Merge pull request #15 from gjbex/development

Adapt for pandas 2.x

Author: gjbex

environment.yml

@@ -1,7 +1,6 @@
 name: python_for_data_science
 channels:
   - conda-forge
-  - defaults
 dependencies:
   - gdal
   - networkx
@@ -41,4 +40,8 @@ dependencies:
   - sqlalchemy
   - plotly
   - beautifulsoup4
-prefix: /home/gjb/miniconda3/envs/python_for_data_science
+  - lxml
+  - ca-certificates
+  - certifi
+  - openssl
+prefix: /home/gjb/mambaforge/envs/python_for_data_science

python_for_data_science_linux64_conda_specs.txt

@@ -1,2 +1,3 @@
 .ipynb_checkpoints
 random_data.csv
+genes_table.html

source-code/pandas/.gitignore

@@ -22,6 +22,5 @@ easy to use.
 1. `patients.ipynb`: runninng example used in the Python slides.
 1. `patient_data.ipynb`: extended version of therunninng example used
     in the Python slides.
-1. `bokeh_plot.ipynb`: using Bokeh as a plotting beackdnd for pandas.
 1. `pipes.ipynb`: consolidating data processing using pipes.
 1. `screenshots`: screenshots made for the slides.

source-code/pandas/README.md

@@ -0,0 +1,12 @@
+# Bokeh
+
+You can use Bokeh as a plotting backend for pandas.
+
+## What is it?
+
+1. `bokeh_plot.ipynb`: using Bokeh as a plotting beackdnd for pandas.
+1. `environment.yml`: conda environment required to run the notebook.
+1. `pandas_bokeh_linux64_conda_specs.txt`: conda environment specification.
+
+*Note:* currently (2023-03-22) the bokeh backend for pandas requires
+bokeh 2.x, and that has to be specified as an explicit dependency.

source-code/pandas/agt_analysis.ipynb

@@ -0,0 +1,12 @@
+name: pandas_bokeh
+channels:
+  - conda-forge
+  - patrikhlobil
+dependencies:
+  - pandas-bokeh
+  - bokeh==2.4.3
+  - pandas
+  - jupyterlab
+  - ca-certificates
+  - openssl
+prefix: /home/gjb/mambaforge/envs/pandas_bokeh

source-code/pandas/bokeh/README.md

@@ -0,0 +1,161 @@
+# This file may be used to create an environment using:
+# $ conda create --name <env> --file <this file>
+# platform: linux-64
+@EXPLICIT
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