a01e..f04f978 100644 --- a/notebooks/00-jupyter_introduction.md +++ b/notebooks/00-jupyter_introduction.md @@ -5,7 +5,7 @@ jupytext: extension: .md format_name: myst format_version: 0.13 - jupytext_version: 1.16.6 + jupytext_version: 1.18.1 kernelspec: display_name: Python 3 (ipykernel) language: python @@ -14,7 +14,7 @@ kernelspec:

Jupyter notebook INTRODUCTION

-> *© 2025, Joris Van den Bossche and Stijn Van Hoey (, ). Licensed under [CC BY 4.0 Creative Commons](http://creativecommons.org/licenses/by/4.0/)* +> *© 2026, Joris Van den Bossche and Stijn Van Hoey (, ). Licensed under [CC BY 4.0 Creative Commons](http://creativecommons.org/licenses/by/4.0/)* --- diff --git a/notebooks/case1_bike_count.ipynb b/notebooks/case1_bike_count.ipynb index dcdcd47..465dc20 100644 --- a/notebooks/case1_bike_count.ipynb +++ b/notebooks/case1_bike_count.ipynb @@ -8,7 +8,7 @@ "source": [ "

CASE - Bike count data

\n", "\n", - "> *© 2025, Joris Van den Bossche and Stijn Van Hoey (, ). Licensed under [CC BY 4.0 Creative Commons](http://creativecommons.org/licenses/by/4.0/)*\n", + "> *© 2026, Joris Van den Bossche and Stijn Van Hoey (, ). Licensed under [CC BY 4.0 Creative Commons](http://creativecommons.org/licenses/by/4.0/)*\n", "\n", "---" ] @@ -2806,6 +2806,7 @@ "metadata": { "celltoolbar": "Nbtutor - export exercises", "jupytext": { + "default_lexer": "ipython3", "formats": "ipynb,md:myst" }, "kernelspec": { @@ -2823,7 +2824,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.12.8" + "version": "3.13.11" }, "nav_menu": {}, "toc": { diff --git a/notebooks/case1_bike_count.md b/notebooks/case1_bike_count.md index 720c2d9..2ad42de 100644 --- a/notebooks/case1_bike_count.md +++ b/notebooks/case1_bike_count.md @@ -5,7 +5,7 @@ jupytext: extension: .md format_name: myst format_version: 0.13 - jupytext_version: 1.16.6 + jupytext_version: 1.18.1 kernelspec: display_name: Python 3 (ipykernel) language: python @@ -14,7 +14,7 @@ kernelspec:

CASE - Bike count data

-> *© 2025, Joris Van den Bossche and Stijn Van Hoey (, ). Licensed under [CC BY 4.0 Creative Commons](http://creativecommons.org/licenses/by/4.0/)* +> *© 2026, Joris Van den Bossche and Stijn Van Hoey (, ). Licensed under [CC BY 4.0 Creative Commons](http://creativecommons.org/licenses/by/4.0/)* --- diff --git a/notebooks/case2_observations.ipynb b/notebooks/case2_observations.ipynb index 78987f8..44da2c8 100644 --- a/notebooks/case2_observations.ipynb +++ b/notebooks/case2_observations.ipynb @@ -6,7 +6,7 @@ "source": [ "

CASE - Observation data

\n", "\n", - "> *© 2025, Joris Van den Bossche and Stijn Van Hoey (, ). Licensed under [CC BY 4.0 Creative Commons](http://creativecommons.org/licenses/by/4.0/)*\n", + "> *© 2026, Joris Van den Bossche and Stijn Van Hoey (, ). Licensed under [CC BY 4.0 Creative Commons](http://creativecommons.org/licenses/by/4.0/)*\n", "\n", "---" ] @@ -4552,6 +4552,7 @@ "metadata": { "celltoolbar": "Nbtutor - export exercises", "jupytext": { + "default_lexer": "ipython3", "formats": "ipynb,md:myst" }, "kernelspec": { @@ -4569,7 +4570,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.12.8" + "version": "3.13.11" }, "nav_menu": {}, "toc": { diff --git a/notebooks/case2_observations.md b/notebooks/case2_observations.md index bf36f98..9967e25 100644 --- a/notebooks/case2_observations.md +++ b/notebooks/case2_observations.md @@ -5,7 +5,7 @@ jupytext: extension: .md format_name: myst format_version: 0.13 - jupytext_version: 1.16.6 + jupytext_version: 1.18.1 kernelspec: display_name: Python 3 (ipykernel) language: python @@ -14,7 +14,7 @@ kernelspec:

CASE - Observation data

-> *© 2025, Joris Van den Bossche and Stijn Van Hoey (, ). Licensed under [CC BY 4.0 Creative Commons](http://creativecommons.org/licenses/by/4.0/)* +> *© 2026, Joris Van den Bossche and Stijn Van Hoey (, ). Licensed under [CC BY 4.0 Creative Commons](http://creativecommons.org/licenses/by/4.0/)* --- diff --git a/notebooks/case3_bacterial_resistance_lab_experiment.ipynb b/notebooks/case3_bacterial_resistance_lab_experiment.ipynb index b5965a6..3326fa6 100644 --- a/notebooks/case3_bacterial_resistance_lab_experiment.ipynb +++ b/notebooks/case3_bacterial_resistance_lab_experiment.ipynb @@ -8,7 +8,7 @@ "source": [ "

CASE - Bacterial resistance experiment

\n", "\n", - "> *© 2025, Joris Van den Bossche and Stijn Van Hoey (, ). Licensed under [CC BY 4.0 Creative Commons](http://creativecommons.org/licenses/by/4.0/)*\n", + "> *© 2026, Joris Van den Bossche and Stijn Van Hoey (, ). Licensed under [CC BY 4.0 Creative Commons](http://creativecommons.org/licenses/by/4.0/)*\n", "\n", "---" ] @@ -1742,6 +1742,7 @@ "metadata": { "celltoolbar": "Nbtutor - export exercises", "jupytext": { + "default_lexer": "ipython3", "formats": "ipynb,md:myst" }, "kernelspec": { @@ -1759,7 +1760,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.12.8" + "version": "3.13.11" }, "widgets": { "application/vnd.jupyter.widget-state+json": { diff --git a/notebooks/case3_bacterial_resistance_lab_experiment.md b/notebooks/case3_bacterial_resistance_lab_experiment.md index 74302d6..c072ea7 100644 --- a/notebooks/case3_bacterial_resistance_lab_experiment.md +++ b/notebooks/case3_bacterial_resistance_lab_experiment.md @@ -5,7 +5,7 @@ jupytext: extension: .md format_name: myst format_version: 0.13 - jupytext_version: 1.16.6 + jupytext_version: 1.18.1 kernelspec: display_name: Python 3 (ipykernel) language: python @@ -14,7 +14,7 @@ kernelspec:

CASE - Bacterial resistance experiment

-> *© 2025, Joris Van den Bossche and Stijn Van Hoey (, ). Licensed under [CC BY 4.0 Creative Commons](http://creativecommons.org/licenses/by/4.0/)* +> *© 2026, Joris Van den Bossche and Stijn Van Hoey (, ). Licensed under [CC BY 4.0 Creative Commons](http://creativecommons.org/licenses/by/4.0/)* --- diff --git a/notebooks/case4_air_quality_analysis.ipynb b/notebooks/case4_air_quality_analysis.ipynb index 0a88172..fc66e2a 100644 --- a/notebooks/case4_air_quality_analysis.ipynb +++ b/notebooks/case4_air_quality_analysis.ipynb @@ -8,7 +8,7 @@ "source": [ "

CASE - air quality data of European monitoring stations (AirBase)

\n", "\n", - "> *© 2025, Joris Van den Bossche and Stijn Van Hoey (, ). Licensed under [CC BY 4.0 Creative Commons](http://creativecommons.org/licenses/by/4.0/)*\n", + "> *© 2026, Joris Van den Bossche and Stijn Van Hoey (, ). Licensed under [CC BY 4.0 Creative Commons](http://creativecommons.org/licenses/by/4.0/)*\n", "\n", "---" ] @@ -2652,6 +2652,7 @@ "metadata": { "celltoolbar": "Nbtutor - export exercises", "jupytext": { + "default_lexer": "ipython3", "formats": "ipynb,md:myst" }, "kernelspec": { @@ -2669,7 +2670,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.12.8" + "version": "3.13.11" }, "nav_menu": {}, "toc": { diff --git a/notebooks/case4_air_quality_analysis.md b/notebooks/case4_air_quality_analysis.md index dbc507f..a527b53 100644 --- a/notebooks/case4_air_quality_analysis.md +++ b/notebooks/case4_air_quality_analysis.md @@ -5,7 +5,7 @@ jupytext: extension: .md format_name: myst format_version: 0.13 - jupytext_version: 1.16.6 + jupytext_version: 1.18.1 kernelspec: display_name: Python 3 (ipykernel) language: python @@ -14,7 +14,7 @@ kernelspec:

CASE - air quality data of European monitoring stations (AirBase)

-> *© 2025, Joris Van den Bossche and Stijn Van Hoey (, ). Licensed under [CC BY 4.0 Creative Commons](http://creativecommons.org/licenses/by/4.0/)* +> *© 2026, Joris Van den Bossche and Stijn Van Hoey (, ). Licensed under [CC BY 4.0 Creative Commons](http://creativecommons.org/licenses/by/4.0/)* --- diff --git a/notebooks/case4_air_quality_processing.ipynb b/notebooks/case4_air_quality_processing.ipynb index b759975..f11dc6e 100644 --- a/notebooks/case4_air_quality_processing.ipynb +++ b/notebooks/case4_air_quality_processing.ipynb @@ -6,7 +6,7 @@ "source": [ "

CASE - air quality data of European monitoring stations (AirBase)

\n", "\n", - "> *© 2025, Joris Van den Bossche and Stijn Van Hoey (, ). Licensed under [CC BY 4.0 Creative Commons](http://creativecommons.org/licenses/by/4.0/)*\n", + "> *© 2026, Joris Van den Bossche and Stijn Van Hoey (, ). Licensed under [CC BY 4.0 Creative Commons](http://creativecommons.org/licenses/by/4.0/)*\n", "\n", "---" ] @@ -1854,6 +1854,7 @@ ], "metadata": { "jupytext": { + "default_lexer": "ipython3", "formats": "ipynb,md:myst" }, "kernelspec": { @@ -1871,7 +1872,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.12.8" + "version": "3.13.11" }, "nav_menu": {}, "toc": { diff --git a/notebooks/case4_air_quality_processing.md b/notebooks/case4_air_quality_processing.md index 1cf0dbb..18d8168 100644 --- a/notebooks/case4_air_quality_processing.md +++ b/notebooks/case4_air_quality_processing.md @@ -5,7 +5,7 @@ jupytext: extension: .md format_name: myst format_version: 0.13 - jupytext_version: 1.16.6 + jupytext_version: 1.18.1 kernelspec: display_name: Python 3 (ipykernel) language: python @@ -14,7 +14,7 @@ kernelspec:

CASE - air quality data of European monitoring stations (AirBase)

-> *© 2025, Joris Van den Bossche and Stijn Van Hoey (, ). Licensed under [CC BY 4.0 Creative Commons](http://creativecommons.org/licenses/by/4.0/)* +> *© 2026, Joris Van den Bossche and Stijn Van Hoey (, ). Licensed under [CC BY 4.0 Creative Commons](http://creativecommons.org/licenses/by/4.0/)* --- diff --git a/notebooks/pandas_01_data_structures.ipynb b/notebooks/pandas_01_data_structures.ipynb index ea77436..3dde303 100644 --- a/notebooks/pandas_01_data_structures.ipynb +++ b/notebooks/pandas_01_data_structures.ipynb @@ -7,7 +7,7 @@ "source": [ "

01 - Pandas: Data Structures

\n", "\n", - "> *© 2025, Joris Van den Bossche and Stijn Van Hoey (, ). Licensed under [CC BY 4.0 Creative Commons](http://creativecommons.org/licenses/by/4.0/)*\n", + "> *© 2026, Joris Van den Bossche and Stijn Van Hoey (, ). Licensed under [CC BY 4.0 Creative Commons](http://creativecommons.org/licenses/by/4.0/)*\n", "\n", "---" ] @@ -1901,6 +1901,7 @@ ], "metadata": { "jupytext": { + "default_lexer": "ipython3", "formats": "ipynb,md:myst" }, "kernelspec": { @@ -1918,7 +1919,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.12.8" + "version": "3.13.11" }, "widgets": { "application/vnd.jupyter.widget-state+json": { diff --git a/notebooks/pandas_01_data_structures.md b/notebooks/pandas_01_data_structures.md index 367c9b8..8d58760 100644 --- a/notebooks/pandas_01_data_structures.md +++ b/notebooks/pandas_01_data_structures.md @@ -5,7 +5,7 @@ jupytext: extension: .md format_name: myst format_version: 0.13 - jupytext_version: 1.16.6 + jupytext_version: 1.18.1 kernelspec: display_name: Python 3 (ipykernel) language: python @@ -14,7 +14,7 @@ kernelspec:

01 - Pandas: Data Structures

-> *© 2025, Joris Van den Bossche and Stijn Van Hoey (, ). Licensed under [CC BY 4.0 Creative Commons](http://creativecommons.org/licenses/by/4.0/)* +> *© 2026, Joris Van den Bossche and Stijn Van Hoey (, ). Licensed under [CC BY 4.0 Creative Commons](http://creativecommons.org/licenses/by/4.0/)* --- diff --git a/notebooks/pandas_02_basic_operations.ipynb b/notebooks/pandas_02_basic_operations.ipynb index c6dffba..a9db2b3 100644 --- a/notebooks/pandas_02_basic_operations.ipynb +++ b/notebooks/pandas_02_basic_operations.ipynb @@ -8,7 +8,7 @@ "

02 - Pandas: Basic operations on Series and DataFrames

\n", "\n", "\n", - "> *© 2025, Joris Van den Bossche and Stijn Van Hoey (, ). Licensed under [CC BY 4.0 Creative Commons](http://creativecommons.org/licenses/by/4.0/)*\n", + "> *© 2026, Joris Van den Bossche and Stijn Van Hoey (, ). Licensed under [CC BY 4.0 Creative Commons](http://creativecommons.org/licenses/by/4.0/)*\n", "\n", "---" ] @@ -1563,6 +1563,7 @@ ], "metadata": { "jupytext": { + "default_lexer": "ipython3", "formats": "ipynb,md:myst" }, "kernelspec": { @@ -1580,7 +1581,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.12.8" + "version": "3.13.11" }, "widgets": { "application/vnd.jupyter.widget-state+json": { diff --git a/notebooks/pandas_02_basic_operations.md b/notebooks/pandas_02_basic_operations.md index 9c2a00b..4590cdf 100644 --- a/notebooks/pandas_02_basic_operations.md +++ b/notebooks/pandas_02_basic_operations.md @@ -5,7 +5,7 @@ jupytext: extension: .md format_name: myst format_version: 0.13 - jupytext_version: 1.16.6 + jupytext_version: 1.18.1 kernelspec: display_name: Python 3 (ipykernel) language: python @@ -15,7 +15,7 @@ kernelspec:

02 - Pandas: Basic operations on Series and DataFrames

-> *© 2025, Joris Van den Bossche and Stijn Van Hoey (, ). Licensed under [CC BY 4.0 Creative Commons](http://creativecommons.org/licenses/by/4.0/)* +> *© 2026, Joris Van den Bossche and Stijn Van Hoey (, ). Licensed under [CC BY 4.0 Creative Commons](http://creativecommons.org/licenses/by/4.0/)* --- diff --git a/notebooks/pandas_03a_selecting_data.ipynb b/notebooks/pandas_03a_selecting_data.ipynb index 8a824d1..983464c 100755 --- a/notebooks/pandas_03a_selecting_data.ipynb +++ b/notebooks/pandas_03a_selecting_data.ipynb @@ -8,7 +8,7 @@ "

03 - Pandas: Indexing and selecting data - part I

\n", "\n", "\n", - "> *© 2025, Joris Van den Bossche and Stijn Van Hoey (, ). Licensed under [CC BY 4.0 Creative Commons](http://creativecommons.org/licenses/by/4.0/)*\n", + "> *© 2026, Joris Van den Bossche and Stijn Van Hoey (, ). Licensed under [CC BY 4.0 Creative Commons](http://creativecommons.org/licenses/by/4.0/)*\n", "\n", "---" ] @@ -3027,6 +3027,7 @@ ], "metadata": { "jupytext": { + "default_lexer": "ipython3", "formats": "ipynb,md:myst" }, "kernelspec": { @@ -3044,7 +3045,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.12.8" + "version": "3.13.11" }, "widgets": { "application/vnd.jupyter.widget-state+json": { diff --git a/notebooks/pandas_03a_selecting_data.md b/notebooks/pandas_03a_selecting_data.md index 85f9c04..edae20e 100644 --- a/notebooks/pandas_03a_selecting_data.md +++ b/notebooks/pandas_03a_selecting_data.md @@ -5,7 +5,7 @@ jupytext: extension: .md format_name: myst format_version: 0.13 - jupytext_version: 1.16.6 + jupytext_version: 1.18.1 kernelspec: display_name: Python 3 (ipykernel) language: python @@ -15,7 +15,7 @@ kernelspec:

03 - Pandas: Indexing and selecting data - part I

-> *© 2025, Joris Van den Bossche and Stijn Van Hoey (, ). Licensed under [CC BY 4.0 Creative Commons](http://creativecommons.org/licenses/by/4.0/)* +> *© 2026, Joris Van den Bossche and Stijn Van Hoey (, ). Licensed under [CC BY 4.0 Creative Commons](http://creativecommons.org/licenses/by/4.0/)* --- diff --git a/notebooks/pandas_03b_indexing.ipynb b/notebooks/pandas_03b_indexing.ipynb index 55ae1ae..27f7b58 100644 --- a/notebooks/pandas_03b_indexing.ipynb +++ b/notebooks/pandas_03b_indexing.ipynb @@ -7,7 +7,7 @@ "source": [ "

03 - Pandas: Indexing and selecting data - part II

\n", "\n", - "> *© 2025, Joris Van den Bossche and Stijn Van Hoey (, ). Licensed under [CC BY 4.0 Creative Commons](http://creativecommons.org/licenses/by/4.0/)*\n", + "> *© 2026, Joris Van den Bossche and Stijn Van Hoey (, ). Licensed under [CC BY 4.0 Creative Commons](http://creativecommons.org/licenses/by/4.0/)*\n", "\n", "---" ] @@ -1875,6 +1875,7 @@ ], "metadata": { "jupytext": { + "default_lexer": "ipython3", "formats": "ipynb,md:myst" }, "kernelspec": { @@ -1892,7 +1893,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.12.8" + "version": "3.13.11" }, "widgets": { "application/vnd.jupyter.widget-state+json": { diff --git a/notebooks/pandas_03b_indexing.md b/notebooks/pandas_03b_indexing.md index ef89dca..90bd9c9 100644 --- a/notebooks/pandas_03b_indexing.md +++ b/notebooks/pandas_03b_indexing.md @@ -5,7 +5,7 @@ jupytext: extension: .md format_name: myst format_version: 0.13 - jupytext_version: 1.16.6 + jupytext_version: 1.18.1 kernelspec: display_name: Python 3 (ipykernel) language: python @@ -14,7 +14,7 @@ kernelspec:

03 - Pandas: Indexing and selecting data - part II

-> *© 2025, Joris Van den Bossche and Stijn Van Hoey (, ). Licensed under [CC BY 4.0 Creative Commons](http://creativecommons.org/licenses/by/4.0/)* +> *© 2026, Joris Van den Bossche and Stijn Van Hoey (, ). Licensed under [CC BY 4.0 Creative Commons](http://creativecommons.org/licenses/by/4.0/)* --- diff --git a/notebooks/pandas_04_time_series_data.ipynb b/notebooks/pandas_04_time_series_data.ipynb index 8ef676f..d09f866 100644 --- a/notebooks/pandas_04_time_series_data.ipynb +++ b/notebooks/pandas_04_time_series_data.ipynb @@ -9,7 +9,7 @@ "source": [ "

04 - Pandas: Working with time series data

\n", "\n", - "> *© 2025, Joris Van den Bossche and Stijn Van Hoey (, ). Licensed under [CC BY 4.0 Creative Commons](http://creativecommons.org/licenses/by/4.0/)*\n", + "> *© 2026, Joris Van den Bossche and Stijn Van Hoey (, ). Licensed under [CC BY 4.0 Creative Commons](http://creativecommons.org/licenses/by/4.0/)*\n", "\n", "---" ] @@ -2687,6 +2687,7 @@ ], "metadata": { "jupytext": { + "default_lexer": "ipython3", "formats": "ipynb,md:myst" }, "kernelspec": { @@ -2704,7 +2705,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.12.8" + "version": "3.13.11" }, "widgets": { "application/vnd.jupyter.widget-state+json": { diff --git a/notebooks/pandas_04_time_series_data.md b/notebooks/pandas_04_time_series_data.md index ca47377..f21b9f9 100644 --- a/notebooks/pandas_04_time_series_data.md +++ b/notebooks/pandas_04_time_series_data.md @@ -5,7 +5,7 @@ jupytext: extension: .md format_name: myst format_version: 0.13 - jupytext_version: 1.16.6 + jupytext_version: 1.18.1 kernelspec: display_name: Python 3 (ipykernel) language: python @@ -14,7 +14,7 @@ kernelspec:

04 - Pandas: Working with time series data

-> *© 2025, Joris Van den Bossche and Stijn Van Hoey (, ). Licensed under [CC BY 4.0 Creative Commons](http://creativecommons.org/licenses/by/4.0/)* +> *© 2026, Joris Van den Bossche and Stijn Van Hoey (, ). Licensed under [CC BY 4.0 Creative Commons](http://creativecommons.org/licenses/by/4.0/)* --- diff --git a/notebooks/pandas_05_groupby_operations.ipynb b/notebooks/pandas_05_groupby_operations.ipynb index 741a0bb..14d7a37 100644 --- a/notebooks/pandas_05_groupby_operations.ipynb +++ b/notebooks/pandas_05_groupby_operations.ipynb @@ -8,7 +8,7 @@ "

05 - Pandas: \"Group by\" operations

\n", "\n", "\n", - "> *© 2025, Joris Van den Bossche and Stijn Van Hoey (, ). Licensed under [CC BY 4.0 Creative Commons](http://creativecommons.org/licenses/by/4.0/)*\n", + "> *© 2026, Joris Van den Bossche and Stijn Van Hoey (, ). Licensed under [CC BY 4.0 Creative Commons](http://creativecommons.org/licenses/by/4.0/)*\n", "\n", "---" ] @@ -2729,6 +2729,7 @@ ], "metadata": { "jupytext": { + "default_lexer": "ipython3", "formats": "ipynb,md:myst" }, "kernelspec": { @@ -2746,7 +2747,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.12.8" + "version": "3.13.11" }, "widgets": { "application/vnd.jupyter.widget-state+json": { diff --git a/notebooks/pandas_05_groupby_operations.md b/notebooks/pandas_05_groupby_operations.md index 628f0af..e54a6cd 100644 --- a/notebooks/pandas_05_groupby_operations.md +++ b/notebooks/pandas_05_groupby_operations.md @@ -5,7 +5,7 @@ jupytext: extension: .md format_name: myst format_version: 0.13 - jupytext_version: 1.16.6 + jupytext_version: 1.18.1 kernelspec: display_name: Python 3 (ipykernel) language: python @@ -15,7 +15,7 @@ kernelspec:

05 - Pandas: "Group by" operations

-> *© 2025, Joris Van den Bossche and Stijn Van Hoey (, ). Licensed under [CC BY 4.0 Creative Commons](http://creativecommons.org/licenses/by/4.0/)* +> *© 2026, Joris Van den Bossche and Stijn Van Hoey (, ). Licensed under [CC BY 4.0 Creative Commons](http://creativecommons.org/licenses/by/4.0/)* --- diff --git a/notebooks/pandas_06_data_cleaning.ipynb b/notebooks/pandas_06_data_cleaning.ipynb index a6696ff..4d97910 100644 --- a/notebooks/pandas_06_data_cleaning.ipynb +++ b/notebooks/pandas_06_data_cleaning.ipynb @@ -7,7 +7,7 @@ "source": [ "

06 - Pandas: Methods for data cleaning

\n", "\n", - "> *© 2025, Joris Van den Bossche and Stijn Van Hoey (, ). Licensed under [CC BY 4.0 Creative Commons](http://creativecommons.org/licenses/by/4.0/)*\n", + "> *© 2026, Joris Van den Bossche and Stijn Van Hoey (, ). Licensed under [CC BY 4.0 Creative Commons](http://creativecommons.org/licenses/by/4.0/)*\n", "\n", "---" ] @@ -3187,6 +3187,9 @@ } ], "metadata": { + "jupytext": { + "default_lexer": "ipython3" + }, "kernelspec": { "display_name": "Python 3 (ipykernel)", "language": "python", @@ -3202,7 +3205,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.12.8" + "version": "3.13.11" }, "widgets": { "application/vnd.jupyter.widget-state+json": { diff --git a/notebooks/pandas_06_data_cleaning.md b/notebooks/pandas_06_data_cleaning.md index 7e3b525..bcd5683 100644 --- a/notebooks/pandas_06_data_cleaning.md +++ b/notebooks/pandas_06_data_cleaning.md @@ -4,7 +4,7 @@ jupytext: extension: .md format_name: myst format_version: 0.13 - jupytext_version: 1.16.6 + jupytext_version: 1.18.1 kernelspec: display_name: Python 3 (ipykernel) language: python @@ -13,7 +13,7 @@ kernelspec:

06 - Pandas: Methods for data cleaning

-> *© 2025, Joris Van den Bossche and Stijn Van Hoey (, ). Licensed under [CC BY 4.0 Creative Commons](http://creativecommons.org/licenses/by/4.0/)* +> *© 2026, Joris Van den Bossche and Stijn Van Hoey (, ). Licensed under [CC BY 4.0 Creative Commons](http://creativecommons.org/licenses/by/4.0/)* --- diff --git a/notebooks/pandas_07_missing_values.ipynb b/notebooks/pandas_07_missing_values.ipynb index 17149a4..3242f9d 100644 --- a/notebooks/pandas_07_missing_values.ipynb +++ b/notebooks/pandas_07_missing_values.ipynb @@ -8,7 +8,7 @@ "

07 - Pandas: Working with missing data

\n", "\n", "\n", - "> *© 2025, Joris Van den Bossche and Stijn Van Hoey (, ). Licensed under [CC BY 4.0 Creative Commons](http://creativecommons.org/licenses/by/4.0/)*\n", + "> *© 2026, Joris Van den Bossche and Stijn Van Hoey (, ). Licensed under [CC BY 4.0 Creative Commons](http://creativecommons.org/licenses/by/4.0/)*\n", "\n", "---" ] @@ -754,6 +754,7 @@ ], "metadata": { "jupytext": { + "default_lexer": "ipython3", "formats": "ipynb,md:myst" }, "kernelspec": { @@ -771,7 +772,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.12.8" + "version": "3.13.11" }, "widgets": { "application/vnd.jupyter.widget-state+json": { diff --git a/notebooks/pandas_07_missing_values.md b/notebooks/pandas_07_missing_values.md index 18ab96c..6a61bc4 100644 --- a/notebooks/pandas_07_missing_values.md +++ b/notebooks/pandas_07_missing_values.md @@ -5,7 +5,7 @@ jupytext: extension: .md format_name: myst format_version: 0.13 - jupytext_version: 1.16.6 + jupytext_version: 1.18.1 kernelspec: display_name: Python 3 (ipykernel) language: python @@ -15,7 +15,7 @@ kernelspec:

07 - Pandas: Working with missing data

-> *© 2025, Joris Van den Bossche and Stijn Van Hoey (, ). Licensed under [CC BY 4.0 Creative Commons](http://creativecommons.org/licenses/by/4.0/)* +> *© 2026, Joris Van den Bossche and Stijn Van Hoey (, ). Licensed under [CC BY 4.0 Creative Commons](http://creativecommons.org/licenses/by/4.0/)* --- diff --git a/notebooks/pandas_08_reshaping_data.ipynb b/notebooks/pandas_08_reshaping_data.ipynb index 254aa41..5417924 100644 --- a/notebooks/pandas_08_reshaping_data.ipynb +++ b/notebooks/pandas_08_reshaping_data.ipynb @@ -8,7 +8,7 @@ "

08 - Pandas: Tidy data and reshaping

\n", "\n", "\n", - "> *© 2025, Joris Van den Bossche and Stijn Van Hoey (, ). Licensed under [CC BY 4.0 Creative Commons](http://creativecommons.org/licenses/by/4.0/)*\n", + "> *© 2026, Joris Van den Bossche and Stijn Van Hoey (, ). Licensed under [CC BY 4.0 Creative Commons](http://creativecommons.org/licenses/by/4.0/)*\n", "\n", "---" ] @@ -4240,6 +4240,7 @@ ], "metadata": { "jupytext": { + "default_lexer": "ipython3", "formats": "ipynb,md:myst" }, "kernelspec": { @@ -4257,7 +4258,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.12.8" + "version": "3.13.11" }, "widgets": { "application/vnd.jupyter.widget-state+json": { diff --git a/notebooks/pandas_08_reshaping_data.md b/notebooks/pandas_08_reshaping_data.md index 9d21336..53164cf 100644 --- a/notebooks/pandas_08_reshaping_data.md +++ b/notebooks/pandas_08_reshaping_data.md @@ -5,7 +5,7 @@ jupytext: extension: .md format_name: myst format_version: 0.13 - jupytext_version: 1.16.6 + jupytext_version: 1.18.1 kernelspec: display_name: Python 3 (ipykernel) language: python @@ -15,7 +15,7 @@ kernelspec:

08 - Pandas: Tidy data and reshaping

-> *© 2025, Joris Van den Bossche and Stijn Van Hoey (, ). Licensed under [CC BY 4.0 Creative Commons](http://creativecommons.org/licenses/by/4.0/)* +> *© 2026, Joris Van den Bossche and Stijn Van Hoey (, ). Licensed under [CC BY 4.0 Creative Commons](http://creativecommons.org/licenses/by/4.0/)* --- diff --git a/notebooks/pandas_09_combining_datasets.ipynb b/notebooks/pandas_09_combining_datasets.ipynb index 8b71180..5657974 100644 --- a/notebooks/pandas_09_combining_datasets.ipynb +++ b/notebooks/pandas_09_combining_datasets.ipynb @@ -10,7 +10,7 @@ "

09 - Pandas: Combining datasets

\n", "\n", "\n", - "> *© 2025, Joris Van den Bossche and Stijn Van Hoey (, ). Licensed under [CC BY 4.0 Creative Commons](http://creativecommons.org/licenses/by/4.0/)*\n", + "> *© 2026, Joris Van den Bossche and Stijn Van Hoey (, ). Licensed under [CC BY 4.0 Creative Commons](http://creativecommons.org/licenses/by/4.0/)*\n", "\n", "---" ] @@ -4312,6 +4312,7 @@ ], "metadata": { "jupytext": { + "default_lexer": "ipython3", "formats": "ipynb,md:myst" }, "kernelspec": { @@ -4329,7 +4330,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.12.8" + "version": "3.13.11" }, "widgets": { "application/vnd.jupyter.widget-state+json": { diff --git a/notebooks/pandas_09_combining_datasets.md b/notebooks/pandas_09_combining_datasets.md index 826d340..582a9e7 100644 --- a/notebooks/pandas_09_combining_datasets.md +++ b/notebooks/pandas_09_combining_datasets.md @@ -5,7 +5,7 @@ jupytext: extension: .md format_name: myst format_version: 0.13 - jupytext_version: 1.16.6 + jupytext_version: 1.18.1 kernelspec: display_name: Python 3 (ipykernel) language: python @@ -15,7 +15,7 @@ kernelspec:

09 - Pandas: Combining datasets

-> *© 2025, Joris Van den Bossche and Stijn Van Hoey (, ). Licensed under [CC BY 4.0 Creative Commons](http://creativecommons.org/licenses/by/4.0/)* +> *© 2026, Joris Van den Bossche and Stijn Van Hoey (, ). Licensed under [CC BY 4.0 Creative Commons](http://creativecommons.org/licenses/by/4.0/)* --- diff --git a/notebooks/visualization_01_matplotlib.ipynb b/notebooks/visualization_01_matplotlib.ipynb index 9cd8cf2..4baa250 100644 --- a/notebooks/visualization_01_matplotlib.ipynb +++ b/notebooks/visualization_01_matplotlib.ipynb @@ -6,7 +6,7 @@ "source": [ "

Visualization - Matplotlib

\n", "\n", - "> *© 2025, Joris Van den Bossche and Stijn Van Hoey. Licensed under [CC BY 4.0 Creative Commons](http://creativecommons.org/licenses/by/4.0/)*\n", + "> *© 2026, Joris Van den Bossche and Stijn Van Hoey. Licensed under [CC BY 4.0 Creative Commons](http://creativecommons.org/licenses/by/4.0/)*\n", "\n", "---" ] @@ -1587,6 +1587,7 @@ ], "metadata": { "jupytext": { + "default_lexer": "ipython3", "formats": "ipynb,md:myst" }, "kernelspec": { @@ -1604,7 +1605,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.12.8" + "version": "3.13.11" }, "nav_menu": {}, "toc": { diff --git a/notebooks/visualization_01_matplotlib.md b/notebooks/visualization_01_matplotlib.md index 265d282..048f638 100644 --- a/notebooks/visualization_01_matplotlib.md +++ b/notebooks/visualization_01_matplotlib.md @@ -5,7 +5,7 @@ jupytext: extension: .md format_name: myst format_version: 0.13 - jupytext_version: 1.16.6 + jupytext_version: 1.18.1 kernelspec: display_name: Python 3 (ipykernel) language: python @@ -14,7 +14,7 @@ kernelspec:

Visualization - Matplotlib

-> *© 2025, Joris Van den Bossche and Stijn Van Hoey. Licensed under [CC BY 4.0 Creative Commons](http://creativecommons.org/licenses/by/4.0/)* +> *© 2026, Joris Van den Bossche and Stijn Van Hoey. Licensed under [CC BY 4.0 Creative Commons](http://creativecommons.org/licenses/by/4.0/)* --- diff --git a/notebooks/visualization_02_seaborn.ipynb b/notebooks/visualization_02_seaborn.ipynb index 92a0ef1..a9c066e 100644 --- a/notebooks/visualization_02_seaborn.ipynb +++ b/notebooks/visualization_02_seaborn.ipynb @@ -9,7 +9,7 @@ "

Visualisation: Seaborn

\n", "\n", "\n", - "> *© 2025, Joris Van den Bossche and Stijn Van Hoey (, ). Licensed under [CC BY 4.0 Creative Commons](http://creativecommons.org/licenses/by/4.0/)*\n", + "> *© 2026, Joris Van den Bossche and Stijn Van Hoey (, ). Licensed under [CC BY 4.0 Creative Commons](http://creativecommons.org/licenses/by/4.0/)*\n", "\n", "---" ] @@ -2511,6 +2511,7 @@ "metadata": { "celltoolbar": "Nbtutor - export exercises", "jupytext": { + "default_lexer": "ipython3", "formats": "ipynb,md:myst" }, "kernelspec": { @@ -2528,7 +2529,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.12.8" + "version": "3.13.11" }, "nav_menu": {}, "toc": { diff --git a/notebooks/visualization_02_seaborn.md b/notebooks/visualization_02_seaborn.md index b8aeb58..63b2429 100644 --- a/notebooks/visualization_02_seaborn.md +++ b/notebooks/visualization_02_seaborn.md @@ -5,7 +5,7 @@ jupytext: extension: .md format_name: myst format_version: 0.13 - jupytext_version: 1.16.6 + jupytext_version: 1.18.1 kernelspec: display_name: Python 3 (ipykernel) language: python @@ -15,7 +15,7 @@ kernelspec:

Visualisation: Seaborn

-> *© 2025, Joris Van den Bossche and Stijn Van Hoey (, ). Licensed under [CC BY 4.0 Creative Commons](http://creativecommons.org/licenses/by/4.0/)* +> *© 2026, Joris Van den Bossche and Stijn Van Hoey (, ). Licensed under [CC BY 4.0 Creative Commons](http://creativecommons.org/licenses/by/4.0/)* --- diff --git a/notebooks/visualization_03_landscape.ipynb b/notebooks/visualization_03_landscape.ipynb index b52224a..9abbe66 100644 --- a/notebooks/visualization_03_landscape.ipynb +++ b/notebooks/visualization_03_landscape.ipynb @@ -6,7 +6,7 @@ "source": [ "

Visualization - Python's Visualization Landscape

\n", "\n", - "> *© 2025, Joris Van den Bossche and Stijn Van Hoey (, ). Licensed under [CC BY 4.0 Creative Commons](http://creativecommons.org/licenses/by/4.0/)*\n", + "> *© 2026, Joris Van den Bossche and Stijn Van Hoey (, ). Licensed under [CC BY 4.0 Creative Commons](http://creativecommons.org/licenses/by/4.0/)*\n", "\n", "---" ] @@ -1160,6 +1160,7 @@ ], "metadata": { "jupytext": { + "default_lexer": "ipython3", "formats": "ipynb,md:myst" }, "kernelspec": { @@ -1177,7 +1178,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.12.8" + "version": "3.13.11" }, "widgets": { "application/vnd.jupyter.widget-state+json": { diff --git a/notebooks/visualization_03_landscape.md b/notebooks/visualization_03_landscape.md index 75aaa2e..1d31a63 100644 --- a/notebooks/visualization_03_landscape.md +++ b/notebooks/visualization_03_landscape.md @@ -5,7 +5,7 @@ jupytext: extension: .md format_name: myst format_version: 0.13 - jupytext_version: 1.16.6 + jupytext_version: 1.18.1 kernelspec: display_name: Python 3 (ipykernel) language: python @@ -14,7 +14,7 @@ kernelspec:

Visualization - Python's Visualization Landscape

-> *© 2025, Joris Van den Bossche and Stijn Van Hoey (, ). Licensed under [CC BY 4.0 Creative Commons](http://creativecommons.org/licenses/by/4.0/)* +> *© 2026, Joris Van den Bossche and Stijn Van Hoey (, ). Licensed under [CC BY 4.0 Creative Commons](http://creativecommons.org/licenses/by/4.0/)* --- From 8a583a60e4e3b3720995e1f5ee39bb8afaf5567a Mon Sep 17 00:00:00 2001 From: Joris Van den Bossche Date: Tue, 13 Jan 2026 17:57:55 +0100 Subject: [PATCH 3/5] update links in bacterial case study --- notebooks/case3_bacterial_resistance_lab_experiment.ipynb | 8 ++++---- notebooks/case3_bacterial_resistance_lab_experiment.md | 8 ++++---- 2 files changed, 8 insertions(+), 8 deletions(-) diff --git a/notebooks/case3_bacterial_resistance_lab_experiment.ipynb b/notebooks/case3_bacterial_resistance_lab_experiment.ipynb index 3326fa6..bef3651 100644 --- a/notebooks/case3_bacterial_resistance_lab_experiment.ipynb +++ b/notebooks/case3_bacterial_resistance_lab_experiment.ipynb @@ -17,7 +17,7 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "In this case study, we will make use of the open data, affiliated to the following [journal article](http://rsbl.royalsocietypublishing.org/content/12/5/20160064):\n", + "In this case study, we will make use of the open data, affiliated to the following [journal article](https://royalsocietypublishing.org/rsbl/article/12/5/20160064/50398/Effects-of-antibiotic-resistance-alleles-on):\n", "\n", ">Arias-Sánchez FI, Hall A (2016) Effects of antibiotic resistance alleles on bacterial evolutionary responses to viral parasites. Biology Letters 12(5): 20160064. https://doi.org/10.1098/rsbl.2016.0064" ] @@ -33,7 +33,7 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "Check the full paper on the [web version](http://rsbl.royalsocietypublishing.org/content/12/5/20160064). The study handles:\n", + "Check the full paper on the [web version](https://royalsocietypublishing.org/rsbl/article/12/5/20160064/50398/Effects-of-antibiotic-resistance-alleles-on). The study handles:\n", "> Antibiotic resistance has wide-ranging effects on bacterial phenotypes and evolution. However, the influence of antibiotic resistance on bacterial responses to parasitic viruses remains unclear, despite the ubiquity of such viruses in nature and current interest in therapeutic applications. We experimentally investigated this by exposing various Escherichia coli genotypes, including eight antibiotic-resistant genotypes and a mutator, to different viruses (lytic bacteriophages). Across 960 populations, we measured changes in population density and sensitivity to viruses, and tested whether variation among bacterial genotypes was explained by their relative growth in the absence of parasites, or mutation rate towards phage resistance measured by fluctuation tests for each phage" ] }, @@ -1353,9 +1353,9 @@ "tags": [] }, "source": [ - "Check Figure 2 of the original journal paper in the 'correction' part of the pdf:\n", + "Check Figure 2 in the results section of the original paper:\n", "\n", - "" + "" ] }, { diff --git a/notebooks/case3_bacterial_resistance_lab_experiment.md b/notebooks/case3_bacterial_resistance_lab_experiment.md index c072ea7..0d919b1 100644 --- a/notebooks/case3_bacterial_resistance_lab_experiment.md +++ b/notebooks/case3_bacterial_resistance_lab_experiment.md @@ -20,7 +20,7 @@ kernelspec: +++ -In this case study, we will make use of the open data, affiliated to the following [journal article](http://rsbl.royalsocietypublishing.org/content/12/5/20160064): +In this case study, we will make use of the open data, affiliated to the following [journal article](https://royalsocietypublishing.org/rsbl/article/12/5/20160064/50398/Effects-of-antibiotic-resistance-alleles-on): >Arias-Sánchez FI, Hall A (2016) Effects of antibiotic resistance alleles on bacterial evolutionary responses to viral parasites. Biology Letters 12(5): 20160064. https://doi.org/10.1098/rsbl.2016.0064 @@ -30,7 +30,7 @@ In this case study, we will make use of the open data, affiliated to the followi +++ -Check the full paper on the [web version](http://rsbl.royalsocietypublishing.org/content/12/5/20160064). The study handles: +Check the full paper on the [web version](https://royalsocietypublishing.org/rsbl/article/12/5/20160064/50398/Effects-of-antibiotic-resistance-alleles-on). The study handles: > Antibiotic resistance has wide-ranging effects on bacterial phenotypes and evolution. However, the influence of antibiotic resistance on bacterial responses to parasitic viruses remains unclear, despite the ubiquity of such viruses in nature and current interest in therapeutic applications. We experimentally investigated this by exposing various Escherichia coli genotypes, including eight antibiotic-resistant genotypes and a mutator, to different viruses (lytic bacteriophages). Across 960 populations, we measured changes in population density and sensitivity to viruses, and tested whether variation among bacterial genotypes was explained by their relative growth in the absence of parasites, or mutation rate towards phage resistance measured by fluctuation tests for each phage ```{code-cell} ipython3 @@ -294,9 +294,9 @@ sns.catplot(data=density_mean, kind="bar", +++ -Check Figure 2 of the original journal paper in the 'correction' part of the pdf: +Check Figure 2 in the results section of the original paper: - + ```{code-cell} ipython3 falcor.head() From 45713b771144e882ddc6052d14e35dab24911d04 Mon Sep 17 00:00:00 2001 From: Joris Van den Bossche Date: Tue, 13 Jan 2026 18:17:45 +0100 Subject: [PATCH 4/5] update link in air quality notebooks --- notebooks/case4_air_quality_analysis.ipynb | 2 +- notebooks/case4_air_quality_analysis.md | 2 +- notebooks/case4_air_quality_processing.ipynb | 2 +- notebooks/case4_air_quality_processing.md | 2 +- 4 files changed, 4 insertions(+), 4 deletions(-) diff --git a/notebooks/case4_air_quality_analysis.ipynb b/notebooks/case4_air_quality_analysis.ipynb index fc66e2a..64b08e1 100644 --- a/notebooks/case4_air_quality_analysis.ipynb +++ b/notebooks/case4_air_quality_analysis.ipynb @@ -39,7 +39,7 @@ "- BETR802: urban traffic site in Antwerp, Belgium\n", "- BETN029: rural background site in Houtem, Belgium\n", "\n", - "See http://www.eea.europa.eu/themes/air/interactive/no2" + "See https://www.eea.europa.eu/en/topics/in-depth/air-pollution" ] }, { diff --git a/notebooks/case4_air_quality_analysis.md b/notebooks/case4_air_quality_analysis.md index a527b53..60581b3 100644 --- a/notebooks/case4_air_quality_analysis.md +++ b/notebooks/case4_air_quality_analysis.md @@ -31,7 +31,7 @@ We processed some raw data files of the AirBase air quality data. The data conta - BETR802: urban traffic site in Antwerp, Belgium - BETN029: rural background site in Houtem, Belgium -See http://www.eea.europa.eu/themes/air/interactive/no2 +See https://www.eea.europa.eu/en/topics/in-depth/air-pollution +++ diff --git a/notebooks/case4_air_quality_processing.ipynb b/notebooks/case4_air_quality_processing.ipynb index f11dc6e..3dbbd86 100644 --- a/notebooks/case4_air_quality_processing.ipynb +++ b/notebooks/case4_air_quality_processing.ipynb @@ -29,7 +29,7 @@ "- BETR802: urban traffic site in Antwerp, Belgium\n", "- BETN029: rural background site in Houtem, Belgium\n", "\n", - "See http://www.eea.europa.eu/themes/air/interactive/no2" + "See https://www.eea.europa.eu/en/topics/in-depth/air-pollution" ] }, { diff --git a/notebooks/case4_air_quality_processing.md b/notebooks/case4_air_quality_processing.md index 18d8168..2ac9005 100644 --- a/notebooks/case4_air_quality_processing.md +++ b/notebooks/case4_air_quality_processing.md @@ -31,7 +31,7 @@ Some of the data files that are available from AirBase were included in the data - BETR802: urban traffic site in Antwerp, Belgium - BETN029: rural background site in Houtem, Belgium -See http://www.eea.europa.eu/themes/air/interactive/no2 +See https://www.eea.europa.eu/en/topics/in-depth/air-pollution ```{code-cell} ipython3 import pandas as pd From 1fe30653e173d0dfd3c0ed109c52c2f08e2ee81b Mon Sep 17 00:00:00 2001 From: Joris Van den Bossche Date: Tue, 13 Jan 2026 18:18:55 +0100 Subject: [PATCH 5/5] fixup slide change --- web/templates/slides.html.tmpl | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/web/templates/slides.html.tmpl b/web/templates/slides.html.tmpl index f9a6c4c..7ed9e34 100644 --- a/web/templates/slides.html.tmpl +++ b/web/templates/slides.html.tmpl @@ -153,7 +153,7 @@ class: middle, section_background Creating a new environment: ``` -conda create -n my_env python=3.3 pandas +conda create -n my_env python=3.13 pandas # or from environment file conda env create -f environment.yml