zainabnazari

# First, make sure you have a backup of your repository or any important files, as this process is irreversible.
git rm -r folder_name
git commit -m "Remove folder_name from repository"

By default, Git retains the history of commits, even for deleted files or folders.
To delete the history and make it easier to push the changes, you can use the git filter-branch command. Run the following command:
git filter-branch --force --index-filter 'git rm -r --cached --ignore-unmatch folder_name' --prune-empty --tag-name-filter cat -- --all

Once the filter-branch operation completes, the history of the folder will be deleted. However, the commits are still present in your local repository. 
To remove them completely, you can run the following command:

zainabnazari

#!/bin/bash
#SBATCH --job-name=v02n
#SBATCH --partition=regular1
#SBATCH --nodes=1
#SBATCH --ntasks=1
#SBATCH --mem=160G
#SBATCH --cpus-per-task=1
#SBATCH --hint=nomultithread
#SBATCH --time=02:00:00

zainabnazari

result_count_ir3_lb=pd.read_csv(path3/"bl_matrix_counts_ir3.txt",index_col=[0])
result_count_ir3_lb.isnull().values.any()

zainabnazari

final2=pd.read_csv("final.csv", header=None,index_col=[0])
final=final2.rename(columns=final2.iloc[0]).drop(final2.index[0]).reset_index(drop=True)

zainabnazari

import pandas as pd
import numpy as np
from pathlib import Path
import functools


# We put the main path to the folder where 'counts' files are there.
path1=Path("/scratch/znazari/PPMI_ver_sep2022/RNA_Seq_data/star_ir2/counts/")

# We read the file: in the bl.txt is written the name of all files.

zainabnazari

#include <stdio.h>
#include "omp.h"

void main()
{
printf("hi world from the main function\n");
        #pragma omp parallel
        {
        //#pragma omp critical
                {

zainabnazari

// C[] is the elements of matrix multiplication 
// we consider the hash value as zero and add the sum of the elemnt of the matrix as its value
// if the two matrices that we have computed have diffrent hash value then there would be an error in the computation of the matrics.

int hash_value = 0;
int i_m;
for( i_m = 0; i_m < N*N; i_m++) {
    hash_value += C[i_m];
}
// taking a modulo  to shorten  the final result.

zainabnazari

%%time
dfSave = pd.DataFrame()
for i in range(len(bl_files)):
    print(i)
    df = pd.read_csv(path1/bl_files.iloc[i][0],skiprows=1,delimiter='\t')
    dfSave[bl_list[i]] = df.iloc[:,-1:]
    del df

zainabnazari

git rm path/to/large_file.ext
# commit the removal:
git commit -m "Remove large file"
# If you want to keep the previous commit message, use:
git commit --amend --no-edit
# oteherwise
git commit --amend
# then:
git push --force origin branch_name
# force pushing can be disruptive and may affect other collaborators who have already pulled the previous commit.

zainabnazari

#In python instead of

my_list=[]
for i in range(len(my_files)):
    my_list=my_list+[my_function(my_files.iloc[i][0])]  
my_list;

#use:

my_list = [my_function(my_files.iloc[i][0]) for i in range(len(bl_files))]