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Activate/fix rpy2 tests #35396

Merged
merged 13 commits into from
Jun 22, 2024
Merged

Activate/fix rpy2 tests #35396

merged 13 commits into from
Jun 22, 2024

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mkoeppe
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@mkoeppe mkoeppe commented Mar 30, 2023 •
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📚 Description

As a follow-up on:

we make rpy2 a dynamically detected feature, enabling the automatic run of doctests tagged # optional - rpy2; we use a file-level doctest tag for the r.py file.

We also update the spkg documentation for #35347

Resolves #35347

📝 Checklist

  • The title is concise, informative, and self-explanatory.
  • The description explains in detail what this PR is about.
  • I have linked a relevant issue or discussion.
  • I have created tests covering the changes.
  • I have updated the documentation accordingly.

⌛ Dependencies

@mkoeppe mkoeppe self-assigned this Mar 30, 2023
@mkoeppe mkoeppe mentioned this pull request Mar 30, 2023
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github-actions bot commented Apr 16, 2023 •
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Documentation preview for this PR (built with commit 11833d8; changes) is ready! 🎉
This preview will update shortly after each push to this PR.

@mkoeppe mkoeppe force-pushed the doctest_clean_namespace branch 2 times, most recently from d707a6e to f428181 Compare April 17, 2024 05:52
@mkoeppe mkoeppe mentioned this pull request Apr 24, 2024
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@kwankyu
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kwankyu commented Jun 8, 2024

Otherwise lgtm.

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kwankyu commented Jun 9, 2024

There is a genuine failure:

sage -t --random-seed=30511447838430634235757231865836227899 src/sage/interfaces/r.py
**********************************************************************
File "src/sage/interfaces/r.py", line 1312, in sage.interfaces.r.R.plot
Failed example:
    r.library("lattice")
Exception raised:
    Traceback (most recent call last):
      File "/Users/runner/work/sage/sage/src/sage/doctest/forker.py", line 714, in _run
        self.compile_and_execute(example, compiler, test.globs)
      File "/Users/runner/work/sage/sage/src/sage/doctest/forker.py", line 1146, in compile_and_execute
        exec(compiled, globs)
      File "<doctest sage.interfaces.r.R.plot[5]>", line 1, in <module>
        r.library("lattice")
      File "/Users/runner/work/sage/sage/src/sage/interfaces/r.py", line 860, in library
        raise ImportError("R library {} not installed".format(library_name))
    ImportError: R library lattice not installed

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mkoeppe commented Jun 9, 2024

Is that from the conda test?

I added the package name here, but that will only take effect after updating the conda-lock files (as done and to be redone in #37998)

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kwankyu commented Jun 9, 2024

OK.

Thanks.

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mkoeppe commented Jun 9, 2024

Thanks!

vbraun pushed a commit to vbraun/sage that referenced this pull request Jun 10, 2024
sagemathgh-35396: Activate/fix rpy2 tests
111de63 
    
<!-- Please provide a concise, informative and self-explanatory title.
-->
<!-- Don't put issue numbers in the title. Put it in the Description
below. -->
<!-- For example, instead of "Fixes sagemath#12345", use "Add a new method to
multiply two integers" -->

### 📚 Description

<!-- Describe your changes here in detail. -->

As a follow-up on:
- sagemath#35237

we make `rpy2` a dynamically detected feature, enabling the automatic
run of doctests tagged `# optional - rpy2`; we use a file-level doctest
tag for the `r.py` file.

We also update the spkg documentation for sagemath#35347

<!-- Why is this change required? What problem does it solve? -->
<!-- If this PR resolves an open issue, please link to it here. For
example "Fixes sagemath#12345". -->

Resolves sagemath#35347

<!-- If your change requires a documentation PR, please link it
appropriately. -->

### 📝 Checklist

<!-- Put an `x` in all the boxes that apply. It should be `[x]` not `[x
]`. -->

- [x] The title is concise, informative, and self-explanatory.
- [x] The description explains in detail what this PR is about.
- [ ] I have linked a relevant issue or discussion.
- [ ] I have created tests covering the changes.
- [ ] I have updated the documentation accordingly.

### ⌛ Dependencies

<!-- List all open PRs that this PR logically depends on
- sagemath#12345: short description why this is a dependency
- sagemath#34567: ...
-->
- Depends on sagemath#35237
<!-- If you're unsure about any of these, don't hesitate to ask. We're
here to help! -->
    
URL: sagemath#35396
Reported by: Matthias Köppe
Reviewer(s): Kwankyu Lee, Matthias Köppe
vbraun pushed a commit to vbraun/sage that referenced this pull request Jun 16, 2024
sagemathgh-35396: Activate/fix rpy2 tests
7c5c604 
    
<!-- Please provide a concise, informative and self-explanatory title.
-->
<!-- Don't put issue numbers in the title. Put it in the Description
below. -->
<!-- For example, instead of "Fixes sagemath#12345", use "Add a new method to
multiply two integers" -->

### 📚 Description

<!-- Describe your changes here in detail. -->

As a follow-up on:
- sagemath#35237

we make `rpy2` a dynamically detected feature, enabling the automatic
run of doctests tagged `# optional - rpy2`; we use a file-level doctest
tag for the `r.py` file.

We also update the spkg documentation for sagemath#35347

<!-- Why is this change required? What problem does it solve? -->
<!-- If this PR resolves an open issue, please link to it here. For
example "Fixes sagemath#12345". -->

Resolves sagemath#35347

<!-- If your change requires a documentation PR, please link it
appropriately. -->

### 📝 Checklist

<!-- Put an `x` in all the boxes that apply. It should be `[x]` not `[x
]`. -->

- [x] The title is concise, informative, and self-explanatory.
- [x] The description explains in detail what this PR is about.
- [ ] I have linked a relevant issue or discussion.
- [ ] I have created tests covering the changes.
- [ ] I have updated the documentation accordingly.

### ⌛ Dependencies

<!-- List all open PRs that this PR logically depends on
- sagemath#12345: short description why this is a dependency
- sagemath#34567: ...
-->
- Depends on sagemath#35237
<!-- If you're unsure about any of these, don't hesitate to ask. We're
here to help! -->
    
URL: sagemath#35396
Reported by: Matthias Köppe
Reviewer(s): Kwankyu Lee, Matthias Köppe
vbraun pushed a commit to vbraun/sage that referenced this pull request Jun 16, 2024
sagemathgh-35396: Activate/fix rpy2 tests
ddbd4fa 
    
<!-- Please provide a concise, informative and self-explanatory title.
-->
<!-- Don't put issue numbers in the title. Put it in the Description
below. -->
<!-- For example, instead of "Fixes sagemath#12345", use "Add a new method to
multiply two integers" -->

### 📚 Description

<!-- Describe your changes here in detail. -->

As a follow-up on:
- sagemath#35237

we make `rpy2` a dynamically detected feature, enabling the automatic
run of doctests tagged `# optional - rpy2`; we use a file-level doctest
tag for the `r.py` file.

We also update the spkg documentation for sagemath#35347

<!-- Why is this change required? What problem does it solve? -->
<!-- If this PR resolves an open issue, please link to it here. For
example "Fixes sagemath#12345". -->

Resolves sagemath#35347

<!-- If your change requires a documentation PR, please link it
appropriately. -->

### 📝 Checklist

<!-- Put an `x` in all the boxes that apply. It should be `[x]` not `[x
]`. -->

- [x] The title is concise, informative, and self-explanatory.
- [x] The description explains in detail what this PR is about.
- [ ] I have linked a relevant issue or discussion.
- [ ] I have created tests covering the changes.
- [ ] I have updated the documentation accordingly.

### ⌛ Dependencies

<!-- List all open PRs that this PR logically depends on
- sagemath#12345: short description why this is a dependency
- sagemath#34567: ...
-->
- Depends on sagemath#35237
<!-- If you're unsure about any of these, don't hesitate to ask. We're
here to help! -->
    
URL: sagemath#35396
Reported by: Matthias Köppe
Reviewer(s): Kwankyu Lee, Matthias Köppe
@vbraun vbraun merged commit 0df98b3 into sagemath:develop Jun 22, 2024
31 of 42 checks passed
@mkoeppe mkoeppe deleted the doctest_clean_namespace branch June 22, 2024 20:12
@mkoeppe mkoeppe mentioned this pull request Jun 22, 2024
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@mkoeppe mkoeppe mentioned this pull request Jun 25, 2024
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antonio-rojas added a commit to antonio-rojas/sage that referenced this pull request Jun 27, 2024
@antonio-rojas
Filter out R warnings
db5bf6c 
These are causing some doctest failures after sagemath#35396
@antonio-rojas antonio-rojas mentioned this pull request Jun 27, 2024
Merged
@mkoeppe mkoeppe added this to the sage-10.4 milestone Jul 8, 2024
vbraun pushed a commit to vbraun/sage that referenced this pull request Jul 13, 2024
sagemathgh-38294: Filter out R warnings
28d8530 
These are causing some doctest failures after
sagemath#35396

```
**********************************************************************
File "/usr/lib/python3.12/site-packages/sage/interfaces/r.py", line 51,
in sage.interfaces.r
Failed example:
    v = 2*x+y+1; v
Expected:
    [1] 32.2 17.8 10.3 20.2 66.1 21.8 22.6 12.8 16.9 50.8 43.5
Got:
    R[write to console]: Además:
    R[write to console]: Aviso:
    <BLANKLINE>
    R[write to console]: In sage10 + sage6 :
    R[write to console]:
    <BLANKLINE>
    R[write to console]:  longitud de objeto mayor no es múltiplo de la
longitud de uno menor
    <BLANKLINE>
     [1] 32.2 17.8 10.3 20.2 66.1 21.8 22.6 12.8 16.9 50.8 43.5
**********************************************************************
File "/usr/lib/python3.12/site-packages/sage/interfaces/r.py", line 78,
in sage.interfaces.r
Failed example:
    r(-17).sqrt()
Expected:
    [1] NaN
Got:
    R[write to console]: Además:
    R[write to console]: Aviso:
    <BLANKLINE>
    R[write to console]: In sqrt(sage10) :
    R[write to console]:  Se han producido NaNs
    <BLANKLINE>
    [1] NaN
**********************************************************************
File "/usr/lib/python3.12/site-packages/sage/interfaces/r.py", line 356,
in sage.interfaces.r._setup_r_to_sage_converter
Failed example:
    r(-17).sqrt().sage()
Expected:
    nan
Got:
    R[write to console]: Además:
    R[write to console]: Aviso:
    <BLANKLINE>
    R[write to console]: In sqrt(sage4) :
    R[write to console]:  Se han producido NaNs
    <BLANKLINE>
    nan
**********************************************************************
```

URL: sagemath#38294
Reported by: Antonio Rojas
Reviewer(s): Matthias Köppe
vbraun pushed a commit to vbraun/sage that referenced this pull request Jul 16, 2024
sagemathgh-38294: Filter out R warnings
89d1d65 
    
These are causing some doctest failures after
sagemath#35396

```
**********************************************************************
File "/usr/lib/python3.12/site-packages/sage/interfaces/r.py", line 51,
in sage.interfaces.r
Failed example:
    v = 2*x+y+1; v
Expected:
    [1] 32.2 17.8 10.3 20.2 66.1 21.8 22.6 12.8 16.9 50.8 43.5
Got:
    R[write to console]: Además:
    R[write to console]: Aviso:
    <BLANKLINE>
    R[write to console]: In sage10 + sage6 :
    R[write to console]:
    <BLANKLINE>
    R[write to console]:  longitud de objeto mayor no es múltiplo de la
longitud de uno menor
    <BLANKLINE>
     [1] 32.2 17.8 10.3 20.2 66.1 21.8 22.6 12.8 16.9 50.8 43.5
**********************************************************************
File "/usr/lib/python3.12/site-packages/sage/interfaces/r.py", line 78,
in sage.interfaces.r
Failed example:
    r(-17).sqrt()
Expected:
    [1] NaN
Got:
    R[write to console]: Además:
    R[write to console]: Aviso:
    <BLANKLINE>
    R[write to console]: In sqrt(sage10) :
    R[write to console]:  Se han producido NaNs
    <BLANKLINE>
    [1] NaN
**********************************************************************
File "/usr/lib/python3.12/site-packages/sage/interfaces/r.py", line 356,
in sage.interfaces.r._setup_r_to_sage_converter
Failed example:
    r(-17).sqrt().sage()
Expected:
    nan
Got:
    R[write to console]: Además:
    R[write to console]: Aviso:
    <BLANKLINE>
    R[write to console]: In sqrt(sage4) :
    R[write to console]:  Se han producido NaNs
    <BLANKLINE>
    nan
**********************************************************************
```
    
URL: sagemath#38294
Reported by: Antonio Rojas
Reviewer(s): Matthias Köppe
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rpy2: Document that it is a "semistandard" package
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