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Conflicting version requirements for coverage between python-coveralls and pytest-cov #66
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Details: * pytest-cov 2.6.0 has increased its version requirement for the coverage package from coverage>=3.7.1 to coverage>=4.4. That is in conflict with the version requirement of python-coveralls for coverage==4.0.3. As a workaround, this change pins the version of pytest-cov to <2.6. An issue against pytest-cov has been opened: z4r/python-coveralls#66 Once that issue is resolved, the workaround can be removed again, probably 2.6.0 needs to continue to be excluded. Signed-off-by: Andreas Maier <[email protected]>
Details: * pytest-cov 2.6.0 has increased its version requirement for the coverage package from coverage>=3.7.1 to coverage>=4.4. That is in conflict with the version requirement of python-coveralls for coverage==4.0.3. As a workaround, this change pins the version of pytest-cov to <2.6. An issue against pytest-cov has been opened: z4r/python-coveralls#66 Once that issue is resolved, the workaround can be removed again, probably 2.6.0 needs to continue to be excluded. Signed-off-by: Andreas Maier <[email protected]>
Same issue here. |
Details: * pytest-cov 2.6.0 has increased its version requirement for the coverage package from coverage>=3.7.1 to coverage>=4.4. That is in conflict with the version requirement of python-coveralls for coverage==4.0.3. As a workaround, this change pins the version of pytest-cov to <2.6. An issue against pytest-cov has been opened: z4r/python-coveralls#66 Once that issue is resolved, the workaround can be removed again, probably 2.6.0 needs to continue to be excluded. Signed-off-by: Andreas Maier <[email protected]>
Details: * pytest-cov 2.6.0 has increased its version requirement for the coverage package from coverage>=3.7.1 to coverage>=4.4. That is in conflict with the version requirement of python-coveralls for coverage==4.0.3. As a workaround, this change pins the version of pytest-cov to <2.6. An issue against pytest-cov has been opened: z4r/python-coveralls#66 Once that issue is resolved, the workaround can be removed again, probably 2.6.0 needs to continue to be excluded. Signed-off-by: Andreas Maier <[email protected]>
Details: * pytest-cov 2.6.0 has increased its version requirement for the coverage package from coverage>=3.7.1 to coverage>=4.4. That is in conflict with the version requirement of python-coveralls for coverage==4.0.3. As a workaround, this change pins the version of pytest-cov to <2.6. An issue against pytest-cov has been opened: z4r/python-coveralls#66 Once that issue is resolved, the workaround can be removed again, probably 2.6.0 needs to continue to be excluded. Signed-off-by: Andreas Maier <[email protected]>
As a workaround, just force the version of |
Force the coverage version to work around z4r/python-coveralls#66
Details: * pytest-cov 2.6.0 has increased its version requirement for the coverage package from coverage>=3.7.1 to coverage>=4.4. That is in conflict with the version requirement of python-coveralls for coverage==4.0.3. As a workaround, this change pins the version of pytest-cov to <2.6. An issue against pytest-cov has been opened: z4r/python-coveralls#66 Once that issue is resolved, the workaround can be removed again, probably 2.6.0 needs to continue to be excluded. Signed-off-by: Andreas Maier <[email protected]>
Currently, the most recent version of python-coveralls requires `coverage==4.0.3`, while pytest-cov requires `Coverage>=4.4`. The current fix seems to be to pin `pytest-cov` to a previous version. This can be changed once: z4r/python-coveralls#66 has been resolved.
* Attempt to fix coverage dependency issue Currently, the most recent version of python-coveralls requires `coverage==4.0.3`, while pytest-cov requires `Coverage>=4.4`. The current fix seems to be to pin `pytest-cov` to a previous version. This can be changed once: z4r/python-coveralls#66 has been resolved. * Hotfix for MDTraj MOL2 file issues MDTraj has merged a fix for MOL2 file reading mdtraj/mdtraj#1378 However, it has not been included in a new release on `conda` yet. Pinning to an older version without the MOL2 fixes currently. * Forgot to update Appveyor build script
Force the coverage version to work around z4r/python-coveralls#66
Pins version of pytest-cov to 2.5 (z4r/python-coveralls#66)
Quick fix: pin pytest-cov to a previous version -> |
The pinning can be removed once the following issue is fixed: z4r/python-coveralls#66 pytest-cov 2.6.0 increased its version requirement for the coverage package to coverage>=4.4 while python-coveralls requires coverage==4.0.3.
Would it be possible to relax the Line 25 in 286e98f
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* Make foyer an optional dependency * Split dependencies into required and required for development * Update developer requirements * Marked appropriate tests to check if Foyer is installed * Remove duplicate line * Remove openbabel and gsd from Appveyor testing * Attempt to fix coverage dependency issue (#466) * Attempt to fix coverage dependency issue Currently, the most recent version of python-coveralls requires `coverage==4.0.3`, while pytest-cov requires `Coverage>=4.4`. The current fix seems to be to pin `pytest-cov` to a previous version. This can be changed once: z4r/python-coveralls#66 has been resolved. * Hotfix for MDTraj MOL2 file issues MDTraj has merged a fix for MOL2 file reading mdtraj/mdtraj#1378 However, it has not been included in a new release on `conda` yet. Pinning to an older version without the MOL2 fixes currently. * Forgot to update Appveyor build script * Bump to version 0.8.1 * Update changelog to 0.8.1 * Fixes issues with packmol input files (#474) * Fixes issues with packmol input file Also reports error based on process code instead of output, which prevented report of error about input issues. * Bump to version 0.8.1 * Update changelog to 0.8.1 * Small formatting nits * Run `activate base` before `conda build` See ContinuumIO/anaconda-issues#10211 (comment) * Update changelog * Re-pin mdtraj and pytest-cov
* Make foyer an optional dependency * Split dependencies into required and required for development * Update developer requirements * Marked appropriate tests to check if Foyer is installed * Remove duplicate line * Remove openbabel and gsd from Appveyor testing * Attempt to fix coverage dependency issue (mosdef-hub#466) * Attempt to fix coverage dependency issue Currently, the most recent version of python-coveralls requires `coverage==4.0.3`, while pytest-cov requires `Coverage>=4.4`. The current fix seems to be to pin `pytest-cov` to a previous version. This can be changed once: z4r/python-coveralls#66 has been resolved. * Hotfix for MDTraj MOL2 file issues MDTraj has merged a fix for MOL2 file reading mdtraj/mdtraj#1378 However, it has not been included in a new release on `conda` yet. Pinning to an older version without the MOL2 fixes currently. * Forgot to update Appveyor build script * Bump to version 0.8.1 * Update changelog to 0.8.1 * Fixes issues with packmol input files (mosdef-hub#474) * Fixes issues with packmol input file Also reports error based on process code instead of output, which prevented report of error about input issues. * Bump to version 0.8.1 * Update changelog to 0.8.1 * Small formatting nits * Run `activate base` before `conda build` See ContinuumIO/anaconda-issues#10211 (comment) * Update changelog * Re-pin mdtraj and pytest-cov
I had this same issue, after upgrading pip ( |
* Fix too many files being left open in packing.py `tempfile.mkstemp` provides a low level interface for interacting with temporary files. However, garbage collection (closing files, deleting files after use) must be manually taken care of. Packing.py uses temp files when packing or solvating a system, these files are never closed. This can cause the program to reach the limit of open files for a process set by the OS level `ulimit`. These changes migrate from using `mkstemp` to a higher level interface `tempfile.NamedTemporaryFile`, providing the same type of temporary file, but with saner garbage collection and scope. The sections where temp files are made are now contained in `try finally` sections, to ensure proper file closure and deletion when the program finishes, or is interrupted. * Syntax changes NamedTemporaryFile provides a file-like object to interact with compared to mkstemp. To get the full path, the `name` attribute of the NamedTemporaryFile is needed. * remove nested try-finally blocks * Forgot to pass in path for the solvate method. * Move file creation to method, move topology generation to file. * Bump to version 0.8.1 * Update changelog to 0.8.1 * Update gitignore file for VSCode Using Microsoft's VSCode generates an addtional directory and files to assist the various plugins, save states, etc. This is not needed for other users. This has been added to the .gitignore file to prevent these files from being committed erroneously. * Fixes issues with packmol input files (#474) * Fixes issues with packmol input file Also reports error based on process code instead of output, which prevented report of error about input issues. * Bump to version 0.8.1 * Update changelog to 0.8.1 * Small formatting nits * Run `activate base` before `conda build` in Appveyor (#477) * Run `activate base` before `conda build` See ContinuumIO/anaconda-issues#10211 (comment) * Update changelog * GSD files now include 1,4 special pairs for use in OPLS (#473) * Update dependency requirements (#457) * Make foyer an optional dependency * Split dependencies into required and required for development * Update developer requirements * Marked appropriate tests to check if Foyer is installed * Remove duplicate line * Remove openbabel and gsd from Appveyor testing * Attempt to fix coverage dependency issue (#466) * Attempt to fix coverage dependency issue Currently, the most recent version of python-coveralls requires `coverage==4.0.3`, while pytest-cov requires `Coverage>=4.4`. The current fix seems to be to pin `pytest-cov` to a previous version. This can be changed once: z4r/python-coveralls#66 has been resolved. * Hotfix for MDTraj MOL2 file issues MDTraj has merged a fix for MOL2 file reading mdtraj/mdtraj#1378 However, it has not been included in a new release on `conda` yet. Pinning to an older version without the MOL2 fixes currently. * Forgot to update Appveyor build script * Bump to version 0.8.1 * Update changelog to 0.8.1 * Fixes issues with packmol input files (#474) * Fixes issues with packmol input file Also reports error based on process code instead of output, which prevented report of error about input issues. * Bump to version 0.8.1 * Update changelog to 0.8.1 * Small formatting nits * Run `activate base` before `conda build` See ContinuumIO/anaconda-issues#10211 (comment) * Update changelog * Re-pin mdtraj and pytest-cov * Syntax changes NamedTemporaryFile provides a file-like object to interact with compared to mkstemp. To get the full path, the `name` attribute of the NamedTemporaryFile is needed. * Ensure all files generated in the for loops are closed and unlinked * Increase the box dims for testing fill_region a test for `fill_region` was packing a very small volume (~2nm^3) with many water molecules. This led to parts of the molecules outside the defined region. The region has been increased. * Remove support for pytest-ignore-flaky Recently, the tests on travis for the example notebooks are failing due to some internal error with pytest-ignore-flaky plugin. It seems like the feature can be replicated well enough using @pytest.mark.xfail with the strict setting to False. * Update CI as well to remove 'pytest-ignore-flaky' * Change the overlap parameter for a test, was causing floating point errors in PACKMOL * Changelog.md * Include information about the in changelog.md
Fix existing issue with codecov ( z4r/python-coveralls#66 )
Replicates graphql/graphql-js@4ed25af One of the issues for us with coveralls was this: z4r/python-coveralls#66
Cf. z4r/python-coveralls#66 which is causing the problem, and may eventually produce a longer-term fix.
PR #67 (released in version 2.9.2) has addressed this issue by now requiring coverage>=4.4. |
The error may be due to z4r/python-coveralls#66 Solution: drop CI support for Python <= 3.5, except 2.7, and apply a workaround for pypy.
The issue should be closed because it has been fixed, as stated above. As a remark for anyone who is still seeing similar symptoms: |
* Attempt to fix coverage dependency issue Currently, the most recent version of python-coveralls requires `coverage==4.0.3`, while pytest-cov requires `Coverage>=4.4`. The current fix seems to be to pin `pytest-cov` to a previous version. This can be changed once: z4r/python-coveralls#66 has been resolved. * Hotfix for MDTraj MOL2 file issues MDTraj has merged a fix for MOL2 file reading mdtraj/mdtraj#1378 However, it has not been included in a new release on `conda` yet. Pinning to an older version without the MOL2 fixes currently. * Forgot to update Appveyor build script
* Make foyer an optional dependency * Split dependencies into required and required for development * Update developer requirements * Marked appropriate tests to check if Foyer is installed * Remove duplicate line * Remove openbabel and gsd from Appveyor testing * Attempt to fix coverage dependency issue (#466) * Attempt to fix coverage dependency issue Currently, the most recent version of python-coveralls requires `coverage==4.0.3`, while pytest-cov requires `Coverage>=4.4`. The current fix seems to be to pin `pytest-cov` to a previous version. This can be changed once: z4r/python-coveralls#66 has been resolved. * Hotfix for MDTraj MOL2 file issues MDTraj has merged a fix for MOL2 file reading mdtraj/mdtraj#1378 However, it has not been included in a new release on `conda` yet. Pinning to an older version without the MOL2 fixes currently. * Forgot to update Appveyor build script * Bump to version 0.8.1 * Update changelog to 0.8.1 * Fixes issues with packmol input files (#474) * Fixes issues with packmol input file Also reports error based on process code instead of output, which prevented report of error about input issues. * Bump to version 0.8.1 * Update changelog to 0.8.1 * Small formatting nits * Run `activate base` before `conda build` See ContinuumIO/anaconda-issues#10211 (comment) * Update changelog * Re-pin mdtraj and pytest-cov
* Fix too many files being left open in packing.py `tempfile.mkstemp` provides a low level interface for interacting with temporary files. However, garbage collection (closing files, deleting files after use) must be manually taken care of. Packing.py uses temp files when packing or solvating a system, these files are never closed. This can cause the program to reach the limit of open files for a process set by the OS level `ulimit`. These changes migrate from using `mkstemp` to a higher level interface `tempfile.NamedTemporaryFile`, providing the same type of temporary file, but with saner garbage collection and scope. The sections where temp files are made are now contained in `try finally` sections, to ensure proper file closure and deletion when the program finishes, or is interrupted. * Syntax changes NamedTemporaryFile provides a file-like object to interact with compared to mkstemp. To get the full path, the `name` attribute of the NamedTemporaryFile is needed. * remove nested try-finally blocks * Forgot to pass in path for the solvate method. * Move file creation to method, move topology generation to file. * Bump to version 0.8.1 * Update changelog to 0.8.1 * Update gitignore file for VSCode Using Microsoft's VSCode generates an addtional directory and files to assist the various plugins, save states, etc. This is not needed for other users. This has been added to the .gitignore file to prevent these files from being committed erroneously. * Fixes issues with packmol input files (#474) * Fixes issues with packmol input file Also reports error based on process code instead of output, which prevented report of error about input issues. * Bump to version 0.8.1 * Update changelog to 0.8.1 * Small formatting nits * Run `activate base` before `conda build` in Appveyor (#477) * Run `activate base` before `conda build` See ContinuumIO/anaconda-issues#10211 (comment) * Update changelog * GSD files now include 1,4 special pairs for use in OPLS (#473) * Update dependency requirements (#457) * Make foyer an optional dependency * Split dependencies into required and required for development * Update developer requirements * Marked appropriate tests to check if Foyer is installed * Remove duplicate line * Remove openbabel and gsd from Appveyor testing * Attempt to fix coverage dependency issue (#466) * Attempt to fix coverage dependency issue Currently, the most recent version of python-coveralls requires `coverage==4.0.3`, while pytest-cov requires `Coverage>=4.4`. The current fix seems to be to pin `pytest-cov` to a previous version. This can be changed once: z4r/python-coveralls#66 has been resolved. * Hotfix for MDTraj MOL2 file issues MDTraj has merged a fix for MOL2 file reading mdtraj/mdtraj#1378 However, it has not been included in a new release on `conda` yet. Pinning to an older version without the MOL2 fixes currently. * Forgot to update Appveyor build script * Bump to version 0.8.1 * Update changelog to 0.8.1 * Fixes issues with packmol input files (#474) * Fixes issues with packmol input file Also reports error based on process code instead of output, which prevented report of error about input issues. * Bump to version 0.8.1 * Update changelog to 0.8.1 * Small formatting nits * Run `activate base` before `conda build` See ContinuumIO/anaconda-issues#10211 (comment) * Update changelog * Re-pin mdtraj and pytest-cov * Syntax changes NamedTemporaryFile provides a file-like object to interact with compared to mkstemp. To get the full path, the `name` attribute of the NamedTemporaryFile is needed. * Ensure all files generated in the for loops are closed and unlinked * Increase the box dims for testing fill_region a test for `fill_region` was packing a very small volume (~2nm^3) with many water molecules. This led to parts of the molecules outside the defined region. The region has been increased. * Remove support for pytest-ignore-flaky Recently, the tests on travis for the example notebooks are failing due to some internal error with pytest-ignore-flaky plugin. It seems like the feature can be replicated well enough using @pytest.mark.xfail with the strict setting to False. * Update CI as well to remove 'pytest-ignore-flaky' * Change the overlap parameter for a test, was causing floating point errors in PACKMOL * Changelog.md * Include information about the in changelog.md
* remove it from our .gitignore * pin pytest-cov so that it works on Travis (see z4r/python-coveralls#66 for more info) * add 3.7 as a build job * switch to Xenial instead of Trusty as the CI environment * match the file up with the flake8 move that was done in `develop` branch
* Make foyer an optional dependency * Split dependencies into required and required for development * Update developer requirements * Marked appropriate tests to check if Foyer is installed * Remove duplicate line * Remove openbabel and gsd from Appveyor testing * Attempt to fix coverage dependency issue (#466) * Attempt to fix coverage dependency issue Currently, the most recent version of python-coveralls requires `coverage==4.0.3`, while pytest-cov requires `Coverage>=4.4`. The current fix seems to be to pin `pytest-cov` to a previous version. This can be changed once: z4r/python-coveralls#66 has been resolved. * Hotfix for MDTraj MOL2 file issues MDTraj has merged a fix for MOL2 file reading mdtraj/mdtraj#1378 However, it has not been included in a new release on `conda` yet. Pinning to an older version without the MOL2 fixes currently. * Forgot to update Appveyor build script * Bump to version 0.8.1 * Update changelog to 0.8.1 * Fixes issues with packmol input files (#474) * Fixes issues with packmol input file Also reports error based on process code instead of output, which prevented report of error about input issues. * Bump to version 0.8.1 * Update changelog to 0.8.1 * Small formatting nits * Run `activate base` before `conda build` See ContinuumIO/anaconda-issues#10211 (comment) * Update changelog * Re-pin mdtraj and pytest-cov
* Fix too many files being left open in packing.py `tempfile.mkstemp` provides a low level interface for interacting with temporary files. However, garbage collection (closing files, deleting files after use) must be manually taken care of. Packing.py uses temp files when packing or solvating a system, these files are never closed. This can cause the program to reach the limit of open files for a process set by the OS level `ulimit`. These changes migrate from using `mkstemp` to a higher level interface `tempfile.NamedTemporaryFile`, providing the same type of temporary file, but with saner garbage collection and scope. The sections where temp files are made are now contained in `try finally` sections, to ensure proper file closure and deletion when the program finishes, or is interrupted. * Syntax changes NamedTemporaryFile provides a file-like object to interact with compared to mkstemp. To get the full path, the `name` attribute of the NamedTemporaryFile is needed. * remove nested try-finally blocks * Forgot to pass in path for the solvate method. * Move file creation to method, move topology generation to file. * Bump to version 0.8.1 * Update changelog to 0.8.1 * Update gitignore file for VSCode Using Microsoft's VSCode generates an addtional directory and files to assist the various plugins, save states, etc. This is not needed for other users. This has been added to the .gitignore file to prevent these files from being committed erroneously. * Fixes issues with packmol input files (#474) * Fixes issues with packmol input file Also reports error based on process code instead of output, which prevented report of error about input issues. * Bump to version 0.8.1 * Update changelog to 0.8.1 * Small formatting nits * Run `activate base` before `conda build` in Appveyor (#477) * Run `activate base` before `conda build` See ContinuumIO/anaconda-issues#10211 (comment) * Update changelog * GSD files now include 1,4 special pairs for use in OPLS (#473) * Update dependency requirements (#457) * Make foyer an optional dependency * Split dependencies into required and required for development * Update developer requirements * Marked appropriate tests to check if Foyer is installed * Remove duplicate line * Remove openbabel and gsd from Appveyor testing * Attempt to fix coverage dependency issue (#466) * Attempt to fix coverage dependency issue Currently, the most recent version of python-coveralls requires `coverage==4.0.3`, while pytest-cov requires `Coverage>=4.4`. The current fix seems to be to pin `pytest-cov` to a previous version. This can be changed once: z4r/python-coveralls#66 has been resolved. * Hotfix for MDTraj MOL2 file issues MDTraj has merged a fix for MOL2 file reading mdtraj/mdtraj#1378 However, it has not been included in a new release on `conda` yet. Pinning to an older version without the MOL2 fixes currently. * Forgot to update Appveyor build script * Bump to version 0.8.1 * Update changelog to 0.8.1 * Fixes issues with packmol input files (#474) * Fixes issues with packmol input file Also reports error based on process code instead of output, which prevented report of error about input issues. * Bump to version 0.8.1 * Update changelog to 0.8.1 * Small formatting nits * Run `activate base` before `conda build` See ContinuumIO/anaconda-issues#10211 (comment) * Update changelog * Re-pin mdtraj and pytest-cov * Syntax changes NamedTemporaryFile provides a file-like object to interact with compared to mkstemp. To get the full path, the `name` attribute of the NamedTemporaryFile is needed. * Ensure all files generated in the for loops are closed and unlinked * Increase the box dims for testing fill_region a test for `fill_region` was packing a very small volume (~2nm^3) with many water molecules. This led to parts of the molecules outside the defined region. The region has been increased. * Remove support for pytest-ignore-flaky Recently, the tests on travis for the example notebooks are failing due to some internal error with pytest-ignore-flaky plugin. It seems like the feature can be replicated well enough using @pytest.mark.xfail with the strict setting to False. * Update CI as well to remove 'pytest-ignore-flaky' * Change the overlap parameter for a test, was causing floating point errors in PACKMOL * Changelog.md * Include information about the in changelog.md
* Make foyer an optional dependency * Split dependencies into required and required for development * Update developer requirements * Marked appropriate tests to check if Foyer is installed * Remove duplicate line * Remove openbabel and gsd from Appveyor testing * Attempt to fix coverage dependency issue (#466) * Attempt to fix coverage dependency issue Currently, the most recent version of python-coveralls requires `coverage==4.0.3`, while pytest-cov requires `Coverage>=4.4`. The current fix seems to be to pin `pytest-cov` to a previous version. This can be changed once: z4r/python-coveralls#66 has been resolved. * Hotfix for MDTraj MOL2 file issues MDTraj has merged a fix for MOL2 file reading mdtraj/mdtraj#1378 However, it has not been included in a new release on `conda` yet. Pinning to an older version without the MOL2 fixes currently. * Forgot to update Appveyor build script * Bump to version 0.8.1 * Update changelog to 0.8.1 * Fixes issues with packmol input files (#474) * Fixes issues with packmol input file Also reports error based on process code instead of output, which prevented report of error about input issues. * Bump to version 0.8.1 * Update changelog to 0.8.1 * Small formatting nits * Run `activate base` before `conda build` See ContinuumIO/anaconda-issues#10211 (comment) * Update changelog * Re-pin mdtraj and pytest-cov
* Make foyer an optional dependency * Split dependencies into required and required for development * Update developer requirements * Marked appropriate tests to check if Foyer is installed * Remove duplicate line * Remove openbabel and gsd from Appveyor testing * Attempt to fix coverage dependency issue (#466) * Attempt to fix coverage dependency issue Currently, the most recent version of python-coveralls requires `coverage==4.0.3`, while pytest-cov requires `Coverage>=4.4`. The current fix seems to be to pin `pytest-cov` to a previous version. This can be changed once: z4r/python-coveralls#66 has been resolved. * Hotfix for MDTraj MOL2 file issues MDTraj has merged a fix for MOL2 file reading mdtraj/mdtraj#1378 However, it has not been included in a new release on `conda` yet. Pinning to an older version without the MOL2 fixes currently. * Forgot to update Appveyor build script * Bump to version 0.8.1 * Update changelog to 0.8.1 * Fixes issues with packmol input files (#474) * Fixes issues with packmol input file Also reports error based on process code instead of output, which prevented report of error about input issues. * Bump to version 0.8.1 * Update changelog to 0.8.1 * Small formatting nits * Run `activate base` before `conda build` See ContinuumIO/anaconda-issues#10211 (comment) * Update changelog * Re-pin mdtraj and pytest-cov
Cf. z4r/python-coveralls#66 which is causing the problem, and may eventually produce a longer-term fix.
The latest version of 'python-coveralls' (2.9.1, released 4/2017) requires coverage==4.0.3 (see its setup.py).
The latest version of 'pytest-cov' (2.6.0, released today) requires coverage>=4.4.
This breaks the tests of several of our projects. The version conflicts are reported by pip:
The test run finally breaks when py.test cannot load its pytest-cov plugin:
Why is it that python-coveralls needs to require exactly coverage==4.0.3? This was doomed to create such a conflict one day.
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