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uaf-arctic-eco-modeling / dvm-dos-tem

A process based Dynamic Vegetation, Dynamic Organic Soil, Terrestrial Ecosystem Model.
MIT License
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fix paths for building sphinx documentation #701

Open tobeycarman opened 7 months ago

tobeycarman commented 7 months ago

Currently the documentation, specifically Example Experiment 0, requires that the user has the following dataset on their computer:

/data/input-catalog/cru-ts40_ar5_rcp85_ncar-ccsm4_TOOLIK_FIELD_STATION_10x10/

which is not something that comes with a clone of the repository.

Suggest changing so that building the documentation only requires data that ships with the repository.

Additionally there may be issues with missing directories when building for the first time:

$ sphinx-build ./source/ ./build
Running Sphinx v5.1.1
making output directory... done
building [mo]: targets for 0 po files that are out of date
building [html]: targets for 25 source files that are out of date
updating environment: [new config] 25 added, 0 changed, 0 removed
executing example_experiment_0ples_and_tutorials/example_experiment_0                                 
/work/docs_src/sphinx/source/CLI_tools/input.rst:3: WARNING: duplicate label cli_tools/input:positional arguments, other instance in /work/docs_src/sphinx/source/CLI_tools/input.rst
/work/docs_src/sphinx/source/CLI_tools/input.rst:3: WARNING: duplicate label cli_tools/input:named arguments, other instance in /work/docs_src/sphinx/source/CLI_tools/input.rst
/work/docs_src/sphinx/source/CLI_tools/input.rst:3: WARNING: duplicate label cli_tools/input:positional arguments, other instance in /work/docs_src/sphinx/source/CLI_tools/input.rst
/work/docs_src/sphinx/source/CLI_tools/input.rst:3: WARNING: duplicate label cli_tools/input:named arguments, other instance in /work/docs_src/sphinx/source/CLI_tools/input.rst
/work/docs_src/sphinx/source/CLI_tools/input.rst:3: WARNING: duplicate label cli_tools/input:positional arguments, other instance in /work/docs_src/sphinx/source/CLI_tools/input.rst
/work/docs_src/sphinx/source/CLI_tools/qcal.rst:5: ERROR: Failed to import "cmdline_define" from "util.qcal".
No module named 'calibration'

Extension error:
Cell raised uncaught exception:
---------------------------------------------------------------------------
FileNotFoundError                         Traceback (most recent call last)
Cell In[1], line 15
     11 from util.output import load_trsc_dataframe
     13 # This lets us work with shorter paths relative to the experiment
     14 # directory
---> 15 os.chdir('/data/workflows/exp0_jan26_test')

FileNotFoundError: [Errno 2] No such file or directory: '/data/workflows/exp0_jan26_test'

and 

[Errno 2] No such file or directory: b'output/VEGC_yearly_tr.nc'