Add functions that can extract and update phenological status based on MODIS data and enable monthly SDA

Qianyuxuan commented 5 months ago

Description

Add a function to extract MODIS phenological data under "data.remote" package based on user-defined sites' locations and dates.
Add functions that can parameterize leaf-on and leaf-off dates for SIPNET model with MODIS phenological data.
Enable SDA with monthly observations.
Add a pecan.xml template for running single-site SDA.
Fix bugs in Dongchen's new block-based SDA modules "Analysis_sda_block.R".
Motivation and Context

Review Time Estimate

[ ] Immediately
[ ] Within one week
[x] When possible

Types of changes

[x] Bug fix (non-breaking change which fixes an issue)
[x] New feature (non-breaking change which adds functionality)
[x] Breaking change (fix or feature that would cause existing functionality to change)

Checklist:

[ ] My change requires a change to the documentation.
[ ] My name is in the list of CITATION.cff
[ ] I have updated the CHANGELOG.md.
[x] I have updated the documentation accordingly.
[ ] I have read the CONTRIBUTING document.
[ ] I have added tests to cover my changes.
[ ] All new and existing tests passed.

mdietze commented 3 months ago

@Qianyuxuan there's a bunch of errors coming up in the build that suggest that you're missing namespaces on functions

check base/workflow
  0 warnings found in base/workflow.
  1 notes found in base/workflow.
  ── R CMD check comparison ──────────────────────────── PEcAn.workflow 1.7.2 ────
  Status: BROKEN

  ── Fixed

  ✔ checking CRAN incoming feasibility ... WARNING
  ✔ checking DESCRIPTION meta-information ... NOTE

  ── Newly failing

  ✖ checking R code for possible problems ... NOTE

  R check of base/workflow reports the following new problems. Please fix these and resubmit:
  Error: Please fix these and resubmit.
  Execution halted
  checking R code for possible problems ... NOTE
  qsub_parallel: no visible global function definition for
    ‘makeSOCKcluster’
  qsub_parallel: no visible global function definition for
    ‘registerDoSNOW’
  qsub_parallel: no visible global function definition for
    ‘txtProgressBar’
  qsub_parallel : progress: no visible global function definition for
    ‘setTxtProgressBar’
  qsub_parallel: no visible global function definition for ‘%dopar%’
  qsub_parallel: no visible global function definition for ‘foreach’
  qsub_parallel: no visible binding for global variable ‘run’
  qsub_parallel: no visible global function definition for
    ‘remote.execute.cmd’
  qsub_parallel: no visible binding for global variable ‘host’
  qsub_parallel: no visible binding for global variable ‘folder’
  qsub_parallel: no visible global function definition for ‘stopCluster’
  Undefined global functions or variables:
    %dopar% folder foreach host makeSOCKcluster registerDoSNOW
    remote.execute.cmd run setTxtProgressBar stopCluster txtProgressBar

Qianyuxuan commented 3 months ago

@mdietze Sorry I just realized the files "qsub_parallel.R" and "merge_job_files.R" were placed under "/base/workflow" by mistake long ago. They should be under "/base/remote" and they were there now as committed by Dongchen. I will delete these files under the workflow.

mdietze commented 3 months ago

check modules/data.land
  2 warnings found in modules/data.land.
  2 notes found in modules/data.land.
  Error: Please fix these and resubmit.
  R check of modules/data.land returned new problems:
  checking Rd \usage sections ... WARNING: Undocumented arguments in documentation object 'prepare_pools' 'settings'

mdietze commented 3 months ago

check models/sipnet
  2 warnings found in models/sipnet.
  2 notes found in models/sipnet.
  Error: Please fix these and resubmit.
  Execution halted
  R check of models/sipnet returned new problems:
  checking Rd \usage sections ... WARNING: Undocumented arguments in documentation object 'write.config.SIPNET' 'defaults' 'trait.values' 'settings' 'run.id' 'inputs' 'IC' 'restart' 'spinup' 'obs_time' 'update_phenology'

PecanProject / pecan