a
b
c
d
Introduction
Theory
Method
Results
git for everything
Massimo Pinto ENEA-INMRI, Italy
Reid Townson NRC, Canada
Romain Coulon BIPM
Frédéric Tessier NRC, Canada
Frédéric Meynadier BIPM
Introduction
Theory
Method
Results
a
b
c
d
Massimo Pinto ENEA-INMRI, Italy
Frédéric Tessier NRC, Canada
Reid Townson NRC, Canada
Romain Coulon BIPM,
Frédéric Meynadier BIPM
Introduction
Theory
Method
Results
a
b
c
d
Massimo Pinto ENEA-INMRI, Italy
Frédéric Tessier NRC, Canada
Reid Townson NRC, Canada
Romain Coulon BIPM,
Frédéric Meynadier BIPM
Today you will learn (something) about git
- What is version control? Why not simply “Save As...” successive versions of a file?
- What does this have to do with metrology? Is it not just for programmers?
- Why is the free git software efficient compared to alternatives methods?
- Can I start using git today for my work (code, data, papers, quality system, etc.)?
- How could my team edit files collaboratively and concurrently?
- Where can I share my work: github.com, gitlab.com, bitbucket.org?
- Who can offer compelling examples of git applications in metrology?
- Why is it called git anyways? Why is it dubbed the stupid content tracker?
Version control saves you from a “Save as...” fiasco
filenames and timestamps are unreliable for tracking versions
Jorge Cham, phdcomics.com
trying to make sense from the timestamp
Version control saves you from a “Save as...” fiasco
Jorge Cham, phdcomics.com
File system information is not robust:
Filename is arbitrary; timestamp can be updated inadvertently upon saving or copying; or restoring from backup.
Information is lost when the file is deleted.
Multiple copies (versions) make it worse!
What we need:
A robust record of file modifications, to answer the 5 “w’s”: Who, What, When, Where, and Why?
A tool to work collaboratively and concurrently.
Version control is a two-way street
Jonathan McGlone, @jmcglone
Proper version control offers a solid track record of your file modifications, and those of your collaborators.
A version acts as a snapshot in time: any set of changes can be recorded as a version.
Each version is documented.
It’s your diary.
You can inspect and recover any version in your project history,
and compare any two versions.
A long history of version control software:
SCCS, RCS, CVS, subversion, helix core, bazaar, bitkeeper, git, ...
Anyone can explore new ideas and experiment with different versions on the side with branches, without affecting the main project branch.
git is a many-street network
main
your work
someone
else’s work
Anyone can explore new ideas and experiment with different versions on the side with branches, without affecting the main project branch.
You can merge in any successful idea into the main project branch at any point, automatically.
git is a many-street network
your work
someone
else’s work
main
Anyone can explore new ideas and experiment with different versions on the side with branches, without affecting the main project branch.
You can merge in any successful idea into the main project branch at any point, automatically.
A repository is the collection of all commits and branches for a given project.
git is a many-street network
repository
git is a many-street network
clone
clone
clone
you @ office
backup
you @ home
collaborator
Anyone can explore new ideas and experiment with different versions on the side with branches, without affecting the main project branch.
You can merge in any successful idea into the main project branch at any point, automatically.
A repository is the collection of all commits and branches for a given project.
A repository can be duplicated and shared. Every clone gets the full history.
git is a many-street network
you @ office
Anyone can explore new ideas and experiment with different versions on the side with branches, without affecting the main project branch.
You can merge in any successful idea into the main project branch at any point, automatically.
A repository is the collection of all commits and branches for a given project.
A repository can be duplicated and shared. Every clone gets the full history.
distributed
(no central server)
you @ home
collaborator
backup
git is a many-street network
pull
pull
pull
collaborator
backup
you @ office
Anyone can explore new ideas and experiment with different versions on the side with branches, without affecting the main project branch.
You can merge in any successful idea into the main project branch at any point, automatically.
A repository is the collection of all commits and branches for a given project.
A repository can be duplicated and shared. Every clone gets the full history.
you @ home
git enables open science
As you embrace the open science paradigm, you can share your work (code, methods, data, reports, etc.) on a hosting platform, for example:
A penelope code to calculate correction factors for effects in diaphragms in free-air chambers
As you embrace the open science paradigm, you can share your work (code, methods, data, reports, etc.) on a hosting platform, for example:
Kurosawa T, Takata N and Saito N.
Effect of the diaphragm of free-air ionization chamber for X-ray air-kerma measurements, Radiation Protection Dosimetry 146, 195–7 (2011)
git enables open science
A penelope code to calculate correction factors for effects in diaphragms in free-air chambers
git enables open science
As you embrace the open science paradigm, you can share your work (code, methods, data, reports, etc.) on a hosting platform, for example:
A python software tool to generate
x-ray spectra using SpekPy
Bujila R, Omar A and Poludniowski G.
A validation of SpekPy: a software toolkit for modelling X-ray tube spectra,
Physica Medica: European Journal of Medical Physics 75, 44–54 (2020)
As you embrace the open science paradigm, you can share your work (code, methods, data, reports, etc.) on a hosting platform, for example:
Don’t feel intimidated by the breadth of git, or its learning curve: nobody starts using git by actually knowing how it works. As with other software, you learn by doing. Note that most operations in git can be undone, so feel free to experiment!
“git” started today, help is just a click away
Documentation and tutorials:
Introduction
Theory
Method
Results
a
b
c
d
Massimo Pinto ENEA-INMRI, Italy
Frédéric Tessier NRC, Canada
Reid Townson NRC, Canada
Romain Coulon BIPM,
Frédéric Meynadier BIPM
Introduction
Theory
Method
Results
a
b
c
d
Massimo Pinto ENEA-INMRI, Italy
Frédéric Tessier NRC, Canada
Reid Townson NRC, Canada
Romain Coulon BIPM,
Frédéric Meynadier BIPM
git is a file versioning technology
git (command-line)
web hosting
...
GitHub
GitLab
Bitbucket
version “as a service”
...
many apps built for git
or rely on git
Overleaf
Jujutsu
gitless
git is a file versioning technology
git (command-line)
web hosting
...
GitHub
GitLab
Bitbucket
version “as a service”
many apps built for git
or rely on git
Gitpod
Overleaf
Colaboratory
...
Scientists have the right mindset for version control
measurements over time
science
measurement (a datum)
files over time
commit (a change)
git
Scientists have the right mindset for version control
measurements over time
science
traceability
accountability
accuracy
precision
reproducibility
documentation
comparison
measurement (a datum)
files over time
log
commit authorship
commit hash
single-character change
clone
commit message
diff
commit (a change)
git
The git “philosophy” is: a chain of changes
git
repository
folder
traditional
“universe” is the folder
myproject/
The git “philosophy” is: a chain of changes
git
repository
c
d
e
“universe” is the set of folder states
a
b
“universe” is the folder
folder
traditional
myproject/
a
b
c
d
e
git adds a “change” axis to a folder
The git “philosophy” is: a chain of changes
Like snapshots for your work; you decide when to record a snapshot.
a
c
d
e
b
The git “philosophy” is: a chain of changes
git adds a “change” axis to a folder
Think in terms of project states, not files: states pertain to the entire project.
a
c
d
e
b
The git “philosophy” is: a chain of changes
git adds a “change” axis to a folder
A state only records changes.
changes from a
init
changes from b
changes from c
changes from d
changes from a
init
a
c
d
e
b
The git “philosophy” is: a chain of changes
git adds a “change” axis to a folder
changes from c
changes from d
A state only records changes, with respect to a parent state.
changes from b
git’s fundamental “atom” is the commit
c
Most git operations relate directly to commits.
changes from parent
changes from parent
“c”
git’s fundamental “unit” is the commit
3f2f1b8...
blobs and trees
log message
author, date, ...
Most git operations relate directly to commits.
changes from parent
The commit identifier is unequivocal
3f2f1b8...
blobs and trees
The commit identifier is the SHA-1 hash of its content.
log message
author, date, ...
9af0cd4...
SHA-1 hash
40 hexadecimal characters (160 bits)
changes from parent
The commit identifier is unequivocal
3f2f1b8...
blobs and trees
The commit identifier is the SHA-1 hash of its content.
log message
author, date, ...
9af0cd4...
SHA-1 hash
9af0cd4...
40 hexadecimal characters (160 bits)
changes from parent
The commit identifier is unequivocal
3f2f1b8...
blobs and trees
log message
author, date, ...
3f2f1b8...
9af0cd4...
9af0cd4...
SHA-1 hash
The commit identifier is the SHA-1 hash of its content, including the parent identifier.
40 hexadecimal characters (160 bits)
The commit chain guarantees data integrity
Alice
0f3caf9
9af0cd4
25fed04
3f2f1b8
c995654
8ee6494
e1e03b7
5b9adde
bb4325e
bfc5afc
1dc307f
9f4b07d
9456bc3
4534cdd
The git history is a cryptographic “blockchain”
(without proof-of-work).
Bob
9af0cd4
25fed04
3f2f1b8
c995654
8ee6494
e1e03b7
5b9adde
bb4325e
bfc5afc
1dc307f
9f4b07d
9456bc3
4534cdd
0f3caf9
The commit chain guarantees data integrity
Alice
0f3caf9
The git history is a cryptographic “blockchain”
(without proof-of-work).
Bob
9af0cd4
174b7f4
3f2f1b8
c995654
8ee6494
e1e03b7
d601706
a1a1fff
404fd5f
b473e64
9f4b07d
9456bc3
4534cdd
da3d38e
9af0cd4
3f2f1b8
c995654
8ee6494
e1e03b7
9f4b07d
9456bc3
4534cdd
25fed04
5b9adde
bb4325e
bfc5afc
1dc307f
Many commits can share the same parent: branches
Alice
0f3caf9
Bob
da3d38e
174b7f4
d601706
a1a1fff
404fd5f
b473e64
Alice and Bob can work concurrently on the same project.
9af0cd4
3f2f1b8
c995654
8ee6494
e1e03b7
9f4b07d
9456bc3
4534cdd
25fed04
5b9adde
bb4325e
bfc5afc
1dc307f
Many commits can share the same parent: branches
main
0f3caf9
new-feature
da3d38e
174b7f4
d601706
a1a1fff
404fd5f
b473e64
9af0cd4
3f2f1b8
c995654
8ee6494
e1e03b7
9f4b07d
9456bc3
4534cdd
25fed04
5b9adde
bb4325e
bfc5afc
1dc307f
One person can work concurrently on different project tracks.
A commit may have multiple parents: merge
0f3caf9
main
git merges file modifications automatically (or helps you resolve conflicts).
c50c05f
da3d38e
174b7f4
d601706
a1a1fff
404fd5f
b473e64
25fed04
5b9adde
bb4325e
bfc5afc
1dc307f
9af0cd4
3f2f1b8
c995654
8ee6494
e1e03b7
9f4b07d
9456bc3
4534cdd
A commit may have multiple parents: merge
main
Branch labels advance automatically when commits are added.
56f6492
c50c05f
0f3caf9
da3d38e
174b7f4
d601706
a1a1fff
404fd5f
b473e64
25fed04
5b9adde
bb4325e
bfc5afc
1dc307f
9af0cd4
3f2f1b8
c995654
8ee6494
e1e03b7
9f4b07d
9456bc3
4534cdd
You can “time travel” to any commit
56f6492
new-idea
A branch is simply a mnemonic label for a commit hash.
git branch new-idea 8ee6494
git checkout new-ideamain
c50c05f
da3d38e
174b7f4
d601706
a1a1fff
404fd5f
b473e64
8ee6494
0f3caf9
9af0cd4
25fed04
3f2f1b8
c995654
e1e03b7
5b9adde
bb4325e
bfc5afc
1dc307f
9f4b07d
9456bc3
4534cdd
You can “time travel” to any commit
new-idea
A branch is simply a mnemonic label for a commit hash.
b56a084
7f89723
fe620ac
07a73e6
63a61f9
2c1ea58
56f6492
git branch new-idea 8ee6494
git checkout new-ideamain
c50c05f
0f3caf9
9af0cd4
25fed04
3f2f1b8
c995654
8ee6494
e1e03b7
5b9adde
bb4325e
bfc5afc
1dc307f
9f4b07d
9456bc3
4534cdd
da3d38e
174b7f4
d601706
a1a1fff
404fd5f
b473e64
A git repository is a “bag of commits”
7f89723
fe620ac
07a73e6
63a61f9
2c1ea58
56f6492
c50c05f
0f3caf9
174b7f4
d601706
a1a1fff
404fd5f
b473e64
b56a084
9af0cd4
25fed04
3f2f1b8
c995654
8ee6494
e1e03b7
5b9adde
bb4325e
bfc5afc
1dc307f
9f4b07d
9456bc3
4534cdd
da3d38e
new-idea
main
git stores commit objects, there is no “link object” (each commit knows its parent).
A git repository is a “bag of commits”
3f2f1b8
8ee6494
c995654
e1e03b7
9f4b07d
9456bc3
4534cdd
9af0cd4
25fed04
bfc5afc
5b9adde
bb4325e
1dc307f
0f3caf9
c50c05f
174b7f4
404fd5f
d601706
a1a1fff
b473e64
da3d38e
7f89723
63a61f9
fe620ac
07a73e6
2c1ea58
56f6492
main
b56a084
new-idea
myproject/.git/
individual,
self-contained objects
connect the dots !
A git repository is a “bag of commits”
3f2f1b8
8ee6494
c995654
e1e03b7
9f4b07d
9456bc3
4534cdd
9af0cd4
25fed04
bfc5afc
5b9adde
bb4325e
1dc307f
0f3caf9
c50c05f
174b7f4
404fd5f
d601706
a1a1fff
b473e64
da3d38e
7f89723
63a61f9
fe620ac
07a73e6
2c1ea58
56f6492
main
b56a084
new-idea
myproject/.git/
individual,
self-contained objects
204d614
cb4dea8
d8f8b59
566ad69
09717f9
pull
60aceae
alice
sets of commits are portable
commits are persistent
deleting a branch does not delete
the commits
changes from parent
The key to useful version control is the log
blobs and trees
log message
author, date, ...
A repository is only as good as its documentation.
9af0cd4...
SHA-1 hash
3f2f1b8...
The key to useful version control is the log
log messages
$ git log --oneline
a6fc389c Merge #685: develop into master for 2021 release
7b7b9a5b Fix documentation warnings, links, tags, year
78e8745d Tweak README and add links to EGSnrc Discussions
60110c9a Bring 'develop' branch up to date with 'master'
7cfc660c Merge additional small stuff before release 2021
7a478e9f Update README to match EGSnrc web page
7a190b0d Update copyright years and fix duplicate reference
fd24a3fe Merge #684: small stuff for the 2021 release
8a0bcb40 Clarify notation for slab input in xyz geometry
58478a2c Fix loop index compiler warning in egs_cylinders.h
d17c479a Fix typo in egs_kerma documentation
b814bb3a Adjust format, typos, comments, docs, etc.
f57d3dbb Add a comment in getting-started about mingw
2030db2e Fix n_split equation in DOSXYZnrc documentation
30d10d19 Change Google+ community reference to reddit
d2ec76e0 Merge #588: run parallel jobs without a lock file
02258354 Run C preprocessor on Mortran apps to parse #ifdef
b08afa94 Remove -j12 option for testing in CI pipeline
c71955df Adjust eol spaces, remove leftover merge markers
5c4f81e0 Merge #683: add egs++ lattice geometry (see #561)
9b942fc1 Adjust headers, add citation pages and reflow
9edf97df Add egs_lattice geometry to the egs++ Makefile
77664e05 Add a reference to the egs_lattice paper
e91e2c41 Document the egs_lattice geometry variables
cc6d2100 Add egs_lattice geometry and sample input file
c778e2a7 Merge #628: add new set of egs-parallel scripts
01b86ac0 Add command to get thread count on Darwin system
66fea4bc Fix timing and atomic relaxations in CAVRZnrc
da12bc0c Preserve information after DOSXYZnrc parallel run
7ab5e620 Fix lock file errors when using a BEAMnrc library
67d4608d Check uniform RCO job termination in Motran apps
cc477746 Fix total ncase for the job control file object
3910e125 Add -u (--urc) run control option to egs++ apps
a8ed1cd5 Add variable is_uniform_run to EGS_IO structure
3acb191c Update Mortran apps for uniform run control
a868291c Improve SPRRZnrc for parallel jobs
f4f6e356 Tune egs_utilities.mortran for uniform run control
c59d015d Tune egs_parallel.mortran for uniform run control
20c9dfb6 Update egsnrc.macros for uniform run control
3a222f8a Improve output messages for the spherical geometry
ff7a2893 Add sleep option to stagger SGE job submission
2d72f39d Add script to submit jobs on Sun Grid Engine
dc4e55fd Improve the description of run control objects
3f2f1b82 Change the urco default to check finished jobs
3901664c Add environment variable for density corrections
5cbc8fc8 Increase maximum number of jobs to 8192
c4c2fe76 Implement a uniform run control object
8a7311f5 Strip non-alphanumeric lead chars in PBS job name
8df47161 Fix pbsdsh jobnames starting with a period
58b6cd23 Detect failure to launch pbs job in egs-egs_parallel
( 900 lines... )
b6fe81a9 Fix missing comment quote
8e9a08fa Port utils files to github and AGPL-3.0
e255618f Move statement about file revision history
0dcc8d18 Adjust file header format
f9b27b1d Adjust file header format
874f1cb6 Merge branch 'master' of github.com:nrc-cnrc/EGSnrc
9327c077 Port egsnrc source files to github and AGPL-3.0
9990f5c2 Update readme
bbe98a8e Update readme
0ec55e41 Add markdown version of the AGPL-3.0
bb7a404d Port mortran3 files to github
cdab6a2c Port EGSnrc makefiles to github and AGPL 3.0
48fc752f Port EGSnrc cutils files to github
12b0db6b Update README.md
8ee6494f Update README.md
c9956542 Update README.md
e1e03b7b Update README.md
9f4b07de Create LICENCE
9456bc34 Update README.md
4534cdd4 Initial commit
avoid this !
Write a short (50 characters) informative commit title
Jorge Cham, phdcomics.com
The key to useful version control is the log
log messages
$ git log --oneline
a6fc389c Merge #685: develop into master for 2021 release
7b7b9a5b Fix documentation warnings, links, tags, year
78e8745d Tweak README and add links to EGSnrc Discussions
60110c9a Bring 'develop' branch up to date with 'master'
7cfc660c Merge additional small stuff before release 2021
7a478e9f Update README to match EGSnrc web page
7a190b0d Update copyright years and fix duplicate reference
fd24a3fe Merge #684: small stuff for the 2021 release
8a0bcb40 Clarify notation for slab input in xyz geometry
58478a2c Fix loop index compiler warning in egs_cylinders.h
d17c479a Fix typo in egs_kerma documentation
b814bb3a Adjust format, typos, comments, docs, etc.
f57d3dbb Add a comment in getting-started about mingw
2030db2e Fix n_split equation in DOSXYZnrc documentation
30d10d19 Change Google+ community reference to reddit
d2ec76e0 Merge #588: run parallel jobs without a lock file
02258354 Run C preprocessor on Mortran apps to parse #ifdef
b08afa94 Remove -j12 option for testing in CI pipeline
c71955df Adjust eol spaces, remove leftover merge markers
5c4f81e0 Merge #683: add egs++ lattice geometry (see #561)
9b942fc1 Adjust headers, add citation pages and reflow
9edf97df Add egs_lattice geometry to the egs++ Makefile
77664e05 Add a reference to the egs_lattice paper
e91e2c41 Document the egs_lattice geometry variables
cc6d2100 Add egs_lattice geometry and sample input file
c778e2a7 Merge #628: add new set of egs-parallel scripts
01b86ac0 Add command to get thread count on Darwin system
66fea4bc Fix timing and atomic relaxations in CAVRZnrc
da12bc0c Preserve information after DOSXYZnrc parallel run
7ab5e620 Fix lock file errors when using a BEAMnrc library
67d4608d Check uniform RCO job termination in Motran apps
cc477746 Fix total ncase for the job control file object
3910e125 Add -u (--urc) run control option to egs++ apps
a8ed1cd5 Add variable is_uniform_run to EGS_IO structure
3acb191c Update Mortran apps for uniform run control
a868291c Improve SPRRZnrc for parallel jobs
f4f6e356 Tune egs_utilities.mortran for uniform run control
c59d015d Tune egs_parallel.mortran for uniform run control
20c9dfb6 Update egsnrc.macros for uniform run control
3a222f8a Improve output messages for the spherical geometry
ff7a2893 Add sleep option to stagger SGE job submission
2d72f39d Add script to submit jobs on Sun Grid Engine
dc4e55fd Improve the description of run control objects
3f2f1b82 Change the urco default to check finished jobs
3901664c Add environment variable for density corrections
5cbc8fc8 Increase maximum number of jobs to 8192
c4c2fe76 Implement a uniform run control object
8a7311f5 Strip non-alphanumeric lead chars in PBS job name
8df47161 Fix pbsdsh jobnames starting with a period
58b6cd23 Detect failure to launch pbs job in egs-egs_parallel
( 900 lines... )
b6fe81a9 Fix missing comment quote
8e9a08fa Port utils files to github and AGPL-3.0
e255618f Move statement about file revision history
0dcc8d18 Adjust file header format
f9b27b1d Adjust file header format
874f1cb6 Merge branch 'master' of github.com:nrc-cnrc/EGSnrc
9327c077 Port egsnrc source files to github and AGPL-3.0
9990f5c2 Update readme
bbe98a8e Update readme
0ec55e41 Add markdown version of the AGPL-3.0
bb7a404d Port mortran3 files to github
cdab6a2c Port EGSnrc makefiles to github and AGPL 3.0
48fc752f Port EGSnrc cutils files to github
12b0db6b Update README.md
8ee6494f Update README.md
c9956542 Update README.md
e1e03b7b Update README.md
9f4b07de Create LICENCE
9456bc34 Update README.md
4534cdd4 Initial commitavoid this !
Write a short (50 characters) informative commit title
Jorge Cham, phdcomics.com
The key to useful version control is the log
log messages
$ git log --oneline
a6fc389c Merge #685: develop into master for 2021 release
7b7b9a5b Fix documentation warnings, links, tags, year
78e8745d Tweak README and add links to EGSnrc Discussions
60110c9a Bring 'develop' branch up to date with 'master'
7cfc660c Merge additional small stuff before release 2021
7a478e9f Update README to match EGSnrc web page
7a190b0d Update copyright years and fix duplicate reference
fd24a3fe Merge #684: small stuff for the 2021 release
8a0bcb40 Clarify notation for slab input in xyz geometry
58478a2c Fix loop index compiler warning in egs_cylinders.h
d17c479a Fix typo in egs_kerma documentation
b814bb3a Adjust format, typos, comments, docs, etc.
f57d3dbb Add a comment in getting-started about mingw
2030db2e Fix n_split equation in DOSXYZnrc documentation
30d10d19 Change Google+ community reference to reddit
d2ec76e0 Merge #588: run parallel jobs without a lock file
02258354 Run C preprocessor on Mortran apps to parse #ifdef
b08afa94 Remove -j12 option for testing in CI pipeline
c71955df Adjust eol spaces, remove leftover merge markers
5c4f81e0 Merge #683: add egs++ lattice geometry (see #561)
9b942fc1 Adjust headers, add citation pages and reflow
9edf97df Add egs_lattice geometry to the egs++ Makefile
77664e05 Add a reference to the egs_lattice paper
e91e2c41 Document the egs_lattice geometry variables
cc6d2100 Add egs_lattice geometry and sample input file
c778e2a7 Merge #628: add new set of egs-parallel scripts
01b86ac0 Add command to get thread count on Darwin system
66fea4bc Fix timing and atomic relaxations in CAVRZnrc
da12bc0c Preserve information after DOSXYZnrc parallel run
7ab5e620 Fix lock file errors when using a BEAMnrc library
67d4608d Check uniform RCO job termination in Motran apps
cc477746 Fix total ncase for the job control file object
3910e125 Add -u (--urc) run control option to egs++ apps
a8ed1cd5 Add variable is_uniform_run to EGS_IO structure
3acb191c Update Mortran apps for uniform run control
a868291c Improve SPRRZnrc for parallel jobs
f4f6e356 Tune egs_utilities.mortran for uniform run control
c59d015d Tune egs_parallel.mortran for uniform run control
20c9dfb6 Update egsnrc.macros for uniform run control
3a222f8a Improve output messages for the spherical geometry
ff7a2893 Add sleep option to stagger SGE job submission
2d72f39d Add script to submit jobs on Sun Grid Engine
dc4e55fd Improve the description of run control objects
3f2f1b82 Change the urco default to check finished jobs
3901664c Add environment variable for density corrections
5cbc8fc8 Increase maximum number of jobs to 8192
c4c2fe76 Implement a uniform run control object
8a7311f5 Strip non-alphanumeric lead chars in PBS job name
8df47161 Fix pbsdsh jobnames starting with a period
58b6cd23 Detect failure to launch pbs job in egs-egs_parallel
( 900 lines... )
b6fe81a9 Fix missing comment quote
8e9a08fa Port utils files to github and AGPL-3.0
e255618f Move statement about file revision history
0dcc8d18 Adjust file header format
f9b27b1d Adjust file header format
874f1cb6 Merge branch 'master' of github.com:nrc-cnrc/EGSnrc
9327c077 Port egsnrc source files to github and AGPL-3.0
9990f5c2 Update readme
bbe98a8e Update readme
0ec55e41 Add markdown version of the AGPL-3.0
bb7a404d Port mortran3 files to github
cdab6a2c Port EGSnrc makefiles to github and AGPL 3.0
48fc752f Port EGSnrc cutils files to github
12b0db6b Update README.md
8ee6494f Update README.md
c9956542 Update README.md
e1e03b7b Update README.md
9f4b07de Create LICENCE
9456bc34 Update README.md
4534cdd4 Initial commitavoid this !
Write a short (50 characters) informative commit title
inital commit on
28th November 2012
Jorge Cham, phdcomics.com
Follow the “seven rules” for commit messages
log messages
$ git log
commit 697301d6
Author: Ernesto <ernesto.mainegra-hing@nrc-cnrc.gc.ca>
Date: Thu Jan 28 18:05:34 2021 -0500
Fix #661: flag Rayleigh photons as scattered
Include Rayleigh photons as part of the scattered dose component in
DOSRZnrc, using the patch provided by @dworogers. Also adjust comment
lines that were longer than 80 characters.
commit 3fa9be78
Author: Frederic Tessier <ftessier@gmail.com>
Date: Tue Dec 15 11:00:48 2020 -0500
Fix command to get file size in configure script
Use 'wc -c' to obtain the number of bytes in the temporary file when
determining the Fortran record length during EGSnrc configuration. The
problem with 'stat -c' is that it is not standard; for example, there is
no '-c' option in BSD variants (macOS). Using the 'stat' command is
a regression introduced in issue #616 to remove a dependency on the
format of the 'ls' output.
commit 7247e188
Author: Reid Townson <rwtownson@gmail.com>
Date: Wed Aug 19 16:23:05 2020 -0400
Add splitting var in egs_chamber to replace latch
Use a dedicated splitting variable nbr_split, instead of latch, to hold
the splitting number in the egs_chamber application. A new stack
variable nbr_splitting is added to pass its value through the EGSnrc
back end. This avoids overwriting the latch variable in cases where it
is needed otherwise, for example in the phsp scoring object. Ideally,
the meaning of latch should remain consistent with BEAMnrc.
(966 commits...)
commit 4534cdd4
Author: ftessier <ftessier@gmail.com>
Date: Wed Nov 28 11:26:41 2012 -0800
Initial commitChris Beams, @cbeams, https://cbea.ms/git-commit/
The seven rules of a great
git commit message
Keep in mind: this has all been said before
Follow the “seven rules” for commit messages
log messages
$ git log
commit 697301d6
Author: Ernesto <ernesto.mainegra-hing@nrc-cnrc.gc.ca>
Date: Thu Jan 28 18:05:34 2021 -0500
Fix #661: flag Rayleigh photons as scattered
Include Rayleigh photons as part of the scattered dose component in
DOSRZnrc, using the patch provided by @dworogers. Also adjust comment
lines that were longer than 80 characters.
commit 3fa9be78
Author: Frederic Tessier <ftessier@gmail.com>
Date: Tue Dec 15 11:00:48 2020 -0500
Fix command to get file size in configure script
Use 'wc -c' to obtain the number of bytes in the temporary file when
determining the Fortran record length during EGSnrc configuration. The
problem with 'stat -c' is that it is not standard; for example, there is
no '-c' option in BSD variants (macOS). Using the 'stat' command is
a regression introduced in issue #616 to remove a dependency on the
format of the 'ls' output.
commit 7247e188
Author: Reid Townson <rwtownson@gmail.com>
Date: Wed Aug 19 16:23:05 2020 -0400
Add splitting var in egs_chamber to replace latch
Use a dedicated splitting variable nbr_split, instead of latch, to hold
the splitting number in the egs_chamber application. A new stack
variable nbr_splitting is added to pass its value through the EGSnrc
back end. This avoids overwriting the latch variable in cases where it
is needed otherwise, for example in the phsp scoring object. Ideally,
the meaning of latch should remain consistent with BEAMnrc.
(966 commits...)
commit 4534cdd4
Author: ftessier <ftessier@gmail.com>
Date: Wed Nov 28 11:26:41 2012 -0800
Initial commitChris Beams, @cbeams, https://cbea.ms/git-commit/
Keep in mind: this has all been said before
- Separate subject from body with a blank line
- Limit the subject line to 50 characters
- Capitalize the subject line
- Do not end the subject line with a period
- Use the imperative mood in the subject line
The seven rules of a great
git commit message
Follow the “seven rules” for commit messages
log messages
$ git log
commit 697301d6
Author: Ernesto <ernesto.mainegra-hing@nrc-cnrc.gc.ca>
Date: Thu Jan 28 18:05:34 2021 -0500
Fix #661: flag Rayleigh photons as scattered
Include Rayleigh photons as part of the scattered dose component in
DOSRZnrc, using the patch provided by @dworogers. Also adjust comment
lines that were longer than 80 characters.
commit 3fa9be78
Author: Frederic Tessier <ftessier@gmail.com>
Date: Tue Dec 15 11:00:48 2020 -0500
Fix command to get file size in configure script
Use 'wc -c' to obtain the number of bytes in the temporary file when
determining the Fortran record length during EGSnrc configuration. The
problem with 'stat -c' is that it is not standard; for example, there is
no '-c' option in BSD variants (macOS). Using the 'stat' command is
a regression introduced in issue #616 to remove a dependency on the
format of the 'ls' output.
commit 7247e188
Author: Reid Townson <rwtownson@gmail.com>
Date: Wed Aug 19 16:23:05 2020 -0400
Add splitting var in egs_chamber to replace latch
Use a dedicated splitting variable nbr_split, instead of latch, to hold
the splitting number in the egs_chamber application. A new stack
variable nbr_splitting is added to pass its value through the EGSnrc
back end. This avoids overwriting the latch variable in cases where it
is needed otherwise, for example in the phsp scoring object. Ideally,
the meaning of latch should remain consistent with BEAMnrc.
(966 commits...)
commit 4534cdd4
Author: ftessier <ftessier@gmail.com>
Date: Wed Nov 28 11:26:41 2012 -0800
Initial commitChris Beams, @cbeams, https://cbea.ms/git-commit/
Keep in mind: this has all been said before
- Wrap the message lines at 72 characters
- Use the body to explain what and why vs. how
The seven rules of a great
git commit message
- Separate subject from body with a blank line
- Limit the subject line to 50 characters
- Capitalize the subject line
- Do not end the subject line with a period
- Use the imperative mood in the subject line
Follow the “seven rules” for commit messages
log messages
$ git show 697301d6
commit 697301d6
Author: Ernesto <ernesto.mainegra-hing@nrc-cnrc.gc.ca>
Date: Thu Jan 28 18:05:34 2021 -0500
Fix #661: flag Rayleigh photons as scattered
Include Rayleigh photons as part of the scattered dose component in
DOSRZnrc, using the patch provided by @dworogers. Also adjust comment
lines that were longer than 80 characters.
diff --git a/HEN_HOUSE/user_codes/dosrznrc/dosrznrc.mortran b/HEN_HOUSE/user_codes/dosrznrc/dosrznrc.mortran
index 2abb1ff..a4d4856 100644
--- a/HEN_HOUSE/user_codes/dosrznrc/dosrznrc.mortran
+++ b/HEN_HOUSE/user_codes/dosrznrc/dosrznrc.mortran
@@ -1358,8 +1358,8 @@ REPLACE {$VERSION} WITH {
" ESAVEIN (R) If ELECTRON RANGE REJECTION is on, discard an
" electron when E< ESAVEIN and RANGE < CDIST
" where CDIST is closest distance to region of
-" interest specified below. This ignores bremsstrahlung
-" losses below ESAVEIN.
+" interest specified below (ignores bremsstrahlung
+" losses below ESAVEIN).
" This parameter must be input even if not used.
" ESAVEIN is a total energy.
"
@@ -2583,6 +2583,7 @@ IF(IFULL = 1 | IFULL = 3 | IKERMA = 1) [
iausfl(19) = 1; "after compt"
iausfl(20) = 1; "before photo"
iausfl(21) = 1; "after photo"
+ iausfl(25) = 1; "after Rayleigh"
iausfl(32) = 1; "before eii"
iausfl(33) = 1; "after eii"
iausfl(34) = 1; "after sub-threshold fluorescent photon discarded"Chris Beams, @cbeams, https://cbea.ms/git-commit/
Keep in mind: this has all been said before
- Wrap the message lines at 72 characters
- Use the body to explain what and why vs. how
The seven rules of a great
git commit message
- Separate subject from body with a blank line
- Limit the subject line to 50 characters
- Capitalize the subject line
- Do not end the subject line with a period
- Use the imperative mood in the subject line
git trades a little overhead for robust version control
Your new workflow to manage documents: start today!
mypaper/
.git/
git init
git stage
+
work
+
git trades a little overhead for robust version control
Your new workflow to manage documents: start today!
mypaper/
.git/
git init
git stage
git commit
+
work
+
9456bc3
.git/
git trades a little overhead for robust version control
Your new workflow to manage documents: start today!
mypaper/
.git/
git init
git commit
work
work
some more
+
git stage
+
+
9456bc3
.git/
git trades a little overhead for robust version control
Your new workflow to manage documents: start today!
mypaper/
.git/
git init
work
work
some more
235f0f1
+
9456bc3
git commit
git stage
+
+
.git/
git trades a little overhead for robust version control
Your new workflow to manage documents: start today!
mypaper/
.git/
git init
work
work
some more
235f0f1
git commit
git stage
+
4407e0b
+
+
9456bc3
.git/
git trades a little overhead for robust version control
Your new workflow to manage documents: start today!
mypaper/
.git/
git init
work
work
some more
235f0f1
git commit
git stage
+
4407e0b
+
9456bc3
94583fc
.git/
accuracy
precision
comparison
reproducibility
accountability
documentation
Example: checking modifications
Introduction
Theory
Method
Results
a
b
c
d
Massimo Pinto ENEA-INMRI, Italy
Frédéric Tessier NRC, Canada
Reid Townson NRC, Canada
Romain Coulon BIPM,
Frédéric Meynadier BIPM
Introduction
Theory
Method
Results
a
b
c
d
Massimo Pinto ENEA-INMRI, Italy
Frédéric Tessier NRC, Canada
Reid Townson NRC, Canada
Romain Coulon BIPM
Frédéric Meynadier BIPM
BIPM Ionizing Radiation Department GitHub repository
BIPM Time Department GitLab instance
Install git: this is easy!
Linux
$ sudo apt install git-all # on systems relying on .deb packages
$ sudo yum install git-all # on systems relying on .rpm packagesmacOS
$ git --version # if not installed, will prompt to install itWindows
1. Download installer: https://gitforwindows.org/
2. Open the Git BASH application to run terminal git commands.
There are dozens of guis for git
Visual Studio Code
gitk
GitHub Desktop
Sourcetree
GitKraken
Tell git who you are: git config
- Specify a name and email that will be associated with your commits.
This is essential for collaborative work and public repositories.
$ git config --global user.name "Firstname Lastname"
$ git config --global user.email "firstname.lastname@email.com"- You can inspect your git configuration variables at any time:
$ git config --list
user.email=firstname.lastname@email.com
user.name=Firstname Lastname
core.editor=vim
core.autocrlf=input
log.abbrevcommit=true
color.ui=auto
init.defaultbranch=main
- There is a long list of configuration variables, see the git-config manual
Create a repository: git init
-
Create a new directory for our project:
$ mkdir myproject- Go inside that directory and initialize git:
$ cd myproject/
$ git init
Initialized empty Git repository in /home/user/myproject/.git/
- The hidden .git directory is the repository (don’t remove it!)
$ ls -al
total 0
drwxr-xr-x 3 user staff 96 7 Feb 10:58 .
drwxr-xr-x 63 user staff 2016 7 Feb 10:57 ..
drwxr-xr-x 9 user staff 288 7 Feb 10:58 .git
myproject/
.git/
Check the current state of the project: git status
- Check the status of our new, empty repository:
$ git status
On branch main
No commits yet
nothing to commit (create/copy files and use "git stage" to track)- After creating a new file myproject/myfile.txt:
$ git status
On branch main
No commits yet
Untracked files:
(use "git stage <file>..." to include in what will be committed)
myfile.txt
nothing added to commit but untracked files present (use "git stage" to track)reminders in the status
git ignores untracked files
- We must add files to the repository explicitly. By default, new files
are untracked (ignored by git).
+
Stage changes to build a commit: git stage (git add)
- Creating a commit involves two steps:
+
working “tree”
myproject/
Stage changes to build a commit: git stage (git add)
- Stage new files (or file modifications) to start building a new commit:
$ git stage myfile.txt
$ git status
On branch main
No commits yet
Changes to be committed:
(use "git rm --cached <file>..." to unstage)
new file: myfile.txt- Creating a commit involves two steps:
stage
working “tree”
myproject/
git stage
+
reminder of command to unstage
Record the commit in the repository: git commit
- When our commit is ready, we record it in the repository:
$ git commit -m "Initial commit"
[main (root-commit) b753721] Initial commit
1 file changed, 0 insertions(+), 0 deletions(-)
create mode 100644 myFile.txt
$ git status
On branch main
nothing to commit, working tree clean
stage
working “tree”
myproject/
+
repository
myproject/.git/
git commit
-m “Commit message”
(or git opens a text editor)
- Creating a commit involves two steps:
git stage
Find out what has changed: git diff
- For each file, differences are displayed, line by line in “diff” format:
$ echo "Here is my change" >> myfile.txt
$ git diff
diff --git a/myfile.txt b/myfile.txt
index e69de29..7381106 100644
--- a/myfile.txt
+++ b/myfile.txt
@@ -0,0 +1 @@
+Here is my change.$ git diff --name-status
M myfile.txt- Many output options are available, here for example a more concise one:
- It is possible to compare any two commits in the repository by specifying two commit references (hashes, branch names, etc.), for example:
$ git diff e69de29 7381106 # any two commit references (here two commit hashes)the difference between the current working
copy and what is stored in the repository (.git/)
Revisit history: git log
- The log only lists the commits (not the working or staged changes):
$ git log
commit b753721
Author: Reid Townson <myemail@email.com>
Date: Thu Nov 25 14:40:00 2021 -0500
Initial commit$ git stage myfile.txt # stage changes
$ git commit -m "Insert a line to illustrate a modification" # commit them
$ git log
commit b48f500
Author: Reid Townson <myemail@email.com>
Date: Fri Dec 10 12:31:37 2021 -0500
Insert a line to illustrate a modification
commit b753721
Author: Reid Townson <myemail@email.com>
Date: Thu Nov 25 14:40:00 2021 -0500
Initial commit- Stage and commit our change, and see it appear in the log:
useful to find commit hashes of older commits!
Collaborate: host a repository on github.com
EGSnrc/
.git/
Pick your hosting service: github.com, gitlab.com, bitbucket.org.
Duplicate a repository: git clone
EGSnrc/
.git/
$ git clone https://github.com/nrc-cnrc/EGSnrc.git
Cloning into 'EGSnrc'...
remote: Enumerating objects: 13850, done.
remote: Counting objects: 100% (141/141), done.
remote: Compressing objects: 100% (125/125), done.
remote: Total 13850 (delta 57), reused 49 (delta 16), pack-reused 13709
Receiving objects: 100% (13850/13850), 54.38 MiB | 2.27 MiB/s, done.
Resolving deltas: 100% (9215/9215), done.
Updating files: 100% (2448/2448), done.Cloning means duplicating the repository locally, including the entire history, branches, etc.
Send changes to the remote: git push
- Repositories you are linked to are called remotes. To view these links:
$ cd myproject/
$ git remote -v
origin https://github.com/myname/myproject.git (fetch)
origin https://github.com/myname/myproject.git (push)$ git push origin
Enter passphrase for key '/home/myname/.ssh/id_rsa':
...
To github.com:myname/myproject.git
b680987..ffa4138 main -> main- After making local changes, you can push them to the “origin” remote:
$ git status
On branch main
Your branch is up to date with 'origin/main'.
nothing to commit, working tree clean- As always, check the status to confirm:
a remote can be any URL
Receive changes from the remote: git pull
- If there are new commits in the remote, we need to update the local repo:
$ git pull
...
From github.com:myname/myproject
ffa4138..a9700ea main -> origin/main
Updating ffa4138..a9700ea
Fast-forward
myFile.txt | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)$ git pull
Auto-merging myFile.txt
CONFLICT (content): Merge conflict in myFile.txt
Automatic merge failed; fix conflicts and then commit the result.- If there are merge conflicts, git asks you to fix them manually:
a summary of the changes that were pulled in the local repo
- Resolving conflicts is an advanced topic. To cancel the entire pull operation at this point, issue the command:
git merge --abort
git data flow cheat sheet
stage
working “tree”
local repo
remote repo
.git/
git stage
git commit
git push
git pull
git fetch
git merge
We surveyed the basic git operations
- init
- status
- stage
- commit
- diff
- log
- clone
- push
- pull
All the advanced topics are easier to grasp once you
figure out the basics: what a commit is, how git operates.
Basic concepts
- branches
- remotes
- tags
- searching
- merging
- rebasing
- resolving conflicts
- resetting
- cherry-picking
- interactive staging
- cleaning, rewriting history
- submodules
- git workflows
- set up an internal git server
- ...
More advanced topics
Introduction
Theory
Method
Results
a
b
c
d
Massimo Pinto ENEA-INMRI, Italy
Frédéric Tessier NRC, Canada
Reid Townson NRC, Canada
Romain Coulon BIPM
Frédéric Meynadier BIPM
BIPM Ionizing Radiation Department GitHub repository
BIPM Time Department GitLab instance
Introduction
Theory
Method
a
b
c
Massimo Pinto ENEA-INMRI, Italy
Frédéric Tessier NRC, Canada
Reid Townson NRC, Canada
Contributions
Massimo Pinto explained how version control promotes file management that is robust, reliable, and how it enables collaboration and open science.
Frédéric Tessier articulated a fundamental picture of the git philosophy and its inner workings, to accelerate the learning of git concepts and git operations.
Reid Townson taught the basic git commands with practical examples so that you can start managing your individual or collaborative projects with git right away.
Romain Coulon and Frédéric Meynadier showcased two real-life scenarios at the BIPM where git is enabling a project management approach that complies de facto with ISO 17025 principles.
In ISO/IEC 17025:2017
“7.5.2 The laboratory shall ensure that amendments to technical records can be tracked to previous versions or to original observations. Both the original and amended data and files shall be retained, including the date of alteration, an indication of the altered aspects and the personnel responsible for the alterations.”