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Update documentation
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Luke Marsden committed Apr 19, 2024
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11 changes: 6 additions & 5 deletions 01_opening_and_understanding.html

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47 changes: 24 additions & 23 deletions 02_creating_plots.html

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75 changes: 38 additions & 37 deletions 03_extracting_data_to_different_formats.html

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277 changes: 139 additions & 138 deletions 04_creating_a_cfnetcdf_file.html

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265 changes: 133 additions & 132 deletions 05_how_to_structure_your_NetCDF_file_or_files.html

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11 changes: 6 additions & 5 deletions 06_creating_multiple_cfnetcdf_files_in_one_go.html

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17 changes: 3 additions & 14 deletions 07_combing_data_from_multiple_netcdf_files.html

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41 changes: 26 additions & 15 deletions 08_ancillary_variables.html

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371 changes: 82 additions & 289 deletions 09_cells_and_cell_methods.html

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2 changes: 1 addition & 1 deletion _sources/03_extracting_data_to_different_formats.ipynb
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"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.11.4"
"version": "3.11.5"
}
},
"nbformat": 4,
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6 changes: 3 additions & 3 deletions _sources/04_creating_a_cfnetcdf_file.ipynb
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"And remember we might want to select additional applicable global attributes from this section of the CF conventions:\n",
"https://cfconventions.org/Data/cf-conventions/cf-conventions-1.11/cf-conventions.html#attribute-appendix\n",
"\n",
"Go through and add each required attribute and any others you wish to. You are also welcome to add any global attributes from the CF conventions as well as any custom attributes on top of these requirements. Similarly to variable attributes, this can either be done one by one or all in one in a dictionary. "
"Go through and add each required attribute and any others you wish to. You are also welcome to add any custom attributes on top of these requirements. Similarly to variable attributes, this can either be done one by one or all in one in a dictionary. "
]
},
{
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"id": "3d9fd5f0",
"metadata": {},
"source": [
"In this case, it makes sense to some attributes based on information we have already provided."
"In this case, it makes sense to add some attributes based on information we have already provided."
]
},
{
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"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.11.4"
"version": "3.11.5"
}
},
"nbformat": 4,
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18 changes: 9 additions & 9 deletions _sources/08_ancillary_variables.ipynb
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"\n",
"We need to create a new variable for the flags.\n",
"\n",
"Flags are stored as numbers, and with the meanings for the numbers stored as a variable attribute. The `flag_meanings` should be separated by spaces - so don't include spaces in any of the terms you use! The length of the `flag values` and `flag_meanings` should be the same. "
"Flags are stored as numbers, and with the meanings for the numbers stored as a variable attribute. The *flag_meanings* should be separated by spaces - so don't include spaces in any of the terms you use! The length of the *flag values* and *flag_meanings* should be the same. "
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"id": "96a656ec",
"metadata": {},
"source": [
"So for example, a value of 2 means 'probably_good_data'\n",
"So for example, a value of 2 means *probably_good_data*.\n",
"\n",
"You might wonder which conventions these quality flag values and meanings adhere to. In this case, we are following the OceanSITES Manual v 1.4.\n",
"http://www.oceansites.org/docs/oceansites_data_format_reference_manual.pdf\n",
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"id": "ad00e25c",
"metadata": {},
"source": [
"Now we need to state that the new 'Chlorophyll_A_quality_flags' variable is related to the 'Chlorophyll A' variable."
"Now we need to state that the new *Chlorophyll_A_quality_flags* variable is related to the *Chlorophyll A* variable."
]
},
{
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"id": "3ba86208",
"metadata": {},
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"Finally we need to add our metadata to the ancillary variable to describe it. There are a lot of standard names for different types of flags. Search for 'flag' here to find a suitable `standard_name` for you. \n",
"Finally we need to add our metadata to the ancillary variable to describe it. There are a lot of standard names for different types of flags. Search for *flag* here to find a suitable *standard_name* for you. \n",
"https://cfconventions.org/Data/cf-standard-names/current/build/cf-standard-name-table.html\n",
"\n",
"The CF conventions also has standardised variable attributes you can use for `flag_values`and `flag_meanings`. You often see the `valid_range` attribute used here too to explicitely show that any values outside of that range are invalid. You could use `valid_min` and `valid_max` used instead."
"The CF conventions also has standardised variable attributes you can use for *flag_values* and *flag_meanings*. You often see the *valid_range* attribute used here too to explicitely show that any values outside of that range are invalid. You could use *valid_min* and *valid_max* used instead."
]
},
{
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"id": "667e8976",
"metadata": {},
"source": [
"Make sure you refer to the conventions you are following for your quality flags in your `Conventions` global attribute, for example"
"Make sure you refer to the conventions you are following for your quality flags in your *Conventions* global attribute, for example"
]
},
{
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"metadata": {},
"source": [
"## Retrieving only good_quality data\n",
"Suppose we want to retrieve only the good_quality `Chlorophyll_A` data, where `Chlorophyll_A_quality_flags = 1`"
"Suppose we want to retrieve only the good_quality *Chlorophyll_A* data, where *Chlorophyll_A_quality_flags = 1*"
]
},
{
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"id": "8e994299",
"metadata": {},
"source": [
"More work needs to be done to expand the CF conventions to standardise ancillary data. At the time of writing, a `standard_name` for the volume of sea water filtered does not exist. \n",
"More work needs to be done to expand the CF conventions to standardise ancillary data. At the time of writing, a *standard_name* for the volume of sea water filtered does not exist. \n",
"\n",
"This is where the scientific community can help! \n",
"\n",
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