Use pytest to run doctests

[mkoeppe]

As suggested in #33232 comment:1, ./sage --pytest now uses pytest to discover and run doctests.

To test, run ./sage --pytest src/sage/manifolds/. This results in

48 failed, 1416 passed, 7 warnings

With many of the failed tests being due to some issues with assumptions and/or symbolic variables and/or deprecation warnings.
To see examples of these failures, run pytest on

src/sage/manifolds/differentiable/examples/sphere.py
src/sage/manifolds/utilities.py
src/sage/manifolds/chart.py

We also add tests that verify that sage --pytest (and sage -t) correctly complain about failing doctests.

Follow-ups:

• pytest - fix scope in which doctests are run #33826 Fix these issues
• Use pytest-xdist to run pytest in parallel #33825 Use pytest-parallel or pytest-xdist to run pytest in parallel
• Run doctests defined in cython files using pytest-cython #33827 Also run doctests defined in cython files using https://github.com/lgpage/pytest-cython

Depends on #33572

CC: @tobiasdiez @tornaria

Component: doctest framework

Author: Tobias Diez

Branch: cc19e92

Reviewer: Matthias Koeppe

Issue created by migration from https://trac.sagemath.org/ticket/33546

[mkoeppe]

Dependencies: #33549

[tobiasdiez]

Description changed:

--- 
+++ 
@@ -2,3 +2,4 @@
 
 In this context, the limitation of pytest to Python files matching the pytest file pattern (#31924) will be reverted.
 
+For cython files: https://github.com/lgpage/pytest-cython

[tobiasdiez]

Changed dependencies from #33549 to none

[tobiasdiez]

Branch: public/tests/pytest_doctests

[sagetrac-git]

Branch pushed to git repo; I updated commit sha1. New commits:

f67476f

Add some test and prelimary code

[sagetrac-git]

Commit: f67476f

[tobiasdiez]

Dependencies: #33572

[tobiasdiez]

comment:7

In principle this seems to work now. To test, run ./sage --pytest src/test_doctest.py. Feedback welcome.

Any idea why the import of Integer is necessary in test_doctest.py and how to do this on a global level? How is this done for sage -t?

[sagetrac-git]

Changed commit from f67476f to 538ead3

[sagetrac-git]

Branch pushed to git repo; I updated commit sha1. New commits:

9385501	src/bin/sage: Implement 'sage --pytest'
abbb61f	src/conftest.py: import sage.all to avoid cyclic import errors
9bb72ea	src/conftest.py: Add # type: ignore, add reference to trac ticket
2c16704	src/conftest.py: Remove outdated text
30642ba	src/bin/sage: Handle 'sage -pytest' without file args
f805567	Merge remote-tracking branch 'origin/u/mkoeppe/sage__pytest' into public/tests/pytest_doctests
538ead3	First working prototype

[tobiasdiez]

Description changed:

--- 
+++ 
@@ -1,5 +1,19 @@
-As suggested in [#33232 comment:1](https://github.com/sagemath/sage/issues/33232#comment:1)
+As suggested in [#33232 comment:1](https://github.com/sagemath/sage/issues/33232#comment:1), `./sage --pytest` now uses pytest to discover and run doctests.
 
-In this context, the limitation of pytest to Python files matching the pytest file pattern (#31924) will be reverted.
+To test, run `./sage --pytest src/sage/manifolds/`. This results in 
 
-For cython files: https://github.com/lgpage/pytest-cython
+```
+48 failed, 1416 passed, 7 warnings
+```
+With many of the failed tests being due to some issues with assumptions and/or symbolic  variables and/or deprecation warnings.
+To see examples of these failures, run pytest on
+
+```
+src/sage/manifolds/differentiable/examples/sphere.py
+src/sage/manifolds/utilities.py
+src/sage/manifolds/chart.py
+```
+
+Follow-ups:
+- Fix these issues
+- Also run doctests defined in cython files using https://github.com/lgpage/pytest-cython

[tobiasdiez]

comment:9

There are still a few issues, but as a first version it should be good to go.

[sagetrac-git]

Changed commit from 538ead3 to 58e11d7