Run activate base before conda build in Appveyor
#477
Merged
Conversation
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
justinGilmer
approved these changes
Dec 11, 2018
|
🚀 |
|
Actually, @mattwthompson , can you add a brief blurb of this PR in changelog.md? Then we can merge. |
justinGilmer
pushed a commit
to justinGilmer/mbuild
that referenced
this pull request
Jan 7, 2019
* Run `activate base` before `conda build` See ContinuumIO/anaconda-issues#10211 (comment) * Update changelog
justinGilmer
added a commit
that referenced
this pull request
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
mikemhenry
pushed a commit
to mikemhenry/mbuild
that referenced
this pull request
Jan 28, 2019
* Run `activate base` before `conda build` See ContinuumIO/anaconda-issues#10211 (comment) * Update changelog
mikemhenry
pushed a commit
to mikemhenry/mbuild
that referenced
this pull request
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
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
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
This at least gets it to build the conda package (before and after). Not sure about the tests at the moment.