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(need two lines before ..versionchanged)
- deprecate in 1.0.0 - remove in 2.0.0 - adjusted tests that test for warnings: only test for UserWarning and match the message with regex in pytest.warns() instead manually looking through the WarningReport object: the problem is that the deprecation warning changes the number of entries
These tests are not necessary because gridDataFormats is a dependency.
- close #2502 - DensityAnalysis is based on @nawtrey's pmda.density.DensityAnalysis but replace _reduce with accumulation in _single_frame - added tests (based on the Test_density_from_universe): both give the same answer as they pass the same tests; test specific exceptions in DensityAnalysis - update docs (also write ångström consistently throughout) - update CHANGELOG
When density_from_universe() is gone we will not need the function factory either.
- density_from_PDB is terrible code (I wrote it) and not used: deprecated and to be removed for 2.0.0 - added test so that it is covered - fixed bug that was uncovered by test (us ag.tempfactors) - added test for Bfactors2RMSF - test for deprecation warnings - organized in classes - shortened test names for density_from_universe()
Fixed the attribute error (#2396). Added test cases that check the ids and indices of atoms in a hydrogen bond. Co-authored-by: p-j-smith <[email protected]>
Tidied up the mock universe in TestHydrogenBondAnalysisMock. Using numpy asserts rather than bare asserts.
Co-authored-by: p-j-smith <[email protected]>
It is a million times faster to access. See #2396 (comment)
* fix #2593 * Changes the :meth:PSAnalysis.generate_paths defaults for store and filename defaults to those originally documented in the docstring. * Updates the test for :meth:PSAnalysis.save_paths and :meth:PSAnalysis.load so it no longer fails. * Also some blank line PEP8 changes, because I got carried away * Update CHANGELOG
* Implement CHEMFILES reader and writer Co-authored-by: richardjgowers <[email protected]> Co-authored-by: Max Linke <[email protected]>
Commit title: Increase coverage of leaflet.py (#2603) Contents of commit: ============= 1) This commit adds a series of tests to `analysis/leaflet.py` which cover parts of the code which did not use to be tested (Issue #2600). As of this commit, coverage is now at over 95% for this module. 2) This commit also fixes a missing import for the selection module (#2612). Unaltered commit history: ================= * _get_graph without self.pbc for leaflet.py * using update * add test for leaflet write_selection and fix one missing module in leaflet.py * tyop * check expected lipids contact are returned when pbc on * check leaflet write_selection output * remove unused codes * add more tests on update function * cover three options for sparse * add test on components index in group & add name CHANGELOG * add test on update without cutoff * PEP8 formatting * exclude valueerror in matrix cal from coverage * add author
* use try:except to wrap 'read_numpy_offsets' to catch if offsets file fails to load. provide warning to user and read offsets from trajectory instead Co-authored-by: Oliver Beckstein <[email protected]>
Partially fixes #2502 (completes PR #2537) ## PR contents: This PR by @wvandertoorn finalises the work done as part of #2537 Key commits: - Fixes docstring (adds .. deprecated information). - Adds back :class:`TestGridImport`. - Reduces precision matching of `test_density_from_PDB`. - CHANGELOG and AUTHORS updated accordingly.
Fixes #2618 ## PR details In light of recently pytest changes (5.4.0), this PR switches some tests over to explicitly declared fixtures. Also included are some typo and PEP8 corrections.
Fixed the run() method of analysis.hydrogenbonds.hbond_analysis method to use atom indices instead of ids
Fixes issue #2575 ## Work done in this PR: Here the always-empty `details` dictionary which used to be returned by ClusterMethods has been removed. ## Files changed - ClusterMethods.py (removed details). - test_encore.py (removed details). - cluster.py (removed details). - AUTHORS and CHANGELOG updated accordingly.
added test for alignto and fasta2select
remove dead code
Added warning for 1 A^3 CRYST1 Record
print message if C extension not installed
#2256) * Summary of changes The main issue with HydrogenBondLifetimes (besides the bug #2247) is that it defined its own definition of a hydrogen bond, without allowing the user to change it. It should be clear that the hydrogen bonds first have to be computed by the user, and then the autocorrelation for the bonds can be found. This is achieved with the autocorrelation() function, which is now made available in a separate module, `MDAnalysis.lib.correlations` so that it can be used by any code. * Provides well defined autocorrelation which can be used for both, SurvivalProbability and HydrogenLifetimes (and more?) in new module MDAnalysis/lib/correlations.py * Autocorrelation function and intermittency function are now independant with their own test cases * Removed the class HydrogenBondLifetimes and moved the autocorrelation functionality into the hbond_analysis class as a .autocorrelation method. This method should replace also hbond_autocorrel.py file in the future. * New test cases for the method .autocorrelation (HydrogenBondAnalysis) were added * Added a test cases that, with our definition of intermittency, would fail in the case of the hbond_autocorrel.py. * Fixes the issue #2247 * Detailed code comments * new module MDAnalysis/lib/correlations.py * Extracting the autocorrelation and intermittency from SP into their own functions with their own test cases. * A more general documentation in the autocorrelation. * The documentation updated with the code. The HydrogenBondAnalysis should ideally be extracted from the HydrogenBondLifetime and fed into it in the constructor. * Removed the class HydrogenBondLifetimes and moved the autocorrelation functionality into the hbond_analysis class as a .autocorrelation method. This method should replace also hbond_autocorrel.py file. Test cases for the new method .autocorrelation are added. * Updated logging. * Added __future__ imports. * Remove deprecation warning for HydrogenBondLifetime. This function will be removed in a future PR once a replacement that uses the new hydrogen bond class is in place. * Added checks for parameters types and dimensions. * reST citations * Detailed test comments * Updated test cases to illuminate the bug in #2247. * Correction for the test to make it consistent with the previous author's test. Our end index is inclusive (5th frame, giving 6 frames). But the other author's analysis was done on 0-4 frames (5 frames). * Exhaustive testing for autocorrelation. It will now return 1 at tau=0. Now the function can be embedded into HydrogenBondLifetime. * Exceptions marked as not covered Co-authored-by: Paul Smith <[email protected]> Co-authored-by: Oliver Beckstein <[email protected]>
* fixes #2661 * added frames and times * changed hole test * added deprecation warning, docs, pep8 fixes * added test and doc change * removed timesteps attribute from hydrogenbonds.hbond_analysis and all 1.0 versionchanged notes * updated CHANGELOG
* fixes #2669 * fixes #2672 * fixes "same residue" and "same segment" selections * Use resindices of resids for same residue selection * Use segindices of segids for same segment selection * Use resindices for byres selection * add failing test * failing tests with correct number of atoms * fix same selection * add failing byres test * fix byres test * add comments * updated changelog
* Fixes #2681 * use the upstream `pytest` temporary file/path handling instead of using/maintaining our own * no residual test artifacts were observed when the full test suite passed locally for this feature branch Co-authored-by: Oliver Beckstein <[email protected]>
* resize image in readme * add raw tag * fix spacing * resize * try center * try rst center * try html center class * remove centering * use numfocus template * fix link * add line break manually * alt text
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