astropy: Cannot collect tests : pytest.PytestDeprecationWarning

Description

I have no idea what’s happened to my setup, but suddenly nothing is working. I tried now started entirely from scratch, including removing my ~/.astropy and making a fresh env for testing.

Test collection fails early with:

ERROR  - pytest.PytestDeprecationWarning: direct construction of DocTestModulePlus has been deprecated, please use DocTestModulePlus.from_parent

Steps to Reproduce

astropy) ➜  astropy git:(master)  conda create -n astropy2 python=3.6      
Collecting package metadata (current_repodata.json): done
Solving environment: done

## Package Plan ##

  environment location: /Users/aldcroft/miniconda3/envs/astropy2

  added / updated specs:
    - python=3.6


The following NEW packages will be INSTALLED:

  ca-certificates    pkgs/main/osx-64::ca-certificates-2020.1.1-0
  certifi            pkgs/main/osx-64::certifi-2020.4.5.1-py36_0
  libcxx             pkgs/main/osx-64::libcxx-4.0.1-hcfea43d_1
  libcxxabi          pkgs/main/osx-64::libcxxabi-4.0.1-hcfea43d_1
  libedit            pkgs/main/osx-64::libedit-3.1.20181209-hb402a30_0
  libffi             pkgs/main/osx-64::libffi-3.2.1-h0a44026_6
  ncurses            pkgs/main/osx-64::ncurses-6.2-h0a44026_1
  openssl            pkgs/main/osx-64::openssl-1.1.1g-h1de35cc_0
  pip                pkgs/main/osx-64::pip-20.0.2-py36_1
  python             pkgs/main/osx-64::python-3.6.10-hc70fcce_1
  readline           pkgs/main/osx-64::readline-8.0-h1de35cc_0
  setuptools         pkgs/main/osx-64::setuptools-46.1.3-py36_0
  sqlite             pkgs/main/osx-64::sqlite-3.31.1-h5c1f38d_1
  tk                 pkgs/main/osx-64::tk-8.6.8-ha441bb4_0
  wheel              pkgs/main/osx-64::wheel-0.34.2-py36_0
  xz                 pkgs/main/osx-64::xz-5.2.5-h1de35cc_0
  zlib               pkgs/main/osx-64::zlib-1.2.11-h1de35cc_3


Proceed ([y]/n)? y

Preparing transaction: done
Verifying transaction: done
Executing transaction: done
#
# To activate this environment, use
#
#     $ conda activate astropy2
#
# To deactivate an active environment, use
#
#     $ conda deactivate

(astropy) ➜  astropy git:(master)  conda activate astropy2

(astropy2) ➜  astropy git:(master)  git clean -fxd         
Removing .pytest_cache/
...
Removing astropy/wcs/src/docstrings.c
Skipping repository astropy_helpers/
Removing build/
Removing docs/__pycache__/

(astropy2) ➜  astropy git:(master)  pip install -e '.[test]'
Obtaining file:///Users/aldcroft/git/astropy
  Installing build dependencies ... done
  Getting requirements to build wheel ... done
    Preparing wheel metadata ... done
Collecting numpy>=1.16
  Using cached numpy-1.18.3-cp36-cp36m-macosx_10_9_x86_64.whl (15.2 MB)
Collecting objgraph; extra == "test"
  Using cached objgraph-3.4.1-py2.py3-none-any.whl (17 kB)
Collecting coverage; extra == "test"
  Using cached coverage-5.1-cp36-cp36m-macosx_10_13_x86_64.whl (203 kB)
Collecting skyfield>=1.20; extra == "test"
  Downloading skyfield-1.20.tar.gz (262 kB)
     |████████████████████████████████| 262 kB 1.6 MB/s 
Collecting ipython; extra == "test"
  Downloading ipython-7.14.0-py3-none-any.whl (782 kB)
     |████████████████████████████████| 782 kB 6.1 MB/s 
Collecting pytest-astropy>=0.8; extra == "test"
  Using cached pytest_astropy-0.8.0-py3-none-any.whl (3.3 kB)
Collecting pytest-xdist; extra == "test"
  Using cached pytest_xdist-1.31.0-py2.py3-none-any.whl (36 kB)
Collecting sgp4; extra == "test"
  Downloading sgp4-2.7-cp36-cp36m-macosx_10_6_intel.whl (165 kB)
     |████████████████████████████████| 165 kB 563 bytes/s 
Collecting graphviz
  Downloading graphviz-0.14-py2.py3-none-any.whl (18 kB)
Requirement already satisfied: certifi>=2017.4.17 in /Users/aldcroft/miniconda3/envs/astropy2/lib/python3.6/site-packages (from skyfield>=1.20; extra == "test"->astropy==4.1.dev1534+g7d2a91538.d20200502) (2020.4.5.1)
Processing /Users/aldcroft/Library/Caches/pip/wheels/48/67/ed/21bb8af8724f9889e7f1f0bb77093a9a71b3f9296574a14837/jplephem-2.14-py3-none-any.whl
Collecting pickleshare
  Using cached pickleshare-0.7.5-py2.py3-none-any.whl (6.9 kB)
Collecting prompt-toolkit!=3.0.0,!=3.0.1,<3.1.0,>=2.0.0
  Using cached prompt_toolkit-3.0.5-py3-none-any.whl (351 kB)
Requirement already satisfied: setuptools>=18.5 in /Users/aldcroft/miniconda3/envs/astropy2/lib/python3.6/site-packages (from ipython; extra == "test"->astropy==4.1.dev1534+g7d2a91538.d20200502) (46.1.3.post20200330)
Collecting pexpect; sys_platform != "win32"
  Using cached pexpect-4.8.0-py2.py3-none-any.whl (59 kB)
Collecting pygments
  Using cached Pygments-2.6.1-py3-none-any.whl (914 kB)
Collecting decorator
  Using cached decorator-4.4.2-py2.py3-none-any.whl (9.2 kB)
Processing /Users/aldcroft/Library/Caches/pip/wheels/b4/cb/f1/d142b3bb45d488612cf3943d8a1db090eb95e6687045ba61d1/backcall-0.1.0-py3-none-any.whl
Collecting jedi>=0.10
  Using cached jedi-0.17.0-py2.py3-none-any.whl (1.1 MB)
Collecting traitlets>=4.2
  Using cached traitlets-4.3.3-py2.py3-none-any.whl (75 kB)
Collecting appnope; sys_platform == "darwin"
  Using cached appnope-0.1.0-py2.py3-none-any.whl (4.0 kB)
Collecting pytest-doctestplus>=0.2.0
  Using cached pytest_doctestplus-0.5.0-py2.py3-none-any.whl (17 kB)
Collecting pytest-arraydiff>=0.1
  Using cached pytest_arraydiff-0.3-py2.py3-none-any.whl (8.2 kB)
Collecting pytest-astropy-header>=0.1.2
  Using cached pytest_astropy_header-0.1.2-py2.py3-none-any.whl (7.4 kB)
Collecting pytest-filter-subpackage>=0.1
  Using cached pytest_filter_subpackage-0.1.1-py2.py3-none-any.whl (5.1 kB)
Collecting hypothesis>=5.1
  Downloading hypothesis-5.10.4-py3-none-any.whl (292 kB)
     |████████████████████████████████| 292 kB 2.6 MB/s 
Collecting pytest-openfiles>=0.3.1
  Using cached pytest_openfiles-0.5.0-py3-none-any.whl (6.5 kB)
Collecting pytest-remotedata>=0.3.1
  Using cached pytest_remotedata-0.3.2-py2.py3-none-any.whl (8.3 kB)
Collecting pytest>=4.6
  Using cached pytest-5.4.1-py3-none-any.whl (246 kB)
Collecting pytest-cov>=2.0
  Using cached pytest_cov-2.8.1-py2.py3-none-any.whl (18 kB)
Collecting pytest-forked
  Using cached pytest_forked-1.1.3-py2.py3-none-any.whl (4.5 kB)
Collecting execnet>=1.1
  Using cached execnet-1.7.1-py2.py3-none-any.whl (39 kB)
Collecting six
  Using cached six-1.14.0-py2.py3-none-any.whl (10 kB)
Collecting wcwidth
  Using cached wcwidth-0.1.9-py2.py3-none-any.whl (19 kB)
Collecting ptyprocess>=0.5
  Using cached ptyprocess-0.6.0-py2.py3-none-any.whl (39 kB)
Collecting parso>=0.7.0
  Using cached parso-0.7.0-py2.py3-none-any.whl (100 kB)
Collecting ipython-genutils
  Using cached ipython_genutils-0.2.0-py2.py3-none-any.whl (26 kB)
Collecting attrs>=19.2.0
  Using cached attrs-19.3.0-py2.py3-none-any.whl (39 kB)
Collecting sortedcontainers<3.0.0,>=2.1.0
  Using cached sortedcontainers-2.1.0-py2.py3-none-any.whl (28 kB)
Processing /Users/aldcroft/Library/Caches/pip/wheels/a1/d9/f2/b5620c01e9b3e858c6877b1045fda5b115cf7df6490f883382/psutil-5.7.0-cp36-cp36m-macosx_10_9_x86_64.whl
Collecting pluggy<1.0,>=0.12
  Using cached pluggy-0.13.1-py2.py3-none-any.whl (18 kB)
Collecting packaging
  Using cached packaging-20.3-py2.py3-none-any.whl (37 kB)
Collecting py>=1.5.0
  Using cached py-1.8.1-py2.py3-none-any.whl (83 kB)
Collecting more-itertools>=4.0.0
  Using cached more_itertools-8.2.0-py3-none-any.whl (43 kB)
Collecting importlib-metadata>=0.12; python_version < "3.8"
  Using cached importlib_metadata-1.6.0-py2.py3-none-any.whl (30 kB)
Collecting apipkg>=1.4
  Using cached apipkg-1.5-py2.py3-none-any.whl (4.9 kB)
Collecting pyparsing>=2.0.2
  Using cached pyparsing-2.4.7-py2.py3-none-any.whl (67 kB)
Collecting zipp>=0.5
  Using cached zipp-3.1.0-py3-none-any.whl (4.9 kB)
Building wheels for collected packages: skyfield
  Building wheel for skyfield (setup.py) ... done
  Created wheel for skyfield: filename=skyfield-1.20-py3-none-any.whl size=297372 sha256=33c228a291bfc2ec55964457b418dc3a51fd8ac8ee13ded05d66283ab83d5607
  Stored in directory: /Users/aldcroft/Library/Caches/pip/wheels/e9/9d/45/451b32f65b27ab00717c980a1df6e41938825840b0ac657922
Successfully built skyfield
Installing collected packages: numpy, graphviz, objgraph, coverage, jplephem, sgp4, skyfield, pickleshare, wcwidth, prompt-toolkit, ptyprocess, pexpect, pygments, decorator, backcall, parso, jedi, six, ipython-genutils, traitlets, appnope, ipython, zipp, importlib-metadata, pluggy, pyparsing, packaging, py, attrs, more-itertools, pytest, pytest-doctestplus, pytest-arraydiff, pytest-astropy-header, pytest-filter-subpackage, sortedcontainers, hypothesis, psutil, pytest-openfiles, pytest-remotedata, pytest-cov, pytest-astropy, pytest-forked, apipkg, execnet, pytest-xdist, astropy
  Running setup.py develop for astropy

Successfully installed apipkg-1.5 appnope-0.1.0 astropy attrs-19.3.0 backcall-0.1.0 coverage-5.1 decorator-4.4.2 execnet-1.7.1 graphviz-0.14 hypothesis-5.10.4 importlib-metadata-1.6.0 ipython-7.14.0 ipython-genutils-0.2.0 jedi-0.17.0 jplephem-2.14 more-itertools-8.2.0 numpy-1.18.3 objgraph-3.4.1 packaging-20.3 parso-0.7.0 pexpect-4.8.0 pickleshare-0.7.5 pluggy-0.13.1 prompt-toolkit-3.0.5 psutil-5.7.0 ptyprocess-0.6.0 py-1.8.1 pygments-2.6.1 pyparsing-2.4.7 pytest-5.4.1 pytest-arraydiff-0.3 pytest-astropy-0.8.0 pytest-astropy-header-0.1.2 pytest-cov-2.8.1 pytest-doctestplus-0.5.0 pytest-filter-subpackage-0.1.1 pytest-forked-1.1.3 pytest-openfiles-0.5.0 pytest-remotedata-0.3.2 pytest-xdist-1.31.0 sgp4-2.7 six-1.14.0 skyfield-1.20 sortedcontainers-2.1.0 traitlets-4.3.3 wcwidth-0.1.9 zipp-3.1.0

(astropy2) ➜  astropy git:(master) pytest astropy/io/ascii
==================================================================== test session starts =====================================================================
platform darwin -- Python 3.6.10, pytest-5.4.1, py-1.8.1, pluggy-0.13.1

Running tests with Astropy version 4.1.dev1534+g7d2a91538.d20200502.
Running tests in astropy/io/ascii.

Date: 2020-05-02T15:05:04

Platform: Darwin-19.2.0-x86_64-i386-64bit

Executable: /Users/aldcroft/miniconda3/envs/astropy2/bin/python

Full Python Version: 
3.6.10 |Anaconda, Inc.| (default, Mar 25 2020, 18:53:43) 
[GCC 4.2.1 Compatible Clang 4.0.1 (tags/RELEASE_401/final)]

encodings: sys: utf-8, locale: UTF-8, filesystem: utf-8
byteorder: little
float info: dig: 15, mant_dig: 15

Package versions: 
Numpy: 1.18.3
Scipy: not available
Matplotlib: not available
h5py: not available
Pandas: not available
Cython: not available
Scikit-image: not available
asdf: not available

Using Astropy options: remote_data: none.

rootdir: /Users/aldcroft/git/astropy, inifile: setup.cfg
plugins: arraydiff-0.3, remotedata-0.3.2, xdist-1.31.0, hypothesis-5.10.4, filter-subpackage-0.1.1, openfiles-0.5.0, forked-1.1.3, doctestplus-0.5.0, astropy-header-0.1.2, cov-2.8.1
collected 0 items / 1 error                                                                                                                                  

=========================================================================== ERRORS ===========================================================================
_______________________________________________________________ ERROR collecting test session ________________________________________________________________
../../miniconda3/envs/astropy2/lib/python3.6/site-packages/pluggy/hooks.py:286: in __call__
    return self._hookexec(self, self.get_hookimpls(), kwargs)
../../miniconda3/envs/astropy2/lib/python3.6/site-packages/pluggy/manager.py:93: in _hookexec
    return self._inner_hookexec(hook, methods, kwargs)
../../miniconda3/envs/astropy2/lib/python3.6/site-packages/pluggy/manager.py:87: in <lambda>
    firstresult=hook.spec.opts.get("firstresult") if hook.spec else False,
../../miniconda3/envs/astropy2/lib/python3.6/site-packages/pytest_doctestplus/plugin.py:456: in pytest_collect_file
    return self._doctest_module_item_cls(path, parent)
../../miniconda3/envs/astropy2/lib/python3.6/site-packages/_pytest/nodes.py:83: in __call__
    warnings.warn(NODE_USE_FROM_PARENT.format(name=self.__name__), stacklevel=2)
E   pytest.PytestDeprecationWarning: direct construction of DocTestModulePlus has been deprecated, please use DocTestModulePlus.from_parent
================================================================== short test summary info ===================================================================
ERROR  - pytest.PytestDeprecationWarning: direct construction of DocTestModulePlus has been deprecated, please use DocTestModulePlus.from_parent
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! Interrupted: 1 error during collection !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
====================================================================== 1 error in 0.52s ======================================================================

System Details

Darwin-19.2.0-x86_64-i386-64bit Python 3.6.10 |Anaconda, Inc.| (default, Mar 25 2020, 18:53:43) [GCC 4.2.1 Compatible Clang 4.0.1 (tags/RELEASE_401/final)] Numpy 1.18.3 astropy 4.1.dev1534+g7d2a91538.d20200502