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Conflicting version requirements for coverage between python-coveralls and pytest-cov #66

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andy-maier opened this issue Sep 3, 2018 · 7 comments

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@andy-maier
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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:

...
python-coveralls 2.9.1 has requirement coverage==4.0.3, but you'll have coverage 4.5.1 which is incompatible.
...
pytest-cov 2.6.0 has requirement coverage>=4.4, but you'll have coverage 4.0.3 which is incompatible.
...

The test run finally breaks when py.test cannot load its pytest-cov plugin:

pluggy.manager.PluginValidationError: Plugin 'pytest_cov' could not be loaded: (coverage 4.0.3 (/home/travis/virtualenv/python2.7.14/lib/python2.7/site-packages), Requirement.parse('coverage>=4.4'))!

Why is it that python-coveralls needs to require exactly coverage==4.0.3? This was doomed to create such a conflict one day.

andy-maier added a commit to zhmcclient/python-zhmcclient that referenced this issue Sep 4, 2018
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]>
andy-maier added a commit to zhmcclient/python-zhmcclient that referenced this issue Sep 4, 2018
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]>
@inkhey
Copy link

inkhey commented Sep 5, 2018

Same issue here.

andy-maier added a commit to pywbem/pywbem that referenced this issue Sep 5, 2018
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]>
andy-maier added a commit to pywbem/pywbem that referenced this issue Sep 5, 2018
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]>
andy-maier added a commit to pywbem/pywbem that referenced this issue Sep 6, 2018
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]>
haasad added a commit to LCA-ActivityBrowser/activity-browser that referenced this issue Sep 6, 2018
@dkfellows
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As a workaround, just force the version of coverage to be at least 4.4 by pip-installing that over the top; that seems to work with our tests. (OK, they're not thorough tests of whether this is correct, but it seems to work.)

dkfellows added a commit to SpiNNakerManchester/sPyNNaker that referenced this issue Sep 7, 2018
Force the coverage version to work around z4r/python-coveralls#66
andy-maier added a commit to pywbem/pywbem that referenced this issue Sep 7, 2018
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]>
loicpw added a commit to loicpw/clichain that referenced this issue Sep 13, 2018
justinGilmer added a commit to justinGilmer/mbuild that referenced this issue Oct 15, 2018
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.
summeraz pushed a commit to mosdef-hub/mbuild that referenced this issue Oct 15, 2018
* 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
tbhartman added a commit to tbhartman/abaqus2dyna that referenced this issue Oct 23, 2018
Force the coverage version to work around z4r/python-coveralls#66
jan-matthis added a commit to mackelab/delfi that referenced this issue Nov 5, 2018
Pins version of pytest-cov to 2.5 (z4r/python-coveralls#66)
@carlomazzaferro
Copy link

Quick fix: pin pytest-cov to a previous version -> pytest-cov==2.5.0

spiccinini added a commit to satellogic/orbit-predictor that referenced this issue Dec 7, 2018
jnns added a commit to jnns/mkepub that referenced this issue Dec 12, 2018
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.
@jakirkham
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Contributor

Would it be possible to relax the coverage constraint here and merely require 4.0.3 as a minimum? Any ideas as to what motivated that constraint initially?

'coverage==4.0.3',

astrojuanlu pushed a commit to astrojuanlu/orbit-predictor that referenced this issue Dec 28, 2018
justinGilmer pushed a commit to mosdef-hub/mbuild that referenced this issue Jan 7, 2019
* 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
justinGilmer pushed a commit to justinGilmer/mbuild that referenced this issue Jan 7, 2019
* 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
@stoltzmaniac
Copy link

I had this same issue, after upgrading pip ( pip install --upgrade pip ) I didn't have the problem, not sure why this would have done anything though.

justinGilmer added a commit to mosdef-hub/mbuild that referenced this issue Jan 8, 2019
* 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
praiskup added a commit to praiskup/distgen that referenced this issue Jan 11, 2019
praiskup added a commit to devexp-db/distgen that referenced this issue Jan 13, 2019
matsoftware added a commit to matsoftware/swift-code-metrics that referenced this issue Feb 10, 2019
matsoftware added a commit to matsoftware/swift-code-metrics that referenced this issue Feb 10, 2019
elupus added a commit to elupus/nibeuplink that referenced this issue Mar 1, 2019
sirex added a commit to sirex/manopozicija.lt that referenced this issue Apr 2, 2019
Cito added a commit to graphql-python/graphql-core that referenced this issue Apr 18, 2019
Replicates graphql/graphql-js@4ed25af

One of the issues for us with coveralls was this:
z4r/python-coveralls#66
j2kun added a commit to pim-book/programmers-introduction-to-mathematics that referenced this issue Apr 27, 2019
Cf. z4r/python-coveralls#66 which is causing
the problem, and may eventually produce a longer-term fix.
arrrobase added a commit to SivyerLab/pystim that referenced this issue May 8, 2019
abeelen pushed a commit to abeelen/nikamap that referenced this issue May 29, 2019
shuttle1987 added a commit to persephone-tools/persephone that referenced this issue Jun 27, 2019
@andy-maier
Copy link
Author

PR #67 (released in version 2.9.2) has addressed this issue by now requiring coverage>=4.4.

abeelen pushed a commit to abeelen/nikamap that referenced this issue Jun 25, 2020
MaxGaukler added a commit to MaxGaukler/mpmath that referenced this issue Sep 16, 2020
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.
@MaxGaukler
Copy link

The issue should be closed because it has been fixed, as stated above.

As a remark for anyone who is still seeing similar symptoms:
The same symptom pluggy.manager.PluginValidationError can also occur due to a bug in pip's dependency resolver. This can be solved by using pip >= 20.3 (will be released soon). For details, see https://pip.pypa.io/en/stable/user_guide/#resolver-changes-2020

umesh-timalsina pushed a commit to mosdef-hub/molbox that referenced this issue Jun 26, 2021
* 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
umesh-timalsina pushed a commit to mosdef-hub/molbox that referenced this issue Jun 26, 2021
* 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
umesh-timalsina pushed a commit to mosdef-hub/molbox that referenced this issue Jun 26, 2021
* 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
NicolasBenjamin pushed a commit to NicolasBenjamin/Python-Flask-Docker that referenced this issue Dec 29, 2021
* 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
umesh-timalsina pushed a commit to GOMC-WSU/MoSDeF-GOMC that referenced this issue Mar 22, 2022
* 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
umesh-timalsina pushed a commit to GOMC-WSU/MoSDeF-GOMC that referenced this issue Mar 22, 2022
* 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
umesh-timalsina pushed a commit to umesh-timalsina/MoSDeF-GOMC that referenced this issue Oct 12, 2022
* 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
umesh-timalsina pushed a commit to umesh-timalsina/MoSDeF-GOMC that referenced this issue Oct 12, 2022
* 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
tonicanada pushed a commit to tonicanada/programmers-introduction-to-mathematics that referenced this issue Oct 1, 2023
Cf. z4r/python-coveralls#66 which is causing
the problem, and may eventually produce a longer-term fix.
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