Forem: anatlavitzkovitz

osdc-2023-assignment8

anatlavitzkovitz — Sun, 19 Mar 2023 07:41:59 +0000

Running local tests

assignment 8
I cloned requests git, build a docker and run the tests, follwing this link:

git clone git@github.com:psf/requests.git
docker run -it --rm --workdir /opt -v$(pwd):/opt python:3.11 bash
pip install -r requirements-dev.txt
pip install tox
make test

this is the print:

tox -p
py38-use_chardet_on_py3: SKIP ⚠ in 0.3 seconds
py37-default: SKIP ⚠ in 0.33 seconds
py38-default: SKIP ⚠ in 0.36 seconds
py310-use_chardet_on_py3: SKIP ⚠ in 0.37 seconds
py37-use_chardet_on_py3: SKIP ⚠ in 0.39 seconds
py310-default: SKIP ⚠ in 0.38 seconds
⠴ [4/10] py39-default | py39-use_chardet_on_py3 | py311-default | py311-use_chardet_on_py3
⠧ [4/10] py39-default | py39-use_chardet_on_py3 | py311-default | py311-use_chardet_on_py3
py39-default: OK ✔ in 1 minute 32.45 seconds
py39-use_chardet_on_py3: OK ✔ in 1 minute 32.68 seconds
py311-default: OK ✔ in 1 minute 32.79 seconds
py37-default: SKIP (0.32 seconds)
py37-use_chardet_on_py3: SKIP (0.39 seconds)
py38-default: SKIP (0.36 seconds)
py38-use_chardet_on_py3: SKIP (0.30 seconds)
py39-default: OK (92.44=setup[19.63]+cmd[72.81] seconds)
py39-use_chardet_on_py3: OK (92.68=setup[19.59]+cmd[73.09] seconds)
py310-default: SKIP (0.35 seconds)
py310-use_chardet_on_py3: SKIP (0.36 seconds)
py311-default: OK (92.79=setup[19.96]+cmd[72.83] seconds)
py311-use_chardet_on_py3: OK (92.90=setup[20.11]+cmd[72.79] seconds)
congratulations :) (92.99 seconds)

pip install pytest-random-order pytest-coverage
pytest -svv --random-order --cov-config .coveragerc --cov=requests --cov-report html --cov-report term --cov-branch

This is the result:

---------- coverage: platform linux, python 3.11.2-final-0 -----------

Name Stmts Miss Branch BrPart Cover

requests/init.py 68 68 10 0 0%
requests/version.py 10 10 0 0 0%
requests/_internal_utils.py 21 11 2 0 52%
requests/adapters.py 216 62 78 8 76%
requests/api.py 19 12 2 0 43%
requests/auth.py 173 53 60 15 70%
requests/certs.py 4 4 2 0 0%
requests/compat.py 30 30 2 0 0%
requests/cookies.py 239 116 104 9 52%
requests/exceptions.py 37 29 2 0 26%
requests/help.py 62 20 18 5 59%
requests/hooks.py 14 3 10 0 88%
requests/models.py 456 121 212 18 76%
requests/packages.py 17 17 10 0 0%
requests/sessions.py 268 61 100 4 82%
requests/status_codes.py 14 14 10 0 0%
requests/structures.py 39 18 8 0 62%

requests/utils.py 485 158 224 12 71%

TOTAL 2172 807 854 71 66%
Coverage HTML written to dir htmlcov

class notes:

My last change in author name will not be shown in pydigger, because it takes the data from pypi and not from github.

Webhooks:
whenever there is a change, github sends a json file with an update. updates the website with new slides with every push.
You can add a url via settings.
This can be set that only if github actions works, the slides are updated.

stash

What if I have some local changes but I need to pull the last version? start from the beginning? I can save my changes with stash, pull the repo and than pop the stashed data. how?

git stash  # saves local changes on the side.
git pull
git stash pop  #takes the last change and adds or number. if there is no conflict, it will be deleted.
git stash list
git stash show (0/1) #shows the last

patch is the same as diff
git stash drop 0 # will through away 0

docker

docker image: playground
How to build a docker image and publish it in dockerhub?

docker login
docker build -t szabgab/playground:latest #build an image from a docker file
docker push #push to dockerhub

This will first search locally for an image, or will pull from dockerhub if doesn't exist:

docker run -it -rm ...szabgab/playground:latest # pulls from dockerhub

run python tests localy

Gabor cloned python requests.

jinja - a good example for a good repo (same as flask)

Gabor has a dev.to on this with a docker image run command.
via .github/actions you can understand how to run the test.
runs a make.
goto makfile.

make test #- dosent work
make
pytest test #-random_order #will run in a random order.
```

osdc-2023-assignment7

anatlavitzkovitz — Mon, 06 Mar 2023 21:16:03 +0000

Contributing to open projects

assignment 7

Contribute to pydigger: I decided to contribute an author name for pydigger

I found this repo, without an author name.

This is what I wrote in my pull request:
"Hi. I am taking an open source project course https://github.com/OSDC-Code-Maven/osdc-2023-01-public
and try to contribute to projects without an author name. to be added here: https://pydigger.com/."

my pull request

Waiting for a reply!

update: My pull request was excepted and merged! (-:

Running R tests locally

This is my next task...
I work with a package in R called CrispRVariants.

I cloned it to my server and activated an R conda environment I have there.
Now I could do:

Rscript testthat.R

I received the following message:

Loading required package: CrispRVariants
Loading required package: ggplot2

[ FAIL 0 | WARN 2 | SKIP 0 | PASS 20 ]

seems that something worked.
Also I found that there is a package to test coverage similar to python in (here)[https://github.com/IainMcl/R-Unit-Testing]

install.packages(covr)
library(covr)
report()

I need to test this.

Lesson notes:

Example on how to write an issue
Problem in dev.to:
in dev.to if you do save changes your are out of the editor. how can this be fixed? maybe add an automated saving, or save and keep on editing.
If we go down on GitHub page there is a link to Forem. Going to forem and link to github. one repo is forem.
Forem/forem issues - search for autosave
shuly suggested an issue to add autosave here but got no reply.

another example: zarr-python
First search the issues - maybe someone else had a similar problem?

codecove - which lines were running during the test
this can show absence of tests
this can show us if a code was not tested after a change.
but if a test was not written, a piece of code will not be tested. high coverage doesn't mean good code but low coverage will show that not all the code is being tested.

You can try to promote a pull request

What if it doesn't work and you don't want to wait?
you can fix the issue locally and put in pypl with shaw - not recommended.
or you can make a fork and accept the pull request.

how?
dr - a basic docker file with alias in basrc for Gabor called dr.
Gabor has it in GitHub.

git clone ...
git fetch origin (default name) pull/1357/head
git checkout -b b1357 FETCH_HEAD
git lg
git show HEAD
git checkout main
git checkout -b szabgab
git merge 1357
gitk --all

now you can use this repo.
better that he would do rebase...

Now we can add another PR:

git checkout -b b1299 FETCH_HEAD

but this time there is a conflict.

a conflict
If you make a change in a different line - no problem to merge branch and main. changes to the same line- merge has a conflict. The change is in the text itself, not the raw number.
Now you can manually edit the new file and add it after that.

You can cancel the commit like this:

git merge --abort

how to find projects in R?

explore/topics 'r'
add languages : R
recently updated better than more stars.

wcgenesummary
add contribution, find tests that can be run locally. this is the best practice for running the test.

ggplots - open issue how to run a test?
testhat? maybe this is very simple to run.

to do
how to run a test, open a pull request. how to make test coverage? send a pull requst. what test is missing, write it.
good way - run the test case and compare to the output. make this as a test.

osdc-2023-assignment5

anatlavitzkovitz — Thu, 09 Feb 2023 20:15:00 +0000

How to make my own repository and edit it locally?

Unfortunately I missed lesson 4, but I was in Amsterdam so at least had some fun.
I decided to make my own R plot repository in GitHub, as I use R a lot and many times I repeat my code. I think this could be useful although I am sure there are many similar repositories.

How?
I wrote a first piece of R code and put that in a linux server which have R installed. I wrote a short R script and saved it, and did:

git status
git add 'main.R'
git commit -m "my first script in my new R rep0"

Now I went to GitHub and opened a new repo.

back to the remote I wrote:

git remote add origin git@github.com:anatlavitzkovitz/visualization_with_R.git
git branch -M main
git push -u origin main

but...
Permission denied (publickey).
fatal: Could not read from remote repository.

oh.... I forgot to add the ssh key to my GitHub keys.
After doing that (explained in more details here)- it worked.

I added a README file via GitHub with some details. It still needs a lot more work but I hope to add some more details and code soon.

##########

How to clone and make local changes to another open source project?

I entered some of my colleagues Shuly's repo
and Adi's repo and added
some issues.

now I want to make some pull requests to my friend's repos @shulyavraham:

git clone git@github.com:ShulyAvraham/LIMS_results_validation.git
git checkout -b addrequirements

Now add some changed such as:
added #test to requirements.txt (not a very useful package..)

git add requirements.txt
git commit -m "updated requirements.txt"
git push

ERROR: Permission to ShulyAvraham/LIMS_results_validation.git denied to anatlavitzkovitz.
fatal: Could not read from remote repository.

Please make sure you have the correct access rights
and the repository exists.

ha ha... I need to make my fork and than a pull request from there!

I went to Shuly's repo
and made a fork. back to my remote now:

git remote add fork git@github.com:anatlavitzkovitz/LIMS_results_validation.git

git remote -v
fork    https://github.com/anatlavitzkovitz/LIMS_results_validation (fetch)
fork    https://github.com/anatlavitzkovitz/LIMS_results_validation (push)
origin  git@github.com:ShulyAvraham/LIMS_results_validation.git (fetch)
origin  git@github.com:anatlavitzkovitz/LIMS_results_validation.git (push)

git push --set-upstream fork addrequirements

now I have a pull request in my fork. send to Shuly!

osdc-2023-assignment3

anatlavitzkovitz — Fri, 27 Jan 2023 20:20:02 +0000

In our 3rd lesson of osdc we learnt how to work locally. Our assignment was to work locally on windows, clone our GitHub website, make some changes and push back to the main repo.
How?
I installed git on my windows laptop, and opened git bash.
In the terminal I wrote:
ssh-keygen.exe
in .ssh/ I found a paired-key, public and private.
cat .ssh/id_rsa.pub and place in GitHub - go to my profile setting-> SSH and GPG keys-> new SSH key. give it a title, paste the key and press 'Add SSH key'.
Now I can go to my repository on GitHub, press the green "code" button on the upper right corner, copy the SSH one and do 'git clone copied SSH address' in the terminal.
Doing this on my local git bash, allowed me to clone the repo.

But...It only worked when I defined driver C as my home directory and worked without VPN.

I could now add a file named "test_locally.txt" to the docs folder, and than do:

git status
git add test_locally.txt
git commit -m "test working locally"
git push

It works!

But than my pull request failed. I don't know why )-:

osdc-2023-assignment2

anatlavitzkovitz — Mon, 16 Jan 2023 19:06:23 +0000

My first assignment in osdc 2 was to follow all my course friends who already have a dev.to account:
@shulyavraham
@adieg
@yoadk
@silent_mobius
@dshisher
@anatlavitzkovitz
@avivyunker

Next, I created GitHub page. How?
in My GitHub I created a new repository with my name, in general: github_username.github.io.
Within this rep I create a docs folder and in the docs folder create a file called index.md. containing the context of my website and even with a painting of me done by my talented mom.
I added links to my GitHub and GitLab repositories, to my blog at dev.to and to the course.

I added my CV in Markdown to docs/cv.md: cv

In the setting of my webpage, I changed pages to deploy main branch from docs/. how? like this:
Go to Settings->Pages->Deploy from a branch->main ->Select /Docs->Save.

To add a colored background I added a file to docs/ called _config.yml, containing the following markdown colored theme:
theme: jekyll-theme-cayman.

Finally, I pushed this post in to my json in OSDC:
pull request

Time investment:
2.5 hours

osdc-2023-assignment1

anatlavitzkovitz — Mon, 09 Jan 2023 20:34:41 +0000

I just started OSDC 2023 course with @szabgab OSDC and here is my first assignment:

This is my github

This is my Gitlab

I chose baby yoda as my profile picture because me and my family like watching Star Wars movies together, and I like the idea of a small guy who is more than meets the eye..

A little about me

-I am a bioinformatician and I love biology.

-I program mainly in R, Python and Shell.

-Here are some packages I use:

-What do I want to accomplish in this course?
First to learn and enjoy. Than to gain practical knowledge that will improve my daily work.

-Which open source projects would you like to contribute to?
Maybe one of the above I mentioned, still need to think about it.

Time investment:

1.5 hour for: open gitLab account, define participants json, create dev account, update linkedin url, send pull request, update github and dev profile picture.
1 hour for: write the blog, fixing pull requests issues.
1 hour for: find github for corporations and universities, update the blog.

a note about a pull request:
pull request
As my gitlab user name was not corrected in the json file, there was a special test just for me in the test_json.py file. after updating the username in the json file I had also to update the match regex that finds the username to also include a dot, as my user name 'anat.lavitz' contains a dot.

What are friends for?
Here is a link to my team mate Shuly and her post:
blog1

blog2

updating the corporations repos with 3 sequencing companies:
Illumina
nanopore
Pacbio
This is the pull request:
pull request

and the non-profit repo with the Broad institute git:
Broad Institute
This is the pull request:
pull request