GIT
Basic
The git commands to update, commit and push your local repository are:
$ git status
$ git add -u
$ git add new_files
$ git commit -m "my commit comment"
$ git push origin master
then go to the github repository your fork originated from and create a pull request, then merge it.
Remove large files
To remove large files from a github repository
Let’s say you want to remove all tiff files from the all commit history of a github repository e.g. https://github.com/decarlof/holotomocupy_bq.git. First you want to delete the unwanted files from the last commit:
$ git clone https://github.com/decarlof/holotomocupy_bq.git
$ cd holotomocupy_bq
$ find . -type f \( -iname \*.tif -o -iname \*.tiff \)
./examples_synthetic/data/beta-chip-192.tiff
./examples_synthetic/data/delta-chip-192.tiff
./examples_synthetic/data/prb_id16a/prb_abs_1024.tiff
./examples_synthetic/data/prb_id16a/prb_abs_192.tiff
./examples_synthetic/data/prb_id16a/prb_abs_2048.tiff
./examples_synthetic/data/prb_id16a/prb_abs_256.tiff
./examples_synthetic/data/prb_id16a/prb_abs_384.tiff
./examples_synthetic/data/prb_id16a/prb_abs_512.tiff
./examples_synthetic/data/prb_id16a/prb_phase_1024.tiff
./examples_synthetic/data/prb_id16a/prb_phase_192.tiff
./examples_synthetic/data/prb_id16a/prb_phase_2048.tiff
./examples_synthetic/data/prb_id16a/prb_phase_256.tiff
./examples_synthetic/data/prb_id16a/prb_phase_384.tiff
./examples_synthetic/data/prb_id16a/prb_phase_512.tiff
$ rm -rf ./examples_synthetic/data/beta-chip-192.tiff
$ rm -rf ./examples_synthetic/data/delta-chip-192.tiff
$ rm -rf ./examples_synthetic/data/prb_id16a/prb_abs_1024.tiff
$ rm -rf ./examples_synthetic/data/prb_id16a/prb_abs_192.tiff
$ rm -rf ./examples_synthetic/data/prb_id16a/prb_abs_2048.tiff
$ rm -rf ./examples_synthetic/data/prb_id16a/prb_abs_256.tiff
$ rm -rf ./examples_synthetic/data/prb_id16a/prb_abs_384.tiff
$ rm -rf ./examples_synthetic/data/prb_id16a/prb_abs_512.tiff
$ rm -rf ./examples_synthetic/data/prb_id16a/prb_phase_1024.tiff
$ rm -rf ./examples_synthetic/data/prb_id16a/prb_phase_192.tiff
$ rm -rf ./examples_synthetic/data/prb_id16a/prb_phase_2048.tiff
$ rm -rf ./examples_synthetic/data/prb_id16a/prb_phase_256.tiff
$ rm -rf ./examples_synthetic/data/prb_id16a/prb_phase_384.tiff
$ rm -rf ./examples_synthetic/data/prb_id16a/prb_phase_512.tiff
$ git add -u
$ git commit -m "removed tiff files"
$ git push
Install bfg repo cleaner to obtain the latest version of bfg then clone the repository using the –mirror option:
$ cd ..
$ git clone --mirror https://github.com/decarlof/holotomocupy_bq.git
$ java -jar ~/Downloads/bfg-1.14.0.jar -D "*.tiff" holotomocupy_bq.git/
Using repo : /Users/decarlo/conda/holotomocupy_bq.git
Found 35 objects to protect
Found 2 commit-pointing refs : HEAD, refs/heads/master
Protected commits
-----------------
These are your protected commits, and so their contents will NOT be altered:
* commit 626411d5 (protected by 'HEAD')
Cleaning
--------
Found 65 commits
Cleaning commits: 100% (65/65)
Cleaning commits completed in 134 ms.
Updating 1 Ref
--------------
Ref Before After
---------------------------------------
refs/heads/master | 626411d5 | 35529ff1
Updating references: 100% (1/1)
...Ref update completed in 14 ms.
Commit Tree-Dirt History
------------------------
Earliest Latest
| |
.......DDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDm
D = dirty commits (file tree fixed)
m = modified commits (commit message or parents changed)
. = clean commits (no changes to file tree)
Before After
-------------------------------------------
First modified commit | c8f5ff5f | 8a11c799
Last dirty commit | 0dd743b5 | 7307f3af
Deleted files
-------------
Filename Git id
----------------------------------------------------------------
beta-chip-192.tiff | 5817f483 (27.0 MB)
data_chip_384_0.tiff | d134a399 (50.6 MB)
data_chip_384_1.tiff | 88452e45 (50.6 MB)
data_chip_384_2.tiff | d89fb163 (50.6 MB)
data_chip_384_3.tiff | a6e464f7 (50.6 MB)
data_phantom_384_0.tiff | ef07a76a (576.3 KB)
data_phantom_384_1.tiff | a0c64c93 (576.3 KB)
data_phantom_384_2.tiff | 6be72afc (576.3 KB)
data_phantom_384_3.tiff | 02530ed1 (576.3 KB)
delta-chip-192.tiff | af0b8a5c (27.0 MB)
flat_chip_384_0.tiff | 655cf599 (576.3 KB)
flat_chip_384_1.tiff | f3f1cca6 (576.3 KB)
flat_chip_384_2.tiff | 4e0900f2 (576.3 KB)
flat_chip_384_3.tiff | d35c35ea (576.3 KB)
flat_phantom_384_0.tiff | 9fc7e4af (576.3 KB)
...
In total, 153 object ids were changed. Full details are logged here:
/Users/decarlo/conda/holotomocupy_bq.git.bfg-report/2024-06-18/14-36-21
BFG run is complete! When ready, run: git reflog expire --expire=now --all && git gc --prune=now --aggressive
$ cd holotomocupy_bq.git/
$ git reflog expire --expire=now --all && git gc --prune=now --aggressive
$ git push
The repository on github is now clear of all .tiff files from its history. You can clone again with:
$ git clone https://github.com/decarlof/holotomocupy_bq.git holotomocupy_bq_cleaned
and delete the old holotomocupy_bq folder.