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Merge branch 'master' of https://github.com/vincefn/objcryst into upstream-objcryst
2 parents f60cf2e + c5ea86c commit 8e8a68c

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ChangeLog.txt

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#### 2020.1 (January 2021)
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#### 2022.1 (May 2022)
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NEW FEATURES
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* Add cylindrical absorption correction (mu*R)
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* Access to Crystallography Open Database now uses an http access without
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need for MySQL, and should work through firewalls
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* Added more internal functions for the pyobjcryst Python interface.
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See https://pyobjcryst.readthedocs.io/en/latest/examples/index.html
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IMPROVEMENTS
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* Improve indexing: use the integrated goodness-of-fit based on P1 integration
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intervals as a default indicator, normalised by the number of reflections
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used (* nb_refl / nb_refl_P1)
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* Switched to wxWidgets 3.1
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* When using --cif2pattern, do not convert atoms to a Molecule (faster)
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* Fox grid allows a working directory with spaces in the path.
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* In the XML output, the atom list inside a RigidGroup will now be
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valid XML. NB: older Fox versions will not be able to read correctly
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the list of atoms inside the group.
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BUG FIXES
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* Correct EstimateCellVolume estimation for orthorombic F
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* Correct calculation of integrated figures of merit (Rwp, etc..)
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with multiple crystalline phases (https://github.com/vincefn/objcryst/pull/53)
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* + several minor issues
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#### 2017.2 (28 June 2017)

Fox/Fox.xcodeproj/project.pbxproj

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Fox/Fox_vc12.sln

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Global
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Fox/Fox_vc12.vcxproj

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Fox/bc32.mak

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