Test that everything can be imported during ci #36591

tobiasdiez · 2023-10-30T12:10:03Z

Currently you cannot import many modules directly. We use pytest --collect-only to test during ci that the imports are working. As a first step, we run pytest through sage, which makes sure that sage.all is loaded. Once the reported errors are fixed (e.g. by filtering out modules that fail because of FeatureNotPresentError), we can check that importing without sage.all works.

📝 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 · 2023-10-30T16:12:02Z

This produces 47K lines of output, and various unexplained error messages.
Are there currently modules that cannot be imported? How does one spot them in the 47K lines of output?

error: option -c not recognized
ERROR sage/categories/finite_dimensional_lie_algebras_with_basis.py - RuntimeError: dictionary changed size during iteration
ERROR sage/combinat/root_system/coxeter_group.py - ModuleNotFoundError: No module named 'from sage'
ERROR sage/combinat/root_system/coxeter_group.py - ModuleNotFoundError: No module named 'from sage'
ERROR sage/crypto/__init__.py - RuntimeError: dictionary changed size during iteration
ERROR sage/crypto/mq/__init__.py - RuntimeError: dictionary changed size during iteration
ERROR sage/crypto/mq/__init__.py - RuntimeError: dictionary changed size during iteration
ERROR sage/ext_data/nbconvert/postprocess.py - FileNotFoundError: [Errno 2] No such file or directory: '-c'
ERROR sage/geometry/polyhedron/backend_normaliz.py - sage.features.FeatureNotPresentError: pynormaliz is not available.
Importing NmzResult failed: No module named 'PyNormaliz'
No equivalent system packages for debian are known to Sage.
To install pynormaliz using the Sage package manager, you can try to run:
  !sage -i pynormaliz
To install pynormaliz using the pip package manager, you can try to run:

tobiasdiez · 2023-10-31T09:30:17Z

At the end you find a summary, if you scroll up a little bit more you find the full exception stack trace. I've now silenced the other output as much as possible (it still shows how much tests are collected per file).

.github/workflows/build.yml

tobiasdiez · 2023-11-11T00:31:19Z

That's the summary now:

ERROR sage/categories/finite_dimensional_lie_algebras_with_basis.py - RuntimeError: dictionary changed size during iteration
ERROR sage/combinat/root_system/coxeter_group.py - ModuleNotFoundError: No module named 'from sage'
ERROR sage/combinat/root_system/coxeter_group.py - ModuleNotFoundError: No module named 'from sage'
ERROR sage/crypto/__init__.py - RuntimeError: dictionary changed size during iteration
ERROR sage/crypto/mq/__init__.py - RuntimeError: dictionary changed size during iteration
ERROR sage/crypto/mq/__init__.py - RuntimeError: dictionary changed size during iteration
ERROR sage/ext_data/nbconvert/postprocess.py - FileNotFoundError: [Errno 2] No such file or directory: '-c'
ERROR sage/geometry/polyhedron/backend_normaliz.py - sage.features.FeatureNotPresentError: pynormaliz is not available.
Importing NmzResult failed: No module named 'PyNormaliz'
No equivalent system packages for debian are known to Sage.
To install pynormaliz using the Sage package manager, you can try to run:
  !sage -i pynormaliz
To install pynormaliz using the pip package manager, you can try to run:
!sage -pip install pynormaliz==2.18
ERROR sage/geometry/polyhedron/backend_normaliz.py - sage.features.FeatureNotPresentError: pynormaliz is not available.
Importing NmzResult failed: No module named 'PyNormaliz'
No equivalent system packages for debian are known to Sage.
To install pynormaliz using the Sage package manager, you can try to run:
  !sage -i pynormaliz
To install pynormaliz using the pip package manager, you can try to run:
!sage -pip install pynormaliz==2.18
ERROR sage/graphs/graph_editor.py - sage.features.FeatureNotPresentError: phitigra is not available.
Importing GraphEditor failed: No module named 'phitigra'
No equivalent system packages for debian are known to Sage.
To install phitigra using the Sage package manager, you can try to run:
  !sage -i phitigra
No equivalent system packages for pip are known to Sage.
ERROR sage/graphs/graph_editor.py - sage.features.FeatureNotPresentError: phitigra is not available.
Importing GraphEditor failed: No module named 'phitigra'
No equivalent system packages for debian are known to Sage.
To install phitigra using the Sage package manager, you can try to run:
  !sage -i phitigra
No equivalent system packages for pip are known to Sage.
ERROR sage/interfaces/r.py - ModuleNotFoundError: No module named 'rpy2'
ERROR sage/interfaces/r.py - ModuleNotFoundError: No module named 'rpy2'
ERROR sage/repl/ipython_kernel/__main__.py - SystemExit: 2
ERROR sage/sat/solvers/cryptominisat.py - sage.features.FeatureNotPresentError: pycryptosat is not available.
Importing Solver failed: No module named 'pycryptosat'
No equivalent system packages for debian are known to Sage.
To install pycryptosat using the Sage package manager, you can try to run:
  !sage -i cryptominisat
No equivalent system packages for pip are known to Sage.
ERROR sage/sat/solvers/cryptominisat.py - sage.features.FeatureNotPresentError: pycryptosat is not available.
Importing Solver failed: No module named 'pycryptosat'
No equivalent system packages for debian are known to Sage.
To install pycryptosat using the Sage package manager, you can try to run:
  !sage -i cryptominisat
No equivalent system packages for pip are known to Sage.
ERROR sage/sat/solvers/picosat.py - sage.features.FeatureNotPresentError: pycosat is not available.
Importing solve failed: No module named 'pycosat'
No equivalent system packages for debian are known to Sage.
To install pycosat using the Sage package manager, you can try to run:
  !sage -i pycosat
No equivalent system packages for pip are known to Sage.
ERROR sage/sat/solvers/picosat.py - sage.features.FeatureNotPresentError: pycosat is not available.
Importing solve failed: No module named 'pycosat'
No equivalent system packages for debian are known to Sage.
To install pycosat using the Sage package manager, you can try to run:
  !sage -i pycosat
No equivalent system packages for pip are known to Sage.
ERROR sage/tests/memcheck/symbolic_expression.py - ModuleNotFoundError: No module named 'valgrind'
ERROR sage/tests/memcheck/verify_no_leak.py - ModuleNotFoundError: No module named 'valgrind'
ERROR sage_setup/autogen/giacpy-mkkeywords.py - FileNotFoundError: [Errno 2] No such file or directory: 'aide_cas.txt'

(more details in the logs)

mkoeppe · 2023-11-11T03:40:52Z

ERROR sage/combinat/root_system/coxeter_group.py - ModuleNotFoundError: No module named 'from sage'
ERROR sage/combinat/root_system/coxeter_group.py - ModuleNotFoundError: No module named 'from sage'

I've fixed this bizarre looking error in #36698

mkoeppe · 2023-11-11T03:42:21Z

ERROR sage/tests/memcheck/symbolic_expression.py - ModuleNotFoundError: No module named 'valgrind'
ERROR sage/tests/memcheck/verify_no_leak.py - ModuleNotFoundError: No module named 'valgrind'
ERROR sage_setup/autogen/giacpy-mkkeywords.py - FileNotFoundError: [Errno 2] No such file or directory: 'aide_cas.txt'

I'd suggest to just exclude these (sage.test and sage_setup) from anything "pytest"

mkoeppe · 2023-11-11T03:43:08Z

ERROR sage/repl/ipython_kernel/main.py - SystemExit: 2

Also __main__.py files probably best to exclude from pytest globally if you can

mkoeppe · 2023-11-11T03:43:37Z

ERROR sage/ext_data/nbconvert/postprocess.py - FileNotFoundError: [Errno 2] No such file or directory: '-c'

Exclude please

tobiasdiez · 2023-11-21T05:32:19Z

ERROR sage/tests/memcheck/symbolic_expression.py - ModuleNotFoundError: No module named 'valgrind'
ERROR sage/tests/memcheck/verify_no_leak.py - ModuleNotFoundError: No module named 'valgrind'
ERROR sage_setup/autogen/giacpy-mkkeywords.py - FileNotFoundError: [Errno 2] No such file or directory: 'aide_cas.txt'

I'd suggest to just exclude these (sage.test and sage_setup) from anything "pytest"

There are doctests in these modules, so I think completely ignoring them is to coarse.

tobiasdiez · 2023-11-21T05:38:59Z

ERROR sage/repl/ipython_kernel/main.py - SystemExit: 2

Also __main__.py files probably best to exclude from pytest globally if you can

Done

ERROR sage/ext_data/nbconvert/postprocess.py - FileNotFoundError: [Errno 2] No such file or directory: '-c'

Exclude please

Done

mkoeppe · 2023-12-21T18:10:00Z

The log has 2000 lines of the form

conftest_inputtest.py: 1
conftest_test.py: 2
sage/algebras/affine_nil_temperley_lieb.py: 12
sage/algebras/algebra.py: 1
sage/algebras/askey_wilson.py: 22
sage/algebras/associated_graded.py: 10
sage/algebras/cellular_basis.py: 11
sage/algebras/clifford_algebra.py: 71
sage/algebras/cluster_algebra.py: 84
sage/algebras/commutative_dga.py: 95

https://github.com/sagemath/sage/actions/runs/7285981360/job/19853897084?pr=36591#step:16:26

Could you add a message to the log please that explains what it is?

mkoeppe · 2023-12-21T18:10:51Z

best to exclude setup.py

______________________________________________ ERROR collecting setup.py _______________________________________________
../local/var/lib/sage/venv-python3.11.1/lib/python3.11/site-packages/setuptools/_distutils/fancy_getopt.py:246: in getopt
    opts, args = getopt.getopt(args, short_opts, self.long_opts)
../local/var/lib/sage/venv-python3.11.1/lib/python3.11/getopt.py:95: in getopt
    opts, args = do_shorts(opts, args[0][1:], shortopts, args[1:])
../local/var/lib/sage/venv-python3.11.1/lib/python3.11/getopt.py:195: in do_shorts
    if short_has_arg(opt, shortopts):
../local/var/lib/sage/venv-python3.11.1/lib/python3.11/getopt.py:211: in short_has_arg
    raise GetoptError(_('option -%s not recognized') % opt, opt)
E   getopt.GetoptError: option -c not recognized

mkoeppe · 2023-12-21T18:14:31Z

There are lots of error messages related to optional packages, for example https://github.com/sagemath/sage/actions/runs/7285981360/job/19853897084?pr=36591#step:16:3134

sage/geometry/polyhedron/backend_normaliz.py - sage.features.FeatureNotPresentError: pynormaliz is not available.
Importing NmzResult failed: No module named 'PyNormaliz'
No equivalent system packages for debian are known to Sage.
To install pynormaliz using the Sage package manager, you can try to run:
  !sage -i pynormaliz
To install pynormaliz using the pip package manager, you can try to run:
!sage -pip install pynormaliz==2.18

Would it be easy to skip the files that are marked as depending on an optional feature?

.github/workflows/build.yml

Co-authored-by: Matthias Köppe <mkoeppe@math.ucdavis.edu>

tobiasdiez · 2023-12-28T12:57:10Z

The log has 2000 lines of the form
conftest_inputtest.py: 1
conftest_test.py: 2
sage/algebras/affine_nil_temperley_lieb.py: 12
sage/algebras/algebra.py: 1
sage/algebras/askey_wilson.py: 22
sage/algebras/associated_graded.py: 10
sage/algebras/cellular_basis.py: 11
sage/algebras/clifford_algebra.py: 71
sage/algebras/cluster_algebra.py: 84
sage/algebras/commutative_dga.py: 95
https://github.com/sagemath/sage/actions/runs/7285981360/job/19853897084?pr=36591#step:16:26

Could you add a message to the log please that explains what it is?

Done.

There are lots of error messages related to optional packages, for example https://github.com/sagemath/sage/actions/runs/7285981360/job/19853897084?pr=36591#step:16:3134
sage/geometry/polyhedron/backend_normaliz.py - sage.features.FeatureNotPresentError: pynormaliz is not available.
Importing NmzResult failed: No module named 'PyNormaliz'
No equivalent system packages for debian are known to Sage.
To install pynormaliz using the Sage package manager, you can try to run:
  !sage -i pynormaliz
To install pynormaliz using the pip package manager, you can try to run:
!sage -pip install pynormaliz==2.18
Would it be easy to skip the files that are marked as depending on an optional feature?

Will look into this as follow-up. (It is really not the point of this PR to fix/exclude any of these failing imports)

github-actions · 2023-12-28T13:34:18Z

Documentation preview for this PR (built with commit cc3792f; changes) is ready! 🎉

mkoeppe · 2023-12-28T18:04:47Z

.github/workflows/build.yml

@@ -174,6 +174,9 @@ jobs:

      - name: Check that all modules can be imported
        run: |
+          # The following command checks that all modules can be imported.
+          # The output also includes a long list of modules together with the number of tests in each module.
+          # This can be ignored.


Is the output intended? Do you use this information? Or should everyone ignore it?

It's safe to ignore (but pytest doesn't support a way to hide it)

Fine. I assume that you mean that you also do not use this information. We'll iterate the cosmetics in follow-up PRs.

Currently you cannot import many modules directly. We use `pytest --collect-only` to test during ci that the imports are working. As a first step, we run pytest through sage, which makes sure that `sage.all` is loaded. Once the reported errors are fixed (e.g. by filtering out modules that fail because of FeatureNotPresentError), we can check that importing without `sage.all` works. ### 📝 Checklist     - [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   URL: sagemath#36591 Reported by: Tobias Diez Reviewer(s): Matthias Köppe, Tobias Diez

@kwankyu

As reported in https://groups.google.com/g/sage- devel/c/mLtXcaypU3Q/m/jHoVjQ9oAAAJ @kwankyu This failure was introduced as a side effect of sagemath#36591: The pytest discovery of modules disagrees with `sage_setup`'s notion of package directories vs. data directories. We repair it by making `sage.tests.books` an ordinary package directory (correct because the whole thing is shipped by **sagemath-repl**).   Fixes sagemath#37216  ### 📝 Checklist     - [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   URL: sagemath#37185 Reported by: Matthias Köppe Reviewer(s): Gonzalo Tornaría

Test that everything can be imported during ci

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tobiasdiez added the s: needs review label Oct 30, 2023

tobiasdiez requested a review from mkoeppe October 30, 2023 13:01

Silence output as much as possible

7d9b2a1

Merge branch 'develop' into test_imports

78b42b8

mkoeppe reviewed Oct 31, 2023

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Merge branch 'develop' into test_imports

33b54d8

vbraun force-pushed the develop branch 2 times, most recently from 883e05f to e349b00 Compare November 12, 2023 16:25

tobiasdiez added 2 commits November 16, 2023 10:28

Merge branch 'develop' into test_imports

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Merge branch 'develop' into test_imports

259e1a6

tobiasdiez added 4 commits November 21, 2023 06:34

Skip a few files from doctestsing with pytest

e84cb91

Merge branch 'develop' into test_imports

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Merge branch 'develop' into test_imports

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Merge branch 'develop' into test_imports

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tobiasdiez and others added 2 commits December 28, 2023 20:47

Update .github/workflows/build.yml

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Co-authored-by: Matthias Köppe <mkoeppe@math.ucdavis.edu>

Add message to explain long list of modules during check

97a2548

Merge branch 'develop' into test_imports

cc3792f

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vbraun merged commit 1044a6c into sagemath:develop Jan 14, 2024
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Fix sage_setup.clean doctest #37185

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Test that everything can be imported during ci #36591

Test that everything can be imported during ci #36591

tobiasdiez commented Oct 30, 2023 •

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Test that everything can be imported during ci #36591

Test that everything can be imported during ci #36591

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tobiasdiez commented Oct 30, 2023 • edited

📝 Checklist

⌛ Dependencies

mkoeppe commented Oct 30, 2023

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