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feat : source docs sample added #34

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@Namyalg Namyalg commented Apr 27, 2022

A sample source documentation has been created in this PR.

Namyalg and others added 30 commits April 27, 2022 20:36
@Namyalg
source docs sample
4c58b91
@Namyalg
removed extra files
663d110
@Adexandria
source docs
0f6aa95
@Namyalg
Merge pull request #1 from Adexandria/source-docs
0ec3fe1 
source docs sample for cbmaggregatorlandunitdata
@Namyalg
docs: cbmaggregatorlandunitdata documented
5c20aab
@Adexandria
source-docs sample
3d33347
@Adexandria
Merge branch 'Namyalg:source-docs' into source-docs
969681a
@Namyalg
Merge pull request #2 from Adexandria/source-docs
5c8b564 
Source docs sample for cbmaggregatorlibpqxxwriter
@Namyalg
source docs generated for cbmaggregatorlibpqxxwriter.cpp
aeb1706
@Namyalg
add cbmaggregatorlibpqxxwriter to index.rst, add runs-on to build-doc…
4783755 
…s.yml
@Namyalg
Update build-docs.yml
e13dc34
@Namyalg
Update build-docs.yml
e5195ae
@Namyalg
Update build-docs.yml
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@Namyalg
Update build-docs.yml
8e4639f
@Namyalg
Add GHA to deploy to Netlify
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@Namyalg
Update build-docs.yml
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@Namyalg
ci: add doxygen as dependency
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@Namyalg
Merge branch 'source-docs' of https://github.com/Namyalg/moja.canada …
ac6538e 
…into source-docs
@Namyalg
add class description to cbmaggregatorlibpqxxwriter, increase timeout…
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… for site deploy in build-docs
@Namyalg
in prod: true
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@Namyalg
remove production branch
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@Namyalg
in prod: true
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@Namyalg
modify doxygen config
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@Adexandria
added description to ln 115 method
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@Adexandria
source docs sample
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@Adexandria
Merge branch 'Namyalg:source-docs' into source-docs
a1f31dc
@Adexandria
Fixed spacing issues
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line 110 -112
@Adexandria
fixed spacing issues
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@Namyalg
Merge pull request #3 from Adexandria/source-docs
1468e36 
Source docs sample for cbmaggregatorpostgresqlwriter
@Namyalg
build source docs for cbmaggregatorpostgresqlwriter'
e517017
Namyalg and others added 28 commits August 3, 2022 16:03
@Namyalg
docs: update standcomponent and cbmspinupsequencer
6b572ce
@Namyalg
docs: update flatrecord.cpp
f06ef2b
@Namyalg
chore: event descriptions added to glossary
f6fd2b6
@Adexandria @Namyalg
docs: source docs added for moja.modules.cbm
33474bd
@Namyalg
fix: merge conflict in cbmaggregatorcsvwriter.cpp
58b5953
@Namyalg
Updated/tested to use applied annual water table depth in turnover an…
9d7d0c2 
…d decay.

1) applied annual WTD is set in turnover module (spinup and foward), and later used in decay module.
2) spinup turnover will use spinup longterm WTD for annual WTD in spinup turnover and decay
3) forward turnover will use regular annual drought code to compute the WTD for turnover and decay
4) disturbance trigged WTD modifier only applies to forward run
@Namyalg
csv output is now split into subdirectories by year for more efficien…
02407a4 
…t processing.
@Namyalg
Made splitting csv output into files by year optional, off by default.
de0fc55 
Fixed missing quotation marks in error output file.

chore: add clang format and git hooks for moja.canada (moja-global#35)

Signed-off-by: HarshCasper <[email protected]>
@Namyalg
Added header to files in debug mode.
478a7b4
@Namyalg
Fix error message strings with nested quotes.
df5256a
@Namyalg
# This is a combination of 32 commits.
6af7219 
# This is the 1st commit message:

In CBMSpinupSequencer, updated to read peatlandId from peatland map, and set variable peatland_class with the peatlandId. Enable peatland_class is writabler to prepare the transition from original peatland to different type peatland after certain disturbance.

# This is the commit message #2:

Update build-docs.yml
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Create requirements.txt
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modified source sample doc

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source docs format updated

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update ageclasshelper

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update ageClassHelper

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chore: change documentation theme to doxygen

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updated cbmbuildlandunitmodule

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updated cbmdisturbanceeventmodule

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updated cbmdecaymodule

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updated cbmbuildlandunitmodule

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update: docs for ageclasshelper

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update: docs for ageclasshelper

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update ageClassHelper

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update docs for cbmageindicators

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update docs

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update docs

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add: source docs for peatlandparameters

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verify AgeClassHelper

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verify cbmageindicators

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add: docs for TreeSpecies

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docs for componentbiomasscarboncurve

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updated source for cbmflataggregatorlandunitdata

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review cbmlandunitmodule

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updated
@Namyalg
change docs_sphinx to docs
0ee6e34
@Adexandria @Namyalg
updated source docs for cbmdisturbancelistener
3d705ab
@Namyalg
# This is a combination of 46 commits.
6fbbab1 
# This is the 1st commit message:

In CBMSpinupSequencer, updated to read peatlandId from peatland map, and set variable peatland_class with the peatlandId. Enable peatland_class is writabler to prepare the transition from original peatland to different type peatland after certain disturbance.

# This is the commit message #2:

Update build-docs.yml
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Create requirements.txt
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modified source sample doc

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source docs format updated

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update ageclasshelper

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update ageClassHelper

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chore: change documentation theme to doxygen

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updated cbmbuildlandunitmodule

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updated cbmdisturbanceeventmodule

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updated cbmdecaymodule

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updated cbmbuildlandunitmodule

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updated cbmdecaymodule

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update: docs for ageclasshelper

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update: docs for ageclasshelper

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update ageClassHelper

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update docs for cbmageindicators

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update docs

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update docs

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add: source docs for peatlandparameters

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verify AgeClassHelper

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verify cbmageindicators

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add: docs for TreeSpecies

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docs for componentbiomasscarboncurve

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updated source for cbmflataggregatorlandunitdata

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review cbmlandunitmodule

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updated

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change docs_sphinx to docs

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Test github pages on GHA

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Update build-docs.yml
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Update build-docs.yml
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Update build-docs.yml
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Update build-docs.yml
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Update build-docs.yml
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review libpqxx and postgresql writer

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review sql writer

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review landunitdatatransform

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review docs, update peatlandaftercbmmodule

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updated source doc for cbmlandclasstransitionmodule
@Namyalg
fix: merge conflict cbmlandunitdatatransform.cpp
a4dbf2e
@Namyalg
# This is a combination of 49 commits.
e5d534d 
# This is the 1st commit message:

In CBMSpinupSequencer, updated to read peatlandId from peatland map, and set variable peatland_class with the peatlandId. Enable peatland_class is writabler to prepare the transition from original peatland to different type peatland after certain disturbance.

# This is the commit message #2:

Update build-docs.yml
# This is the commit message #3:

Create requirements.txt
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modified source sample doc

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source docs format updated

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update ageclasshelper

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Update build-docs.yml
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Update build-docs.yml
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Update build-docs.yml
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update ageClassHelper

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chore: change documentation theme to doxygen

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updated cbmbuildlandunitmodule

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updated cbmdisturbanceeventmodule

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updated cbmdecaymodule

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updated cbmbuildlandunitmodule

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updated cbmdecaymodule

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update: docs for ageclasshelper

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update: docs for ageclasshelper

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update ageClassHelper

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update docs for cbmageindicators

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update docs

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update docs

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add: source docs for peatlandparameters

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verify AgeClassHelper

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verify cbmageindicators

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add: docs for TreeSpecies

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docs for componentbiomasscarboncurve

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updated source for cbmflataggregatorlandunitdata

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review cbmlandunitmodule

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updated

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change docs_sphinx to docs

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Test github pages on GHA

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Update build-docs.yml
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Update build-docs.yml
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Update build-docs.yml
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Update build-docs.yml
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Update build-docs.yml
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Update build-docs.yml
# This is the commit message moja-global#41:

Update build-docs.yml
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review libpqxx and postgresql writer

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review sql writer

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review landunitdatatransform

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review docs, update peatlandaftercbmmodule

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updated source doc for cbmlandclasstransitionmodule

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updated sourec doc for cbmlandunitdatatransform

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updated

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update README
@Namyalg
# This is a combination of 66 commits.
231bb2c 
# This is the 1st commit message:

In CBMSpinupSequencer, updated to read peatlandId from peatland map, and set variable peatland_class with the peatlandId. Enable peatland_class is writabler to prepare the transition from original peatland to different type peatland after certain disturbance.

# This is the commit message #2:

Update build-docs.yml
# This is the commit message #3:

Create requirements.txt
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modified source sample doc

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source docs format updated

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update ageclasshelper

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Update build-docs.yml
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Update build-docs.yml
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Update build-docs.yml
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update ageClassHelper

# This is the commit message moja-global#11:

chore: change documentation theme to doxygen

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updated cbmbuildlandunitmodule

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updated cbmdisturbanceeventmodule

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updated cbmdecaymodule

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updated cbmbuildlandunitmodule

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updated cbmdecaymodule

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Update build-docs.yml
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update: docs for ageclasshelper

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update: docs for ageclasshelper

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update ageClassHelper

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update docs for cbmageindicators

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update docs

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update docs

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add: source docs for peatlandparameters

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verify AgeClassHelper

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verify cbmageindicators

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add: docs for TreeSpecies

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docs for componentbiomasscarboncurve

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updated source for cbmflataggregatorlandunitdata

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review cbmlandunitmodule

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updated

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change docs_sphinx to docs

# This is the commit message moja-global#34:

Test github pages on GHA

# This is the commit message moja-global#35:

Update build-docs.yml
# This is the commit message moja-global#36:

Update build-docs.yml
# This is the commit message moja-global#37:

Update build-docs.yml
# This is the commit message moja-global#38:

Update build-docs.yml
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Update build-docs.yml
# This is the commit message moja-global#40:

Update build-docs.yml
# This is the commit message moja-global#41:

Update build-docs.yml
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review libpqxx and postgresql writer

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review sql writer

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review landunitdatatransform

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review docs, update peatlandaftercbmmodule

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updated source doc for cbmlandclasstransitionmodule

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updated sourec doc for cbmlandunitdatatransform

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updated

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update README

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updated

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review CBMLandClassTransitionModule

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updated for CBMPeatlandSpinupOutput

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updated CBMPeatlandSpinupOutput

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updated

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review CBMLandClassTransitionModule

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review CBMLandClassTransitionModule

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docs for DynamicGrowthCurveLookupTransform

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updated

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review CBMPeatlandSpinupOutput

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docs for peatlandturnoverparameters

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update docs

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docs for peatlandgrowthcurvetransform

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source docs for CBMSequencer

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review PeatlandDisturbance

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docs for peatlandgrowthcurvetransform and peatlandgrowthmodule

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review cbmsequencer
@Namyalg
fix: merge conflict in cbmlandunitdatatransform.cpp
1194c8d
@Namyalg
fix: merge conflict in cbmspinupdisturbancemodule.cpp
5417a31
@Namyalg
# This is a combination of 74 commits.
d9cfe85 
# This is the 1st commit message:

In CBMSpinupSequencer, updated to read peatlandId from peatland map, and set variable peatland_class with the peatlandId. Enable peatland_class is writabler to prepare the transition from original peatland to different type peatland after certain disturbance.

# This is the commit message #2:

Update build-docs.yml
# This is the commit message #3:

Create requirements.txt
# This is the commit message #4:

modified source sample doc

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source docs format updated

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update ageclasshelper

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Update build-docs.yml
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Update build-docs.yml
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Update build-docs.yml
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update ageClassHelper

# This is the commit message moja-global#11:

chore: change documentation theme to doxygen

# This is the commit message moja-global#12:

updated cbmbuildlandunitmodule

# This is the commit message moja-global#13:

updated cbmdisturbanceeventmodule

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updated cbmdecaymodule

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updated cbmbuildlandunitmodule

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updated cbmdecaymodule

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Update build-docs.yml
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Update build-docs.yml
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update: docs for ageclasshelper

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update: docs for ageclasshelper

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update ageClassHelper

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update docs for cbmageindicators

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update docs

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update docs

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add: source docs for peatlandparameters

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verify AgeClassHelper

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verify cbmageindicators

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add: docs for TreeSpecies

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docs for componentbiomasscarboncurve

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updated source for cbmflataggregatorlandunitdata

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review cbmlandunitmodule

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updated

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change docs_sphinx to docs

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Test github pages on GHA

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Update build-docs.yml
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Update build-docs.yml
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Update build-docs.yml
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Update build-docs.yml
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Update build-docs.yml
# This is the commit message moja-global#40:

Update build-docs.yml
# This is the commit message moja-global#41:

Update build-docs.yml
# This is the commit message moja-global#42:

review libpqxx and postgresql writer

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review sql writer

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review landunitdatatransform

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review docs, update peatlandaftercbmmodule

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updated source doc for cbmlandclasstransitionmodule

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updated sourec doc for cbmlandunitdatatransform

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updated

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update README

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updated

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review CBMLandClassTransitionModule

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updated for CBMPeatlandSpinupOutput

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updated CBMPeatlandSpinupOutput

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updated

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review CBMLandClassTransitionModule

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review CBMLandClassTransitionModule

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docs for DynamicGrowthCurveLookupTransform

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updated

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review CBMPeatlandSpinupOutput

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docs for peatlandturnoverparameters

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update docs

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docs for peatlandgrowthcurvetransform

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source docs for CBMSequencer

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review PeatlandDisturbance

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docs for peatlandgrowthcurvetransform and peatlandgrowthmodule

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review cbmsequencer

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review files, add description to files

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docs for cbmspinupdisturbancemodule

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review cbmsequencer

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review CBMSequencer

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update cbmdisturbancelistener.cpp

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source docs for PeatlandDecayParameters

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source doc for PeatlandDecayParameters

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source docs for PeatlandFireParameters
@Namyalg
fix: merge conflict
ca5715d
@Namyalg
fix: merge conflict
7fbd8d3
@Namyalg
fix: merge conflict
4129ca7
@Namyalg
fix: merge conflict
4983094
@Namyalg
# This is a combination of 80 commits.
51eb3bd 
# This is the 1st commit message:

In CBMSpinupSequencer, updated to read peatlandId from peatland map, and set variable peatland_class with the peatlandId. Enable peatland_class is writabler to prepare the transition from original peatland to different type peatland after certain disturbance.

# This is the commit message #2:

Update build-docs.yml
# This is the commit message #3:

Create requirements.txt
# This is the commit message #4:

modified source sample doc

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source docs format updated

# This is the commit message #6:

update ageclasshelper

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Update build-docs.yml
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Update build-docs.yml
# This is the commit message #9:

Update build-docs.yml
# This is the commit message #10:

update ageClassHelper

# This is the commit message moja-global#11:

chore: change documentation theme to doxygen

# This is the commit message moja-global#12:

updated cbmbuildlandunitmodule

# This is the commit message moja-global#13:

updated cbmdisturbanceeventmodule

# This is the commit message moja-global#14:

updated cbmdecaymodule

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updated cbmbuildlandunitmodule

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updated cbmdecaymodule

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update: docs for ageclasshelper

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update: docs for ageclasshelper

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update ageClassHelper

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add: source docs for peatlandparameters

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verify AgeClassHelper

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verify cbmageindicators

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add: docs for TreeSpecies

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docs for componentbiomasscarboncurve

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updated source for cbmflataggregatorlandunitdata

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review cbmlandunitmodule

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updated

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change docs_sphinx to docs

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Test github pages on GHA

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review libpqxx and postgresql writer

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review landunitdatatransform

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review docs, update peatlandaftercbmmodule

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updated source doc for cbmlandclasstransitionmodule

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updated sourec doc for cbmlandunitdatatransform

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updated

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update README

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updated CBMPeatlandSpinupOutput

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updated

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review
@Namyalg
fix: merge conflict
0d620fb
@Namyalg
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In CBMSpinupSequencer, updated to read peatlandId from peatland map, and set variable peatland_class with the peatlandId. Enable peatland_class is writabler to prepare the transition from original peatland to different type peatland after certain disturbance.

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source docs format updated

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update ageclasshelper

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chore: change documentation theme to doxygen

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updated cbmbuildlandunitmodule

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updated cbmdisturbanceeventmodule

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updated cbmbuildlandunitmodule

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update: docs for ageclasshelper

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add: source docs for peatlandparameters

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verify AgeClassHelper

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add: docs for TreeSpecies

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docs for componentbiomasscarboncurve

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updated source for cbmflataggregatorlandunitdata

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review cbmlandunitmodule

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change docs_sphinx to docs

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Test github pages on GHA

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review libpqxx and postgresql writer

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review sql writer

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review landunitdatatransform

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review docs, update peatlandaftercbmmodule

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updated source doc for cbmlandclasstransitionmodule

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source docs for PeatlandDecayParameters

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include .h docs in .cpp file, write docs for standgrowthcurve

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docs for growthmultipliermodule, growthcurvetransform

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source docs for CBMTransitionRulesModule

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docs for mossdecaymodule, mossdisturbance

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docs for mossgrowthmodule, mossturnovermodule

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update

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docs for standbiomasscarboncurve

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docs for esgymspinupsequencer

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source docs for record

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review record

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docs:timeseriesidxfromflintdatatransform

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source documentation for cbmsequencer

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docs: peatlandspinupnext.cpp

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update: peatlandspinupnext.cpp
@Namyalg
In CBMSpinupSequencer, updated to read peatlandId from peatland map, …
460afc2 
…and set variable peatland_class with the peatlandId. Enable peatland_class is writabler to prepare the transition from original peatland to different type peatland after certain disturbance.

docs: build source docs
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@Namyalg @Adexandria