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Let pygmt.info load datetime columns into a str dtype array - #960

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weiji14 merged 3 commits into
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info_load_datetime_as_str
Mar 3, 2021
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Let pygmt.info load datetime columns into a str dtype array#960
weiji14 merged 3 commits into
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info_load_datetime_as_str

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@weiji14weiji14 commented Feb 24, 2021•
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Description of proposed changes

Fixes problem with pygmt.info not being able to handle datetime64 inputs. I.e. ValueError: could not convert string to float: '2021-01-01T12:34:56'.

However, users will still need to usepygmt.info(..., f="0T") until upstream issue at GenericMappingTools/gmt#4241 is resolved. Something like so:

importpandasaspdimportpygmttable=pd.date_range(start="2020-01-01", periods=5).to_numpy()
output=pygmt.info(table=table, per_column=True, f="0T")
print(output)
# ['2020-01-01T00:00:00' '2020-01-05T00:00:00']

Also added two extra unit tests using numpy datetime64 types.

References:

Addresses #597 on the pygmt side using fix mentioned in #597 (comment). Assuming that GenericMappingTools/gmt#4241 is fixed in GMT 6.2.0, then issue #597 can be closed once PyGMT bumps minimum required GMT version to 6.2.0.

Reminders

  • Run make format and make check to make sure the code follows the style guide.
  • Add tests for new features or tests that would have caught the bug that you're fixing.
  • Add new public functions/methods/classes to doc/api/index.rst.
  • Write detailed docstrings for all functions/methods.
  • If adding new functionality, add an example to docstrings or tutorials.

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specific operations. Supported slash commands are:

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  • /test-gmt-dev: run full tests on the latest GMT development version

@weiji14
Let pygmt.info load datetime columns into a str dtype array
7b38109
Fixes problem with pygmt.info not being able to handle datetime64 inputs.
I.e. `ValueError: could not convert string to float: '2021-01-01T12:34:56'`
However, users will still need to use`pygmt.info(..., f="0T")` until
upstream issue at GenericMappingTools/gmt#4241
is resolved. Also added two extra unit tests using numpy datetime64 types.
@weiji14weiji14 added the bug Something isn't working label Feb 24, 2021
@weiji14weiji14 added this to the 0.3.1 milestone Feb 24, 2021
weiji14
weiji14 commented Feb 24, 2021
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Comment threadpygmt/tests/test_info.py Outdated
Comment threadpygmt/tests/test_info.py Outdated
seisman
seisman reviewed Feb 25, 2021
View reviewed changes
Comment threadpygmt/src/info.py
@weiji14weiji14 mentioned this pull request Mar 3, 2021
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weiji14 added a commit that referenced this pull request Mar 3, 2021
@weiji14
Add common alias coltypes (-f) for specifying i/o data types
132d5ce
Used to specify data types of input and/or output
columns (time or geographical data). See also:
- https://docs.generic-mapping-tools.org/6.1/gmt.html#f-full
- https://github.com/GenericMappingTools/gmt/blob/6.1.1/doc/rst/source/explain_-f.rst_
- https://github.com/GenericMappingTools/gmt/blob/master/doc/rst/source/explain_-f_full.rst_
- https://docs.generic-mapping-tools.org/6.1/cookbook/options.html#data-type-selection-the-f-option
Needed for the workaround datetime bugfix at #960
@weiji14weiji14 mentioned this pull request Mar 3, 2021
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weiji14 added a commit that referenced this pull request Mar 3, 2021
@weiji14
Add common alias coltypes (-f) for specifying i/o data types (#994)
eb2bcc5
Used to specify data types of input and/or output
columns (time or geographical data). See also:
- https://docs.generic-mapping-tools.org/6.1/gmt.html#f-full
- https://github.com/GenericMappingTools/gmt/blob/6.1.1/doc/rst/source/explain_-f.rst_
- https://github.com/GenericMappingTools/gmt/blob/master/doc/rst/source/explain_-f_full.rst_
- https://docs.generic-mapping-tools.org/6.1/cookbook/options.html#data-type-selection-the-f-option
Needed for the workaround datetime bugfix at #960
@weiji14
weiji14 marked this pull request as ready for review March 3, 2021 21:19
@weiji14

weiji14 commented Mar 3, 2021

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Hmm, that crash on the Windows GMT dev test at https://github.com/GenericMappingTools/pygmt/runs/2025836161?check_suite_focus=true#step:15:86 at the start (before any tests got run) doesn't look nice.

@seisman

seisman commented Mar 3, 2021•
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/test-gmt-dev

Hmm, that crash on the Windows GMT dev test at GenericMappingTools/pygmt/runs/2025836161?check_suite_focus=true#step:15:86 at the start (before any tests got run) doesn't look nice.

It may be just a sporadic crash. Just re-triggered the dev tests.

Edit: Jobs at https://github.com/GenericMappingTools/pygmt/actions/runs/619017413

@weiji14

weiji14 commented Mar 3, 2021•
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Thanks! Windows tests have passed at https://github.com/GenericMappingTools/pygmt/runs/2026019634?check_suite_focus=true#step:15:867. Any other comment on this PR?

@weiji14
weiji14 merged commit 52dbd7a into masterMar 3, 2021
@weiji14
weiji14 deleted the info_load_datetime_as_str branch March 3, 2021 22:17
@weiji14weiji14 mentioned this pull request Mar 3, 2021
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sixy6e pushed a commit to sixy6e/pygmt that referenced this pull request Dec 21, 2022
@weiji14Josh Sixsmith
Add common alias coltypes (-f) for specifying i/o data types (Generic…
8a1945b
…MappingTools#994)
Used to specify data types of input and/or output
columns (time or geographical data). See also:
- https://docs.generic-mapping-tools.org/6.1/gmt.html#f-full
- https://github.com/GenericMappingTools/gmt/blob/6.1.1/doc/rst/source/explain_-f.rst_
- https://github.com/GenericMappingTools/gmt/blob/master/doc/rst/source/explain_-f_full.rst_
- https://docs.generic-mapping-tools.org/6.1/cookbook/options.html#data-type-selection-the-f-option
Needed for the workaround datetime bugfix at GenericMappingTools#960
sixy6e pushed a commit to sixy6e/pygmt that referenced this pull request Dec 21, 2022
@weiji14Josh Sixsmith
Let pygmt.info load datetime columns into a str dtype array (GenericM…
f57277d
…appingTools#960)
Fixes problem with pygmt.info not being able to handle datetime64 inputs.
I.e. `ValueError: could not convert string to float: '2021-01-01T12:34:56'`
However, users will still need to use`pygmt.info(..., coltypes="0T")` until
upstream issue at GenericMappingTools/gmt#4241
is resolved. Also added two extra unit tests using numpy datetime64 types.
* Use common alias coltypes (f) in tests and make a note on the workaround
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