Update dependency requirements #457
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Something else to think about would be pinning all of our dependencies. This seems to be the general best practice, the downside being the need to update the versions periodically. |
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👍 Although we'd want to be careful about pinning packages unless we know of breaking issues. That severely restricts end users who want to integrate a library like mbuild into a larger workflow that may have other dependency requirements. E.g. if you pin numpy to 1.11 here but someone is building a workflow with numpy==1.12 then they can't use mbuild. Also from that blog post you linked: |
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@ctk3b That's a good point. I think the optimal route (from looking at this) would be to pin dependencies in |
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Basically what you don't want is to pin dependencies on whatever users install via |
* 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
* 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
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Not sure why this branch went dormant, but it's still good after merging master back into it. The red X from travis is due to an unrelated issue on Python 2.7 macOS builds only. I think this is ready to merge, after which we should make a release and then do the same thing in foyer. |
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Yeah, this looks good to me. That issue about too many open files should be resolved today. Ill go ahead and merge. |
justinGilmer
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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
justinGilmer
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that referenced
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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
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mikemhenry
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Jan 28, 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
mikemhenry
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Jan 28, 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 (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` in Appveyor (mosdef-hub#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 (mosdef-hub#473) * Update dependency requirements (mosdef-hub#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 (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 * 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
This was referenced Feb 21, 2019
umesh-timalsina
referenced
this pull request
in GOMC-WSU/MoSDeF-GOMC
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
referenced
this pull request
in GOMC-WSU/MoSDeF-GOMC
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
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We've had issues with a dependency loop due to
mbuildandfoyerboth having each other as a required dependency. To fix this, and to make MoSDeF more modular, this PR separatesfoyerout as an optional dependency, though still required for development and testing.To specify that
foyeris required for testing, this PR also separates out from ourrequirements.txtfile arequirements-dev.txtfile that lists all packages required for development and testing ofmbuild.requirements.txtnow contains only the subset of packages that are required to actually usembuild.