Savetxt unit #1085

fiolj · 2026-01-05T22:38:06Z

This PR aims to add optional arguments to savetxt, that behave similar to numpy's savetxt.

This is associated with Issue 263 and this discussion thread.

It add the possibility of supplying the unit of an open file instead of a filename (which could be used for output_unit for instance)

This implementation is quite simple. The main changes are:

Add optional header and footer (that could be commented out with a character, currently defaults to '#')
Changes delimiter to an arbitrary length string. I am not completely sure that is really useful. Initially I've added this because np.savetxt (Numpy's) allows character or arbitrary strings but np.loadtxt requires it to be a length 1 char.
Add the possibility to override default format for saving data

codecov · 2026-01-05T23:12:32Z

Codecov Report

❌ Patch coverage is 50.00000% with 4 lines in your changes missing coverage. Please review.
✅ Project coverage is 68.61%. Comparing base (6e8669d) to head (8403d30).

Files with missing lines	Patch %	Lines
example/io/example_savetxt.f90	0.00%	4 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##           master    #1085      +/-   ##
==========================================
- Coverage   68.62%   68.61%   -0.01%     
==========================================
  Files         394      394              
  Lines       12730    12734       +4     
  Branches     1376     1376              
==========================================
+ Hits         8736     8738       +2     
- Misses       3994     3996       +2

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jalvesz · 2026-01-06T07:12:09Z

Thanks for this @fiolj. Would you mind reverting the changes not related to the implementation? (styling) There are too many and it renders difficult to read through the PR. You can check the style_guide for info https://github.com/fortran-lang/stdlib/blob/master/STYLE_GUIDE.md

One thing, white spaces in-between parentheses and an intrinsic function are not recommended ( open (...), allocate (...), etc )

fiolj · 2026-01-06T12:54:26Z

Thanks @jalvesz, I've fixed the formatting

jvdp1

Thank you @fiolj . Here are some suggestions

jvdp1 · 2026-01-14T21:42:44Z

doc/specs/stdlib_io.md

 `array`: Shall be a rank-2 array of type `real`, `complex` or `integer`.

-`delimiter` (optional): Shall be a character expression of length 1 that contains the delimiter used to separate the columns. The default is `' '`.
+`filename or unit`: Shall be either a character expression containing the name of the file or an integer containing the unit of an already open file, that will contain the 2D `array`. Setting the two of them shall give an error


Suggested change

`filename or unit`: Shall be either a character expression containing the name of the file or an integer containing the unit of an already open file, that will contain the 2D `array`. Setting the two of them shall give an error

`filename or unit`: Shall be either a character expression containing the name of the file or an integer containing the unit of an already open file, that will contain the 2D `array`. Setting the two of them shall give an error.

jvdp1 · 2026-01-14T21:46:50Z

src/stdlib_io.fypp

  use stdlib_optval, only: optval
  use stdlib_ascii, only: is_blank
  use stdlib_string_type, only : string_type, assignment(=), move
+  ! use stdlib_strings, only: replace_all


Suggested change

! use stdlib_strings, only: replace_all

jvdp1 · 2026-01-14T21:52:11Z

src/stdlib_io.fypp

+      character(len=*), intent(in), optional :: delimiter  ! Column delimiter. Default is a space.
+      character(len=*), intent(in), optional :: header  !< If present, text to write before data.
+      character(len=*), intent(in), optional :: footer  !< If present, text to write after data.
+      character(len=1), intent(in), optional :: comments  !< Comment character. Default "#"


Is it in all languages only one character? (furthermore, I don't think that there will be a check if the lenght is mentioned)

Suggested change

character(len=1), intent(in), optional :: comments !< Comment character. Default "#"

character(len=*), intent(in), optional :: comments !< Comment character. Default "#"

jvdp1 · 2026-01-14T21:54:40Z

src/stdlib_io.fypp

      character(len=3) :: delim_str
+      character(len=:), allocatable :: default_fmt
      character(len=:), allocatable :: fmt_
+      character(len=1), allocatable :: comments_


Suggested change

character(len=1), allocatable :: comments_

character(len=:), allocatable :: comments_

src/stdlib_io.fypp

jvdp1 · 2026-01-14T22:02:25Z

src/stdlib_io.fypp

+  pure function prepend(Sin, comment) result(Sout)
+    character(len=*), intent(in) :: Sin
+    character(len=:), allocatable :: Sout
+    character(len=1), intent(in) :: comment 


Suggested change

character(len=1), intent(in) :: comment

character(len=*), intent(in) :: comment

jvdp1 · 2026-01-14T22:03:08Z

src/stdlib_io.fypp

+    character(len=*), intent(in) :: Sin
+    character(len=:), allocatable :: Sout
+    character(len=1), intent(in) :: comment 
+    character(len=3) :: com_


To keep some flexibility:

Suggested change

character(len=3) :: com_

character(len=:), allocatable :: com_

jvdp1 · 2026-01-14T22:07:21Z

src/stdlib_io.fypp


-      s = open(filename, "w")
+      !! Write the header if non-empty
+      ! prepend function may be replaced by use of replace_all but currently stdlib_strings


It is probably something that we should solve at a later stage.

jvdp1 · 2026-01-14T22:09:10Z

doc/specs/stdlib_io.md

+
+`footer`: (optional) Shall be a character expression that will be written at the end of the file.
+
+`comments`: (optional) : Shall  be a character expression of length 1 that will be prepended to the ``header`` and ``footer`` strings to mark them as comments. Default: `# `.


Could we keep the lenght of comments undefined? (E.g., what about is a user would like to pass !# as comments?

Yes, I agree.

doc/specs/stdlib_io.md

fiolj · 2026-01-15T13:29:33Z

Reviewing the arguments of savetxt I've rechecked and Numpy's has the following order:
np.savetxt(fname, X, fmt, delimiter, newline, header, footer, comments, encoding)

Currently, we have the order of fmt and delimiter inverted. Should we make it as Numpy or should we keep it?

jvdp1 · 2026-01-19T06:10:26Z

Reviewing the arguments of savetxt I've rechecked and Numpy's has the following order: np.savetxt(fname, X, fmt, delimiter, newline, header, footer, comments, encoding)

Currently, we have the order of fmt and delimiter inverted. Should we make it as Numpy or should we keep it?

As savetxt is still experimental and as both fmt and delimiter are optional, I think that inverting both args is doable.

fiolj · 2026-01-19T15:13:50Z

Reviewing the arguments of savetxt I've rechecked and Numpy's has the following order: np.savetxt(fname, X, fmt, delimiter, newline, header, footer, comments, encoding)
Currently, we have the order of fmt and delimiter inverted. Should we make it as Numpy or should we keep it?

As savetxt is still experimental and as both fmt and delimiter are optional, I think that inverting both args is doable.

Thanks, I agree. Last uploaded commit has the new order and some small cleanup of the code.
Following the suggestion of @certik in the thread I've searched savetxt in numpy's commit history and found no issues or complains related to these arguments.

I think that it this version is close to apt to be merged, except for the codecov failings (which I have no idea what they mean).

jvdp1 · 2026-01-19T15:23:35Z

xcept for the codecov failings (which I have no idea what they mean).

It is related to the examples that are not covered by these pipelines. I think that @jalvesz got a similar issue with another PR.
It should not stop us for merging this PR (provided it is not related to the changes proposed in this PR).

jalvesz · 2026-01-19T16:09:14Z

The fails with codecov are valid in my opinion. In #1074 we avoided codecov from analyzing the examples as a metric for coverage. But in this case, it is a valid fail because there are API changes which are not being tested. It is not enough to just add an example to ensure correctness.

jvdp1 · 2026-01-19T16:22:18Z

The fails with codecov are valid in my opinion. In #1074 we avoided codecov from analyzing the examples as a metric for coverage. But in this case, it is a valid fail because there are API changes which are not being tested.

I am confused. This shows that some lines of example_savetxt are not covered. Or do I miss-interpret the report?

It is not enough to just add an example to ensure correctness.

I agree with you.

src/stdlib_io.fypp

Co-authored-by: Jeremie Vandenplas <[email protected]>

jvdp1 · 2026-01-19T16:28:05Z

I think that it this version is close to apt to be merged, except for the codecov failings (which I have no idea what they mean).

@fiolj could you update the tests to cover the different changes in the API?

fiolj · 2026-01-19T19:46:13Z

I think that it this version is close to apt to be merged, except for the codecov failings (which I have no idea what they mean).

@fiolj could you update the tests to cover the different changes in the API?

Yes. I've commited some tests.
I noticed that loadtxt is currently setting delimiter to a single char, thus I've kept the same convention to savetxt.
It is quite easy to change savetxt to arbitrary length strings; I would wait until loadtxt is also modified.

jalvesz · 2026-01-20T07:32:06Z

I am confused. This shows that some lines of example_savetxt are not covered. Or do I miss-interpret the report?

I'm also confused now, codecov is supposed to ignore files in the examples directory after the PR #1074 ... I would say for the moment to ignore this false error.

fiolj and others added 17 commits December 22, 2025 11:59

Added optional arguments: header, footer, comment to savetxt

d6cc685

Fixed missing dummy args in savetxt

e2d1c09

Merge branch 'master' into savetxt

94c36cc

updated savetxt spec

af2137b

implemented arbitrary-length delimiter

4db2dd0

Added optional fmt argument to savetxt (after header and delimiter)

5c8397c

Overloaded savetxt version with unit instead of filename

eb4acc6

Fixed error in default format

dc2c9f8

Fixed introduced error in savetxt format

e6a02f7

Merge branch 'fortran-lang:master' into savetxt-header

d390d79

Fixed typo and added short example with headings

9cd8e51

fixed typo in code (comment -> comments)

b75e631

Fixed mistake (allocatable length 1 char)

036ce25

Merge branch 'savetxt-header' into savetxt-fmt

ab357fa

Merge branch 'savetxt-fmt' into savetxt-unit

e6af81a

Added "correctly" header and footer

04061b8

Merge branch 'master' into savetxt-unit

fbe6d0a

jalvesz linked an issue Jan 6, 2026 that may be closed by this pull request

Add optional arguments to savetxt #1076

Open

Fixed formatting for easier reveiew

3f6aff3

fiolj added 2 commits January 9, 2026 18:48

Merge branch 'master' into savetxt-unit

d491c8f

Merge branch 'master' into savetxt-unit

390857d

jvdp1 reviewed Jan 14, 2026

View reviewed changes

Corrected arguments, made comments arbitrary length, check open unit

4e574eb

fiolj added 3 commits January 15, 2026 10:40

Corrected specs. filename and unit in different calls

d470409

Added option newline as in Numpy savetxt

6c43047

Corrected introduced errors in savetxt

a01ffe7

Merge branch 'savetxt-unit' of github.com:fiolj/stdlib into savetxt-unit

e3c13f3

jvdp1 reviewed Jan 19, 2026

View reviewed changes

src/stdlib_io.fypp Outdated Show resolved Hide resolved

correct IF -> if in src/stdlib_io.fypp

86fa060

Co-authored-by: Jeremie Vandenplas <[email protected]>

Fixed error in footer of savetxt and added tests

8403d30

	`filename or unit`: Shall be either a character expression containing the name of the file or an integer containing the unit of an already open file, that will contain the 2D `array`. Setting the two of them shall give an error
	`filename or unit`: Shall be either a character expression containing the name of the file or an integer containing the unit of an already open file, that will contain the 2D `array`. Setting the two of them shall give an error.

	character(len=1), intent(in), optional :: comments !< Comment character. Default "#"
	character(len=*), intent(in), optional :: comments !< Comment character. Default "#"

	character(len=1), allocatable :: comments_
	character(len=:), allocatable :: comments_

	character(len=1), intent(in) :: comment
	character(len=*), intent(in) :: comment

	character(len=3) :: com_
	character(len=:), allocatable :: com_


		`footer`: (optional) Shall be a character expression that will be written at the end of the file.

		`comments`: (optional) : Shall be a character expression of length 1 that will be prepended to the ``header`` and ``footer`` strings to mark them as comments. Default: `# `.

Savetxt unit #1085

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Savetxt unit #1085

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