Allow passing arguments containing spaces into pygmt functions #1487

weiji14 · 2021-09-07T01:10:45Z

Description of proposed changes

To allow for spaces in arguments to PyGMT functions, this pull request modifies the build_arg_string function in pygmt/helpers/utils.py to replace space characters ( ) with the equivalent octal code (\040). This enables users to do this:

import pygmt

fig = pygmt.Figure()
fig.basemap(region=[0, 2, 4, 8], projection="X2c", frame=r"WSne+tPlot Zero")
fig.show()

Note that no nested double quotes ('"some word"') are needed anymore!

I have also removed some hacky workarounds that allowed for text inputs with spaces into:

subplot's autolabel(-A) and title (-T) parameters - workaround added in Convert booleans arguments in build_arg_string, not in kwargs_to_strings #1125 and Wrap subplot using with statement #822
text's -F parameter
psconvert's prefix (-F) parameter - workaround added in Let Figure.savefig support filenames with spaces #1116

Also updated some unit tests for fig.legend and fig.rose that had used arguments like '"Some text"'.

Special handling of functions where spaces can't just be converted to `\040`:

Ensure that pygmt.config(FORMAT_DATE_MAP="o dd") works (c29e632)
Make sure that fig.savefig() saves filenames with spaces properly (Let Figure.savefig support filenames with spaces #1116) without \040 octal code characters in the filename (83c8c3b)
Ensure that PROJ4 projections with spaces (e.g. projection="+proj4=+longlat +ellipsoid=someplanet") work, xref -JEPSG:4326 not writing CRS to netcdf in surface #655 (comment) (3ec7727)

Fixes #247 🎉 🎉 🎉

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.

Slash Commands

You can write slash commands (/command) in the first line of a comment to perform
specific operations. Supported slash commands are:

/format: automatically format and lint the code
/test-gmt-dev: run full tests on the latest GMT development version

Modifying build_arg_string function to replace blank space characters with octal code 040, and added a doctest to check various combinations with single and double quotes included.

Supersedes workaround for subplot's autolabel (-A) and title (-T) parameters in a9d167d, 4126c16, and eadb847.

Doesn't work yet, as the filename will contain the 040 octal code, but committing to have the diff available for review.

github-actions · 2021-09-07T01:12:16Z

Summary of changed images

This is an auto-generated report of images that have changed on the DVC remote

Status	Path
added	pygmt/tests/baseline/test_basemap_utm_projection.png
added	pygmt/tests/baseline/test_config_format_date_map.png
modified	pygmt/tests/baseline/test_rose_no_sectors.png

Image diff(s)

Added images

pygmt/tests/baseline/test_basemap_utm_projection.png

pygmt/tests/baseline/test_config_format_date_map.png

Modified images

Path	Old	New
test_rose_no_sectors.png

Report last updated at commit a526d45

weiji14 · 2021-09-07T01:23:25Z

pygmt/tests/test_figure.py

 with GMTTempFile(prefix="pygmt-filename with spaces", suffix=".png") as imgfile:
 fig.savefig(imgfile.name)
+ assert r"\040" not in os.path.abspath(imgfile.name)
 assert os.path.exists(imgfile.name)


A problem with this PR is that running fig.savefig with filenames that have spaces (introduced in #1116) will produce an output like "pygmt-filename\040with\040spaces.png". This test currently passes still, but it is a false positive, because Python's os.path.exists reads "pygmt-filename\040with\040spaces.png" as ""pygmt-filename with spaces.png"".

Any ideas how to improve the test and/or implementation of psconvert?

Ok, I've manually worked around the problem in 83c8c3b so filenames with spaces will be saved as usual (without \040 in the name).

willschlitzer · 2021-10-27T16:53:38Z

@weiji14 I'm assuming this won't be done by Friday? Should I bump it to a later version?

weiji14 · 2021-10-27T21:37:38Z

@weiji14 I'm assuming this won't be done by Friday? Should I bump it to a later version?

Yes, the bugfix here needs a thorough review and more tests I think, plus I haven't figured out how to resolve #1487 (comment). So let's move it to v0.6.0.

seisman · 2022-01-10T11:15:36Z

xref: https://forum.generic-mapping-tools.org/t/errors-in-pygmt-when-there-are-spaces-in-string-arguments/2494/3

Also added a regression test for FORMAT_DATE_MAP="o dd".

weiji14 · 2022-01-10T15:34:29Z

pygmt/src/config.py

@@ -55,7 +55,7 @@ def __init__(self, **kwargs):
 self.old_defaults[key] = lib.get_default(key)

 # call gmt set to change GMT defaults
- arg_str = " ".join([f"{key}={value}" for key, value in kwargs.items()])
+ arg_str = " ".join([f'{key}="{value}"' for key, value in kwargs.items()])


xref: https://forum.generic-mapping-tools.org/t/errors-in-pygmt-when-there-are-spaces-in-string-arguments/2494/3

Ok, I've fixed the FORMAT_DATE_MAP="o dd" issue reported in the forum by wrapping the arguments in double quotes here in commit c29e632. Didn't use \040 because o\040dd doesn't work. The problem with this solution is that the workaround suggested in the forum (use FORMAT_DATE_MAP='"o dd"') will break in PyGMT v0.6.0, but I think that's acceptable since that workaround isn't intuitive anyway.

So that fig.savefig won't insert `\040` characters when saving filenames with spaces. Resolves problem mentioned in https://github.com/GenericMappingTools/pygmt/pull/1487/files#r703116544

maxrjones · 2022-03-12T20:58:32Z

pygmt/figure.py

+ # Manually handle prefix -F argument so spaces aren't converted to \040
+ # by build_arg_string function. For more information, see
+ # https://github.com/GenericMappingTools/pygmt/pull/1487
+ prefix = kwargs.pop("F")


Should there be a check before this that prefix is provided so that the user doesn't get a KeyError here? Or you could raise GMTInvalidInput in an except statement.

Good point. Looking at the docs at https://docs.generic-mapping-tools.org/6.3/psconvert.html, it reads like prefix/-F is optional, but when I tried running psconvert without the -F option, it throws an error: psconvert [ERROR]: Modern GMT mode requires the -F option. See https://github.com/GenericMappingTools/gmt/blob/adb244afa51ca7246cc051080c9d47193087d6c2/src/psconvert.c#L1041-L1042

So since PyGMT is modern mode only, it should be fine to keep this line intact.

The docs say "If no input files are given, will convert the current active figure (see pygmt.figure). In this case, an output name must be given using parameter prefix." How does one provide other input files than the current figure using pygmt.Figure.psconvert?

If we chose not to support operations analogous to psconvert -Tg test.ps (which uses the same prefix as the original file name), I think we should make prefix required in the function signature or raise an invalid input exception to avoid the traceback below. I don't think it's obvious to that the error is caused by not using prefix.

How does one provide other input files than the current figure using pygmt.Figure.psconvert?

We can't, because it has not been implemented yet. The current fig.psconvert is a method of the pygmt.Figure() class and is tied to the fig, and can only 'psconvert' the active figure.

If we chose not to support operations analogous to psconvert -Tg test.ps (which uses the same prefix as the original file name), I think we should make prefix required in the function signature or raise an invalid input exception to avoid the traceback below. I don't think it's obvious to that the error is caused by not using prefix.

Ok, I've added a try-except block in 801ba01 to raise a GMTInvalidInput if prefix/-F is not given.

maxrjones · 2022-03-12T21:29:54Z

I tried for a while to break it. Nice work on this complicated issue!

The two issues that I came across relate to the outgrid and outfile parameters.

Outgrid parameter

The following will produce a filename with spaces using the main branch but the filename contains "\040" with this branch:

pygmt.grdcut("@earth_relief_01d", region=[0, 1, 0, 1], outgrid="test grid output.nc")

Outfile parameter

File outputs with spaces still require using the trick of wrapping double quotes in single quotes (this could be addressed separately from this PR).

pygmt.blockmean(data="@ship_15.txt", region=[245, 255, 20, 30], spacing="5m", outfile='"Test file output.txt"') # Works
pygmt.blockmean(data="@ship_15.txt", region=[245, 255, 20, 30], spacing="5m", outfile="Test file output.txt") # Doesn't work

weiji14 · 2022-03-12T22:25:47Z

I tried for a while to break it. Nice work on this complicated issue!

Thanks for testing this! I still have a nagging feeling that there's a random edge case that will break this, but we'll find out once this gets released into the wild 😈

The two issues that I came across relate to the outgrid and outfile parameters.

Outgrid parameter

The following will produce a filename with spaces using the main branch but the filename contains "\040" with this branch:
pygmt.grdcut("@earth_relief_01d", region=[0, 1, 0, 1], outgrid="test grid output.nc")
Outfile parameter

File outputs with spaces still require using the trick of wrapping double quotes in single quotes (this could be addressed separately from this PR).
pygmt.blockmean(data="@ship_15.txt", region=[245, 255, 20, 30], spacing="5m", outfile='"Test file output.txt"') # Works
pygmt.blockmean(data="@ship_15.txt", region=[245, 255, 20, 30], spacing="5m", outfile="Test file output.txt") # Doesn't work

Right, fixing this would require a workaround like the one applied to fig.savefig mentioned in #1487 (comment), but it'll be a lot of work to apply it individually to all the functions having an outgrid/outfile parameter. Maybe leave it for another time, and honestly, we really need to discourage people from having spaces in filenames in the first place.

maxrjones

There are still a couple issues to work out as mentioned in https://github.com/GenericMappingTools/pygmt/pull/1487/files#r825371307 and #1487 (comment), but this is a big improvement that would benefit users in v0.6.0.

seisman · 2022-03-13T12:21:32Z

The one thing that makes little sense to me is shown in the following example:

import pygmt
fig = pygmt.Figure()
fig.basemap(region=[0, 2, 4, 8], projection="X10c", frame=["WSne+tPlot Zero", "xaf+lX label+uK"])
fig.show()

As you can see, I have to use "xaf+lX label+uK", not "xaf+l'X label'+uK" or 'xaf+l"X label"+uK'. For me, the last two are much easier to read.

weiji14 · 2022-03-13T12:45:27Z

As you can see, I have to use "xaf+lX label+uK", not "xaf+l'X label'+uK" or 'xaf+l"X label"+uK'. For me, the last two are much easier to read.

I just tested all three examples and only "xaf+l'X label'+uK" doesn't work properly (it prints 'X label instead of X label), but that's a known issue with using single quotes. This branch should be backwards compatible with the 'xaf+l"X label"+uK' method, and it now allows for "xaf+lX label+uK" which isn't nice but works if people like that format.

seisman · 2022-03-13T12:59:04Z

As you can see, I have to use "xaf+lX label+uK", not "xaf+l'X label'+uK" or 'xaf+l"X label"+uK'. For me, the last two are much easier to read.

I just tested all three examples and only "xaf+l'X label'+uK" doesn't work properly (it prints 'X label instead of X label), but that's a known issue with using single quotes. This branch should be backwards compatible with the 'xaf+l"X label"+uK' method, and it now allows for "xaf+lX label+uK" which isn't nice but works if people like that format.

Ah, you're right. Good to know that I can still use 'xaf+l"X label"+uK'.

I'm reading how GMT parses a long text string https://github.com/GenericMappingTools/gmt/blob/434ed1848a1e8886931694b2de4c352e4c6cddae/src/gmt_parse.c#L600, it seems it ignores double quotes (that's why 'xaf+l"X label"+uK'), but doesn't ignore single quotes (so "xaf+l'X label'+uK" doesn't work).

pygmt/helpers/utils.py

seisman · 2022-03-13T13:08:34Z

pygmt/helpers/utils.py

+ if key != "J": # non-projection parameters
+ _value = str(kwargs[key]).replace(" ", r"\040")
+ else:
+ # special handling if key == "J" (projection)
+ # remove any spaces in PROJ4 string
+ _value = str(kwargs[key]).replace(" ", "")
+ gmt_args.append(rf"-{key}{_value}")


I know almost nothing about PROJ4, but does a PROJ4 string always contains +proj=xxx or EPSG? If yes, then we can simplify the if-test to something like:

if key != "J" or (key == "J" and "+proj" not in value and "EPSG" not in value): _value = str(kwargs[key]).replace(" ", r"\040") else: # special handling if -J + PROJ4 string # remove any spaces in PROJ4 string _value = str(kwargs[key]).replace(" ", "") gmt_args.append(rf"-{key}{_value}")

The motivation is, since PROJ4 is not commonly used, it seems a waste of time to do call the replace method for GMT-style -J.

Not sure if all PROJ-strings have either +proj=xxx or EPSG (see https://proj.org/operations/projections/index.html), but they probably do? I know that there's +init=EPSG:xxx which kinda works when I tried here, but that's actually deprecated syntax (see https://pyproj4.github.io/pyproj/stable/gotchas.html#init-auth-auth-code-should-be-replaced-with-auth-auth-code) and probably not something we want to allow.

Also unsure if 2 extra if-checks saves time, considering that either way, a str.replace still needs to happen for the space character - either to \040 or to nothing ``.

Co-Authored-By: Dongdong Tian <[email protected]>

weiji14 · 2022-03-13T15:43:43Z

Thanks team! I'll merge this in and close that almost 4 year old #247 bug!!

…icMappingTools#1487) * Replace spaces in arguments with octal code 040 Modifying build_arg_string function to replace blank space characters with octal code 040, and added a doctest to check various combinations with single and double quotes included. * Remove workarounds for spaces in fig.subplot's autolabel and title args Supersedes workaround for subplot's autolabel (-A) and title (-T) parameters in a9d167d, 4126c16, and eadb847. * Remove workaround for spaces in fig.text's -F argument * Remove double quotes around legend label test examples * Edit test_rose_no_sectors to remove single quotes from title * Remove workaround for spaces in fig.psconvert prefix Doesn't work yet, as the filename will contain the 040 octal code, but committing to have the diff available for review. * Ensure spaces in pygmt.config arguments can work Also added a regression test for FORMAT_DATE_MAP="o dd". * Manually handle prefix -F in psconvert So that fig.savefig won't insert `\040` characters when saving filenames with spaces. Resolves problem mentioned in https://github.com/GenericMappingTools/pygmt/pull/1487/files#r703116544 * Handle PROJ4 strings with spaces Instead of converting spaces to \040 in proj4 strings, just remove them directly. Added parametrized unit tests to basemap and grdproject to check that it works. * Use Modifier Letter Colon instead of regular colon to fix WIndows tests Adapted from https://stackoverflow.com/questions/10386344/how-to-get-a-file-in-windows-with-a-colon-in-the-filename/25477235#25477235. * Try using underscore instead of Modifier Letter Colon * Raise GMTInvalidInput if no prefix argument is passed to psconvert Co-authored-by: Dongdong Tian <[email protected]>

weiji14 added 6 commits September 7, 2021 12:01

Replace spaces in arguments with octal code 040

b5ad405

Modifying build_arg_string function to replace blank space characters with octal code 040, and added a doctest to check various combinations with single and double quotes included.

Remove workarounds for spaces in fig.subplot's autolabel and title args

14648c2

Supersedes workaround for subplot's autolabel (-A) and title (-T) parameters in a9d167d, 4126c16, and eadb847.

Remove workaround for spaces in fig.text's -F argument

924f439

Remove double quotes around legend label test examples

707745f

Edit test_rose_no_sectors to remove single quotes from title

03e4308

Remove workaround for spaces in fig.psconvert prefix

095449a

Doesn't work yet, as the filename will contain the 040 octal code, but committing to have the diff available for review.

weiji14 added the bug Something isn't working label Sep 7, 2021

weiji14 added this to the 0.5.0 milestone Sep 7, 2021

weiji14 self-assigned this Sep 7, 2021

vercel bot temporarily deployed to Preview September 7, 2021 01:13 Inactive

Format using blackdoc and fix flake8 error

d81b80b

weiji14 force-pushed the arg_with_space branch from 869b43a to d81b80b Compare September 7, 2021 01:20

weiji14 changed the title ~~Arg with space~~ Fix problem with arguments with spaces into pygmt functions Sep 7, 2021

vercel bot temporarily deployed to Preview September 7, 2021 01:22 Inactive

weiji14 changed the title ~~Fix problem with arguments with spaces into pygmt functions~~ Allow passing arguments containing spaces into pygmt functions Sep 7, 2021

weiji14 commented Sep 7, 2021

View reviewed changes

weiji14 modified the milestones: 0.5.0, 0.6.0 Oct 27, 2021

weiji14 mentioned this pull request Nov 26, 2021

Dynamic legend labels with space in it #1632

Closed

weiji14 linked an issue Nov 26, 2021 that may be closed by this pull request

Dynamic legend labels with space in it #1632

Closed

weiji14 mentioned this pull request Dec 30, 2021

Add an "add a title" to starter tutorial #1688

Merged

6 tasks

weiji14 added 2 commits January 10, 2022 09:28

Merge branch 'main' into arg_with_space

dd849cb

Ensure spaces in pygmt.config arguments can work

c29e632

Also added a regression test for FORMAT_DATE_MAP="o dd".

vercel bot temporarily deployed to Preview January 10, 2022 15:31 Inactive

weiji14 commented Jan 10, 2022

View reviewed changes

Manually handle prefix -F in psconvert

83c8c3b

So that fig.savefig won't insert `\040` characters when saving filenames with spaces. Resolves problem mentioned in https://github.com/GenericMappingTools/pygmt/pull/1487/files#r703116544

vercel bot temporarily deployed to Preview March 11, 2022 18:28 Inactive

maxrjones reviewed Mar 12, 2022

View reviewed changes

Merge branch 'main' into arg_with_space

4770396

maxrjones approved these changes Mar 13, 2022

View reviewed changes

Release v0.6.x automation moved this from In progress to Reviewer approved Mar 13, 2022

maxrjones added the final review call This PR requires final review and approval from a second reviewer label Mar 13, 2022

Raise GMTInvalidInput if no prefix argument is passed to psconvert

801ba01

vercel bot temporarily deployed to Preview March 13, 2022 01:57 Inactive

seisman reviewed Mar 13, 2022

View reviewed changes

weiji14 and others added 2 commits March 13, 2022 09:54

Merge branch 'main' into arg_with_space

ecb580e

Fix rst syntax in pygmt/helpers/utils.py

a526d45

Co-Authored-By: Dongdong Tian <[email protected]>

vercel bot temporarily deployed to Preview March 13, 2022 13:55 Inactive

seisman approved these changes Mar 13, 2022

View reviewed changes

weiji14 merged commit b173c69 into main Mar 13, 2022

Release v0.6.x automation moved this from Reviewer approved to Done Mar 13, 2022

weiji14 deleted the arg_with_space branch March 13, 2022 15:46

weiji14 removed the final review call This PR requires final review and approval from a second reviewer label Mar 13, 2022

weiji14 mentioned this pull request Mar 26, 2022

Plot labels do not allow spaces #1849

Closed

weiji14 mentioned this pull request May 10, 2022

Add the anatomy of a figure tutorial GenericMappingTools/egu22pygmt#7

Merged

seisman mentioned this pull request Jun 12, 2022

Update the description of setting titles in tutorial #1950

Merged

yvonnefroehlich mentioned this pull request Jul 19, 2022

Inconsistent handling of whitespaces in titles and labels across gallery and tutorial examples #2013

Closed

seisman mentioned this pull request Jan 4, 2023

pygmt.config doesn't work with values that have whitespaces #2298

Closed

seisman mentioned this pull request Mar 21, 2024

Refactor all wrappers to pass an argument list to Session.call_module #3132

Merged

10 tasks

Provide feedback

Saved searches

Use saved searches to filter your results more quickly

Allow passing arguments containing spaces into pygmt functions #1487

Allow passing arguments containing spaces into pygmt functions #1487

weiji14 commented Sep 7, 2021 •

edited

Loading

github-actions bot commented Sep 7, 2021 •

edited

Loading

Added images

Modified images

weiji14 Sep 7, 2021

weiji14 Jan 13, 2022

willschlitzer commented Oct 27, 2021

weiji14 commented Oct 27, 2021

seisman commented Jan 10, 2022

weiji14 Jan 10, 2022

maxrjones Mar 12, 2022 •

edited

Loading

weiji14 Mar 12, 2022

maxrjones Mar 13, 2022

weiji14 Mar 13, 2022

maxrjones commented Mar 12, 2022

weiji14 commented Mar 12, 2022

Outgrid parameter

Outfile parameter

maxrjones left a comment

seisman commented Mar 13, 2022

weiji14 commented Mar 13, 2022 •

edited

Loading

seisman commented Mar 13, 2022

seisman Mar 13, 2022

weiji14 Mar 13, 2022 •

edited

Loading

weiji14 commented Mar 13, 2022

Allow passing arguments containing spaces into pygmt functions #1487

Allow passing arguments containing spaces into pygmt functions #1487

Conversation

weiji14 commented Sep 7, 2021 • edited Loading

Special handling of functions where spaces can't just be converted to \040:

github-actions bot commented Sep 7, 2021 • edited Loading

Summary of changed images

Image diff(s)

Added images

Modified images

weiji14 Sep 7, 2021

Choose a reason for hiding this comment

weiji14 Jan 13, 2022

Choose a reason for hiding this comment

willschlitzer commented Oct 27, 2021

weiji14 commented Oct 27, 2021

seisman commented Jan 10, 2022

weiji14 Jan 10, 2022

Choose a reason for hiding this comment

maxrjones Mar 12, 2022 • edited Loading

Choose a reason for hiding this comment

weiji14 Mar 12, 2022

Choose a reason for hiding this comment

maxrjones Mar 13, 2022

Choose a reason for hiding this comment

weiji14 Mar 13, 2022

Choose a reason for hiding this comment

maxrjones commented Mar 12, 2022

Outgrid parameter

Outfile parameter

weiji14 commented Mar 12, 2022

Outgrid parameter

Outfile parameter

maxrjones left a comment

Choose a reason for hiding this comment

seisman commented Mar 13, 2022

weiji14 commented Mar 13, 2022 • edited Loading

seisman commented Mar 13, 2022

seisman Mar 13, 2022

Choose a reason for hiding this comment

weiji14 Mar 13, 2022 • edited Loading

Choose a reason for hiding this comment

weiji14 commented Mar 13, 2022

weiji14 commented Sep 7, 2021 •

edited

Loading

Special handling of functions where spaces can't just be converted to `\040`:

github-actions bot commented Sep 7, 2021 •

edited

Loading

maxrjones Mar 12, 2022 •

edited

Loading

weiji14 commented Mar 13, 2022 •

edited

Loading

weiji14 Mar 13, 2022 •

edited

Loading