add docs for analysis.align.AverageStructure (backport)#2945
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add docs for analysis.align.AverageStructure (backport)#2945
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Conflicts: package/CHANGELOG package/MDAnalysis/version.py testsuite/CHANGELOG testsuite/setup.py
Conflicts: maintainer/conda/MDAnalysis/meta.yaml package/CHANGELOG package/MDAnalysis/version.py package/setup.py testsuite/CHANGELOG testsuite/MDAnalysisTests/__init__.py testsuite/setup.py
- updated all modules - removed any code that guards against scipy or matplotlib import - conforms to style guide https://github.com/MDAnalysis/mdanalysis/wiki/Style-Guide#module-imports-in-mdanalysisanalysis - fixes #1159 - fixes #1361
Conflicts: package/CHANGELOG
Release 0.16.2
(List was messed up in a previous cherry-pick and not fully correct then.)
- removed superfluous coordinates/dcdtimeseries.c - removed execute permissions from module NAMDBI.py
* Make the TPR parser a bit faster A function in the TPR parser calls list.pop thousands of times, which is slow. This commit avoids that exansive call. Taking the TPR from https://github.com/bioexcel/covid_modelling_simulation_data/tree/master/spike_protein/full_spike/trimer the parsing time on my computer goes from 25.6s to 9.39s. On a more pathological TPR file, it goes from 3 minutes to about 6s. * Update changelog for #2804 Co-authored-by: Richard Gowers <richardjgowers@gmail.com>
* Fixes #2814 * changes in ChainReader: * new `_read_frame` and `__iter__` are now properly connected (previously, they moved independently, which could lead to the ChainReader being in an inconsistent state) * remove `_chained_iterator`. * add `__next__` * add an extra attribute `__current_frame` to internally monitor absolute current frame * add tests * update CHANGELOG
* decorate Selection.apply to ignore empty atomgroups * added test for global selection off empty AG * fix for global selections and empty AG * decorate functions instead * update CHANGELOG Co-authored-by: richard <richard@nextmovesoftware.com> (cherry picked from commit 016f2c6)
* Fix Issue #2848 * An attribute error is thrown when finding D-H pairs via the topology if hydrogens is an empty AtomGroup. This has been fixed so that an empty donors group is created, rather than assigning donors = 0. * Added a test case that raises the attribute without the fix. * Updated CHANGELOG * add @bieniekmateusz and @p-j-smith to CHANGELOG 1.0.1 author section (was forgotten in PR #2849) Co-authored-by: bieniekmateusz <bieniekmat@gmail.com> (cherry picked from commit 575c027)
* partially addresses #1387 for the DMS parser * Changes made in this Pull Request: * Repeated residues are not squashed * Multiple segids are created when multiple chains are present * Implemented extraction of chains from DMS formats * Properly split repeating segids: ["A", "B", "A"] -> ["A", "B"] * tests: New DMS file that includes multiple segids Derived from adk_closed.dms and edited in sqlite3 ```sql UPDATE particle SET segid = "CORE"; UPDATE particle SET segid = "NMP" WHERE resid BETWEEN 30 AND 59; UPDATE particle SET segid = "LID" WHERE resid BETWEEN 122 AND 159; ``` where the domain definitions can be found in: Seyler SL, Kumar A, Thorpe MF, Beckstein O (2015) Path Similarity Analysis: A Method for Quantifying Macromolecular Pathways. PLoS Comput Biol 11(10): e1004568. https://doi.org/10.1371/journal.pcbi.1004568 * tests: - Modified atom selections in test_dms.py - added new selections in test_dms.py and relabeled previous selections - Added DMS with no segid * Updated CHANGELOG (cherry picked from commit 2f16a16)
- fix #2734 (docs now build with sphinx 2.3) - formally deprecated lib.log.echo() (CHANGELOG, @deprecate, and test) - explicitly added docs to ProgressMeter - avoids sphinx failure due to wrong formatting in tqdm.auto.tqdm - add specific example for MDA - document our own verbose kwarg - improved markup - not documented: gui kwarg (discouraged in original docs) (cherry picked from commit 5e68617)
* fix #2751 * Python 2.7/3 backport of PR #2755 (use six.string_types, update CHANGELOG and versionchanged as 1.0.1) * modified AtomNames topologyattr to include lookup table index * rework atom name selection to use lookup tables * fixed test supplying integer as atom name * Update test_topologyattrs.py * use dict-lookup string attrs EVERYWHERERE * made protein selection faster, 48ms -> 0.5ms on GRO testfile * improved nucleic/backbone selections * Added explicit tests for Resnames topologyattr tests now provide str types for resnames/icodes * use fnmatchcase to be case sensitive (this was a small unreported bug in 1.0.0: the matching was done case-insensitive) Co-authored-by: Irfan Alibay <IAlibay@users.noreply.github.com> Co-authored-by: Oliver Beckstein <orbeckst@gmail.com> (cherry picked from commit 45e56e8)
- pinning ensures that chemfiles conda package pulls the last working
netcdf4 package in; otherwise we get failures such as
OSError: libnetcdf.so.18: cannot open shared object file: No such file or directory
- #2798 (comment)
Co-authored-by: Guillaume Fraux <luthaf@luthaf.fr>
- explicit PYPI_CHECK in script section - switch travis to beta for config validation - https://docs.travis-ci.com/user/build-config-validation - get feedback on problems with the config yml file Note: Use ci-helper's algorithm for installing numpy and don't pin a numpy version, not even for the simple PYPI_CHECK section (cherry picked from commit bbc3dcb)
- generate LONG_DESCRIPTION from README.rst
- remove SUMMARY.txt (out of date)
- read top-level repository README.rst for LONG_DESCRIPTION
- changed README.rst
- add installation instruction (link)
- add links to Quickstart Guide, User Guide, and API docs
- add links to issue tracker and mailing list in text (Contributing)
- replaced links to wiki with links to User Guide
- remove raw html from README (raw html not allowed on PyPi)
- replace NumFOCUS logo image with reduced size version (200 x 61 px) and standard reST
image syntax (logo added to web site in commit
MDAnalysis/MDAnalysis.github.io@ec4fe2c )
- fix broken link
- tutorials direct to Examples in User Guide
- add link to video section of "Learning MDAnalysis"
- passes `twine check`
- cleaned up MANIFEST.in (for pypi packages)
- fixed links in Py files
- Make sure that we always use the SSL url of the home page
git grep -l 'http://www\.mdanalysis\.org' | xargs perl -wpi~ -e 's(https://www\.mdanalysis\.org)(https://www.mdanalysis.org)'
- fixed link to issue tracker in files
git grep -l 'issues.mdanalysis.org' | xargs perl -wpi~ -e 's(https?://issues\.mdanalysis\.org)(https://github.com/MDAnalysis/mdanalysis/issues)
- fixed PEP8 issues in files
- various updates in testsuite/README (link to userguide, update badges)
- use User Guide as style reference
Co-authored-by: Lily Wang <31115101+lilyminium@users.noreply.github.com>
(cherry picked from commit d0b03e6)
- see #2920 - add deprecation note to as_Universe - add deprecation notice to LeafletFinder: filename instead of Universe will be removed (uses as_Universe so users will see the DeprecationWarning from as_Universe) - add test - update CHANGELOG for 1.0.1
- fixes The output files had all the the floating point numbers joined in a single string. - see PR #2733 - update AUTHORS - update CHANGELOG
Work around conda-weirdness which just fails to properly resolve the pinned chemfiles-lib that would be compatible with the last working Py 2.7 version of netcdf4.
Co-authored-by: Irfan Alibay <IAlibay@users.noreply.github.com> Co-authored-by: Lily Wang <lilyminium@users.noreply.github.com>
* deprecate helanal, to be removed in 2.0.0 (use analysis.helix_analysis in 2.0 from PR #2622) * add deprecation warnings to analysis.helanal * update CHANGELOG
- Fixes #2768 - backport fixes from 2.0.0 development version to the 1.0.x branch (master) - includes backports of all fixes tagged with Milestone 1.0.x (currently 1.0.1) via cherry-picked commits
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Fixes #2943
Changes made in this Pull Request:
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