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ENH: Add carbontracker to track pipeline energy consumption and carbon footprint #94

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ENH: Add carbontracker to track pipeline energy consumption and carbon footprint #94

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sebastientourbier
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Test to use carbontracker (https://pypi.org/project/carbontracker/) to track environmental impact of running of CMP3

@sebastientourbier
Merge branch 'release/v3.0.0' of github.com:connectomicslab/connectom…
3f5c135 
…emapper3 into enh/release/v3.0.0/custom_anatomical
@sebastientourbier
MAINT: Move extract_base_directory to cmtklib/util and rename to extr…
228d98e 
…act_reconall_base_dir
@sebastientourbier
REF: Move 2 duplicated util functions to cmtklib/utils.py
ee77571
@sebastientourbier
ENH: Implement custom segmentation inputs compliant with BIDS derivat…
8cd4cd3 
…ives
@sebastientourbier
STY: Correct typo
fec9243
@sebastientourbier
REF: move get_basename() from parcellation.py to cmtklib/utils.py
b8f23ac
@sebastientourbier
STY: Run BLACK on parcellation.py
69486bd
@sebastientourbier
STY: Run BLACK on segmentation.py
74b03c8
@sebastientourbier
FIX: Add gzip to dockerfile
30529e8
@sebastientourbier
ENH: Add json for custom segmentations
8c527a8
@sebastientourbier
ENH: Update setup.py to manage JSON of cmp.config
7ec58ad
@sebastientourbier
ENH: Add __init__.py to cmp/config
e9073c5
@sebastientourbier
STY: Run BLACK on setup.py
5b38a34
@sebastientourbier
STY: Run BLACK on cmtklib/util.py
a7af6e1
@sebastientourbier
STY: Run BLACK on cmtklib/config.py
98da3a4
@sebastientourbier
STY: Run BLACK on cmtklib/connectome.py and clean comments
930d3ac
@sebastientourbier
ENH: Add custom bids dir and json for segmentation in graphical compo…
1289516 
…nent
@sebastientourbier
STY: Run BLACK on cmpbidsappmanager/stages/segmentation
6f03f45
@sebastientourbier
STY: Run BLACK on all the rest of the cmp/cmtklib files
5459135
@sebastientourbier
FIX: Review way matlab runtime is installed for freesurfer in dockerfile
fa11024
@sebastientourbier
FIX: Dockerfile
9d9386d
@sebastientourbier
FIX: Review way matlab runtime is installed for freesurfer in dockerfile
0aaf043
@sebastientourbier
ENH: Add json for custom segmentation / parcellation
fe0407b
@sebastientourbier
FIX: Add unzip for new script that install FS matlab runtime
77f830c
@sebastientourbier
ENH: Add subject and session as stage attributes
8e916c6
@sebastientourbier
ENH: Update construction of segmentation and parcellation stage with …
98fac16 
…subject and session
@sebastientourbier
ENH: Add custom bids derivatives directory and json to `cmp/stages/pa…
4b0337d 
…rcellation`
@sebastientourbier
Merge branch 'release/v3.0.0' into enh/release/v3.0.0/custom_anatomical
c55eeec
@sebastientourbier
Merge branch 'release/v3.0.0' into enh/release/v3.0.0/custom_anatomical
5a04dcb
@sebastientourbier
Merge branch 'release/v3.0.0' into enh/release/v3.0.0/custom_anatomical
a2eda54
@sebastientourbier
MAINT: Improve code for datasinker substitution of anatomical pipeline
4e16988
@sebastientourbier
STY: Review flow connect layout and protect from being BLACK formatted
51d1ee0
@sebastientourbier
Merge remote-tracking branch 'origin/enh/release/v3.0.0/custom_anatom…
cdd0007 
…ical' into enh/release/v3.0.0/custom_anatomical
@sebastientourbier
REF: Refactor create_pipeline_workflow() of anatomical pipeline
f9b328e
@sebastientourbier
ENH: Create function create_datasinker_node() of anatomical pipeline
ea0893d
@sebastientourbier
FIX: Review datasinker for NativeFreesurfer
9a9553c
@sebastientourbier
STY: Handle function arguments of cmat() with None and initialization…
40b6d10 
… of an empty dictionary
@sebastientourbier
MAINT: Use fstring to show nb_threads in cmp/project.py
a97bf9f
@sebastientourbier
STY: Review code layout and protect flow connects in `stages/parcella…
1cf8df1 
…tion/parcellation.py`
@sebastientourbier
ENH: Generation of BIDS ROI label/index mapping file
fc729a3
@sebastientourbier
CI: Comment test of list of outputs for new BIDS ROI label/index mapp…
f20866c 
…ing file
@sebastientourbier
STY: Correct code style issues
e175ae0
@sebastientourbier
MAINT: Review conditions to handle Custom parcellation in `parcellati…
1c40c0e 
…on.py`
@sebastientourbier
MAINT: clean and make consistent tools and versions in conda environm…
c87d3b4 
…ents
@sebastientourbier
ENH: Add carbontracker to be installed in the conda environment
dba1b9c
@sebastientourbier
STY: review code style in tracker
cd90b36
@sebastientourbier
ENH: Add carbontracker to BIDS App "run.py" entrypoint script
7eaa384
@sebastientourbier sebastientourbier added the enhancement New feature or request label May 6, 2021
@sebastientourbier sebastientourbier self-assigned this May 6, 2021
@sebastientourbier
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Due to challenges in accessing host hardware consumptions from within a Docker container with no root privileges, I am closing this PR.
An alternative approach would be to integrate the carbon tracker at the level of the python container wrappers that were introduced in #113 and #112.

@sebastientourbier sebastientourbier deleted the enh/release/v3.0.0/carbon_tracker branch January 3, 2022 08:38
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