add content from EDS-213 lesson

preserve_computing-env.qmd

@@ -15,4 +15,357 @@ In Python:
 
 ### Virtual environments
 
-You can even go a step further and help others to recreate the same computing environment that you used independently of what versions you have installed on your machine: <https://rstudio.github.io/renv/articles/renv.html>
+You can even go a step further and help others to recreate the same computing environment that you used independently of what versions you have installed on your machine.
+
+[Level up!](https://media.giphy.com/media/v1.Y2lkPTc5MGI3NjExemkwd3RnMzA4a3FocHZ2bWJscHgxNG9yaW4yeGZ6YzZpaXgzNHJhciZlcD12MV9pbnRlcm5hbF9naWZfYnlfaWQmY3Q9Zw/x2woMnCz4W0Vy/giphy.gif)
+
+
+
+#### R
+
+Here is a short introduction to `renv`, an R package that creates virtual environment to encapsulate your R work. ![source: https://rstudio.github.io/renv/articles/renv.html](../../img/renv.png)
+
+We are going to add renv to our shorebird data cleaning project. Make
+sure you have the renv package installed:
+
+```r
+install.packages("renv")
+```
+
+You may also choose Tools>Project Options>Environments and check "use
+renv for this project"
+
+Or at the R console:
+
+```r
+renv::init( )
+```
+
+Let's check the new files that we have...
+
+- Look at the .gitignore
+- Look at the renv.lock file
+
+Let's say we reworked our script and suppose we would need the
+[naniar](https://cran.r-project.org/web/packages/naniar/vignettes/getting-started-w-naniar.html)
+R package to deal with the NAs. Let's update or virtual environment:
+
+```r
+renv::install("naniar")
+```
+Add some R code using this package, for example
+
+```r
+library(naniar)
+
+snowsurvey_csv %>% 
+  miss_var_summary()
+```
+
+Alright, now that the installation is completed and we added this package to our code, we can save, and take a snapshot:
+
+```r
+renv::snapshot()
+```
+
+This action will update the lock file, and we will see naniar and all
+its dependencies included.
+
+Let's check. If updated, you should be good to go. If your attempts to
+update packages introduced new problems, you may run `renv::restore()` to
+revert to the previous state as encoded in the lockfile.
+
+Use `.libPaths()` to confirm where package installations are located!
+
+Want to know more? here is a good resource to get started: <https://rstudio.github.io/renv/articles/renv.html>
+
+
+#### Python
+
+[`virtualenv`](https://docs.python-guide.org/dev/virtualenvs/#lower-level-virtualenv) is a tool to create Python virtual environments. In a nutsheel here are the steps to follow:
+
+ Create a new folder, your project folder. I will use EDS213. Make
+    sure you set the path to this folder.
+
+-   Note: The environment will be created in the current version of
+    Python that you are running (in Conda we can specify the version we
+    want).
+
+To create the environment: (second venv is the name of the environment)
+
+```bash
+python3 -m venv venv213
+```
+
+-   The `-m` flag makes sure you are creating a pip that is tied to the
+    active Python executable
+
+**Time to activate it:**
+
+```bash
+source venv213/bin/activate
+```
+
+You can tell it is activated because it shows (venv213) in the prompt.
+
+Let's check which packages are there with a new `pip list`
+
+Nothing, right? Only setup tools, and pip). Nothing to worry about, it
+should be this way! Let's proceed.
+
+**Install libraries:**
+
+We will be installing two packages for this exercise.
+
+First:
+
+```bash
+pip install numpy
+```
+
+And then:
+
+```bash
+pip install pandas
+```
+
+_This should take a little longer!_
+
+Another `pip list`
+
+Alright, the packages and dependencies installed are right there!
+
+
+**Export and allow future replication of the environment:**
+
+Let's save the packages and dependencies we have after the installs.
+
+```bash
+pip freeze
+```
+
+That should be stored in a `requirements.txt file
+
+So let's get it redirected to the required file:
+
+```bash
+pip freeze > requirements.txt
+```
+
+Question: This file won't leave inside the venv folder, but rather in
+the project root folder any idea why?
+
+Well, you only need that file to reproduce the environment. And the venv
+should be should throw away and be able to rebuild easily! So, do not
+include any project file in that folder and treat that as disposable
+after the pip freeze
+
+To double-check if all is good, we can run the following command:
+
+```bash
+cat requirements.txt
+```
+
+This file should be included in your repository to let others
+reinstall your packages and dependencies as needed.
+
+**Deactivate**
+
+If you are done with that, you should deactivate that environment by
+typing:
+
+```bash
+deactivate
+```
+
+Then, you will see you no longer have the environment we created in our
+prompt.
+
+If you are willing to delete the environment altogether, you should
+delete the directory for the virtual environment
+
+Remove folder:
+
+```bash
+rm -rf venv213/
+```
+
+**Reusing the Requirements**
+
+*Create a new project folder to reuse the requirements*
+
+```bash
+mkdir my-project
+```
+
+*Create a virtual env for it*
+
+```bash
+python3 -m venv my-project/venv
+```
+
+*Activate it*
+
+```bash
+source my-project/venv/bin/activate
+```
+
+*Install required packages*
+
+```bash
+pip install -r requirements.txt
+```
+
+-   Attention! Never include project files in the venv folder.
+
+-   Do not commit your venv file to the environment itself to source
+    control (git ignore)
+
+-   You may install more packages and update the requirements.txt with
+    the pip freeze command
+
+-   You should commit /share only your requirements.txt file. That is
+    all that others and your future self need to recreate the
+    environment.
+
+-   The environment should be something you should throw away and be
+    able to rebuild easily.
+
+-   Make sure to deactivate when done using it.
+
+
+#### If you are using Conda
+
+**Checking what is in the system:**
+
+conda list
+
+To create the environment:
+
+```bash
+conda create --name env213
+```
+
+proceed (\[y\]/n)? y
+
+Time to activate it
+
+conda activate env213 only work on conda 4.6 and later versions. For
+Conda versions prior to 4.6, run:
+
+-   Windows: activate or Linux and macOS: source activate
+
+You can tell it is activated because it shows (venv213) in the prompt.
+
+Let's check which packages are there with a new 
+
+```bash
+conda list env213
+```
+
+Empty, right? Nothing to worry about, it should be this way! Let's
+proceed.
+
+**Install packages:**
+
+We will be installing two packages for this exercise.
+
+First:
+
+```bash
+conda install numpy
+```
+
+proceed (\[y\]/n)? y
+
+And then, one more package:
+
+```bash
+conda install Pandas
+```
+
+proceed (\[y\]/n)? y
+
+Now check which packages are in the specific environment we are working
+on:
+
+```bash
+conda list
+```
+
+Alright, the packages and dependencies installed are right there!
+
+**Export and allow future replication of the environment:**
+
+Let's save the packages and dependencies we have after the installs.
+
+```bash
+conda list --export
+```
+
+That should be stored in a environments.yml file
+
+So let's get it redirected to the required file:
+
+```bash
+conda list -e > environment.yml
+```
+
+This file should be included in your research compendium to let others
+reinstall your packages and dependencies as needed.
+
+**Deactivate it:**
+
+If you are done with that, you should deactivate that environment by
+typing:
+
+```bash
+conda deactivate
+```
+
+Note: only works on conda 4.6 and later versions. For conda
+versions before 4.6, run:
+
+Windows: `deactivate` or Linux and macOS: `source deactivate`
+
+Then, you will see you no longer have the environment we created in our
+prompt.
+
+If you are willing to delete the environment altogether, you should
+delete the directory for the virtual environment
+
+**Back to base we can create a new environment based on the .yml
+packages and dependencies by running (this is noted on top of the yml
+file):**
+
+```bash
+conda create --name my-env --file environment.yml
+```
+
+proceed (\[y\]/n)? y
+
+**Activate it:**
+
+```bash
+conda activate my-env (or see above if conda version \< 4.6)
+```
+
+proceed (\[y\]/n)? Y
+
+**Check if packages are there:**
+
+```bash
+conda list
+```
+**Remember to deactivate it when done:**
+
+```bash
+conda deactivate (or see above if conda version \< 4.6)
+```
+
+Check all your environments `conda env list`
+
+More info:
+[[https://conda.io/projects/conda/en/latest/user-guide/tasks/manage-environments.html]{.underline}](https://conda.io/projects/conda/en/latest/user-guide/tasks/manage-environments.html)
+
+