CHANGELOG.md

CHANGELOG

v0.3.2 (2025-01-22)

🐛

• 🐛 Fix heuristic Operation.origin code that gave wrong results in cubic system (8ad71d1)

• 🐛 Fix some trigonal systems being mistaken for cubic (51e50d1)

• 🐛 Fix test which wrongly assumed that diagonal 3-fold screw axes should extinct -hhh, h-hh, and hh-h reflections (38bff51)

• 🐛 Fix test which wrongly assumed that diagonal 3-fold screw axes should extinct -hhh, h-hh, and hh-h reflections (6b98f10)

• 🐛 Make Group.auto_generated_code a single word (67c01c7)

• 🐛 Properly attach Group.name and .number when reading catalog from json (1952454)

• 🐛 Split SymmOp into Operation and BoundedOperation whose translation is fixed to [0,1) (5352e54)

• 🐛 The direction of screw axes should align with their glide (ea7c587)

⏪

• ⏪ Revert "🧪 Add failing test for auto-generated space group names" (0f0cb4c)

This reverts commit 50c96c21928f208b7834e54e25f2979885e08ad8.

Other

• 💡 Remove TODO comment associated with completed code update (80189b8)

• 🚧 Add hikari.utility.Singleton to be potentially used later (a051311)

• 🚧 Add rudimentary hm_symbol property that better aligns with crystallographic tables (8b850b0)

• 📝 Improve documentation, type hints in hikari.dataframes.cif (2018a6c)

• 📝 Improve documentation, type hints in hikari.dataframes.cif (941c6a1)

• 📝 Improve type hints for hikari.symmetry.Operations (ce974d0)

• 📝 Streamline operations.py type hints to rely on typing only (3d003ab)

• 🧪 Add failing test for auto-generated space group names (50c96c2)

• ✅ Make (ub)bounded a property, add/improve all Operation tests (ad33a95)

• Merge remote-tracking branch 'origin/development' into development (321bc56)

• 🔀 Merge pull request #43 from Baharis/development (c2f66e9)

Split SymmOp into Operation and BoundedOperation

v0.3.1 (2024-12-10)

🐛

• 🐛 Fix GroupCatalog.values, .items (81d700c)

• 🐛 Fix all space groups being "standard" due to wrong type in json (ebe9b7d)

📦

• 📦 Add MANIFEST.in to potentially help adding resources to wheel (2875cf7)

Other

• ⚰️ Remove dead resources function _load_bytes (de35f29)

• 👷 In continuous integration, run rapid tests only (49bc6a9)

• 💚 Fix continuous integration to properly publish hikari under name hikari-toolkit (3992db7)

• ✅ Add even more tests for GroupCatalog (b6b17d6)

• ✅ Add further tests for GroupCatalog (1723078)

• ✅ Skip the potency map tests on python 3.13.0 only (b8f178a)

• 🔀 Merge pull request #42 from Baharis/development (fe1ca24)

Fix GroupCatalog, fix and expand GroupCatalog testing

v0.3.0 (2024-12-02)

✏️

• ✏️ Fix typo in pyproject.toml path (4dde1ef)

✨

• ✨ Increase overall quality of handling, storing, selecting Groups, Increase user experience quality and code safety, Bug fixes. (ec6aac6)

Other

• .* suffix can only be used with == or != operators (181004d)

• 🍻 Add forgotten type fix (30f65d7)

• 💚 Add hikari API tokens (847188d)

• 💚 Can't install scipy on newest macs, maybe issue with 3.13; skip for now (3a613bc)

• 💚 Make macos install gfortran (9d5da57)

• 💚 Make macos install gfortran 2 (85d3d9e)

• 💚 Make macos install gfortran 3 (b349f92)

• 💚 Make macos install gfortran 4 (32175c0)

• 📝 Align documentation style with that of picometer (f25ab46)

• 🎉 Move to poetry package control, bump required python version to 3.9 (38397d1)

• 🚚 Rename test directory to tests, remove some mentions of picometer (279926f)

• groupcatalogue to make group dicts, hikari.typing, a->e (491b1cb)

• Add a custom AmbiguousGroupAccessorWarning for clarity (8c8ab2e)

• Add JSON files to git (414d047)

• Add P21/n to the list of known structures (but not to pickles) (fa4d928)

• Add P21/n to the list of known structures2 (but not to pickles) (b624353)

• Add python 3.10 to test builds (6d87228)

• Add some type hints (67d00de)

• Add tests for hkl completeness scripts (1026827)

• Add tests for HklFrame, including writing hkl and res (cd2d59f)

• Add windows and mac os to test environments (e528da4)

• Americanize all instances of Catalogue to Catalog (3438f82)

• Apparently np.warnings doesn't exist in some versions; just try (f897412)

• Apparently np.warnings doesn't exist in some versions; just try (62b62e6)

• Apparently one refl is not always read correctly in Python3.10 (9159136)

• Automatically generate the GroupCatalogue based on provided GroupCatalogueKey data (c6096a1)

• Automatically get correct space group based on index, HM, HM-short*, or Hall name (b9ee7f8)

• Bugfix: correctly type hint Match, remove fixed TODOs (fff5255)

• Compose a Hall_symbol_PG.dat for point groups only (6009f6d)

• Define all keys using clearer OOP syntax with registry (98e79ee)

• Define new HklKeyDict to substitute old ambiguous HklKeys (c06d0e3)

• Do not use >= when specified starred version of dependency (c03b44a)

• Don't suggest buggy pandas 1.5.0 in requirements.txt (9908054)

• Except ax.dist deprecation; any alternatives? (1ea5270)

• Fix mpl deprecation issues, uncertainties not supported... (7e37464)

• Fix code test environment to ubuntu-20.04 (7764931)

• Fix error in shelx_4 hkl format docstring (6c7ae78)

• Fix implementation for point groups (4fed404)

• Fix issues with new HklKeyDict and HklKeyRegistrar (fea9177)

• Fix platform-specific np.str to np.str_ (7400d26)

• Fix python version 3.10 being interpreted as float (e9a55d1)

• Fix temporary completeness statistics test (e44fe89)

• Fix tests of similarity index comparisons to ignore heared lines (9f0907d)

• Fix typo in test_space_groups_picked_match_hall (22594c0)

• Fix wrong definition of d in HallSymbols (0d89742)

• In catalog, change pickling protocol to 4 to support python 3.7 and 3.8 loader (8016a9c)

• In catalog, replace f'{var=}' syntax from python 3.9 with f'var={var}' (a20a175)

• In resources, replace importlib.resources.files from python 3.9 with open_binary & open_text (2c46c6c)

• In type hints, replace collections.abc.Buffer from python 3.12 with simple bytes (0b27187)

• Increased HklKeyRadius precision to float64 (f41abe8)

• Make all docstrings and regexes with backslash raw (af20f77)

• Make all docstrings and regexes with backslash raw 2 (278c5ee)

• Merge branch 'development' (aa8476b)

• Merge pull request #38 from Baharis/futureproof (9a96455)

Futureproof

• Merge pull request #39 from Baharis/futureproof (87bfc47)

Futureproof

• Merge pull request #40 from Baharis/hall_symbols (cd58abe)

Increase overall quality of handling, storing, selecting Groups; Increase user experience quality and code safety; Bug fixes.

• Merge pull request #41 from Baharis/development (36888c6)

🔀 Bump minimum python to 3.9 and manage versioning with poetry

• Merge remote-tracking branch 'origin/futureproof' into futureproof (08778c9)

• Minor style and docstring improvements (f7258a8)

• Modify implementation to account for point groups without '-p' at the beginning (12900b7)

• Most of the HallSymbols work, some errors still to fix (f6e52bc)

• One test is unpredictable on ubuntu-latest, no idea why (707b140)

• Only check "older" python3.6 on ubuntu-20.04 (1505106)

• Preserve hkl key 'equiv' to consistently be of dtype np.int64 (3bf53f6)

• Preserve hkl key 'equiv' to consistently be of dtype np.int64 (3724333)

• Prevent deprecation failure by adding observed=False to hkl table groupby (fa05b53)

• Regenerate pickles and update pickle-dumping/loading mechanism (841e6f3)

• Remove HklFrame.keys and HklIo.keys altogether (de8a67d)

• Remove all usage of pickle from the code (4362cdd)

• Remove debug print statements (d6d5f0f)

• Remove ReST references to deleted modules, minor fixes (6aebac0)

• Replace deprecated pandas delim_whitespace with sep='\s+' (5f91c8f)

• Rewrite resources to use importlib.resources. Drop Python 3.7 support for resources and __future__.annotations. (cf8a606)

• Since we drop __future__.annotations, replace Tuple, List, OrderedDict with tuple, list, dict (c9f53b9)

• Skip tests that rely on tk GUI for development purposes until Python 3.13.1 fixes init.tcl (b5da0ea)

• Switch serializer from pickle to JSON to avoid version conflicts and increase security (81d927c)

• Tests fail @ Python 3.10, TODO: fix matplotlib deprecation (cabf95b)

• Todos; fix BaseFrame reading angles from incorrect fields (88e6380)

• Tweak, move HallSymbol to separate file (5ab853c)

• Update SG pickle, simplify its dumping, add strong Group tests (2168209)

• Wip: Start implementing generating SGs from Hall Symbols (2aba1de)

• Write docstring, ultimately remove point/space_group.py/.json, adapt tests (f6fa4f0)

v0.2.3 (2022-08-12)

Other

• animate_similarity_index now accepts list of transformations instead of single step transformation (3574282)

• animate_similarity_index now fixes axes to same length and shows SI plot < 10 only (687cd61)

• animate_similarity_index now plots using four individual axes (0303209)

• hklframe.fill now uses 4x less memory when creating initial hkl list to cut (2be4e4d)

• Added animate_similarity_index for making simple animations (559d62d)

• Added animate_similarity_index to scripts.__init__ (223f1f2)

• Added a dedicated test case for HklFrame.fill (c7db318)

• Added description of m80 format to HklIo.format docstring (fbcbeb0)

• Added docstring and fixed text placement mistake in animate_similarity_index (704e65b)

• Bumped hikari version to 0.2.3 (304ee6b)

• Changed try/except loops to catch errors when reading hkl whenever fixed-width line is too short (c28f1d5)

• Created utility.numpy_tools.str2array to read compact matrix representations (3547788)

• Created test suite for utility.numpy_tools.str2array (5762401)

• Defined HklFrame.fill2 method in order to optimise memory use when filling with reflections (b957ff8)

• Defined a basic structure of the Selling class (2e13f9c)

• Defined a very bare-bones m80 reflection file type in hkl_formats_defined.json (da566de)

• Defined an empty dummy key type _ in HklKeys to hold irrelevant data (4fd12dc)

• Fixed and tested HklFrame.fill2. Now it won't produce hkl > HKL_LIMIT and is 2-3x faster (628194b)

• Implemented HklFrame.fill3, which is still 2-3x faster and severely less memory hungry than fill2 (be9a05a)

• In dataframes.base defined new class Selling and its matrices to handle Selling reduction (cc3ca38)

• In HklFrame.fill, in hkl_walls changed l to l_ to avoid ambiguity (89d25ca)

• Increased HKL_LIMIT to 127. New fill uses less memory and is 9x faster for very oblique cells (d5f02f4)

• Increased readability of HklFrame.fill (e5e0411)

• Merge pull request #34 from Baharis/animation (f19ef43)

Animation

• Merge pull request #35 from Baharis/m80 (0053f2d)

M80

• Merge pull request #36 from Baharis/animation (0e12e30)

Similarity index animations fix

• Merge pull request #37 from Baharis/reduction (5f0fa00)

Reduction

• Moved Selling reduction tools from dataframes.base file into BaseFrame (2ab2b2c)

• Redefined empty/trash entry type in hkl files from _ to None (f8eda14)

• Removed attempts to define partially reduced cell - maybe useful in the future, too much work now (c6282ac)

• Renamed reduction to semi-reduction, as it doesn;t need unique and fixed ordering (9cc6de4)

• Started animate_similarity_index based on so #7819498 question (526c7fc)

• Substituted old fill with new, faster and less demanding one (9fb1b6f)

• Tested HklFrame.fill3 tu be 2-3x/~1.5x faster in problematic/standard case, Replaced fill (3e042af)

v0.2.2 (2022-06-20)

Other

• angular_explorer now prints values of property in focus points to the listing file (501780f)

• baseframe.fill_from_cif_block now correctly raises KeyError on missing data if fragile (16f0fcf)

• cifblock.get_as_type now correctly returns unmodified default if given (09ae41d)

• cifframe.get_as_type now correctly does not raise KeyErrors (63445f8)

• cifreader.databuffer moved to CifIO and made abstract (6c8af86)

• cifreader now does not store last '\n' in multilines; accordingly, CifWriter adds it (110ccaf)

• cifwritebuffer now correctly clears lists when flushing (b854b51)

• cifwriter.write method made to work after some tests (9b3c497)

• cifwriter.write method now writes the last data of each block correctly (fd43fd9)

• cifwriter.write now forcibly enquotes single multiline cif entries (b49d292)

• cifwriterbuffer now clumps cif-core-missing entries together if they are similar enough (3c6a90a)

• hikari.scripts.calculate_similarity_indices now returns 1 for negative adps (41c8e93)

• Added MULTILINE_QUOTE_REGEX to prevent commented "\ndata" from triggering as block (acaf5c9)

• Added a NaCl_negative_ADPs block to test NaCl cif file (8694104)

• Added a bunch of tests for hikari.dataframes.cif objects (808f72b)

• Added a few tests for hikari.scripts.calculate_similarity_indices (27e21b2)

• Added to-be-tested write methods to CifFrame and CifBlock (2f19333)

• Added two simple tests for creating potency_maps (432147d)

• Added two simple tests for writing cif files in a reproducible way (f7de3cb)

• Bumped hikari version to 0.2.2 (5796393)

• Cleared TODOs and misleading if-name-main (04088e8)

• Fixed CifReader and CifWriter docstring to generate documentation correctly (c659e45)

• Fixed error with quoted comments by protecting quotes before stripping comments (3c139ba)

• Fixed looped multilines being incorrectly assigned to loop_keys in CifReader (688ef19)

• Fixed multilines being one newline too long after CifWriter (39048bd)

• Implemented CifValidator.get__category to check groups in cif validator (4434883)

• Implemented CifValidator.get__list to check if _list is 'yes' in cif dict (09c199f)

• Implemented CifWriterBuffer to write individual data elements to cif file (ebd2a3f)

• Merge pull request #31 from Baharis/CifIO (0fe1d1a)

Cif io

• Merge pull request #32 from Baharis/similarity (97056be)

Similarity

• Merge pull request #33 from Baharis/property_at_focus (2cbd25c)

Property at focus

• Modified regex expressions used in CifReader (a9e0ebc)

• One can now get hidden keys from CifValidator (such as _atom_site_aniso_B_11) without expanding (4a2368c)

• Overloaded contains method of CifValidator based on results of get (cfe5935)

• Registered "\n" as whitespace and added DATA_BLOCK_REGEX to CifReader (80a2663)

• Removed "# noinspection PyTypeChecker" from code to prevent type misinterpretation by git (8f06ad4)

• Restricted CifReader.DataBuffer (now IOBuffer) to a very general abstract class (39beec0)

• Restructured buffer classes out of IO classes; they are going to play a large role (9e68088)

• Shortened regex expressions, found error with quoted pound signs (24447c8)

• Simplified calculate_similarity_indices docstring using type hints (67a0834)

• Simplified CifReader and CifReaderBuffer by protecting multilines (770c79a)

• Since CifBlock.get_as_type is now allowed to return None, modify tests to check that (ff172ec)

• Slightly optimised the regex (0f8eab7)

• Started creating CifWriter and CifWriter.WriterBuffer (f0fdb52)

• Started reconstructing CifReader using more regex expressions (dc7a471)

• Successfully tested calculate_similarity_indices script against MW's datasets (4b52e5f)

v0.2.1 (2022-06-10)

Other

• Added missing package data to the setup file (b81726d)

• Bumped hikari version to 0.2.1 (a1f868b)

• Merge pull request #30 from Baharis/package_optimisation (e460d25)

Resources hotfix

v0.2.0 (2022-06-09)

Other

• 'cifblock.get_as_type' now correctly turns lists into lists instead of maps (45ce7b2)

• 'hikari.dataframes.baseframe' can again read cif blocks using fill_from_cif_block (8c025b2)

• baseframe.imported_from_cif is now name-indexed dict of 3-els instead of list of 4-els (f3a8b09)

• cifframe.get_as_type uses default value now, raises KeyError if no default nor value found (be25b58)

• cifio.__init__() now checks whether item should be a list based on length and CifValidator data (702bd5d)

• cifio now correctly reads singletons as lists via CifValidator (6c02c7e)

• cifreader now correctly ignores comments by calling strip_comments when reading (788823f)

• det3x3 renamed from udet, moved from UBaseFrame to hikari.utility.mathtools, and made used by BaseFrame (0fd3109)

• hikari.dataframes.cif.cifblock now properly raises Error when no default nor value are found (cb9fa7a)

• revert_whitespace now acts on single string; Created CifWrite from CifIO (68348a7)

• test_dataframes constants now are correctly uppercase (9d1405a)

• ubaseframe tested, moved to its own file, and added to hikari.dataframes.__init__ (5ef6a7d)

• utilities.deg2rad can now /correctly/ handle ufloats (ad9b880)

• utilities.deg2rad can now handle ufloats (8e91472)

• utility.det3x3 now uses indexing instead of slicing to properly communicate with unumpy.matrix (478d111)

• Adapted README.md to include e.g. fcf/cif support (412e8ae)

• Added __init__.py to test folder for coverage integration (c5a350f)

• Added CifBlock to hikari.dataframes.__init__ to accessible from outside (26b739b)

• Added compare_adps to hikari.scripts submodule (139826e)

• Added get_as_type method to CifBlock (b5f8a3f)

• Added nacl_cif, nacl_fcf, and cif_core_dict to hikari.resources (edfbede)

• Added read method to CifBlock (c74a1eb)

• Added a CifValidator object to hikari.dataframes.cif (c3a5e4a)

• Added a common_prefix function to hikari.dataframes.cif. Cif reader needs rewriting... (4fe2cce)

• Added a generic script for calculated similarity index for one atom (be8341a)

• Added a shameful codecov badge (7735cca)

• Added a simple reformat_hkl script to match readme (aed1335)

• Added and commented some basic script for many-atom compare_adp script (bcb9b57)

• Added and updated tests for BaseFrame, CifBlock, CifFrame, and UBaseFrame (03aa1ad)

• Added CI tests badge (ce8f2c7)

• Added cif dictionary to the resources (4b0f21c)

• Added codecov workflow (c5f1ec3)

• Added docstrings to hikari.dataframes.CifIO methods (83756a3)

• Added inactive validate to CifIO.__init__() to prevent CifValidator infinite loop (482d69b)

• Added other NaCl files to the resources for the purpose of testing (67b0d16)

• Added project requirements.txt to Sphinx requirements (270df0a)

• Added readthedocs files to try and fix empty documentation problem (534ab09)

• Added reminder tofix the documentation later on (b09e5c0)

• Added requirement for uncertainties package version 3+ (550e1fe)

• Added tests for hikari.utility.certain_float submodule (7cdd941)

• Added, updated, corrected tests for CifBlock (5efb750)

• All cell parameters of UBaseFrame are now ufloats (6511006)

• Bumped hikari version to 0.2.0 (ff31b56)

• Bumped the version to check whether this impacts documentation (301a492)

• Changed CifFrame class to be a subclass of OrderedDict (d5c42b8)

• Changed CifReader.MATCHING_QUOTES_REGEX to disregard quotes not followed by whitespace (a4b8dbc)

• Changed CifReader.MATCHING_QUOTES_REGEX to not count '' as quote (9ec480d)

• Changed CifReader to be able to read cif dictionary, but with problems (78f65ce)

• Changed CifReader to correctly protect and release quoted words (e654168)

• Changed test_dataframes.py so that files are created only once (55dabc7)

• Cleaned BaseFrame and UBaseFrame inits' code (7244d2f)

• Corrected grammar in README.md (c2a1ee3)

• Corrected order inside CifReader.substitute_quoted_whitespace (22ce28d)

• Create .readthedocs.yaml (ee0a18c)

• Created empty CifBlock class to handle individual blocks of hikari.dataframes.CifFrame (c00ef01)

• Defined cfloat "type" (str2ufloat2float converter) to hikari.utility (edd2f51)

• Documentation corrected throughout the project to include empty line between descriptions and parameters (48b57dc)

• Extended tests for hikari.dataframes submodule (5bd29d2)

• Extended tests for hikari.utility.math_tools submodule, changed bug in rotation_from(a, to=-a) (a4c29d3)

• Extended tests for hikari.utility.chem_tools submodule (21d77df)

• Extended tests for hikari.utility.interval submodule (which itself was simplified a bit) (0e3ef97)

• Extracted CifReader out of CifIO class (7dfa2d3)

• Fixed cfloat to really return nominal value instead of ufloat (47219cf)

• Fixed CifReader.parse to flush DataBuffer at the start of a "loop_" (aa18bef)

• Fixed minor formatting errors (9d0ca06)

• Fixed problem with premature termination of reading in CifIO (ab6e123)

• Fixed regex and loop bugs in substitute_whitespace_in_quotes in CifIO (bb798a2)

• Fixed unnecessary hyphen in .readthedocs.yaml (a5ddebd)

• Implemented blocks property in CifIO (61e8e15)

• Implemented first version of UBaseFrame, subclass of BaseFrame capable of handling uncertainty (747ac01)

• Improved code clarity regarding floats and ufloats in calculate_similarity_indices (ef371f6)

• Improved output clarity in calculate_similarity_indices (f919218)

• In BaseFrame and UBaseFrame, removed padding to increase maintainability (232d9a1)

• Included recently added submodules to documentation (04185a9)

• Increased code maintainability as suggested by 'codefactor' in multiple files (80ceb53)

• Many BaseFrame attributes are now protected instead of private to allow changes in descendants (090e080)

• Merge pull request #19 from Baharis/Readthedocs-integration (69ba4ce)

Integrated repository with readthedocs and accordingly added badges to the README.md file

• Merge pull request #20 from Baharis/cif_frame (ef97b36)

Cif frame

• Merge pull request #21 from Baharis/cif_frame (8a614d6)

Cif frame

• Merge pull request #22 from Baharis/UBaseFrame (294e9f0)

UBaseFrame

• Merge pull request #23 from Baharis/similarity (8f2e525)

Fixed the problem with requirements not being correctly read after specifying readthedocs configuration

• Merge pull request #24 from Baharis/similarity (4a436a9)

Similarity

• Merge pull request #25 from Baharis/similarity (2d67538)

Similarity

• Merge pull request #26 from Baharis/tests (3e82126)

Tests

• Merge pull request #27 from Baharis/tests (561cf78)

Modified tests to accommodate codecov integration

• Merge pull request #28 from Baharis/cif_dictionary (2a184f8)

Cif dictionary

• Merge pull request #29 from Baharis/package_optimisation (00697c5)

Package optimisation

• Merge remote-tracking branch 'origin/tests' into tests (e50d355)

• Minor style fixes in hikari.dataframes (689c08e)

• Mixed too short lines in documentation (f58ff33)

• Moch-import uncertainties to check whether this package does cause problems (8e4862e)

• Modified CifIO and CifFrame to read all blocks instead of one specified (d904462)

• Modified hikari.dataframes.CifFrame to read using new CifIO and added docstrings (c920e40)

• Modified sphinx configuration files to avoid documentation errors in the future (0869493)

• Modified the compare_adps script to match its docstring (b8b23ca)

• Moved NaCl files to test, as they are not an essential part of the package (4f4d25d)

• Parameter normalize of calculate_similarity_index now correctly normalises (359ec38)

• Parameter prepend added to CifReader.read() to get correct block names in CifValidator (ae80b9f)

• Prepared a docstring for hikari.scripts.compare_adps.compare_adps (f05d8aa)

• Prepared a rough draft of a CifIO class for reading cif files (8a88b58)

• Prepared a successful test version of hikari.scripts.compare_adps.compare_adps script (bc0e655)

• Re-added doc html static path due to new docs problems (6367384)

• Re-added doc requirements and specified them (f748c1c)

• Re-added fail on warning (2896498)

• Reduced CifBlock to a pure OrderedDict clone and made it item type in CifFrame (c5f767d)

• Remove python requirements for building the docs (f6f2c7e)

• Removed '_static' from sphinx' html_static_path (2860c09)

• Removed _static reference, as it does not look like its connected to LaTeX errors (e5e0d86)

• Removed common_prefix function from hikari.dataframes.cif as its functionality was found dispensable (e7aa7fd)

• Removed prepend method attribute from CifIO, as it won't be needed with expanding... (ccf22e7)

• Removed ustrip function from hikari.dataframes.cif for the sake of including uncertainties later (c353a46)

• Removed dangerous setters from BaseFrame (after setting other pars wouldn't update) (0f1c929)

• Removed misleading if-name-main line in hikari.dataframes.base used for testing (c4a216e)

• Removed misleading if-name-self in hikari.dataframes.cif (55b6caf)

• Removed old TODO; CifFrame will exist besides PyCifRW (977739c)

• Removed older compare_adp script (c8eea1a)

• Removed project requirements.txt (f76d263)

• Removed trailing spaces from .readthedocs.yaml (19c781d)

• Removed whitespace padding from BaseFrame and UBaseFrame to increase maintainability (ec267d9)

• Renamed compare_adps script to more fitting calculate_similarity_indices (cba17e0)

• Renamed ambiguous DataBuffer.parse to DataBuffer.add_word (f15c948)

• Script calculate_similarity_index now uses unit cell parameters from both cif blocks. (4777f30)

• Setup now correctly imports uncertainties package, making wheels and documentation - hopefully - work (e521f27)

• Simplified CifIO.DataBuffer reset and added tab handling (50e8623)

• Split revert_whitespace and regex compiler out of substitute_whitespace_in_quotes in CifIO (27f3c3a)

• Testing sphinx integration of python typing for euler_rodrigues_matrix function (a0f0825)

• Tests now use NaCl files in test folder instead of resources (2413ac7)

• Turned off pdf/epub generation to prevent LaTeX issues (98a32d0)

• Update codecov.yml (00673d0)

• Update codecov.yml (faa3785)

• Update codecov.yml (047755b)

• Update codecov.yml (9e138b4)

• Update codecov.yml (26ff4a1)

• Update README.md (4c762e1)

• Updated wrong link in README.md (86e398c)

v0.1.5 (2022-05-28)

Other

• angularheatmapartist.focus is now a tuple instead of dict. (32f38c8)

• angularpropertyexplorers and consequently r1_map and potency_map now also correctly accept orientation vector (2f72a0c)

• hikari.scrips.r1_map and hikari.scrips.potency_map bug-fixed and splightly simplified (61e8f95)

• hikari.scrips.r1_map moved to the scripts namespace and made to use angular heatmap artists (f663cef)

• matplotlibangularheatmapartist now properly plots (100), (010), (001) arrows and focus points (30b3a58)

• potency_map now draws focus points correctly in trigonal and hexagonal systems (9f28ad2)

• potency_map now logs average and quartiles of potency based on map data (342ceeb)

• r1_map and potency_map scrips were adapted to utilise hikari.utility.Interval (64509d0)

• r1_map now correctly determines trim area using radians, not degrees (09bdf32)

• Added Interval class docstring (127d11a)

• All scripts use path created by make_abspath instead of raw strings (71c0bff)

• Angularpotencyexplorer now correctly uses keys potency and R1 instead of cplt and r1 (767c460)

• Border lines are now drawn correctly in gnuplot_angular_heatmap_template (e1a2288)

• Bumped hikari version to 0.1.5 (f3dc57b)

• Changed property_theoretical_minimum and ..._maximum to abstract in AngularPropertyExplorer (4df899f)

• Changed a number of attributes to properties in AngularPropertyExplorer (but still not functional) (890b886)

• Changed explore to abc method in AngularPropertyExplorer (3bc1cd0)

• Created a AngularPropertyExplorerFactory for unified handling of angular property (r1, potency) maps (5eec073)

• Directional axes on MatplotlibAngularHeatmapArtist are now properly labelled (100), (010), and (001) (43e8329)

• Drafted first version of AngularPotencyExplorer and AngularR1Explorer based on AngularPropertyExplorer (969b672)

• Fixed wrong z_axis setter in AngularHeatmapArtist (22bb896)

• Further changes (property limit, class settings) introduces to still-wip AngularPropertyExplorer (cfe8393)

• Further minor docstring and naming changes of scripts in potency_map.py (067ab6c)

• Generated documentation (sphinx make html/clean) for hikari version 0.1.5 (f0567c4)

• Groups and limits in AngularPropertyExplorer are now set by space_group setters, making code almost as fast as previously (2373929)

• Hack-fixed matplotlib Axis3D aspect ratio by plotting invisible [1,1,1] and [-1,-1,-1] points (ff16db4)

• Histogram made constant-width and map moved left in gnuplot_angular_heatmap_template (501fd5e)

• Implemented cartesian2spherical and spherical2cartesian conversion functions (3f46d3c)

• Implemented histogram option in potency_map, for now does not draw (cabf6a2)

• Implemented a weighted_quantile in utility.math_tools which approximates quartiles in weighted distribution (e7dfdc4)

• Implemented method arange in hikari.utility.Interval (05d87e6)

• Implemented method comb_with in hikari.utility.Interval (a14206c)

• Implemented method mesh_with in hikari.utility.Interval (4779be3)

• Implemented unit tests for hikari.utility.Interval (8cacef0)

• In MatplotlibAngularHeatmapArtist made a bit more space for colorbox key (aff4037)

• Included histogram-making in gnuplot_angular_heatmap_template, fixed pathing issues (742eb8b)

• Introduced line_subset module from pruby.utility.line_subset (7c9517f)

• Merge pull request #15 from Baharis/paths (66f1450)

All scripts use path created by make_abspath instead of raw strings

• Merge pull request #16 from Baharis/potency_map (5f64466)

Potency map

• Merge pull request #17 from Baharis/interval (3dc913f)

Interval

• Merge pull request #18 from Baharis/angular_explorer (a1b5785)

Angular explorer

• Merged all set_ methodsinto oneset_up, registered AngularPropertyExplorersin Factory, and replaced oldr1_mapandpotency_map with new ones ([a59f1de`](https://github.com/Baharis/hikari/commit/a59f1de52635bd9fc86ea8b1b4be9630d973f459))

• Minor clarity improvements after introducing spherical2cartesian function (575d5ee)

• Minor docstring and changes, unused items removes in hikari.utility.artists and hikari.scripts.hkl_potency (122ccf5)

• Minor docstring and naming changes of scripts in potency_map.py (c79c0cf)

• Modified MatplotlibAngularHeatmapArtist to plot larger maps (although histogram it too complicated to bother) (f249f4f)

• Modified and merged previously imported LineSubset and LineSegment (109232e)

• Modified recursive _min and _max functions used by LineSegment (20e5379)

• Move utility.artists to artist_factory and unified plotting in AngularPropertyExplorers (390cef4)

• Moved PG and SG declarations from resources to symmetry to avoid circular imports (fcce0c6)

• Moved gnuplot spherical heatmap plotting capability to hikari.utility.artists (9d1bfef)

• Moved matplotlib angular heatmap plotting capabilities to hikari.utility.MatplotlibAngularHeatmapArtist (f7a7d63)

• Potency map accepts argument orientation and appropriately plots focus point on the map (a900099)

• Removed old documentation (899d5a0)

• Renamed cartesian2spherical and spherical2cartesian to cart2sph and sph2cart (d661340)

• Renamed cplt_map_template to gnuplot_angular_heatmap_template (b2824a7)

• Reorganised imports in hikari.utility.__init__ to prevent import errors (00f59cb)

• Simplifications and style changes in gnuplot_angular_heatmap_template (f9f0b63)

• Simplified _min and _max functions to be at most 1-deep recursive (657be28)

• Simplified potency_map using new spherical2cartesian function (de94025)

• Spherical heatmap now draws (100), (010), and (001) labels next to arrows (acdce23)

• Started creating a AngularPropertyExplorer for handling of angular property (r1, potency) maps, not yet functional (168d0df)

• Tested and fixed new potency_map2 and r1_map2 based on AngularPropertyExplorer (d88faf9)

• Triclinic and monoclinic systems have half and quadrant drawn. (e92db08)

• Updated __main__ script contents in hkl_completeness.py in hikari.scripts (3375bf5)

• Updated potency_map.py and r1_map.py __main__ scripts and added basic r1_map docstring (4cebc36)

• Updated potency_vs_dac_opening_angle for potency and Python3.6 syntax (cec0efd)

• Updted Interval unit tests to use modern np.array_equal instead of depreciated (A==B).all() syntax (569d22f)

• Upgraded and renamed _assert_iterable_length to _assert_is_iterable in Artist (d77332e)

• Vectorised orientation_weight to speed up AngularPropertyExplorer (71ce337)

v0.1.4 (2022-04-20)

Other

• Added and checked SFactors for Na+ and Cl- in NaCl, improvement only on low-res (37309f1)

• Added atomic_form_factor function to hikari.utility.chem_tools. Import errors still present. (e61a559)

• Added correct orientation handling to the structure factor formula in ResFrame (c9e7bb6)

• Added docstrings to ResFrame and calculate_sample_form_factors script (06d1265)

• Added split_atom_label function to utility.chem_tools (f8742c8)

• Added temporary script to find best formula for temperature factor (0a7e7f1)

• Added temporary temp_calculate_other_form_factors function to fcf scripts (bbb40f3)

• Added two rough methods to approximate structure factors, inaccurate for large sintl (1faa66e)

• Added Xray_atomic_form_factors to hikari.resources (402c601)

• Changed formula to the one from Grosse-Kunstleve (2002) (6268fe9)

• Corrected Uij order as given in res file. Transformed Uijs are correct. (c35d1cb)

• Fixed the formula for atomic form factor, again (fc3d251)

• Group.is_symmorphic is a bit slower, but works even if generators are unspecified or unconventional (0d4b4e3)

• Group.name appends now +/- sense to axes. Inconsequent with ITC in cubic system, where the concept of axis direction is complicated (577fb1a)

• Hexagonal R-centred cells should are now called correctly (3c6e9ff)

• Introduced dummy LstFrame to look for value of R1 (145ed9a)

• Merge pull request #13 from Baharis/Rmap (287f0b5)

Rmap

• Merge pull request #14 from Baharis/res_frame (f0081ee)

Res frame

• Morphed temps into a bare-bones script for fcf prediction (b738828)

• Prepared a simple script to map R1 using shelxl (904d8da)

• Prepared setup.py file and introduced as hikari-toolkit to pypi (1043ef2)

• Slightly rewritten existing read method of ResFrame to understand syntax (1826a24)

• Source of Xray_atomic_form_factors added to csv. Some circular import errors found. (22842e3)

• Split atomic_form_factor and temperature_factor into separate methods (dbd13a3)

• Symmop.orientation now utilises a direct formula instead of invariants. Rotations still have funny names in cubic system. (e6a9db8)

• Update README.md (eb98381)

• Vectorised atomic_form_factor, temperature_factor, and form_factor methods (a4da118)

v0.1.3 (2022-01-22)

Other

• Added additional simple tests for SymmOp (de7ff2d)

• Added comparison methods to hikari.symmetry.Group (a01297e)

• Added crystallographic matrices A and G to BaseFrame (79eefd4)

• Added hkl.msd style file to resources, printed with each res (e1e4c0b)

• Added human&computer-readable representation of SymmOp (7660c47)

• Added sample unittest for hikari.symmetry.operations (3d6ea13)

• Added simple tests for hikari.utility (9dc37bb)

• Based DAC definition on matrix A (340264f)

• Changed definition of BaseFrame.v to determinant of matrix BaseFrame.A (597f3ec)

• Characteristic radiation wavelengths moved from HklFrame.la to json in resources (30ed90c)

• Cplt_map_template.gnu renamed and moved to new directory resources (f4e068e)

• Created fully vector dac_count unfortunately has enough memory only for small system, so reverting to hybrid approach (d07a5b0)

• Dac_count of HklFrame accepts only one vector now, but is 2x faster then previous solution due to vectorisation (b168530)

• Dac_potency_around_axis script changed to utilise new rotation from math_tools (91f9ee7)

• Dacs_count now splits input into chunks not to exceed hikari.MEMORY_SIZE (3f39710)

• Defined rotation matrix in math_tools using Euler-Rodrigues formula (29f8d23)

• Duplicated potency_map function for further edition (c9d6849)

• First draft of fully vectorised dac_count function for maps (b528fdb)

• Fixed (temporarly?) circular import issue in hikari.dataframes.hkl (246715e)

• Fixed extinct method of HklFrame broken after last name changes (cf37198)

• Fixed HklFrame.HklIo fixed parser, which for some bizarre reason returned None (1bb4d3b)

• Fixed x/y/z definitions in new converter and changed it to default artist in HklFrame (2c57a11)

• Hikari.dataframes.hklframes().extinct() now correctly uses Group().operations (7c688ab)

• Hkl format dictionaries moved to resources and supplied directly as dict (1bf71e5)

• Hklframe._in_dac further optimised by calculating norm directly (29a8931)

• Hklframe._in_dac removed, all references rerouted to vectorised _in_dacs (1375add)

• Hklframe.fill simplified to use reshape instead of nested concatenates (a77ee4e)

• Hklframe.merge docstring abbreviated (c4aacd9)

• Hklframe.stats now returns correctly cplt and I/si (e94ffab)

• Implemented 1st draft of HklToResConverter to replace HklArtist (61d3112)

• Implemented proper str, repr and eq methods for Group (ba52cb6)

• Introduced more advanced tests for HklFrame, for trim, place etc (a87828b)

• Introduced simple tests for all utility functions and symmetry.operations (e5f72f9)

• Introduced simple tests for HklFrame (d43b6e5)

• Introduced simple tests to control BaseFrame algebra (4366031)

• Merge branch 'master' into unittest (2dd837c)

• Merge pull request #10 from Baharis/fibonacci (53647f6)

Fibonacci sphere algorithm

• Merge pull request #11 from Baharis/scripts_simplified (ad552ad)

dacs_count debugging

• Merge pull request #12 from Baharis/frame_tests (22c812f)

Frame tests

• Merge pull request #3 from Baharis/resources (51e0f1b)

Resources management optimisation

• Merge pull request #4 from Baharis/representations (f7229d5)

Representations

• Merge pull request #5 from Baharis/hkl_artist (9f7ebc9)

Replaced HklArtist with simpler HklToResConverter

• Merge pull request #6 from Baharis/stats (8742bdf)

Method stats of HklFrame used to return wrong completeness statistics for merged datasets. After this fix, stats not only calculates completeness correctly, but also "I/si(I)". This might fail whenever for some reason the file does not feature I or si.

• Merge pull request #7 from Baharis/hklframe (f9c40fb)

hikari.dataframes.hkl.HklFrame methods and doc-strings simplified, circular import fixed.

• Merge pull request #8 from Baharis/dac_count (ac79fc6)

dac method optimised and split into dac_count and dac_trim

• Merge pull request #9 from Baharis/unittest (9bcdb0a)

Simple unittest-s for utility functions and symmetry.operations

• Minor import optimisations (1617786)

• Minor modifications, potency_map 1 and 2 merged (0b9f36b)

• Moved priority rules from Group().auto_generated_rules to Group attributes (aacfb8b)

• Point and space groups are now loaded in resources and only aliased in symmetry's init (282469c)

• Point_groups.json and space_groups.json moved to resources (5a78d9a)

• Point_groups.pickle and space_groups.pickle moved to resources (53dc41d)

• Potency_map code clarity fixes (2d5bc8a)

• Potency_violin_plot script changed to utilise new dacs_count (3f2e2aa)

• Potency_vs_oa script changed to be more precise and use new dacs_count (cef7470)

• Re-implemented fully-vectorised dacs_count added and removed in a previous commit (06dbcba)

• Re-implemented fully-vectorised potency_map script, which is 10-20% faster (0fa2266)

• Refactored HklFrame.duplicate to HklFrame.copy (150fb3b)

• Removed dac_count as redundant, simplified docstrings (d72ad28)

• Removed memory logging and other comments from dacs_count (f18569f)

• Removed old, more complicated hkl-to-res converter. (1b45f42)

• Renamed script files, moved all potency methods to separate file (a71af82)

• Save pickle moved to hikari.resources (8611057)

• Scripts modified to accept space group string or int instead of Group instance (1784514)

• Shortened some docstrings, but still no bugfix (7159e75)

• Simplified and fixed previously-bugged BaseFrame._refresh_cell (ca0753e)

• Simplified BaseFrame documentation, removed x/y/z attributes to introduce orthogonal vectors later (db31cd7)

• Simplified docstring of hikari.scripts.potency_map (84f4782)

• Simplified HklFrame.stats docstring (90be715)

• Simplified some tests to control BaseFrame algebra (6a6256f)

• Single vector HklFrame.dac_count restored not to use caching, which was buggy (3b2d41f)

• Split HklFrame.dac into dac_count and dac_trim based on vectorised _in_dac, adapted potency_map (6914e25)

• Symmop's hash now uses hash of SymmOp's repr (3ce639c)

• Tested and found fully-vectorised method to be just as fast as bugged-heuristic looping dac_trim (0739c55)

• Uniformity tests of fibonacci_sphere now uses larger sphere of 99k elements (4b4f5fd)

• Utilised A_r in HklFrame.place() (df753b0)

• Vectorised hikari.utility.math_tools.fibonacci_sphere using numpy (ff6c969)

v0.1.2 (2021-11-04)

Other

• Added and modified some properties of hikari.symmetry.group (40cd5b6)

• Added approximate group naming capability. Group.system now has property directions. (fa44d89)

• Added number to group (default 0). Re-pickled PG & SG dicts. (b5dd93c)

• Code minor corrections and simplifications in scripts.hkl (a8bc84c)

• Fixed bugs: 3>-3 and occasional 21>2 rules in Group.auto_generated_name (18e3558)

• Group.name hidden as Group._generated_name as it might be useful later (eb5ddd2)

• Hikari.utility.home_directory deleted, as new make_abspath makes it obsolete (890083d)

• Implemented Group.transform() to enable using undefined settings. (e7702cf)

• Introduced/reintroduced point/space group json files. (8150895)

• Make_abspath now correctly returns string instead of Path object (dac3346)

• Make_abspath renamed, now uses pathlib and correctly expands '~' & '..' (ca1866f)

• Merge remote-tracking branch 'origin/master' (126ac6a)

• Output of pandas.describe() does not collapse horizontally anymore (2aae422)

• Output of pandas.describe() is now appended to potency_violin_plot() log file (619702d)

• Palettes.py in utility simplified, unused sns palettes removed (524c128)

• Removed 'uncertainties' from requirements.txt (0b9af79)

• Removed unused imports from CifFrame and ResFrame (24db35a)

• Simplified definitions and docstrings in hikari.symmetry.group (980d8c3)

• Typo fix in README.md (5d9b18d)

v0.1.1 (2021-10-20)

Other

• Abbreviated Group.CrystalSystem to Group.System Fixed wrong definition in Group.system() which made mmm monoclinic (b3ba4c9)

• Added legacy folder to .gitignore (7f3cc87)

• Changed HklKeys.__equiv type from tuple to int, resulting in 1.5-3x speedup. (8ec4e46)

• In scripts.hkl renamed completeness_map to potency_map. (dc53830)

• Minor code clarity corrections. (3b04e52)

• Moved fcf and potency_map scripts to separate files, heavily optimised and renamed completeness_violin_plot to potency_violin_plot, merged dac_point_group_statistics into potency_violin_plot (e2af144)

• Point groups are now read from point_groups.pickle (28cc3c9)

• Removed legacy is#n functions from hikari.utility. (f1c10cf)

• Removed legacy subfolder from repository (0f00b54)

• Removed trimming in Hkl.dac(), increasing speed when called many times. (7047e98)

• Space groups are now read from space_groups.pickle (4723c51)

v0.1.0 (2021-10-13)

Other

• A lot of script modifications, fixed wrong transformation in hkl dataframe, slightly modified map palettes (8499ded)

• A lot of stuff I don't remember (c3d4b30)

• Added crystal system; about to modify group/space group (3915e47)

• Added documentation and increased overall clarity of symmetry module. (33c6d1e)

• Added documentation and increased overall clarity of utility module. (d139c11)

• Added example folder, generalised rescale method of HklFrame (5fffc76)

• Added extinction functionality (9d02c6f)

• Added free format read/write (untested) (3bc335d)

• Added new concept of symmetry operation management (b2b7561)

• Added rotoinversion type and into methods (0f2a486)

• Added some sphinx files (cb4808c)

• All SGs have been defined in json file (74ff2cc)

• Alternative SG origins have been defined in json file (fe69c1c)

• Changed names of point groups in documentation For various scripts: > Fixed completeness to calculate unique reflections instead of all resymmetrified (cplt1 instead of 2) > Added legacy_cplt to calculate cplt1 (f3c64b4)

• Changed paths in gnuplot to absolute Fixed transform to act as resymmetrify before Changed disc-transforming ops to chiral_ops (d15cf20)

• Changed point group to dictionary Simplified symmetry structure Simplified wavelength description Extended 'edit_wavelength' method (36dab53)

• Changed SGs to rely on ITC-A generator definitions SGs are now stored in json file (1f64765)

• Completeness vs DAC orientation script added (718db7c)

• Cplt map script for plotting in gnuplot simplified (f7f8190)

• Created taskmasters, Added normalized direction vectors x,y,z/v,w (77a0ab8)

• Defined nnp, simple statistical tools and axis-specific colormaps (388fe3c)

• Defined space groups 1-46 (7f05615)

• Delete 1%2E1686607.pdf (eca521d)

• Deleted scripts dir (9d8a899)

• Diamond anvil cell completeness map drawing script introduced (916aaf0)

• During DAC tests (a083b38)

• Finished clearing files, removed old components, added manual file (862d4be)

• Fixed colormap in matplotlib to show actual colors Added "fix_scale" option to completeness map script/taskmaster (5e795cd)

• Fixed reciprocal definition (caedf1d)

• Fixed SettingWithCopyWarning and some legacy code from numpy (0c69296)

• Fixed, cleaned and documented new SymmOp (241981c)

• Generalized extinct to accept tuple or string with ':' Added separate 'find_equivalents' method (bdcf053)

• Hikari and pRuby imported (7b6c0f8)

• Hkl calculating moved (57c5e3f)

• Hklio introduced to handle reading and writing (75acd2e)

• Hklres visualiser added (b5e3954)

• Hklres visualiser added (f05d6fa)

• I made this (7d366e1)

• Initial commit (ed432e3)

• License and readme added (c353c2d)

• License and readme added (4dcbefd)

• License and readme added (1932d6f)

• License file updated for year 2021. (512822d)

• Made hkl frame accept fcf files Prepared script for BayCoNs and partially npps (d2195b6)

• Merge pull request #1 from Baharis/dataframes (f84fc81)

Dataframes

• Merge pull request #2 from Baharis/dataframes (0b879eb)

Dataframes

• Merged 'resymmetrify' and 'transform' Fixed 'make_stats' for given symmetry (780fee1)

• Minor changes to new symmetry operation algebra (46c55b4)

• Minor correction to check git connection (07d0678)

• Minor naming corrections from kesshou to hikari. (6f2cfe0)

• Move unused code to external folder with stubs, fix documentation errors (8d1973c)

• Moved all group and symmetry functionality to new class (219d1bd)

• Moved all project files to new folder (4ad116f)

• Moved all relevant scripts to taskmasters (4b579c5)

• Moved completeness maps to taskmasters, removed some old scripts (c6faace)

• Moved HklFrame.Crystal to BaseFrame Made HklFrame a sub-class of BaseFrame (6845870)

• Moved kesshou/scripts/crysalis to separate project and removed from kesshou as it does not fit central theme. Fixed resolution having to be given in A instead of A-1 radius in completeness_map script. (c3226a3)

• Moved kesshou/scripts/png to separate project and removed from kesshou as it does not fit central theme (3e323bd)

• Moved scripts to common module Added first docstrings to the strings (0c2f785)

• Optimised imports, basic documentation all code in hkl dataframe. Renamed data to table. (ffbcfaf)

• Pdf file renamed (8310efe)

• Prepared tutorial in readme (81216f5)

• Provided initial documentation to HklFrame and BaseFrame. (e30dd22)

• Read dat introduced Read hkl reintroduced (fb6ebe2)

• Read dat introduced Read hkl reintroduced (d77b735)

• Read dat introduced Read hkl reintroduced (711a6dd)

• Recalculating I and si to F and sf ready (ff3ca02)

• Refactored all instances of "kesshou" to "hikari" (692049c)

• Removed all pycache files (b5a92e2)

• Removed redundant matmul functionality of SymmOps Moved potential symm ops matrices to docs (ec5496c)

• Removed some redundant or unused code from .hkl file (94277be)

• Removed test files (a466f89)

• Reshkl moved to HklArtise, removed 2D draw (355e0d6)

• Resolution calculation introduced (3dbd99a)

• Resolution calculation moved to "place" of method of hkl dataframe (230efd9)

• Restucturised for dataframes (494a5b8)

• Rewritten to *Frames (eaf2497)

• Rewritten to *Frames (04a582d)

• Script for checking completeness some degrees around vector (f60901f)

• Scripts added (abf12a4)

• Scripts moved to main directory (4484a00)

• Sg generation now relies only on json definitions (1128c9d)

• Some additions I already forgot about (213048a)

• Some files renamed, increased readability, added manual-type files (2d79c5e)

• Sphinx added. Dataframes moved to scripts A few minor methods removed from HklFrame (69eb346)

• Split HklIo into HklReader and HklWriter (d8f67be)

• Superclassed pointgroup using group, added parity functions (3c70203)

• Tools for merging RGB-layers, alt #14&#31 SG definitions, modified dac-stats script (445fbc0)

• Transformation and translation are now stored internally using ints to avoid approximations (fbf0f27)

• Updated requirements, removed drop_zero, removed find_reflection, optimised trim (be82419)

• Vectorised 'calculate_uncertainty' method (a65fae5)

• Vectorised 'dac' method (172f95a)

• Vectorised 'generate_ball' method and renamed it to 'make_ball' (4be0bdf)

• Vectorised 'place' method (6f5d4fd)