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Fixes issue #2939 ## Work done in this PR - Adds missing file types of testsuite/setup.py (*top, *in, *sdf, and the contents of data/gromacs/gromos54a7_edited.ff/*).
* fix hip with reaction
- fix #2934 - use unistd.h in ENCORE's spe.c when not WIN32 (e.g. __unix__ or __APPLE__ but to be consistent with other uses in the code base we do not specifically test for __unix__ || __APPLE__) - update CHANGELOG
ensure that unistd.h is included on recent clang
Towards #2739 ## Work done in this PR Removes the old helanal code in favour of helix_analysis
* Update README.rst * Remove bolding from tutorials (does not work as a reST link)
* invalid escape sequences in `str/bytes` are deprecated in newer versions of Python: https://bugs.python.org/issue27364 * fix the various `DeprecationWarning: invalid escape sequence \..` warnings emitted by our full test suite, mostly by using raw strings `r'...'` to allow use of internal `\` * full test suite warning count drops slightly from 30,298 to 30,276
* invalid escape sequence usage is now treated as an error in our full test suite to prevent regressions * CHANGELOG update
- mostly convert strings to raw strings - removed a number of embedded newlines from raw strings (because they do not work in raw strins as expected) - fixed heading of MDAnalysis/core/topologyattrs.py - fixed reST in Janin
MAINT: fix invalid escape seqs
- Copies the latest release to https://docs.mdanalysis.org/stable/ - Copies latest dev docs to https://docs.mdanalysis.org/dev - Allows docs to be intersphinxed at above URLs
Fixes #2979 ## Work done in this PR The file test_bat_IO.npy was created in one test and used in another one. This leads to the second test possibly failing when the tests are run in parallel. This commit moves creating the file into a fixture that the two tests depends. The new fixture also uses the tmpdir fixture to avoid the file created during the tests to remain in the test directory.
Not an issue targetted fix. ## Overview mamba is a dropin replacement for the conda CLI but faster ## Work done in this PR Enabled the `MAMBA` environment variable keyword for the CI helper.
* Fixes #2990 * Update indexing in Charges and Masses get_residues: Avoid indexing a numpy array with a list of arrays, use a tuple of array instead. Multidimensional indexing of arrays with a non-tuple argument is deprecated. * Turn warnings into errors to avoid regression over #2990 * Update CHANGELOG
* TST, CI: add ARM64 Graviton 2 to CI * start testing MDAnalysis on ARM64 using new AWS Graviton 2 architecture available in Travis CI * testing on my fork shows only two failures in the MDAnalysis test suite using a fairly minimal set of dependencies; we can probably either fix those or skip them and open an issue * the test failures are: `test_written_remarks_property` `TestEncoreClustering.test_clustering_three_ensembles_two_identical` * run time for this CI entry is about 23 minutes, which is solid for ARM; we save a lot of time using experimental upstream wheels in some cases and excluding (source builds of) dependencies where possible until the ARM64 binary wheel ecosystem matures a bit more * MAINT: ARM64 shims * adjust `CAffinityPropagation()` C-level function to use `double` instead of `float` in some strategic locations that allow the `test_clustering_three_ensembles_two_identical()` test to pass on gcc115 ARM64 machine * mark `test_written_remarks_property()` as a known failure on ARM64; it fails in Travis CI on that platform, but not on gcc115 ARM64 machine; that said, this test is already known to be flaky on Windows 32-bit (may depend on character settings on machine?) * MAINT: MR 2956 revisions * reduce optimization level of MDAnalysis builds on ARM64 to avoid problems with `ap.c` causing test failures on that architecture * revert any source changes to `ap.c`
Fixes issue #1989, completes PR #2956 ## Work done in this PR * Switches CI to using recently released SciPy `1.5.3` with "official" Linux ARM64 wheels over the weekend, instead of the previous "special"/unreleased wheels * Add a `CHANGELOG` entry to reflect preliminary MDAnalysis support for the Linux ARM64 platform (minimal dependencies)
Fixes #2993 Redirect URLs in stable/sitemap.xml and dev/sitemap.xml to correct locations
* Add a reindex argument to the PDBWritter * Tests for PDB reindex * Remove extra print * Test PDB CONECT with reindex=False * Update CHANGELOG * More precise version change for PDB reindex * Fix long lines * Increase test coverage for #2886 Also silence some warnings for the tests in the PR. * Remove useless branch in PDB.py There was a test in PDBWriter._write_pdb_bonds about writing the bonds for an atomgroup that does not have AG.ids but asking to not reindex. The test was silencing the problem and would lead to the bonds not being written. However, that part of the code would never be reached because writing the atoms would have raised an exception before that method is called. This commit removes this test. Now, if that part of the code is called (which should not happen), an exception is raised when the method tries to access AG.ids.
- Fixes #1845 - Adds dummy method with documentation of original method - Dummy method gets replaced by actual method on instantiation
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Hello @viral28! Thanks for opening this PR. We checked the lines you've touched for PEP 8 issues, and found:
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