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 91.37931% with 5 lines in your changes missing coverage. Please review.
✅ Project coverage is 68.66%. Comparing base (de3e59f) to head (20c1a3f).
⚠️ Report is 21 commits behind head on master.

Files with missing lines	Patch %	Lines
example/io/example_savetxt.f90	0.00%	4 Missing ⚠️
example/linalg/example_solve_custom.f90	0.00%	1 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##           master    #1085      +/-   ##
==========================================
+ Coverage   68.55%   68.66%   +0.10%     
==========================================
  Files         396      396              
  Lines       12746    12803      +57     
  Branches     1376     1381       +5     
==========================================
+ Hits         8738     8791      +53     
- Misses       4008     4012       +4

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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

doc/specs/stdlib_io.md

src/stdlib_io.fypp

src/io/stdlib_io.fypp

src/stdlib_io.fypp

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.

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.

Copilot

Pull request overview

This PR adds optional arguments to the savetxt function to provide more flexibility when saving 2D arrays to text files, making it more similar to NumPy's savetxt functionality.

Changes:

Added ability to specify an already-opened file unit instead of a filename, enabling writing to stdout or appending to files
Added optional header and footer parameters that are automatically commented with a configurable comment character
Added optional fmt parameter to customize output format
Modified format string construction to support custom delimiters (though delimiter parameter still limited to single character)

Reviewed changes

Copilot reviewed 4 out of 4 changed files in this pull request and generated 18 comments.

File	Description
src/io/stdlib_io.fypp	Core implementation: generates two variants of savetxt (filename and unit), adds format customization, header/footer support via new prepend helper function
test/io/test_savetxt.f90	Updated tests to exercise new delimiter, fmt, header, footer, and comments parameters
doc/specs/stdlib_io.md	Updated documentation to describe new optional parameters and unit-based interface
example/io/example_savetxt.f90	Added examples demonstrating new features including writing to stdout

💡 Add Copilot custom instructions for smarter, more guided reviews. Learn how to get started.

Copilot · 2026-01-29T13:08:02Z

src/io/stdlib_io.fypp

+        default_fmt = FMT_REAL_${k1}$(2:len(FMT_REAL_${k1}$)-1)
      #:elif 'complex' in t1
-        fmt_ = "(*"//FMT_COMPLEX_${k1}$(1:11)//delim_str//FMT_COMPLEX_${k1}$(14:23)//",:,"//delim_str//"))"
+        default_fmt = FMT_COMPLEX_${k1}$(2:11)//delim_str//FMT_COMPLEX_${k1}$ (14:23)


The substring indices for extracting the second format descriptor for complex numbers are incorrect. For FMT_COMPLEX_SP = '(es15.08e2,1x,es15.08e2)', the substring (14:23) starts at the comma and extracts ,es15.08e2, which includes an unwanted leading comma. The correct indices should be (15:23) to extract just es15.08e2. The same issue affects all complex kinds (DP, XDP, QP) with appropriately adjusted indices based on their format string lengths.

Suggested change

default_fmt = FMT_COMPLEX_${k1}$(2:11)//delim_str//FMT_COMPLEX_${k1}$ (14:23)

default_fmt = FMT_COMPLEX_${k1}$(2:11)//delim_str//FMT_COMPLEX_${k1}$ (15:23)

Copilot · 2026-01-29T13:08:03Z

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 that will be prepended to the ``header`` and ``footer`` strings to mark them as comments. Default: `#`.


There is an extra colon and space after comments in the parameter description. It should be comments (optional): not comments: (optional) : for consistency with other parameter descriptions in the documentation.

Suggested change

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

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

Copilot · 2026-01-29T13:08:03Z

src/io/stdlib_io.fypp

+      ! prepend function may be replaced by use of replace_all but currently stdlib_strings
+      ! is being compiled after stdlib_io
+      ! if (header_ /= '') write (unit, '(A)') comments_//replace_all(header_, nl, nl//comments_)
+      if (header_ /= '') write (unit, '(A)', iostat=ios, iomsg=iomsg) prepend(header_, comments_)


The write statement for the header does not check the iostat value after writing. If the write fails (e.g., due to permissions or disk space issues), the error is silently ignored and execution continues. Consider adding error handling similar to the data writing loop (lines 319-327) to ensure write failures are caught and reported.

Suggested change

if (header_ /= '') write (unit, '(A)', iostat=ios, iomsg=iomsg) prepend(header_, comments_)

if (header_ /= '') then

write (unit, '(A)', iostat=ios, iomsg=iomsg) prepend(header_, comments_)

if (ios /= 0) then

write (msgout,1) trim(iomsg),size(d,2),0,&

#:if 'filename' in arg1

trim(filename)

#:else

unit

#:endif

call error_stop(msg=trim(msgout))

end if

end if

Copilot · 2026-01-29T13:08:03Z

src/io/stdlib_io.fypp

-      close(s)
-
+      ! if (footer_ /= '') write (unit, '(A)') comments_//replace_all(footer_, nl, nl//comments_)
+      if (footer_ /= '') write (unit, '(A)') prepend(footer_, comments_)


The write statement for the footer does not check the iostat value after writing. If the write fails (e.g., due to permissions or disk space issues), the error is silently ignored. Consider adding error handling similar to the data writing loop (lines 319-327) to ensure write failures are caught and reported.

Suggested change

if (footer_ /= '') write (unit, '(A)') prepend(footer_, comments_)

if (footer_ /= '') then

write (unit, '(A)', iostat=ios, iomsg=iomsg) prepend(footer_, comments_)

if (ios /= 0) then

write (msgout,'(a)') trim(iomsg)

call error_stop(msg=trim(msgout))

end if

end if

Copilot · 2026-01-29T13:08:03Z

src/io/stdlib_io.fypp

+      #:endif
      ${t1}$, intent(in) :: d(:,:)           ! The 2D array to save
-      character(len=1), intent(in), optional :: delimiter  ! Column delimiter. Default is a space.
+      character(len=1), intent(in), optional :: delimiter  ! Column delimiter. Default is a space ' '.


The delimiter parameter is still constrained to character(len=1), but the PR description states that one goal is to "change delimiter to an arbitrary length string" to support delimiters like ', ' (comma followed by spaces). This inconsistency means the feature is incomplete. Consider changing the delimiter parameter type to character(len=*) to match the stated goal and documentation changes.

Suggested change

character(len=1), intent(in), optional :: delimiter ! Column delimiter. Default is a space ' '.

character(len=*), intent(in), optional :: delimiter ! Column delimiter. Default is a space ' '.

Copilot · 2026-01-29T13:08:06Z

src/io/stdlib_io.fypp

+        default_fmt = FMT_REAL_${k1}$(2:len(FMT_REAL_${k1}$)-1)
      #:elif 'complex' in t1
-        fmt_ = "(*"//FMT_COMPLEX_${k1}$(1:11)//delim_str//FMT_COMPLEX_${k1}$(14:23)//",:,"//delim_str//"))"
+        default_fmt = FMT_COMPLEX_${k1}$(2:11)//delim_str//FMT_COMPLEX_${k1}$ (14:23)


There is an extra space before the opening parenthesis in FMT_COMPLEX_${k1}$ (14:23). This should be FMT_COMPLEX_${k1}$(14:23) without the space to avoid a syntax error when the template is expanded.

Suggested change

default_fmt = FMT_COMPLEX_${k1}$(2:11)//delim_str//FMT_COMPLEX_${k1}$ (14:23)

default_fmt = FMT_COMPLEX_${k1}$(2:11)//delim_str//FMT_COMPLEX_${k1}$(14:23)

Copilot · 2026-01-29T13:08:06Z

doc/specs/stdlib_io.md

+
+`fmt`: (optional): Fortran format specifier for the text save. Defaults to the write format for the data type.
+
+`header`: (optional) Shall be a character expression that will be written at the beginning of the file.


There is an extra colon after header in the parameter description. It should be header (optional): not header: (optional) for consistency with other parameter descriptions in the documentation.

Suggested change

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

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

Copilot · 2026-01-29T13:08:06Z

test/io/test_savetxt.f90

+        call savetxt(outpath, e, fmt='(g0.7)', header="Three values per line", footer="Total size = 6", comments='#!')
+        call loadtxt(outpath, d2, fmt='*', skiprows=1, max_rows=2)


The new unit-based interface for savetxt is not tested. The example code includes a call to savetxt(output_unit, x, header='...'), but there are no automated tests verifying this functionality works correctly. Consider adding a test case that opens a file with a specific unit number, writes to it using the unit variant of savetxt, closes it, and then verifies the content was written correctly.

Copilot · 2026-01-29T13:08:06Z

test/io/test_savetxt.f90

        e = reshape([1, 2, 3, 4, 5, 6], [2, 3])
-        call savetxt(outpath, e)
-        call loadtxt(outpath, d2)
+        call savetxt(outpath, e, fmt='(g0.7)', header="Three values per line", footer="Total size = 6", comments='#!')


The test uses comments='#!' (two characters), but the comments parameter documentation states it's for "a character expression" and defaults to #. The implementation allows arbitrary length comment strings (via optval(comments, comment_default) where comments is character(len=*)), which is good, but this should be explicitly documented. The current documentation at line 127 is unclear about whether multiple characters are supported.

Suggested change

call savetxt(outpath, e, fmt='(g0.7)', header="Three values per line", footer="Total size = 6", comments='#!')

call savetxt(outpath, e, fmt='(g0.7)', header="Three values per line", footer="Total size = 6", comments='#')

Copilot · 2026-01-29T13:08:06Z

test/io/test_savetxt.f90

+        call savetxt(outpath, e, fmt='(g0.7)', header="Three values per line", footer="Total size = 6", comments='#!')
+        call loadtxt(outpath, d2, fmt='*', skiprows=1, max_rows=2)


The test saves data with header and footer, but only validates that the data can be read back using skiprows=1 to skip the header and max_rows=2 to read only the data rows. The footer is never verified to have been written correctly. Consider adding a test that reads the entire file as text and verifies both header and footer are present and correctly formatted with comment characters.

jvdp1

Thank oyu @fiolj . Overall it looks good. Here are some minor suggestions.

jvdp1 · 2026-01-29T12:58:17Z

doc/specs/stdlib_io.md

-`delimiter` (optional): Shall be a character expression of length 1 that contains the delimiter used to separate the columns. The default is `' '`.
+`delimiter` (optional): Shall be a character expression of any length that contains the delimiter used to separate the columns. The default is a single space `' '`.
+
+`fmt`: (optional): Fortran format specifier for the text save. Defaults to the write format for the data type.


what is the write format?

It currently is (and was also in the original) the (may be little) documented Formatting constants. I've added the reference now in the spec

doc/specs/stdlib_io.md

jvdp1 · 2026-01-29T13:00:41Z

src/io/stdlib_io.fypp

    !!
    !! Saves a 2D array into a text file
    !! ([Specification](../page/specs/stdlib_io.html#description_2))
+    #:for a1 in ['f', 'u']


Suggested change

#:for a1 in ['f', 'u']

#:for arg1 in ['f'ilename, 'unit']

jvdp1 · 2026-01-29T13:00:50Z

src/io/stdlib_io.fypp

+    #:for a1 in ['f', 'u']
    #:for k1, t1 in KINDS_TYPES
-      module procedure savetxt_${t1[0]}$${k1}$
+      module procedure savetxt_${t1[0]}$${k1}$${a1}$


Suggested change

module procedure savetxt_${t1[0]}$${k1}$${a1}$

module procedure savetxt_${t1[0]}$${k1}$${arg1}$

I can use arg1 but I was thinking on only using the first letter to identify the name of the routine, as in the definition (arg1[0]):

#:for arg1 in ['filename', 'unit']
#:for k1, t1 in KINDS_TYPES
subroutine savetxt_${t1[0]}$${k1}$${arg1[0]}$ (${arg1}$, d, delimiter, fmt, header, footer, comments)

src/io/stdlib_io.fypp

jvdp1 · 2026-01-29T13:21:34Z

src/io/stdlib_io.fypp

+    character(len=*), intent(in) :: Sin
+    character(len=:), allocatable :: Sout
+    character(len=*), intent(in) :: comment 
+    character(len=len(comment)+2) :: com_


Why "+2"? It seems that only 1 space is attended at the end of comment?

yes, corrected

jvdp1 · 2026-01-29T13:24:15Z

test/io/test_savetxt.f90

        d = reshape([1, 2, 3, 4, 5, 6], [3, 2])
-        call savetxt(outpath, d)
-        call loadtxt(outpath, d2)
+        call savetxt(outpath, d, delimiter=',')


Could we keep the initial tests, and add new ones for delimiter=','?

jvdp1 · 2026-01-29T13:25:07Z

test/io/test_savetxt.f90

        e = reshape([1, 2, 3, 4, 5, 6], [2, 3])
-        call savetxt(outpath, e)
-        call loadtxt(outpath, d2)
+        call savetxt(outpath, e, fmt='(g0.7)', header="Three values per line", footer="Total size = 6", comments='#!')


Same comment here: could we keep the initial tests and add new ones for delimiter='``?

Done, please check if the new tests are ok if you have time

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

Juan Fiol and others added 3 commits January 23, 2026 11:45

Merge branch 'master' into savetxt-unit

241e146

Merge branch 'master' into savetxt-unit

45ee7c2

Merge branch 'master' into savetxt-unit

672ad8a

jvdp1 requested a review from Copilot January 29, 2026 12:57

Copilot started reviewing on behalf of jvdp1 January 29, 2026 12:57 View session

Copilot AI reviewed Jan 29, 2026

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jvdp1 reviewed Jan 29, 2026

View reviewed changes

Juan Fiol and others added 3 commits January 30, 2026 16:31

test_headfoot is failing now

2b16ff3

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

5ecd021

Added individual tests for optional arguments to savetxt

20c1a3f

	default_fmt = FMT_COMPLEX_${k1}$(2:11)//delim_str//FMT_COMPLEX_${k1}$ (14:23)
	default_fmt = FMT_COMPLEX_${k1}$(2:11)//delim_str//FMT_COMPLEX_${k1}$ (15:23)


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

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

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

-      if (header_ /= '') write (unit, '(A)', iostat=ios, iomsg=iomsg) prepend(header_, comments_)
+      if (header_ /= '') then
+         write (unit, '(A)', iostat=ios, iomsg=iomsg) prepend(header_, comments_)
+         if (ios /= 0) then
+            write (msgout,1) trim(iomsg),size(d,2),0,&
+            #:if 'filename' in arg1
+              trim(filename)
+            #:else
+              unit
+            #:endif
+            call error_stop(msg=trim(msgout))
+         end if
+      end if

	character(len=1), intent(in), optional :: delimiter ! Column delimiter. Default is a space ' '.
	character(len=*), intent(in), optional :: delimiter ! Column delimiter. Default is a space ' '.


		`fmt`: (optional): Fortran format specifier for the text save. Defaults to the write format for the data type.

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

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

		call savetxt(outpath, e, fmt='(g0.7)', header="Three values per line", footer="Total size = 6", comments='#!')
		call loadtxt(outpath, d2, fmt='*', skiprows=1, max_rows=2)

	module procedure savetxt_${t1[0]}$${k1}$${a1}$
	module procedure savetxt_${t1[0]}$${k1}$${arg1}$

Savetxt unit #1085

Are you sure you want to change the base?

Savetxt unit #1085

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fiolj commented Jan 5, 2026 •

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codecov bot commented Jan 5, 2026 •

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